Diff of the two buildlogs: -- --- b1/build.log 2021-05-18 23:08:01.137165187 +0000 +++ b2/build.log 2021-05-18 23:08:47.307370082 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue May 18 11:01:05 -12 2021 -I: pbuilder-time-stamp: 1621378865 +I: Current time: Tue Jun 21 19:31:02 +14 2022 +I: pbuilder-time-stamp: 1655789462 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 [./discosnp_4.4.4-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.cSooo2Jf/trustedkeys.kbx': General error -gpgv: Signature made Thu Oct 1 00:57:13 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.i8OKCjEd/trustedkeys.kbx': General error +gpgv: Signature made Fri Oct 2 02:57:13 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -36,137 +36,171 @@ dpkg-source: info: applying shell_syntax.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/20908/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/24244/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 +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/24244/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/24244/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=10' - 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=18' + 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='7aa3249afad749a387f8ad4b29ee75fd' - 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='20908' - PS1='# ' - PS2='> ' + INVOCATION_ID=894eb88dbe7e4354938ddfe379f85326 + 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=24244 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.MqjotJPQ7W/pbuilderrc_MqNe --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.MqjotJPQ7W/b1 --logfile b1/build.log discosnp_4.4.4-1.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://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/tmp.MqjotJPQ7W/pbuilderrc_fN0l --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.MqjotJPQ7W/b2 --logfile b2/build.log --extrapackages usrmerge discosnp_4.4.4-1.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://85.184.249.68:3128 I: uname -a - Linux ionos12-i386 4.19.0-16-686-pae #1 SMP Debian 4.19.181-1 (2021-03-19) i686 GNU/Linux + Linux i-capture-the-hostname 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux I: ls -l /bin - total 5836 - -rwxr-xr-x 1 root root 1367848 Feb 24 08:57 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 01:23 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 02:38 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 02:38 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 100952 Mar 2 11:30 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 02:38 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 02:38 more - -rwsr-xr-x 1 root root 50720 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 13856 Feb 7 02:38 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 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Feb 24 08:57 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 May 17 21:35 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 02:38 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 602584 Feb 16 21:55 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 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 Feb 7 02:38 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/20908/tmp/hooks/D02_print_environment finished + total 5776 + -rwxr-xr-x 1 root root 1367848 Feb 25 2021 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 2020 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 2021 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 2021 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 100952 Mar 3 2021 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 2021 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 2021 more + -rwsr-xr-x 1 root root 50720 Feb 8 2021 mount + -rwxr-xr-x 1 root root 13856 Feb 8 2021 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 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Feb 25 2021 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 Jun 21 19:31 sh -> bash + lrwxrwxrwx 1 root root 4 Jun 20 05:47 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 2021 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 602584 Feb 17 2021 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 2021 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Feb 8 2021 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 Feb 8 2021 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/24244/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -300,7 +334,7 @@ Get: 82 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo-dev i386 1:2.0.6-4 [299 kB] Get: 83 http://deb.debian.org/debian bullseye/main i386 libjpeg-dev i386 1:2.0.6-4 [67.8 kB] Get: 84 http://deb.debian.org/debian bullseye/main i386 libhdf5-dev i386 1.10.6+repack-2 [2594 kB] -Fetched 57.1 MB in 23s (2514 kB/s) +Fetched 57.1 MB in 1s (92.5 MB/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.) @@ -654,8 +688,44 @@ 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 (4029 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 ... 41735 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/discosnp-4.4.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/discosnp-4.4.4/ && 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 discosnp dpkg-buildpackage: info: source version 4.4.4-1 dpkg-buildpackage: info: source distribution unstable @@ -712,7 +782,7 @@ -- Build files have been written to: /build/discosnp-4.4.4/obj-i686-linux-gnu dh_auto_build - cd obj-i686-linux-gnu && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-i686-linux-gnu && make -j18 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' /usr/bin/cmake -S/build/discosnp-4.4.4 -B/build/discosnp-4.4.4/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/discosnp-4.4.4/obj-i686-linux-gnu/CMakeFiles /build/discosnp-4.4.4/obj-i686-linux-gnu//CMakeFiles/progress.marks @@ -721,90 +791,84 @@ make -f tools/kissnp2/CMakeFiles/kissnp2.dir/build.make tools/kissnp2/CMakeFiles/kissnp2.dir/depend make -f tools/kissreads2/CMakeFiles/kissreads2.dir/build.make tools/kissreads2/CMakeFiles/kissreads2.dir/depend make -f tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/build.make tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/depend +make -f tools/read_file_names/CMakeFiles/read_file_names.dir/build.make tools/read_file_names/CMakeFiles/read_file_names.dir/depend make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' cd /build/discosnp-4.4.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-4.4.4 /build/discosnp-4.4.4/tools/kissnp2 /build/discosnp-4.4.4/obj-i686-linux-gnu /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2 /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2/CMakeFiles/kissnp2.dir/DependInfo.cmake --color= -make -f tools/read_file_names/CMakeFiles/read_file_names.dir/build.make tools/read_file_names/CMakeFiles/read_file_names.dir/depend make -f tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build.make tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/depend make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' -cd /build/discosnp-4.4.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-4.4.4 /build/discosnp-4.4.4/tools/QHC /build/discosnp-4.4.4/obj-i686-linux-gnu /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' cd /build/discosnp-4.4.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-4.4.4 /build/discosnp-4.4.4/tools/kissreads2 /build/discosnp-4.4.4/obj-i686-linux-gnu /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2/CMakeFiles/kissreads2.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' -cd /build/discosnp-4.4.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-4.4.4 /build/discosnp-4.4.4/tools/create_coverage_h5_file /build/discosnp-4.4.4/obj-i686-linux-gnu /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/create_coverage_h5_file /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/DependInfo.cmake --color= +cd /build/discosnp-4.4.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-4.4.4 /build/discosnp-4.4.4/tools/QHC /build/discosnp-4.4.4/obj-i686-linux-gnu /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' cd /build/discosnp-4.4.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-4.4.4 /build/discosnp-4.4.4/tools/read_file_names /build/discosnp-4.4.4/obj-i686-linux-gnu /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names/CMakeFiles/read_file_names.dir/DependInfo.cmake --color= -Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names/CMakeFiles/read_file_names.dir/DependInfo.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names/CMakeFiles/read_file_names.dir/depend.internal". -Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names/CMakeFiles/read_file_names.dir/depend.internal". -Scanning dependencies of target read_file_names -make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' -Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/DependInfo.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/depend.internal". -Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/depend.internal". -make -f tools/read_file_names/CMakeFiles/read_file_names.dir/build.make tools/read_file_names/CMakeFiles/read_file_names.dir/build +make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' +cd /build/discosnp-4.4.4/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-4.4.4 /build/discosnp-4.4.4/tools/create_coverage_h5_file /build/discosnp-4.4.4/obj-i686-linux-gnu /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/create_coverage_h5_file /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/DependInfo.cmake --color= Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2/CMakeFiles/kissnp2.dir/DependInfo.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2/CMakeFiles/kissnp2.dir/depend.internal". -Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2/CMakeFiles/kissnp2.dir/depend.internal". Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2/CMakeFiles/kissreads2.dir/DependInfo.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2/CMakeFiles/kissreads2.dir/depend.internal". Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2/CMakeFiles/kissreads2.dir/depend.internal". -Scanning dependencies of target quick_hierarchical_clustering +Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2/CMakeFiles/kissnp2.dir/depend.internal". +Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/DependInfo.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/depend.internal". +Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/depend.internal". +Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names/CMakeFiles/read_file_names.dir/DependInfo.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names/CMakeFiles/read_file_names.dir/depend.internal". +Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names/CMakeFiles/read_file_names.dir/depend.internal". Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/DependInfo.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/depend.internal". Dependee "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/discosnp-4.4.4/obj-i686-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/depend.internal". +Scanning dependencies of target quick_hierarchical_clustering +Scanning dependencies of target read_file_names +Scanning dependencies of target create_coverage_h5_file +Scanning dependencies of target kissnp2 +make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' make -f tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/build.make tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/build -make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' -make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' -Scanning dependencies of target kissnp2 make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' make -f tools/kissnp2/CMakeFiles/kissnp2.dir/build.make tools/kissnp2/CMakeFiles/kissnp2.dir/build -make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' +make -f tools/read_file_names/CMakeFiles/read_file_names.dir/build.make tools/read_file_names/CMakeFiles/read_file_names.dir/build +make -f tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build.make tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build Scanning dependencies of target kissreads2 +make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' +make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' -[ 4%] Building CXX object tools/read_file_names/CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o make -f tools/kissreads2/CMakeFiles/kissreads2.dir/build.make tools/kissreads2/CMakeFiles/kissreads2.dir/build -cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/read_file_names/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -c /build/discosnp-4.4.4/tools/read_file_names/src/get_read_file_names.cpp make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' -[ 13%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Bubble.cpp.o -Scanning dependencies of target create_coverage_h5_file -[ 13%] Building CXX object tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o +make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' +make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' +[ 4%] Building CXX object tools/read_file_names/CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o +[ 8%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Filter.cpp.o +cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/read_file_names/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -c /build/discosnp-4.4.4/tools/read_file_names/src/get_read_file_names.cpp +cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissnp2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissnp2.dir/src/Filter.cpp.o -c /build/discosnp-4.4.4/tools/kissnp2/src/Filter.cpp +[ 13%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/commons.cpp.o +[ 17%] Building CXX object tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o +[ 21%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Bubble.cpp.o +cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/commons.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/commons.cpp +[ 26%] Building CXX object tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissnp2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissnp2.dir/src/Bubble.cpp.o -c /build/discosnp-4.4.4/tools/kissnp2/src/Bubble.cpp +cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/create_coverage_h5_file && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/create_coverage_h5_file/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o -c /build/discosnp-4.4.4/tools/create_coverage_h5_file/src/create_coverage_h5_file.cpp cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/QHC/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -c /build/discosnp-4.4.4/tools/QHC/src/quick_hierarchical_clustering.cpp -make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' -make -f tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build.make tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build -[ 17%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Filter.cpp.o -cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissnp2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissnp2.dir/src/Filter.cpp.o -c /build/discosnp-4.4.4/tools/kissnp2/src/Filter.cpp -[ 21%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o -make[3]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' -[ 26%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/main.cpp.o +[ 30%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o +[ 34%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o +[ 39%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/couple.cpp.o +[ 43%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/main.cpp.o cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissnp2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o -c /build/discosnp-4.4.4/tools/kissnp2/src/Kissnp2.cpp +[ 52%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/extension_algorithm.cpp.o +[ 52%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissnp2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissnp2.dir/src/main.cpp.o -c /build/discosnp-4.4.4/tools/kissnp2/src/main.cpp -[ 30%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/commons.cpp.o -[ 34%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o -cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/commons.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/commons.cpp cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/Kissreads2.cpp -[ 39%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/couple.cpp.o +[ 56%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment_info.cpp.o cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/couple.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/couple.cpp -[ 43%] Building CXX object tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o -cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/create_coverage_h5_file && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/create_coverage_h5_file/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o -c /build/discosnp-4.4.4/tools/create_coverage_h5_file/src/create_coverage_h5_file.cpp -[ 47%] Linking CXX executable ../../bin/quick_hierarchical_clustering -cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC && /usr/bin/cmake -E cmake_link_script CMakeFiles/quick_hierarchical_clustering.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -o ../../bin/quick_hierarchical_clustering -L/usr/lib/i386-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/i386-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz -make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' -[ 47%] Built target quick_hierarchical_clustering -[ 52%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/extension_algorithm.cpp.o cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/extension_algorithm.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/extension_algorithm.cpp -[ 56%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o -[ 60%] Linking CXX executable ../../bin/read_file_names cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/fragment_index.cpp -cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names && /usr/bin/cmake -E cmake_link_script CMakeFiles/read_file_names.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -o ../../bin/read_file_names -L/usr/lib/i386-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/i386-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz -[ 65%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment_info.cpp.o cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/fragment_info.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/fragment_info.cpp -[ 69%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/interface_libchash.cpp.o +[ 60%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/interface_libchash.cpp.o +[ 65%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/libchash.cpp.o cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/interface_libchash.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/interface_libchash.cpp -make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' -[ 69%] Built target read_file_names -[ 73%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/list.cpp.o -cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/list.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/list.cpp -[ 78%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/libchash.cpp.o +[ 69%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/list.cpp.o cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/libchash.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp +[ 73%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/main.cpp.o +cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/list.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/list.cpp +[ 78%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/outputs.cpp.o +cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/main.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/main.cpp +cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/outputs.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/outputs.cpp /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp: In function 'HTItem* HashFind(HashTable*, u_long)': /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ @@ -895,10 +959,16 @@ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:622:3: note: in expansion of macro 'READ_UL' 622 | READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]); | ^~~~~~~ -[ 82%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/main.cpp.o -cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/main.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/main.cpp -[ 86%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/outputs.cpp.o -cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/outputs.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/outputs.cpp +[ 82%] Linking CXX executable ../../bin/quick_hierarchical_clustering +cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/QHC && /usr/bin/cmake -E cmake_link_script CMakeFiles/quick_hierarchical_clustering.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -o ../../bin/quick_hierarchical_clustering -L/usr/lib/i386-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/i386-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz +make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' +[ 82%] Built target quick_hierarchical_clustering +[ 86%] Linking CXX executable ../../bin/read_file_names +cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/read_file_names && /usr/bin/cmake -E cmake_link_script CMakeFiles/read_file_names.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -o ../../bin/read_file_names -L/usr/lib/i386-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/i386-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz +make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' +[ 86%] Built target read_file_names [ 91%] Linking CXX executable ../../bin/create_coverage_h5_file cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/create_coverage_h5_file && /usr/bin/cmake -E cmake_link_script CMakeFiles/create_coverage_h5_file.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o -o ../../bin/create_coverage_h5_file -L/usr/lib/i386-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/i386-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz @@ -911,9 +981,9 @@ cd /build/discosnp-4.4.4/obj-i686-linux-gnu/tools/kissnp2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/kissnp2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/kissnp2.dir/src/Bubble.cpp.o CMakeFiles/kissnp2.dir/src/Filter.cpp.o CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o CMakeFiles/kissnp2.dir/src/main.cpp.o -o ../../bin/kissnp2 -L/usr/lib/i386-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/i386-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' -[100%] Built target kissnp2 -make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' [100%] Built target kissreads2 +make[3]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' +[100%] Built target kissnp2 make[2]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/discosnp-4.4.4/obj-i686-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' @@ -921,7 +991,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-i686-linux-gnu && make -j10 install DESTDIR=/build/discosnp-4.4.4/debian/discosnp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-i686-linux-gnu && make -j18 install DESTDIR=/build/discosnp-4.4.4/debian/discosnp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/discosnp-4.4.4/obj-i686-linux-gnu' /usr/bin/cmake -S/build/discosnp-4.4.4 -B/build/discosnp-4.4.4/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -959,7 +1029,6 @@ cp -a debian/mans/*.sh.1 debian/discosnp/usr/share/man/man1 make[1]: Leaving directory '/build/discosnp-4.4.4' dh_python3 -I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/discoSnpRAD/clustering_scripts/fasta_and_cluster_to_filtered_vcf.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/create_filtered_vcf.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/vcf_formatting_functions.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_common.py @@ -967,6 +1036,7 @@ I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_compacted_paths_to_fa.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_msr_to_gfa.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_node_ids_to_node_sequences.py +I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/discoSnpRAD/clustering_scripts/fasta_and_cluster_to_filtered_vcf.py dh_lintian dh_perl dh_link @@ -982,20 +1052,22 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'discosnp-dbgsym' in '../discosnp-dbgsym_4.4.4-1_i386.deb'. dpkg-deb: building package 'discosnp' in '../discosnp_4.4.4-1_i386.deb'. +dpkg-deb: building package 'discosnp-dbgsym' in '../discosnp-dbgsym_4.4.4-1_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../discosnp_4.4.4-1_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/24244/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/24244/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/20908 and its subdirectories -I: Current time: Tue May 18 11:08:00 -12 2021 -I: pbuilder-time-stamp: 1621379280 +I: removing directory /srv/workspace/pbuilder/24244 and its subdirectories +I: Current time: Tue Jun 21 19:31:46 +14 2022 +I: pbuilder-time-stamp: 1655789506