Diff of the two buildlogs: -- --- b1/build.log 2021-06-11 12:59:11.300410267 +0000 +++ b2/build.log 2021-06-11 13:09:14.437575520 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jul 14 07:19:21 -12 2022 -I: pbuilder-time-stamp: 1657826361 +I: Current time: Sat Jun 12 02:59:31 +14 2021 +I: pbuilder-time-stamp: 1623416371 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 [./smalt_0.7.6-9.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.fjJHnt7p/trustedkeys.kbx': General error -gpgv: Signature made Fri Jan 3 07:41:23 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.zDE14L_1/trustedkeys.kbx': General error +gpgv: Signature made Sat Jan 4 09:41:23 2020 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./smalt_0.7.6-9.dsc @@ -29,137 +29,171 @@ dpkg-source: info: applying 2to3.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/10760/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/23539/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/23539/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/23539/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='e854d6d9f23a40ea9fdd6dedf61ab1a4' - 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='10760' - PS1='# ' - PS2='> ' + INVOCATION_ID=ef9993b765f847678040953306cf8df4 + 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=23539 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.nmcxHjiO5S/pbuilderrc_iL38 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.nmcxHjiO5S/b1 --logfile b1/build.log smalt_0.7.6-9.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.nmcxHjiO5S/pbuilderrc_vXmz --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.nmcxHjiO5S/b2 --logfile b2/build.log --extrapackages usrmerge smalt_0.7.6-9.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 ionos16-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 Jul 13 03:46 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/10760/tmp/hooks/D02_print_environment finished + total 5780 + -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 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 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 Jun 12 03:01 sh -> bash + lrwxrwxrwx 1 root root 4 Jun 10 23:27 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/23539/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -264,7 +298,7 @@ Get: 59 http://deb.debian.org/debian bullseye/main i386 libhts3 i386 1.11-4 [408 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 libncurses6 i386 6.2+20201114-2 [110 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 samtools i386 1.11-1 [576 kB] -Fetched 28.4 MB in 3s (10.4 MB/s) +Fetched 28.4 MB in 2s (17.2 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 ... 19675 files and directories currently installed.) @@ -530,9 +564,41 @@ Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). -0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +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 59.5 kB of archives. +After this operation, 157 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 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (1118 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 ... 22593 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_25_all.deb ... +Unpacking usrmerge (25) ... +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 (25) ... +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/smalt-0.7.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/smalt-0.7.6/ && 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 smalt dpkg-buildpackage: info: source version 0.7.6-9 dpkg-buildpackage: info: source distribution unstable @@ -561,7 +627,7 @@ CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a thread-safe mkdir -p... /bin/mkdir -p +checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -591,8 +657,8 @@ checking for BAMBAMC... yes checking for gzread in -lz... yes checking how to run the C preprocessor... gcc -E -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes @@ -628,8 +694,8 @@ checking emmintrin.h usability... yes checking emmintrin.h presence... yes checking for emmintrin.h... yes -checking build system type... x86_64-pc-linux-gnu -checking host system type... x86_64-pc-linux-gnu +checking build system type... i686-pc-linux-gnu +checking host system type... i686-pc-linux-gnu checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes @@ -643,7 +709,7 @@ config.status: executing depfiles commands make[1]: Leaving directory '/build/smalt-0.7.6' dh_auto_build - make -j18 + make -j10 make[1]: Entering directory '/build/smalt-0.7.6' make all-recursive make[2]: Entering directory '/build/smalt-0.7.6' @@ -659,14 +725,39 @@ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-swsimd.o -MD -MP -MF .deps/libsgm_a-swsimd.Tpo -c -o libsgm_a-swsimd.o `test -f 'swsimd.c' || echo './'`swsimd.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-sort.o -MD -MP -MF .deps/libsgm_a-sort.Tpo -c -o libsgm_a-sort.o `test -f 'sort.c' || echo './'`sort.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-array.o -MD -MP -MF .deps/libsgm_a-array.Tpo -c -o libsgm_a-array.o `test -f 'array.c' || echo './'`array.c +score.c:49:21: warning: 'LN0P25' defined but not used [-Wunused-const-variable=] + 49 | static const double LN0P25 = -1.386294; /* natural logarithm of 1/4 */ + | ^~~~~~ +alignment.c:478:13: warning: 'blankALITRACK' defined but not used [-Wunused-function] + 478 | static void blankALITRACK(ALITRACK *trackp, const ALIBAND *bandp) + | ^~~~~~~~~~~~~ +sequence.c: In function 'seqFastqGetConstSequence': +sequence.c:2079:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 2079 | if (length) + | ^~ +sequence.c:2081:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 2081 | return NULL; + | ^~~~~~ +sequence.c: In function 'seqFastqGetSequence': +sequence.c:2094:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 2094 | if (length) + | ^~ +sequence.c:2096:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 2096 | return NULL; + | ^~~~~~ +sequence.c: In function 'seqIOopen': +sequence.c:489:5: warning: this statement may fall through [-Wimplicit-fallthrough=] + 489 | strcpy(p->fmode, "r"); + | ^~~~~~~~~~~~~~~~~~~~~ +sequence.c:491:3: note: here + 491 | case SEQIO_WRITE_GZIP_FASTA: + | ^~~~ +mv -f .deps/libsgm_a-array.Tpo .deps/libsgm_a-array.Po +mv -f .deps/libsgm_a-alibuffer.Tpo .deps/libsgm_a-alibuffer.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-interval.o -MD -MP -MF .deps/libsgm_a-interval.Tpo -c -o libsgm_a-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-hashidx.o -MD -MP -MF .deps/libsgm_a-hashidx.Tpo -c -o libsgm_a-hashidx.o `test -f 'hashidx.c' || echo './'`hashidx.c +mv -f .deps/filio.Tpo .deps/filio.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-hashhit.o -MD -MP -MF .deps/libsgm_a-hashhit.Tpo -c -o libsgm_a-hashhit.o `test -f 'hashhit.c' || echo './'`hashhit.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-segment.o -MD -MP -MF .deps/libsgm_a-segment.Tpo -c -o libsgm_a-segment.o `test -f 'segment.c' || echo './'`segment.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-smalt.o -MD -MP -MF .deps/smalt-smalt.Tpo -c -o smalt-smalt.o `test -f 'smalt.c' || echo './'`smalt.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-menu.o -MD -MP -MF .deps/smalt-menu.Tpo -c -o smalt-menu.o `test -f 'menu.c' || echo './'`menu.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-threads.o -MD -MP -MF .deps/smalt-threads.Tpo -c -o smalt-threads.o `test -f 'threads.c' || echo './'`threads.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-infmt.o -MD -MP -MF .deps/smalt-infmt.Tpo -c -o smalt-infmt.o `test -f 'infmt.c' || echo './'`infmt.c hashidx.c: In function 'countPerfectKey': hashidx.c:191:77: warning: unused parameter 'tuplectr' [-Wunused-parameter] 191 | static int countPerfectKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) @@ -690,75 +781,49 @@ hashidx.c:63:19: warning: 'HASHTABFIL_READERRMSG' defined but not used [-Wunused-const-variable=] 63 | static const char HASHTABFIL_READERRMSG[] = "when reading hash table file"; | ^~~~~~~~~~~~~~~~~~~~~ -score.c:49:21: warning: 'LN0P25' defined but not used [-Wunused-const-variable=] - 49 | static const double LN0P25 = -1.386294; /* natural logarithm of 1/4 */ - | ^~~~~~ -sequence.c: In function 'seqFastqGetConstSequence': -sequence.c:2079:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 2079 | if (length) - | ^~ -sequence.c:2081:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 2081 | return NULL; - | ^~~~~~ -sequence.c: In function 'seqFastqGetSequence': -sequence.c:2094:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 2094 | if (length) - | ^~ -sequence.c:2096:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 2096 | return NULL; - | ^~~~~~ -alignment.c:478:13: warning: 'blankALITRACK' defined but not used [-Wunused-function] - 478 | static void blankALITRACK(ALITRACK *trackp, const ALIBAND *bandp) - | ^~~~~~~~~~~~~ +mv -f .deps/libsgm_a-swsimd.Tpo .deps/libsgm_a-swsimd.Po +mv -f .deps/libsgm_a-interval.Tpo .deps/libsgm_a-interval.Po +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-segment.o -MD -MP -MF .deps/libsgm_a-segment.Tpo -c -o libsgm_a-segment.o `test -f 'segment.c' || echo './'`segment.c +mv -f .deps/elib.Tpo .deps/elib.Po +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-smalt.o -MD -MP -MF .deps/smalt-smalt.Tpo -c -o smalt-smalt.o `test -f 'smalt.c' || echo './'`smalt.c +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-menu.o -MD -MP -MF .deps/smalt-menu.Tpo -c -o smalt-menu.o `test -f 'menu.c' || echo './'`menu.c +mv -f .deps/libsgm_a-score.Tpo .deps/libsgm_a-score.Po +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-threads.o -MD -MP -MF .deps/smalt-threads.Tpo -c -o smalt-threads.o `test -f 'threads.c' || echo './'`threads.c segment.c:1375:12: warning: 'checkCANDARRsequential' defined but not used [-Wunused-function] 1375 | static int checkCANDARRsequential(const CANDARR candr, SEGNUM_t *rvc_offs) | ^~~~~~~~~~~~~~~~~~~~~~ segment.c:1330:13: warning: 'labelSEGCANDWithinInsertRange' defined but not used [-Wunused-function] 1330 | static void labelSEGCANDWithinInsertRange (SEGCAND *candAp, SEGNUM_t nsegA, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mv -f .deps/libsgm_a-array.Tpo .deps/libsgm_a-array.Po -sequence.c: In function 'seqIOopen': -sequence.c:489:5: warning: this statement may fall through [-Wimplicit-fallthrough=] - 489 | strcpy(p->fmode, "r"); - | ^~~~~~~~~~~~~~~~~~~~~ -sequence.c:491:3: note: here - 491 | case SEQIO_WRITE_GZIP_FASTA: - | ^~~~ -mv -f .deps/libsgm_a-alibuffer.Tpo .deps/libsgm_a-alibuffer.Po -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-results.o -MD -MP -MF .deps/smalt-results.Tpo -c -o smalt-results.o `test -f 'results.c' || echo './'`results.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-resultpairs.o -MD -MP -MF .deps/smalt-resultpairs.Tpo -c -o smalt-resultpairs.o `test -f 'resultpairs.c' || echo './'`resultpairs.c +mv -f .deps/libsgm_a-sort.Tpo .deps/libsgm_a-sort.Po +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-infmt.o -MD -MP -MF .deps/smalt-infmt.Tpo -c -o smalt-infmt.o `test -f 'infmt.c' || echo './'`infmt.c smalt.c: In function 'cleanupSmaltOutput': smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter] 659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op) | ~~~~~~~~^~~~~~~ -mv -f .deps/libsgm_a-interval.Tpo .deps/libsgm_a-interval.Po -mv -f .deps/filio.Tpo .deps/filio.Po +mv -f .deps/smalt-infmt.Tpo .deps/smalt-infmt.Po +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-results.o -MD -MP -MF .deps/smalt-results.Tpo -c -o smalt-results.o `test -f 'results.c' || echo './'`results.c +mv -f .deps/smalt-threads.Tpo .deps/smalt-threads.Po +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-resultpairs.o -MD -MP -MF .deps/smalt-resultpairs.Tpo -c -o smalt-resultpairs.o `test -f 'resultpairs.c' || echo './'`resultpairs.c +mv -f .deps/libsgm_a-alignment.Tpo .deps/libsgm_a-alignment.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-report.o -MD -MP -MF .deps/smalt-report.Tpo -c -o smalt-report.o `test -f 'report.c' || echo './'`report.c +mv -f .deps/libsgm_a-diffstr.Tpo .deps/libsgm_a-diffstr.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-rmap.o -MD -MP -MF .deps/smalt-rmap.Tpo -c -o smalt-rmap.o `test -f 'rmap.c' || echo './'`rmap.c -mv -f .deps/smalt-infmt.Tpo .deps/smalt-infmt.Po -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-insert.o -MD -MP -MF .deps/smalt-insert.Tpo -c -o smalt-insert.o `test -f 'insert.c' || echo './'`insert.c results.c: In function 'resultSetInferInsertSize': results.c:2470:11: warning: self-comparison always evaluates to true [-Wtautological-compare] 2470 | rp->sidx == rp->sidx) { | ^~ -mv -f .deps/libsgm_a-swsimd.Tpo .deps/libsgm_a-swsimd.Po -mv -f .deps/elib.Tpo .deps/elib.Po -mv -f .deps/smalt-threads.Tpo .deps/smalt-threads.Po -mv -f .deps/libsgm_a-score.Tpo .deps/libsgm_a-score.Po -mv -f .deps/libsgm_a-sort.Tpo .deps/libsgm_a-sort.Po -mv -f .deps/libsgm_a-alignment.Tpo .deps/libsgm_a-alignment.Po +mv -f .deps/libsgm_a-hashidx.Tpo .deps/libsgm_a-hashidx.Po +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-insert.o -MD -MP -MF .deps/smalt-insert.Tpo -c -o smalt-insert.o `test -f 'insert.c' || echo './'`insert.c +mv -f .deps/libsgm_a-hashhit.Tpo .deps/libsgm_a-hashhit.Po +mv -f .deps/smalt-smalt.Tpo .deps/smalt-smalt.Po mv -f .deps/smalt-resultpairs.Tpo .deps/smalt-resultpairs.Po +mv -f .deps/libsgm_a-segment.Tpo .deps/libsgm_a-segment.Po mv -f .deps/smalt-menu.Tpo .deps/smalt-menu.Po -mv -f .deps/smalt-smalt.Tpo .deps/smalt-smalt.Po mv -f .deps/smalt-insert.Tpo .deps/smalt-insert.Po -mv -f .deps/libsgm_a-hashhit.Tpo .deps/libsgm_a-hashhit.Po -mv -f .deps/libsgm_a-hashidx.Tpo .deps/libsgm_a-hashidx.Po -mv -f .deps/libsgm_a-segment.Tpo .deps/libsgm_a-segment.Po mv -f .deps/smalt-rmap.Tpo .deps/smalt-rmap.Po -mv -f .deps/libsgm_a-diffstr.Tpo .deps/libsgm_a-diffstr.Po -mv -f .deps/smalt-report.Tpo .deps/smalt-report.Po -mv -f .deps/smalt-results.Tpo .deps/smalt-results.Po mv -f .deps/sequence.Tpo .deps/sequence.Po +mv -f .deps/smalt-report.Tpo .deps/smalt-report.Po rm -f libseq.a ar cru libseq.a elib.o filio.o sequence.o ar: `u' modifier ignored since `D' is the default (see `U') @@ -766,6 +831,7 @@ rm -f libsgm.a ar cru libsgm.a libsgm_a-score.o libsgm_a-diffstr.o libsgm_a-alibuffer.o libsgm_a-alignment.o libsgm_a-swsimd.o libsgm_a-sort.o libsgm_a-array.o libsgm_a-interval.o libsgm_a-hashidx.o libsgm_a-hashhit.o libsgm_a-segment.o libseq.a ar: `u' modifier ignored since `D' is the default (see `U') +mv -f .deps/smalt-results.Tpo .deps/smalt-results.Po ranlib libsgm.a gcc -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o smalt smalt-smalt.o smalt-menu.o smalt-threads.o smalt-infmt.o smalt-results.o smalt-resultpairs.o smalt-report.o smalt-rmap.o smalt-insert.o libsgm.a libseq.a -lbambamc -lz -lm -lpthread -lz make[3]: Leaving directory '/build/smalt-0.7.6/src' @@ -787,25 +853,25 @@ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT trunkreads.o -MD -MP -MF .deps/trunkreads.Tpo -c -o trunkreads.o trunkreads.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT basqcol.o -MD -MP -MF .deps/basqcol.Tpo -c -o basqcol.o basqcol.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT basqual.o -MD -MP -MF .deps/basqual.Tpo -c -o basqual.o basqual.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT simqual.o -MD -MP -MF .deps/simqual.Tpo -c -o simqual.o simqual.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT diffstr.o -MD -MP -MF .deps/diffstr.Tpo -c -o diffstr.o `test -f '../src/diffstr.c' || echo './'`../src/diffstr.c -mv -f .deps/trunkreads.Tpo .deps/trunkreads.Po -gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o trunkreads trunkreads.o ../src/libseq.a -lz mv -f .deps/readstats.Tpo .deps/readstats.Po -mv -f .deps/splitreads.Tpo .deps/splitreads.Po -gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o readstats readstats.o ../src/libseq.a -lz -gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o splitreads splitreads.o ../src/libseq.a -lz +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT simqual.o -MD -MP -MF .deps/simqual.Tpo -c -o simqual.o simqual.c mv -f .deps/rsample.Tpo .deps/rsample.Po +mv -f .deps/splitreads.Tpo .deps/splitreads.Po mv -f .deps/splitmates.Tpo .deps/splitmates.Po -gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o splitmates splitmates.o ../src/libseq.a -lz +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT diffstr.o -MD -MP -MF .deps/diffstr.Tpo -c -o diffstr.o `test -f '../src/diffstr.c' || echo './'`../src/diffstr.c +mv -f .deps/trunkreads.Tpo .deps/trunkreads.Po mv -f .deps/fetchseq.Tpo .deps/fetchseq.Po -gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fetchseq fetchseq.o ../src/libseq.a -lz mv -f .deps/basqcol.Tpo .deps/basqcol.Po +mv -f .deps/basqual.Tpo .deps/basqual.Po +gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fetchseq fetchseq.o ../src/libseq.a -lz mv -f .deps/mixreads.Tpo .deps/mixreads.Po +gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o splitreads splitreads.o ../src/libseq.a -lz +gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o splitmates splitmates.o ../src/libseq.a -lz +gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o readstats readstats.o ../src/libseq.a -lz +gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o trunkreads trunkreads.o ../src/libseq.a -lz +gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o basqcol basqcol.o basqual.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o mixreads mixreads.o ../src/libseq.a -lz mv -f .deps/simqual.Tpo .deps/simqual.Po -mv -f .deps/basqual.Tpo .deps/basqual.Po -gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o basqcol basqcol.o basqual.o ../src/libseq.a -lz mv -f .deps/simread.Tpo .deps/simread.Po gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o simread simread.o rsample.o ../src/libsgm.a ../src/libseq.a -lm -lz mv -f .deps/diffstr.Tpo .deps/diffstr.Po @@ -816,7 +882,7 @@ make[2]: Leaving directory '/build/smalt-0.7.6' make[1]: Leaving directory '/build/smalt-0.7.6' dh_auto_test - make -j18 check VERBOSE=1 + make -j10 check VERBOSE=1 make[1]: Entering directory '/build/smalt-0.7.6' Making check in src make[2]: Entering directory '/build/smalt-0.7.6/src' @@ -837,6 +903,8 @@ gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-insert.o -MD -MP -MF .deps/smalt_Xali_test-insert.Tpo -c -o smalt_Xali_test-insert.o `test -f '../src/insert.c' || echo './'`../src/insert.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-report.o -MD -MP -MF .deps/smalt_Xali_test-report.Tpo -c -o smalt_Xali_test-report.o `test -f '../src/report.c' || echo './'`../src/report.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-rmap.o -MD -MP -MF .deps/smalt_Xali_test-rmap.Tpo -c -o smalt_Xali_test-rmap.o `test -f '../src/rmap.c' || echo './'`../src/rmap.c +mv -f .deps/sequenceReverseComplement_test.Tpo .deps/sequenceReverseComplement_test.Po +gcc -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o sequenceReverseComplement_test sequenceReverseComplement_test.o ../src/libseq.a -lz ../src/results.c: In function 'resultSetInferInsertSize': ../src/results.c:2470:11: warning: self-comparison always evaluates to true [-Wtautological-compare] 2470 | rp->sidx == rp->sidx) { @@ -845,14 +913,12 @@ ../src/smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter] 659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op) | ~~~~~~~~^~~~~~~ -mv -f .deps/sequenceReverseComplement_test.Tpo .deps/sequenceReverseComplement_test.Po -gcc -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o sequenceReverseComplement_test sequenceReverseComplement_test.o ../src/libseq.a -lz mv -f .deps/smalt_Xali_test-infmt.Tpo .deps/smalt_Xali_test-infmt.Po mv -f .deps/smalt_Xali_test-threads.Tpo .deps/smalt_Xali_test-threads.Po -mv -f .deps/smalt_Xali_test-resultpairs.Tpo .deps/smalt_Xali_test-resultpairs.Po mv -f .deps/smalt_Xali_test-insert.Tpo .deps/smalt_Xali_test-insert.Po -mv -f .deps/smalt_Xali_test-menu.Tpo .deps/smalt_Xali_test-menu.Po +mv -f .deps/smalt_Xali_test-resultpairs.Tpo .deps/smalt_Xali_test-resultpairs.Po mv -f .deps/smalt_Xali_test-smalt.Tpo .deps/smalt_Xali_test-smalt.Po +mv -f .deps/smalt_Xali_test-menu.Tpo .deps/smalt_Xali_test-menu.Po mv -f .deps/smalt_Xali_test-report.Tpo .deps/smalt_Xali_test-report.Po mv -f .deps/smalt_Xali_test-rmap.Tpo .deps/smalt_Xali_test-rmap.Po mv -f .deps/smalt_Xali_test-results.Tpo .deps/smalt_Xali_test-results.Po @@ -917,8 +983,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'smalt' in '../smalt_0.7.6-9_i386.deb'. dpkg-deb: building package 'smalt-dbgsym' in '../smalt-dbgsym_0.7.6-9_i386.deb'. +dpkg-deb: building package 'smalt' in '../smalt_0.7.6-9_i386.deb'. dpkg-deb: building package 'smalt-examples' in '../smalt-examples_0.7.6-9_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../smalt_0.7.6-9_i386.changes @@ -926,12 +992,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/23539/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/23539/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/10760 and its subdirectories -I: Current time: Thu Jul 14 07:22:08 -12 2022 -I: pbuilder-time-stamp: 1657826528 +I: removing directory /srv/workspace/pbuilder/23539 and its subdirectories +I: Current time: Sat Jun 12 03:09:13 +14 2021 +I: pbuilder-time-stamp: 1623416953