Diff of the two buildlogs: -- --- b1/build.log 2023-05-13 09:44:24.233605438 +0000 +++ b2/build.log 2023-05-13 09:50:25.101782021 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 12 21:39:03 -12 2023 -I: pbuilder-time-stamp: 1683970743 +I: Current time: Sat Jun 15 06:07:29 +14 2024 +I: pbuilder-time-stamp: 1718381249 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./crac_2.5.2+dfsg.orig.tar.xz] I: copying [./crac_2.5.2+dfsg-5.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Nov 7 09:33:37 2021 -12 +gpgv: Signature made Mon Nov 8 11:33:37 2021 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -35,135 +35,167 @@ dpkg-source: info: applying tempfile.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3143674/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3397530/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 15 06:07 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3397530/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3397530/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='a95edae1023440e693aff3a04759bc81' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - 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='3143674' - PS1='# ' - PS2='> ' + INVOCATION_ID=e42369e56da845fdbf11cb0f96886c2a + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-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=3397530 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.TLe9K2T1/pbuilderrc_b2Xt --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.TLe9K2T1/b1 --logfile b1/build.log crac_2.5.2+dfsg-5.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.TLe9K2T1/pbuilderrc_WlDV --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.TLe9K2T1/b2 --logfile b2/build.log --extrapackages usrmerge crac_2.5.2+dfsg-5.dsc' + SUDO_GID=110 + SUDO_UID=105 + 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 ionos11-amd64 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Apr 23 09:23 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more - -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount - -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:23 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/3143674/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Apr 24 2023 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 2023 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 2023 more + -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount + -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 Jun 15 06:07 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 2023 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar + -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/3397530/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -272,7 +304,7 @@ Get: 57 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] -Fetched 24.8 MB in 1s (19.5 MB/s) +Fetched 24.8 MB in 1s (22.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpopt0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) @@ -524,8 +556,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/crac-2.5.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../crac_2.5.2+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/3397530/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/3397530/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/crac-2.5.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../crac_2.5.2+dfsg-5_source.changes dpkg-buildpackage: info: source package crac dpkg-buildpackage: info: source version 2.5.2+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -565,7 +608,7 @@ ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a race-free mkdir -p... /bin/mkdir -p +checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -594,10 +637,10 @@ checking whether make sets $(MAKE)... (cached) yes checking whether ln -s works... yes checking how to print strings... printf -checking for a sed that does not truncate output... /bin/sed -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E -checking for fgrep... /bin/grep -F +checking for a sed that does not truncate output... /usr/bin/sed +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E +checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B @@ -617,8 +660,8 @@ checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no -checking for a working dd... /bin/dd -checking how to truncate binary pipes... /bin/dd bs=4096 count=1 +checking for a working dd... /usr/bin/dd +checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes @@ -737,7 +780,7 @@ config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build - make -j15 + make -j16 make[1]: Entering directory '/build/crac-2.5.2+dfsg' Making all in src make[2]: Entering directory '/build/crac-2.5.2+dfsg/src' @@ -767,6 +810,10 @@ samHeader.cpp:160:15: warning: ignoring return value of 'int sam_hdr_write(samFile*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 160 | sam_hdr_write(out,h); | ~~~~~~~~~~~~~^~~~~~~ +samLine.cpp: In constructor 'OptionalField::OptionalField(const char*, char)': +samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] + 60 | strncpy(tag,tag_name,2); + | ^ In file included from ../libReadsReader/readsReader.h:57, from ../Read.h:55, from ../ReadIndex.h:52, @@ -782,10 +829,6 @@ ../libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ -samLine.cpp: In constructor 'OptionalField::OptionalField(const char*, char)': -samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] - 60 | strncpy(tag,tag_name,2); - | ^ samLine.cpp: In constructor 'CharOptionalField::CharOptionalField(const char*, char)': samLine.cpp:60:10: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation] samLine.cpp: In constructor 'IntOptionalField::IntOptionalField(const char*, int)': @@ -824,18 +867,6 @@ g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SSA.o SSA.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o utils.cpp g++ -DHAVE_CONFIG_H -I. -I../../config -I/build/crac-2.5.2+dfsg -I/build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GenomeInfo.o GenomeInfo.cpp -In file included from /usr/include/libGkArrays/readsReader.h:109, - from locateTags.h:60, - from locateTags.cpp:53: -/usr/include/libGkArrays/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] - 169 | static int kseq_read(kseq_t *seq) \ - | ^~~~~~~~~ -/usr/include/libGkArrays/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' - 227 | __KSEQ_READ - | ^~~~~~~~~~~ -/usr/include/libGkArrays/readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' - 111 | KSEQ_INIT(gzFile, gzread) - | ^~~~~~~~~ cracIndex.cpp:85:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 85 | cerr << "\tCompiled on " <<__DATE__ << endl << endl; | ^~~~~~~~ @@ -860,6 +891,18 @@ ./seqan/sequence/lexical.h:239:45: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] 239 | typedef typename Value::Type TLeftValue; | ^~~~~~~~~~ +In file included from /usr/include/libGkArrays/readsReader.h:109, + from locateTags.h:60, + from locateTags.cpp:53: +/usr/include/libGkArrays/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] + 169 | static int kseq_read(kseq_t *seq) \ + | ^~~~~~~~~ +/usr/include/libGkArrays/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' + 227 | __KSEQ_READ + | ^~~~~~~~~~~ +/usr/include/libGkArrays/readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' + 111 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ In file included from ./seqan/sequence.h:51: ./seqan/sequence/string_base.h: In function 'void seqan::assign(String&, const TSource&, Tag)': ./seqan/sequence/string_base.h:811:51: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] @@ -966,10 +1009,6 @@ ./seqan/index/shape_gapped.h:415:89: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] 415 | typedef typename Value< Shape > >::Type THValue; | ^~~~~~~ -rm -f libSSA.a -ar cru libSSA.a bitarray.o bitrankw32int.o chrPosition.o HuffAlphabetRank.o Huffman_Codes.o locateOnGenome.o locateTags.o SSA.o utils.o GenomeInfo.o -ar: `u' modifier ignored since `D' is the default (see `U') -ranlib libSSA.a In file included from ./seqan/file.h:66, from /build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/multikey_qsort.h:6, from /build/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:8, @@ -1049,6 +1088,10 @@ ./seqan/basic/basic_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here 57 | struct SimpleType | ^~~~~~~~~~ +rm -f libSSA.a +ar cru libSSA.a bitarray.o bitrankw32int.o chrPosition.o HuffAlphabetRank.o Huffman_Codes.o locateOnGenome.o locateTags.o SSA.o utils.o GenomeInfo.o +ar: `u' modifier ignored since `D' is the default (see `U') +ranlib libSSA.a In file included from ./seqan/basic.h:61: In function 'void seqan::allocate(T&, TValue*&, TSize, Tag) [with T = String >; TValue = unsigned int; TSize = long unsigned int; TUsage = TagAllocateStorage_]', inlined from 'seqan::Value >, 0>::Type* seqan::_allocateStorage(String >&, size_t)' at ./seqan/sequence/string_alloc.h:294:11, @@ -1074,7 +1117,7 @@ /usr/include/c++/12/new:126:26: note: in a call to allocation function 'void* operator new(std::size_t)' declared here 126 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lm -lpthread -lSSA -L/build/crac-2.5.2+dfsg/src/libSSA/ -Wl,-z,relro -Wl,-z,now -o crac-index cracIndex.o libSSA.a -lhts -lz -lpthread -lm +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lm -lpthread -lSSA -L/build/crac-2.5.2+dfsg/src/libSSA/ -Wl,-z,relro -Wl,-z,now -o crac-index cracIndex.o libSSA.a -lhts -lz -lpthread -lm libtool: link: g++ -g -O2 -ffile-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o crac-index cracIndex.o -lSSA -L/build/crac-2.5.2+dfsg/src/libSSA/ libSSA.a -lhts -lz -lpthread -lm make[3]: Leaving directory '/build/crac-2.5.2+dfsg/src/libSSA' Making all in libReadsReader @@ -1254,62 +1297,6 @@ libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' 59 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ -In file included from libReadsReader/readsReader.h:57, - from Read.h:55, - from ReadIndex.h:52, - from Support.h:59, - from SupportBreak.cpp:55: -libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] - 169 | static int kseq_read(kseq_t *seq) \ - | ^~~~~~~~~ -libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' - 227 | __KSEQ_READ - | ^~~~~~~~~~~ -libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' - 59 | KSEQ_INIT(gzFile, gzread) - | ^~~~~~~~~ -In file included from libReadsReader/readsReader.h:57, - from Read.h:55, - from ReadIndex.h:52, - from Support.h:59, - from Support.cpp:57: -libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] - 169 | static int kseq_read(kseq_t *seq) \ - | ^~~~~~~~~ -libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' - 227 | __KSEQ_READ - | ^~~~~~~~~~~ -libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' - 59 | KSEQ_INIT(gzFile, gzread) - | ^~~~~~~~~ -In file included from libReadsReader/readsReader.h:57, - from Read.h:55, - from ReadIndex.h:52, - from classifyTags.h:53, - from classifyTags.cpp:52: -libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] - 169 | static int kseq_read(kseq_t *seq) \ - | ^~~~~~~~~ -libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' - 227 | __KSEQ_READ - | ^~~~~~~~~~~ -libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' - 59 | KSEQ_INIT(gzFile, gzread) - | ^~~~~~~~~ -In file included from ./libReadsReader/readsReader.h:57, - from ./Read.h:55, - from ./ReadIndex.h:52, - from ./Classifier.h:56, - from Classifier.cpp:52: -./libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] - 169 | static int kseq_read(kseq_t *seq) \ - | ^~~~~~~~~ -./libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' - 227 | __KSEQ_READ - | ^~~~~~~~~~~ -./libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' - 59 | KSEQ_INIT(gzFile, gzread) - | ^~~~~~~~~ In file included from /usr/include/libGkArrays/bitvector.hxx:104, from /usr/include/libGkArrays/solArray.h:106, from /usr/include/libGkArrays/gkArrays.h:112, @@ -1365,13 +1352,6 @@ /usr/include/libGkArrays/largebinvect.hxx:208:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 208 | inline LargeBinVect &operator--() throw (BinVectOverflow); | ^~~~~ -locateServer.cpp: In function 'void* launchSubServer(void*)': -locateServer.cpp:464:8: warning: unused variable 'threshold' [-Wunused-variable] - 464 | uint threshold = indexTags->getFactorLength(); - | ^~~~~~~~~ -locateServer.cpp:466:9: warning: variable 'dontCare' set but not used [-Wunused-but-set-variable] - 466 | char *dontCare, *variable, *tag_length, *factor; - | ^~~~~~~~ /usr/include/libGkArrays/largebinvect.hxx:210:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 210 | inline LargeBinVect operator--(int) throw (BinVectOverflow, std::bad_alloc); | ^~~~~ @@ -1388,22 +1368,46 @@ /usr/include/libGkArrays/largebinvect.cxx:147:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 147 | LargeBinVect::LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc) { | ^~~~~ +In file included from libReadsReader/readsReader.h:57, + from Read.h:55, + from ReadIndex.h:52, + from classifyTags.h:53, + from classifyTags.cpp:52: +libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] + 169 | static int kseq_read(kseq_t *seq) \ + | ^~~~~~~~~ +libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' + 227 | __KSEQ_READ + | ^~~~~~~~~~~ +libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' + 59 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ /usr/include/libGkArrays/largebinvect.cxx:167:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | LargeBinVect::LargeBinVect(const LargeBinVect &v) throw (std::bad_alloc) | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:184:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 184 | LargeBinVect &LargeBinVect::operator=(const LargeBinVect &v) throw (std::bad_alloc) { | ^~~~~ +In file included from libReadsReader/readsReader.h:57, + from Read.h:55, + from ReadIndex.h:52, + from Support.h:59, + from SupportBreak.cpp:55: +libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] + 169 | static int kseq_read(kseq_t *seq) \ + | ^~~~~~~~~ +libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' + 227 | __KSEQ_READ + | ^~~~~~~~~~~ +libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' + 59 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ /usr/include/libGkArrays/largebinvect.cxx:339:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 339 | LargeBinVect LargeBinVect::operator()(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) { | ^~~~~ /usr/include/libGkArrays/largebinvect.cxx:363:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 363 | unsigned long int LargeBinVect::GetValue(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) { | ^~~~~ -locateServer.cpp: In function 'void locateServer(ClassifyTags*, const char*, const char*)': -locateServer.cpp:717:9: warning: variable 'dontCare' set but not used [-Wunused-but-set-variable] - 717 | char *dontCare; - | ^~~~~~~~ /usr/include/libGkArrays/largebinvect.cxx:397:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 397 | bool LargeBinVect::operator[](const CountWordSize i) const throw (std::out_of_range) { | ^~~~~ @@ -1449,6 +1453,45 @@ /usr/include/libGkArrays/solArray.h:202:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 202 | void realloc(uintSA nbElements) throw (logic_error); | ^~~~~ +locateServer.cpp: In function 'void* launchSubServer(void*)': +locateServer.cpp:464:8: warning: unused variable 'threshold' [-Wunused-variable] + 464 | uint threshold = indexTags->getFactorLength(); + | ^~~~~~~~~ +locateServer.cpp:466:9: warning: variable 'dontCare' set but not used [-Wunused-but-set-variable] + 466 | char *dontCare, *variable, *tag_length, *factor; + | ^~~~~~~~ +locateServer.cpp: In function 'void locateServer(ClassifyTags*, const char*, const char*)': +locateServer.cpp:717:9: warning: variable 'dontCare' set but not used [-Wunused-but-set-variable] + 717 | char *dontCare; + | ^~~~~~~~ +In file included from libReadsReader/readsReader.h:57, + from Read.h:55, + from ReadIndex.h:52, + from Support.h:59, + from Support.cpp:57: +libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] + 169 | static int kseq_read(kseq_t *seq) \ + | ^~~~~~~~~ +libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' + 227 | __KSEQ_READ + | ^~~~~~~~~~~ +libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' + 59 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ +In file included from ./libReadsReader/readsReader.h:57, + from ./Read.h:55, + from ./ReadIndex.h:52, + from ./Classifier.h:56, + from Classifier.cpp:52: +./libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] + 169 | static int kseq_read(kseq_t *seq) \ + | ^~~~~~~~~ +./libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' + 227 | __KSEQ_READ + | ^~~~~~~~~~~ +./libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT' + 59 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ In file included from libReadsReader/readsReader.h:57, from Read.h:55, from ReadIndex.h:52, @@ -1510,7 +1553,7 @@ Classifier.cpp:187:33: note: 'bioundetermined_type' was declared here 187 | BioUndeterminedInfo::Type bioundetermined_type; | ^~~~~~~~~~~~~~~~~~~~ -/bin/bash ../libtool --tag=CXX --mode=link g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -ljellyfish-2.0 -lm -lpthread -lhts -lSSA -lReadsInfo -lReadsReader -lgzstream -L/build/crac-2.5.2+dfsg/src/libSSA -L/build/crac-2.5.2+dfsg/src/libReadsInfo -L/build/crac-2.5.2+dfsg/src/libReadsReader -ljellyfish-2.0 -lGkArrays -lProgressBar -Wl,-z,relro -Wl,-z,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o /build/crac-2.5.2+dfsg/src/libSSA/libSSA.a /build/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /build/crac-2.5.2+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm +/bin/sh ../libtool --tag=CXX --mode=link g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -ljellyfish-2.0 -lm -lpthread -lhts -lSSA -lReadsInfo -lReadsReader -lgzstream -L/build/crac-2.5.2+dfsg/src/libSSA -L/build/crac-2.5.2+dfsg/src/libReadsInfo -L/build/crac-2.5.2+dfsg/src/libReadsReader -ljellyfish-2.0 -lGkArrays -lProgressBar -Wl,-z,relro -Wl,-z,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o /build/crac-2.5.2+dfsg/src/libSSA/libSSA.a /build/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /build/crac-2.5.2+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm libtool: link: g++ -std=c++0x -g -O2 -ffile-prefix-map=/build/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o -lSSA -lReadsInfo -lReadsReader -lgzstream -L/build/crac-2.5.2+dfsg/src/libSSA -L/build/crac-2.5.2+dfsg/src/libReadsInfo -L/build/crac-2.5.2+dfsg/src/libReadsReader /usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so -lGkArrays -lProgressBar /build/crac-2.5.2+dfsg/src/libSSA/libSSA.a /build/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /build/crac-2.5.2+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm make[3]: Leaving directory '/build/crac-2.5.2+dfsg/src' make[2]: Leaving directory '/build/crac-2.5.2+dfsg/src' @@ -1649,8 +1692,8 @@ Making install in libSSA make[3]: Entering directory '/build/crac-2.5.2+dfsg/src/libSSA' make[4]: Entering directory '/build/crac-2.5.2+dfsg/src/libSSA' - /bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c crac-index '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' + /usr/bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c crac-index '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' libtool: install: /usr/bin/install -c crac-index /build/crac-2.5.2+dfsg/debian/crac/usr/bin/crac-index make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/crac-2.5.2+dfsg/src/libSSA' @@ -1661,7 +1704,7 @@ make[4]: Entering directory '/build/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[5]: Entering directory '/build/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[5]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/include/crac-2.5.2/kseq' + /usr/bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/include/crac-2.5.2/kseq' /usr/bin/install -c -m 644 kseq.h '/build/crac-2.5.2+dfsg/debian/crac/usr/include/crac-2.5.2/kseq' make[5]: Leaving directory '/build/crac-2.5.2+dfsg/src/libReadsReader/kseq' make[4]: Leaving directory '/build/crac-2.5.2+dfsg/src/libReadsReader/kseq' @@ -1674,8 +1717,8 @@ make[3]: Leaving directory '/build/crac-2.5.2+dfsg/src/libReadsReader' make[3]: Entering directory '/build/crac-2.5.2+dfsg/src' make[4]: Entering directory '/build/crac-2.5.2+dfsg/src' - /bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' - /bin/bash ../libtool --mode=install /usr/bin/install -c crac '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' + /usr/bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' + /bin/sh ../libtool --mode=install /usr/bin/install -c crac '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' libtool: install: /usr/bin/install -c crac /build/crac-2.5.2+dfsg/debian/crac/usr/bin/crac make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/crac-2.5.2+dfsg/src' @@ -1685,14 +1728,14 @@ make[2]: Entering directory '/build/crac-2.5.2+dfsg/man' make[3]: Entering directory '/build/crac-2.5.2+dfsg/man' make[3]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/share/man/man1' + /usr/bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/share/man/man1' /usr/bin/install -c -m 644 crac.1 '/build/crac-2.5.2+dfsg/debian/crac/usr/share/man/man1' make[3]: Leaving directory '/build/crac-2.5.2+dfsg/man' make[2]: Leaving directory '/build/crac-2.5.2+dfsg/man' Making install in scripts make[2]: Entering directory '/build/crac-2.5.2+dfsg/scripts' make[3]: Entering directory '/build/crac-2.5.2+dfsg/scripts' - /bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' + /usr/bin/mkdir -p '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' /usr/bin/install -c crac-client '/build/crac-2.5.2+dfsg/debian/crac/usr/bin' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/crac-2.5.2+dfsg/scripts' @@ -1775,12 +1818,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3397530/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3397530/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/3143674 and its subdirectories -I: Current time: Fri May 12 21:44:23 -12 2023 -I: pbuilder-time-stamp: 1683971063 +I: removing directory /srv/workspace/pbuilder/3397530 and its subdirectories +I: Current time: Sat Jun 15 06:13:27 +14 2024 +I: pbuilder-time-stamp: 1718381607