Diff of the two buildlogs: -- --- b1/build.log 2023-04-16 05:32:45.729778899 +0000 +++ b2/build.log 2023-04-16 05:37:13.557887626 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 17 23:52:17 -12 2024 -I: pbuilder-time-stamp: 1716033137 +I: Current time: Sun Apr 16 19:32:47 +14 2023 +I: pbuilder-time-stamp: 1681623167 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 [./hinge_0.5.0.orig.tar.gz] I: copying [./hinge_0.5.0-7.debian.tar.xz] I: Extracting source -gpgv: Signature made Tue Dec 21 19:23:38 2021 -12 +gpgv: Signature made Wed Dec 22 21:23:38 2021 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -32,135 +32,167 @@ dpkg-source: info: applying spdlog-1.5.0.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2416617/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1425028/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 Apr 16 19:32 /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/1425028/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1425028/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=16' - 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=15' + 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='012184e7e6164d2b928717e4b73e7111' - 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='2416617' - PS1='# ' - PS2='> ' + INVOCATION_ID=668c9d1ed29c47d0bb577fa41e9df96c + 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=1425028 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.AuZQ17u3/pbuilderrc_4U3W --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.AuZQ17u3/b1 --logfile b1/build.log hinge_0.5.0-7.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://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/r-b-build.AuZQ17u3/pbuilderrc_L72n --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.AuZQ17u3/b2 --logfile b2/build.log --extrapackages usrmerge hinge_0.5.0-7.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://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Feb 12 2023 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 2023 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 2023 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 2023 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 2022 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 2023 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 2023 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 2023 more - -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount - -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Feb 12 2023 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 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 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 2023 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 2023 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 2023 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 2023 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 2023 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 2022 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/2416617/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Feb 13 10:05 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 03:20 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 00:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 04:43 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 03:33 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 00:02 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 00:02 more + -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount + -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Feb 13 10:05 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 06:31 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 Apr 16 19:32 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 00:02 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 14520 Nov 3 06:31 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 22:35 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 00:02 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 00:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 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/1425028/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -449,7 +481,7 @@ Get: 217 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.20.0+ds-3+b1 [1681 kB] Get: 218 http://deb.debian.org/debian bookworm/main amd64 python3-pbcore all 2.1.2+dfsg-5 [2830 kB] Get: 219 http://deb.debian.org/debian bookworm/main amd64 python3-ujson amd64 5.7.0-1 [24.2 kB] -Fetched 199 MB in 2s (97.3 MB/s) +Fetched 199 MB in 3s (76.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal: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.) @@ -1354,8 +1386,19 @@ 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/hinge-0.5.0/ && 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 > ../hinge_0.5.0-7_source.changes +I: user script /srv/workspace/pbuilder/1425028/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/1425028/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/hinge-0.5.0/ && 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 > ../hinge_0.5.0-7_source.changes dpkg-buildpackage: info: source package hinge dpkg-buildpackage: info: source version 0.5.0-7 dpkg-buildpackage: info: source distribution unstable @@ -1441,7 +1484,7 @@ -- Build files have been written to: /build/hinge-0.5.0/obj-x86_64-linux-gnu dh_auto_build - cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/hinge-0.5.0 -B/build/hinge-0.5.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hinge-0.5.0/obj-x86_64-linux-gnu/CMakeFiles /build/hinge-0.5.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -1451,15 +1494,15 @@ make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/depend make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/depend make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/depend -make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' -cd /build/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src /build/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/CMakeFiles/man.dir/DependInfo.cmake --color= make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/depend make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' +cd /build/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src /build/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/CMakeFiles/man.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/ini.dir/DependInfo.cmake --color= +make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/DB.dir/DependInfo.cmake --color= -make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/LA.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' @@ -1469,44 +1512,44 @@ make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/DW_banded.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' +make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/build make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' -make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/build -make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/build -make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' +make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/build make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' -make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/build make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' -make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/build -make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/build +make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' -make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' +make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build +make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' +make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' +make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' -[ 3%] Building C object bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o -[ 6%] Building CXX object bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o -[ 10%] Building C object bin/lib/CMakeFiles/LA.dir/align.c.o -[ 13%] Building C object bin/lib/CMakeFiles/ini.dir/ini.c.o -[ 20%] Building C object bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -[ 20%] Building C object bin/lib/CMakeFiles/DB.dir/DB.c.o -[ 24%] Generating hinge.1 -cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o -MF CMakeFiles/DW_banded.dir/DW_banded.c.o.d -o CMakeFiles/DW_banded.dir/DW_banded.c.o -c /build/hinge-0.5.0/src/lib/DW_banded.c -[ 27%] Building C object bin/lib/CMakeFiles/PAF.dir/paf.c.o +[ 10%] Building C object bin/lib/CMakeFiles/DB.dir/DB.c.o +[ 10%] Building C object bin/lib/CMakeFiles/ini.dir/ini.c.o +[ 10%] Building C object bin/lib/CMakeFiles/DB.dir/QV.c.o +[ 13%] Building CXX object bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o +[ 17%] Generating hinge.1 +cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DB.dir/QV.c.o -MF CMakeFiles/DB.dir/QV.c.o.d -o CMakeFiles/DB.dir/QV.c.o -c /build/hinge-0.5.0/src/lib/QV.c +cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/ini.dir/ini.c.o -MF CMakeFiles/ini.dir/ini.c.o.d -o CMakeFiles/ini.dir/ini.c.o -c /build/hinge-0.5.0/src/lib/ini.c +[ 20%] Building C object bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DB.dir/DB.c.o -MF CMakeFiles/DB.dir/DB.c.o.d -o CMakeFiles/DB.dir/DB.c.o -c /build/hinge-0.5.0/src/lib/DB.c -cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -MF CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o.d -o CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -c /build/hinge-0.5.0/src/lib/kmer_lookup.c -cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/LA.dir/align.c.o -MF CMakeFiles/LA.dir/align.c.o.d -o CMakeFiles/LA.dir/align.c.o -c /build/hinge-0.5.0/src/lib/align.c cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin && /usr/bin/pandoc --from markdown --to man -s /build/hinge-0.5.0/src/hinge.1.md -o hinge.1 -[ 31%] Building C object bin/lib/CMakeFiles/DB.dir/QV.c.o -cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/ini.dir/ini.c.o -MF CMakeFiles/ini.dir/ini.c.o.d -o CMakeFiles/ini.dir/ini.c.o -c /build/hinge-0.5.0/src/lib/ini.c -cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DB.dir/QV.c.o -MF CMakeFiles/DB.dir/QV.c.o.d -o CMakeFiles/DB.dir/QV.c.o -c /build/hinge-0.5.0/src/lib/QV.c -cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/PAF.dir/paf.c.o -MF CMakeFiles/PAF.dir/paf.c.o.d -o CMakeFiles/PAF.dir/paf.c.o -c /build/hinge-0.5.0/src/lib/paf.c cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/c++ -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o -MF CMakeFiles/ini.dir/INIReader.cpp.o.d -o CMakeFiles/ini.dir/INIReader.cpp.o -c /build/hinge-0.5.0/src/lib/INIReader.cpp +cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o -MF CMakeFiles/DW_banded.dir/DW_banded.c.o.d -o CMakeFiles/DW_banded.dir/DW_banded.c.o -c /build/hinge-0.5.0/src/lib/DW_banded.c +[ 24%] Building C object bin/lib/CMakeFiles/LA.dir/align.c.o +cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/LA.dir/align.c.o -MF CMakeFiles/LA.dir/align.c.o.d -o CMakeFiles/LA.dir/align.c.o -c /build/hinge-0.5.0/src/lib/align.c +[ 27%] Building C object bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o +cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -MF CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o.d -o CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -c /build/hinge-0.5.0/src/lib/kmer_lookup.c +[ 31%] Building C object bin/lib/CMakeFiles/PAF.dir/paf.c.o +cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/PAF.dir/paf.c.o -MF CMakeFiles/PAF.dir/paf.c.o.d -o CMakeFiles/PAF.dir/paf.c.o -c /build/hinge-0.5.0/src/lib/paf.c make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' [ 31%] Built target man /build/hinge-0.5.0/src/lib/DB.c: In function 'Load_QVs': @@ -1519,6 +1562,11 @@ /build/hinge-0.5.0/src/lib/DB.c:925:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 925 | { fscanf(istub,DB_FDATA,&last,fname,prolog); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 34%] Linking C static library libPAF.a +cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/PAF.dir/cmake_clean_target.cmake +cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/PAF.dir/link.txt --verbose=1 +[ 37%] Linking C static library libDW_banded.a +cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/DW_banded.dir/cmake_clean_target.cmake /build/hinge-0.5.0/src/lib/kmer_lookup.c: In function 'find_best_aln_range': /build/hinge-0.5.0/src/lib/kmer_lookup.c:347:14: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 347 | q_coor = calloc( km_ptr->count, sizeof(seq_coor_t) ); @@ -1533,19 +1581,14 @@ /usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here 556 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ -[ 34%] Linking C static library libPAF.a -cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/PAF.dir/cmake_clean_target.cmake -[ 37%] Linking C static library libDW_banded.a -cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/DW_banded.dir/cmake_clean_target.cmake -cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/PAF.dir/link.txt --verbose=1 -cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DW_banded.dir/link.txt --verbose=1 /usr/bin/ar qc libPAF.a CMakeFiles/PAF.dir/paf.c.o /usr/bin/ranlib libPAF.a +cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DW_banded.dir/link.txt --verbose=1 +make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' /usr/bin/ar qc libDW_banded.a CMakeFiles/DW_banded.dir/DW_banded.c.o /usr/bin/ranlib libDW_banded.a -make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' [ 37%] Built target PAF +make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' [ 37%] Built target DW_banded /build/hinge-0.5.0/src/lib/DB.c: In function 'Open_DB': /build/hinge-0.5.0/src/lib/DB.c:533:11: warning: 'free' called on pointer 'p' with nonzero offset 40 [-Wfree-nonheap-object] @@ -1571,6 +1614,13 @@ make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' [ 44%] Building C object bin/lib/CMakeFiles/falcon.dir/falcon.c.o cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/falcon.dir/falcon.c.o -MF CMakeFiles/falcon.dir/falcon.c.o.d -o CMakeFiles/falcon.dir/falcon.c.o -c /build/hinge-0.5.0/src/lib/falcon.c +[ 48%] Linking C static library libfalcon.a +cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/falcon.dir/cmake_clean_target.cmake +cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/falcon.dir/link.txt --verbose=1 +/usr/bin/ar qc libfalcon.a CMakeFiles/falcon.dir/falcon.c.o +/usr/bin/ranlib libfalcon.a +make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' +[ 48%] Built target falcon /build/hinge-0.5.0/src/lib/DB.c: In function 'Read_All_Sequences': /build/hinge-0.5.0/src/lib/DB.c:1587:15: warning: 'free' called on pointer 'p' with nonzero offset 1 [-Wfree-nonheap-object] 1587 | free(seq); @@ -1580,22 +1630,15 @@ /build/hinge-0.5.0/src/lib/DB.c:84:12: note: returned from 'malloc' 84 | if ((p = malloc(size)) == NULL) | ^~~~~~~~~~~~ -[ 48%] Linking C static library libfalcon.a -cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/falcon.dir/cmake_clean_target.cmake -cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/falcon.dir/link.txt --verbose=1 -/usr/bin/ar qc libfalcon.a CMakeFiles/falcon.dir/falcon.c.o -/usr/bin/ranlib libfalcon.a -make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' -[ 48%] Built target falcon [ 51%] Linking C static library libDB.a cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/DB.dir/cmake_clean_target.cmake cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DB.dir/link.txt --verbose=1 /usr/bin/ar qc libDB.a CMakeFiles/DB.dir/DB.c.o CMakeFiles/DB.dir/QV.c.o /usr/bin/ranlib libDB.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' -[ 51%] Built target DB [ 55%] Linking CXX static library libini.a cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/ini.dir/cmake_clean_target.cmake +[ 55%] Built target DB cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/ini.dir/link.txt --verbose=1 /usr/bin/ar qc libini.a CMakeFiles/ini.dir/ini.c.o CMakeFiles/ini.dir/INIReader.cpp.o /usr/bin/ranlib libini.a @@ -1631,44 +1674,44 @@ make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' [ 65%] Built target LAInterface make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/depend -make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/depend -make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/depend -make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/depend -make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/filter /build/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter/CMakeFiles/Reads_filter.dir/DependInfo.cmake --color= +make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/maximal /build/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal/CMakeFiles/get_maximal_reads.dir/DependInfo.cmake --color= +make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/consensus /build/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus/CMakeFiles/draft_assembly.dir/DependInfo.cmake --color= +make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/consensus /build/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus/CMakeFiles/consensus.dir/DependInfo.cmake --color= +make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/layout /build/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout/CMakeFiles/hinging.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' -make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/build -make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' -make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/build -make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/build make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' -make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build -make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' +make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/build +make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' +make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/build +make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' +make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' -[ 68%] Building CXX object bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o -[ 72%] Building CXX object bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o -[ 79%] Building CXX object bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -[ 79%] Building CXX object bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o +[ 68%] Building CXX object bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o +[ 72%] Building CXX object bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o +cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o -MF CMakeFiles/Reads_filter.dir/filter.cpp.o.d -o CMakeFiles/Reads_filter.dir/filter.cpp.o -c /build/hinge-0.5.0/src/filter/filter.cpp +cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -MF CMakeFiles/get_maximal_reads.dir/maximal.cpp.o.d -o CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -c /build/hinge-0.5.0/src/maximal/maximal.cpp +[ 75%] Building CXX object bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o -MF CMakeFiles/draft_assembly.dir/draft.cpp.o.d -o CMakeFiles/draft_assembly.dir/draft.cpp.o -c /build/hinge-0.5.0/src/consensus/draft.cpp +[ 79%] Building CXX object bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o -MF CMakeFiles/consensus.dir/consensus.cpp.o.d -o CMakeFiles/consensus.dir/consensus.cpp.o -c /build/hinge-0.5.0/src/consensus/consensus.cpp -cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o -MF CMakeFiles/Reads_filter.dir/filter.cpp.o.d -o CMakeFiles/Reads_filter.dir/filter.cpp.o -c /build/hinge-0.5.0/src/filter/filter.cpp [ 82%] Building CXX object bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o -cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -MF CMakeFiles/get_maximal_reads.dir/maximal.cpp.o.d -o CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -c /build/hinge-0.5.0/src/maximal/maximal.cpp cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o -MF CMakeFiles/hinging.dir/hinging.cpp.o.d -o CMakeFiles/hinging.dir/hinging.cpp.o -c /build/hinge-0.5.0/src/layout/hinging.cpp [ 86%] Linking CXX executable consensus cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus && /usr/bin/cmake -E cmake_link_script CMakeFiles/consensus.dir/link.txt --verbose=1 @@ -1680,16 +1723,16 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -o get_maximal_reads -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' [ 89%] Built target get_maximal_reads -[ 93%] Linking CXX executable Reads_filter -cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter && /usr/bin/cmake -E cmake_link_script CMakeFiles/Reads_filter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/Reads_filter.dir/filter.cpp.o -o Reads_filter -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz -make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' -[ 93%] Built target Reads_filter -[ 96%] Linking CXX executable draft_assembly +[ 93%] Linking CXX executable draft_assembly cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus && /usr/bin/cmake -E cmake_link_script CMakeFiles/draft_assembly.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/draft_assembly.dir/draft.cpp.o -o draft_assembly -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libfalcon.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz ../lib/libkmer_lookup.a ../lib/libDW_banded.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' -[ 96%] Built target draft_assembly +[ 93%] Built target draft_assembly +[ 96%] Linking CXX executable Reads_filter +cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter && /usr/bin/cmake -E cmake_link_script CMakeFiles/Reads_filter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/Reads_filter.dir/filter.cpp.o -o Reads_filter -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz +make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' +[ 96%] Built target Reads_filter [100%] Linking CXX executable hinging cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout && /usr/bin/cmake -E cmake_link_script CMakeFiles/hinging.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hinging.dir/hinging.cpp.o -o hinging -lfmt ../lib/libLAInterface.a ../lib/libini.a /usr/lib/x86_64-linux-gnu/libboost_graph.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz /usr/lib/x86_64-linux-gnu/libboost_regex.a @@ -1702,7 +1745,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/hinge/ - cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/hinge-0.5.0/debian/hinge AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/hinge-0.5.0/debian/hinge AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/hinge-0.5.0 -B/build/hinge-0.5.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -1810,12 +1853,14 @@ 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/1425028/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1425028/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/2416617 and its subdirectories -I: Current time: Fri May 17 23:55:46 -12 2024 -I: pbuilder-time-stamp: 1716033346 +I: removing directory /srv/workspace/pbuilder/1425028 and its subdirectories +I: Current time: Sun Apr 16 19:37:13 +14 2023 +I: pbuilder-time-stamp: 1681623433