Diff of the two buildlogs: -- --- b1/build.log 2023-05-05 05:17:21.653878557 +0000 +++ b2/build.log 2023-05-05 05:55:25.849613035 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jun 5 23:27:49 -12 2024 -I: pbuilder-time-stamp: 1717673269 +I: Current time: Fri May 5 19:17:27 +14 2023 +I: pbuilder-time-stamp: 1683263847 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 [./abyss_2.3.5+dfsg.orig.tar.xz] I: copying [./abyss_2.3.5+dfsg-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Fri Oct 21 23:36:18 2022 -12 +gpgv: Signature made Sun Oct 23 01:36:18 2022 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key @@ -29,135 +29,167 @@ dpkg-source: info: applying fix-privacy-breach.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1050698/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1880974/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 May 5 19:18 /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/1880974/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1880974/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='e6bc35003759477b91a11686c92d5bc7' - 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='1050698' - PS1='# ' - PS2='> ' + INVOCATION_ID=3b94cc359e7f474d956d401e301f0bcc + 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=1880974 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.9Fgzdmb5/pbuilderrc_x3rl --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.9Fgzdmb5/b1 --logfile b1/build.log abyss_2.3.5+dfsg-2.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.9Fgzdmb5/pbuilderrc_3knJ --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.9Fgzdmb5/b2 --logfile b2/build.log --extrapackages usrmerge abyss_2.3.5+dfsg-2.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.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Apr 23 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 Apr 23 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/1050698/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 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 Apr 24 11:23 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 09:55 sed + lrwxrwxrwx 1 root root 9 May 5 19:18 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 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 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/1880974/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -317,7 +349,7 @@ Get: 106 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] -Fetched 71.7 MB in 1s (91.4 MB/s) +Fetched 71.7 MB in 5s (15.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-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 ... 19596 files and directories currently installed.) @@ -767,8 +799,19 @@ 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/abyss-2.3.5+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 > ../abyss_2.3.5+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/1880974/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/1880974/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/abyss-2.3.5+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 > ../abyss_2.3.5+dfsg-2_source.changes dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 2.3.5+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -807,14 +850,14 @@ checking whether g++ supports C++11 features with -std=c++11... yes 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 checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking dependency style of g++ -std=c++11... none checking for gawk... (cached) mawk @@ -964,7 +1007,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/abyss-2.3.5+dfsg' dh_auto_build - make -j16 + make -j15 make[2]: Entering directory '/build/abyss-2.3.5+dfsg' make all-recursive make[3]: Entering directory '/build/abyss-2.3.5+dfsg' @@ -1011,8 +1054,8 @@ ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdatalayer.a -g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/DataLayer' Making all in DataBase make[4]: Entering directory '/build/abyss-2.3.5+dfsg/DataBase' @@ -1057,12 +1100,17 @@ gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o prob.o prob.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o translate.o translate.c -alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined - 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, - | ^~~~~~~~~~~~~~ -alig.c:13:20: warning: inline function 'calc_weight' declared but never defined - 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, - | ^~~~~~~~~~~ +io.c: In function 'read_scr_matrix': +io.c:270:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 270 | fscanf( fp, "%i", &is); + | ^~~~~~~~~~~~~~~~~~~~~~ +io.c:282:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 282 | fscanf(fp, "%s\n", rline); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +io.c: In function 'read_diag_prob_dist': +io.c:371:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 371 | fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assemble.c:40:20: warning: inline function 'align_diag' declared but never defined 40 | extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); | ^~~~~~~~~~ @@ -1078,20 +1126,15 @@ assemble.c:13:20: warning: inline function 'calc_weight' declared but never defined 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, | ^~~~~~~~~~~ +alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined + 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, + | ^~~~~~~~~~~~~~ +alig.c:13:20: warning: inline function 'calc_weight' declared but never defined + 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, + | ^~~~~~~~~~~ diag.c:1456:17: warning: 'real_calc_weight' is static but used in inline function 'find_diags_dyn' which is not static 1456 | real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn); | ^~~~~~~~~~~~~~~~ -io.c: In function 'read_scr_matrix': -io.c:270:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 270 | fscanf( fp, "%i", &is); - | ^~~~~~~~~~~~~~~~~~~~~~ -io.c:282:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 282 | fscanf(fp, "%s\n", rline); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -io.c: In function 'read_diag_prob_dist': -io.c:371:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 371 | fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rm -f libdialign.a ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o ar: `u' modifier ignored since `D' is the default (see `U') @@ -1130,8 +1173,8 @@ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp -g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg-mpi abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Parallel' Making all in Bloom make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Bloom' @@ -1165,8 +1208,8 @@ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp -g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/DistanceEst' Making all in KAligner make[4]: Entering directory '/build/abyss-2.3.5+dfsg/KAligner' @@ -1191,8 +1234,8 @@ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm -g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Map' Making all in MergePaths @@ -1200,8 +1243,8 @@ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp -g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PathConsensus PathConsensus-PathConsensus.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o MergePaths MergePaths-MergePaths.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/MergePaths' Making all in Overlap @@ -1226,8 +1269,8 @@ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm -g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/ParseAligns' Making all in PathOverlap make[4]: Entering directory '/build/abyss-2.3.5+dfsg/PathOverlap' @@ -1312,7 +1355,7 @@ markdown README.md > README.html make[1]: Leaving directory '/build/abyss-2.3.5+dfsg' dh_auto_test - make -j16 check "TESTSUITEFLAGS=-j16 --verbose" VERBOSE=1 + make -j15 check "TESTSUITEFLAGS=-j15 --verbose" VERBOSE=1 make[1]: Entering directory '/build/abyss-2.3.5+dfsg' Making check in bin make[2]: Entering directory '/build/abyss-2.3.5+dfsg/bin' @@ -1528,7 +1571,6 @@ g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomFilter Konnector/BloomFilter-BloomFilter.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloom Konnector/DBGBloom-DBGBloomTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloomAlgorithms Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBFSVisitor Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_BidirectionalBFS Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_AllPathsSearch Graph/graph_AllPathsSearch-AllPathsSearchTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_HashGraph Graph/graph_HashGraph-HashGraphTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm @@ -1538,18 +1580,19 @@ g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_KmerPair PairedDBG/KmerPair-KmerPairTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_Dinuc PairedDBG/Dinuc-DinucTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_BranchRecord PairedDBG/BranchRecord-BranchRecordTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_MaskedKmer BloomDBG/MaskedKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_SpacedSeed BloomDBG/SpacedSeedTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHash BloomDBG/RollingHashTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHashIterator BloomDBG/RollingHashIteratorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_MaskedKmer BloomDBG/MaskedKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_SpacedSeed BloomDBG/SpacedSeedTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_LoadAlgorithm PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o ../PairedDBG/libpaireddbg.a ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_LightweightKmer BloomDBG/LightweightKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBFSVisitor Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ExtendPath Graph/graph_ExtendPath-ExtendPathTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBidiBFSVisitor Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_CountingBloomFilter BloomDBG/CountingBloomFilter-CountingBloomFilterTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_HashAgnosticCascadingBloom BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_BloomDBG BloomDBG/BloomDBG-BloomDBGTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_konnector Konnector/konnector-konnectorTest.o ../Align/libalign.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_CountingBloomFilter BloomDBG/CountingBloomFilter-CountingBloomFilterTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_BloomDBG BloomDBG/BloomDBG-BloomDBGTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBidiBFSVisitor Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingBloomDBG BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Unittest' make check-TESTS @@ -1560,35 +1603,35 @@ PASS: common_bitutil PASS: common_kmer PASS: common_sequence -PASS: common_sam PASS: common_KmerIterator -PASS: BloomFilter +PASS: common_sam PASS: common_sam_ssq -PASS: Konnector_DBGBloom +PASS: BloomFilter PASS: Konnector_DBGBloomAlgorithms +PASS: Konnector_DBGBloom PASS: graph_ConstrainedBFSVisitor PASS: graph_BidirectionalBFS PASS: graph_AllPathsSearch PASS: graph_HashGraph PASS: graph_ConstrainedBidiBFSVisitor -PASS: graph_ExtendPath PASS: graph_DotIO -PASS: graph_UndirectedGraph +PASS: graph_ExtendPath PASS: Konnector_konnector +PASS: graph_UndirectedGraph PASS: PairedDBG_KmerPair -PASS: PairedDBG_Dinuc PASS: PairedDBG_BranchRecord +PASS: PairedDBG_Dinuc PASS: BloomDBG_BloomDBG -PASS: BloomDBG_RollingHash PASS: BloomDBG_RollingHashIterator +PASS: BloomDBG_RollingHash PASS: BloomDBG_HashAgnosticCascadingBloom PASS: BloomDBG_CountingBloomFilter PASS: BloomDBG_RollingBloomDBG PASS: BloomDBG_MaskedKmer PASS: BloomDBG_SpacedSeed PASS: BloomDBG_LightweightKmer -PASS: PairedDBG_LoadAlgorithm PASS: DBG_LoadAlgorithm +PASS: PairedDBG_LoadAlgorithm ============================================================================ Testsuite summary for ABySS 2.3.5 ============================================================================ @@ -1611,12 +1654,12 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/abyss-2.3.5+dfsg' dh_auto_install --destdir=debian/tmp - make -j16 install DESTDIR=/build/abyss-2.3.5\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no + make -j15 install DESTDIR=/build/abyss-2.3.5\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/abyss-2.3.5+dfsg' Making install in bin make[3]: Entering directory '/build/abyss-2.3.5+dfsg/bin' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/bin' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk abyss-dida abyss-stack-size '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/bin' @@ -1625,7 +1668,7 @@ make[3]: Entering directory '/build/abyss-2.3.5+dfsg/doc' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/doc' make[4]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/share/doc/abyss' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/build/abyss-2.3.5+dfsg/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/doc' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/doc' @@ -1639,7 +1682,7 @@ Making install in Graph make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Graph' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Graph' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-gc abyss-todot '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Graph' @@ -1647,7 +1690,7 @@ Making install in DataLayer make[3]: Entering directory '/build/abyss-2.3.5+dfsg/DataLayer' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/DataLayer' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-fac abyss-tofastq '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/DataLayer' @@ -1655,8 +1698,8 @@ Making install in DataBase make[3]: Entering directory '/build/abyss-2.3.5+dfsg/DataBase' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/DataBase' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-db-csv '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-txt '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' @@ -1686,7 +1729,7 @@ Making install in Align make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Align' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Align' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-align abyss-mergepairs '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Align' @@ -1694,7 +1737,7 @@ Making install in ABYSS make[3]: Entering directory '/build/abyss-2.3.5+dfsg/ABYSS' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/ABYSS' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c ABYSS '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/ABYSS' @@ -1702,7 +1745,7 @@ Making install in Parallel make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Parallel' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Parallel' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Parallel' @@ -1710,7 +1753,7 @@ Making install in Bloom make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Bloom' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Bloom' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-bloom '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Bloom' @@ -1718,7 +1761,7 @@ Making install in BloomDBG make[3]: Entering directory '/build/abyss-2.3.5+dfsg/BloomDBG' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/BloomDBG' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-bloom-dbg '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/BloomDBG' @@ -1726,23 +1769,23 @@ Making install in Konnector make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Konnector' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Konnector' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c konnector '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Konnector' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Konnector' Making install in Consensus make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Consensus' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Consensus' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c Consensus '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Consensus' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Consensus' Making install in DAssembler make[3]: Entering directory '/build/abyss-2.3.5+dfsg/DAssembler' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/DAssembler' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c DAssembler '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/DAssembler' @@ -1750,7 +1793,7 @@ Making install in DistanceEst make[3]: Entering directory '/build/abyss-2.3.5+dfsg/DistanceEst' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/DistanceEst' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c DistanceEst DistanceEst-ssq '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/DistanceEst' @@ -1758,7 +1801,7 @@ Making install in KAligner make[3]: Entering directory '/build/abyss-2.3.5+dfsg/KAligner' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/KAligner' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c KAligner '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/KAligner' @@ -1766,23 +1809,23 @@ Making install in Layout make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Layout' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Layout' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-layout '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Layout' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Layout' Making install in LogKmerCount make[3]: Entering directory '/build/abyss-2.3.5+dfsg/LogKmerCount' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/LogKmerCount' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c logcounter '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/LogKmerCount' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/LogKmerCount' Making install in Map make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Map' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Map' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Map' @@ -1790,15 +1833,15 @@ Making install in MergePaths make[3]: Entering directory '/build/abyss-2.3.5+dfsg/MergePaths' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/MergePaths' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c MergePaths MergeContigs PathConsensus '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/MergePaths' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/MergePaths' Making install in Overlap make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Overlap' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Overlap' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c Overlap '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Overlap' @@ -1806,16 +1849,16 @@ Making install in PairedDBG make[3]: Entering directory '/build/abyss-2.3.5+dfsg/PairedDBG' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/PairedDBG' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-paired-dbg '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/PairedDBG' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/PairedDBG' Making install in ParseAligns make[3]: Entering directory '/build/abyss-2.3.5+dfsg/ParseAligns' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/ParseAligns' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/ParseAligns' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/ParseAligns' @@ -1823,14 +1866,14 @@ make[3]: Entering directory '/build/abyss-2.3.5+dfsg/PathOverlap' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/PathOverlap' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c PathOverlap '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/PathOverlap' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/PathOverlap' Making install in PopBubbles make[3]: Entering directory '/build/abyss-2.3.5+dfsg/PopBubbles' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/PopBubbles' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c PopBubbles '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/PopBubbles' @@ -1838,7 +1881,7 @@ Making install in Scaffold make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Scaffold' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Scaffold' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Scaffold' @@ -1847,7 +1890,7 @@ make[3]: Entering directory '/build/abyss-2.3.5+dfsg/SimpleGraph' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/SimpleGraph' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c SimpleGraph '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/SimpleGraph' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/SimpleGraph' @@ -1861,7 +1904,7 @@ Making install in FilterGraph make[3]: Entering directory '/build/abyss-2.3.5+dfsg/FilterGraph' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/FilterGraph' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-filtergraph '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/FilterGraph' @@ -1869,7 +1912,7 @@ Making install in GapFiller make[3]: Entering directory '/build/abyss-2.3.5+dfsg/GapFiller' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/GapFiller' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-gapfill '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/GapFiller' @@ -1877,23 +1920,23 @@ Making install in Sealer make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Sealer' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Sealer' - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-sealer '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Sealer' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Sealer' Making install in RResolver make[3]: Entering directory '/build/abyss-2.3.5+dfsg/RResolver' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/RResolver' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-rresolver-short '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/RResolver' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/RResolver' Making install in AdjList make[3]: Entering directory '/build/abyss-2.3.5+dfsg/AdjList' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/AdjList' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c AdjList '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/AdjList' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/AdjList' @@ -1921,16 +1964,16 @@ make[3]: Entering directory '/build/abyss-2.3.5+dfsg' make[4]: Entering directory '/build/abyss-2.3.5+dfsg' make[4]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/share/doc/abyss' + /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md '/build/abyss-2.3.5+dfsg/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg' make[2]: Leaving directory '/build/abyss-2.3.5+dfsg' mkdir -p debian/tmp/usr/share/man/man1 -PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games help2man --no-info \ +PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path help2man --no-info \ -n "Estimate distances between contigs using paired-end alignments." \ DistanceEst > debian/tmp/usr/share/man/man1/DistanceEst.1 -PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games help2man --no-info \ +PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path help2man --no-info \ -n "Fill the paired-end fields of SAM alignments" abyss-fixmate \ > debian/tmp/usr/share/man/man1/abyss-fixmate.1 make[1]: Leaving directory '/build/abyss-2.3.5+dfsg' @@ -1958,8 +2001,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'abyss' in '../abyss_2.3.5+dfsg-2_amd64.deb'. dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.3.5+dfsg-2_amd64.deb'. +dpkg-deb: building package 'abyss' in '../abyss_2.3.5+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../abyss_2.3.5+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../abyss_2.3.5+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1967,12 +2010,14 @@ 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/1880974/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1880974/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/1050698 and its subdirectories -I: Current time: Wed Jun 5 23:40:22 -12 2024 -I: pbuilder-time-stamp: 1717674022 +I: removing directory /srv/workspace/pbuilder/1880974 and its subdirectories +I: Current time: Fri May 5 19:55:25 +14 2023 +I: pbuilder-time-stamp: 1683266125