Diff of the two buildlogs: -- --- b1/build.log 2022-08-26 07:16:31.619393984 +0000 +++ b2/build.log 2022-08-26 07:50:02.804063433 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Sep 28 01:09:31 -12 2023 -I: pbuilder-time-stamp: 1695906571 +I: Current time: Fri Aug 26 21:16:35 +14 2022 +I: pbuilder-time-stamp: 1661498195 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Mon Dec 24 02:47:04 2018 -12 +gpgv: Signature made Tue Dec 25 04:47:04 2018 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./jellyfish_2.2.10-2.dsc @@ -32,136 +32,171 @@ dpkg-source: info: applying fix_replacement_of_-L_option.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2609232/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2751546/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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +lrwxrwxrwx 1 root root 4 Aug 26 21:17 /bin/sh -> 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/2751546/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2751546/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='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(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= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='d50733253129480baffd0b05053c6115' - 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='2609232' - PS1='# ' - PS2='> ' + INVOCATION_ID=b702b02b20054d6a840f6c08610b0d10 + 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=2751546 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.zQO9rNdLRu/pbuilderrc_4PFa --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.zQO9rNdLRu/b1 --logfile b1/build.log jellyfish_2.2.10-2.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.zQO9rNdLRu/pbuilderrc_7FYO --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.zQO9rNdLRu/b2 --logfile b2/build.log jellyfish_2.2.10-2.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 ionos5-amd64 5.18.0-0.deb11.3-amd64 #1 SMP PREEMPT_DYNAMIC Debian 5.18.14-1~bpo11+1 (2022-07-28) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-17-amd64 #1 SMP Debian 5.10.136-1 (2022-08-13) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Sep 9 02:47 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/2609232/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 26 21:17 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 7 22:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/2751546/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -322,7 +357,7 @@ Get: 101 http://deb.debian.org/debian buster/main amd64 swig amd64 3.0.12-2 [310 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 time amd64 1.7-25.1+b1 [31.6 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 yaggo all 1.5.10-2 [18.9 kB] -Fetched 121 MB in 4s (30.0 MB/s) +Fetched 121 MB in 13s (9483 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0: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 ... 19195 files and directories currently installed.) @@ -769,7 +804,8 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/jellyfish-2.2.10/ && 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 > ../jellyfish_2.2.10-2_source.changes +hostname: Name or service not known +I: Running cd /build/jellyfish-2.2.10/ && 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 > ../jellyfish_2.2.10-2_source.changes dpkg-buildpackage: info: source package jellyfish dpkg-buildpackage: info: source version 2.2.10-2 dpkg-buildpackage: info: source distribution unstable @@ -918,7 +954,7 @@ checking for x86-AVX xgetbv output... unknown checking for x86 cpuid 0x00000000 output... d:68747541:444d4163:69746e65 checking for x86 cpuid 0x80000000 output... 8000001a:68747541:444d4163:69746e65 -checking for x86 cpuid 0x00000001 output... 600f12:800:9eb82203:78bfbff +checking for x86 cpuid 0x00000001 output... 600f12:9000800:9eb82203:78bfbff checking for x86 cpuid 0x00000007 output... 0:0:0:0 checking for x86 cpuid 0x80000001 output... 600f12:0:10be7:2dd3fbff checking for x86-AVX xgetbv 0x00000000 output... 7:0 @@ -1042,37 +1078,37 @@ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/cite_main.o sub_commands/cite_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/mem_main.o sub_commands/mem_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/merge_files.o jellyfish/merge_files.cc -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c -o lib/rectangular_binary_matrix.lo lib/rectangular_binary_matrix.cc +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c -o lib/rectangular_binary_matrix.lo lib/rectangular_binary_matrix.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c lib/rectangular_binary_matrix.cc -fPIC -DPIC -o lib/.libs/rectangular_binary_matrix.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c lib/rectangular_binary_matrix.cc -o lib/rectangular_binary_matrix.o >/dev/null 2>&1 -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c -o lib/mer_dna.lo lib/mer_dna.cc +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. 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libjellyfish-2.0.la +/bin/sh ./libtool --tag=CXX --mode=link g++ -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.28.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/8/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -Wl,-rpath -Wl,/build/jellyfish-2.2.10/.libs -lpthread ./.libs/libjellyfish-2.0.so -L/usr/lib/gcc/x86_64-linux-gnu/8 -L/usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/8/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/8/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: link: (cd "swig/perl5/.libs" && rm -f "jellyfish.so.0" && ln -s "jellyfish.so.0.0.0" "jellyfish.so.0") libtool: link: (cd "swig/perl5/.libs" && rm -f "jellyfish.so" && ln -s "jellyfish.so.0.0.0" "jellyfish.so") @@ -1098,7 +1134,7 @@ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/mersenne.o jellyfish/mersenne.cpp g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/backtrace.o jellyfish/backtrace.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dbg.o jellyfish/dbg.cc -/bin/bash ./libtool --tag=CXX --mode=link g++ -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -lpthread -o bin/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o jellyfish/backtrace.o jellyfish/dbg.o libjellyfish-2.0.la +/bin/sh ./libtool --tag=CXX --mode=link g++ -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -lpthread -o bin/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o jellyfish/backtrace.o jellyfish/dbg.o libjellyfish-2.0.la libtool: link: g++ -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o jellyfish/backtrace.o jellyfish/dbg.o -lpthread ./.libs/libjellyfish-2.0.so -pthread g++ -DHAVE_CONFIG_H -I. -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_main.o `test -f 'unit_tests/test_main.cc' || echo './'`unit_tests/test_main.cc g++ -DHAVE_CONFIG_H -I. -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_misc.o `test -f 'unit_tests/test_misc.cc' || echo './'`unit_tests/test_misc.cc @@ -1126,23 +1162,23 @@ g++ -DHAVE_CONFIG_H -I. -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_atomic_bits_array.o `test -f 'unit_tests/test_atomic_bits_array.cc' || echo './'`unit_tests/test_atomic_bits_array.cc g++ -DHAVE_CONFIG_H -I. -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_stdio_filebuf.o `test -f 'unit_tests/test_stdio_filebuf.cc' || echo './'`unit_tests/test_stdio_filebuf.cc g++ -DHAVE_CONFIG_H -I. -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/bin_test_all-backtrace.o `test -f 'jellyfish/backtrace.cc' || echo './'`jellyfish/backtrace.cc -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/gtest/src/libgtest_la-gtest-all.lo `test -f 'unit_tests/gtest/src/gtest-all.cc' || echo './'`unit_tests/gtest/src/gtest-all.cc +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/gtest/src/libgtest_la-gtest-all.lo `test -f 'unit_tests/gtest/src/gtest-all.cc' || echo './'`unit_tests/gtest/src/gtest-all.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c unit_tests/gtest/src/gtest-all.cc -fPIC -DPIC -o unit_tests/gtest/src/.libs/libgtest_la-gtest-all.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c unit_tests/gtest/src/gtest-all.cc -o unit_tests/gtest/src/libgtest_la-gtest-all.o >/dev/null 2>&1 -/bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -lpthread -o libgtest.la unit_tests/gtest/src/libgtest_la-gtest-all.lo +/bin/sh ./libtool --tag=CXX --mode=link g++ -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -lpthread -o libgtest.la unit_tests/gtest/src/libgtest_la-gtest-all.lo libtool: link: ar cru .libs/libgtest.a unit_tests/gtest/src/.libs/libgtest_la-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libgtest.a libtool: link: ( cd ".libs" && rm -f "libgtest.la" && ln -s "../libgtest.la" "libgtest.la" ) -/bin/bash ./libtool --tag=CXX --mode=link g++ -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -lpthread -o bin/test_all unit_tests/bin_test_all-test_main.o unit_tests/bin_test_all-test_misc.o unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_rectangular_binary_matrix.o unit_tests/bin_test_all-test_mer_dna.o unit_tests/bin_test_all-test_large_hash_array.o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o unit_tests/bin_test_all-test_file_header.o unit_tests/bin_test_all-test_mer_iterator.o unit_tests/bin_test_all-test_hash_counter.o unit_tests/bin_test_all-test_mer_heap.o unit_tests/bin_test_all-test_stream_iterator.o unit_tests/bin_test_all-test_token_ring.o unit_tests/bin_test_all-test_text_dumper.o unit_tests/bin_test_all-test_dumpers.o unit_tests/bin_test_all-test_mapped_file.o unit_tests/bin_test_all-test_int128.o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o unit_tests/bin_test_all-test_whole_sequence_parser.o unit_tests/bin_test_all-test_allocators_mmap.o unit_tests/bin_test_all-test_cooperative_pool2.o unit_tests/bin_test_all-test_generator_manager.o unit_tests/bin_test_all-test_atomic_bits_array.o unit_tests/bin_test_all-test_stdio_filebuf.o jellyfish/bin_test_all-backtrace.o libgtest.la libjellyfish-2.0.la +/bin/sh ./libtool --tag=CXX --mode=link g++ -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -lpthread -o bin/test_all unit_tests/bin_test_all-test_main.o unit_tests/bin_test_all-test_misc.o unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_rectangular_binary_matrix.o unit_tests/bin_test_all-test_mer_dna.o unit_tests/bin_test_all-test_large_hash_array.o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o unit_tests/bin_test_all-test_file_header.o unit_tests/bin_test_all-test_mer_iterator.o unit_tests/bin_test_all-test_hash_counter.o unit_tests/bin_test_all-test_mer_heap.o unit_tests/bin_test_all-test_stream_iterator.o unit_tests/bin_test_all-test_token_ring.o unit_tests/bin_test_all-test_text_dumper.o unit_tests/bin_test_all-test_dumpers.o unit_tests/bin_test_all-test_mapped_file.o unit_tests/bin_test_all-test_int128.o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o unit_tests/bin_test_all-test_whole_sequence_parser.o unit_tests/bin_test_all-test_allocators_mmap.o unit_tests/bin_test_all-test_cooperative_pool2.o unit_tests/bin_test_all-test_generator_manager.o unit_tests/bin_test_all-test_atomic_bits_array.o unit_tests/bin_test_all-test_stdio_filebuf.o jellyfish/bin_test_all-backtrace.o libgtest.la libjellyfish-2.0.la libtool: link: g++ -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/test_all unit_tests/bin_test_all-test_main.o unit_tests/bin_test_all-test_misc.o unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_rectangular_binary_matrix.o unit_tests/bin_test_all-test_mer_dna.o unit_tests/bin_test_all-test_large_hash_array.o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o unit_tests/bin_test_all-test_file_header.o unit_tests/bin_test_all-test_mer_iterator.o unit_tests/bin_test_all-test_hash_counter.o unit_tests/bin_test_all-test_mer_heap.o unit_tests/bin_test_all-test_stream_iterator.o unit_tests/bin_test_all-test_token_ring.o unit_tests/bin_test_all-test_text_dumper.o unit_tests/bin_test_all-test_dumpers.o unit_tests/bin_test_all-test_mapped_file.o unit_tests/bin_test_all-test_int128.o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o unit_tests/bin_test_all-test_whole_sequence_parser.o unit_tests/bin_test_all-test_allocators_mmap.o unit_tests/bin_test_all-test_cooperative_pool2.o unit_tests/bin_test_all-test_generator_manager.o unit_tests/bin_test_all-test_atomic_bits_array.o unit_tests/bin_test_all-test_stdio_filebuf.o jellyfish/bin_test_all-backtrace.o ./.libs/libgtest.a -lpthread ./.libs/libjellyfish-2.0.so -pthread g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/fastq2sam.o jellyfish/fastq2sam.cc -/bin/bash ./libtool --tag=CXX --mode=link g++ -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -lpthread -o bin/fastq2sam jellyfish/fastq2sam.o libjellyfish-2.0.la +/bin/sh ./libtool --tag=CXX --mode=link g++ -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -lpthread -o bin/fastq2sam jellyfish/fastq2sam.o libjellyfish-2.0.la libtool: link: g++ -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/fastq2sam jellyfish/fastq2sam.o -lpthread ./.libs/libjellyfish-2.0.so -pthread make[2]: Leaving directory '/build/jellyfish-2.2.10' make[1]: Leaving directory '/build/jellyfish-2.2.10' dh_auto_test - make -j16 check VERBOSE=1 + make -j15 check VERBOSE=1 make[1]: Entering directory '/build/jellyfish-2.2.10' make check-am make[2]: Entering directory '/build/jellyfish-2.2.10' @@ -1152,10 +1188,10 @@ make[3]: 'bin/fastq2sam' is up to date. make[3]: 'bin/test_all' is up to date. make[3]: 'libgtest.la' is up to date. -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/gtest/src/libgtest_main_la-gtest_main.lo `test -f 'unit_tests/gtest/src/gtest_main.cc' || echo './'`unit_tests/gtest/src/gtest_main.cc +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/gtest/src/libgtest_main_la-gtest_main.lo `test -f 'unit_tests/gtest/src/gtest_main.cc' || echo './'`unit_tests/gtest/src/gtest_main.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c unit_tests/gtest/src/gtest_main.cc -fPIC -DPIC -o unit_tests/gtest/src/.libs/libgtest_main_la-gtest_main.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -c unit_tests/gtest/src/gtest_main.cc -o unit_tests/gtest/src/libgtest_main_la-gtest_main.o >/dev/null 2>&1 -/bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -lpthread -o libgtest_main.la unit_tests/gtest/src/libgtest_main_la-gtest_main.lo libgtest.la +/bin/sh ./libtool --tag=CXX --mode=link g++ -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -lpthread -o libgtest_main.la unit_tests/gtest/src/libgtest_main_la-gtest_main.lo libgtest.la libtool: link: (cd .libs/libgtest_main.lax/libgtest.a && ar x "/build/jellyfish-2.2.10/./.libs/libgtest.a") libtool: link: ar cru .libs/libgtest_main.a unit_tests/gtest/src/.libs/libgtest_main_la-gtest_main.o .libs/libgtest_main.lax/libgtest.a/libgtest_la-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') @@ -1168,8 +1204,8 @@ make[4]: Entering directory '/build/jellyfish-2.2.10' SKIP: tests/big.sh PASS: tests/generate_sequence.sh -SKIP: tests/sam.sh SKIP: tests/swig_python.sh +SKIP: tests/sam.sh SKIP: tests/swig_ruby.sh PASS: tests/small_mers.sh PASS: tests/subset_hashing.sh @@ -1178,311 +1214,106 @@ PASS: tests/multi_file.sh PASS: tests/large_key.sh PASS: tests/merge.sh -PASS: tests/swig_perl.sh +FAIL: tests/swig_perl.sh PASS: tests/parallel_hashing.sh PASS: unit_tests/unit_tests.sh -============================================================================ -Testsuite summary for jellyfish 2.2.10 -============================================================================ +======================================== + jellyfish 2.2.10: ./test-suite.log +======================================== + # TOTAL: 15 -# PASS: 11 +# PASS: 10 # SKIP: 4 # XFAIL: 0 -# FAIL: 0 +# FAIL: 1 # XPASS: 0 # ERROR: 0 -============================================================================ -make[4]: Leaving directory '/build/jellyfish-2.2.10' -make[3]: Leaving directory '/build/jellyfish-2.2.10' -make[2]: Leaving directory '/build/jellyfish-2.2.10' -make[1]: Leaving directory '/build/jellyfish-2.2.10' - create-stamp debian/debhelper-build-stamp - fakeroot debian/rules binary -dh binary # --with python3 - dh_testroot - dh_prep - debian/rules override_dh_auto_install -make[1]: Entering directory '/build/jellyfish-2.2.10' -dh_auto_install -- install-data - make -j1 install DESTDIR=/build/jellyfish-2.2.10/debian/tmp AM_UPDATE_INFO_DIR=no install-data -make[2]: Entering directory '/build/jellyfish-2.2.10' -make install-am -make[3]: Entering directory '/build/jellyfish-2.2.10' -make[4]: Entering directory '/build/jellyfish-2.2.10' - /bin/mkdir -p '/build/jellyfish-2.2.10/debian/tmp/usr/lib/x86_64-linux-gnu' - /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/jellyfish-2.2.10/debian/tmp/usr/lib/x86_64-linux-gnu' -libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/jellyfish-2.2.10/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 -libtool: install: (cd /build/jellyfish-2.2.10/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) -libtool: install: (cd /build/jellyfish-2.2.10/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) -libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /build/jellyfish-2.2.10/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la -libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/jellyfish-2.2.10/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a -libtool: install: chmod 644 /build/jellyfish-2.2.10/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a -libtool: install: ranlib /build/jellyfish-2.2.10/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a -libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' - /bin/mkdir -p '/build/jellyfish-2.2.10/debian/tmp/usr/bin' - /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/jellyfish-2.2.10/debian/tmp/usr/bin' -libtool: warning: 'libjellyfish-2.0.la' has not been installed in '/usr/lib/x86_64-linux-gnu' -libtool: install: /usr/bin/install -c bin/.libs/jellyfish /build/jellyfish-2.2.10/debian/tmp/usr/bin/jellyfish - /bin/mkdir -p '/build/jellyfish-2.2.10/debian/tmp/usr/include/jellyfish-2.2.10/jellyfish' - /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/build/jellyfish-2.2.10/debian/tmp/usr/include/jellyfish-2.2.10/jellyfish' - /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/build/jellyfish-2.2.10/debian/tmp/usr/include/jellyfish-2.2.10/jellyfish' - /bin/mkdir -p '/build/jellyfish-2.2.10/debian/tmp/usr/share/man/man1' - /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-2.2.10/debian/tmp/usr/share/man/man1/jellyfish.1' - /bin/mkdir -p '/build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0' - /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0' -libtool: warning: relinking 'swig/perl5/jellyfish.la' -libtool: install: (cd /build/jellyfish-2.2.10; /bin/bash "/build/jellyfish-2.2.10/libtool" --tag CXX --mode=relink g++ -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.28.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-2.2.10/debian/tmp) -libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/8/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.2.10/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/8 -L/usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/8/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/8/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 -libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0/jellyfish.so.0.0.0 -libtool: install: (cd /build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) -libtool: install: (cd /build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) -libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0/jellyfish.la -libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0/jellyfish.a -libtool: install: chmod 644 /build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0/jellyfish.a -libtool: install: ranlib /build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0/jellyfish.a -libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.28.0' - /bin/mkdir -p '/build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0' - /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0' - /bin/mkdir -p '/build/jellyfish-2.2.10/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' - /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-2.2.10/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' -make[4]: Leaving directory '/build/jellyfish-2.2.10' -make[3]: Leaving directory '/build/jellyfish-2.2.10' - /bin/mkdir -p '/build/jellyfish-2.2.10/debian/tmp/usr/include/jellyfish-2.2.10/jellyfish' - /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/build/jellyfish-2.2.10/debian/tmp/usr/include/jellyfish-2.2.10/jellyfish' - /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/build/jellyfish-2.2.10/debian/tmp/usr/include/jellyfish-2.2.10/jellyfish' - /bin/mkdir -p '/build/jellyfish-2.2.10/debian/tmp/usr/share/man/man1' - /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-2.2.10/debian/tmp/usr/share/man/man1/jellyfish.1' - /bin/mkdir -p '/build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0' - /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0' -libtool: warning: relinking 'swig/perl5/jellyfish.la' -libtool: install: (cd /build/jellyfish-2.2.10; /bin/bash "/build/jellyfish-2.2.10/libtool" --tag CXX --mode=relink g++ -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.28.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-2.2.10/debian/tmp) -libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/8/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.2.10/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/8 -L/usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/8/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/8/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 -libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0/jellyfish.so.0.0.0 -libtool: install: (cd /build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) -libtool: install: (cd /build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) -libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0/jellyfish.la -libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0/jellyfish.a -libtool: install: chmod 644 /build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0/jellyfish.a -libtool: install: ranlib /build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0/jellyfish.a -libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.28.0' - /bin/mkdir -p '/build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0' - /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-2.2.10/debian/tmp/usr/lib/perl/5.28.0' - /bin/mkdir -p '/build/jellyfish-2.2.10/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' - /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-2.2.10/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' -make[2]: Leaving directory '/build/jellyfish-2.2.10' -make[1]: Leaving directory '/build/jellyfish-2.2.10' - debian/rules override_dh_install -make[1]: Entering directory '/build/jellyfish-2.2.10' -# dh_install -X*.a -X*.la -Xpkgconfig -dh_auto_configure --sourcedirectory=swig/perl5 - cd swig/perl5 && perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lpthread" --I/build/jellyfish-2.2.10/debian/tmp//usr/include/jellyfish-2.2.10 --L/build/jellyfish-2.2.10/debian/tmp//usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -lpthread --L/build/jellyfish-2.2.10/debian/tmp//usr/lib/x86_64-linux-gnu -Generating a Unix-style Makefile -Writing Makefile for jellyfish -Writing MYMETA.yml and MYMETA.json -dh_auto_build --sourcedirectory=swig/perl5 - cd swig/perl5 && make -j16 -make[2]: Entering directory '/build/jellyfish-2.2.10/swig/perl5' -Running Mkbootstrap for jellyfish () -cp jellyfish.pm blib/lib/jellyfish.pm -g++ -c -std=c++0x -I/build/jellyfish-2.2.10/debian/tmp//usr/include/jellyfish-2.2.10 -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.0.1\" -DXS_VERSION=\"0.0.1\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.28/CORE" swig_wrap.cpp -chmod 644 "jellyfish.bs" -"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- jellyfish.bs blib/arch/auto/jellyfish/jellyfish.bs 644 -rm -f blib/arch/auto/jellyfish/jellyfish.so -LD_RUN_PATH="/build/jellyfish-2.2.10/debian/tmp//usr/lib/x86_64-linux-gnu" x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/jellyfish-2.2.10=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lpthread -shared -L/usr/local/lib -fstack-protector-strong swig_wrap.o -o blib/arch/auto/jellyfish/jellyfish.so \ - -L/build/jellyfish-2.2.10/debian/tmp//usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -lpthread \ - -chmod 755 blib/arch/auto/jellyfish/jellyfish.so -make[2]: Leaving directory '/build/jellyfish-2.2.10/swig/perl5' -dh_auto_install --sourcedirectory=swig/perl5 - cd swig/perl5 && make -j16 install DESTDIR=/build/jellyfish-2.2.10/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr -make[2]: Entering directory '/build/jellyfish-2.2.10/swig/perl5' -"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- jellyfish.bs blib/arch/auto/jellyfish/jellyfish.bs 644 -Files found in blib/arch: installing files in blib/lib into architecture dependent library tree -Installing /build/jellyfish-2.2.10/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.28/auto/jellyfish/jellyfish.so -Installing /build/jellyfish-2.2.10/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.28/jellyfish.pm -make[2]: Leaving directory '/build/jellyfish-2.2.10/swig/perl5' -chrpath --delete debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so -dh_install -d-shlibmove --commit \ - --multiarch \ - --devunversioned \ - --movedev "debian/tmp/usr/include/jellyfish*/jellyfish/*.hpp" usr/include/jellyfish \ - --movedev "debian/tmp/usr/include/jellyfish*/jellyfish/*.h" usr/include/jellyfish \ - debian/tmp/usr/lib/*/libjellyfish-*.so -Library package automatic movement utility -set -e -install -d -m 755 debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu -install -d -m 755 debian/libjellyfish-2.0-2/usr/lib/x86_64-linux-gnu -mv debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu -mv debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu || true -mv debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu -mv /build/jellyfish-2.2.10/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2 debian/libjellyfish-2.0-2/usr/lib/x86_64-linux-gnu -mv /build/jellyfish-2.2.10/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 debian/libjellyfish-2.0-2/usr/lib/x86_64-linux-gnu -PKGDEV=libjellyfish-2.0-dev -PKGSHL=libjellyfish-2.0-2 -install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish -mv debian/tmp/usr/include/jellyfish*/jellyfish/*.hpp debian/libjellyfish-2.0-dev/usr/include/jellyfish -install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish -mv debian/tmp/usr/include/jellyfish*/jellyfish/*.h debian/libjellyfish-2.0-dev/usr/include/jellyfish -sed -i "/dependency_libs/ s/'.*'/''/" ./debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu/*.la -make[1]: Leaving directory '/build/jellyfish-2.2.10' - dh_installdocs - dh_installchangelogs - debian/rules override_dh_installexamples -make[1]: Entering directory '/build/jellyfish-2.2.10' -dh_installexamples -sed '/SRCDIR=/d' debian/jellyfish-examples/usr/share/doc/jellyfish-examples/examples/compat.sh* -if [ -z "$nCPUs" ]; then - nCPUs=$(grep -c '^processor' /proc/cpuinfo 2>/dev/null || sysctl -n hw.ncpu) -fi -pref=$(basename $0 .sh) -DIR=../bin -JF="$DIR/jellyfish" -[ -n "$VALGRIND" ] && JF="valgrind $JF" -BUILDDIR=/build/jellyfish-2.2.10 - -check () { - cut -d\ -f 2 $1 | xargs md5sum | sed 's/ \*/ /' | sort -k2,2 | diff -w $DIFFFLAGS $1 - -} -ENABLE_RUBY_BINDING="" -RUBY="" -ENABLE_PYTHON_BINDING="" -PYTHON="" -ENABLE_PERL_BINDING="/usr/lib/perl/5.28.0" -PERL="/usr/bin/perl" -SAMTOOLS="" +.. contents:: :depth: 2 -if [ -n "$DEBUG" ]; then - set -x; - DIFFFLAGS="-y" -fi - -set -e -if [ -z "$nCPUs" ]; then - nCPUs=$(grep -c '^processor' /proc/cpuinfo 2>/dev/null || sysctl -n hw.ncpu) -fi -pref=$(basename $0 .sh) -DIR=../bin -JF="$DIR/jellyfish" -[ -n "$VALGRIND" ] && JF="valgrind $JF" -BUILDDIR=@abs_top_builddir@ +SKIP: tests/big +=============== -check () { - cut -d\ -f 2 $1 | xargs @MD5@ | sed 's/ \*/ /' | sort -k2,2 | diff -w $DIFFFLAGS $1 - -} - -ENABLE_RUBY_BINDING="@RUBY_EXT_LIB@" -RUBY="@RUBY@" -ENABLE_PYTHON_BINDING="@PYTHON@" -PYTHON="@PYTHON@" -ENABLE_PERL_BINDING="@PERL_EXT_LIB@" -PERL="@PERL@" -SAMTOOLS="@SAMTOOLS@" - -if [ -n "$DEBUG" ]; then - set -x; - DIFFFLAGS="-y" -fi +Skip big test +SKIP tests/big.sh (exit status: 77) -set -e -sed '/BUILDDIR=/d' debian/jellyfish-examples/usr/share/doc/jellyfish-examples/examples/compat.sh* -if [ -z "$nCPUs" ]; then - nCPUs=$(grep -c '^processor' /proc/cpuinfo 2>/dev/null || sysctl -n hw.ncpu) -fi -pref=$(basename $0 .sh) -DIR=../bin -JF="$DIR/jellyfish" -[ -n "$VALGRIND" ] && JF="valgrind $JF" -SRCDIR=/build/jellyfish-2.2.10 +SKIP: tests/sam +=============== -check () { - cut -d\ -f 2 $1 | xargs md5sum | sed 's/ \*/ /' | sort -k2,2 | diff -w $DIFFFLAGS $1 - -} +Skip SAM/BAM/CRAM file format test +SKIP tests/sam.sh (exit status: 77) -ENABLE_RUBY_BINDING="" -RUBY="" -ENABLE_PYTHON_BINDING="" -PYTHON="" -ENABLE_PERL_BINDING="/usr/lib/perl/5.28.0" -PERL="/usr/bin/perl" -SAMTOOLS="" +SKIP: tests/swig_python +======================= -if [ -n "$DEBUG" ]; then - set -x; - DIFFFLAGS="-y" -fi +SKIP tests/swig_python.sh (exit status: 77) -set -e -if [ -z "$nCPUs" ]; then - nCPUs=$(grep -c '^processor' /proc/cpuinfo 2>/dev/null || sysctl -n hw.ncpu) -fi -pref=$(basename $0 .sh) -DIR=../bin -JF="$DIR/jellyfish" -[ -n "$VALGRIND" ] && JF="valgrind $JF" -SRCDIR=@abs_top_srcdir@ +SKIP: tests/swig_ruby +===================== -check () { - cut -d\ -f 2 $1 | xargs @MD5@ | sed 's/ \*/ /' | sort -k2,2 | diff -w $DIFFFLAGS $1 - -} +SKIP tests/swig_ruby.sh (exit status: 77) -ENABLE_RUBY_BINDING="@RUBY_EXT_LIB@" -RUBY="@RUBY@" -ENABLE_PYTHON_BINDING="@PYTHON@" -PYTHON="@PYTHON@" -ENABLE_PERL_BINDING="@PERL_EXT_LIB@" -PERL="@PERL@" -SAMTOOLS="@SAMTOOLS@" +FAIL: tests/swig_perl +===================== -if [ -n "$DEBUG" ]; then - set -x; - DIFFFLAGS="-y" -fi +Test test_mer_file.t +ok 1 - require jellyfish; +ok 2 - Histogram +ok 3 - Dump +ok 4 - Query identical to read +1..4 +Test test_hash_counter.t +ok 1 - require jellyfish; +ok 2 - mer_dna k +ok 3 - Hash size +ok 4 - Hash value length +not ok 5 - Value in hash +# Failed test 'Value in hash' +# at /build/jellyfish-2.2.10/swig/perl5/t/test_hash_counter.t line 37. +not ok 6 - Adding mer to hash +# Failed test 'Adding mer to hash' +# at /build/jellyfish-2.2.10/swig/perl5/t/test_hash_counter.t line 41. +1..6 +# Looks like you failed 2 tests of 6. +FAIL tests/swig_perl.sh (exit status: 2) -set -e -rm -f debian/jellyfish-examples/usr/share/doc/jellyfish-examples/examples/swig* +============================================================================ +Testsuite summary for jellyfish 2.2.10 +============================================================================ +# TOTAL: 15 +# PASS: 10 +# SKIP: 4 +# XFAIL: 0 +# FAIL: 1 +# XPASS: 0 +# ERROR: 0 +============================================================================ +See ./test-suite.log +Please report to gmarcais@umd.edu +============================================================================ +make[4]: *** [Makefile:2384: test-suite.log] Error 1 +make[4]: Leaving directory '/build/jellyfish-2.2.10' +make[3]: *** [Makefile:2492: check-TESTS] Error 2 +make[3]: Leaving directory '/build/jellyfish-2.2.10' +make[2]: *** [Makefile:2692: check-am] Error 2 +make[2]: Leaving directory '/build/jellyfish-2.2.10' +make[1]: *** [Makefile:2694: check] Error 2 make[1]: Leaving directory '/build/jellyfish-2.2.10' - dh_installman - dh_lintian - dh_perl - dh_link - dh_strip_nondeterminism - dh_compress - dh_fixperms - dh_missing - dh_strip - dh_makeshlibs - dh_shlibdeps - dh_installdeb - dh_gencontrol - dh_md5sums - dh_builddeb -dpkg-deb: building package 'libjellyfish-2.0-dev' in '../libjellyfish-2.0-dev_2.2.10-2_amd64.deb'. -dpkg-deb: building package 'libjellyfish-2.0-2' in '../libjellyfish-2.0-2_2.2.10-2_amd64.deb'. -dpkg-deb: building package 'libjellyfish-2.0-2-dbgsym' in '../libjellyfish-2.0-2-dbgsym_2.2.10-2_amd64.deb'. -dpkg-deb: building package 'libjellyfish-perl' in '../libjellyfish-perl_2.2.10-2_amd64.deb'. -dpkg-deb: building package 'jellyfish-examples-dbgsym' in '../jellyfish-examples-dbgsym_2.2.10-2_amd64.deb'. -dpkg-deb: building package 'jellyfish-dbgsym' in '../jellyfish-dbgsym_2.2.10-2_amd64.deb'. -dpkg-deb: building package 'jellyfish' in '../jellyfish_2.2.10-2_amd64.deb'. -dpkg-deb: building package 'jellyfish-examples' in '../jellyfish-examples_2.2.10-2_amd64.deb'. -dpkg-deb: building package 'libjellyfish-perl-dbgsym' in '../libjellyfish-perl-dbgsym_2.2.10-2_amd64.deb'. - dpkg-genbuildinfo --build=binary - dpkg-genchanges --build=binary >../jellyfish_2.2.10-2_amd64.changes -dpkg-genchanges: info: binary-only upload (no source code included) - dpkg-source --after-build . -dpkg-buildpackage: info: binary-only upload (no source included) -dpkg-genchanges: info: not including original source code in upload +dh_auto_test: make -j15 check VERBOSE=1 returned exit code 2 +make: *** [debian/rules:19: build] Error 2 +dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 I: copying local configuration +E: Failed autobuilding of package +I: user script /srv/workspace/pbuilder/2751546/tmp/hooks/C01_cleanup starting +debug output: disk usage on i-capture-the-hostname at Fri Aug 26 07:49:57 UTC 2022 +Filesystem Size Used Avail Use% Mounted on +tmpfs 24G 0 24G 0% /dev/shm + +I: user script /srv/workspace/pbuilder/2751546/tmp/hooks/C01_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/2609232 and its subdirectories -I: Current time: Thu Sep 28 01:39:34 -12 2023 -I: pbuilder-time-stamp: 1695908374 +I: removing directory /srv/workspace/pbuilder/2751546 and its subdirectories