Diff of the two buildlogs:
--
--- b1/build.log 2021-11-29 07:51:29.139290728 +0000
+++ b2/build.log 2021-11-29 08:10:58.171172275 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Sun Jan 1 02:07:54 -12 2023
-I: pbuilder-time-stamp: 1672582074
+I: Current time: Mon Nov 29 21:51:31 +14 2021
+I: pbuilder-time-stamp: 1638172291
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 Sun Feb 17 01:20:28 2019 -12
+gpgv: Signature made Mon Feb 18 03:20:28 2019 +14
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./abyss_2.1.5-7.dsc
@@ -35,136 +35,170 @@
dpkg-source: info: applying spelling
I: using fakeroot in build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/2150296/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/862613/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos11-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'
+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/862613/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/862613/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='94fc609b61dd47dfa1f7e08570613c6c'
- 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='2150296'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=a30ae840ba6645a9923b7e2e1e3ec9f4
+ 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=862613
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.7CccSBudTb/pbuilderrc_H5oo --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.7CccSBudTb/b1 --logfile b1/build.log abyss_2.1.5-7.dsc'
- SUDO_GID='111'
- SUDO_UID='106'
- SUDO_USER='jenkins'
- TERM='unknown'
- TZ='/usr/share/zoneinfo/Etc/GMT+12'
- USER='root'
- _='/usr/bin/systemd-run'
- http_proxy='http://85.184.249.68:3128'
+ PWD=/
+ SHELL=/bin/bash
+ SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+ SHLVL=3
+ SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.7CccSBudTb/pbuilderrc_20LE --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.7CccSBudTb/b2 --logfile b2/build.log abyss_2.1.5-7.dsc'
+ SUDO_GID=111
+ SUDO_UID=106
+ 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 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux
+ Linux i-capture-the-hostname 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) 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 Dec 10 16:20 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/2150296/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 Nov 29 21:51 sh -> bash
+ lrwxrwxrwx 1 root root 4 Nov 8 11:58 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/862613/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -327,7 +361,7 @@
Get: 107 http://deb.debian.org/debian buster/main amd64 pkg-config amd64 0.29-6 [63.5 kB]
Get: 108 http://deb.debian.org/debian buster/main amd64 python-pkg-resources all 40.8.0-1 [182 kB]
Get: 109 http://deb.debian.org/debian buster/main amd64 python-markdown all 3.0.1-3 [60.6 kB]
-Fetched 49.0 MB in 1s (81.2 MB/s)
+Fetched 49.0 MB in 2s (25.8 MB/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.)
@@ -792,7 +826,8 @@
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/abyss-2.1.5/ && 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_2.1.5-7_source.changes
+hostname: Name or service not known
+I: Running cd /build/abyss-2.1.5/ && 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_2.1.5-7_source.changes
dpkg-buildpackage: info: source package abyss
dpkg-buildpackage: info: source version 2.1.5-7
dpkg-buildpackage: info: source distribution unstable
@@ -1029,7 +1064,7 @@
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/abyss-2.1.5'
dh_auto_build
- make -j16
+ make -j15
make[2]: Entering directory '/build/abyss-2.1.5'
make all-recursive
make[3]: Entering directory '/build/abyss-2.1.5'
@@ -1084,11 +1119,11 @@
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc
-g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm
rm -f libdb.a
ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libdb.a
+g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm
make[4]: Leaving directory '/build/abyss-2.1.5/DataBase'
Making all in FMIndex
make[4]: Entering directory '/build/abyss-2.1.5/FMIndex'
@@ -1099,8 +1134,8 @@
ar cru libfmindex.a libfmindex_a-bit_array.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libfmindex.a
-g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm
g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm
+g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm
make[4]: Leaving directory '/build/abyss-2.1.5/FMIndex'
Making all in Assembly
make[4]: Entering directory '/build/abyss-2.1.5/Assembly'
@@ -1122,15 +1157,6 @@
gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parameters.o parameters.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o prob.o prob.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o translate.o translate.c
-diag.c:1456:3: warning: 'real_calc_weight' is static but used in inline function 'find_diags_dyn' which is not static
- real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn);
- ^~~~~~~~~~~~~~~~
-alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined
- 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
- extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
- ^~~~~~~~~~~
assemble.c:40:20: warning: inline function 'align_diag' declared but never defined
extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
^~~~~~~~~~
@@ -1146,6 +1172,12 @@
assemble.c:13:20: warning: inline function 'calc_weight' declared but never defined
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
+ 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
+ extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
+ ^~~~~~~~~~~
io.c: In function 'read_scr_matrix':
io.c:270:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf( fp, "%i", &is);
@@ -1157,6 +1189,9 @@
io.c:371:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight );
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+diag.c:1456:3: warning: 'real_calc_weight' is static but used in inline function 'find_diags_dyn' which is not static
+ real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn);
+ ^~~~~~~~~~~~~~~~
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')
@@ -1195,8 +1230,8 @@
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/Parallel'
Making all in Bloom
make[4]: Entering directory '/build/abyss-2.1.5/Bloom'
@@ -1230,8 +1265,8 @@
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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
make[4]: Leaving directory '/build/abyss-2.1.5/DistanceEst'
Making all in KAligner
make[4]: Entering directory '/build/abyss-2.1.5/KAligner'
@@ -1256,8 +1291,8 @@
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/Map'
Making all in MergePaths
@@ -1294,8 +1329,8 @@
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/ParseAligns'
Making all in PathOverlap
@@ -1372,7 +1407,7 @@
markdown_py -f README.html README.md
make[1]: Leaving directory '/build/abyss-2.1.5'
dh_auto_test
- make -j16 check VERBOSE=1
+ make -j15 check VERBOSE=1
make[1]: Entering directory '/build/abyss-2.1.5'
Making check in bin
make[2]: Entering directory '/build/abyss-2.1.5/bin'
@@ -1533,20 +1568,28 @@
g++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_main_a-gtest_main.o `test -f 'src/gtest_main.cc' || echo './'`src/gtest_main.cc
g++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_main_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc
-rm -f libgtest.a
-ar cru libgtest.a src/libgtest_a-gtest-all.o
-ar: `u' modifier ignored since `D' is the default (see `U')
-ranlib libgtest.a
rm -f libgtest_main.a
ar cru libgtest_main.a src/libgtest_main_a-gtest_main.o src/libgtest_main_a-gtest-all.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libgtest_main.a
+rm -f libgtest.a
+ar cru libgtest.a src/libgtest_a-gtest-all.o
+ar: `u' modifier ignored since `D' is the default (see `U')
+ranlib libgtest.a
make[3]: Leaving directory '/build/abyss-2.1.5/lib/gtest-1.7.0'
make[2]: Leaving directory '/build/abyss-2.1.5/lib/gtest-1.7.0'
Making check in Unittest
make[2]: Entering directory '/build/abyss-2.1.5/Unittest'
make common_stringutil common_histogram common_bitutil common_kmer common_sequence common_KmerIterator common_sam BloomFilter Konnector_DBGBloom Konnector_DBGBloomAlgorithms graph_ConstrainedBFSVisitor graph_BidirectionalBFS graph_AllPathsSearch graph_HashGraph graph_ConstrainedBidiBFSVisitor graph_ExtendPath graph_DotIO graph_UndirectedGraph Konnector_konnector DBG_LoadAlgorithm PairedDBG_LoadAlgorithm PairedDBG_KmerPair PairedDBG_Dinuc PairedDBG_BranchRecord BloomDBG_BloomDBG BloomDBG_RollingHash BloomDBG_RollingHashIterator BloomDBG_HashAgnosticCascadingBloom BloomDBG_RollingBloomDBG BloomDBG_MaskedKmer BloomDBG_SpacedSeed BloomDBG_LightweightKmer
make[3]: Entering directory '/build/abyss-2.1.5/Unittest'
+g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/konnector-konnectorTest.o `test -f 'Konnector/konnectorTest.cpp' || echo './'`Konnector/konnectorTest.cpp
+g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/StringUtilTest.o Common/StringUtilTest.cpp
+g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/HistogramTest.o Common/HistogramTest.cpp
+g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/BitUtilTest.o Common/BitUtilTest.cpp
+g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerTest.o Common/KmerTest.cpp
+g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/Sequence.o Common/Sequence.cc
+g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerIteratorTest.o Common/KmerIteratorTest.cpp
+g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/SAM.o Common/SAM.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/BloomFilter-BloomFilter.o `test -f 'Konnector/BloomFilter.cc' || echo './'`Konnector/BloomFilter.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/DBGBloom-DBGBloomTest.o `test -f 'Konnector/DBGBloomTest.cpp' || echo './'`Konnector/DBGBloomTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o `test -f 'Konnector/DBGBloomAlgorithmsTest.cpp' || echo './'`Konnector/DBGBloomAlgorithmsTest.cpp
@@ -1558,7 +1601,6 @@
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ExtendPath-ExtendPathTest.o `test -f 'Graph/ExtendPathTest.cpp' || echo './'`Graph/ExtendPathTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_DotIO-DotIOTest.o `test -f 'Graph/DotIOTest.cpp' || echo './'`Graph/DotIOTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/UndirectedGraphTest.o Graph/UndirectedGraphTest.cpp
-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/konnector-konnectorTest.o `test -f 'Konnector/konnectorTest.cpp' || echo './'`Konnector/konnectorTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'DBG/LoadAlgorithmTest.cpp' || echo './'`DBG/LoadAlgorithmTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'PairedDBG/LoadAlgorithmTest.cpp' || echo './'`PairedDBG/LoadAlgorithmTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/KmerPair-KmerPairTest.o `test -f 'PairedDBG/KmerPairTest.cc' || echo './'`PairedDBG/KmerPairTest.cc
@@ -1572,81 +1614,74 @@
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/MaskedKmerTest.o BloomDBG/MaskedKmerTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/SpacedSeedTest.o BloomDBG/SpacedSeedTest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/LightweightKmerTest.o BloomDBG/LightweightKmerTest.cpp
-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/StringUtilTest.o Common/StringUtilTest.cpp
-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/HistogramTest.o Common/HistogramTest.cpp
-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/BitUtilTest.o Common/BitUtilTest.cpp
-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerTest.o Common/KmerTest.cpp
-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/Sequence.o Common/Sequence.cc
-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerIteratorTest.o Common/KmerIteratorTest.cpp
-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/SAM.o Common/SAM.cc
+g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 common_stringutil Common/StringUtilTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
+g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 common_histogram Common/HistogramTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
+g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 common_bitutil Common/BitUtilTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
+g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 common_kmer Common/KmerTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
+g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 common_sequence Common/Sequence.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
+g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 common_KmerIterator Common/KmerIteratorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
+g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 common_sam Common/SAM.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
+g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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_DotIO Graph/graph_DotIO-DotIOTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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_UndirectedGraph Graph/UndirectedGraphTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 DBG_LoadAlgorithm DBG/LoadAlgorithm-LoadAlgorithmTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
-g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
-g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
-g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
-g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
-g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
-g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 common_histogram Common/HistogramTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
-g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 common_kmer Common/KmerTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
-g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 common_sequence Common/Sequence.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
+g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
+g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
+g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
+g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
+g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
+g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
-g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
-g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 common_KmerIterator Common/KmerIteratorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
-g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 common_bitutil Common/BitUtilTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
-g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
-g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 common_stringutil Common/StringUtilTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
-g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 common_sam Common/SAM.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm
make[3]: Leaving directory '/build/abyss-2.1.5/Unittest'
make check-TESTS
make[3]: Entering directory '/build/abyss-2.1.5/Unittest'
make[4]: Entering directory '/build/abyss-2.1.5/Unittest'
-PASS: common_sequence
+PASS: common_stringutil
PASS: common_histogram
-PASS: common_KmerIterator
-PASS: common_kmer
PASS: common_bitutil
-PASS: common_stringutil
-PASS: Konnector_DBGBloom
-PASS: graph_BidirectionalBFS
-PASS: BloomFilter
+PASS: common_kmer
+PASS: common_sequence
PASS: common_sam
-PASS: Konnector_DBGBloomAlgorithms
+PASS: BloomFilter
+PASS: common_KmerIterator
+PASS: Konnector_DBGBloom
PASS: graph_ConstrainedBFSVisitor
+PASS: Konnector_DBGBloomAlgorithms
PASS: graph_AllPathsSearch
+PASS: graph_BidirectionalBFS
PASS: graph_ConstrainedBidiBFSVisitor
PASS: graph_HashGraph
PASS: graph_ExtendPath
PASS: graph_DotIO
-PASS: Konnector_konnector
PASS: graph_UndirectedGraph
-PASS: BloomDBG_BloomDBG
+PASS: Konnector_konnector
PASS: PairedDBG_KmerPair
-PASS: BloomDBG_HashAgnosticCascadingBloom
PASS: PairedDBG_Dinuc
-PASS: BloomDBG_RollingHash
-PASS: BloomDBG_MaskedKmer
-PASS: BloomDBG_LightweightKmer
PASS: PairedDBG_BranchRecord
-PASS: BloomDBG_SpacedSeed
+PASS: BloomDBG_BloomDBG
+PASS: BloomDBG_RollingHash
PASS: BloomDBG_RollingHashIterator
+PASS: BloomDBG_HashAgnosticCascadingBloom
+PASS: BloomDBG_MaskedKmer
PASS: BloomDBG_RollingBloomDBG
-PASS: PairedDBG_LoadAlgorithm
+PASS: BloomDBG_SpacedSeed
+PASS: BloomDBG_LightweightKmer
PASS: DBG_LoadAlgorithm
+PASS: PairedDBG_LoadAlgorithm
============================================================================
Testsuite summary for ABySS 2.1.5
============================================================================
@@ -1672,7 +1707,7 @@
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/abyss-2.1.5'
dh_auto_install --destdir=debian/tmp
- make -j16 install DESTDIR=/build/abyss-2.1.5/debian/tmp AM_UPDATE_INFO_DIR=no
+ make -j15 install DESTDIR=/build/abyss-2.1.5/debian/tmp AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/build/abyss-2.1.5'
Making install in bin
make[3]: Entering directory '/build/abyss-2.1.5/bin'
@@ -1721,8 +1756,8 @@
make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin'
/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin'
- /usr/bin/install -c abyss-db-csv '/build/abyss-2.1.5/debian/tmp/usr/bin'
/usr/bin/install -c abyss-db-txt '/build/abyss-2.1.5/debian/tmp/usr/bin'
+ /usr/bin/install -c abyss-db-csv '/build/abyss-2.1.5/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/abyss-2.1.5/DataBase'
make[3]: Leaving directory '/build/abyss-2.1.5/DataBase'
Making install in FMIndex
@@ -1765,8 +1800,8 @@
Making install in Parallel
make[3]: Entering directory '/build/abyss-2.1.5/Parallel'
make[4]: Entering directory '/build/abyss-2.1.5/Parallel'
-make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/build/abyss-2.1.5/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-2.1.5/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/abyss-2.1.5/Parallel'
make[3]: Leaving directory '/build/abyss-2.1.5/Parallel'
@@ -1789,8 +1824,8 @@
Making install in Konnector
make[3]: Entering directory '/build/abyss-2.1.5/Konnector'
make[4]: Entering directory '/build/abyss-2.1.5/Konnector'
-make[4]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin'
+make[4]: Nothing to be done for 'install-data-am'.
/usr/bin/install -c konnector '/build/abyss-2.1.5/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/abyss-2.1.5/Konnector'
make[3]: Leaving directory '/build/abyss-2.1.5/Konnector'
@@ -1883,8 +1918,8 @@
Making install in ParseAligns
make[3]: Entering directory '/build/abyss-2.1.5/ParseAligns'
make[4]: Entering directory '/build/abyss-2.1.5/ParseAligns'
- /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin'
make[4]: Nothing to be done for 'install-data-am'.
+ /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin'
/usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/build/abyss-2.1.5/debian/tmp/usr/bin'
make[4]: Leaving directory '/build/abyss-2.1.5/ParseAligns'
make[3]: Leaving directory '/build/abyss-2.1.5/ParseAligns'
@@ -1994,10 +2029,10 @@
make[4]: Leaving directory '/build/abyss-2.1.5'
make[3]: Leaving directory '/build/abyss-2.1.5'
make[2]: Leaving directory '/build/abyss-2.1.5'
-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-2.1.5'
@@ -2034,12 +2069,14 @@
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/862613/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/862613/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/2150296 and its subdirectories
-I: Current time: Sun Jan 1 02:14:32 -12 2023
-I: pbuilder-time-stamp: 1672582472
+I: removing directory /srv/workspace/pbuilder/862613 and its subdirectories
+I: Current time: Mon Nov 29 22:10:57 +14 2021
+I: pbuilder-time-stamp: 1638173457