Diff of the two buildlogs: -- --- b1/build.log 2022-03-18 13:57:33.101581189 +0000 +++ b2/build.log 2022-03-18 14:15:53.263320775 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Apr 20 08:11:31 -12 2023 -I: pbuilder-time-stamp: 1682021491 +I: Current time: Sat Mar 19 03:57:37 +14 2022 +I: pbuilder-time-stamp: 1647611857 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 Tue Oct 9 04:10:34 2018 -12 +gpgv: Signature made Wed Oct 10 06:10:34 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -31,136 +31,170 @@ dpkg-source: info: applying gcc-6.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1455767/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3677834/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' +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/3677834/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3677834/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='9c50d4664b6b4c668d4d4fa0bbe2975c' - 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='1455767' - PS1='# ' - PS2='> ' + INVOCATION_ID=e02ce23189ee4c69a8594100fc293dac + 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=3677834 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.CYNfdPTF3x/pbuilderrc_ZN0i --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.CYNfdPTF3x/b1 --logfile b1/build.log consensuscore_1.1.1+dfsg-1.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.CYNfdPTF3x/pbuilderrc_vz7M --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.CYNfdPTF3x/b2 --logfile b2/build.log consensuscore_1.1.1+dfsg-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 5.16.0-0.bpo.3-amd64 #1 SMP PREEMPT Debian 5.16.11-1~bpo11+1 (2022-03-02) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-12-amd64 #1 SMP Debian 5.10.103-1 (2022-03-07) 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 Apr 9 02:46 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/1455767/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 Mar 19 03:58 sh -> bash + lrwxrwxrwx 1 root root 4 Mar 7 22:26 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/3677834/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -308,7 +342,7 @@ Get: 90 http://deb.debian.org/debian buster/main amd64 python3-setuptools all 40.8.0-1 [306 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 swig3.0 amd64 3.0.12-2 [1397 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 swig amd64 3.0.12-2 [310 kB] -Fetched 132 MB in 3s (43.4 MB/s) +Fetched 132 MB in 5s (27.6 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.) @@ -705,7 +739,8 @@ 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/consensuscore-1.1.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../consensuscore_1.1.1+dfsg-1_source.changes +hostname: Name or service not known +I: Running cd /build/consensuscore-1.1.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../consensuscore_1.1.1+dfsg-1_source.changes dpkg-buildpackage: info: source package consensuscore dpkg-buildpackage: info: source version 1.1.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -768,15 +803,18 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SseRecursor.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SimpleRecursor.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Sequence.o -MM src/C++/Sequence.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Sequence.d -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/ReadScorer.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Utils.o -MM src/C++/Utils.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Utils.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/ReadScorer.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConsensus.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o -MM src/C++/Quiver/ReadScorer.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConfig.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Version.o -MM src/C++/Version.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Version.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationScorer.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o -MM src/C++/Quiver/detail/RecursorBase.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Read.o -MM src/C++/Read.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Read.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationEnumerator.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o -MM src/C++/Quiver/detail/RecursorBase.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MultiReadMutationScorer.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o -MM src/C++/Quiver/QuiverConfig.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.d src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor; ConsensusCore::MutationScorer::EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:190:16: required from here src/C++/Quiver/MutationScorer.cpp:30:7: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] @@ -800,52 +838,49 @@ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; ConsensusCore::MutationScorer::EvaluatorType = ConsensusCore::EdnaEvaluator]’: src/C++/Quiver/MutationScorer.cpp:196:16: required from here src/C++/Quiver/MutationScorer.cpp:30:7: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Read.o -MM src/C++/Read.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Read.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Binomial.o -MM src/C++/Statistics/Binomial.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Binomial.d -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MultiReadMutationScorer.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/Diploid.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Diploid.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o -MM src/C++/Quiver/QuiverConfig.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o -MM src/C++/Quiver/MutationEnumerator.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/Diploid.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Diploid.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/RangeFinder.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphTraversals.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Diploid.o -MM src/C++/Quiver/Diploid.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Diploid.d -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphImpl.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o -MM src/C++/Quiver/QuiverConsensus.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphImpl.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraph.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o -MM src/C++/Quiver/SimpleRecursor.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o -MM src/C++/Quiver/MutationScorer.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaConsensus.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Mutation.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Mutation.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o -MM src/C++/Poa/PoaConsensus.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o -MM src/C++/Poa/PoaGraph.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/SparseMatrix.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o -MM src/C++/Poa/PoaConsensus.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/DenseMatrix.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o -MM src/C++/Matrix/SparseMatrix.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.d -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Logging/Logging.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Logging.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o -MM src/C++/Poa/RangeFinder.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Logging/Logging.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Logging.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o -MM src/C++/Matrix/SparseMatrix.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o -MM src/C++/Quiver/MultiReadMutationScorer.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Features.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Features.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o -MM src/C++/Matrix/DenseMatrix.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Logging.o -MM src/C++/Logging/Logging.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Logging.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Feature.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Feature.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Edna/EdnaCounts.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o -MM src/C++/Matrix/DenseMatrix.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Coverage.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Coverage.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Feature.o -MM src/C++/Feature.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Feature.d -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Checksum.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Checksum.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Coverage.o -MM src/C++/Coverage.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Coverage.d -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o -MM src/C++/Poa/PoaGraphTraversals.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.d -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Features.o -MM src/C++/Features.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Features.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Checksum.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Checksum.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/PairwiseAlignment.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Features.o -MM src/C++/Features.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Features.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o -MM src/C++/Edna/EdnaCounts.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o -MM src/C++/Poa/PoaGraphTraversals.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/LinearAlignment.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AlignConfig.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o -MM src/C++/Quiver/SseRecursor.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o -MM src/C++/Align/AlignConfig.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AffineAlignment.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Mutation.o -MM src/C++/Mutation.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Mutation.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o -MM src/C++/Align/PairwiseAlignment.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.d -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o -MM src/C++/Align/AffineAlignment.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o -MM src/C++/Align/LinearAlignment.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.d -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o -MM src/C++/Quiver/SseRecursor.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o -MM src/C++/Align/AffineAlignment.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.d +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Mutation.o -MM src/C++/Mutation.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Mutation.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Checksum.o -MM src/C++/Checksum.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Checksum.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o -MM src/C++/Poa/PoaGraphImpl.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.d ar crs /build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a /build/consensuscore-1.1.1+dfsg/build/C++/Version.o /build/consensuscore-1.1.1+dfsg/build/C++/Utils.o /build/consensuscore-1.1.1+dfsg/build/C++/Binomial.o /build/consensuscore-1.1.1+dfsg/build/C++/Sequence.o /build/consensuscore-1.1.1+dfsg/build/C++/Read.o /build/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o /build/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o /build/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o /build/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o /build/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o /build/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o /build/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o /build/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o /build/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o /build/consensuscore-1.1.1+dfsg/build/C++/Diploid.o /build/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o /build/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o /build/consensuscore-1.1.1+dfsg/build/C++/Mutation.o /build/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o /build/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o /build/consensuscore-1.1.1+dfsg/build/C++/Logging.o /build/consensuscore-1.1.1+dfsg/build/C++/Features.o /build/consensuscore-1.1.1+dfsg/build/C++/Feature.o /build/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o /build/consensuscore-1.1.1+dfsg/build/C++/Coverage.o /build/consensuscore-1.1.1+dfsg/build/C++/Checksum.o /build/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o /build/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o /build/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o /build/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o @@ -950,13 +985,13 @@ [ RUN ] RecursorTest/0.SmallMergeTest [ OK ] RecursorTest/0.SmallMergeTest (0 ms) [ RUN ] RecursorTest/0.MediumSizedTest -[ OK ] RecursorTest/0.MediumSizedTest (3 ms) +[ OK ] RecursorTest/0.MediumSizedTest (4 ms) [ RUN ] RecursorTest/0.LinkTest [ OK ] RecursorTest/0.LinkTest (0 ms) [ RUN ] RecursorTest/0.ExtendAlphaTest [ OK ] RecursorTest/0.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/0.ExtendBetaTest -[ OK ] RecursorTest/0.ExtendBetaTest (1 ms) +[ OK ] RecursorTest/0.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/0 (4 ms total) [----------] 7 tests from RecursorTest/1, where TypeParam = ConsensusCore::SseRecursor @@ -967,14 +1002,14 @@ [ RUN ] RecursorTest/1.SmallMergeTest [ OK ] RecursorTest/1.SmallMergeTest (0 ms) [ RUN ] RecursorTest/1.MediumSizedTest -[ OK ] RecursorTest/1.MediumSizedTest (2 ms) +[ OK ] RecursorTest/1.MediumSizedTest (4 ms) [ RUN ] RecursorTest/1.LinkTest [ OK ] RecursorTest/1.LinkTest (0 ms) [ RUN ] RecursorTest/1.ExtendAlphaTest [ OK ] RecursorTest/1.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/1.ExtendBetaTest -[ OK ] RecursorTest/1.ExtendBetaTest (1 ms) -[----------] 7 tests from RecursorTest/1 (3 ms total) +[ OK ] RecursorTest/1.ExtendBetaTest (0 ms) +[----------] 7 tests from RecursorTest/1 (4 ms total) [----------] 7 tests from RecursorTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorTest/2.SmallMatchTest @@ -984,14 +1019,14 @@ [ RUN ] RecursorTest/2.SmallMergeTest [ OK ] RecursorTest/2.SmallMergeTest (0 ms) [ RUN ] RecursorTest/2.MediumSizedTest -[ OK ] RecursorTest/2.MediumSizedTest (2 ms) +[ OK ] RecursorTest/2.MediumSizedTest (3 ms) [ RUN ] RecursorTest/2.LinkTest [ OK ] RecursorTest/2.LinkTest (0 ms) [ RUN ] RecursorTest/2.ExtendAlphaTest [ OK ] RecursorTest/2.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/2.ExtendBetaTest -[ OK ] RecursorTest/2.ExtendBetaTest (0 ms) -[----------] 7 tests from RecursorTest/2 (2 ms total) +[ OK ] RecursorTest/2.ExtendBetaTest (1 ms) +[----------] 7 tests from RecursorTest/2 (4 ms total) [----------] 7 tests from RecursorTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorTest/3.SmallMatchTest @@ -1001,96 +1036,96 @@ [ RUN ] RecursorTest/3.SmallMergeTest [ OK ] RecursorTest/3.SmallMergeTest (0 ms) [ RUN ] RecursorTest/3.MediumSizedTest -[ OK ] RecursorTest/3.MediumSizedTest (3 ms) +[ OK ] RecursorTest/3.MediumSizedTest (5 ms) [ RUN ] RecursorTest/3.LinkTest [ OK ] RecursorTest/3.LinkTest (0 ms) [ RUN ] RecursorTest/3.ExtendAlphaTest [ OK ] RecursorTest/3.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/3.ExtendBetaTest [ OK ] RecursorTest/3.ExtendBetaTest (0 ms) -[----------] 7 tests from RecursorTest/3 (3 ms total) +[----------] 7 tests from RecursorTest/3 (5 ms total) [----------] 5 tests from RecursorFuzzTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/0.AlphaBetaConcordance -[ OK ] RecursorFuzzTest/0.AlphaBetaConcordance (75 ms) +[ OK ] RecursorFuzzTest/0.AlphaBetaConcordance (94 ms) [ RUN ] RecursorFuzzTest/0.Alignment -[ OK ] RecursorFuzzTest/0.Alignment (77 ms) +[ OK ] RecursorFuzzTest/0.Alignment (91 ms) [ RUN ] RecursorFuzzTest/0.LinkAlphaBeta -[ OK ] RecursorFuzzTest/0.LinkAlphaBeta (89 ms) +[ OK ] RecursorFuzzTest/0.LinkAlphaBeta (102 ms) [ RUN ] RecursorFuzzTest/0.ExtendAlpha -[ OK ] RecursorFuzzTest/0.ExtendAlpha (26 ms) +[ OK ] RecursorFuzzTest/0.ExtendAlpha (33 ms) [ RUN ] RecursorFuzzTest/0.ExtendBeta -[ OK ] RecursorFuzzTest/0.ExtendBeta (25 ms) -[----------] 5 tests from RecursorFuzzTest/0 (292 ms total) +[ OK ] RecursorFuzzTest/0.ExtendBeta (31 ms) +[----------] 5 tests from RecursorFuzzTest/0 (352 ms total) [----------] 5 tests from RecursorFuzzTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/1.AlphaBetaConcordance -[ OK ] RecursorFuzzTest/1.AlphaBetaConcordance (61 ms) +[ OK ] RecursorFuzzTest/1.AlphaBetaConcordance (75 ms) [ RUN ] RecursorFuzzTest/1.Alignment -[ OK ] RecursorFuzzTest/1.Alignment (65 ms) +[ OK ] RecursorFuzzTest/1.Alignment (77 ms) [ RUN ] RecursorFuzzTest/1.LinkAlphaBeta -[ OK ] RecursorFuzzTest/1.LinkAlphaBeta (74 ms) +[ OK ] RecursorFuzzTest/1.LinkAlphaBeta (77 ms) [ RUN ] RecursorFuzzTest/1.ExtendAlpha -[ OK ] RecursorFuzzTest/1.ExtendAlpha (30 ms) +[ OK ] RecursorFuzzTest/1.ExtendAlpha (32 ms) [ RUN ] RecursorFuzzTest/1.ExtendBeta -[ OK ] RecursorFuzzTest/1.ExtendBeta (30 ms) -[----------] 5 tests from RecursorFuzzTest/1 (260 ms total) +[ OK ] RecursorFuzzTest/1.ExtendBeta (32 ms) +[----------] 5 tests from RecursorFuzzTest/1 (294 ms total) [----------] 5 tests from RecursorFuzzTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/2.AlphaBetaConcordance -[ OK ] RecursorFuzzTest/2.AlphaBetaConcordance (72 ms) +[ OK ] RecursorFuzzTest/2.AlphaBetaConcordance (92 ms) [ RUN ] RecursorFuzzTest/2.Alignment -[ OK ] RecursorFuzzTest/2.Alignment (85 ms) +[ OK ] RecursorFuzzTest/2.Alignment (114 ms) [ RUN ] RecursorFuzzTest/2.LinkAlphaBeta -[ OK ] RecursorFuzzTest/2.LinkAlphaBeta (112 ms) +[ OK ] RecursorFuzzTest/2.LinkAlphaBeta (115 ms) [ RUN ] RecursorFuzzTest/2.ExtendAlpha -[ OK ] RecursorFuzzTest/2.ExtendAlpha (22 ms) +[ OK ] RecursorFuzzTest/2.ExtendAlpha (23 ms) [ RUN ] RecursorFuzzTest/2.ExtendBeta [ OK ] RecursorFuzzTest/2.ExtendBeta (23 ms) -[----------] 5 tests from RecursorFuzzTest/2 (315 ms total) +[----------] 5 tests from RecursorFuzzTest/2 (367 ms total) [----------] 5 tests from RecursorFuzzTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/3.AlphaBetaConcordance -[ OK ] RecursorFuzzTest/3.AlphaBetaConcordance (87 ms) +[ OK ] RecursorFuzzTest/3.AlphaBetaConcordance (88 ms) [ RUN ] RecursorFuzzTest/3.Alignment -[ OK ] RecursorFuzzTest/3.Alignment (88 ms) +[ OK ] RecursorFuzzTest/3.Alignment (89 ms) [ RUN ] RecursorFuzzTest/3.LinkAlphaBeta -[ OK ] RecursorFuzzTest/3.LinkAlphaBeta (88 ms) +[ OK ] RecursorFuzzTest/3.LinkAlphaBeta (91 ms) [ RUN ] RecursorFuzzTest/3.ExtendAlpha -[ OK ] RecursorFuzzTest/3.ExtendAlpha (21 ms) +[ OK ] RecursorFuzzTest/3.ExtendAlpha (22 ms) [ RUN ] RecursorFuzzTest/3.ExtendBeta -[ OK ] RecursorFuzzTest/3.ExtendBeta (22 ms) -[----------] 5 tests from RecursorFuzzTest/3 (307 ms total) +[ OK ] RecursorFuzzTest/3.ExtendBeta (23 ms) +[----------] 5 tests from RecursorFuzzTest/3 (313 ms total) [----------] 5 tests from QvEvaluatorTest [ RUN ] QvEvaluatorTest.IncVsInc4 -[ OK ] QvEvaluatorTest.IncVsInc4 (52 ms) +[ OK ] QvEvaluatorTest.IncVsInc4 (51 ms) [ RUN ] QvEvaluatorTest.DelVsDel4 -[ OK ] QvEvaluatorTest.DelVsDel4 (53 ms) +[ OK ] QvEvaluatorTest.DelVsDel4 (58 ms) [ RUN ] QvEvaluatorTest.ExtraVsExtra4 -[ OK ] QvEvaluatorTest.ExtraVsExtra4 (58 ms) +[ OK ] QvEvaluatorTest.ExtraVsExtra4 (57 ms) [ RUN ] QvEvaluatorTest.MergeVsMerge4 -[ OK ] QvEvaluatorTest.MergeVsMerge4 (44 ms) +[ OK ] QvEvaluatorTest.MergeVsMerge4 (42 ms) [ RUN ] QvEvaluatorTest.BadTagTest -[ OK ] QvEvaluatorTest.BadTagTest (5 ms) -[----------] 5 tests from QvEvaluatorTest (213 ms total) +[ OK ] QvEvaluatorTest.BadTagTest (6 ms) +[----------] 5 tests from QvEvaluatorTest (214 ms total) [----------] 4 tests from PoaGraph [ RUN ] PoaGraph.SmallBasicTest [ OK ] PoaGraph.SmallBasicTest (0 ms) [ RUN ] PoaGraph.SmallExtraTests -[ OK ] PoaGraph.SmallExtraTests (0 ms) +[ OK ] PoaGraph.SmallExtraTests (1 ms) [ RUN ] PoaGraph.SmallMismatchTests -[ OK ] PoaGraph.SmallMismatchTests (1 ms) +[ OK ] PoaGraph.SmallMismatchTests (0 ms) [ RUN ] PoaGraph.SmallDeletionTests [ OK ] PoaGraph.SmallDeletionTests (0 ms) [----------] 4 tests from PoaGraph (1 ms total) [----------] 8 tests from PoaConsensus [ RUN ] PoaConsensus.TestSimple -[ OK ] PoaConsensus.TestSimple (0 ms) +[ OK ] PoaConsensus.TestSimple (1 ms) [ RUN ] PoaConsensus.TestOverhangSecond -[ OK ] PoaConsensus.TestOverhangSecond (1 ms) +[ OK ] PoaConsensus.TestOverhangSecond (0 ms) [ RUN ] PoaConsensus.SmallSemiglobalTest [ OK ] PoaConsensus.SmallSemiglobalTest (0 ms) [ RUN ] PoaConsensus.SmallTilingTest @@ -1099,13 +1134,13 @@ [ OK ] PoaConsensus.TestVerboseGraphVizOutput (0 ms) [ RUN ] PoaConsensus.TestLocalStaggered dot -Tpng local-staggered.dot > local-staggered.png -sh: 1: dot: not found -[ OK ] PoaConsensus.TestLocalStaggered (8 ms) +sh: dot: käsku ei ole +[ OK ] PoaConsensus.TestLocalStaggered (9 ms) [ RUN ] PoaConsensus.TestLongInsert [ OK ] PoaConsensus.TestLongInsert (1 ms) [ RUN ] PoaConsensus.NondeterminismRegressionTest -[ OK ] PoaConsensus.NondeterminismRegressionTest (862 ms) -[----------] 8 tests from PoaConsensus (872 ms total) +[ OK ] PoaConsensus.NondeterminismRegressionTest (968 ms) +[----------] 8 tests from PoaConsensus (980 ms total) [----------] 3 tests from PairwiseAlignmentTests [ RUN ] PairwiseAlignmentTests.RepresentationTests @@ -1113,15 +1148,15 @@ [ RUN ] PairwiseAlignmentTests.GlobalAlignmentTests [ OK ] PairwiseAlignmentTests.GlobalAlignmentTests (0 ms) [ RUN ] PairwiseAlignmentTests.TargetPositionsInQueryTest -[ OK ] PairwiseAlignmentTests.TargetPositionsInQueryTest (1 ms) -[----------] 3 tests from PairwiseAlignmentTests (1 ms total) +[ OK ] PairwiseAlignmentTests.TargetPositionsInQueryTest (0 ms) +[----------] 3 tests from PairwiseAlignmentTests (0 ms total) [----------] 2 tests from AffineAlignmentTests [ RUN ] AffineAlignmentTests.BasicTests [ OK ] AffineAlignmentTests.BasicTests (0 ms) [ RUN ] AffineAlignmentTests.LargeGapTest -[ OK ] AffineAlignmentTests.LargeGapTest (18 ms) -[----------] 2 tests from AffineAlignmentTests (18 ms total) +[ OK ] AffineAlignmentTests.LargeGapTest (20 ms) +[----------] 2 tests from AffineAlignmentTests (20 ms total) [----------] 1 test from IupacAlignmentTests [ RUN ] IupacAlignmentTests.BasicTest @@ -1147,8 +1182,8 @@ [ RUN ] MutationTest.MutationsToTranscript [ OK ] MutationTest.MutationsToTranscript (0 ms) [ RUN ] MutationTest.MutatedTemplatePositionsTest -[ OK ] MutationTest.MutatedTemplatePositionsTest (0 ms) -[----------] 7 tests from MutationTest (0 ms total) +[ OK ] MutationTest.MutatedTemplatePositionsTest (1 ms) +[----------] 7 tests from MutationTest (1 ms total) [----------] 8 tests from MutationScorerTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/0.BasicTest @@ -1156,7 +1191,7 @@ [ RUN ] MutationScorerTest/0.CopyTest [ OK ] MutationScorerTest/0.CopyTest (0 ms) [ RUN ] MutationScorerTest/0.MutationsAtBeginning -[ OK ] MutationScorerTest/0.MutationsAtBeginning (1 ms) +[ OK ] MutationScorerTest/0.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/0.MutationsAtEnd [ OK ] MutationScorerTest/0.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/0.TinyTemplate @@ -1164,7 +1199,7 @@ [ RUN ] MutationScorerTest/0.TemplateMutationWorkflow [ OK ] MutationScorerTest/0.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/0.DinucleotideInsertionTest -[ OK ] MutationScorerTest/0.DinucleotideInsertionTest (2 ms) +[ OK ] MutationScorerTest/0.DinucleotideInsertionTest (3 ms) [ RUN ] MutationScorerTest/0.DinucleotideDeletionTest [ OK ] MutationScorerTest/0.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/0 (4 ms total) @@ -1183,10 +1218,10 @@ [ RUN ] MutationScorerTest/1.TemplateMutationWorkflow [ OK ] MutationScorerTest/1.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/1.DinucleotideInsertionTest -[ OK ] MutationScorerTest/1.DinucleotideInsertionTest (2 ms) +[ OK ] MutationScorerTest/1.DinucleotideInsertionTest (3 ms) [ RUN ] MutationScorerTest/1.DinucleotideDeletionTest [ OK ] MutationScorerTest/1.DinucleotideDeletionTest (1 ms) -[----------] 8 tests from MutationScorerTest/1 (3 ms total) +[----------] 8 tests from MutationScorerTest/1 (4 ms total) [----------] 8 tests from MutationScorerTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/2.BasicTest @@ -1200,12 +1235,12 @@ [ RUN ] MutationScorerTest/2.TinyTemplate [ OK ] MutationScorerTest/2.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/2.TemplateMutationWorkflow -[ OK ] MutationScorerTest/2.TemplateMutationWorkflow (0 ms) +[ OK ] MutationScorerTest/2.TemplateMutationWorkflow (1 ms) [ RUN ] MutationScorerTest/2.DinucleotideInsertionTest [ OK ] MutationScorerTest/2.DinucleotideInsertionTest (2 ms) [ RUN ] MutationScorerTest/2.DinucleotideDeletionTest [ OK ] MutationScorerTest/2.DinucleotideDeletionTest (1 ms) -[----------] 8 tests from MutationScorerTest/2 (3 ms total) +[----------] 8 tests from MutationScorerTest/2 (4 ms total) [----------] 8 tests from MutationScorerTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/3.BasicTest @@ -1221,18 +1256,18 @@ [ RUN ] MutationScorerTest/3.TemplateMutationWorkflow [ OK ] MutationScorerTest/3.TemplateMutationWorkflow (1 ms) [ RUN ] MutationScorerTest/3.DinucleotideInsertionTest -[ OK ] MutationScorerTest/3.DinucleotideInsertionTest (1 ms) +[ OK ] MutationScorerTest/3.DinucleotideInsertionTest (2 ms) [ RUN ] MutationScorerTest/3.DinucleotideDeletionTest -[ OK ] MutationScorerTest/3.DinucleotideDeletionTest (1 ms) +[ OK ] MutationScorerTest/3.DinucleotideDeletionTest (0 ms) [----------] 8 tests from MutationScorerTest/3 (3 ms total) [----------] 4 tests from MutationEnumerationTest [ RUN ] MutationEnumerationTest.TestAllMutations -[ OK ] MutationEnumerationTest.TestAllMutations (0 ms) +[ OK ] MutationEnumerationTest.TestAllMutations (1 ms) [ RUN ] MutationEnumerationTest.TestUniqueMutations [ OK ] MutationEnumerationTest.TestUniqueMutations (0 ms) [ RUN ] MutationEnumerationTest.TestUniqueNearbyMutations -[ OK ] MutationEnumerationTest.TestUniqueNearbyMutations (2 ms) +[ OK ] MutationEnumerationTest.TestUniqueNearbyMutations (1 ms) [ RUN ] MutationEnumerationTest.TestDinucleotideMutations [ OK ] MutationEnumerationTest.TestDinucleotideMutations (0 ms) [----------] 4 tests from MutationEnumerationTest (2 ms total) @@ -1257,7 +1292,7 @@ [ RUN ] MultiReadMutationScorerTest/0.BasicTest [ OK ] MultiReadMutationScorerTest/0.BasicTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.ManyMutationTest -[ OK ] MultiReadMutationScorerTest/0.ManyMutationTest (1 ms) +[ OK ] MultiReadMutationScorerTest/0.ManyMutationTest (2 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyConstructorTest [ OK ] MultiReadMutationScorerTest/0.CopyConstructorTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.ReverseStrandTest @@ -1265,16 +1300,16 @@ [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning (0 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtEnd -[ OK ] MultiReadMutationScorerTest/0.TestMutationsAtEnd (0 ms) +[ OK ] MultiReadMutationScorerTest/0.TestMutationsAtEnd (1 ms) [ RUN ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 [ OK ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 (1 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyTest -[ OK ] MultiReadMutationScorerTest/0.CopyTest (1 ms) +[ OK ] MultiReadMutationScorerTest/0.CopyTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds (0 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds -[ OK ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds (0 ms) -[----------] 11 tests from MultiReadMutationScorerTest/0 (5 ms total) +[ OK ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds (1 ms) +[----------] 11 tests from MultiReadMutationScorerTest/0 (7 ms total) [----------] 11 tests from MatrixTest/0, where TypeParam = ConsensusCore::DenseMatrix [ RUN ] MatrixTest/0.Basic @@ -1295,12 +1330,12 @@ [ OK ] MatrixTest/0.Holes (0 ms) [ RUN ] MatrixTest/0.BigBandedMatrix N13ConsensusCore11DenseMatrixE : 1000000 -[ OK ] MatrixTest/0.BigBandedMatrix (6 ms) +[ OK ] MatrixTest/0.BigBandedMatrix (8 ms) [ RUN ] MatrixTest/0.BigIrregularBandedMatrix [ OK ] MatrixTest/0.BigIrregularBandedMatrix (0 ms) [ RUN ] MatrixTest/0.CopyTest [ OK ] MatrixTest/0.CopyTest (0 ms) -[----------] 11 tests from MatrixTest/0 (6 ms total) +[----------] 11 tests from MatrixTest/0 (8 ms total) [----------] 11 tests from MatrixTest/1, where TypeParam = ConsensusCore::SparseMatrix [ RUN ] MatrixTest/1.Basic @@ -1321,12 +1356,12 @@ [ OK ] MatrixTest/1.Holes (0 ms) [ RUN ] MatrixTest/1.BigBandedMatrix N13ConsensusCore12SparseMatrixE : 1001976 -[ OK ] MatrixTest/1.BigBandedMatrix (6 ms) +[ OK ] MatrixTest/1.BigBandedMatrix (7 ms) [ RUN ] MatrixTest/1.BigIrregularBandedMatrix [ OK ] MatrixTest/1.BigIrregularBandedMatrix (0 ms) [ RUN ] MatrixTest/1.CopyTest [ OK ] MatrixTest/1.CopyTest (0 ms) -[----------] 11 tests from MatrixTest/1 (7 ms total) +[----------] 11 tests from MatrixTest/1 (8 ms total) [----------] 3 tests from CoverageTests [ RUN ] CoverageTests.CoverageInWindowTest @@ -1338,7 +1373,7 @@ [----------] 3 tests from CoverageTests (0 ms total) [----------] Global test environment tear-down -[==========] 158 tests from 29 test cases ran. (2324 ms total) +[==========] 158 tests from 29 test cases ran. (2599 ms total) [ PASSED ] 158 tests. make[3]: Leaving directory '/build/consensuscore-1.1.1+dfsg' make[2]: Leaving directory '/build/consensuscore-1.1.1+dfsg' @@ -1487,9 +1522,6 @@ dpkg-gencontrol: warning: Depends field of package libconsensuscore-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package libconsensuscore-dev: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package libconsensuscore-dev: substitution variable ${python:Depends} unused, but is defined -dpkg-gencontrol: warning: package python3-pbconsensuscore: substitution variable ${python3:Provides} unused, but is defined -dpkg-gencontrol: warning: package python3-pbconsensuscore: substitution variable ${python3:Versions} unused, but is defined -dpkg-gencontrol: warning: package python3-pbconsensuscore: substitution variable ${python:Depends} unused, but is defined dpkg-gencontrol: warning: package python-pbconsensuscore: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package python-pbconsensuscore: substitution variable ${python:Provides} unused, but is defined dpkg-gencontrol: warning: package python-pbconsensuscore: substitution variable ${python:Versions} unused, but is defined @@ -1499,13 +1531,16 @@ dpkg-gencontrol: warning: package python-pbconsensuscore: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package python-pbconsensuscore: substitution variable ${python:Provides} unused, but is defined dpkg-gencontrol: warning: package python-pbconsensuscore: substitution variable ${python:Versions} unused, but is defined +dpkg-gencontrol: warning: package python3-pbconsensuscore: substitution variable ${python3:Provides} unused, but is defined +dpkg-gencontrol: warning: package python3-pbconsensuscore: substitution variable ${python3:Versions} unused, but is defined +dpkg-gencontrol: warning: package python3-pbconsensuscore: substitution variable ${python:Depends} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'libconsensuscore-dev' in '../libconsensuscore-dev_1.1.1+dfsg-1_amd64.deb'. +dpkg-deb: building package 'python3-pbconsensuscore-dbgsym' in '../python3-pbconsensuscore-dbgsym_1.1.1+dfsg-1_amd64.deb'. +dpkg-deb: building package 'python-pbconsensuscore-dbgsym' in '../python-pbconsensuscore-dbgsym_1.1.1+dfsg-1_amd64.deb'. dpkg-deb: building package 'python-pbconsensuscore' in '../python-pbconsensuscore_1.1.1+dfsg-1_amd64.deb'. +dpkg-deb: building package 'libconsensuscore-dev' in '../libconsensuscore-dev_1.1.1+dfsg-1_amd64.deb'. dpkg-deb: building package 'python3-pbconsensuscore' in '../python3-pbconsensuscore_1.1.1+dfsg-1_amd64.deb'. -dpkg-deb: building package 'python-pbconsensuscore-dbgsym' in '../python-pbconsensuscore-dbgsym_1.1.1+dfsg-1_amd64.deb'. -dpkg-deb: building package 'python3-pbconsensuscore-dbgsym' in '../python3-pbconsensuscore-dbgsym_1.1.1+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../consensuscore_1.1.1+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1513,12 +1548,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3677834/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3677834/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/1455767 and its subdirectories -I: Current time: Thu Apr 20 08:20:33 -12 2023 -I: pbuilder-time-stamp: 1682022033 +I: removing directory /srv/workspace/pbuilder/3677834 and its subdirectories +I: Current time: Sat Mar 19 04:15:52 +14 2022 +I: pbuilder-time-stamp: 1647612952