Diff of the two buildlogs: -- --- b1/build.log 2020-08-11 09:33:27.839762035 +0000 +++ b2/build.log 2020-08-11 09:40:09.283376382 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Aug 10 21:07:37 -12 2020 -I: pbuilder-time-stamp: 1597136857 +I: Current time: Tue Sep 14 05:56:29 +14 2021 +I: pbuilder-time-stamp: 1631548589 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ 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 @@ -32,138 +32,172 @@ dpkg-source: info: applying gcc-6.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/16305/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2788/tmp/hooks/D01_modify_environment starting +debug: Running on profitbricks-build6-i386. +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/2788/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2788/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=18' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='6122959b75d84cd8b067e34e26d758f1' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='16305' - PS1='# ' - PS2='> ' + INVOCATION_ID=af4a5fb96b6d4a668d11465a9cca1c27 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=2788 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.mlfVnw9CNR/pbuilderrc_4hC2 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.mlfVnw9CNR/b1 --logfile b1/build.log consensuscore_1.1.1+dfsg-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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.mlfVnw9CNR/pbuilderrc_UIGH --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.mlfVnw9CNR/b2 --logfile b2/build.log consensuscore_1.1.1+dfsg-1.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux profitbricks-build2-i386 4.19.0-10-686-pae #1 SMP Debian 4.19.132-1 (2020-07-24) i686 GNU/Linux + Linux i-capture-the-hostname 4.19.0-10-amd64 #1 SMP Debian 4.19.132-1 (2020-07-24) x86_64 GNU/Linux I: ls -l /bin - total 5500 - -rwxr-xr-x 1 root root 1302248 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38280 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38280 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 38280 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 17768 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 38692 Feb 28 2019 cat - -rwxr-xr-x 1 root root 75588 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 63268 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 75588 Feb 28 2019 chown - -rwxr-xr-x 1 root root 153732 Feb 28 2019 cp - -rwxr-xr-x 1 root root 132820 Jan 17 2019 dash - -rwxr-xr-x 1 root root 120676 Feb 28 2019 date - -rwxr-xr-x 1 root root 92040 Feb 28 2019 dd - -rwxr-xr-x 1 root root 100620 Feb 28 2019 df - -rwxr-xr-x 1 root root 149736 Feb 28 2019 dir - -rwxr-xr-x 1 root root 79412 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 34532 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 34532 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 67700 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 30112 Apr 22 07:38 fusermount - -rwxr-xr-x 1 root root 206392 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 100952 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 21916 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 79752 Feb 28 2019 ln - -rwxr-xr-x 1 root root 55400 Jul 26 2018 login - -rwxr-xr-x 1 root root 149736 Feb 28 2019 ls - -rwxr-xr-x 1 root root 112032 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 87972 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 79748 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 46916 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 42348 Jan 9 2019 more - -rwsr-xr-x 1 root root 50592 Jan 9 2019 mount - -rwxr-xr-x 1 root root 13724 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 157832 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 38660 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 46852 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 75588 Feb 28 2019 rm - -rwxr-xr-x 1 root root 42756 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 22276 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 9 22:10 sh -> dash - -rwxr-xr-x 1 root root 34532 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 79652 Feb 28 2019 stty - -rwsr-xr-x 1 root root 71072 Jan 9 2019 su - -rwxr-xr-x 1 root root 34564 Feb 28 2019 sync - -rwxr-xr-x 1 root root 504024 Apr 23 2019 tar - -rwxr-xr-x 1 root root 13860 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 104292 Feb 28 2019 touch - -rwxr-xr-x 1 root root 34532 Feb 28 2019 true - -rwxr-xr-x 1 root root 17768 Apr 22 07:38 ulockmgr_server - -rwsr-xr-x 1 root root 30108 Jan 9 2019 umount - -rwxr-xr-x 1 root root 34532 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 149736 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34208 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/16305/tmp/hooks/D02_print_environment finished + total 5476 + -rwxr-xr-x 1 root root 1302248 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38280 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 38280 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 17768 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 38692 Mar 1 2019 cat + -rwxr-xr-x 1 root root 75588 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 63268 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 75588 Mar 1 2019 chown + -rwxr-xr-x 1 root root 153732 Mar 1 2019 cp + -rwxr-xr-x 1 root root 132820 Jan 18 2019 dash + -rwxr-xr-x 1 root root 120676 Mar 1 2019 date + -rwxr-xr-x 1 root root 92040 Mar 1 2019 dd + -rwxr-xr-x 1 root root 100620 Mar 1 2019 df + -rwxr-xr-x 1 root root 149736 Mar 1 2019 dir + -rwxr-xr-x 1 root root 79412 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 34532 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 34532 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 67700 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 30112 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 206392 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 100952 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 21916 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 79752 Mar 1 2019 ln + -rwxr-xr-x 1 root root 55400 Jul 27 2018 login + -rwxr-xr-x 1 root root 149736 Mar 1 2019 ls + -rwxr-xr-x 1 root root 112032 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 87972 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 79748 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 46916 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 42348 Jan 10 2019 more + -rwsr-xr-x 1 root root 50592 Jan 10 2019 mount + -rwxr-xr-x 1 root root 13724 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 157832 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 38660 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 46852 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 75588 Mar 1 2019 rm + -rwxr-xr-x 1 root root 42756 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 22276 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Sep 14 05:56 sh -> bash + lrwxrwxrwx 1 root root 4 Sep 14 04:47 sh.distrib -> dash + -rwxr-xr-x 1 root root 34532 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 79652 Mar 1 2019 stty + -rwsr-xr-x 1 root root 71072 Jan 10 2019 su + -rwxr-xr-x 1 root root 34564 Mar 1 2019 sync + -rwxr-xr-x 1 root root 504024 Apr 24 2019 tar + -rwxr-xr-x 1 root root 13860 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 104292 Mar 1 2019 touch + -rwxr-xr-x 1 root root 34532 Mar 1 2019 true + -rwxr-xr-x 1 root root 17768 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 30108 Jan 10 2019 umount + -rwxr-xr-x 1 root root 34532 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 149736 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34208 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/2788/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -311,7 +345,7 @@ Get: 90 http://deb.debian.org/debian buster/main i386 python3-setuptools all 40.8.0-1 [306 kB] Get: 91 http://deb.debian.org/debian buster/main i386 swig3.0 i386 3.0.12-2 [1456 kB] Get: 92 http://deb.debian.org/debian buster/main i386 swig i386 3.0.12-2 [310 kB] -Fetched 131 MB in 35s (3755 kB/s) +Fetched 131 MB in 2s (83.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19234 files and directories currently installed.) @@ -708,7 +742,7 @@ 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 +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 dpkg-buildpackage: info: source package consensuscore dpkg-buildpackage: info: source version 1.1.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -758,36 +792,55 @@ DEBUG = CPP_STD = c++14 -make[1]: Entering directory '/build/consensuscore-1.1.1+dfsg' +make[1]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird betreten make -f make/Cpp.mk -j8 -make[2]: Entering directory '/build/consensuscore-1.1.1+dfsg' +make[2]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird betreten mkdir -p /build/consensuscore-1.1.1+dfsg/build/C++ 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 -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 -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++/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/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 -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++/Statistics/Binomial.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Binomial.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++/Utils.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Utils.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++/Read.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Read.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++/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 -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 -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 -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++/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/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++/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++/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++/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++/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++/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++/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++/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++/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++/Sequence.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Sequence.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++/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++/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 -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++/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++/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/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/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++/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++/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++/Version.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Version.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++/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++/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++/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++/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/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++/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 -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/detail/RecursorBase.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.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 -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++/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/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 -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++/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/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++/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++/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 -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 -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++/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++/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++/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++/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++/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++/Mutation.o -MM src/C++/Mutation.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Mutation.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=] @@ -811,59 +864,40 @@ 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 -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 -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++/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++/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++/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 -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++/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++/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++/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 -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++/Utils.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Utils.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 -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++/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++/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++/Statistics/Binomial.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Binomial.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 -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++/Version.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Version.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++/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 -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++/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++/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 -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++/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++/Sequence.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Sequence.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++/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++/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++/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 -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++/Read.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Read.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 -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++/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++/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/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/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++/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 -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++/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++/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 -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++/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++/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 -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++/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 -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++/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++/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++/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 -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++/PoaGraphImpl.o -MM src/C++/Poa/PoaGraphImpl.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.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++/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++/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++/Read.o -MM src/C++/Read.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Read.d -ar crs /build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a /build/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o /build/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o /build/consensuscore-1.1.1+dfsg/build/C++/Feature.o /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o /build/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o /build/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.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++/SseRecursor.o /build/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o /build/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o /build/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o /build/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.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++/QuiverConfig.o /build/consensuscore-1.1.1+dfsg/build/C++/Mutation.o /build/consensuscore-1.1.1+dfsg/build/C++/Logging.o /build/consensuscore-1.1.1+dfsg/build/C++/Utils.o /build/consensuscore-1.1.1+dfsg/build/C++/Checksum.o /build/consensuscore-1.1.1+dfsg/build/C++/Binomial.o /build/consensuscore-1.1.1+dfsg/build/C++/Version.o /build/consensuscore-1.1.1+dfsg/build/C++/Coverage.o /build/consensuscore-1.1.1+dfsg/build/C++/Features.o /build/consensuscore-1.1.1+dfsg/build/C++/Sequence.o /build/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o /build/consensuscore-1.1.1+dfsg/build/C++/Read.o /build/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o /build/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o /build/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o /build/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o +ar crs /build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a /build/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o /build/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o /build/consensuscore-1.1.1+dfsg/build/C++/Binomial.o /build/consensuscore-1.1.1+dfsg/build/C++/Utils.o /build/consensuscore-1.1.1+dfsg/build/C++/Read.o /build/consensuscore-1.1.1+dfsg/build/C++/Features.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++/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++/Sequence.o /build/consensuscore-1.1.1+dfsg/build/C++/Checksum.o /build/consensuscore-1.1.1+dfsg/build/C++/Feature.o /build/consensuscore-1.1.1+dfsg/build/C++/Version.o /build/consensuscore-1.1.1+dfsg/build/C++/Mutation.o /build/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o /build/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o /build/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o /build/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o /build/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o /build/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o /build/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o /build/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.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++/Diploid.o /build/consensuscore-1.1.1+dfsg/build/C++/Logging.o /build/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o /build/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o /build/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o /build/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o /build/consensuscore-1.1.1+dfsg/build/C++/Coverage.o touch /build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -make[2]: Leaving directory '/build/consensuscore-1.1.1+dfsg' +make[2]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird verlassen make -f make/Python.mk -make[2]: Entering directory '/build/consensuscore-1.1.1+dfsg' +make[2]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird betreten mkdir -p /build/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:27: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /build/consensuscore-1.1.1+dfsg/include/ConsensusCore/Poa/PoaConsensus.hpp:24: Warning 309: private inheritance from base 'noncopyable' (ignored). 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 -pthread -shared -Wl,-O1 -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I /usr/include/python2.7 -I /usr/lib/python2.7/dist-packages/numpy/core/include /build/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so -make[2]: Leaving directory '/build/consensuscore-1.1.1+dfsg' -make[1]: Leaving directory '/build/consensuscore-1.1.1+dfsg' +make[2]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird verlassen +make[1]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird verlassen I: pybuild base:217: /usr/bin/python3 setup.py build WARNING: '' not a valid package name; please use only .-separated package names in setup.py running build @@ -878,126 +912,134 @@ DEBUG = CPP_STD = c++14 -make[1]: Entering directory '/build/consensuscore-1.1.1+dfsg' +make[1]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird betreten make -f make/Cpp.mk -j8 -make[2]: Entering directory '/build/consensuscore-1.1.1+dfsg' -make[2]: '/build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. -make[2]: Leaving directory '/build/consensuscore-1.1.1+dfsg' +make[2]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird betreten +make[2]: „/build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a“ ist bereits aktuell. +make[2]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird verlassen make -f make/Python.mk -make[2]: Entering directory '/build/consensuscore-1.1.1+dfsg' +make[2]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird betreten mkdir -p /build/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:27: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /build/consensuscore-1.1.1+dfsg/include/ConsensusCore/Poa/PoaConsensus.hpp:24: Warning 309: private inheritance from base 'noncopyable' (ignored). 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 -pthread -shared -Wl,-O1 -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.7m -I /usr/lib/python3/dist-packages/numpy/core/include /build/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so -make[2]: Leaving directory '/build/consensuscore-1.1.1+dfsg' -make[1]: Leaving directory '/build/consensuscore-1.1.1+dfsg' +make[2]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird verlassen +make[1]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird verlassen debian/rules override_dh_auto_test -make[1]: Entering directory '/build/consensuscore-1.1.1+dfsg' +make[1]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird betreten /usr/bin/make test -make[2]: Entering directory '/build/consensuscore-1.1.1+dfsg' +make[2]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird betreten /usr/bin/make -f make/Cpp.mk -j8 -make[3]: Entering directory '/build/consensuscore-1.1.1+dfsg' -make[3]: '/build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. -make[3]: Leaving directory '/build/consensuscore-1.1.1+dfsg' -make[3]: Entering directory '/build/consensuscore-1.1.1+dfsg' +make[3]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird betreten +make[3]: „/build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a“ ist bereits aktuell. +make[3]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird verlassen +make[3]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird betreten mkdir -p /build/consensuscore-1.1.1+dfsg/build/Tests -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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestMutationEnumerator.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestMatrixFacades.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o mkdir -p /build/consensuscore-1.1.1+dfsg/build/Tests -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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestSparseVector.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestQvEvaluator.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o mkdir -p /build/consensuscore-1.1.1+dfsg/build/Tests -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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestMutations.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestCoverage.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestCoverage.o mkdir -p /build/consensuscore-1.1.1+dfsg/build/Tests -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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestPairwiseAlignment.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/ParameterSettings.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.o mkdir -p /build/consensuscore-1.1.1+dfsg/build/Tests 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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestRecursors.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestRecursors.o mkdir -p /build/consensuscore-1.1.1+dfsg/build/Tests -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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/ParameterSettings.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.o -mkdir -p /build/consensuscore-1.1.1+dfsg/build/Tests -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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestCoverage.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestCoverage.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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestPoaConsensus.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o mkdir -p /build/consensuscore-1.1.1+dfsg/build/Tests 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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestMutationScorer.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.o mkdir -p /build/consensuscore-1.1.1+dfsg/build/Tests -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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestMatrixFacades.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o -mkdir -p /build/consensuscore-1.1.1+dfsg/build/Tests -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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestPoaConsensus.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestMultiReadMutationScorer.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o mkdir -p /build/consensuscore-1.1.1+dfsg/build/Tests 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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestDiploidQuiver.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.o mkdir -p /build/consensuscore-1.1.1+dfsg/build/Tests -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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestMultiReadMutationScorer.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestMutationEnumerator.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o mkdir -p /build/consensuscore-1.1.1+dfsg/build/Tests -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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestQvEvaluator.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.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 /build/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestRecursors.o /build/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestCoverage.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o /build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 /build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0/gmock-gtest-all.cc /build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0/gmock_main.cc -lpthread -o /build/consensuscore-1.1.1+dfsg/build/Tests/test-runner +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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestMutations.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o +mkdir -p /build/consensuscore-1.1.1+dfsg/build/Tests +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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestSparseVector.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.o +mkdir -p /build/consensuscore-1.1.1+dfsg/build/Tests +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 -O0 -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 -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-1.1.1+dfsg/src/Tests/TestPairwiseAlignment.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.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 /build/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestCoverage.o /build/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestRecursors.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.o /build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -I/build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 /build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0/gmock-gtest-all.cc /build/consensuscore-1.1.1+dfsg/external/gmock-1.7.0/gmock_main.cc -lpthread -o /build/consensuscore-1.1.1+dfsg/build/Tests/test-runner GTEST_OUTPUT="xml:tests-summary.xml" /build/consensuscore-1.1.1+dfsg/build/Tests/test-runner Running main() from gmock_main.cc [==========] Running 158 tests from 29 test cases. [----------] Global test environment set-up. -[----------] 4 tests from MutationEnumerationTest -[ RUN ] MutationEnumerationTest.TestAllMutations -[ OK ] MutationEnumerationTest.TestAllMutations (0 ms) -[ RUN ] MutationEnumerationTest.TestUniqueMutations -[ OK ] MutationEnumerationTest.TestUniqueMutations (1 ms) -[ RUN ] MutationEnumerationTest.TestUniqueNearbyMutations -[ OK ] MutationEnumerationTest.TestUniqueNearbyMutations (4 ms) -[ RUN ] MutationEnumerationTest.TestDinucleotideMutations -[ OK ] MutationEnumerationTest.TestDinucleotideMutations (1 ms) -[----------] 4 tests from MutationEnumerationTest (6 ms total) - -[----------] 2 tests from SparseVectorTest -[ RUN ] SparseVectorTest.BasicTest -[ OK ] SparseVectorTest.BasicTest (0 ms) -[ RUN ] SparseVectorTest.BasicTest2 -[ OK ] SparseVectorTest.BasicTest2 (0 ms) -[----------] 2 tests from SparseVectorTest (0 ms total) - -[----------] 1 test from SparseVector -[ RUN ] SparseVector.CopyTest -[ OK ] SparseVector.CopyTest (0 ms) -[----------] 1 test from SparseVector (0 ms total) - -[----------] 7 tests from MutationTest -[ RUN ] MutationTest.BasicTest -[ OK ] MutationTest.BasicTest (0 ms) -[ RUN ] MutationTest.DeleteTest -[ OK ] MutationTest.DeleteTest (0 ms) -[ RUN ] MutationTest.InsertTest -[ OK ] MutationTest.InsertTest (0 ms) -[ RUN ] MutationTest.ApplyMutationsTest -[ OK ] MutationTest.ApplyMutationsTest (0 ms) -[ RUN ] MutationTest.ApplyMutationsToSamePositionTest -[ OK ] MutationTest.ApplyMutationsToSamePositionTest (0 ms) -[ RUN ] MutationTest.MutationsToTranscript -[ OK ] MutationTest.MutationsToTranscript (0 ms) -[ RUN ] MutationTest.MutatedTemplatePositionsTest -[ OK ] MutationTest.MutatedTemplatePositionsTest (0 ms) -[----------] 7 tests from MutationTest (0 ms total) - -[----------] 3 tests from PairwiseAlignmentTests -[ RUN ] PairwiseAlignmentTests.RepresentationTests -[ OK ] PairwiseAlignmentTests.RepresentationTests (0 ms) -[ RUN ] PairwiseAlignmentTests.GlobalAlignmentTests -[ OK ] PairwiseAlignmentTests.GlobalAlignmentTests (0 ms) -[ RUN ] PairwiseAlignmentTests.TargetPositionsInQueryTest -[ OK ] PairwiseAlignmentTests.TargetPositionsInQueryTest (1 ms) -[----------] 3 tests from PairwiseAlignmentTests (1 ms total) +[----------] 11 tests from MatrixTest/0, where TypeParam = ConsensusCore::DenseMatrix +[ RUN ] MatrixTest/0.Basic +[ OK ] MatrixTest/0.Basic (0 ms) +[ RUN ] MatrixTest/0.Nullability +[ OK ] MatrixTest/0.Nullability (0 ms) +[ RUN ] MatrixTest/0.Ranges +[ OK ] MatrixTest/0.Ranges (0 ms) +[ RUN ] MatrixTest/0.IsColumnEmpty +[ OK ] MatrixTest/0.IsColumnEmpty (0 ms) +[ RUN ] MatrixTest/0.SSE +[ OK ] MatrixTest/0.SSE (0 ms) +[ RUN ] MatrixTest/0.ToHostArray +[ OK ] MatrixTest/0.ToHostArray (0 ms) +[ RUN ] MatrixTest/0.NonSequentialAccess +[ OK ] MatrixTest/0.NonSequentialAccess (0 ms) +[ RUN ] MatrixTest/0.Holes +[ OK ] MatrixTest/0.Holes (0 ms) +[ RUN ] MatrixTest/0.BigBandedMatrix +N13ConsensusCore11DenseMatrixE : 1000000 +[ OK ] MatrixTest/0.BigBandedMatrix (5 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 (5 ms total) -[----------] 2 tests from AffineAlignmentTests -[ RUN ] AffineAlignmentTests.BasicTests -[ OK ] AffineAlignmentTests.BasicTests (0 ms) -[ RUN ] AffineAlignmentTests.LargeGapTest -[ OK ] AffineAlignmentTests.LargeGapTest (28 ms) -[----------] 2 tests from AffineAlignmentTests (28 ms total) +[----------] 11 tests from MatrixTest/1, where TypeParam = ConsensusCore::SparseMatrix +[ RUN ] MatrixTest/1.Basic +[ OK ] MatrixTest/1.Basic (0 ms) +[ RUN ] MatrixTest/1.Nullability +[ OK ] MatrixTest/1.Nullability (0 ms) +[ RUN ] MatrixTest/1.Ranges +[ OK ] MatrixTest/1.Ranges (0 ms) +[ RUN ] MatrixTest/1.IsColumnEmpty +[ OK ] MatrixTest/1.IsColumnEmpty (0 ms) +[ RUN ] MatrixTest/1.SSE +[ OK ] MatrixTest/1.SSE (0 ms) +[ RUN ] MatrixTest/1.ToHostArray +[ OK ] MatrixTest/1.ToHostArray (0 ms) +[ RUN ] MatrixTest/1.NonSequentialAccess +[ OK ] MatrixTest/1.NonSequentialAccess (0 ms) +[ RUN ] MatrixTest/1.Holes +[ OK ] MatrixTest/1.Holes (0 ms) +[ RUN ] MatrixTest/1.BigBandedMatrix +N13ConsensusCore12SparseMatrixE : 1001976 +[ 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 (8 ms total) -[----------] 1 test from IupacAlignmentTests -[ RUN ] IupacAlignmentTests.BasicTest -[ OK ] IupacAlignmentTests.BasicTest (0 ms) -[----------] 1 test from IupacAlignmentTests (0 ms total) +[----------] 5 tests from QvEvaluatorTest +[ RUN ] QvEvaluatorTest.IncVsInc4 +[ OK ] QvEvaluatorTest.IncVsInc4 (51 ms) +[ RUN ] QvEvaluatorTest.DelVsDel4 +[ OK ] QvEvaluatorTest.DelVsDel4 (54 ms) +[ RUN ] QvEvaluatorTest.ExtraVsExtra4 +[ OK ] QvEvaluatorTest.ExtraVsExtra4 (59 ms) +[ RUN ] QvEvaluatorTest.MergeVsMerge4 +[ OK ] QvEvaluatorTest.MergeVsMerge4 (43 ms) +[ RUN ] QvEvaluatorTest.BadTagTest +[ OK ] QvEvaluatorTest.BadTagTest (4 ms) +[----------] 5 tests from QvEvaluatorTest (213 ms total) -[----------] 1 test from LinearAlignmentTests -[ RUN ] LinearAlignmentTests.BasicTest -[ OK ] LinearAlignmentTests.BasicTest (1 ms) -[----------] 1 test from LinearAlignmentTests (1 ms total) +[----------] 3 tests from CoverageTests +[ RUN ] CoverageTests.CoverageInWindowTest +[ OK ] CoverageTests.CoverageInWindowTest (0 ms) +[ RUN ] CoverageTests.CoveredIntervalsTest +[ OK ] CoverageTests.CoveredIntervalsTest (0 ms) +[ RUN ] CoverageTests.CoveredIntervalsTest2 +[ OK ] CoverageTests.CoveredIntervalsTest2 (0 ms) +[----------] 3 tests from CoverageTests (0 ms total) [----------] 7 tests from RecursorTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorTest/0.SmallMatchTest @@ -1007,14 +1049,14 @@ [ RUN ] RecursorTest/0.SmallMergeTest [ OK ] RecursorTest/0.SmallMergeTest (0 ms) [ RUN ] RecursorTest/0.MediumSizedTest -[ OK ] RecursorTest/0.MediumSizedTest (5 ms) +[ OK ] RecursorTest/0.MediumSizedTest (3 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 (0 ms) -[----------] 7 tests from RecursorTest/0 (5 ms total) +[----------] 7 tests from RecursorTest/0 (3 ms total) [----------] 7 tests from RecursorTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorTest/1.SmallMatchTest @@ -1024,14 +1066,14 @@ [ RUN ] RecursorTest/1.SmallMergeTest [ OK ] RecursorTest/1.SmallMergeTest (0 ms) [ RUN ] RecursorTest/1.MediumSizedTest -[ OK ] RecursorTest/1.MediumSizedTest (5 ms) +[ OK ] RecursorTest/1.MediumSizedTest (3 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 (0 ms) -[----------] 7 tests from RecursorTest/1 (6 ms total) +[----------] 7 tests from RecursorTest/1 (3 ms total) [----------] 7 tests from RecursorTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorTest/2.SmallMatchTest @@ -1041,14 +1083,14 @@ [ RUN ] RecursorTest/2.SmallMergeTest [ OK ] RecursorTest/2.SmallMergeTest (0 ms) [ RUN ] RecursorTest/2.MediumSizedTest -[ OK ] RecursorTest/2.MediumSizedTest (4 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 (4 ms total) +[----------] 7 tests from RecursorTest/2 (3 ms total) [----------] 7 tests from RecursorTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorTest/3.SmallMatchTest @@ -1058,75 +1100,98 @@ [ RUN ] RecursorTest/3.SmallMergeTest [ OK ] RecursorTest/3.SmallMergeTest (0 ms) [ RUN ] RecursorTest/3.MediumSizedTest -[ OK ] RecursorTest/3.MediumSizedTest (5 ms) +[ OK ] RecursorTest/3.MediumSizedTest (3 ms) [ RUN ] RecursorTest/3.LinkTest [ OK ] RecursorTest/3.LinkTest (0 ms) [ RUN ] RecursorTest/3.ExtendAlphaTest -[ OK ] RecursorTest/3.ExtendAlphaTest (1 ms) +[ OK ] RecursorTest/3.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/3.ExtendBetaTest [ OK ] RecursorTest/3.ExtendBetaTest (0 ms) -[----------] 7 tests from RecursorTest/3 (6 ms total) +[----------] 7 tests from RecursorTest/3 (3 ms total) [----------] 5 tests from RecursorFuzzTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/0.AlphaBetaConcordance -[ OK ] RecursorFuzzTest/0.AlphaBetaConcordance (133 ms) +[ OK ] RecursorFuzzTest/0.AlphaBetaConcordance (74 ms) [ RUN ] RecursorFuzzTest/0.Alignment -[ OK ] RecursorFuzzTest/0.Alignment (135 ms) +[ OK ] RecursorFuzzTest/0.Alignment (72 ms) [ RUN ] RecursorFuzzTest/0.LinkAlphaBeta -[ OK ] RecursorFuzzTest/0.LinkAlphaBeta (149 ms) +[ OK ] RecursorFuzzTest/0.LinkAlphaBeta (81 ms) [ RUN ] RecursorFuzzTest/0.ExtendAlpha -[ OK ] RecursorFuzzTest/0.ExtendAlpha (47 ms) +[ OK ] RecursorFuzzTest/0.ExtendAlpha (26 ms) [ RUN ] RecursorFuzzTest/0.ExtendBeta -[ OK ] RecursorFuzzTest/0.ExtendBeta (45 ms) -[----------] 5 tests from RecursorFuzzTest/0 (509 ms total) +[ OK ] RecursorFuzzTest/0.ExtendBeta (25 ms) +[----------] 5 tests from RecursorFuzzTest/0 (279 ms total) [----------] 5 tests from RecursorFuzzTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/1.AlphaBetaConcordance -[ OK ] RecursorFuzzTest/1.AlphaBetaConcordance (115 ms) +[ OK ] RecursorFuzzTest/1.AlphaBetaConcordance (58 ms) [ RUN ] RecursorFuzzTest/1.Alignment -[ OK ] RecursorFuzzTest/1.Alignment (117 ms) +[ OK ] RecursorFuzzTest/1.Alignment (58 ms) [ RUN ] RecursorFuzzTest/1.LinkAlphaBeta -[ OK ] RecursorFuzzTest/1.LinkAlphaBeta (119 ms) +[ OK ] RecursorFuzzTest/1.LinkAlphaBeta (59 ms) [ RUN ] RecursorFuzzTest/1.ExtendAlpha -[ OK ] RecursorFuzzTest/1.ExtendAlpha (48 ms) +[ OK ] RecursorFuzzTest/1.ExtendAlpha (25 ms) [ RUN ] RecursorFuzzTest/1.ExtendBeta -[ OK ] RecursorFuzzTest/1.ExtendBeta (47 ms) -[----------] 5 tests from RecursorFuzzTest/1 (446 ms total) +[ OK ] RecursorFuzzTest/1.ExtendBeta (25 ms) +[----------] 5 tests from RecursorFuzzTest/1 (225 ms total) [----------] 5 tests from RecursorFuzzTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/2.AlphaBetaConcordance -[ OK ] RecursorFuzzTest/2.AlphaBetaConcordance (134 ms) +[ OK ] RecursorFuzzTest/2.AlphaBetaConcordance (75 ms) [ RUN ] RecursorFuzzTest/2.Alignment -[ OK ] RecursorFuzzTest/2.Alignment (134 ms) +[ OK ] RecursorFuzzTest/2.Alignment (75 ms) [ RUN ] RecursorFuzzTest/2.LinkAlphaBeta -[ OK ] RecursorFuzzTest/2.LinkAlphaBeta (163 ms) +[ OK ] RecursorFuzzTest/2.LinkAlphaBeta (95 ms) [ RUN ] RecursorFuzzTest/2.ExtendAlpha -[ OK ] RecursorFuzzTest/2.ExtendAlpha (35 ms) +[ OK ] RecursorFuzzTest/2.ExtendAlpha (21 ms) [ RUN ] RecursorFuzzTest/2.ExtendBeta -[ OK ] RecursorFuzzTest/2.ExtendBeta (35 ms) -[----------] 5 tests from RecursorFuzzTest/2 (501 ms total) +[ OK ] RecursorFuzzTest/2.ExtendBeta (20 ms) +[----------] 5 tests from RecursorFuzzTest/2 (286 ms total) [----------] 5 tests from RecursorFuzzTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/3.AlphaBetaConcordance -[ OK ] RecursorFuzzTest/3.AlphaBetaConcordance (136 ms) +[ OK ] RecursorFuzzTest/3.AlphaBetaConcordance (72 ms) [ RUN ] RecursorFuzzTest/3.Alignment -[ OK ] RecursorFuzzTest/3.Alignment (135 ms) +[ OK ] RecursorFuzzTest/3.Alignment (73 ms) [ RUN ] RecursorFuzzTest/3.LinkAlphaBeta -[ OK ] RecursorFuzzTest/3.LinkAlphaBeta (138 ms) +[ OK ] RecursorFuzzTest/3.LinkAlphaBeta (73 ms) [ RUN ] RecursorFuzzTest/3.ExtendAlpha -[ OK ] RecursorFuzzTest/3.ExtendAlpha (34 ms) +[ OK ] RecursorFuzzTest/3.ExtendAlpha (20 ms) [ RUN ] RecursorFuzzTest/3.ExtendBeta -[ OK ] RecursorFuzzTest/3.ExtendBeta (35 ms) -[----------] 5 tests from RecursorFuzzTest/3 (479 ms total) +[ OK ] RecursorFuzzTest/3.ExtendBeta (21 ms) +[----------] 5 tests from RecursorFuzzTest/3 (259 ms total) -[----------] 3 tests from CoverageTests -[ RUN ] CoverageTests.CoverageInWindowTest -[ OK ] CoverageTests.CoverageInWindowTest (0 ms) -[ RUN ] CoverageTests.CoveredIntervalsTest -[ OK ] CoverageTests.CoveredIntervalsTest (1 ms) -[ RUN ] CoverageTests.CoveredIntervalsTest2 -[ OK ] CoverageTests.CoveredIntervalsTest2 (0 ms) -[----------] 3 tests from CoverageTests (1 ms total) +[----------] 4 tests from PoaGraph +[ RUN ] PoaGraph.SmallBasicTest +[ OK ] PoaGraph.SmallBasicTest (0 ms) +[ RUN ] PoaGraph.SmallExtraTests +[ OK ] PoaGraph.SmallExtraTests (1 ms) +[ RUN ] PoaGraph.SmallMismatchTests +[ 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 (1 ms) +[ RUN ] PoaConsensus.TestOverhangSecond +[ OK ] PoaConsensus.TestOverhangSecond (0 ms) +[ RUN ] PoaConsensus.SmallSemiglobalTest +[ OK ] PoaConsensus.SmallSemiglobalTest (0 ms) +[ RUN ] PoaConsensus.SmallTilingTest +[ OK ] PoaConsensus.SmallTilingTest (0 ms) +[ RUN ] PoaConsensus.TestVerboseGraphVizOutput +[ OK ] PoaConsensus.TestVerboseGraphVizOutput (0 ms) +[ RUN ] PoaConsensus.TestLocalStaggered +dot -Tpng local-staggered.dot > local-staggered.png +sh: dot: Kommando nicht gefunden. +[ OK ] PoaConsensus.TestLocalStaggered (5 ms) +[ RUN ] PoaConsensus.TestLongInsert +[ OK ] PoaConsensus.TestLongInsert (1 ms) +[ RUN ] PoaConsensus.NondeterminismRegressionTest +[ OK ] PoaConsensus.NondeterminismRegressionTest (601 ms) +[----------] 8 tests from PoaConsensus (608 ms total) [----------] 8 tests from MutationScorerTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/0.BasicTest @@ -1136,16 +1201,16 @@ [ RUN ] MutationScorerTest/0.MutationsAtBeginning [ OK ] MutationScorerTest/0.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/0.MutationsAtEnd -[ OK ] MutationScorerTest/0.MutationsAtEnd (0 ms) +[ OK ] MutationScorerTest/0.MutationsAtEnd (1 ms) [ RUN ] MutationScorerTest/0.TinyTemplate [ OK ] MutationScorerTest/0.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/0.TemplateMutationWorkflow -[ OK ] MutationScorerTest/0.TemplateMutationWorkflow (1 ms) +[ OK ] MutationScorerTest/0.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/0.DinucleotideInsertionTest -[ OK ] MutationScorerTest/0.DinucleotideInsertionTest (3 ms) +[ OK ] MutationScorerTest/0.DinucleotideInsertionTest (2 ms) [ RUN ] MutationScorerTest/0.DinucleotideDeletionTest -[ OK ] MutationScorerTest/0.DinucleotideDeletionTest (2 ms) -[----------] 8 tests from MutationScorerTest/0 (6 ms total) +[ OK ] MutationScorerTest/0.DinucleotideDeletionTest (1 ms) +[----------] 8 tests from MutationScorerTest/0 (4 ms total) [----------] 8 tests from MutationScorerTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/1.BasicTest @@ -1157,14 +1222,14 @@ [ RUN ] MutationScorerTest/1.MutationsAtEnd [ OK ] MutationScorerTest/1.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/1.TinyTemplate -[ OK ] MutationScorerTest/1.TinyTemplate (1 ms) +[ OK ] MutationScorerTest/1.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/1.TemplateMutationWorkflow -[ OK ] MutationScorerTest/1.TemplateMutationWorkflow (0 ms) +[ OK ] MutationScorerTest/1.TemplateMutationWorkflow (1 ms) [ RUN ] MutationScorerTest/1.DinucleotideInsertionTest -[ OK ] MutationScorerTest/1.DinucleotideInsertionTest (3 ms) +[ OK ] MutationScorerTest/1.DinucleotideInsertionTest (2 ms) [ RUN ] MutationScorerTest/1.DinucleotideDeletionTest -[ OK ] MutationScorerTest/1.DinucleotideDeletionTest (2 ms) -[----------] 8 tests from MutationScorerTest/1 (6 ms total) +[ OK ] MutationScorerTest/1.DinucleotideDeletionTest (1 ms) +[----------] 8 tests from MutationScorerTest/1 (4 ms total) [----------] 8 tests from MutationScorerTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/2.BasicTest @@ -1174,16 +1239,16 @@ [ RUN ] MutationScorerTest/2.MutationsAtBeginning [ OK ] MutationScorerTest/2.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/2.MutationsAtEnd -[ OK ] MutationScorerTest/2.MutationsAtEnd (1 ms) +[ OK ] MutationScorerTest/2.MutationsAtEnd (0 ms) [ 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 (3 ms) +[ OK ] MutationScorerTest/2.DinucleotideInsertionTest (1 ms) [ RUN ] MutationScorerTest/2.DinucleotideDeletionTest -[ OK ] MutationScorerTest/2.DinucleotideDeletionTest (2 ms) -[----------] 8 tests from MutationScorerTest/2 (6 ms total) +[ OK ] MutationScorerTest/2.DinucleotideDeletionTest (0 ms) +[----------] 8 tests from MutationScorerTest/2 (3 ms total) [----------] 8 tests from MutationScorerTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/3.BasicTest @@ -1191,102 +1256,18 @@ [ RUN ] MutationScorerTest/3.CopyTest [ OK ] MutationScorerTest/3.CopyTest (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtBeginning -[ OK ] MutationScorerTest/3.MutationsAtBeginning (1 ms) +[ OK ] MutationScorerTest/3.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtEnd [ OK ] MutationScorerTest/3.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/3.TinyTemplate [ OK ] MutationScorerTest/3.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/3.TemplateMutationWorkflow -[ OK ] MutationScorerTest/3.TemplateMutationWorkflow (0 ms) +[ OK ] MutationScorerTest/3.TemplateMutationWorkflow (1 ms) [ RUN ] MutationScorerTest/3.DinucleotideInsertionTest -[ OK ] MutationScorerTest/3.DinucleotideInsertionTest (4 ms) +[ OK ] MutationScorerTest/3.DinucleotideInsertionTest (2 ms) [ RUN ] MutationScorerTest/3.DinucleotideDeletionTest -[ OK ] MutationScorerTest/3.DinucleotideDeletionTest (2 ms) -[----------] 8 tests from MutationScorerTest/3 (7 ms total) - -[----------] 11 tests from MatrixTest/0, where TypeParam = ConsensusCore::DenseMatrix -[ RUN ] MatrixTest/0.Basic -[ OK ] MatrixTest/0.Basic (0 ms) -[ RUN ] MatrixTest/0.Nullability -[ OK ] MatrixTest/0.Nullability (0 ms) -[ RUN ] MatrixTest/0.Ranges -[ OK ] MatrixTest/0.Ranges (0 ms) -[ RUN ] MatrixTest/0.IsColumnEmpty -[ OK ] MatrixTest/0.IsColumnEmpty (0 ms) -[ RUN ] MatrixTest/0.SSE -[ OK ] MatrixTest/0.SSE (0 ms) -[ RUN ] MatrixTest/0.ToHostArray -[ OK ] MatrixTest/0.ToHostArray (0 ms) -[ RUN ] MatrixTest/0.NonSequentialAccess -[ OK ] MatrixTest/0.NonSequentialAccess (0 ms) -[ RUN ] MatrixTest/0.Holes -[ OK ] MatrixTest/0.Holes (0 ms) -[ RUN ] MatrixTest/0.BigBandedMatrix -N13ConsensusCore11DenseMatrixE : 1000000 -[ OK ] MatrixTest/0.BigBandedMatrix (9 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 (10 ms total) - -[----------] 11 tests from MatrixTest/1, where TypeParam = ConsensusCore::SparseMatrix -[ RUN ] MatrixTest/1.Basic -[ OK ] MatrixTest/1.Basic (0 ms) -[ RUN ] MatrixTest/1.Nullability -[ OK ] MatrixTest/1.Nullability (0 ms) -[ RUN ] MatrixTest/1.Ranges -[ OK ] MatrixTest/1.Ranges (0 ms) -[ RUN ] MatrixTest/1.IsColumnEmpty -[ OK ] MatrixTest/1.IsColumnEmpty (0 ms) -[ RUN ] MatrixTest/1.SSE -[ OK ] MatrixTest/1.SSE (0 ms) -[ RUN ] MatrixTest/1.ToHostArray -[ OK ] MatrixTest/1.ToHostArray (0 ms) -[ RUN ] MatrixTest/1.NonSequentialAccess -[ OK ] MatrixTest/1.NonSequentialAccess (0 ms) -[ RUN ] MatrixTest/1.Holes -[ OK ] MatrixTest/1.Holes (0 ms) -[ RUN ] MatrixTest/1.BigBandedMatrix -N13ConsensusCore12SparseMatrixE : 1001976 -[ OK ] MatrixTest/1.BigBandedMatrix (14 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 (14 ms total) - -[----------] 4 tests from PoaGraph -[ RUN ] PoaGraph.SmallBasicTest -[ OK ] PoaGraph.SmallBasicTest (0 ms) -[ RUN ] PoaGraph.SmallExtraTests -[ OK ] PoaGraph.SmallExtraTests (0 ms) -[ RUN ] PoaGraph.SmallMismatchTests -[ OK ] PoaGraph.SmallMismatchTests (1 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 (1 ms) -[ RUN ] PoaConsensus.TestOverhangSecond -[ OK ] PoaConsensus.TestOverhangSecond (0 ms) -[ RUN ] PoaConsensus.SmallSemiglobalTest -[ OK ] PoaConsensus.SmallSemiglobalTest (0 ms) -[ RUN ] PoaConsensus.SmallTilingTest -[ OK ] PoaConsensus.SmallTilingTest (0 ms) -[ RUN ] PoaConsensus.TestVerboseGraphVizOutput -[ OK ] PoaConsensus.TestVerboseGraphVizOutput (0 ms) -[ RUN ] PoaConsensus.TestLocalStaggered -dot -Tpng local-staggered.dot > local-staggered.png -sh: 1: dot: not found -[ OK ] PoaConsensus.TestLocalStaggered (6 ms) -[ RUN ] PoaConsensus.TestLongInsert -[ OK ] PoaConsensus.TestLongInsert (1 ms) -[ RUN ] PoaConsensus.NondeterminismRegressionTest -[ OK ] PoaConsensus.NondeterminismRegressionTest (1185 ms) -[----------] 8 tests from PoaConsensus (1194 ms total) +[ OK ] MutationScorerTest/3.DinucleotideDeletionTest (1 ms) +[----------] 8 tests from MutationScorerTest/3 (4 ms total) [----------] 1 test from QuiverConfigTableTests [ RUN ] QuiverConfigTableTests.IllegalChemistry @@ -1306,46 +1287,99 @@ [ RUN ] MultiReadMutationScorerTest/0.Template [ OK ] MultiReadMutationScorerTest/0.Template (0 ms) [ RUN ] MultiReadMutationScorerTest/0.BasicTest -[ OK ] MultiReadMutationScorerTest/0.BasicTest (2 ms) +[ OK ] MultiReadMutationScorerTest/0.BasicTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.ManyMutationTest -[ OK ] MultiReadMutationScorerTest/0.ManyMutationTest (3 ms) +[ OK ] MultiReadMutationScorerTest/0.ManyMutationTest (2 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyConstructorTest [ OK ] MultiReadMutationScorerTest/0.CopyConstructorTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.ReverseStrandTest -[ OK ] MultiReadMutationScorerTest/0.ReverseStrandTest (2 ms) +[ OK ] MultiReadMutationScorerTest/0.ReverseStrandTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning (0 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtEnd [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtEnd (0 ms) [ RUN ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 -[ OK ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 (2 ms) +[ OK ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 (1 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyTest -[ OK ] MultiReadMutationScorerTest/0.CopyTest (0 ms) +[ OK ] MultiReadMutationScorerTest/0.CopyTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds -[ OK ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds (1 ms) +[ OK ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds (0 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds (0 ms) -[----------] 11 tests from MultiReadMutationScorerTest/0 (10 ms total) +[----------] 11 tests from MultiReadMutationScorerTest/0 (6 ms total) -[----------] 5 tests from QvEvaluatorTest -[ RUN ] QvEvaluatorTest.IncVsInc4 -[ OK ] QvEvaluatorTest.IncVsInc4 (93 ms) -[ RUN ] QvEvaluatorTest.DelVsDel4 -[ OK ] QvEvaluatorTest.DelVsDel4 (93 ms) -[ RUN ] QvEvaluatorTest.ExtraVsExtra4 -[ OK ] QvEvaluatorTest.ExtraVsExtra4 (102 ms) -[ RUN ] QvEvaluatorTest.MergeVsMerge4 -[ OK ] QvEvaluatorTest.MergeVsMerge4 (74 ms) -[ RUN ] QvEvaluatorTest.BadTagTest -[ OK ] QvEvaluatorTest.BadTagTest (9 ms) -[----------] 5 tests from QvEvaluatorTest (371 ms total) +[----------] 4 tests from MutationEnumerationTest +[ RUN ] MutationEnumerationTest.TestAllMutations +[ OK ] MutationEnumerationTest.TestAllMutations (0 ms) +[ RUN ] MutationEnumerationTest.TestUniqueMutations +[ OK ] MutationEnumerationTest.TestUniqueMutations (0 ms) +[ RUN ] MutationEnumerationTest.TestUniqueNearbyMutations +[ OK ] MutationEnumerationTest.TestUniqueNearbyMutations (2 ms) +[ RUN ] MutationEnumerationTest.TestDinucleotideMutations +[ OK ] MutationEnumerationTest.TestDinucleotideMutations (0 ms) +[----------] 4 tests from MutationEnumerationTest (2 ms total) + +[----------] 7 tests from MutationTest +[ RUN ] MutationTest.BasicTest +[ OK ] MutationTest.BasicTest (0 ms) +[ RUN ] MutationTest.DeleteTest +[ OK ] MutationTest.DeleteTest (0 ms) +[ RUN ] MutationTest.InsertTest +[ OK ] MutationTest.InsertTest (0 ms) +[ RUN ] MutationTest.ApplyMutationsTest +[ OK ] MutationTest.ApplyMutationsTest (0 ms) +[ RUN ] MutationTest.ApplyMutationsToSamePositionTest +[ OK ] MutationTest.ApplyMutationsToSamePositionTest (0 ms) +[ RUN ] MutationTest.MutationsToTranscript +[ OK ] MutationTest.MutationsToTranscript (0 ms) +[ RUN ] MutationTest.MutatedTemplatePositionsTest +[ OK ] MutationTest.MutatedTemplatePositionsTest (0 ms) +[----------] 7 tests from MutationTest (0 ms total) + +[----------] 2 tests from SparseVectorTest +[ RUN ] SparseVectorTest.BasicTest +[ OK ] SparseVectorTest.BasicTest (0 ms) +[ RUN ] SparseVectorTest.BasicTest2 +[ OK ] SparseVectorTest.BasicTest2 (0 ms) +[----------] 2 tests from SparseVectorTest (0 ms total) + +[----------] 1 test from SparseVector +[ RUN ] SparseVector.CopyTest +[ OK ] SparseVector.CopyTest (0 ms) +[----------] 1 test from SparseVector (0 ms total) + +[----------] 3 tests from PairwiseAlignmentTests +[ RUN ] PairwiseAlignmentTests.RepresentationTests +[ OK ] PairwiseAlignmentTests.RepresentationTests (0 ms) +[ RUN ] PairwiseAlignmentTests.GlobalAlignmentTests +[ OK ] PairwiseAlignmentTests.GlobalAlignmentTests (0 ms) +[ RUN ] PairwiseAlignmentTests.TargetPositionsInQueryTest +[ OK ] PairwiseAlignmentTests.TargetPositionsInQueryTest (0 ms) +[----------] 3 tests from PairwiseAlignmentTests (1 ms total) + +[----------] 2 tests from AffineAlignmentTests +[ RUN ] AffineAlignmentTests.BasicTests +[ OK ] AffineAlignmentTests.BasicTests (0 ms) +[ RUN ] AffineAlignmentTests.LargeGapTest +[ OK ] AffineAlignmentTests.LargeGapTest (13 ms) +[----------] 2 tests from AffineAlignmentTests (13 ms total) + +[----------] 1 test from IupacAlignmentTests +[ RUN ] IupacAlignmentTests.BasicTest +[ OK ] IupacAlignmentTests.BasicTest (0 ms) +[----------] 1 test from IupacAlignmentTests (0 ms total) + +[----------] 1 test from LinearAlignmentTests +[ RUN ] LinearAlignmentTests.BasicTest +[ OK ] LinearAlignmentTests.BasicTest (0 ms) +[----------] 1 test from LinearAlignmentTests (0 ms total) [----------] Global test environment tear-down -[==========] 158 tests from 29 test cases ran. (3618 ms total) +[==========] 158 tests from 29 test cases ran. (1934 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' -make[1]: Leaving directory '/build/consensuscore-1.1.1+dfsg' +make[3]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird verlassen +make[2]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird verlassen +make[1]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird verlassen create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python2,python3 --buildsystem=pybuild @@ -1366,21 +1400,21 @@ DEBUG = CPP_STD = c++14 -make[1]: Entering directory '/build/consensuscore-1.1.1+dfsg' +make[1]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird betreten make -f make/Cpp.mk -j8 -make[2]: Entering directory '/build/consensuscore-1.1.1+dfsg' -make[2]: '/build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. -make[2]: Leaving directory '/build/consensuscore-1.1.1+dfsg' +make[2]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird betreten +make[2]: „/build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a“ ist bereits aktuell. +make[2]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird verlassen make -f make/Python.mk -make[2]: Entering directory '/build/consensuscore-1.1.1+dfsg' +make[2]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird betreten mkdir -p /build/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:27: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /build/consensuscore-1.1.1+dfsg/include/ConsensusCore/Poa/PoaConsensus.hpp:24: Warning 309: private inheritance from base 'noncopyable' (ignored). 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 -pthread -shared -Wl,-O1 -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I /usr/include/python2.7 -I /usr/lib/python2.7/dist-packages/numpy/core/include /build/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so -make[2]: Leaving directory '/build/consensuscore-1.1.1+dfsg' -make[1]: Leaving directory '/build/consensuscore-1.1.1+dfsg' +make[2]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird verlassen +make[1]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird verlassen running install running install_lib running build_py @@ -1391,8 +1425,8 @@ creating /build/consensuscore-1.1.1+dfsg/debian/python-pbconsensuscore/usr/lib creating /build/consensuscore-1.1.1+dfsg/debian/python-pbconsensuscore/usr/lib/python2.7 creating /build/consensuscore-1.1.1+dfsg/debian/python-pbconsensuscore/usr/lib/python2.7/dist-packages -copying /build/consensuscore-1.1.1+dfsg/.pybuild/cpython2_2.7_pbconsensuscore/build/_ConsensusCore.so -> /build/consensuscore-1.1.1+dfsg/debian/python-pbconsensuscore/usr/lib/python2.7/dist-packages copying /build/consensuscore-1.1.1+dfsg/.pybuild/cpython2_2.7_pbconsensuscore/build/ConsensusCore.py -> /build/consensuscore-1.1.1+dfsg/debian/python-pbconsensuscore/usr/lib/python2.7/dist-packages +copying /build/consensuscore-1.1.1+dfsg/.pybuild/cpython2_2.7_pbconsensuscore/build/_ConsensusCore.so -> /build/consensuscore-1.1.1+dfsg/debian/python-pbconsensuscore/usr/lib/python2.7/dist-packages byte-compiling /build/consensuscore-1.1.1+dfsg/debian/python-pbconsensuscore/usr/lib/python2.7/dist-packages/ConsensusCore.py to ConsensusCore.pyc running install_egg_info running egg_info @@ -1420,21 +1454,21 @@ DEBUG = CPP_STD = c++14 -make[1]: Entering directory '/build/consensuscore-1.1.1+dfsg' +make[1]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird betreten make -f make/Cpp.mk -j8 -make[2]: Entering directory '/build/consensuscore-1.1.1+dfsg' -make[2]: '/build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. -make[2]: Leaving directory '/build/consensuscore-1.1.1+dfsg' +make[2]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird betreten +make[2]: „/build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a“ ist bereits aktuell. +make[2]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird verlassen make -f make/Python.mk -make[2]: Entering directory '/build/consensuscore-1.1.1+dfsg' +make[2]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird betreten mkdir -p /build/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:27: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /build/consensuscore-1.1.1+dfsg/include/ConsensusCore/Poa/PoaConsensus.hpp:24: Warning 309: private inheritance from base 'noncopyable' (ignored). 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 -pthread -shared -Wl,-O1 -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.7m -I /usr/lib/python3/dist-packages/numpy/core/include /build/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so -make[2]: Leaving directory '/build/consensuscore-1.1.1+dfsg' -make[1]: Leaving directory '/build/consensuscore-1.1.1+dfsg' +make[2]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird verlassen +make[1]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird verlassen running install running install_lib running build_py @@ -1445,8 +1479,8 @@ creating /build/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib creating /build/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.7 creating /build/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.7/dist-packages -copying /build/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.7_pbconsensuscore/build/_ConsensusCore.so -> /build/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.7/dist-packages copying /build/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.7_pbconsensuscore/build/ConsensusCore.py -> /build/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.7/dist-packages +copying /build/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.7_pbconsensuscore/build/_ConsensusCore.so -> /build/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.7/dist-packages byte-compiling /build/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.7/dist-packages/ConsensusCore.py to ConsensusCore.cpython-37.pyc running install_egg_info running egg_info @@ -1462,17 +1496,17 @@ dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_python2 -make[1]: Entering directory '/build/consensuscore-1.1.1+dfsg' +make[1]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird betreten dh_python2 I: dh_python2 fs:343: renaming _ConsensusCore.so to _ConsensusCore.i386-linux-gnu.so dh_numpy -make[1]: Leaving directory '/build/consensuscore-1.1.1+dfsg' +make[1]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird verlassen debian/rules override_dh_python3 -make[1]: Entering directory '/build/consensuscore-1.1.1+dfsg' +make[1]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird betreten dh_python3 I: dh_python3 fs:343: renaming _ConsensusCore.so to _ConsensusCore.cpython-37m-i386-linux-gnu.so dh_numpy3 -make[1]: Leaving directory '/build/consensuscore-1.1.1+dfsg' +make[1]: Verzeichnis „/build/consensuscore-1.1.1+dfsg“ wird verlassen dh_installinit -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild @@ -1496,31 +1530,33 @@ 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 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 +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_i386.deb'. -dpkg-deb: building package 'python-pbconsensuscore' in '../python-pbconsensuscore_1.1.1+dfsg-1_i386.deb'. -dpkg-deb: building package 'python3-pbconsensuscore' in '../python3-pbconsensuscore_1.1.1+dfsg-1_i386.deb'. -dpkg-deb: building package 'python3-pbconsensuscore-dbgsym' in '../python3-pbconsensuscore-dbgsym_1.1.1+dfsg-1_i386.deb'. -dpkg-deb: building package 'python-pbconsensuscore-dbgsym' in '../python-pbconsensuscore-dbgsym_1.1.1+dfsg-1_i386.deb'. +dpkg-deb: Paket »libconsensuscore-dev« wird in »../libconsensuscore-dev_1.1.1+dfsg-1_i386.deb« gebaut. +dpkg-deb: Paket »python-pbconsensuscore« wird in »../python-pbconsensuscore_1.1.1+dfsg-1_i386.deb« gebaut. +dpkg-deb: Paket »python-pbconsensuscore-dbgsym« wird in »../python-pbconsensuscore-dbgsym_1.1.1+dfsg-1_i386.deb« gebaut. +dpkg-deb: Paket »python3-pbconsensuscore-dbgsym« wird in »../python3-pbconsensuscore-dbgsym_1.1.1+dfsg-1_i386.deb« gebaut. +dpkg-deb: Paket »python3-pbconsensuscore« wird in »../python3-pbconsensuscore_1.1.1+dfsg-1_i386.deb« gebaut. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../consensuscore_1.1.1+dfsg-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/2788/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2788/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/16305 and its subdirectories -I: Current time: Mon Aug 10 21:33:27 -12 2020 -I: pbuilder-time-stamp: 1597138407 +I: removing directory /srv/workspace/pbuilder/2788 and its subdirectories +I: Current time: Tue Sep 14 06:03:08 +14 2021 +I: pbuilder-time-stamp: 1631548988