I: pbuilder: network access will be disabled during build
I: Current time: Tue May 28 05:43:03 -12 2024
I: pbuilder-time-stamp: 1716918183
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [consensuscore_1.1.1+dfsg-4.dsc]
I: copying [./consensuscore_1.1.1+dfsg.orig.tar.xz]
I: copying [./consensuscore_1.1.1+dfsg-4.debian.tar.xz]
I: Extracting source
gpgv: Signature made Mon Nov 14 01:38:02 2022 -12
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./consensuscore_1.1.1+dfsg-4.dsc: no acceptable signature found
dpkg-source: info: extracting consensuscore in consensuscore-1.1.1+dfsg
dpkg-source: info: unpacking consensuscore_1.1.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking consensuscore_1.1.1+dfsg-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying compiler-flags.patch
dpkg-source: info: applying gcc-6.patch
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying check_boost_version.patch
dpkg-source: info: applying sequence_setuptools.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/2185933/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16'
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='30a541f0414046f686b458f7075ccbd7'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='2185933'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Hji0Bc0w/pbuilderrc_L1mV --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Hji0Bc0w/b1 --logfile b1/build.log consensuscore_1.1.1+dfsg-4.dsc'
SUDO_GID='110'
SUDO_UID='105'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://85.184.249.68:3128'
I: uname -a
Linux ionos5-amd64 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux
I: ls -l /bin
total 5632
-rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 44016 Sep 20 2022 cat
-rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 72752 Sep 20 2022 chown
-rwxr-xr-x 1 root root 151152 Sep 20 2022 cp
-rwxr-xr-x 1 root root 125640 Jan 5 2023 dash
-rwxr-xr-x 1 root root 121904 Sep 20 2022 date
-rwxr-xr-x 1 root root 89240 Sep 20 2022 dd
-rwxr-xr-x 1 root root 102200 Sep 20 2022 df
-rwxr-xr-x 1 root root 151344 Sep 20 2022 dir
-rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname
-rwxr-xr-x 1 root root 43856 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 2023 egrep
-rwxr-xr-x 1 root root 35664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep
-rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt
-rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount
-rwxr-xr-x 1 root root 203152 Jan 24 2023 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname
-rwxr-xr-x 1 root root 72824 Sep 20 2022 ln
-rwxr-xr-x 1 root root 53024 Mar 23 2023 login
-rwxr-xr-x 1 root root 151344 Sep 20 2022 ls
-rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk
-rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 59712 Mar 22 2023 more
-rwsr-xr-x 1 root root 59704 Mar 22 2023 mount
-rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint
-rwxr-xr-x 1 root root 142968 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash
-rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 72752 Sep 20 2022 rm
-rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 126424 Jan 5 2023 sed
lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash
-rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 85008 Sep 20 2022 stty
-rwsr-xr-x 1 root root 72000 Mar 22 2023 su
-rwxr-xr-x 1 root root 39824 Sep 20 2022 sync
-rwxr-xr-x 1 root root 531984 Apr 6 2023 tar
-rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 109616 Sep 20 2022 touch
-rwxr-xr-x 1 root root 35664 Sep 20 2022 true
-rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server
-rwsr-xr-x 1 root root 35128 Mar 22 2023 umount
-rwxr-xr-x 1 root root 43888 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/2185933/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), dh-python, dh-exec, libboost-dev, swig, python3-setuptools, python3-all-dev, python3-numpy
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19596 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on dh-python; however:
Package dh-python is not installed.
pbuilder-satisfydepends-dummy depends on dh-exec; however:
Package dh-exec is not installed.
pbuilder-satisfydepends-dummy depends on libboost-dev; however:
Package libboost-dev is not installed.
pbuilder-satisfydepends-dummy depends on swig; however:
Package swig is not installed.
pbuilder-satisfydepends-dummy depends on python3-setuptools; however:
Package python3-setuptools is not installed.
pbuilder-satisfydepends-dummy depends on python3-all-dev; however:
Package python3-all-dev is not installed.
pbuilder-satisfydepends-dummy depends on python3-numpy; however:
Package python3-numpy is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libboost-dev{a} libboost1.74-dev{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-numpy{a} python3-pkg-resources{a} python3-setuptools{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} swig{a} swig4.0{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl javascript-common libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 68 newly installed, 0 to remove and 0 not upgraded.
Need to get 54.3 MB of archives. After unpacking 326 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB]
Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB]
Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB]
Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB]
Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB]
Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB]
Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB]
Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB]
Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B]
Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB]
Get: 12 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 13 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB]
Get: 14 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB]
Get: 15 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB]
Get: 16 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB]
Get: 17 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get: 18 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB]
Get: 19 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB]
Get: 20 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB]
Get: 21 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB]
Get: 22 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB]
Get: 23 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB]
Get: 24 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 25 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 26 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB]
Get: 27 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 28 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB]
Get: 29 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 30 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 31 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get: 32 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 33 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 34 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB]
Get: 35 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB]
Get: 36 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get: 37 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB]
Get: 38 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB]
Get: 39 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 40 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 41 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB]
Get: 42 http://deb.debian.org/debian bookworm/main amd64 dh-exec amd64 0.27 [27.8 kB]
Get: 43 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-2 [76.2 kB]
Get: 44 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-2 [131 kB]
Get: 45 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB]
Get: 46 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB]
Get: 47 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-20 [9510 kB]
Get: 48 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B]
Get: 49 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB]
Get: 50 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB]
Get: 51 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 52 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 53 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB]
Get: 54 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB]
Get: 55 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6 [1988 kB]
Get: 56 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB]
Get: 57 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6 [4738 kB]
Get: 58 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B]
Get: 59 http://deb.debian.org/debian bookworm/main amd64 libpython3-all-dev amd64 3.11.2-1+b1 [1068 B]
Get: 60 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B]
Get: 61 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6 [615 kB]
Get: 62 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB]
Get: 63 http://deb.debian.org/debian bookworm/main amd64 python3-all-dev amd64 3.11.2-1+b1 [1072 B]
Get: 64 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB]
Get: 65 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB]
Get: 66 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB]
Get: 67 http://deb.debian.org/debian bookworm/main amd64 swig4.0 amd64 4.1.0-0.2 [1388 kB]
Get: 68 http://deb.debian.org/debian bookworm/main amd64 swig all 4.1.0-0.2 [321 kB]
Fetched 54.3 MB in 2s (26.2 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libpython3.11-minimal:amd64.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19596 files and directories currently installed.)
Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ...
Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ...
Unpacking libexpat1:amd64 (2.5.0-1) ...
Selecting previously unselected package python3.11-minimal.
Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ...
Unpacking python3.11-minimal (3.11.2-6) ...
Setting up libpython3.11-minimal:amd64 (3.11.2-6) ...
Setting up libexpat1:amd64 (2.5.0-1) ...
Setting up python3.11-minimal (3.11.2-6) ...
Selecting previously unselected package python3-minimal.
(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 ... 19912 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ...
Unpacking python3-minimal (3.11.2-1+b1) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_10.0.0_all.deb ...
Unpacking media-types (10.0.0) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ...
Unpacking readline-common (8.2-1.3) ...
Selecting previously unselected package libreadline8:amd64.
Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ...
Unpacking libreadline8:amd64 (8.2-1.3) ...
Selecting previously unselected package libpython3.11-stdlib:amd64.
Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ...
Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ...
Selecting previously unselected package python3.11.
Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ...
Unpacking python3.11 (3.11.2-6) ...
Selecting previously unselected package libpython3-stdlib:amd64.
Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ...
Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ...
Setting up python3-minimal (3.11.2-1+b1) ...
Selecting previously unselected package python3.
(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 ... 20346 files and directories currently installed.)
Preparing to unpack .../00-python3_3.11.2-1+b1_amd64.deb ...
Unpacking python3 (3.11.2-1+b1) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../02-libmagic-mgc_1%3a5.44-3_amd64.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:amd64.
Preparing to unpack .../03-libmagic1_1%3a5.44-3_amd64.deb ...
Unpacking libmagic1:amd64 (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../04-file_1%3a5.44-3_amd64.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../05-gettext-base_0.21-12_amd64.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:amd64.
Preparing to unpack .../06-libuchardet0_0.0.7-1_amd64.deb ...
Unpacking libuchardet0:amd64 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../07-groff-base_1.22.4-10_amd64.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../08-bsdextrautils_2.38.1-5+b1_amd64.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:amd64.
Preparing to unpack .../09-libpipeline1_1.5.7-1_amd64.deb ...
Unpacking libpipeline1:amd64 (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../10-man-db_2.11.2-2_amd64.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../11-m4_1.4.19-3_amd64.deb ...
Unpacking m4 (1.4.19-3) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../12-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../15-autopoint_0.21-12_all.deb ...
Unpacking autopoint (0.21-12) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../16-libdebhelper-perl_13.11.4_all.deb ...
Unpacking libdebhelper-perl (13.11.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../17-libtool_2.4.7-5_all.deb ...
Unpacking libtool (2.4.7-5) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../18-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../20-libsub-override-perl_0.09-4_all.deb ...
Unpacking libsub-override-perl (0.09-4) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../22-dh-strip-nondeterminism_1.13.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libelf1:amd64.
Preparing to unpack .../23-libelf1_0.188-2.1_amd64.deb ...
Unpacking libelf1:amd64 (0.188-2.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../24-dwz_0.15-1_amd64.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package libicu72:amd64.
Preparing to unpack .../25-libicu72_72.1-3_amd64.deb ...
Unpacking libicu72:amd64 (72.1-3) ...
Selecting previously unselected package libxml2:amd64.
Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.2_amd64.deb ...
Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../27-gettext_0.21-12_amd64.deb ...
Unpacking gettext (0.21-12) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../30-debhelper_13.11.4_all.deb ...
Unpacking debhelper (13.11.4) ...
Selecting previously unselected package dh-exec.
Preparing to unpack .../31-dh-exec_0.27_amd64.deb ...
Unpacking dh-exec (0.27) ...
Selecting previously unselected package python3-lib2to3.
Preparing to unpack .../32-python3-lib2to3_3.11.2-2_all.deb ...
Unpacking python3-lib2to3 (3.11.2-2) ...
Selecting previously unselected package python3-distutils.
Preparing to unpack .../33-python3-distutils_3.11.2-2_all.deb ...
Unpacking python3-distutils (3.11.2-2) ...
Selecting previously unselected package dh-python.
Preparing to unpack .../34-dh-python_5.20230130_all.deb ...
Unpacking dh-python (5.20230130) ...
Selecting previously unselected package libblas3:amd64.
Preparing to unpack .../35-libblas3_3.11.0-2_amd64.deb ...
Unpacking libblas3:amd64 (3.11.0-2) ...
Selecting previously unselected package libboost1.74-dev:amd64.
Preparing to unpack .../36-libboost1.74-dev_1.74.0+ds1-20_amd64.deb ...
Unpacking libboost1.74-dev:amd64 (1.74.0+ds1-20) ...
Selecting previously unselected package libboost-dev:amd64.
Preparing to unpack .../37-libboost-dev_1.74.0.3_amd64.deb ...
Unpacking libboost-dev:amd64 (1.74.0.3) ...
Selecting previously unselected package libexpat1-dev:amd64.
Preparing to unpack .../38-libexpat1-dev_2.5.0-1_amd64.deb ...
Unpacking libexpat1-dev:amd64 (2.5.0-1) ...
Selecting previously unselected package libgfortran5:amd64.
Preparing to unpack .../39-libgfortran5_12.2.0-14_amd64.deb ...
Unpacking libgfortran5:amd64 (12.2.0-14) ...
Selecting previously unselected package libjs-jquery.
Preparing to unpack .../40-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Selecting previously unselected package libjs-underscore.
Preparing to unpack .../41-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ...
Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
Selecting previously unselected package libjs-sphinxdoc.
Preparing to unpack .../42-libjs-sphinxdoc_5.3.0-4_all.deb ...
Unpacking libjs-sphinxdoc (5.3.0-4) ...
Selecting previously unselected package liblapack3:amd64.
Preparing to unpack .../43-liblapack3_3.11.0-2_amd64.deb ...
Unpacking liblapack3:amd64 (3.11.0-2) ...
Selecting previously unselected package libpython3.11:amd64.
Preparing to unpack .../44-libpython3.11_3.11.2-6_amd64.deb ...
Unpacking libpython3.11:amd64 (3.11.2-6) ...
Selecting previously unselected package zlib1g-dev:amd64.
Preparing to unpack .../45-zlib1g-dev_1%3a1.2.13.dfsg-1_amd64.deb ...
Unpacking zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ...
Selecting previously unselected package libpython3.11-dev:amd64.
Preparing to unpack .../46-libpython3.11-dev_3.11.2-6_amd64.deb ...
Unpacking libpython3.11-dev:amd64 (3.11.2-6) ...
Selecting previously unselected package libpython3-dev:amd64.
Preparing to unpack .../47-libpython3-dev_3.11.2-1+b1_amd64.deb ...
Unpacking libpython3-dev:amd64 (3.11.2-1+b1) ...
Selecting previously unselected package libpython3-all-dev:amd64.
Preparing to unpack .../48-libpython3-all-dev_3.11.2-1+b1_amd64.deb ...
Unpacking libpython3-all-dev:amd64 (3.11.2-1+b1) ...
Selecting previously unselected package python3-all.
Preparing to unpack .../49-python3-all_3.11.2-1+b1_amd64.deb ...
Unpacking python3-all (3.11.2-1+b1) ...
Selecting previously unselected package python3.11-dev.
Preparing to unpack .../50-python3.11-dev_3.11.2-6_amd64.deb ...
Unpacking python3.11-dev (3.11.2-6) ...
Selecting previously unselected package python3-dev.
Preparing to unpack .../51-python3-dev_3.11.2-1+b1_amd64.deb ...
Unpacking python3-dev (3.11.2-1+b1) ...
Selecting previously unselected package python3-all-dev.
Preparing to unpack .../52-python3-all-dev_3.11.2-1+b1_amd64.deb ...
Unpacking python3-all-dev (3.11.2-1+b1) ...
Selecting previously unselected package python3-pkg-resources.
Preparing to unpack .../53-python3-pkg-resources_66.1.1-1_all.deb ...
Unpacking python3-pkg-resources (66.1.1-1) ...
Selecting previously unselected package python3-numpy.
Preparing to unpack .../54-python3-numpy_1%3a1.24.2-1_amd64.deb ...
Unpacking python3-numpy (1:1.24.2-1) ...
Selecting previously unselected package python3-setuptools.
Preparing to unpack .../55-python3-setuptools_66.1.1-1_all.deb ...
Unpacking python3-setuptools (66.1.1-1) ...
Selecting previously unselected package swig4.0.
Preparing to unpack .../56-swig4.0_4.1.0-0.2_amd64.deb ...
Unpacking swig4.0 (4.1.0-0.2) ...
Selecting previously unselected package swig.
Preparing to unpack .../57-swig_4.1.0-0.2_all.deb ...
Unpacking swig (4.1.0-0.2) ...
Setting up media-types (10.0.0) ...
Setting up libpipeline1:amd64 (1.5.7-1) ...
Setting up libboost1.74-dev:amd64 (1.74.0+ds1-20) ...
Setting up libicu72:amd64 (72.1-3) ...
Setting up bsdextrautils (2.38.1-5+b1) ...
Setting up libmagic-mgc (1:5.44-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.11.4) ...
Setting up libmagic1:amd64 (1:5.44-3) ...
Setting up gettext-base (0.21-12) ...
Setting up m4 (1.4.19-3) ...
Setting up file (1:5.44-3) ...
Setting up autotools-dev (20220109.1) ...
Setting up libblas3:amd64 (3.11.0-2) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
Setting up libexpat1-dev:amd64 (2.5.0-1) ...
Setting up autopoint (0.21-12) ...
Setting up libgfortran5:amd64 (12.2.0-14) ...
Setting up autoconf (2.71-3) ...
Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ...
Setting up sensible-utils (0.0.17+nmu1) ...
Setting up libuchardet0:amd64 (0.0.7-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libboost-dev:amd64 (1.74.0.3) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up swig4.0 (4.1.0-0.2) ...
Setting up libelf1:amd64 (0.188-2.1) ...
Setting up readline-common (8.2-1.3) ...
Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ...
Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up liblapack3:amd64 (3.11.0-2) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
Setting up gettext (0.21-12) ...
Setting up swig (4.1.0-0.2) ...
Setting up libtool (2.4.7-5) ...
Setting up libreadline8:amd64 (8.2-1.3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up libjs-sphinxdoc (5.3.0-4) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.22.4-10) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ...
Setting up man-db (2.11.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ...
Setting up python3.11 (3.11.2-6) ...
Setting up libpython3.11:amd64 (3.11.2-6) ...
Setting up debhelper (13.11.4) ...
Setting up python3 (3.11.2-1+b1) ...
Setting up dh-exec (0.27) ...
Setting up libpython3.11-dev:amd64 (3.11.2-6) ...
Setting up python3-lib2to3 (3.11.2-2) ...
Setting up python3-pkg-resources (66.1.1-1) ...
Setting up python3-distutils (3.11.2-2) ...
Setting up dh-python (5.20230130) ...
Setting up libpython3-dev:amd64 (3.11.2-1+b1) ...
Setting up python3-setuptools (66.1.1-1) ...
Setting up python3.11-dev (3.11.2-6) ...
Setting up python3-all (3.11.2-1+b1) ...
Setting up libpython3-all-dev:amd64 (3.11.2-1+b1) ...
Setting up python3-dev (3.11.2-1+b1) ...
Setting up python3-numpy (1:1.24.2-1) ...
Setting up python3-all-dev (3.11.2-1+b1) ...
Processing triggers for libc-bin (2.36-9) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/consensuscore-1.1.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../consensuscore_1.1.1+dfsg-4_source.changes
dpkg-buildpackage: info: source package consensuscore
dpkg-buildpackage: info: source version 1.1.1+dfsg-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean --with python3 --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:240: python3.11 setup.py clean
WARNING: '' not a valid package name; please use only .-separated package names in setup.py
running clean
removing '/build/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.11_pbconsensuscore/build' (and everything under it)
'build/bdist.linux-x86_64' does not exist -- can't clean it
'build/scripts-3.11' does not exist -- can't clean it
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary
dh binary --with python3 --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:240: python3.11 setup.py config
WARNING: '' not a valid package name; please use only .-separated package names in setup.py
running config
dh_auto_build -O--buildsystem=pybuild
I: pybuild base:240: /usr/bin/python3 setup.py build
WARNING: '' not a valid package name; please use only .-separated package names in setup.py
running build
ConsensusCore configuration summary
-----------------------------------
BOOST = /usr/include/
SWIG = /usr/bin/swig
SWIG_LIB = /usr/share/swig4.0
PYTHON_INCLUDE = /usr/include/python3.11
NUMPY_INCLUDE = /usr/lib/python3/dist-packages/numpy/core/include
DEBUG =
CPP_STD = c++14
make[1]: Entering directory '/build/consensuscore-1.1.1+dfsg'
make -f make/Cpp.mk -j8
make[2]: Entering directory '/build/consensuscore-1.1.1+dfsg'
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++/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 -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++/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++/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++/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++/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 -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SseRecursor.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SimpleRecursor.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Sequence.o -MM src/C++/Sequence.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Sequence.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/ReadScorer.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Utils.o -MM src/C++/Utils.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Utils.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConsensus.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o -MM src/C++/Quiver/ReadScorer.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConfig.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Version.o -MM src/C++/Version.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Version.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationScorer.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o -MM src/C++/Quiver/detail/RecursorBase.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Read.o -MM src/C++/Read.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Read.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationEnumerator.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -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
src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer<R>::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor<ConsensusCore::DenseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>; EvaluatorType = ConsensusCore::QvEvaluator]’:
src/C++/Quiver/MutationScorer.cpp:190:16: required from here
src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=]
30 | } catch (AlphaBetaMismatchException e) {
| ^
src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer<R>::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor<ConsensusCore::DenseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>; EvaluatorType = ConsensusCore::QvEvaluator]’:
src/C++/Quiver/MutationScorer.cpp:191:16: required from here
src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=]
src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer<R>::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor<ConsensusCore::SparseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>; EvaluatorType = ConsensusCore::QvEvaluator]’:
src/C++/Quiver/MutationScorer.cpp:192:16: required from here
src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=]
src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer<R>::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor<ConsensusCore::SparseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::SumProductCombiner>; EvaluatorType = ConsensusCore::QvEvaluator]’:
src/C++/Quiver/MutationScorer.cpp:193:16: required from here
src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=]
src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer<R>::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor<ConsensusCore::SparseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>; EvaluatorType = ConsensusCore::QvEvaluator]’:
src/C++/Quiver/MutationScorer.cpp:194:16: required from here
src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=]
src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer<R>::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor<ConsensusCore::SparseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::SumProductCombiner>; EvaluatorType = ConsensusCore::QvEvaluator]’:
src/C++/Quiver/MutationScorer.cpp:195:16: required from here
src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=]
src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer<R>::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor<ConsensusCore::SparseMatrix, ConsensusCore::EdnaEvaluator, ConsensusCore::detail::SumProductCombiner>; EvaluatorType = ConsensusCore::EdnaEvaluator]’:
src/C++/Quiver/MutationScorer.cpp:196:16: required from here
src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=]
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/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/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++/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++/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 -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++/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++/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 -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Diploid.o -MM src/C++/Quiver/Diploid.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Diploid.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphImpl.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -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++/MutationScorer.o -MM src/C++/Quiver/MutationScorer.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaConsensus.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -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++/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++/PoaGraph.o -MM src/C++/Poa/PoaGraph.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/SparseMatrix.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o -MM src/C++/Poa/PoaConsensus.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/DenseMatrix.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o -MM src/C++/Matrix/SparseMatrix.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Logging/Logging.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Logging.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/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++/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++/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++/Logging.o -MM src/C++/Logging/Logging.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Logging.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Feature.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/Feature.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o -MM src/C++/Matrix/DenseMatrix.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/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++/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++/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++/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++/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++/PoaGraphTraversals.o -MM src/C++/Poa/PoaGraphTraversals.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/Features.o -MM src/C++/Features.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/Features.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/LinearAlignment.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AlignConfig.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o -MM src/C++/Align/AlignConfig.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AffineAlignment.cpp -o /build/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/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++/LinearAlignment.o -MM src/C++/Align/LinearAlignment.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-1.1.1+dfsg/build/C++/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++/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++/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++/PoaGraphImpl.o -MM src/C++/Poa/PoaGraphImpl.cpp > /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.d
ar crs /build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a /build/consensuscore-1.1.1+dfsg/build/C++/Version.o /build/consensuscore-1.1.1+dfsg/build/C++/Utils.o /build/consensuscore-1.1.1+dfsg/build/C++/Binomial.o /build/consensuscore-1.1.1+dfsg/build/C++/Sequence.o /build/consensuscore-1.1.1+dfsg/build/C++/Read.o /build/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o /build/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o /build/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o /build/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o /build/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o /build/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o /build/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o /build/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o /build/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o /build/consensuscore-1.1.1+dfsg/build/C++/Diploid.o /build/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o /build/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o /build/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o /build/consensuscore-1.1.1+dfsg/build/C++/Mutation.o /build/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o /build/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o /build/consensuscore-1.1.1+dfsg/build/C++/Logging.o /build/consensuscore-1.1.1+dfsg/build/C++/Features.o /build/consensuscore-1.1.1+dfsg/build/C++/Feature.o /build/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o /build/consensuscore-1.1.1+dfsg/build/C++/Coverage.o /build/consensuscore-1.1.1+dfsg/build/C++/Checksum.o /build/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o /build/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o /build/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o /build/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o
touch /build/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a
make[2]: Leaving directory '/build/consensuscore-1.1.1+dfsg'
make -f make/Python.mk
make[2]: Entering directory '/build/consensuscore-1.1.1+dfsg'
mkdir -p /build/consensuscore-1.1.1+dfsg/build/Python
SWIG_LIB=/usr/share/swig4.0 /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/python3.11 -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'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/consensuscore-1.1.1+dfsg'
/usr/bin/make test
make[2]: Entering directory '/build/consensuscore-1.1.1+dfsg'
/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'
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/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/TestQvEvaluator.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o
In file included from /usr/include/boost/bind.hpp:30,
from /build/consensuscore-1.1.1+dfsg/src/Tests/TestQvEvaluator.cpp:5:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
36 | BOOST_PRAGMA_MESSAGE(
| ^~~~~~~~~~~~~~~~~~~~
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
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
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
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/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/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/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/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/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/ParameterSettings.cpp -o /build/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.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/TestSparseVector.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestRecursors.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o /build/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.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/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.
[----------] 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 RecursorTest/0, where TypeParam = ConsensusCore::SimpleRecursor<ConsensusCore::DenseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>
[ RUN ] RecursorTest/0.SmallMatchTest
[ OK ] RecursorTest/0.SmallMatchTest (0 ms)
[ RUN ] RecursorTest/0.SmallMismatchTest
[ OK ] RecursorTest/0.SmallMismatchTest (0 ms)
[ RUN ] RecursorTest/0.SmallMergeTest
[ OK ] RecursorTest/0.SmallMergeTest (0 ms)
[ RUN ] RecursorTest/0.MediumSizedTest
[ OK ] RecursorTest/0.MediumSizedTest (9 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 (9 ms total)
[----------] 7 tests from RecursorTest/1, where TypeParam = ConsensusCore::SseRecursor<ConsensusCore::DenseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>
[ RUN ] RecursorTest/1.SmallMatchTest
[ OK ] RecursorTest/1.SmallMatchTest (1 ms)
[ RUN ] RecursorTest/1.SmallMismatchTest
[ OK ] RecursorTest/1.SmallMismatchTest (0 ms)
[ RUN ] RecursorTest/1.SmallMergeTest
[ OK ] RecursorTest/1.SmallMergeTest (0 ms)
[ RUN ] RecursorTest/1.MediumSizedTest
[ 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 (4 ms total)
[----------] 7 tests from RecursorTest/2, where TypeParam = ConsensusCore::SimpleRecursor<ConsensusCore::SparseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>
[ RUN ] RecursorTest/2.SmallMatchTest
[ OK ] RecursorTest/2.SmallMatchTest (8 ms)
[ RUN ] RecursorTest/2.SmallMismatchTest
[ OK ] RecursorTest/2.SmallMismatchTest (0 ms)
[ RUN ] RecursorTest/2.SmallMergeTest
[ OK ] RecursorTest/2.SmallMergeTest (0 ms)
[ RUN ] RecursorTest/2.MediumSizedTest
[ 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 (11 ms total)
[----------] 7 tests from RecursorTest/3, where TypeParam = ConsensusCore::SseRecursor<ConsensusCore::SparseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>
[ RUN ] RecursorTest/3.SmallMatchTest
[ OK ] RecursorTest/3.SmallMatchTest (0 ms)
[ RUN ] RecursorTest/3.SmallMismatchTest
[ OK ] RecursorTest/3.SmallMismatchTest (0 ms)
[ RUN ] RecursorTest/3.SmallMergeTest
[ OK ] RecursorTest/3.SmallMergeTest (0 ms)
[ RUN ] RecursorTest/3.MediumSizedTest
[ OK ] RecursorTest/3.MediumSizedTest (11 ms)
[ RUN ] RecursorTest/3.LinkTest
[ OK ] RecursorTest/3.LinkTest (0 ms)
[ RUN ] RecursorTest/3.ExtendAlphaTest
[ OK ] RecursorTest/3.ExtendAlphaTest (0 ms)
[ RUN ] RecursorTest/3.ExtendBetaTest
[ OK ] RecursorTest/3.ExtendBetaTest (0 ms)
[----------] 7 tests from RecursorTest/3 (11 ms total)
[----------] 5 tests from RecursorFuzzTest/0, where TypeParam = ConsensusCore::SimpleRecursor<ConsensusCore::DenseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>
[ RUN ] RecursorFuzzTest/0.AlphaBetaConcordance
[ OK ] RecursorFuzzTest/0.AlphaBetaConcordance (65 ms)
[ RUN ] RecursorFuzzTest/0.Alignment
[ OK ] RecursorFuzzTest/0.Alignment (70 ms)
[ RUN ] RecursorFuzzTest/0.LinkAlphaBeta
[ OK ] RecursorFuzzTest/0.LinkAlphaBeta (87 ms)
[ RUN ] RecursorFuzzTest/0.ExtendAlpha
[ OK ] RecursorFuzzTest/0.ExtendAlpha (82 ms)
[ RUN ] RecursorFuzzTest/0.ExtendBeta
[ OK ] RecursorFuzzTest/0.ExtendBeta (82 ms)
[----------] 5 tests from RecursorFuzzTest/0 (396 ms total)
[----------] 5 tests from RecursorFuzzTest/1, where TypeParam = ConsensusCore::SseRecursor<ConsensusCore::DenseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>
[ RUN ] RecursorFuzzTest/1.AlphaBetaConcordance
[ OK ] RecursorFuzzTest/1.AlphaBetaConcordance (169 ms)
[ RUN ] RecursorFuzzTest/1.Alignment
[ OK ] RecursorFuzzTest/1.Alignment (177 ms)
[ RUN ] RecursorFuzzTest/1.LinkAlphaBeta
[ OK ] RecursorFuzzTest/1.LinkAlphaBeta (135 ms)
[ RUN ] RecursorFuzzTest/1.ExtendAlpha
[ OK ] RecursorFuzzTest/1.ExtendAlpha (61 ms)
[ RUN ] RecursorFuzzTest/1.ExtendBeta
[ OK ] RecursorFuzzTest/1.ExtendBeta (62 ms)
[----------] 5 tests from RecursorFuzzTest/1 (615 ms total)
[----------] 5 tests from RecursorFuzzTest/2, where TypeParam = ConsensusCore::SimpleRecursor<ConsensusCore::SparseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>
[ RUN ] RecursorFuzzTest/2.AlphaBetaConcordance
[ OK ] RecursorFuzzTest/2.AlphaBetaConcordance (140 ms)
[ RUN ] RecursorFuzzTest/2.Alignment
[ OK ] RecursorFuzzTest/2.Alignment (146 ms)
[ RUN ] RecursorFuzzTest/2.LinkAlphaBeta
[ OK ] RecursorFuzzTest/2.LinkAlphaBeta (162 ms)
[ RUN ] RecursorFuzzTest/2.ExtendAlpha
[ OK ] RecursorFuzzTest/2.ExtendAlpha (51 ms)
[ RUN ] RecursorFuzzTest/2.ExtendBeta
[ OK ] RecursorFuzzTest/2.ExtendBeta (45 ms)
[----------] 5 tests from RecursorFuzzTest/2 (549 ms total)
[----------] 5 tests from RecursorFuzzTest/3, where TypeParam = ConsensusCore::SseRecursor<ConsensusCore::SparseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>
[ RUN ] RecursorFuzzTest/3.AlphaBetaConcordance
[ OK ] RecursorFuzzTest/3.AlphaBetaConcordance (127 ms)
[ RUN ] RecursorFuzzTest/3.Alignment
[ OK ] RecursorFuzzTest/3.Alignment (142 ms)
[ RUN ] RecursorFuzzTest/3.LinkAlphaBeta
[ OK ] RecursorFuzzTest/3.LinkAlphaBeta (186 ms)
[ RUN ] RecursorFuzzTest/3.ExtendAlpha
[ OK ] RecursorFuzzTest/3.ExtendAlpha (61 ms)
[ RUN ] RecursorFuzzTest/3.ExtendBeta
[ OK ] RecursorFuzzTest/3.ExtendBeta (55 ms)
[----------] 5 tests from RecursorFuzzTest/3 (571 ms total)
[----------] 5 tests from QvEvaluatorTest
[ RUN ] QvEvaluatorTest.IncVsInc4
[ OK ] QvEvaluatorTest.IncVsInc4 (120 ms)
[ RUN ] QvEvaluatorTest.DelVsDel4
[ OK ] QvEvaluatorTest.DelVsDel4 (110 ms)
[ RUN ] QvEvaluatorTest.ExtraVsExtra4
[ OK ] QvEvaluatorTest.ExtraVsExtra4 (138 ms)
[ RUN ] QvEvaluatorTest.MergeVsMerge4
[ OK ] QvEvaluatorTest.MergeVsMerge4 (148 ms)
[ RUN ] QvEvaluatorTest.BadTagTest
[ OK ] QvEvaluatorTest.BadTagTest (13 ms)
[----------] 5 tests from QvEvaluatorTest (529 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 (1 ms)
[ RUN ] PoaGraph.SmallDeletionTests
[ OK ] PoaGraph.SmallDeletionTests (12 ms)
[----------] 4 tests from PoaGraph (14 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 (1 ms)
[ RUN ] PoaConsensus.TestLocalStaggered
dot -Tpng local-staggered.dot > local-staggered.png
sh: 1: dot: not found
[ OK ] PoaConsensus.TestLocalStaggered (26 ms)
[ RUN ] PoaConsensus.TestLongInsert
[ OK ] PoaConsensus.TestLongInsert (1 ms)
[ RUN ] PoaConsensus.NondeterminismRegressionTest
[ OK ] PoaConsensus.NondeterminismRegressionTest (2928 ms)
[----------] 8 tests from PoaConsensus (2957 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 (0 ms total)
[----------] 2 tests from AffineAlignmentTests
[ RUN ] AffineAlignmentTests.BasicTests
[ OK ] AffineAlignmentTests.BasicTests (0 ms)
[ RUN ] AffineAlignmentTests.LargeGapTest
[ OK ] AffineAlignmentTests.LargeGapTest (35 ms)
[----------] 2 tests from AffineAlignmentTests (35 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 (8 ms)
[----------] 1 test from LinearAlignmentTests (8 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)
[----------] 8 tests from MutationScorerTest/0, where TypeParam = ConsensusCore::SimpleRecursor<ConsensusCore::DenseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>
[ RUN ] MutationScorerTest/0.BasicTest
[ OK ] MutationScorerTest/0.BasicTest (0 ms)
[ RUN ] MutationScorerTest/0.CopyTest
[ OK ] MutationScorerTest/0.CopyTest (0 ms)
[ RUN ] MutationScorerTest/0.MutationsAtBeginning
[ OK ] MutationScorerTest/0.MutationsAtBeginning (0 ms)
[ RUN ] MutationScorerTest/0.MutationsAtEnd
[ OK ] MutationScorerTest/0.MutationsAtEnd (0 ms)
[ RUN ] MutationScorerTest/0.TinyTemplate
[ OK ] MutationScorerTest/0.TinyTemplate (0 ms)
[ RUN ] MutationScorerTest/0.TemplateMutationWorkflow
[ OK ] MutationScorerTest/0.TemplateMutationWorkflow (0 ms)
[ RUN ] MutationScorerTest/0.DinucleotideInsertionTest
[ OK ] MutationScorerTest/0.DinucleotideInsertionTest (1 ms)
[ RUN ] MutationScorerTest/0.DinucleotideDeletionTest
[ OK ] MutationScorerTest/0.DinucleotideDeletionTest (1 ms)
[----------] 8 tests from MutationScorerTest/0 (3 ms total)
[----------] 8 tests from MutationScorerTest/1, where TypeParam = ConsensusCore::SseRecursor<ConsensusCore::DenseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>
[ RUN ] MutationScorerTest/1.BasicTest
[ OK ] MutationScorerTest/1.BasicTest (0 ms)
[ RUN ] MutationScorerTest/1.CopyTest
[ OK ] MutationScorerTest/1.CopyTest (0 ms)
[ RUN ] MutationScorerTest/1.MutationsAtBeginning
[ OK ] MutationScorerTest/1.MutationsAtBeginning (0 ms)
[ RUN ] MutationScorerTest/1.MutationsAtEnd
[ OK ] MutationScorerTest/1.MutationsAtEnd (0 ms)
[ RUN ] MutationScorerTest/1.TinyTemplate
[ OK ] MutationScorerTest/1.TinyTemplate (0 ms)
[ RUN ] MutationScorerTest/1.TemplateMutationWorkflow
[ OK ] MutationScorerTest/1.TemplateMutationWorkflow (0 ms)
[ RUN ] MutationScorerTest/1.DinucleotideInsertionTest
[ OK ] MutationScorerTest/1.DinucleotideInsertionTest (10 ms)
[ RUN ] MutationScorerTest/1.DinucleotideDeletionTest
[ OK ] MutationScorerTest/1.DinucleotideDeletionTest (0 ms)
[----------] 8 tests from MutationScorerTest/1 (10 ms total)
[----------] 8 tests from MutationScorerTest/2, where TypeParam = ConsensusCore::SimpleRecursor<ConsensusCore::SparseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>
[ RUN ] MutationScorerTest/2.BasicTest
[ OK ] MutationScorerTest/2.BasicTest (0 ms)
[ RUN ] MutationScorerTest/2.CopyTest
[ OK ] MutationScorerTest/2.CopyTest (0 ms)
[ RUN ] MutationScorerTest/2.MutationsAtBeginning
[ OK ] MutationScorerTest/2.MutationsAtBeginning (1 ms)
[ RUN ] MutationScorerTest/2.MutationsAtEnd
[ 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)
[ RUN ] MutationScorerTest/2.DinucleotideInsertionTest
[ OK ] MutationScorerTest/2.DinucleotideInsertionTest (1 ms)
[ RUN ] MutationScorerTest/2.DinucleotideDeletionTest
[ OK ] MutationScorerTest/2.DinucleotideDeletionTest (9 ms)
[----------] 8 tests from MutationScorerTest/2 (11 ms total)
[----------] 8 tests from MutationScorerTest/3, where TypeParam = ConsensusCore::SseRecursor<ConsensusCore::SparseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>
[ RUN ] MutationScorerTest/3.BasicTest
[ OK ] MutationScorerTest/3.BasicTest (0 ms)
[ RUN ] MutationScorerTest/3.CopyTest
[ OK ] MutationScorerTest/3.CopyTest (0 ms)
[ RUN ] MutationScorerTest/3.MutationsAtBeginning
[ OK ] MutationScorerTest/3.MutationsAtBeginning (1 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)
[ RUN ] MutationScorerTest/3.DinucleotideInsertionTest
[ OK ] MutationScorerTest/3.DinucleotideInsertionTest (1 ms)
[ RUN ] MutationScorerTest/3.DinucleotideDeletionTest
[ OK ] MutationScorerTest/3.DinucleotideDeletionTest (1 ms)
[----------] 8 tests from MutationScorerTest/3 (3 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 (6 ms)
[ RUN ] MutationEnumerationTest.TestDinucleotideMutations
[ OK ] MutationEnumerationTest.TestDinucleotideMutations (0 ms)
[----------] 4 tests from MutationEnumerationTest (6 ms total)
[----------] 1 test from QuiverConfigTableTests
[ RUN ] QuiverConfigTableTests.IllegalChemistry
[ OK ] QuiverConfigTableTests.IllegalChemistry (0 ms)
[----------] 1 test from QuiverConfigTableTests (0 ms total)
[----------] 3 tests from MutationOrientationTests
[ RUN ] MutationOrientationTests.ReadScoresMutation1
[ OK ] MutationOrientationTests.ReadScoresMutation1 (0 ms)
[ RUN ] MutationOrientationTests.ReadScoresMutation2
[ OK ] MutationOrientationTests.ReadScoresMutation2 (0 ms)
[ RUN ] MutationOrientationTests.OrientedMutation
[ OK ] MutationOrientationTests.OrientedMutation (0 ms)
[----------] 3 tests from MutationOrientationTests (0 ms total)
[----------] 11 tests from MultiReadMutationScorerTest/0, where TypeParam = ConsensusCore::SseRecursor<ConsensusCore::SparseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>
[ RUN ] MultiReadMutationScorerTest/0.Template
[ OK ] MultiReadMutationScorerTest/0.Template (0 ms)
[ RUN ] MultiReadMutationScorerTest/0.BasicTest
[ OK ] MultiReadMutationScorerTest/0.BasicTest (0 ms)
[ RUN ] MultiReadMutationScorerTest/0.ManyMutationTest
[ OK ] MultiReadMutationScorerTest/0.ManyMutationTest (2 ms)
[ RUN ] MultiReadMutationScorerTest/0.CopyConstructorTest
[ OK ] MultiReadMutationScorerTest/0.CopyConstructorTest (0 ms)
[ RUN ] MultiReadMutationScorerTest/0.ReverseStrandTest
[ OK ] MultiReadMutationScorerTest/0.ReverseStrandTest (0 ms)
[ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning
[ OK ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning (1 ms)
[ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtEnd
[ OK ] MultiReadMutationScorerTest/0.TestMutationsAtEnd (0 ms)
[ RUN ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1
[ OK ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 (8 ms)
[ RUN ] MultiReadMutationScorerTest/0.CopyTest
[ OK ] MultiReadMutationScorerTest/0.CopyTest (0 ms)
[ RUN ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds
[ OK ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds (0 ms)
[ RUN ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds
[ OK ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds (0 ms)
[----------] 11 tests from MultiReadMutationScorerTest/0 (12 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 (1 ms)
[ RUN ] MatrixTest/0.BigBandedMatrix
N13ConsensusCore11DenseMatrixE : 1000000
[ OK ] MatrixTest/0.BigBandedMatrix (2 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 (3 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 (23 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 (23 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)
[----------] Global test environment tear-down
[==========] 158 tests from 29 test cases ran. (5781 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'
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=pybuild
dh_prep -O--buildsystem=pybuild
dh_auto_install -O--buildsystem=pybuild
I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore
WARNING: '' not a valid package name; please use only .-separated package names in setup.py
running build
ConsensusCore configuration summary
-----------------------------------
BOOST = /usr/include/
SWIG = /usr/bin/swig
SWIG_LIB = /usr/share/swig4.0
PYTHON_INCLUDE = /usr/include/python3.11
NUMPY_INCLUDE = /usr/lib/python3/dist-packages/numpy/core/include
DEBUG =
CPP_STD = c++14
make[1]: Entering directory '/build/consensuscore-1.1.1+dfsg'
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 -f make/Python.mk
make[2]: Entering directory '/build/consensuscore-1.1.1+dfsg'
mkdir -p /build/consensuscore-1.1.1+dfsg/build/Python
SWIG_LIB=/usr/share/swig4.0 /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/python3.11 -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'
running install
/usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running install_lib
running build_py
copying build/Python/ConsensusCore.py -> /build/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.11_pbconsensuscore/build
copying build/Python/_ConsensusCore.so -> /build/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.11_pbconsensuscore/build
creating /build/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore
creating /build/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr
creating /build/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib
creating /build/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.11
creating /build/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.11/dist-packages
copying /build/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.11_pbconsensuscore/build/_ConsensusCore.so -> /build/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.11/dist-packages
copying /build/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.11_pbconsensuscore/build/ConsensusCore.py -> /build/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.11/dist-packages
byte-compiling /build/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.11/dist-packages/ConsensusCore.py to ConsensusCore.cpython-311.pyc
running install_egg_info
running egg_info
creating build/Python/ConsensusCore.egg-info
writing build/Python/ConsensusCore.egg-info/PKG-INFO
writing dependency_links to build/Python/ConsensusCore.egg-info/dependency_links.txt
writing top-level names to build/Python/ConsensusCore.egg-info/top_level.txt
writing manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt'
reading manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt'
adding license file 'LICENSES'
writing manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt'
Copying build/Python/ConsensusCore.egg-info to /build/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.11/dist-packages/ConsensusCore-1.0.2.egg-info
Skipping SOURCES.txt
running install_scripts
dh_install -O--buildsystem=pybuild
dh_installdocs -O--buildsystem=pybuild
dh_installchangelogs -O--buildsystem=pybuild
debian/rules override_dh_python3
make[1]: Entering directory '/build/consensuscore-1.1.1+dfsg'
dh_python3
I: dh_python3 fs:483: renaming _ConsensusCore.so to _ConsensusCore.cpython-311-x86_64-linux-gnu.so
dh_numpy3
make[1]: Leaving directory '/build/consensuscore-1.1.1+dfsg'
dh_installsystemduser -O--buildsystem=pybuild
dh_perl -O--buildsystem=pybuild
dh_link -O--buildsystem=pybuild
dh_strip_nondeterminism -O--buildsystem=pybuild
dh_compress -O--buildsystem=pybuild
dh_fixperms -O--buildsystem=pybuild
dh_missing -O--buildsystem=pybuild
dh_dwz -a -O--buildsystem=pybuild
dh_strip -a -O--buildsystem=pybuild
dh_makeshlibs -a -O--buildsystem=pybuild
dh_shlibdeps -a -O--buildsystem=pybuild
dh_installdeb -O--buildsystem=pybuild
dh_gencontrol -O--buildsystem=pybuild
dpkg-gencontrol: warning: Depends field of package libconsensuscore-dev: substitution variable ${shlibs:Depends} used, but is not defined
dpkg-gencontrol: warning: package libconsensuscore-dev: substitution variable ${python3:Depends} unused, but is defined
dh_md5sums -O--buildsystem=pybuild
dh_builddeb -O--buildsystem=pybuild
dpkg-deb: building package 'libconsensuscore-dev' in '../libconsensuscore-dev_1.1.1+dfsg-4_amd64.deb'.
dpkg-deb: building package 'python3-pbconsensuscore' in '../python3-pbconsensuscore_1.1.1+dfsg-4_amd64.deb'.
dpkg-deb: building package 'python3-pbconsensuscore-dbgsym' in '../python3-pbconsensuscore-dbgsym_1.1.1+dfsg-4_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../consensuscore_1.1.1+dfsg-4_amd64.buildinfo
dpkg-genchanges --build=binary -O../consensuscore_1.1.1+dfsg-4_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
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/2185933 and its subdirectories
I: Current time: Tue May 28 06:11:28 -12 2024
I: pbuilder-time-stamp: 1716919888