I: pbuilder: network access will be disabled during build
I: Current time: Thu Feb 6 18:41:13 +14 2025
I: pbuilder-time-stamp: 1738816873
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-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: using eatmydata during job
I: Copying source file
I: copying [consensuscore_1.1.1+dfsg-7.1.dsc]
I: copying [./consensuscore_1.1.1+dfsg.orig.tar.xz]
I: copying [./consensuscore_1.1.1+dfsg-7.1.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./consensuscore_1.1.1+dfsg-7.1.dsc: unsupported subcommand
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-7.1.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
dpkg-source: info: applying portable_simd.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/6264/tmp/hooks/D01_modify_environment starting
debug: Running on ionos2-i386.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Feb 6 04:41 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/6264/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/6264/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
BASH_VERSION='5.2.37(1)-release'
BUILDDIR=/build/reproducible-path
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=i386
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 '
DIRSTACK=()
DISTRIBUTION=unstable
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=i686
HOST_ARCH=i386
IFS='
'
INVOCATION_ID=1e96ad2ff27a42fea69a941d706ace35
LANG=C
LANGUAGE=de_CH:de
LC_ALL=C
LD_LIBRARY_PATH=/usr/lib/libeatmydata
LD_PRELOAD=libeatmydata.so
MACHTYPE=i686-pc-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=6264
PS4='+ '
PWD=/
SHELL=/bin/bash
SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
SHLVL=3
SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.YrXVr5fo/pbuilderrc_gWX7 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.YrXVr5fo/b2 --logfile b2/build.log consensuscore_1.1.1+dfsg-7.1.dsc'
SUDO_GID=112
SUDO_UID=107
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://46.16.76.132:3128
I: uname -a
Linux i-capture-the-hostname 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/6264/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: i386
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), architecture-is-little-endian, dh-sequence-python3, dh-exec, libboost-dev, swig, python3-setuptools, python3-all-dev, python3-numpy, libsimde-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19792 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 architecture-is-little-endian; however:
Package architecture-is-little-endian is not installed.
pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however:
Package dh-sequence-python3 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.
pbuilder-satisfydepends-dummy depends on libsimde-dev; however:
Package libsimde-dev 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:
architecture-properties{a} 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} libboost1.83-dev{a} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libsimde-dev{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} swig{a} tzdata{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 96 newly installed, 0 to remove and 0 not upgraded.
Need to get 76.1 MB of archives. After unpacking 435 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main i386 libpython3.13-minimal i386 3.13.2-1 [859 kB]
Get: 2 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.4-1 [107 kB]
Get: 3 http://deb.debian.org/debian unstable/main i386 python3.13-minimal i386 3.13.2-1 [2266 kB]
Get: 4 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.13.1-2 [27.0 kB]
Get: 5 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB]
Get: 6 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian unstable/main i386 tzdata all 2025a-2 [259 kB]
Get: 8 http://deb.debian.org/debian unstable/main i386 libffi8 i386 3.4.6-1 [21.2 kB]
Get: 9 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-6 [69.4 kB]
Get: 10 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-6 [173 kB]
Get: 11 http://deb.debian.org/debian unstable/main i386 libpython3.13-stdlib i386 3.13.2-1 [1985 kB]
Get: 12 http://deb.debian.org/debian unstable/main i386 python3.13 i386 3.13.2-1 [745 kB]
Get: 13 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.13.1-2 [9952 B]
Get: 14 http://deb.debian.org/debian unstable/main i386 python3 i386 3.13.1-2 [28.0 kB]
Get: 15 http://deb.debian.org/debian unstable/main i386 libpython3.12-minimal i386 3.12.9-1 [816 kB]
Get: 16 http://deb.debian.org/debian unstable/main i386 python3.12-minimal i386 3.12.9-1 [2238 kB]
Get: 17 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 18 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 19 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 20 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 21 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.23.1-1 [245 kB]
Get: 22 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 23 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 24 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.4-3 [96.2 kB]
Get: 25 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 26 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 27 http://deb.debian.org/debian unstable/main i386 architecture-properties i386 0.2.5 [2276 B]
Get: 28 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-5 [301 kB]
Get: 29 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB]
Get: 30 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 31 http://deb.debian.org/debian unstable/main i386 automake all 1:1.17-3 [862 kB]
Get: 32 http://deb.debian.org/debian unstable/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 33 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 34 http://deb.debian.org/debian unstable/main i386 libtool all 2.5.4-3 [539 kB]
Get: 35 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 36 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 37 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB]
Get: 38 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.1-1 [8584 B]
Get: 39 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 40 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 41 http://deb.debian.org/debian unstable/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 42 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 43 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 44 http://deb.debian.org/debian unstable/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 45 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 46 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 47 http://deb.debian.org/debian unstable/main i386 debhelper all 13.24.1 [920 kB]
Get: 48 http://deb.debian.org/debian unstable/main i386 dh-exec i386 0.30 [26.2 kB]
Get: 49 http://deb.debian.org/debian unstable/main i386 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 50 http://deb.debian.org/debian unstable/main i386 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 51 http://deb.debian.org/debian unstable/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 52 http://deb.debian.org/debian unstable/main i386 python3-typeguard all 4.4.1-1 [37.0 kB]
Get: 53 http://deb.debian.org/debian unstable/main i386 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 54 http://deb.debian.org/debian unstable/main i386 python3-jaraco.context all 6.0.0-1 [7984 B]
Get: 55 http://deb.debian.org/debian unstable/main i386 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 56 http://deb.debian.org/debian unstable/main i386 python3-pkg-resources all 75.6.0-1 [222 kB]
Get: 57 http://deb.debian.org/debian unstable/main i386 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 58 http://deb.debian.org/debian unstable/main i386 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 59 http://deb.debian.org/debian unstable/main i386 python3-setuptools all 75.6.0-1 [720 kB]
Get: 60 http://deb.debian.org/debian unstable/main i386 dh-python all 6.20250108 [113 kB]
Get: 61 http://deb.debian.org/debian unstable/main i386 libblas3 i386 3.12.1-2 [150 kB]
Get: 62 http://deb.debian.org/debian unstable/main i386 libboost1.83-dev i386 1.83.0-4 [10.6 MB]
Get: 63 http://deb.debian.org/debian unstable/main i386 libboost-dev i386 1.83.0.2+b2 [3840 B]
Get: 64 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.2-1 [24.3 kB]
Get: 65 http://deb.debian.org/debian unstable/main i386 libexpat1-dev i386 2.6.4-1 [165 kB]
Get: 66 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.2.0-16 [735 kB]
Get: 67 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-4 [35.0 kB]
Get: 68 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-4 [83.7 kB]
Get: 69 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B]
Get: 70 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-4 [354 kB]
Get: 71 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-4 [149 kB]
Get: 72 http://deb.debian.org/debian unstable/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 73 http://deb.debian.org/debian unstable/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 74 http://deb.debian.org/debian unstable/main i386 libjs-sphinxdoc all 8.1.3-4 [30.4 kB]
Get: 75 http://deb.debian.org/debian unstable/main i386 liblapack3 i386 3.12.1-2 [2198 kB]
Get: 76 http://deb.debian.org/debian unstable/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 77 http://deb.debian.org/debian unstable/main i386 libtirpc3t64 i386 1.3.4+ds-1.3+b1 [90.5 kB]
Get: 78 http://deb.debian.org/debian unstable/main i386 libnsl2 i386 1.3.0-3+b3 [42.7 kB]
Get: 79 http://deb.debian.org/debian unstable/main i386 libpython3.13 i386 3.13.2-1 [2199 kB]
Get: 80 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Get: 81 http://deb.debian.org/debian unstable/main i386 libpython3.13-dev i386 3.13.2-1 [5181 kB]
Get: 82 http://deb.debian.org/debian unstable/main i386 libpython3-dev i386 3.13.1-2 [10.2 kB]
Get: 83 http://deb.debian.org/debian unstable/main i386 libpython3.12-stdlib i386 3.12.9-1 [1972 kB]
Get: 84 http://deb.debian.org/debian unstable/main i386 libpython3.12t64 i386 3.12.9-1 [2172 kB]
Get: 85 http://deb.debian.org/debian unstable/main i386 libpython3.12-dev i386 3.12.9-1 [5283 kB]
Get: 86 http://deb.debian.org/debian unstable/main i386 libpython3-all-dev i386 3.13.1-2 [1072 B]
Get: 87 http://deb.debian.org/debian unstable/main i386 libsimde-dev all 0.8.2-2 [467 kB]
Get: 88 http://deb.debian.org/debian unstable/main i386 python3.12 i386 3.12.9-1 [681 kB]
Get: 89 http://deb.debian.org/debian unstable/main i386 python3-all i386 3.13.1-2 [1052 B]
Get: 90 http://deb.debian.org/debian unstable/main i386 python3.13-dev i386 3.13.2-1 [505 kB]
Get: 91 http://deb.debian.org/debian unstable/main i386 python3-dev i386 3.13.1-2 [26.1 kB]
Get: 92 http://deb.debian.org/debian unstable/main i386 python3.12-dev i386 3.12.9-1 [505 kB]
Get: 93 http://deb.debian.org/debian unstable/main i386 python3-all-dev i386 3.13.1-2 [1076 B]
Get: 94 http://deb.debian.org/debian unstable/main i386 python3-numpy-dev i386 1:2.2.2+ds-2 [145 kB]
Get: 95 http://deb.debian.org/debian unstable/main i386 python3-numpy i386 1:2.2.2+ds-2 [7536 kB]
Get: 96 http://deb.debian.org/debian unstable/main i386 swig i386 4.3.0-1 [1570 kB]
Fetched 76.1 MB in 1s (91.8 MB/s)
Preconfiguring packages ...
Selecting previously unselected package libpython3.13-minimal:i386.
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Unpacking libpython3.13-minimal:i386 (3.13.2-1) ...
Selecting previously unselected package libexpat1:i386.
Preparing to unpack .../libexpat1_2.6.4-1_i386.deb ...
Unpacking libexpat1:i386 (2.6.4-1) ...
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Preparing to unpack .../python3.13-minimal_3.13.2-1_i386.deb ...
Unpacking python3.13-minimal (3.13.2-1) ...
Setting up libpython3.13-minimal:i386 (3.13.2-1) ...
Setting up libexpat1:i386 (2.6.4-1) ...
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Unpacking python3-minimal (3.13.1-2) ...
Selecting previously unselected package media-types.
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Setting up python3.13 (3.13.2-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up python3 (3.13.1-2) ...
Setting up python3-zipp (3.21.0-1) ...
Setting up python3-autocommand (2.2.2-3) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libpython3.13-dev:i386 (3.13.2-1) ...
Setting up python3-typing-extensions (4.12.2-2) ...
Setting up python3-numpy (1:2.2.2+ds-2) ...
Setting up libnsl2:i386 (1.3.0-3+b3) ...
Setting up python3-more-itertools (10.6.0-1) ...
Setting up libpython3-dev:i386 (3.13.1-2) ...
Setting up python3-jaraco.functools (4.1.0-1) ...
Setting up libpython3.12-stdlib:i386 (3.12.9-1) ...
Setting up python3-jaraco.context (6.0.0-1) ...
Setting up python3.13-dev (3.13.2-1) ...
Setting up python3.12 (3.12.9-1) ...
Setting up python3-typeguard (4.4.1-1) ...
Setting up python3-all (3.13.1-2) ...
Setting up debhelper (13.24.1) ...
Setting up dh-exec (0.30) ...
Setting up libpython3.12t64:i386 (3.12.9-1) ...
Setting up python3-inflect (7.3.1-2) ...
Setting up python3-jaraco.text (4.0.0-1) ...
Setting up python3-dev (3.13.1-2) ...
Setting up python3-pkg-resources (75.6.0-1) ...
Setting up python3-setuptools (75.6.0-1) ...
Setting up libpython3.12-dev:i386 (3.12.9-1) ...
Setting up libpython3-all-dev:i386 (3.13.1-2) ...
Setting up python3.12-dev (3.12.9-1) ...
Setting up dh-python (6.20250108) ...
Setting up python3-all-dev (3.13.1-2) ...
Processing triggers for libc-bin (2.40-6) ...
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: user script /srv/workspace/pbuilder/6264/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/6264/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/consensuscore-1.1.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../consensuscore_1.1.1+dfsg-7.1_source.changes
dpkg-buildpackage: info: source package consensuscore
dpkg-buildpackage: info: source version 1.1.1+dfsg-7.1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Timo Röhling <roehling@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean --buildsystem=pybuild
debian/rules execute_before_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
! test -f src/SWIG/numpy.i.orig || mv -v src/SWIG/numpy.i.orig src/SWIG/numpy.i
make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:311: python3.12 setup.py clean
WARNING: '' not a valid package name; please use only .-separated package names in setup.py
running clean
removing '/build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build' (and everything under it)
'build/bdist.linux-i686' does not exist -- can't clean it
'build/scripts-3.12' does not exist -- can't clean it
I: pybuild base:311: python3.13 setup.py clean
WARNING: '' not a valid package name; please use only .-separated package names in setup.py
running clean
removing '/build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.13_pbconsensuscore/build' (and everything under it)
'build/bdist.linux-i686' does not exist -- can't clean it
'build/scripts-3.13' does not exist -- can't clean it
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary
dh binary --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:311: python3.12 setup.py config
WARNING: '' not a valid package name; please use only .-separated package names in setup.py
running config
I: pybuild base:311: python3.13 setup.py config
WARNING: '' not a valid package name; please use only .-separated package names in setup.py
running config
debian/rules execute_before_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
test -f src/SWIG/numpy.i.orig || mv -v src/SWIG/numpy.i src/SWIG/numpy.i.orig
renamed 'src/SWIG/numpy.i' -> 'src/SWIG/numpy.i.orig'
cp /usr/lib/i386-linux-gnu/python3-numpy/numpy/_core/include/numpy/numpy.i src/SWIG/numpy.i
make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
dh_auto_build -O--buildsystem=pybuild
I: pybuild base:311: /usr/bin/python3.12 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/swig/4.3.0
PYTHON_INCLUDE = /usr/include/python3.12
NUMPY_INCLUDE = /usr/lib/i386-linux-gnu/python3-numpy/numpy/_core/include
DEBUG =
CPP_STD = c++14
make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
make -f make/Cpp.mk -j8
make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/DenseMatrix.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/SparseMatrix.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Feature.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphImpl.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphTraversals.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaConsensus.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/RangeFinder.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraph.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o -MM src/C++/Matrix/SparseMatrix.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MultiReadMutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o -MM src/C++/Feature.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o -MM src/C++/Matrix/DenseMatrix.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/Diploid.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o -MM src/C++/Poa/PoaConsensus.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SseRecursor.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/ReadScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o -MM src/C++/Poa/PoaGraph.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SimpleRecursor.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.o -MM src/C++/Quiver/Diploid.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/detail/RecursorBase.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o -MM src/C++/Quiver/ReadScorer.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConsensus.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o -MM src/C++/Poa/RangeFinder.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o -MM src/C++/Poa/PoaGraphTraversals.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o -MM src/C++/Quiver/detail/RecursorBase.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o -MM src/C++/Quiver/MultiReadMutationScorer.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationEnumerator.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConfig.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.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
190 | template class MutationScorer<SimpleQvRecursor>;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
191 | template class MutationScorer<SseQvRecursor>;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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::SimpleRecursor<ConsensusCore::SparseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>; EvaluatorType = ConsensusCore::QvEvaluator]’:
src/C++/Quiver/MutationScorer.cpp:192:16: required from here
192 | template class MutationScorer<SparseSimpleQvRecursor>;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=]
30 | } catch (AlphaBetaMismatchException e) {
| ^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Mutation.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o
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
193 | template class MutationScorer<SparseSimpleQvSumProductRecursor>;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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::SparseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>; EvaluatorType = ConsensusCore::QvEvaluator]’:
src/C++/Quiver/MutationScorer.cpp:194:16: required from here
194 | template class MutationScorer<SparseSseQvRecursor>;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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::SparseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::SumProductCombiner>; EvaluatorType = ConsensusCore::QvEvaluator]’:
src/C++/Quiver/MutationScorer.cpp:195:16: required from here
195 | template class MutationScorer<SparseSseQvSumProductRecursor>;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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::SparseMatrix, ConsensusCore::EdnaEvaluator, ConsensusCore::detail::SumProductCombiner>; EvaluatorType = ConsensusCore::EdnaEvaluator]’:
src/C++/Quiver/MutationScorer.cpp:196:16: required from here
196 | template class MutationScorer<SparseSseEdnaRecursor>;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=]
30 | } catch (AlphaBetaMismatchException e) {
| ^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o -MM src/C++/Quiver/MutationEnumerator.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o -MM src/C++/Quiver/QuiverConfig.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Logging/Logging.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Utils.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.o -MM src/C++/Utils.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o -MM src/C++/Logging/Logging.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Checksum.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Statistics/Binomial.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o -MM src/C++/Quiver/QuiverConsensus.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Version.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o -MM src/C++/Quiver/MutationScorer.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Coverage.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.o -MM src/C++/Coverage.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o -MM src/C++/Mutation.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Features.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Sequence.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.o -MM src/C++/Sequence.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Edna/EdnaCounts.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.o -MM src/C++/Version.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o -MM src/C++/Checksum.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Read.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o -MM src/C++/Statistics/Binomial.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/LinearAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o -MM src/C++/Quiver/SimpleRecursor.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/PairwiseAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.o -MM src/C++/Features.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AffineAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AlignConfig.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o -MM src/C++/Align/AlignConfig.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o -MM src/C++/Poa/PoaGraphImpl.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o -MM src/C++/Edna/EdnaCounts.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o -MM src/C++/Align/LinearAlignment.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o -MM src/C++/Align/PairwiseAlignment.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o -MM src/C++/Align/AffineAlignment.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.o -MM src/C++/Read.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o -MM src/C++/Quiver/SseRecursor.cpp > /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.d
ar crs /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Feature.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Diploid.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Mutation.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Logging.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Utils.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Checksum.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Binomial.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Version.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Coverage.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Features.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Sequence.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/Read.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o
touch /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a
make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
make -f make/Python.mk
make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python
SWIG_LIB=/usr/share/swig/4.3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i
/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored).
/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:28: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored).
/build/reproducible-path/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/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.12 -I /usr/lib/i386-linux-gnu/python3-numpy/numpy/_core/include /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so
make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
I: pybuild base:311: /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/swig/4.3.0
PYTHON_INCLUDE = /usr/include/python3.13
NUMPY_INCLUDE = /usr/lib/i386-linux-gnu/python3-numpy/numpy/_core/include
DEBUG =
CPP_STD = c++14
make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
make -f make/Cpp.mk -j8
make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
make[2]: '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date.
make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
make -f make/Python.mk
make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python
SWIG_LIB=/usr/share/swig/4.3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i
/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored).
/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:28: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored).
/build/reproducible-path/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/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.13 -I /usr/lib/i386-linux-gnu/python3-numpy/numpy/_core/include /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so
make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
/usr/bin/make test
make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
/usr/bin/make -f make/Cpp.mk -j8
make[3]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
make[3]: '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date.
make[3]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
make[3]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMutationEnumerator.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o
mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestSparseVector.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.o
mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMutations.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o
mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestPairwiseAlignment.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.o
mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestRecursors.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestRecursors.o
mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/ParameterSettings.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.o
mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestCoverage.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestCoverage.o
mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.o
mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMatrixFacades.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o
mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestPoaConsensus.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o
mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestDiploidQuiver.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.o
mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestMultiReadMutationScorer.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o
mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O0 -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/reproducible-path/consensuscore-1.1.1+dfsg/src/Tests/TestQvEvaluator.cpp -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o
In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9,
from /usr/include/boost/bind/bind.hpp:24,
from /usr/include/boost/bind.hpp:29,
from /build/reproducible-path/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(
| ^~~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestRecursors.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestCoverage.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 /build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0/gmock-gtest-all.cc /build/reproducible-path/consensuscore-1.1.1+dfsg/external/gmock-1.7.0/gmock_main.cc -lpthread -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/test-runner
GTEST_OUTPUT="xml:tests-summary.xml" /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Tests/test-runner
Running main() from gmock_main.cc
[==========] Running 158 tests from 29 test cases.
[----------] Global test environment set-up.
[----------] 4 tests from MutationEnumerationTest
[ RUN ] MutationEnumerationTest.TestAllMutations
[ OK ] MutationEnumerationTest.TestAllMutations (0 ms)
[ RUN ] MutationEnumerationTest.TestUniqueMutations
[ OK ] MutationEnumerationTest.TestUniqueMutations (0 ms)
[ RUN ] MutationEnumerationTest.TestUniqueNearbyMutations
[ OK ] MutationEnumerationTest.TestUniqueNearbyMutations (2 ms)
[ RUN ] MutationEnumerationTest.TestDinucleotideMutations
[ OK ] MutationEnumerationTest.TestDinucleotideMutations (0 ms)
[----------] 4 tests from MutationEnumerationTest (2 ms total)
[----------] 2 tests from SparseVectorTest
[ RUN ] SparseVectorTest.BasicTest
[ OK ] SparseVectorTest.BasicTest (0 ms)
[ RUN ] SparseVectorTest.BasicTest2
[ OK ] SparseVectorTest.BasicTest2 (0 ms)
[----------] 2 tests from SparseVectorTest (1 ms total)
[----------] 1 test from SparseVector
[ RUN ] SparseVector.CopyTest
[ OK ] SparseVector.CopyTest (0 ms)
[----------] 1 test from SparseVector (0 ms total)
[----------] 7 tests from MutationTest
[ RUN ] MutationTest.BasicTest
[ OK ] MutationTest.BasicTest (0 ms)
[ RUN ] MutationTest.DeleteTest
[ OK ] MutationTest.DeleteTest (0 ms)
[ RUN ] MutationTest.InsertTest
[ OK ] MutationTest.InsertTest (0 ms)
[ RUN ] MutationTest.ApplyMutationsTest
[ OK ] MutationTest.ApplyMutationsTest (0 ms)
[ RUN ] MutationTest.ApplyMutationsToSamePositionTest
[ OK ] MutationTest.ApplyMutationsToSamePositionTest (0 ms)
[ RUN ] MutationTest.MutationsToTranscript
[ OK ] MutationTest.MutationsToTranscript (0 ms)
[ RUN ] MutationTest.MutatedTemplatePositionsTest
[ OK ] MutationTest.MutatedTemplatePositionsTest (0 ms)
[----------] 7 tests from MutationTest (0 ms total)
[----------] 3 tests from PairwiseAlignmentTests
[ RUN ] PairwiseAlignmentTests.RepresentationTests
[ OK ] PairwiseAlignmentTests.RepresentationTests (0 ms)
[ RUN ] PairwiseAlignmentTests.GlobalAlignmentTests
[ OK ] PairwiseAlignmentTests.GlobalAlignmentTests (0 ms)
[ RUN ] PairwiseAlignmentTests.TargetPositionsInQueryTest
[ OK ] PairwiseAlignmentTests.TargetPositionsInQueryTest (0 ms)
[----------] 3 tests from PairwiseAlignmentTests (1 ms total)
[----------] 2 tests from AffineAlignmentTests
[ RUN ] AffineAlignmentTests.BasicTests
[ OK ] AffineAlignmentTests.BasicTests (0 ms)
[ RUN ] AffineAlignmentTests.LargeGapTest
[ OK ] AffineAlignmentTests.LargeGapTest (31 ms)
[----------] 2 tests from AffineAlignmentTests (31 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 (1 ms)
[----------] 1 test from LinearAlignmentTests (1 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 (1 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 (2 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 (0 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 (5 ms)
[ RUN ] RecursorTest/1.LinkTest
[ OK ] RecursorTest/1.LinkTest (1 ms)
[ RUN ] RecursorTest/1.ExtendAlphaTest
[ OK ] RecursorTest/1.ExtendAlphaTest (0 ms)
[ RUN ] RecursorTest/1.ExtendBetaTest
[ OK ] RecursorTest/1.ExtendBetaTest (0 ms)
[----------] 7 tests from RecursorTest/1 (6 ms total)
[----------] 7 tests from RecursorTest/2, where TypeParam = ConsensusCore::SimpleRecursor<ConsensusCore::SparseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>
[ RUN ] RecursorTest/2.SmallMatchTest
[ OK ] RecursorTest/2.SmallMatchTest (0 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 (4 ms)
[ RUN ] RecursorTest/2.LinkTest
[ OK ] RecursorTest/2.LinkTest (1 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 (5 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 (5 ms)
[ RUN ] RecursorTest/3.LinkTest
[ OK ] RecursorTest/3.LinkTest (0 ms)
[ RUN ] RecursorTest/3.ExtendAlphaTest
[ OK ] RecursorTest/3.ExtendAlphaTest (0 ms)
[ RUN ] RecursorTest/3.ExtendBetaTest
[ OK ] RecursorTest/3.ExtendBetaTest (1 ms)
[----------] 7 tests from RecursorTest/3 (6 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 (34 ms)
[ RUN ] RecursorFuzzTest/0.Alignment
[ OK ] RecursorFuzzTest/0.Alignment (36 ms)
[ RUN ] RecursorFuzzTest/0.LinkAlphaBeta
[ OK ] RecursorFuzzTest/0.LinkAlphaBeta (41 ms)
[ RUN ] RecursorFuzzTest/0.ExtendAlpha
[ OK ] RecursorFuzzTest/0.ExtendAlpha (36 ms)
[ RUN ] RecursorFuzzTest/0.ExtendBeta
[ OK ] RecursorFuzzTest/0.ExtendBeta (37 ms)
[----------] 5 tests from RecursorFuzzTest/0 (185 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 (105 ms)
[ RUN ] RecursorFuzzTest/1.Alignment
[ OK ] RecursorFuzzTest/1.Alignment (108 ms)
[ RUN ] RecursorFuzzTest/1.LinkAlphaBeta
[ OK ] RecursorFuzzTest/1.LinkAlphaBeta (112 ms)
[ RUN ] RecursorFuzzTest/1.ExtendAlpha
[ OK ] RecursorFuzzTest/1.ExtendAlpha (36 ms)
[ RUN ] RecursorFuzzTest/1.ExtendBeta
[ OK ] RecursorFuzzTest/1.ExtendBeta (38 ms)
[----------] 5 tests from RecursorFuzzTest/1 (399 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 (90 ms)
[ RUN ] RecursorFuzzTest/2.Alignment
[ OK ] RecursorFuzzTest/2.Alignment (92 ms)
[ RUN ] RecursorFuzzTest/2.LinkAlphaBeta
[ OK ] RecursorFuzzTest/2.LinkAlphaBeta (109 ms)
[ RUN ] RecursorFuzzTest/2.ExtendAlpha
[ OK ] RecursorFuzzTest/2.ExtendAlpha (30 ms)
[ RUN ] RecursorFuzzTest/2.ExtendBeta
[ OK ] RecursorFuzzTest/2.ExtendBeta (29 ms)
[----------] 5 tests from RecursorFuzzTest/2 (351 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 (113 ms)
[ RUN ] RecursorFuzzTest/3.Alignment
[ OK ] RecursorFuzzTest/3.Alignment (116 ms)
[ RUN ] RecursorFuzzTest/3.LinkAlphaBeta
[ OK ] RecursorFuzzTest/3.LinkAlphaBeta (121 ms)
[ RUN ] RecursorFuzzTest/3.ExtendAlpha
[ OK ] RecursorFuzzTest/3.ExtendAlpha (29 ms)
[ RUN ] RecursorFuzzTest/3.ExtendBeta
[ OK ] RecursorFuzzTest/3.ExtendBeta (28 ms)
[----------] 5 tests from RecursorFuzzTest/3 (409 ms total)
[----------] 3 tests from CoverageTests
[ RUN ] CoverageTests.CoverageInWindowTest
[ OK ] CoverageTests.CoverageInWindowTest (0 ms)
[ RUN ] CoverageTests.CoveredIntervalsTest
[ OK ] CoverageTests.CoveredIntervalsTest (0 ms)
[ RUN ] CoverageTests.CoveredIntervalsTest2
[ OK ] CoverageTests.CoveredIntervalsTest2 (0 ms)
[----------] 3 tests from CoverageTests (0 ms total)
[----------] 8 tests from MutationScorerTest/0, where TypeParam = ConsensusCore::SimpleRecursor<ConsensusCore::DenseMatrix, ConsensusCore::QvEvaluator, ConsensusCore::detail::ViterbiCombiner>
[ RUN ] MutationScorerTest/0.BasicTest
[ OK ] MutationScorerTest/0.BasicTest (1 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 (3 ms)
[ RUN ] MutationScorerTest/0.DinucleotideDeletionTest
[ OK ] MutationScorerTest/0.DinucleotideDeletionTest (1 ms)
[----------] 8 tests from MutationScorerTest/0 (5 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 (3 ms)
[ RUN ] MutationScorerTest/1.DinucleotideDeletionTest
[ OK ] MutationScorerTest/1.DinucleotideDeletionTest (1 ms)
[----------] 8 tests from MutationScorerTest/1 (5 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 (0 ms)
[ RUN ] MutationScorerTest/2.MutationsAtEnd
[ OK ] MutationScorerTest/2.MutationsAtEnd (1 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 (3 ms)
[ RUN ] MutationScorerTest/2.DinucleotideDeletionTest
[ OK ] MutationScorerTest/2.DinucleotideDeletionTest (1 ms)
[----------] 8 tests from MutationScorerTest/2 (5 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 (0 ms)
[ RUN ] MutationScorerTest/3.MutationsAtEnd
[ OK ] MutationScorerTest/3.MutationsAtEnd (1 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 (3 ms)
[ RUN ] MutationScorerTest/3.DinucleotideDeletionTest
[ OK ] MutationScorerTest/3.DinucleotideDeletionTest (1 ms)
[----------] 8 tests from MutationScorerTest/3 (5 ms total)
[----------] 11 tests from MatrixTest/0, where TypeParam = ConsensusCore::DenseMatrix
[ RUN ] MatrixTest/0.Basic
[ OK ] MatrixTest/0.Basic (0 ms)
[ RUN ] MatrixTest/0.Nullability
[ OK ] MatrixTest/0.Nullability (0 ms)
[ RUN ] MatrixTest/0.Ranges
[ OK ] MatrixTest/0.Ranges (0 ms)
[ RUN ] MatrixTest/0.IsColumnEmpty
[ OK ] MatrixTest/0.IsColumnEmpty (0 ms)
[ RUN ] MatrixTest/0.SSE
[ OK ] MatrixTest/0.SSE (0 ms)
[ RUN ] MatrixTest/0.ToHostArray
[ OK ] MatrixTest/0.ToHostArray (0 ms)
[ RUN ] MatrixTest/0.NonSequentialAccess
[ OK ] MatrixTest/0.NonSequentialAccess (0 ms)
[ RUN ] MatrixTest/0.Holes
[ OK ] MatrixTest/0.Holes (0 ms)
[ RUN ] MatrixTest/0.BigBandedMatrix
N13ConsensusCore11DenseMatrixE : 1000000
[ OK ] MatrixTest/0.BigBandedMatrix (5 ms)
[ RUN ] MatrixTest/0.BigIrregularBandedMatrix
[ OK ] MatrixTest/0.BigIrregularBandedMatrix (0 ms)
[ RUN ] MatrixTest/0.CopyTest
[ OK ] MatrixTest/0.CopyTest (0 ms)
[----------] 11 tests from MatrixTest/0 (6 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 (12 ms)
[ RUN ] MatrixTest/1.BigIrregularBandedMatrix
[ OK ] MatrixTest/1.BigIrregularBandedMatrix (0 ms)
[ RUN ] MatrixTest/1.CopyTest
[ OK ] MatrixTest/1.CopyTest (0 ms)
[----------] 11 tests from MatrixTest/1 (14 ms total)
[----------] 4 tests from PoaGraph
[ RUN ] PoaGraph.SmallBasicTest
[ OK ] PoaGraph.SmallBasicTest (0 ms)
[ RUN ] PoaGraph.SmallExtraTests
[ OK ] PoaGraph.SmallExtraTests (1 ms)
[ RUN ] PoaGraph.SmallMismatchTests
[ OK ] PoaGraph.SmallMismatchTests (0 ms)
[ RUN ] PoaGraph.SmallDeletionTests
[ OK ] PoaGraph.SmallDeletionTests (1 ms)
[----------] 4 tests from PoaGraph (2 ms total)
[----------] 8 tests from PoaConsensus
[ RUN ] PoaConsensus.TestSimple
[ OK ] PoaConsensus.TestSimple (0 ms)
[ RUN ] PoaConsensus.TestOverhangSecond
[ OK ] PoaConsensus.TestOverhangSecond (1 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: line 1: dot: command not found
[ OK ] PoaConsensus.TestLocalStaggered (11 ms)
[ RUN ] PoaConsensus.TestLongInsert
[ OK ] PoaConsensus.TestLongInsert (1 ms)
[ RUN ] PoaConsensus.NondeterminismRegressionTest
[ OK ] PoaConsensus.NondeterminismRegressionTest (1174 ms)
[----------] 8 tests from PoaConsensus (1189 ms total)
[----------] 1 test from QuiverConfigTableTests
[ RUN ] QuiverConfigTableTests.IllegalChemistry
[ OK ] QuiverConfigTableTests.IllegalChemistry (1 ms)
[----------] 1 test from QuiverConfigTableTests (1 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 (1 ms)
[----------] 3 tests from MutationOrientationTests (1 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 (1 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 (1 ms)
[ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning
[ OK ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning (0 ms)
[ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtEnd
[ OK ] MultiReadMutationScorerTest/0.TestMutationsAtEnd (0 ms)
[ RUN ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1
[ OK ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 (1 ms)
[ RUN ] MultiReadMutationScorerTest/0.CopyTest
[ OK ] MultiReadMutationScorerTest/0.CopyTest (0 ms)
[ RUN ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds
[ OK ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds (1 ms)
[ RUN ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds
[ OK ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds (0 ms)
[----------] 11 tests from MultiReadMutationScorerTest/0 (7 ms total)
[----------] 5 tests from QvEvaluatorTest
[ RUN ] QvEvaluatorTest.IncVsInc4
[ OK ] QvEvaluatorTest.IncVsInc4 (105 ms)
[ RUN ] QvEvaluatorTest.DelVsDel4
[ OK ] QvEvaluatorTest.DelVsDel4 (107 ms)
[ RUN ] QvEvaluatorTest.ExtraVsExtra4
[ OK ] QvEvaluatorTest.ExtraVsExtra4 (126 ms)
[ RUN ] QvEvaluatorTest.MergeVsMerge4
[ OK ] QvEvaluatorTest.MergeVsMerge4 (77 ms)
[ RUN ] QvEvaluatorTest.BadTagTest
[ OK ] QvEvaluatorTest.BadTagTest (6 ms)
[----------] 5 tests from QvEvaluatorTest (421 ms total)
[----------] Global test environment tear-down
[==========] 158 tests from 29 test cases ran. (3063 ms total)
[ PASSED ] 158 tests.
make[3]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
make[1]: Leaving directory '/build/reproducible-path/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:311: /usr/bin/python3.12 setup.py install --root /build/reproducible-path/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/swig/4.3.0
PYTHON_INCLUDE = /usr/include/python3.12
NUMPY_INCLUDE = /usr/lib/i386-linux-gnu/python3-numpy/numpy/_core/include
DEBUG =
CPP_STD = c++14
make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
make -f make/Cpp.mk -j8
make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
make[2]: '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date.
make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
make -f make/Python.mk
make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python
SWIG_LIB=/usr/share/swig/4.3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i
/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored).
/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:28: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored).
/build/reproducible-path/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/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.12 -I /usr/lib/i386-linux-gnu/python3-numpy/numpy/_core/include /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so
make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
running install
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!
********************************************************************************
Please avoid running ``setup.py`` directly.
Instead, use pypa/build, pypa/installer or other
standards-based tools.
See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
********************************************************************************
!!
self.initialize_options()
running install_lib
running build_py
copying build/Python/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build
copying build/Python/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build
copying build/Python/_ConsensusCore.so -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build
creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages
copying /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build/_ConsensusCore.so -> /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages
copying /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.12_pbconsensuscore/build/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages
byte-compiling /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages/ConsensusCore.py to ConsensusCore.cpython-312.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/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.12/dist-packages/ConsensusCore-1.0.2.egg-info
Skipping SOURCES.txt
running install_scripts
I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/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/swig/4.3.0
PYTHON_INCLUDE = /usr/include/python3.13
NUMPY_INCLUDE = /usr/lib/i386-linux-gnu/python3-numpy/numpy/_core/include
DEBUG =
CPP_STD = c++14
make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
make -f make/Cpp.mk -j8
make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
make[2]: '/build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date.
make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
make -f make/Python.mk
make[2]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
mkdir -p /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python
SWIG_LIB=/usr/share/swig/4.3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i
/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored).
/build/reproducible-path/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:28: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored).
/build/reproducible-path/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/reproducible-path/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -DSIMDE_ENABLE_OPENMP -Wno-psabi -O3 -O3 -DNDEBUG -g -fPIC -fno-omit-frame-pointer -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/build/reproducible-path/consensuscore-1.1.1+dfsg/include -I/build/reproducible-path/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.13 -I /usr/lib/i386-linux-gnu/python3-numpy/numpy/_core/include /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/reproducible-path/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/reproducible-path/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so
make[2]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
running install
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!
********************************************************************************
Please avoid running ``setup.py`` directly.
Instead, use pypa/build, pypa/installer or other
standards-based tools.
See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
********************************************************************************
!!
self.initialize_options()
running install_lib
running build_py
copying build/Python/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.13_pbconsensuscore/build
copying build/Python/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.13_pbconsensuscore/build
copying build/Python/_ConsensusCore.so -> /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.13_pbconsensuscore/build
creating /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.13/dist-packages
copying /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.13_pbconsensuscore/build/_ConsensusCore.so -> /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.13/dist-packages
copying /build/reproducible-path/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.13_pbconsensuscore/build/ConsensusCore.py -> /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.13/dist-packages
byte-compiling /build/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.13/dist-packages/ConsensusCore.py to ConsensusCore.cpython-313.pyc
running install_egg_info
running 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
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/reproducible-path/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.13/dist-packages/ConsensusCore-1.0.2.egg-info
Skipping SOURCES.txt
running install_scripts
dh_install -O--buildsystem=pybuild
debian/rules execute_after_dh_install
make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
find debian -name meson.build -delete
make[1]: Leaving directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
dh_installdocs -O--buildsystem=pybuild
dh_installchangelogs -O--buildsystem=pybuild
dh_python3 -O--buildsystem=pybuild
I: dh_python3 fs:421: renaming _ConsensusCore.so to _ConsensusCore.cpython-312-i386-linux-gnu.so
I: dh_python3 fs:421: renaming _ConsensusCore.so to _ConsensusCore.cpython-313-i386-linux-gnu.so
debian/rules execute_after_dh_python3
make[1]: Entering directory '/build/reproducible-path/consensuscore-1.1.1+dfsg'
dh_numpy3
make[1]: Leaving directory '/build/reproducible-path/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 'python3-pbconsensuscore' in '../python3-pbconsensuscore_1.1.1+dfsg-7.1_i386.deb'.
dpkg-deb: building package 'python3-pbconsensuscore-dbgsym' in '../python3-pbconsensuscore-dbgsym_1.1.1+dfsg-7.1_i386.deb'.
dpkg-deb: building package 'libconsensuscore-dev' in '../libconsensuscore-dev_1.1.1+dfsg-7.1_i386.deb'.
dpkg-genbuildinfo --build=binary -O../consensuscore_1.1.1+dfsg-7.1_i386.buildinfo
dpkg-genchanges --build=binary -O../consensuscore_1.1.1+dfsg-7.1_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/6264/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/6264/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/6264 and its subdirectories
I: Current time: Thu Feb 6 18:52:29 +14 2025
I: pbuilder-time-stamp: 1738817549