I: pbuilder: network access will be disabled during build
I: Current time: Tue Apr 7 01:57:01 +14 2026
I: pbuilder-time-stamp: 1775476621
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-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 [gubbins_3.4-2.dsc]
I: copying [./gubbins_3.4.orig.tar.gz]
I: copying [./gubbins_3.4-2.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./gubbins_3.4-2.dsc: unsupported subcommand
dpkg-source: info: extracting gubbins in gubbins-3.4
dpkg-source: info: unpacking gubbins_3.4.orig.tar.gz
dpkg-source: info: unpacking gubbins_3.4-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying do_not_handle_python_by_upstream_build_system.patch
dpkg-source: info: applying gubbins_exe_in_usr_lib.patch
dpkg-source: info: applying iqtree2.patch
dpkg-source: info: applying autoupdate_configure.ac.patch
dpkg-source: info: applying python3-shebang.patch
dpkg-source: info: applying remove-numba-temporarily.patch
dpkg-source: info: applying numpy2.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/41493/tmp/hooks/D01_modify_environment starting
debug: Running on ionos6-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 Apr 6 11:57 /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/41493/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/41493/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=21 '
DIRSTACK=()
DISTRIBUTION=trixie
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=i686
HOST_ARCH=i386
IFS='
'
INVOCATION_ID=4ce519c553594e77b15ec38cda28766b
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=41493
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.X2VJON10/pbuilderrc_ghTI --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.X2VJON10/b2 --logfile b2/build.log gubbins_3.4-2.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://213.165.73.152:3128
I: uname -a
Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/41493/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), dh-sequence-python3, autoconf-archive, pkgconf, fasttree, iqtree, raxml, python3-setuptools, zlib1g-dev, check, python3, python3-biopython, python3-dendropy, python3-reportlab, tox, python3-scipy, python3-multiprocess, python3-wheel
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19789 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however:
Package dh-sequence-python3 is not installed.
pbuilder-satisfydepends-dummy depends on autoconf-archive; however:
Package autoconf-archive is not installed.
pbuilder-satisfydepends-dummy depends on pkgconf; however:
Package pkgconf is not installed.
pbuilder-satisfydepends-dummy depends on fasttree; however:
Package fasttree is not installed.
pbuilder-satisfydepends-dummy depends on iqtree; however:
Package iqtree is not installed.
pbuilder-satisfydepends-dummy depends on raxml; however:
Package raxml is not installed.
pbuilder-satisfydepends-dummy depends on python3-setuptools; however:
Package python3-setuptools is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on check; however:
Package check is not installed.
pbuilder-satisfydepends-dummy depends on python3; however:
Package python3 is not installed.
pbuilder-satisfydepends-dummy depends on python3-biopython; however:
Package python3-biopython is not installed.
pbuilder-satisfydepends-dummy depends on python3-dendropy; however:
Package python3-dendropy is not installed.
pbuilder-satisfydepends-dummy depends on python3-reportlab; however:
Package python3-reportlab is not installed.
pbuilder-satisfydepends-dummy depends on tox; however:
Package tox is not installed.
pbuilder-satisfydepends-dummy depends on python3-scipy; however:
Package python3-scipy is not installed.
pbuilder-satisfydepends-dummy depends on python3-multiprocess; however:
Package python3-multiprocess is not installed.
pbuilder-satisfydepends-dummy depends on python3-wheel; however:
Package python3-wheel is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} check{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fasttree{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} iqtree{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libhwloc15{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libmpich12{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng16-16t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libsubunit-dev{a} libsubunit0{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-autocommand{a} python3-biopython{a} python3-cachetools{a} python3-cairo{a} python3-chardet{a} python3-colorama{a} python3-decorator{a} python3-dendropy{a} python3-dill{a} python3-distlib{a} python3-filelock{a} python3-freetype{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-multiprocess{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pil{a} python3-pip-whl{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-pyproject-api{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-setuptools{a} python3-setuptools-whl{a} python3-typeguard{a} python3-typing-extensions{a} python3-virtualenv{a} python3-wheel{a} python3-wheel-whl{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} raxml{a} readline-common{a} sensible-utils{a} sgml-base{a} tox{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
curl fonts-dejavu-extra javascript-common libarchive-cpio-perl libglib2.0-data libhwloc-plugins libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-dev python3-olefile python3-pooch shared-mime-info wget xdg-user-dirs
0 packages upgraded, 149 newly installed, 0 to remove and 0 not upgraded.
Need to get 93.8 MB of archives. After unpacking 351 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main i386 autoconf-archive all 20220903-3 [775 kB]
Get: 2 http://deb.debian.org/debian trixie/main i386 libpython3.13-minimal i386 3.13.2-1 [859 kB]
Get: 3 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB]
Get: 4 http://deb.debian.org/debian trixie/main i386 python3.13-minimal i386 3.13.2-1 [2266 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.13.2-1 [27.1 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 media-types all 12.0.0 [28.9 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB]
Get: 8 http://deb.debian.org/debian trixie/main i386 tzdata all 2025a-2 [259 kB]
Get: 9 http://deb.debian.org/debian trixie/main i386 libffi8 i386 3.4.7-1 [21.4 kB]
Get: 10 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-6 [69.4 kB]
Get: 11 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-6 [173 kB]
Get: 12 http://deb.debian.org/debian trixie/main i386 libpython3.13-stdlib i386 3.13.2-1 [1985 kB]
Get: 13 http://deb.debian.org/debian trixie/main i386 python3.13 i386 3.13.2-1 [745 kB]
Get: 14 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.13.2-1 [10.0 kB]
Get: 15 http://deb.debian.org/debian trixie/main i386 python3 i386 3.13.2-1 [28.1 kB]
Get: 16 http://deb.debian.org/debian trixie/main i386 python3-numpy-dev i386 1:2.2.3+ds-2+b1 [145 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.1-2 [150 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14.2.0-16 [735 kB]
Get: 19 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.1-2 [2198 kB]
Get: 20 http://deb.debian.org/debian trixie/main i386 python3-numpy i386 1:2.2.3+ds-2+b1 [5060 kB]
Get: 21 http://deb.debian.org/debian trixie/main i386 sgml-base all 1.31 [15.4 kB]
Get: 22 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 openssl i386 3.4.1-1 [1432 kB]
Get: 24 http://deb.debian.org/debian trixie/main i386 ca-certificates all 20241223 [164 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 27 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.23.1-1 [245 kB]
Get: 29 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 30 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 31 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.4-5 [96.5 kB]
Get: 32 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 33 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 34 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-5 [301 kB]
Get: 35 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 36 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 37 http://deb.debian.org/debian trixie/main i386 automake all 1:1.17-3 [862 kB]
Get: 38 http://deb.debian.org/debian trixie/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 39 http://deb.debian.org/debian trixie/main i386 libsubunit0 i386 1.4.2-3+b1 [6584 B]
Get: 40 http://deb.debian.org/debian trixie/main i386 libsubunit-dev i386 1.4.2-3+b1 [7624 B]
Get: 41 http://deb.debian.org/debian trixie/main i386 check i386 0.15.2-3 [116 kB]
Get: 42 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 43 http://deb.debian.org/debian trixie/main i386 libtool all 2.5.4-3 [539 kB]
Get: 44 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 45 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 46 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 47 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 48 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 49 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 50 http://deb.debian.org/debian trixie/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 51 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 52 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b2 [734 kB]
Get: 53 http://deb.debian.org/debian trixie/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 54 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 55 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 56 http://deb.debian.org/debian trixie/main i386 debhelper all 13.24.1 [920 kB]
Get: 57 http://deb.debian.org/debian trixie/main i386 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 58 http://deb.debian.org/debian trixie/main i386 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 59 http://deb.debian.org/debian trixie/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 60 http://deb.debian.org/debian trixie/main i386 python3-typeguard all 4.4.2-1 [37.3 kB]
Get: 61 http://deb.debian.org/debian trixie/main i386 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 62 http://deb.debian.org/debian trixie/main i386 python3-jaraco.context all 6.0.0-1 [7984 B]
Get: 63 http://deb.debian.org/debian trixie/main i386 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 64 http://deb.debian.org/debian trixie/main i386 python3-pkg-resources all 75.8.0-1 [222 kB]
Get: 65 http://deb.debian.org/debian trixie/main i386 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 66 http://deb.debian.org/debian trixie/main i386 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 67 http://deb.debian.org/debian trixie/main i386 python3-setuptools all 75.8.0-1 [724 kB]
Get: 68 http://deb.debian.org/debian trixie/main i386 dh-python all 6.20250108 [113 kB]
Get: 69 http://deb.debian.org/debian trixie/main i386 fasttree i386 2.1.11-2 [183 kB]
Get: 70 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 71 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 72 http://deb.debian.org/debian trixie/main i386 libfontenc1 i386 1:1.1.8-1+b2 [23.4 kB]
Get: 73 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b7 [299 kB]
Get: 74 http://deb.debian.org/debian trixie/main i386 libpng16-16t64 i386 1.6.47-1 [289 kB]
Get: 75 http://deb.debian.org/debian trixie/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB]
Get: 76 http://deb.debian.org/debian trixie/main i386 x11-common all 1:7.7+24 [217 kB]
Get: 77 http://deb.debian.org/debian trixie/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get: 78 http://deb.debian.org/debian trixie/main i386 xfonts-utils i386 1:7.7+7 [95.1 kB]
Get: 79 http://deb.debian.org/debian trixie/main i386 fonts-urw-base35 all 20200910-8 [10.8 MB]
Get: 80 http://deb.debian.org/debian trixie/main i386 fontconfig-config i386 2.15.0-2 [317 kB]
Get: 81 http://deb.debian.org/debian trixie/main i386 libhwloc15 i386 2.12.0-1 [177 kB]
Get: 82 http://deb.debian.org/debian trixie/main i386 libmpich12 i386 4.2.1-5 [1519 kB]
Get: 83 http://deb.debian.org/debian trixie/main i386 iqtree i386 2.0.7+dfsg-1+b2 [3229 kB]
Get: 84 http://deb.debian.org/debian trixie/main i386 libfontconfig1 i386 2.15.0-2 [402 kB]
Get: 85 http://deb.debian.org/debian trixie/main i386 libpixman-1-0 i386 0.44.0-3 [246 kB]
Get: 86 http://deb.debian.org/debian trixie/main i386 libxau6 i386 1:1.0.11-1 [20.7 kB]
Get: 87 http://deb.debian.org/debian trixie/main i386 libxdmcp6 i386 1:1.1.5-1 [28.2 kB]
Get: 88 http://deb.debian.org/debian trixie/main i386 libxcb1 i386 1.17.0-2+b1 [148 kB]
Get: 89 http://deb.debian.org/debian trixie/main i386 libx11-data all 2:1.8.10-2 [337 kB]
Get: 90 http://deb.debian.org/debian trixie/main i386 libx11-6 i386 2:1.8.10-2 [834 kB]
Get: 91 http://deb.debian.org/debian trixie/main i386 libxcb-render0 i386 1.17.0-2+b1 [116 kB]
Get: 92 http://deb.debian.org/debian trixie/main i386 libxcb-shm0 i386 1.17.0-2+b1 [105 kB]
Get: 93 http://deb.debian.org/debian trixie/main i386 libxext6 i386 2:1.3.4-1+b3 [52.5 kB]
Get: 94 http://deb.debian.org/debian trixie/main i386 libxrender1 i386 1:0.9.10-1.1+b4 [28.8 kB]
Get: 95 http://deb.debian.org/debian trixie/main i386 libcairo2 i386 1.18.2-2 [591 kB]
Get: 96 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.23-1+b1 [48.4 kB]
Get: 97 http://deb.debian.org/debian trixie/main i386 libfribidi0 i386 1.0.16-1 [27.0 kB]
Get: 98 http://deb.debian.org/debian trixie/main i386 libglib2.0-0t64 i386 2.83.4-1 [1582 kB]
Get: 99 http://deb.debian.org/debian trixie/main i386 libgraphite2-3 i386 1.3.14-2+b1 [77.8 kB]
Get: 100 http://deb.debian.org/debian trixie/main i386 libharfbuzz0b i386 10.2.0-1 [504 kB]
Get: 101 http://deb.debian.org/debian trixie/main i386 libimagequant0 i386 2.18.0-1+b2 [36.0 kB]
Get: 102 http://deb.debian.org/debian trixie/main i386 libjbig0 i386 2.1-6.1+b2 [32.2 kB]
Get: 103 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-3.1 [170 kB]
Get: 104 http://deb.debian.org/debian trixie/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 105 http://deb.debian.org/debian trixie/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 106 http://deb.debian.org/debian trixie/main i386 libjs-sphinxdoc all 8.1.3-5 [30.5 kB]
Get: 107 http://deb.debian.org/debian trixie/main i386 liblbfgsb0 i386 3.0+dfsg.4-1+b2 [29.5 kB]
Get: 108 http://deb.debian.org/debian trixie/main i386 liblcms2-2 i386 2.16-2 [171 kB]
Get: 109 http://deb.debian.org/debian trixie/main i386 liblerc4 i386 4.0.0+ds-5 [191 kB]
Get: 110 http://deb.debian.org/debian trixie/main i386 libopenjp2-7 i386 2.5.3-1 [215 kB]
Get: 111 http://deb.debian.org/debian trixie/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB]
Get: 112 http://deb.debian.org/debian trixie/main i386 libraqm0 i386 0.10.2-1 [14.6 kB]
Get: 113 http://deb.debian.org/debian trixie/main i386 libsharpyuv0 i386 1.5.0-0.1 [115 kB]
Get: 114 http://deb.debian.org/debian trixie/main i386 libwebp7 i386 1.5.0-0.1 [329 kB]
Get: 115 http://deb.debian.org/debian trixie/main i386 libtiff6 i386 4.5.1+git230720-5 [339 kB]
Get: 116 http://deb.debian.org/debian trixie/main i386 libwebpdemux2 i386 1.5.0-0.1 [114 kB]
Get: 117 http://deb.debian.org/debian trixie/main i386 libwebpmux3 i386 1.5.0-0.1 [127 kB]
Get: 118 http://deb.debian.org/debian trixie/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB]
Get: 119 http://deb.debian.org/debian trixie/main i386 pkgconf i386 1.8.1-4 [26.2 kB]
Get: 120 http://deb.debian.org/debian trixie/main i386 python3-chardet all 5.2.0+dfsg-2 [108 kB]
Get: 121 http://deb.debian.org/debian trixie/main i386 python3-pil i386 11.1.0-5+b1 [518 kB]
Get: 122 http://deb.debian.org/debian trixie/main i386 python3-cairo i386 1.26.1-2+b2 [116 kB]
Get: 123 http://deb.debian.org/debian trixie/main i386 python3-freetype all 2.5.1-1 [89.3 kB]
Get: 124 http://deb.debian.org/debian trixie/main i386 python3-rlpycairo all 0.3.0-3 [9904 B]
Get: 125 http://deb.debian.org/debian trixie/main i386 python3-reportlab all 4.3.1-1 [1158 kB]
Get: 126 http://deb.debian.org/debian trixie/main i386 xml-core all 0.19 [20.1 kB]
Get: 127 http://deb.debian.org/debian trixie/main i386 w3c-sgml-lib all 1.3-3 [273 kB]
Get: 128 http://deb.debian.org/debian trixie/main i386 python3-biopython i386 1.85+dfsg-2+b1 [1668 kB]
Get: 129 http://deb.debian.org/debian trixie/main i386 python3-cachetools all 5.3.3-1 [13.2 kB]
Get: 130 http://deb.debian.org/debian trixie/main i386 python3-colorama all 0.4.6-4 [36.2 kB]
Get: 131 http://deb.debian.org/debian trixie/main i386 python3-decorator all 5.1.1-5 [15.1 kB]
Get: 132 http://deb.debian.org/debian trixie/main i386 python3-dendropy all 4.6.1-2 [277 kB]
Get: 133 http://deb.debian.org/debian trixie/main i386 python3-dill all 0.3.9-1 [83.5 kB]
Get: 134 http://deb.debian.org/debian trixie/main i386 python3-distlib all 0.3.9-1 [257 kB]
Get: 135 http://deb.debian.org/debian trixie/main i386 python3-filelock all 3.17.0-1 [12.7 kB]
Get: 136 http://deb.debian.org/debian trixie/main i386 python3-multiprocess all 0.70.17-1 [107 kB]
Get: 137 http://deb.debian.org/debian trixie/main i386 python3-packaging all 24.2-1 [55.3 kB]
Get: 138 http://deb.debian.org/debian trixie/main i386 python3-pip-whl all 25.0+dfsg-1 [1522 kB]
Get: 139 http://deb.debian.org/debian trixie/main i386 python3-platformdirs all 4.3.6-1 [16.6 kB]
Get: 140 http://deb.debian.org/debian trixie/main i386 python3-pluggy all 1.5.0-1 [26.9 kB]
Get: 141 http://deb.debian.org/debian trixie/main i386 python3-pyproject-api all 1.9.0-1 [51.6 kB]
Get: 142 http://deb.debian.org/debian trixie/main i386 python3-scipy i386 1.14.1-4+b1 [17.0 MB]
Get: 143 http://deb.debian.org/debian trixie/main i386 python3-setuptools-whl all 75.8.0-1 [1244 kB]
Get: 144 http://deb.debian.org/debian trixie/main i386 python3-wheel-whl all 0.45.1-1 [75.3 kB]
Get: 145 http://deb.debian.org/debian trixie/main i386 python3-virtualenv all 20.29.1+ds-1 [71.6 kB]
Get: 146 http://deb.debian.org/debian trixie/main i386 python3-wheel all 0.45.1-1 [56.7 kB]
Get: 147 http://deb.debian.org/debian trixie/main i386 raxml i386 8.2.13+dfsg-1+b2 [992 kB]
Get: 148 http://deb.debian.org/debian trixie/main i386 tox all 4.24.1-1 [399 kB]
Get: 149 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Fetched 93.8 MB in 5s (18.8 MB/s)
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Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
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-> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/41493/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for trixie
I: user script /srv/workspace/pbuilder/41493/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/gubbins-3.4/ && 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 > ../gubbins_3.4-2_source.changes
dpkg-buildpackage: info: source package gubbins
dpkg-buildpackage: info: source version 3.4-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean
debian/rules override_dh_clean
make[1]: Entering directory '/build/reproducible-path/gubbins-3.4'
dh_clean
rm -rf python/*.egg-info python/build python/Makefile
find . -name "*.pyc" -delete
rm -rf python/output_alignment python/tmp* tests/.deps
make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4'
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:29: installing './compile'
configure.ac:14: installing './config.guess'
configure.ac:14: installing './config.sub'
configure.ac:4: installing './install-sh'
configure.ac:4: installing './missing'
src/Makefile.am: installing './depcomp'
parallel-tests: installing './test-driver'
dh_auto_configure
./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
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configure: creating ./config.status
config.status: creating Makefile
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dh_auto_build
make -j21
make[1]: Entering directory '/build/reproducible-path/gubbins-3.4'
make all-recursive
make[2]: Entering directory '/build/reproducible-path/gubbins-3.4'
Making all in src
make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/src'
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.c
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Newickform.lo Newickform.c
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alignment_file.lo alignment_file.c
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o block_tab_file.lo block_tab_file.c
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o branch_sequences.lo branch_sequences.c
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o string_cat.lo string_cat.c
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fasta_of_snp_sites.lo fasta_of_snp_sites.c
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gff_file.lo gff_file.c
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gubbins.lo gubbins.c
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parse_phylip.lo parse_phylip.c
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parse_vcf.lo parse_vcf.c
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylip_of_snp_sites.lo phylip_of_snp_sites.c
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o seqUtil.lo seqUtil.c
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snp_searching.lo snp_searching.c
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snp_sites.lo snp_sites.c
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tree_statistics.lo tree_statistics.c
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tree_scaling.lo tree_scaling.c
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcf.lo vcf.c
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o csv_of_snp_sites.lo csv_of_snp_sites.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_vcf.c -fPIC -DPIC -o .libs/parse_vcf.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_scaling.c -fPIC -DPIC -o .libs/tree_scaling.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c block_tab_file.c -fPIC -DPIC -o .libs/block_tab_file.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c branch_sequences.c -fPIC -DPIC -o .libs/branch_sequences.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_searching.c -fPIC -DPIC -o .libs/snp_searching.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c string_cat.c -fPIC -DPIC -o .libs/string_cat.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c fasta_of_snp_sites.c -fPIC -DPIC -o .libs/fasta_of_snp_sites.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c gubbins.c -fPIC -DPIC -o .libs/gubbins.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c phylip_of_snp_sites.c -fPIC -DPIC -o .libs/phylip_of_snp_sites.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_phylip.c -fPIC -DPIC -o .libs/parse_phylip.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c Newickform.c -fPIC -DPIC -o .libs/Newickform.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -fPIC -DPIC -o .libs/vcf.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_statistics.c -fPIC -DPIC -o .libs/tree_statistics.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c alignment_file.c -fPIC -DPIC -o .libs/alignment_file.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c seqUtil.c -fPIC -DPIC -o .libs/seqUtil.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c gff_file.c -fPIC -DPIC -o .libs/gff_file.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c csv_of_snp_sites.c -fPIC -DPIC -o .libs/csv_of_snp_sites.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_sites.c -fPIC -DPIC -o .libs/snp_sites.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_sites.c -o snp_sites.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c block_tab_file.c -o block_tab_file.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c seqUtil.c -o seqUtil.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c gff_file.c -o gff_file.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c string_cat.c -o string_cat.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c phylip_of_snp_sites.c -o phylip_of_snp_sites.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_vcf.c -o parse_vcf.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c fasta_of_snp_sites.c -o fasta_of_snp_sites.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_statistics.c -o tree_statistics.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c alignment_file.c -o alignment_file.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_scaling.c -o tree_scaling.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c gubbins.c -o gubbins.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -o vcf.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c csv_of_snp_sites.c -o csv_of_snp_sites.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_searching.c -o snp_searching.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c parse_phylip.c -o parse_phylip.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c Newickform.c -o Newickform.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c branch_sequences.c -o branch_sequences.o >/dev/null 2>&1
/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:1 -Wl,-z,relro -Wl,-z,now -pthread -o libgubbins.la -rpath /usr/lib/i386-linux-gnu Newickform.lo alignment_file.lo block_tab_file.lo branch_sequences.lo string_cat.lo fasta_of_snp_sites.lo gff_file.lo gubbins.lo parse_phylip.lo parse_vcf.lo phylip_of_snp_sites.lo seqUtil.lo snp_searching.lo snp_sites.lo tree_statistics.lo tree_scaling.lo vcf.lo csv_of_snp_sites.lo -lm
libtool: link: gcc -shared -fPIC -DPIC .libs/Newickform.o .libs/alignment_file.o .libs/block_tab_file.o .libs/branch_sequences.o .libs/string_cat.o .libs/fasta_of_snp_sites.o .libs/gff_file.o .libs/gubbins.o .libs/parse_phylip.o .libs/parse_vcf.o .libs/phylip_of_snp_sites.o .libs/seqUtil.o .libs/snp_searching.o .libs/snp_sites.o .libs/tree_statistics.o .libs/tree_scaling.o .libs/vcf.o .libs/csv_of_snp_sites.o -lm -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -Wl,-soname -Wl,libgubbins.so.0 -o .libs/libgubbins.so.0.0.1
libtool: link: (cd ".libs" && rm -f "libgubbins.so.0" && ln -s "libgubbins.so.0.0.1" "libgubbins.so.0")
libtool: link: (cd ".libs" && rm -f "libgubbins.so" && ln -s "libgubbins.so.0.0.1" "libgubbins.so")
libtool: link: ar cr .libs/libgubbins.a Newickform.o alignment_file.o block_tab_file.o branch_sequences.o string_cat.o fasta_of_snp_sites.o gff_file.o gubbins.o parse_phylip.o parse_vcf.o phylip_of_snp_sites.o seqUtil.o snp_searching.o snp_sites.o tree_statistics.o tree_scaling.o vcf.o csv_of_snp_sites.o
libtool: link: ranlib .libs/libgubbins.a
libtool: link: ( cd ".libs" && rm -f "libgubbins.la" && ln -s "../libgubbins.la" "libgubbins.la" )
/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -pthread -o gubbins main.o libgubbins.la -lz -lm
libtool: link: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/gubbins main.o ./.libs/libgubbins.so -lz -lm -pthread
make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/src'
Making all in release
make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/release'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/release'
make[3]: Entering directory '/build/reproducible-path/gubbins-3.4'
make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4'
make[2]: Leaving directory '/build/reproducible-path/gubbins-3.4'
make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/gubbins-3.4'
# make sure test data will not be changed (at least tests/data/multiple_recombinations.tre is removed in the test)
cp -a tests/data tests/data.save
dh_auto_test
make -j21 check "TESTSUITEFLAGS=-j21 --verbose" VERBOSE=1
make[2]: Entering directory '/build/reproducible-path/gubbins-3.4'
Making check in src
make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/src'
make run_all_tests
make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/src'
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_branch_sequences.o `test -f '../tests/check_branch_sequences.c' || echo './'`../tests/check_branch_sequences.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_gubbins.o `test -f '../tests/check_gubbins.c' || echo './'`../tests/check_gubbins.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_parse_phylip.o `test -f '../tests/check_parse_phylip.c' || echo './'`../tests/check_parse_phylip.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_snp_searching.o `test -f '../tests/check_snp_searching.c' || echo './'`../tests/check_snp_searching.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_snp_sites.o `test -f '../tests/check_snp_sites.c' || echo './'`../tests/check_snp_sites.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_vcf_parsing.o `test -f '../tests/check_vcf_parsing.c' || echo './'`../tests/check_vcf_parsing.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-helper_methods.o `test -f '../tests/helper_methods.c' || echo './'`../tests/helper_methods.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-run_all_tests.o `test -f '../tests/run_all_tests.c' || echo './'`../tests/run_all_tests.c
../tests/helper_methods.c: In function 'compare_files':
../tests/helper_methods.c:27:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
27 | fread(expected_buffer, sizeof(char), numbytes, expected_output_fh);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../tests/helper_methods.c:34:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
34 | fread(actual_buffer, sizeof(char), numbytes, actual_output_fh);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/bin/sh ../libtool --tag=CC --mode=link gcc -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -pthread -o run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck libgubbins.la -lz -lm -lrt -lsubunit
libtool: link: gcc -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck ./.libs/libgubbins.so -lz -lm -lrt -lsubunit -pthread
make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/src'
make check-TESTS
make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/src'
make[5]: Entering directory '/build/reproducible-path/gubbins-3.4/src'
PASS: run_all_tests
============================================================================
Testsuite summary for gubbins package_version
============================================================================
# TOTAL: 1
# PASS: 1
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[5]: Leaving directory '/build/reproducible-path/gubbins-3.4/src'
make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/src'
make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/src'
Making check in release
make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/release'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/release'
make[3]: Entering directory '/build/reproducible-path/gubbins-3.4'
make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4'
make[2]: Leaving directory '/build/reproducible-path/gubbins-3.4'
rm -rf tests/data
mv tests/data.save tests/data
make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4'
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/gubbins-3.4'
dh_auto_install
make -j1 install DESTDIR=/build/reproducible-path/gubbins-3.4/debian/gubbins AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/build/reproducible-path/gubbins-3.4'
Making install in src
make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/src'
make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/src'
/usr/bin/mkdir -p '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/i386-linux-gnu'
/bin/sh ../libtool --mode=install /usr/bin/install -c libgubbins.la '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/libgubbins.so.0.0.1 /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1
libtool: install: (cd /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/i386-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so.0 || { rm -f libgubbins.so.0 && ln -s libgubbins.so.0.0.1 libgubbins.so.0; }; })
libtool: install: (cd /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/i386-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so || { rm -f libgubbins.so && ln -s libgubbins.so.0.0.1 libgubbins.so; }; })
libtool: install: /usr/bin/install -c .libs/libgubbins.lai /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.la
libtool: install: /usr/bin/install -c .libs/libgubbins.a /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.a
libtool: install: chmod 644 /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.a
libtool: install: ranlib /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.a
libtool: warning: remember to run 'libtool --finish /usr/lib/i386-linux-gnu'
/usr/bin/mkdir -p '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/bin'
/bin/sh ../libtool --mode=install /usr/bin/install -c gubbins '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/bin'
libtool: warning: 'libgubbins.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/gubbins /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/bin/gubbins
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/src'
make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/src'
Making install in release
make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/release'
make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/release'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/release'
make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/release'
make[3]: Entering directory '/build/reproducible-path/gubbins-3.4'
make[4]: Entering directory '/build/reproducible-path/gubbins-3.4'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4'
make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4'
make[2]: Leaving directory '/build/reproducible-path/gubbins-3.4'
# pybuild --install --system=distutils
cd python && \
python3 setup.py install --root=../debian/gubbins --install-layout=deb --install-lib=/usr/share/gubbins --install-scripts=/usr/share/gubbins
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require'
warnings.warn(msg)
running install
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:79: 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 build
running build_py
creating build/lib/gubbins
copying gubbins/treebuilders.py -> build/lib/gubbins
copying gubbins/utils.py -> build/lib/gubbins
copying gubbins/pyjar.py -> build/lib/gubbins
copying gubbins/PreProcessFasta.py -> build/lib/gubbins
copying gubbins/__init__.py -> build/lib/gubbins
copying gubbins/ValidateFastaAlignment.py -> build/lib/gubbins
copying gubbins/run_gubbins.py -> build/lib/gubbins
copying gubbins/common.py -> build/lib/gubbins
creating build/lib/gubbins/tests
copying gubbins/tests/test_treebuilders.py -> build/lib/gubbins/tests
copying gubbins/tests/test_utils.py -> build/lib/gubbins/tests
copying gubbins/tests/test_tree_methods.py -> build/lib/gubbins/tests
copying gubbins/tests/test_validate_starting_tree.py -> build/lib/gubbins/tests
copying gubbins/tests/test_python_scripts.py -> build/lib/gubbins/tests
copying gubbins/tests/test_alignment_python_methods.py -> build/lib/gubbins/tests
copying gubbins/tests/test_pre_process_fasta.py -> build/lib/gubbins/tests
copying gubbins/tests/test_validate_fasta_input.py -> build/lib/gubbins/tests
copying gubbins/tests/test_converging_recombinations.py -> build/lib/gubbins/tests
copying gubbins/tests/__init__.py -> build/lib/gubbins/tests
copying gubbins/tests/test_dependencies.py -> build/lib/gubbins/tests
running build_scripts
creating build/scripts-3.13
copying and adjusting scripts/generate_ska_alignment.py -> build/scripts-3.13
copying and adjusting scripts/extract_gubbins_clade.py -> build/scripts-3.13
copying and adjusting scripts/mask_gubbins_aln.py -> build/scripts-3.13
copying and adjusting scripts/gubbins_alignment_checker.py -> build/scripts-3.13
copying and adjusting scripts/generate_files_for_clade_analysis.py -> build/scripts-3.13
copying and adjusting scripts/count_recombinations_per_gene.py -> build/scripts-3.13
copying and adjusting scripts/extract_recombinant_sequences.py -> build/scripts-3.13
copying ../R/scripts/plot_gubbins.R -> build/scripts-3.13
changing mode of build/scripts-3.13/generate_ska_alignment.py from 644 to 755
changing mode of build/scripts-3.13/extract_gubbins_clade.py from 644 to 755
changing mode of build/scripts-3.13/mask_gubbins_aln.py from 644 to 755
changing mode of build/scripts-3.13/gubbins_alignment_checker.py from 644 to 755
changing mode of build/scripts-3.13/generate_files_for_clade_analysis.py from 644 to 755
changing mode of build/scripts-3.13/count_recombinations_per_gene.py from 644 to 755
changing mode of build/scripts-3.13/extract_recombinant_sequences.py from 644 to 755
running install_lib
creating ../debian/gubbins/usr/share/gubbins
creating ../debian/gubbins/usr/share/gubbins/gubbins
copying build/lib/gubbins/treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins
copying build/lib/gubbins/utils.py -> ../debian/gubbins/usr/share/gubbins/gubbins
copying build/lib/gubbins/pyjar.py -> ../debian/gubbins/usr/share/gubbins/gubbins
creating ../debian/gubbins/usr/share/gubbins/gubbins/tests
copying build/lib/gubbins/tests/test_treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests
copying build/lib/gubbins/tests/test_utils.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests
copying build/lib/gubbins/tests/test_tree_methods.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests
copying build/lib/gubbins/tests/test_validate_starting_tree.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests
copying build/lib/gubbins/tests/test_python_scripts.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests
copying build/lib/gubbins/tests/test_alignment_python_methods.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests
copying build/lib/gubbins/tests/test_pre_process_fasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests
copying build/lib/gubbins/tests/test_validate_fasta_input.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests
copying build/lib/gubbins/tests/test_converging_recombinations.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests
copying build/lib/gubbins/tests/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests
copying build/lib/gubbins/tests/test_dependencies.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests
copying build/lib/gubbins/PreProcessFasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins
copying build/lib/gubbins/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins
copying build/lib/gubbins/ValidateFastaAlignment.py -> ../debian/gubbins/usr/share/gubbins/gubbins
copying build/lib/gubbins/run_gubbins.py -> ../debian/gubbins/usr/share/gubbins/gubbins
copying build/lib/gubbins/common.py -> ../debian/gubbins/usr/share/gubbins/gubbins
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/treebuilders.py to treebuilders.cpython-313.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/utils.py to utils.cpython-313.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/pyjar.py to pyjar.cpython-313.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_treebuilders.py to test_treebuilders.cpython-313.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_utils.py to test_utils.cpython-313.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_tree_methods.py to test_tree_methods.cpython-313.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_starting_tree.py to test_validate_starting_tree.cpython-313.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_python_scripts.py to test_python_scripts.cpython-313.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_alignment_python_methods.py to test_alignment_python_methods.cpython-313.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_pre_process_fasta.py to test_pre_process_fasta.cpython-313.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_fasta_input.py to test_validate_fasta_input.cpython-313.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_converging_recombinations.py to test_converging_recombinations.cpython-313.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/__init__.py to __init__.cpython-313.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_dependencies.py to test_dependencies.cpython-313.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/PreProcessFasta.py to PreProcessFasta.cpython-313.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/__init__.py to __init__.cpython-313.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/ValidateFastaAlignment.py to ValidateFastaAlignment.cpython-313.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/run_gubbins.py to run_gubbins.cpython-313.pyc
byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/common.py to common.cpython-313.pyc
running install_egg_info
running egg_info
creating gubbins.egg-info
writing gubbins.egg-info/PKG-INFO
writing dependency_links to gubbins.egg-info/dependency_links.txt
writing entry points to gubbins.egg-info/entry_points.txt
writing requirements to gubbins.egg-info/requires.txt
writing top-level names to gubbins.egg-info/top_level.txt
writing manifest file 'gubbins.egg-info/SOURCES.txt'
reading manifest file 'gubbins.egg-info/SOURCES.txt'
adding license file 'LICENSE.txt'
writing manifest file 'gubbins.egg-info/SOURCES.txt'
Copying gubbins.egg-info to ../debian/gubbins/usr/share/gubbins/gubbins-3.4.egg-info
Skipping SOURCES.txt
running install_scripts
copying build/scripts-3.13/generate_files_for_clade_analysis.py -> ../debian/gubbins/usr/share/gubbins
copying build/scripts-3.13/mask_gubbins_aln.py -> ../debian/gubbins/usr/share/gubbins
copying build/scripts-3.13/extract_gubbins_clade.py -> ../debian/gubbins/usr/share/gubbins
copying build/scripts-3.13/gubbins_alignment_checker.py -> ../debian/gubbins/usr/share/gubbins
copying build/scripts-3.13/plot_gubbins.R -> ../debian/gubbins/usr/share/gubbins
copying build/scripts-3.13/extract_recombinant_sequences.py -> ../debian/gubbins/usr/share/gubbins
copying build/scripts-3.13/count_recombinations_per_gene.py -> ../debian/gubbins/usr/share/gubbins
copying build/scripts-3.13/generate_ska_alignment.py -> ../debian/gubbins/usr/share/gubbins
changing mode of ../debian/gubbins/usr/share/gubbins/generate_files_for_clade_analysis.py to 755
changing mode of ../debian/gubbins/usr/share/gubbins/mask_gubbins_aln.py to 755
changing mode of ../debian/gubbins/usr/share/gubbins/extract_gubbins_clade.py to 755
changing mode of ../debian/gubbins/usr/share/gubbins/gubbins_alignment_checker.py to 755
changing mode of ../debian/gubbins/usr/share/gubbins/plot_gubbins.R to 775
changing mode of ../debian/gubbins/usr/share/gubbins/extract_recombinant_sequences.py to 755
changing mode of ../debian/gubbins/usr/share/gubbins/count_recombinations_per_gene.py to 755
changing mode of ../debian/gubbins/usr/share/gubbins/generate_ska_alignment.py to 755
Installing run_gubbins.py script to ../debian/gubbins/usr/share/gubbins
make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4'
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/gubbins-3.4'
dh_install
find debian -name "*.la" -delete
find debian -name "*.a" -delete
mkdir -p debian/gubbins/usr/lib/gubbins
mv debian/gubbins/usr/bin/gubbins debian/gubbins/usr/lib/gubbins
make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4'
dh_installdocs
dh_installchangelogs
dh_installman
dh_python3
dh_lintian
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dwz: debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1: DWARF compression not beneficial - old size 60788 new size 61918
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: symbol gzopen used by debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzread used by debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzclose used by debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gubbins/usr/lib/gubbins/gubbins was not linked against libz.so.1 (it uses none of the library's symbols)
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'gubbins-dbgsym' in '../gubbins-dbgsym_3.4-2_i386.deb'.
dpkg-deb: building package 'gubbins' in '../gubbins_3.4-2_i386.deb'.
dpkg-genbuildinfo --build=binary -O../gubbins_3.4-2_i386.buildinfo
dpkg-genchanges --build=binary -O../gubbins_3.4-2_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/41493/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/41493/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/41493 and its subdirectories
I: Current time: Tue Apr 7 02:02:43 +14 2026
I: pbuilder-time-stamp: 1775476963