I: pbuilder: network access will be disabled during build I: Current time: Sun Jan 4 10:39:02 +14 2026 I: pbuilder-time-stamp: 1767472742 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 [gubbins_3.4-1.dsc] I: copying [./gubbins_3.4.orig.tar.gz] I: copying [./gubbins_3.4-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Nov 30 18:13:39 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./gubbins_3.4-1.dsc: no acceptable signature found dpkg-source: info: extracting gubbins in gubbins-3.4 dpkg-source: info: unpacking gubbins_3.4.orig.tar.gz dpkg-source: info: unpacking gubbins_3.4-1.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/24066/tmp/hooks/D01_modify_environment starting debug: Running on infom08-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 Jan 3 20:39 /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/24066/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/24066/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]="32" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.32(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=5 ' 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=2ce0739eceff4c54aa2458b12dc65085 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=24066 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.Z3JXES3N/pbuilderrc_CclD --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.Z3JXES3N/b2 --logfile b2/build.log gubbins_3.4-1.dsc' SUDO_GID=111 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' I: uname -a Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) 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/24066/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 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 ... 19956 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} libcom-err2{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhwloc15{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libmpich12{a} libnsl2{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng16-16t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libsubunit-dev{a} libsubunit0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{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-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} python3.12{a} python3.12-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 krb5-locales 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, 155 newly installed, 0 to remove and 0 not upgraded. Need to get 96.4 MB of archives. After unpacking 405 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libpython3.12-minimal i386 3.12.7-3 [814 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.4-1 [107 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 python3.12-minimal i386 3.12.7-3 [2236 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.12.7-1 [26.8 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 tzdata all 2024b-3 [255 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.2~rc1-1 [23.9 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 13 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libtirpc3t64 i386 1.3.4+ds-1.3+b1 [90.5 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 libnsl2 i386 1.3.0-3+b3 [42.7 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-5 [69.3 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-5 [173 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 libpython3.12-stdlib i386 3.12.7-3 [1964 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 python3.12 i386 3.12.7-3 [671 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.12.7-1 [9712 B] Get: 23 http://deb.debian.org/debian unstable/main i386 python3 i386 3.12.7-1 [27.8 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 sgml-base all 1.31 [15.4 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 openssl i386 3.3.2-2 [1387 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 ca-certificates all 20240203 [158 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-11 [95.6 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-2 [723 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 libsubunit0 i386 1.4.2-3+b1 [6584 B] Get: 43 http://deb.debian.org/debian unstable/main i386 libsubunit-dev i386 1.4.2-3+b1 [7624 B] Get: 44 http://deb.debian.org/debian unstable/main i386 check i386 0.15.2-2+b1 [116 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-8 [517 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 51 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 debhelper all 13.20 [915 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 python3-inflect all 7.3.1-2 [32.4 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 65 http://deb.debian.org/debian unstable/main i386 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 python3-zipp all 3.21.0-1 [10.6 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 python3-setuptools all 75.2.0-1 [731 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 dh-python all 6.20241024 [109 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 fasttree i386 2.1.11-2 [183 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 libfontenc1 i386 1:1.1.8-1+b1 [23.4 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 libpng16-16t64 i386 1.6.44-2 [288 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 x11-common all 1:7.7+23.1 [216 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 xfonts-utils i386 1:7.7+7 [95.1 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 82 http://deb.debian.org/debian unstable/main i386 fontconfig-config i386 2.15.0-1.1+b1 [318 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.2.0-8 [735 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 libhwloc15 i386 2.11.2-1 [177 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 libmpich12 i386 4.2.0-14 [1518 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 iqtree i386 2.0.7+dfsg-1+b2 [3229 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 libblas3 i386 3.12.0-4 [143 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 libfontconfig1 i386 2.15.0-1.1+b1 [402 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 libpixman-1-0 i386 0.44.0-3 [246 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 libxau6 i386 1:1.0.11-1 [20.7 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 libxdmcp6 i386 1:1.1.5-1 [28.2 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 libxcb1 i386 1.17.0-2+b1 [148 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 libx11-data all 2:1.8.10-2 [337 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 libx11-6 i386 2:1.8.10-2 [834 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 libxcb-render0 i386 1.17.0-2+b1 [116 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 libxcb-shm0 i386 1.17.0-2+b1 [105 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 libxext6 i386 2:1.3.4-1+b2 [52.6 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 libxrender1 i386 1:0.9.10-1.1+b2 [28.9 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 libcairo2 i386 1.18.2-2 [591 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.22-1 [48.1 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 libfribidi0 i386 1.0.15-1 [72.4 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 libglib2.0-0t64 i386 2.82.2-3 [1571 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 libgraphite2-3 i386 1.3.14-2+b1 [77.8 kB] Get: 104 http://deb.debian.org/debian unstable/main i386 libharfbuzz0b i386 10.0.1-1 [503 kB] Get: 105 http://deb.debian.org/debian unstable/main i386 libimagequant0 i386 2.18.0-1+b2 [36.0 kB] Get: 106 http://deb.debian.org/debian unstable/main i386 libjbig0 i386 2.1-6.1+b2 [32.2 kB] Get: 107 http://deb.debian.org/debian unstable/main i386 libjpeg62-turbo i386 1:2.1.5-3+b1 [171 kB] Get: 108 http://deb.debian.org/debian unstable/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 109 http://deb.debian.org/debian unstable/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 110 http://deb.debian.org/debian unstable/main i386 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 111 http://deb.debian.org/debian unstable/main i386 liblapack3 i386 3.12.0-4 [2194 kB] Get: 112 http://deb.debian.org/debian unstable/main i386 liblbfgsb0 i386 3.0+dfsg.4-1+b2 [29.5 kB] Get: 113 http://deb.debian.org/debian unstable/main i386 liblcms2-2 i386 2.16-2 [171 kB] Get: 114 http://deb.debian.org/debian unstable/main i386 liblerc4 i386 4.0.0+ds-5 [191 kB] Get: 115 http://deb.debian.org/debian unstable/main i386 libopenjp2-7 i386 2.5.0-2+b4 [210 kB] Get: 116 http://deb.debian.org/debian unstable/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB] Get: 117 http://deb.debian.org/debian unstable/main i386 libraqm0 i386 0.10.1-1+b2 [14.8 kB] Get: 118 http://deb.debian.org/debian unstable/main i386 libsharpyuv0 i386 1.4.0-0.1+b1 [113 kB] Get: 119 http://deb.debian.org/debian unstable/main i386 libwebp7 i386 1.4.0-0.1+b1 [322 kB] Get: 120 http://deb.debian.org/debian unstable/main i386 libtiff6 i386 4.5.1+git230720-5 [339 kB] Get: 121 http://deb.debian.org/debian unstable/main i386 libwebpdemux2 i386 1.4.0-0.1+b1 [111 kB] Get: 122 http://deb.debian.org/debian unstable/main i386 libwebpmux3 i386 1.4.0-0.1+b1 [125 kB] Get: 123 http://deb.debian.org/debian unstable/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB] Get: 124 http://deb.debian.org/debian unstable/main i386 pkgconf i386 1.8.1-4 [26.2 kB] Get: 125 http://deb.debian.org/debian unstable/main i386 python3-numpy i386 1:1.26.4+ds-12 [4752 kB] Get: 126 http://deb.debian.org/debian unstable/main i386 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 127 http://deb.debian.org/debian unstable/main i386 python3-pil i386 10.4.0-1+b1 [513 kB] Get: 128 http://deb.debian.org/debian unstable/main i386 python3-cairo i386 1.26.1-2+b1 [131 kB] Get: 129 http://deb.debian.org/debian unstable/main i386 python3-freetype all 2.5.1-1 [89.3 kB] Get: 130 http://deb.debian.org/debian unstable/main i386 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 131 http://deb.debian.org/debian unstable/main i386 python3-reportlab all 4.2.5-1 [1117 kB] Get: 132 http://deb.debian.org/debian unstable/main i386 xml-core all 0.19 [20.1 kB] Get: 133 http://deb.debian.org/debian unstable/main i386 w3c-sgml-lib all 1.3-3 [273 kB] Get: 134 http://deb.debian.org/debian unstable/main i386 python3-biopython i386 1.84+dfsg-4+b1 [1648 kB] Get: 135 http://deb.debian.org/debian unstable/main i386 python3-cachetools all 5.3.3-1 [13.2 kB] Get: 136 http://deb.debian.org/debian unstable/main i386 python3-colorama all 0.4.6-4 [36.2 kB] Get: 137 http://deb.debian.org/debian unstable/main i386 python3-decorator all 5.1.1-5 [15.1 kB] Get: 138 http://deb.debian.org/debian unstable/main i386 python3-dendropy all 4.6.1-1 [277 kB] Get: 139 http://deb.debian.org/debian unstable/main i386 python3-dill all 0.3.9-1 [83.5 kB] Get: 140 http://deb.debian.org/debian unstable/main i386 python3-distlib all 0.3.9-1 [257 kB] Get: 141 http://deb.debian.org/debian unstable/main i386 python3-filelock all 3.16.1-1 [12.6 kB] Get: 142 http://deb.debian.org/debian unstable/main i386 python3-multiprocess all 0.70.17-1 [107 kB] Get: 143 http://deb.debian.org/debian unstable/main i386 python3-packaging all 24.2-1 [55.3 kB] Get: 144 http://deb.debian.org/debian unstable/main i386 python3-pip-whl all 24.3.1+dfsg-1 [1501 kB] Get: 145 http://deb.debian.org/debian unstable/main i386 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 146 http://deb.debian.org/debian unstable/main i386 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 147 http://deb.debian.org/debian unstable/main i386 python3-pyproject-api all 1.8.0-1 [51.7 kB] Get: 148 http://deb.debian.org/debian unstable/main i386 python3-scipy i386 1.14.1-2 [20.1 MB] Get: 149 http://deb.debian.org/debian unstable/main i386 python3-setuptools-whl all 75.2.0-1 [1249 kB] Get: 150 http://deb.debian.org/debian unstable/main i386 python3-wheel-whl all 0.45.1-1 [75.3 kB] Get: 151 http://deb.debian.org/debian unstable/main i386 python3-virtualenv all 20.28.0+ds-1 [71.3 kB] Get: 152 http://deb.debian.org/debian unstable/main i386 python3-wheel all 0.45.1-1 [56.7 kB] Get: 153 http://deb.debian.org/debian unstable/main i386 raxml i386 8.2.13+dfsg-1+b1 [992 kB] Get: 154 http://deb.debian.org/debian unstable/main i386 tox all 4.23.0-1 [393 kB] Get: 155 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] Fetched 96.4 MB in 1s (114 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package autoconf-archive. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19956 files and directories currently installed.) Preparing to unpack .../autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package libpython3.12-minimal:i386. Preparing to unpack .../libpython3.12-minimal_3.12.7-3_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.7-3) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.4-1_i386.deb ... Unpacking libexpat1:i386 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_i386.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:i386 (3.12.7-3) ... Setting up libexpat1:i386 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21458 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_i386.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:i386. Preparing to unpack .../04-libkrb5support0_1.21.3-3_i386.deb ... Unpacking libkrb5support0:i386 (1.21.3-3) ... Selecting previously unselected package libcom-err2:i386. Preparing to unpack .../05-libcom-err2_1.47.2~rc1-1_i386.deb ... Unpacking libcom-err2:i386 (1.47.2~rc1-1) ... Selecting previously unselected package libk5crypto3:i386. Preparing to unpack .../06-libk5crypto3_1.21.3-3_i386.deb ... Unpacking libk5crypto3:i386 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:i386. Preparing to unpack .../07-libkeyutils1_1.6.3-4_i386.deb ... Unpacking libkeyutils1:i386 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:i386. Preparing to unpack .../08-libkrb5-3_1.21.3-3_i386.deb ... Unpacking libkrb5-3:i386 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:i386. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_i386.deb ... Unpacking libgssapi-krb5-2:i386 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:i386. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3 to /lib/i386-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3.0.0 to /lib/i386-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:i386. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_i386.deb ... Unpacking libnsl2:i386 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:i386. Preparing to unpack .../14-libreadline8t64_8.2-5_i386.deb ... 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' Unpacking libreadline8t64:i386 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:i386. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_i386.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../17-libpython3-stdlib_3.12.7-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 22519 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_i386.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.3.2-2_i386.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../006-libmagic1t64_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.45-3+b1_i386.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.22.5-2_i386.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../009-libuchardet0_0.0.8-1+b2_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.23.0-5_i386.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.40.2-11_i386.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../012-libpipeline1_1.5.8-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.13.0-1_i386.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../014-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../015-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../016-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../017-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../018-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libsubunit0:i386. Preparing to unpack .../019-libsubunit0_1.4.2-3+b1_i386.deb ... Unpacking libsubunit0:i386 (1.4.2-3+b1) ... Selecting previously unselected package libsubunit-dev:i386. Preparing to unpack .../020-libsubunit-dev_1.4.2-3+b1_i386.deb ... Unpacking libsubunit-dev:i386 (1.4.2-3+b1) ... Selecting previously unselected package check:i386. Preparing to unpack .../021-check_0.15.2-2+b1_i386.deb ... Unpacking check:i386 (0.15.2-2+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../022-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../023-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../024-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../025-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../026-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../027-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:i386. Preparing to unpack .../028-libelf1t64_0.192-4_i386.deb ... Unpacking libelf1t64:i386 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../029-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../030-libicu72_72.1-5+b1_i386.deb ... Unpacking libicu72:i386 (72.1-5+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../031-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_i386.deb ... Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../032-gettext_0.22.5-2_i386.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../033-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../034-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../035-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../036-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../037-python3-more-itertools_10.5.0-1_all.deb ... Unpacking python3-more-itertools (10.5.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../038-python3-typing-extensions_4.12.2-2_all.deb ... Unpacking python3-typing-extensions (4.12.2-2) ... Selecting previously unselected package python3-typeguard. 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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/24066/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/24066/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_3.4-1_source.changes dpkg-buildpackage: info: source package gubbins dpkg-buildpackage: info: source version 3.4-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier 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 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking how to create a pax tar archive... gnutar checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... 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(cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking whether to build with code coverage support... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for zlib... yes checking for zlib.h... yes checking for math.h... yes checking for a Python interpreter with version >= 3.8... python3 checking for python3... /usr/bin/python3 checking for python3 version... 3.12 checking for python3 platform... linux checking for GNU default python3 prefix... ${prefix} checking for GNU default python3 exec_prefix... ${exec_prefix} checking for python3 script directory (pythondir)... ${PYTHON_PREFIX}/lib/python3.12/site-packages checking for python3 extension module directory (pyexecdir)... ${PYTHON_EXEC_PREFIX}/lib/python3.12/site-packages checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating release/Makefile config.status: creating python/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j5 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 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 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 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 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string_cat.c -fPIC -DPIC -o .libs/string_cat.o /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 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 fasta_of_snp_sites.c -fPIC -DPIC -o .libs/fasta_of_snp_sites.o /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 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 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 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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 gubbins.c -fPIC -DPIC -o .libs/gubbins.o /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 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 branch_sequences.c -o branch_sequences.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 -fPIC -DPIC -o .libs/parse_phylip.o /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 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 phylip_of_snp_sites.c -fPIC -DPIC -o .libs/phylip_of_snp_sites.o /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 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 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 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 parse_phylip.c -o parse_phylip.o >/dev/null 2>&1 /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 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 /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 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 /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 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 tree_statistics.c -fPIC -DPIC -o .libs/tree_statistics.o /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 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 /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 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 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 tree_scaling.c -o tree_scaling.o >/dev/null 2>&1 /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 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 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 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 /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 -fstack-protector-strong -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 -j5 check "TESTSUITEFLAGS=-j5 --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:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) 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 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/run_gubbins.py -> build/lib/gubbins copying gubbins/__init__.py -> build/lib/gubbins copying gubbins/PreProcessFasta.py -> build/lib/gubbins copying gubbins/common.py -> build/lib/gubbins copying gubbins/ValidateFastaAlignment.py -> build/lib/gubbins creating build/lib/gubbins/tests copying gubbins/tests/test_validate_fasta_input.py -> build/lib/gubbins/tests copying gubbins/tests/test_treebuilders.py -> build/lib/gubbins/tests copying gubbins/tests/test_converging_recombinations.py -> build/lib/gubbins/tests copying gubbins/tests/test_utils.py -> build/lib/gubbins/tests copying gubbins/tests/test_dependencies.py -> build/lib/gubbins/tests copying gubbins/tests/test_validate_starting_tree.py -> build/lib/gubbins/tests copying gubbins/tests/test_alignment_python_methods.py -> build/lib/gubbins/tests copying gubbins/tests/__init__.py -> build/lib/gubbins/tests copying gubbins/tests/test_python_scripts.py -> build/lib/gubbins/tests copying gubbins/tests/test_tree_methods.py -> build/lib/gubbins/tests copying gubbins/tests/test_pre_process_fasta.py -> build/lib/gubbins/tests running build_scripts creating build/scripts-3.12 copying and adjusting scripts/generate_ska_alignment.py -> build/scripts-3.12 copying and adjusting scripts/extract_gubbins_clade.py -> build/scripts-3.12 copying and adjusting scripts/mask_gubbins_aln.py -> build/scripts-3.12 copying and adjusting scripts/gubbins_alignment_checker.py -> build/scripts-3.12 copying and adjusting scripts/generate_files_for_clade_analysis.py -> build/scripts-3.12 copying and adjusting scripts/count_recombinations_per_gene.py -> build/scripts-3.12 copying and adjusting scripts/extract_recombinant_sequences.py -> build/scripts-3.12 copying ../R/scripts/plot_gubbins.R -> build/scripts-3.12 changing mode of build/scripts-3.12/generate_ska_alignment.py from 644 to 755 changing mode of build/scripts-3.12/extract_gubbins_clade.py from 644 to 755 changing mode of build/scripts-3.12/mask_gubbins_aln.py from 644 to 755 changing mode of build/scripts-3.12/gubbins_alignment_checker.py from 644 to 755 changing mode of build/scripts-3.12/generate_files_for_clade_analysis.py from 644 to 755 changing mode of build/scripts-3.12/count_recombinations_per_gene.py from 644 to 755 changing mode of build/scripts-3.12/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 creating ../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_treebuilders.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/test_utils.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/tests/test_validate_starting_tree.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/__init__.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_tree_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/pyjar.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/run_gubbins.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/PreProcessFasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/common.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/ValidateFastaAlignment.py -> ../debian/gubbins/usr/share/gubbins/gubbins byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/treebuilders.py to treebuilders.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/utils.py to utils.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_fasta_input.py to test_validate_fasta_input.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_treebuilders.py to test_treebuilders.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_converging_recombinations.py to test_converging_recombinations.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_utils.py to test_utils.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_dependencies.py to test_dependencies.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_starting_tree.py to test_validate_starting_tree.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_alignment_python_methods.py to test_alignment_python_methods.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/__init__.py to __init__.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_python_scripts.py to test_python_scripts.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_tree_methods.py to test_tree_methods.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_pre_process_fasta.py to test_pre_process_fasta.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/pyjar.py to pyjar.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/run_gubbins.py to run_gubbins.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/__init__.py to __init__.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/PreProcessFasta.py to PreProcessFasta.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/common.py to common.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/ValidateFastaAlignment.py to ValidateFastaAlignment.cpython-312.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-3.12/plot_gubbins.R -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/count_recombinations_per_gene.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/extract_recombinant_sequences.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/extract_gubbins_clade.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/mask_gubbins_aln.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/generate_ska_alignment.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/gubbins_alignment_checker.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/generate_files_for_clade_analysis.py -> ../debian/gubbins/usr/share/gubbins changing mode of ../debian/gubbins/usr/share/gubbins/plot_gubbins.R to 775 changing mode of ../debian/gubbins/usr/share/gubbins/count_recombinations_per_gene.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/extract_recombinant_sequences.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/mask_gubbins_aln.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/generate_ska_alignment.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/generate_files_for_clade_analysis.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 gzclose 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 gzopen 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' in '../gubbins_3.4-1_i386.deb'. dpkg-deb: building package 'gubbins-dbgsym' in '../gubbins-dbgsym_3.4-1_i386.deb'. dpkg-genbuildinfo --build=binary -O../gubbins_3.4-1_i386.buildinfo dpkg-genchanges --build=binary -O../gubbins_3.4-1_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: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/24066/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/24066/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/24066 and its subdirectories I: Current time: Sun Jan 4 10:41:20 +14 2026 I: pbuilder-time-stamp: 1767472880