I: pbuilder: network access will be disabled during build I: Current time: Sat Aug 24 08:47:23 +14 2024 I: pbuilder-time-stamp: 1724438843 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 [busco_5.5.0-2.dsc] I: copying [./busco_5.5.0.orig.tar.gz] I: copying [./busco_5.5.0-2.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Dec 19 16:28:54 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./busco_5.5.0-2.dsc: no acceptable signature found dpkg-source: info: extracting busco in busco-5.5.0 dpkg-source: info: unpacking busco_5.5.0.orig.tar.gz dpkg-source: info: unpacking busco_5.5.0-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-and-disable-tests.patch dpkg-source: info: applying find-bbmap-instead-of-bbtools.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/30669/tmp/hooks/D01_modify_environment starting debug: Running on infom07-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 Aug 23 18:47 /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/30669/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/30669/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=2a21536d924445ac9e689c11683cdc52 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=30669 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.7I566lrp/pbuilderrc_qtXV --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.7I566lrp/b2 --logfile b2/build.log busco_5.5.0-2.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 6.1.0-23-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.99-1 (2024-07-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/30669/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, python3-all, python3-biopython, python3-pandas, python3-setuptools, hmmer dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19717 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 python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on hmmer; however: Package hmmer is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{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} hmmer{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libdebhelper-perl{a} libdeflate0{a} libdivsufsort3{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} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{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} po-debconf{a} python3{a} python3-all{a} python3-autocommand{a} python3-biopython{a} python3-cairo{a} python3-chardet{a} python3-dateutil{a} python3-freetype{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pkg-resources{a} python3-reportlab{a} python3-rlpycairo{a} python3-setuptools{a} python3-six{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra krb5-locales libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-bottleneck python3-bs4 python3-html5lib python3-jinja2 python3-lxml python3-matplotlib python3-numexpr python3-odf python3-olefile python3-openpyxl python3-scipy python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 124 newly installed, 0 to remove and 0 not upgraded. Need to get 69.8 MB of archives. After unpacking 265 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 libpython3.12-minimal i386 3.12.5-4 [812 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.2-1 [107 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 python3.12-minimal i386 3.12.5-4 [2242 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.12.5-1 [26.7 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.1-1 [23.1 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-3 [9432 B] Get: 12 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 libtirpc3t64 i386 1.3.4+ds-1.3 [90.2 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libnsl2 i386 1.3.0-3+b2 [42.4 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-5 [173 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libpython3.12-stdlib i386 3.12.5-4 [1957 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 python3.12 i386 3.12.5-4 [667 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.12.5-1 [9588 B] Get: 22 http://deb.debian.org/debian unstable/main i386 python3 i386 3.12.5-1 [27.6 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 sgml-base all 1.31 [15.4 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3 [42.9 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-7 [101 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 man-db i386 2.12.1-3 [1422 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-2 [723 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-7 [517 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 45 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.191-2 [194 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5 [9550 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg-3+b1 [704 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 debhelper all 13.20 [915 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 python3-more-itertools all 10.3.0-1 [62.0 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 python3-inflect all 7.3.1-1 [42.2 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 59 http://deb.debian.org/debian unstable/main i386 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 python3-pkg-resources all 73.0.1-1 [212 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 python3-zipp all 3.20.0-1 [10.5 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 python3-setuptools all 73.0.1-1 [748 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 dh-python all 6.20240603 [109 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 libfontenc1 i386 1:1.1.8-1 [23.1 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b4 [309 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 libpng16-16t64 i386 1.6.43-5 [286 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 libfreetype6 i386 2.13.2+dfsg-1+b4 [449 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 x11-common all 1:7.7+23.1 [216 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 xfonts-utils i386 1:7.7+6 [95.2 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 74 http://deb.debian.org/debian unstable/main i386 fontconfig-config i386 2.15.0-1.1 [317 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 libdivsufsort3 i386 2.0.1-6 [48.9 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 hmmer i386 3.4+dfsg-2 [1094 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 libfontconfig1 i386 2.15.0-1.1 [401 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 libpixman-1-0 i386 0.42.2-1+b1 [555 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 libxau6 i386 1:1.0.9-1+b1 [18.5 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 libxdmcp6 i386 1:1.1.2-3+b1 [24.8 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 libxcb1 i386 1.17.0-2 [148 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 libx11-6 i386 2:1.8.7-1+b1 [822 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 libxcb-render0 i386 1.17.0-2 [116 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 libxcb-shm0 i386 1.17.0-2 [105 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 libxrender1 i386 1:0.9.10-1.1+b1 [28.8 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 libcairo2 i386 1.18.0-3+b1 [588 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.21-1 [48.0 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 libfribidi0 i386 1.0.15-1 [72.4 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.2.0-3 [735 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 libglib2.0-0t64 i386 2.81.2-1 [1568 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 libgraphite2-3 i386 1.3.14-2 [77.7 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 libharfbuzz0b i386 9.0.0-1 [500 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 libimagequant0 i386 2.18.0-1+b1 [35.9 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 libjbig0 i386 2.1-6.1+b1 [31.8 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 libjpeg62-turbo i386 1:2.1.5-3 [169 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 liblapack3 i386 3.12.0-3 [2167 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 liblcms2-2 i386 2.14-2+b1 [165 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 liblerc4 i386 4.0.0+ds-4+b1 [180 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 libopenjp2-7 i386 2.5.0-2+b3 [197 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 libraqm0 i386 0.10.1-1+b1 [14.7 kB] Get: 104 http://deb.debian.org/debian unstable/main i386 libsharpyuv0 i386 1.4.0-0.1 [113 kB] Get: 105 http://deb.debian.org/debian unstable/main i386 libwebp7 i386 1.4.0-0.1 [318 kB] Get: 106 http://deb.debian.org/debian unstable/main i386 libtiff6 i386 4.5.1+git230720-5 [339 kB] Get: 107 http://deb.debian.org/debian unstable/main i386 libwebpdemux2 i386 1.4.0-0.1 [111 kB] Get: 108 http://deb.debian.org/debian unstable/main i386 libwebpmux3 i386 1.4.0-0.1 [125 kB] Get: 109 http://deb.debian.org/debian unstable/main i386 python3-all i386 3.12.5-1 [1044 B] Get: 110 http://deb.debian.org/debian unstable/main i386 python3-numpy i386 1:1.26.4+ds-11 [4299 kB] Get: 111 http://deb.debian.org/debian unstable/main i386 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 112 http://deb.debian.org/debian unstable/main i386 python3-pil i386 10.4.0-1 [503 kB] Get: 113 http://deb.debian.org/debian unstable/main i386 python3-cairo i386 1.26.1-1+b1 [116 kB] Get: 114 http://deb.debian.org/debian unstable/main i386 python3-freetype all 2.4.0-2 [78.6 kB] Get: 115 http://deb.debian.org/debian unstable/main i386 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 116 http://deb.debian.org/debian unstable/main i386 python3-reportlab all 4.2.2-1 [1150 kB] Get: 117 http://deb.debian.org/debian unstable/main i386 xml-core all 0.19 [20.1 kB] Get: 118 http://deb.debian.org/debian unstable/main i386 w3c-sgml-lib all 1.3-3 [273 kB] Get: 119 http://deb.debian.org/debian unstable/main i386 python3-biopython i386 1.83+dfsg1-3+b1 [1602 kB] Get: 120 http://deb.debian.org/debian unstable/main i386 python3-six all 1.16.0-7 [16.4 kB] Get: 121 http://deb.debian.org/debian unstable/main i386 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 122 http://deb.debian.org/debian unstable/main i386 python3-tz all 2024.1-2 [30.9 kB] Get: 123 http://deb.debian.org/debian unstable/main i386 python3-pandas-lib i386 2.2.2+dfsg-4+b1 [3998 kB] Get: 124 http://deb.debian.org/debian unstable/main i386 python3-pandas all 2.2.2+dfsg-4 [3095 kB] Fetched 69.8 MB in 1s (92.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19717 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.5-4_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.5-4) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.2-1_i386.deb ... Unpacking libexpat1:i386 (2.6.2-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.5-4_i386.deb ... Unpacking python3.12-minimal (3.12.5-4) ... Setting up libpython3.12-minimal:i386 (3.12.5-4) ... Setting up libexpat1:i386 (2.6.2-1) ... Setting up python3.12-minimal (3.12.5-4) ... 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 ... 20037 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.5-1_i386.deb ... 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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) ... Selecting previously unselected package libnsl2:i386. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_i386.deb ... Unpacking libnsl2:i386 (1.3.0-3+b2) ... 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_3.12.5-4_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.5-4) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.5-4_i386.deb ... Unpacking python3.12 (3.12.5-4) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../17-libpython3-stdlib_3.12.5-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.12.5-1) ... Setting up python3-minimal (3.12.5-1) ... 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 ... 21109 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.5-1_i386.deb ... Unpacking python3 (3.12.5-1) ... Selecting previously unselected package sgml-base. 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Setting up libgraphite2-3:i386 (1.3.14-2) ... Setting up liblcms2-2:i386 (2.14-2+b1) ... Setting up libpixman-1-0:i386 (0.42.2-1+b1) ... Setting up libsharpyuv0:i386 (1.4.0-0.1) ... Setting up libxau6:i386 (1:1.0.9-1+b1) ... Setting up libxdmcp6:i386 (1:1.1.2-3+b1) ... Setting up libkeyutils1:i386 (1.6.3-3) ... Setting up libxcb1:i386 (1.17.0-2) ... Setting up libicu72:i386 (72.1-5) ... Setting up liblerc4:i386 (4.0.0+ds-4+b1) ... Setting up bsdextrautils (2.40.2-7) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libxcb-render0:i386 (1.17.0-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:i386 (1.1.0-2+b4) ... Setting up libmagic1t64:i386 (1:5.45-3) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libdeflate0:i386 (1.21-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libxcb-shm0:i386 (1.17.0-2) ... Setting up libcom-err2:i386 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libjbig0:i386 (2.1-6.1+b1) ... Setting up libelf1t64:i386 (0.191-2) ... Setting up libkrb5support0:i386 (1.21.3-3) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Aug 23 18:47:54 UTC 2024. Universal Time is now: Fri Aug 23 18:47:54 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:i386 (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:i386 (2.81.2-1) ... No schema files found: doing nothing. Setting up libblas3:i386 (3.12.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libjpeg62-turbo:i386 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... 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Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:i386 (3.12.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libxrender1:i386 (1:0.9.10-1.1+b1) ... Setting up libtool (2.4.7-7) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:i386 (1.4.0-0.1) ... Setting up libxext6:i386 (2:1.3.4-1+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libfreetype6:i386 (2.13.2+dfsg-1+b4) ... Setting up libgssapi-krb5-2:i386 (1.21.3-3) ... Setting up libreadline8t64:i386 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up hmmer (3.4+dfsg-2) ... Setting up libharfbuzz0b:i386 (9.0.0-1) ... Setting up libfontconfig1:i386 (2.15.0-1.1) ... Setting up libtirpc3t64:i386 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.12.1-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:i386 (1.18.0-3+b1) ... Setting up libraqm0:i386 (0.10.1-1+b1) ... Setting up libnsl2:i386 (1.3.0-3+b2) ... Setting up libpython3.12-stdlib:i386 (3.12.5-4) ... Setting up python3.12 (3.12.5-4) ... Setting up debhelper (13.20) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libpython3-stdlib:i386 (3.12.5-1) ... Setting up python3 (3.12.5-1) ... Setting up python3-zipp (3.20.0-1) ... Setting up python3-freetype (2.4.0-2) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-tz (2024.1-2) ... Setting up python3-six (1.16.0-7) ... Setting up python3-pil:i386 (10.4.0-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-more-itertools (10.3.0-1) ... Setting up python3-cairo (1.26.1-1+b1) ... Setting up python3-jaraco.functools (4.0.2-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-all (3.12.5-1) ... Setting up python3-inflect (7.3.1-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-pkg-resources (73.0.1-1) ... Setting up python3-setuptools (73.0.1-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up python3-reportlab (4.2.2-1) ... Setting up dh-python (6.20240603) ... Setting up python3-pandas-lib:i386 (2.2.2+dfsg-4+b1) ... Setting up python3-pandas (2.2.2+dfsg-4) ... Processing triggers for libc-bin (2.39-7) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.83+dfsg1-3+b1) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/30669/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/30669/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/busco-5.5.0/ && 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 > ../busco_5.5.0-2_source.changes dpkg-buildpackage: info: source package busco dpkg-buildpackage: info: source version 5.5.0-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Komolehin Israel Timilehin dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py clean 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/busco-5.5.0' dh_auto_test -- --test-custom --test-args '{interpreter} -m unittest tests/unittest_runner.py -v' I: pybuild base:311: cd /build/reproducible-path/busco-5.5.0/.pybuild/cpython3_3.12/build; python3.12 -m unittest tests/unittest_runner.py -v /build/reproducible-path/busco-5.5.0/.pybuild/cpython3_3.12/build/busco/busco_tools/miniprot.py:200: SyntaxWarning: invalid escape sequence '\*' self.ata_seq = re.sub("\*", "", sta_seq.upper()) /build/reproducible-path/busco-5.5.0/.pybuild/cpython3_3.12/build/busco/BuscoPlacer.py:211: SyntaxWarning: invalid escape sequence '\[' "[^0-9][0-9]*:[0-9]*[^0-9]{0,1}[0-9]*[^0-9]{0,2}[0-9]*\[%s\]" test_cmdline_options_all_long (tests.unittests.run_BUSCO_unittests.TestParams.test_cmdline_options_all_long) ... ok test_cmdline_options_all_short (tests.unittests.run_BUSCO_unittests.TestParams.test_cmdline_options_all_short) ... ok test_cmdline_options_short_minimum (tests.unittests.run_BUSCO_unittests.TestParams.test_cmdline_options_short_minimum) ... ok test_command_line_cpu_type (tests.unittests.run_BUSCO_unittests.TestParams.test_command_line_cpu_type) ... ok test_command_line_evalue_type (tests.unittests.run_BUSCO_unittests.TestParams.test_command_line_evalue_type) ... ok test_command_line_limit_type (tests.unittests.run_BUSCO_unittests.TestParams.test_command_line_limit_type) ... ok test_help_long (tests.unittests.run_BUSCO_unittests.TestParams.test_help_long) ... ok test_help_short (tests.unittests.run_BUSCO_unittests.TestParams.test_help_short) ... ok test_version_long (tests.unittests.run_BUSCO_unittests.TestParams.test_version_long) ... ok test_version_short (tests.unittests.run_BUSCO_unittests.TestParams.test_version_short) ... ok test_config_main_configured (tests.unittests.ConfigManager_unittests.TestConfigManager.test_config_main_configured) ... ok test_config_main_validated (tests.unittests.ConfigManager_unittests.TestConfigManager.test_config_main_validated) ... ok test_get_config_from_env (tests.unittests.ConfigManager_unittests.TestConfigManager.test_get_config_from_env) ... ok test_get_config_from_params (tests.unittests.ConfigManager_unittests.TestConfigManager.test_get_config_from_params) ... ok test_autoconfig_init_adds_specific_parameters (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_autoconfig_init_adds_specific_parameters) ... ok test_autoconfig_init_calls_super (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_autoconfig_init_calls_super) ... ok test_autoconfig_init_creates_paths (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_autoconfig_init_creates_paths) ... ok test_autoconfig_init_downloads_lineage (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_autoconfig_init_downloads_lineage) ... ok test_autoconfig_init_loads_lineage_config (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_autoconfig_init_loads_lineage_config) ... ok test_autoconfig_init_propagates_mainconfig (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_autoconfig_init_propagates_mainconfig) ... 2024-08-24 08:49:34 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. ok test_autoconfig_init_sets_results_dirname (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_autoconfig_init_sets_results_dirname) ... ok test_autolineage_create_path_method_calls_parent (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_autolineage_create_path_method_calls_parent) ... 2024-08-24 08:49:34 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. ok test_batch_mode_false_with_error (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_batch_mode_false_with_error) ... ok test_batch_mode_false_with_file (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_batch_mode_false_with_file) ... ok test_batch_mode_true (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_batch_mode_true) ... ok test_catch_disallowed_keys (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_catch_disallowed_keys) ... 2024-08-24 08:49:34 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-08-24 08:49:34 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-08-24 08:49:34 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-08-24 08:49:34 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-08-24 08:49:34 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-08-24 08:49:34 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-08-24 08:49:34 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-08-24 08:49:34 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-08-24 08:49:34 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-08-24 08:49:34 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-08-24 08:49:34 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-08-24 08:49:34 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. ok test_check_lineage_present_false (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_check_lineage_present_false) ... 2024-08-24 08:49:34 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. ok test_check_lineage_present_true_with_dataset_version_correct (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_check_lineage_present_true_with_dataset_version_correct) ... ok test_check_lineage_present_true_with_dataset_version_mismatch (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_check_lineage_present_true_with_dataset_version_mismatch) ... ok test_check_lineage_present_true_with_invalid_dataset_version (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_check_lineage_present_true_with_invalid_dataset_version) ... ok test_check_lineage_present_true_with_odb_missing (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_check_lineage_present_true_with_odb_missing) ... ok test_config_auto_lineage_both_selected_warning (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_config_auto_lineage_both_selected_warning) ... ok test_config_auto_lineage_dataset_specified_warning (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_config_auto_lineage_dataset_specified_warning) ... ok test_config_auto_lineage_none_selected_no_lineage_warning (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_config_auto_lineage_none_selected_no_lineage_warning) ... ok test_config_auto_lineage_settings (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_config_auto_lineage_settings) ... ok test_config_default_params (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_config_default_params) ... ok test_config_structure (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_config_structure) ... 2024-08-24 08:49:34 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. ok test_config_update_args_bool (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_config_update_args_bool) ... 2024-08-24 08:49:34 INFO: Quiet mode selected. All subsequent INFO log messages to stdout suppressed. Detailed log still available in logs/busco.log ok test_config_update_args_nonbool (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_config_update_args_nonbool) ... ok test_create_required_paths (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_create_required_paths) ... ok test_downloader_initialized (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_downloader_initialized) ... ok test_evalue_default (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_evalue_default) ... ok test_evalue_nondefault (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_evalue_nondefault) ... ok test_expand_all_paths_hmmsearch (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_expand_all_paths_hmmsearch) ... ok test_expand_all_paths_relative_path_current_dir (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_expand_all_paths_relative_path_current_dir) ... ok test_expand_all_paths_relative_path_parent_dir (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_expand_all_paths_relative_path_parent_dir) ... ok test_expand_all_paths_tilde (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_expand_all_paths_tilde) ... ok test_limit_value_out_of_range (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_limit_value_out_of_range) ... ok test_limit_value_within_range (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_limit_value_within_range) ... ok test_log_config (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_log_config) ... ok test_mandatory_keys_check_log (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_mandatory_keys_check_log) ... ok test_mandatory_keys_check_missing_param_in (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_mandatory_keys_check_missing_param_in) ... ok test_mandatory_keys_check_missing_param_mode (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_mandatory_keys_check_missing_param_mode) ... ok test_mandatory_keys_check_missing_param_out (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_mandatory_keys_check_missing_param_out) ... ok test_out_value_check_invalid (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_out_value_check_invalid) ... ok test_out_value_check_valid (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_out_value_check_valid) ... ok test_previous_run_check_with_existing_run_and_restart (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_previous_run_check_with_existing_run_and_restart) ... ok test_previous_run_check_with_existing_run_no_force (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_previous_run_check_with_existing_run_no_force) ... ok test_previous_run_check_with_existing_run_with_force_and_log (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_previous_run_check_with_existing_run_with_force_and_log) ... ok test_previous_run_check_without_existing_run (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_previous_run_check_without_existing_run) ... ok test_previous_run_check_without_existing_run_and_restart (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_previous_run_check_without_existing_run_and_restart) ... ok test_propagate_config (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_propagate_config) ... ok test_read_config_file (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_read_config_file) ... ok test_read_config_file_duplicateerror (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_read_config_file_duplicateerror) ... ok test_read_config_file_ioerror (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_read_config_file_ioerror) ... ok test_read_config_file_parseerror (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_read_config_file_parseerror) ... ok test_required_input_exists_false (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_required_input_exists_false) ... ok test_set_results_dirname (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_set_results_dirname) ... ok test_validation (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_validation) ... ok test_cleanup_disused_runs (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_cleanup_disused_runs) ... ok test_evaluate_first_order_tiebreak (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_evaluate_first_order_tiebreak) ... ok test_evaluate_multiple_runners (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_evaluate_multiple_runners) ... ok test_evaluate_second_order_tiebreak (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_evaluate_second_order_tiebreak) ... ok test_evaluate_single_runner (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_evaluate_single_runner) ... ok test_evaluate_third_order_tiebreak (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_evaluate_third_order_tiebreak) ... ok test_get_best_match_lineage (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_get_best_match_lineage) ... ok test_init_autolineage (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_init_autolineage) ... ok test_record_results_first_run (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_record_results_first_run) ... ok test_record_results_multiple_runs (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_record_results_multiple_runs) ... ok test_run_auto_selector_lineage_lists_no_virus (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_run_auto_selector_lineage_lists_no_virus) ... ok test_run_lineages_initializes_BuscoConfigAuto (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_run_lineages_initializes_BuscoConfigAuto) ... ok test_run_lineages_initializes_BuscoRunner (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_run_lineages_initializes_BuscoRunner) ... skipped 'Skipping for now, ends with Mock iterable error' test_run_lineages_returns_runners (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_run_lineages_returns_runners) ... ok test_run_lineages_runs_analysis (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_run_lineages_runs_analysis) ... ok test_init_eukaryota_augustus_checks_filetype (tests.unittests.GenomeAnalysis_unittests.TestConfigManager.test_init_eukaryota_augustus_checks_filetype) ... ok test_init_tools_eukaryota_augustus (tests.unittests.GenomeAnalysis_unittests.TestConfigManager.test_init_tools_eukaryota_augustus) ... ok test_init_tools_eukaryota_metaeuk (tests.unittests.GenomeAnalysis_unittests.TestConfigManager.test_init_tools_eukaryota_metaeuk) ... ok test_init_tools_prokaryota (tests.unittests.GenomeAnalysis_unittests.TestConfigManager.test_init_tools_prokaryota) ... ok test_run_analysis_metaeuk (tests.unittests.GenomeAnalysis_unittests.TestConfigManager.test_run_analysis_metaeuk) ... ok test_auto_select_lineage_call_function_gets_lineage_dataset (tests.unittests.BuscoRunner_unittests.TestAutoLineage.test_auto_select_lineage_call_function_gets_lineage_dataset) ... ok test_auto_select_lineage_call_function_initializes_asl (tests.unittests.BuscoRunner_unittests.TestAutoLineage.test_auto_select_lineage_call_function_initializes_asl) ... ok test_auto_select_lineage_call_function_returns_lineage_dataset (tests.unittests.BuscoRunner_unittests.TestAutoLineage.test_auto_select_lineage_call_function_returns_lineage_dataset) ... ok test_auto_select_lineage_call_function_returns_parent (tests.unittests.BuscoRunner_unittests.TestAutoLineage.test_auto_select_lineage_call_function_returns_parent) ... ok test_auto_select_lineage_call_function_runs_asl (tests.unittests.BuscoRunner_unittests.TestAutoLineage.test_auto_select_lineage_call_function_runs_asl) ... ok test_auto_select_lineage_call_function_selects_runner (tests.unittests.BuscoRunner_unittests.TestAutoLineage.test_auto_select_lineage_call_function_selects_runner) ... ok test_config_set_parent_dataset_if_not_virus (tests.unittests.BuscoRunner_unittests.TestAutoLineage.test_config_set_parent_dataset_if_not_virus) ... ok test_config_updated_if_lineage_missing (tests.unittests.BuscoRunner_unittests.TestAutoLineage.test_config_updated_if_lineage_missing) ... ok ---------------------------------------------------------------------- Ran 97 tests in 0.976s OK (skipped=1) make[1]: Leaving directory '/build/reproducible-path/busco-5.5.0' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/busco/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/busco-5.5.0/debian/busco /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() /usr/lib/python3.12/dist-packages/busco/busco_tools/miniprot.py:200: SyntaxWarning: invalid escape sequence '\*' /usr/lib/python3.12/dist-packages/busco/BuscoPlacer.py:211: SyntaxWarning: invalid escape sequence '\[' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'busco' in '../busco_5.5.0-2_i386.deb'. dpkg-genbuildinfo --build=binary -O../busco_5.5.0-2_i386.buildinfo dpkg-genchanges --build=binary -O../busco_5.5.0-2_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/30669/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/30669/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/30669 and its subdirectories I: Current time: Sat Aug 24 08:49:45 +14 2024 I: pbuilder-time-stamp: 1724438985