Sun Apr 23 05:14:03 UTC 2023 I: starting to build busco/bookworm/amd64 on jenkins on '2023-04-23 05:13'
Sun Apr 23 05:14:03 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_5/590/console.log
Sun Apr 23 05:14:03 UTC 2023 I: Downloading source for bookworm/busco=5.4.4-1
--2023-04-23 05:14:03-- http://cdn-fastly.deb.debian.org/debian/pool/main/b/busco/busco_5.4.4-1.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 1439 (1.4K) [text/prs.lines.tag]
Saving to: ‘busco_5.4.4-1.dsc’
0K . 100% 60.1M=0s
2023-04-23 05:14:04 (60.1 MB/s) - ‘busco_5.4.4-1.dsc’ saved [1439/1439]
Sun Apr 23 05:14:04 UTC 2023 I: busco_5.4.4-1.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: busco
Binary: busco
Architecture: any
Version: 5.4.4-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://gitlab.com/ezlab/busco
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/busco
Vcs-Git: https://salsa.debian.org/med-team/busco.git
Testsuite: autopkgtest
Testsuite-Triggers: python3-all, quilt
Build-Depends: debhelper-compat (= 13), dh-python, python3-all, python3-biopython <!nocheck>, python3-pandas <!nocheck>, python3-setuptools, hmmer
Package-List:
busco deb science optional arch=any
Checksums-Sha1:
c68a8ba7c21176c8fa7222c4165a43e7752f9767 386069 busco_5.4.4.orig.tar.gz
e433c9d6cd85f4e8a333a405edef83a220b957a8 7884 busco_5.4.4-1.debian.tar.xz
Checksums-Sha256:
91bbbcfd7838e86efa43f54f54515c44f1d5abaa19a6ad2ecb68db1fa9415aaf 386069 busco_5.4.4.orig.tar.gz
1e30f1e3097588e13af0f451158bd3378a177732c1c04afc66a5771f828fe99b 7884 busco_5.4.4-1.debian.tar.xz
Files:
019b6535ff5bfbf9bf7d4a32fca4f918 386069 busco_5.4.4.orig.tar.gz
ae7201a129004b5c0f5a4e58f214b52b 7884 busco_5.4.4-1.debian.tar.xz
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Sun Apr 23 05:14:04 UTC 2023 I: Checking whether the package is not for us
Sun Apr 23 05:14:04 UTC 2023 I: Starting 1st build on remote node ionos11-amd64.debian.net.
Sun Apr 23 05:14:04 UTC 2023 I: Preparing to do remote build '1' on ionos11-amd64.debian.net.
Sun Apr 23 05:18:31 UTC 2023 I: Deleting $TMPDIR on ionos11-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sat Apr 22 17:14:06 -12 2023
I: pbuilder-time-stamp: 1682226846
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [busco_5.4.4-1.dsc]
I: copying [./busco_5.4.4.orig.tar.gz]
I: copying [./busco_5.4.4-1.debian.tar.xz]
I: Extracting source
gpgv: Signature made Fri Dec 30 23:16:56 2022 -12
gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./busco_5.4.4-1.dsc: no acceptable signature found
dpkg-source: info: extracting busco in busco-5.4.4
dpkg-source: info: unpacking busco_5.4.4.orig.tar.gz
dpkg-source: info: unpacking busco_5.4.4-1.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/2674753/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15'
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='ce2bbccffba4439a8fc773c73d51d90e'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='2674753'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.oepsScTz/pbuilderrc_WEes --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oepsScTz/b1 --logfile b1/build.log busco_5.4.4-1.dsc'
SUDO_GID='111'
SUDO_UID='106'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://78.137.99.97:3128'
I: uname -a
Linux ionos11-amd64 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux
I: ls -l /bin
total 5632
-rwxr-xr-x 1 root root 1265648 Feb 12 08:05 bash
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 44016 Sep 20 2022 cat
-rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 72752 Sep 20 2022 chown
-rwxr-xr-x 1 root root 151152 Sep 20 2022 cp
-rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash
-rwxr-xr-x 1 root root 121904 Sep 20 2022 date
-rwxr-xr-x 1 root root 89240 Sep 20 2022 dd
-rwxr-xr-x 1 root root 102200 Sep 20 2022 df
-rwxr-xr-x 1 root root 151344 Sep 20 2022 dir
-rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname
-rwxr-xr-x 1 root root 43856 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep
-rwxr-xr-x 1 root root 35664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep
-rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt
-rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount
-rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname
-rwxr-xr-x 1 root root 72824 Sep 20 2022 ln
-rwxr-xr-x 1 root root 53024 Mar 23 00:40 login
-rwxr-xr-x 1 root root 151344 Sep 20 2022 ls
-rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk
-rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 59712 Mar 22 22:02 more
-rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount
-rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint
-rwxr-xr-x 1 root root 142968 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Feb 12 08:05 rbash -> bash
-rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 72752 Sep 20 2022 rm
-rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 27560 Nov 2 04:31 run-parts
-rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed
lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash
-rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 85008 Sep 20 2022 stty
-rwsr-xr-x 1 root root 72000 Mar 22 22:02 su
-rwxr-xr-x 1 root root 39824 Sep 20 2022 sync
-rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar
-rwxr-xr-x 1 root root 14520 Nov 2 04:31 tempfile
-rwxr-xr-x 1 root root 109616 Sep 20 2022 touch
-rwxr-xr-x 1 root root 35664 Sep 20 2022 true
-rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server
-rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount
-rwxr-xr-x 1 root root 43888 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/2674753/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), dh-python, 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 ... 19596 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on dh-python; however:
Package dh-python is not installed.
pbuilder-satisfydepends-dummy depends on 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} 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} libbsd0{a} libdebhelper-perl{a} libdeflate0{a} libdivsufsort3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} liblapack3{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1{a} libopenjp2-7{a} libpipeline1{a} libpng16-16{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libraqm0{a} libreadline8{a} libsub-override-perl{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} po-debconf{a} python3{a} python3-all{a} python3-biopython{a} python3-dateutil{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-numpy{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pkg-resources{a} python3-renderpm{a} python3-reportlab{a} python3-reportlab-accel{a} python3-setuptools{a} python3-six{a} python3-tz{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{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 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-numba python3-numexpr python3-odf python3-olefile python3-openpyxl python3-scipy python3-tables shared-mime-info wget xdg-user-dirs
0 packages upgraded, 96 newly installed, 0 to remove and 0 not upgraded.
Need to get 62.9 MB of archives. After unpacking 239 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB]
Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB]
Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB]
Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB]
Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB]
Get: 6 http://deb.debian.org/debian bookworm/main amd64 mailcap all 3.70+nmu1 [32.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main amd64 mime-support all 3.66 [10.9 kB]
Get: 8 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB]
Get: 9 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB]
Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB]
Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB]
Get: 12 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B]
Get: 13 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB]
Get: 14 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB]
Get: 15 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 16 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB]
Get: 17 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB]
Get: 18 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB]
Get: 19 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB]
Get: 20 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get: 21 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB]
Get: 22 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB]
Get: 23 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB]
Get: 24 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB]
Get: 25 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB]
Get: 26 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB]
Get: 27 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 28 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 29 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB]
Get: 30 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 31 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB]
Get: 32 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 33 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 34 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get: 35 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 36 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 37 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB]
Get: 38 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB]
Get: 39 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get: 40 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB]
Get: 41 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB]
Get: 42 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 43 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 44 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB]
Get: 45 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-2 [76.2 kB]
Get: 46 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-2 [131 kB]
Get: 47 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB]
Get: 48 http://deb.debian.org/debian bookworm/main amd64 libfontenc1 amd64 1:1.1.4-1 [24.3 kB]
Get: 49 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB]
Get: 50 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB]
Get: 51 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-4 [399 kB]
Get: 52 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB]
Get: 53 http://deb.debian.org/debian bookworm/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get: 54 http://deb.debian.org/debian bookworm/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB]
Get: 55 http://deb.debian.org/debian bookworm/main amd64 fonts-urw-base35 all 20200910-7 [10.8 MB]
Get: 56 http://deb.debian.org/debian bookworm/main amd64 libdivsufsort3 amd64 2.0.1-5 [44.7 kB]
Get: 57 http://deb.debian.org/debian bookworm/main amd64 hmmer amd64 3.3.2+dfsg-1 [1153 kB]
Get: 58 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB]
Get: 59 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB]
Get: 60 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB]
Get: 61 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB]
Get: 62 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB]
Get: 63 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB]
Get: 64 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB]
Get: 65 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB]
Get: 66 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB]
Get: 67 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB]
Get: 68 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB]
Get: 69 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB]
Get: 70 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB]
Get: 71 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB]
Get: 72 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-1+b1 [189 kB]
Get: 73 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4.1 [10.6 kB]
Get: 74 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.1 [285 kB]
Get: 75 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-5 [316 kB]
Get: 76 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.1 [99.2 kB]
Get: 77 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.1 [109 kB]
Get: 78 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB]
Get: 79 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB]
Get: 80 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB]
Get: 81 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B]
Get: 82 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB]
Get: 83 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB]
Get: 84 http://deb.debian.org/debian bookworm/main amd64 python3-renderpm amd64 3.6.12-1+b1 [79.2 kB]
Get: 85 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab-accel amd64 3.6.12-1+b1 [38.6 kB]
Get: 86 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+b1 [472 kB]
Get: 87 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab all 3.6.12-1 [564 kB]
Get: 88 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB]
Get: 89 http://deb.debian.org/debian bookworm/main amd64 w3c-sgml-lib all 1.3-3 [273 kB]
Get: 90 http://deb.debian.org/debian bookworm/main amd64 python3-biopython amd64 1.80+dfsg-4+b1 [1593 kB]
Get: 91 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB]
Get: 92 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB]
Get: 93 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-3 [30.1 kB]
Get: 94 http://deb.debian.org/debian bookworm/main amd64 python3-pandas-lib amd64 1.5.3+dfsg-2 [3499 kB]
Get: 95 http://deb.debian.org/debian bookworm/main amd64 python3-pandas all 1.5.3+dfsg-2 [2885 kB]
Get: 96 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB]
Fetched 62.9 MB in 2s (29.9 MB/s)
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I: Building the package
I: Running cd /build/busco-5.4.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../busco_5.4.4-1_source.changes
dpkg-buildpackage: info: source package busco
dpkg-buildpackage: info: source version 5.4.4-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean --with python3 --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:240: python3.11 setup.py clean
'build/bdist.linux-x86_64' does not exist -- can't clean it
'build/scripts-3.11' does not exist -- can't clean it
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary
dh binary --with python3 --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:240: python3.11 setup.py config
dh_auto_build -O--buildsystem=pybuild
I: pybuild base:240: /usr/bin/python3 setup.py build
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/busco-5.4.4'
dh_auto_test -- --test-custom --test-args '{interpreter} -m unittest tests/unittest_runner.py -v'
I: pybuild base:240: cd /build/busco-5.4.4/.pybuild/cpython3_3.11/build; python3.11 -m unittest tests/unittest_runner.py -v
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) ... 2023-04-22 17:18:21 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) ... 2023-04-22 17:18:21 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) ... 2023-04-22 17:18:21 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.
2023-04-22 17:18:21 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.
2023-04-22 17:18:21 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.
2023-04-22 17:18:21 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.
2023-04-22 17:18:21 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.
2023-04-22 17:18:21 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.
2023-04-22 17:18:21 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.
2023-04-22 17:18:21 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.
2023-04-22 17:18:21 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.
2023-04-22 17:18:21 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.
2023-04-22 17:18:21 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.
2023-04-22 17:18:21 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) ... 2023-04-22 17:18:21 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) ... 2023-04-22 17:18:21 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) ... 2023-04-22 17:18:21 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 1.661s
OK (skipped=1)
make[1]: Leaving directory '/build/busco-5.4.4'
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:240: /usr/bin/python3 setup.py install --root /build/busco-5.4.4/debian/busco
/usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
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_5.4.4-1_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../busco_5.4.4-1_amd64.buildinfo
dpkg-genchanges --build=binary -O../busco_5.4.4-1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: including full source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/2674753 and its subdirectories
I: Current time: Sat Apr 22 17:18:30 -12 2023
I: pbuilder-time-stamp: 1682227110
Sun Apr 23 05:18:31 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net.
Sun Apr 23 05:18:31 UTC 2023 I: Preparing to do remote build '2' on ionos5-amd64.debian.net.
Sun Apr 23 05:20:11 UTC 2023 I: Deleting $TMPDIR on ionos5-amd64.debian.net.
Sun Apr 23 05:20:11 UTC 2023 I: busco_5.4.4-1_amd64.changes:
Format: 1.8
Date: Sat, 31 Dec 2022 16:40:11 +0530
Source: busco
Binary: busco
Architecture: amd64
Version: 5.4.4-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Description:
busco - benchmarking sets of universal single-copy orthologs
Changes:
busco (5.4.4-1) unstable; urgency=medium
.
* Team Upload.
* New upstream version 5.4.4
* Bump Standards-Version to 4.6.2 (no changes needed)
Checksums-Sha1:
9824618f8d37f6e2f828a530d4c89d962fe8b175 6813 busco_5.4.4-1_amd64.buildinfo
7b94e060521e70168f071a5e10d48af9a6f81f66 71788 busco_5.4.4-1_amd64.deb
Checksums-Sha256:
288f94574bc1cec607d68cc2035fe0020db07c985321905843b898b17685b6f8 6813 busco_5.4.4-1_amd64.buildinfo
98891e95d5baf338c3c14ac530f765c064634118e24d2c89b2c84aad3fe2a536 71788 busco_5.4.4-1_amd64.deb
Files:
71ddf2df994624843119db4d951c268d 6813 science optional busco_5.4.4-1_amd64.buildinfo
50c8e27a0d3a3df3da74214c5791c8b7 71788 science optional busco_5.4.4-1_amd64.deb
Sun Apr 23 05:20:13 UTC 2023 I: diffoscope 241 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.oepsScTz/busco_5.4.4-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.oepsScTz/busco_5.4.4-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.oepsScTz/busco_5.4.4-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.oepsScTz/b1/busco_5.4.4-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.oepsScTz/b2/busco_5.4.4-1_amd64.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call abc.DotChangesFile
## main (total time: 0.388s)
0.387s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.017s)
0.017s 12 calls diffoscope.comparators.binary.FilesystemFile
0.000s 10 calls abc.DotChangesFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Sun Apr 23 05:20:15 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists.
Sun Apr 23 05:20:15 UTC 2023 I: busco from bookworm built successfully and reproducibly on amd64.
Sun Apr 23 05:20:17 UTC 2023 I: Submitting .buildinfo files to external archives:
Sun Apr 23 05:20:17 UTC 2023 I: Submitting 8.0K b1/busco_5.4.4-1_amd64.buildinfo.asc
Sun Apr 23 05:20:18 UTC 2023 I: Submitting 8.0K b2/busco_5.4.4-1_amd64.buildinfo.asc
Sun Apr 23 05:20:19 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun Apr 23 05:20:19 UTC 2023 I: Done submitting .buildinfo files.
Sun Apr 23 05:20:19 UTC 2023 I: Removing signed busco_5.4.4-1_amd64.buildinfo.asc files:
removed './b1/busco_5.4.4-1_amd64.buildinfo.asc'
removed './b2/busco_5.4.4-1_amd64.buildinfo.asc'