Sun Mar 9 09:26:04 UTC 2025 I: starting to build pyensembl/unstable/armhf on jenkins on '2025-03-09 09:25'
Sun Mar 9 09:26:04 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_10/7650/console.log
Sun Mar 9 09:26:04 UTC 2025 I: Downloading source for unstable/pyensembl=2.3.13-2
--2025-03-09 09:26:04-- http://deb.debian.org/debian/pool/main/p/pyensembl/pyensembl_2.3.13-2.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2291 (2.2K) [text/prs.lines.tag]
Saving to: ‘pyensembl_2.3.13-2.dsc’
0K .. 100% 367M=0s
2025-03-09 09:26:05 (367 MB/s) - ‘pyensembl_2.3.13-2.dsc’ saved [2291/2291]
Sun Mar 9 09:26:05 UTC 2025 I: pyensembl_2.3.13-2.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: pyensembl
Binary: pyensembl
Architecture: all
Version: 2.3.13-2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://github.com/openvax/pyensembl
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/pyensembl
Vcs-Git: https://salsa.debian.org/med-team/pyensembl.git
Testsuite: autopkgtest, autopkgtest-pkg-pybuild
Testsuite-Triggers: python3-all, python3-pytest
Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-pandas, python3-numpy, python3-datacache, python3-serializable, python3-memoized-property, python3-gtfparse, python3-pytest <!nocheck>
Package-List:
pyensembl deb science optional arch=all
Checksums-Sha1:
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6f22e36bf3d779d62ea266696b5e6125be79cae147dfd1504a018164c90bd110 5448 pyensembl_2.3.13-2.debian.tar.xz
Files:
4c3aa9cc52f322844bbfa1caa4e14c53 60660 pyensembl_2.3.13.orig.tar.xz
7c3be861abe7a1ccc6d0b0572aabdc6d 5448 pyensembl_2.3.13-2.debian.tar.xz
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Sun Mar 9 09:26:05 UTC 2025 I: Checking whether the package is not for us
Sun Mar 9 09:26:05 UTC 2025 I: Starting 1st build on remote node wbq0-armhf-rb.debian.net.
Sun Mar 9 09:26:05 UTC 2025 I: Preparing to do remote build '1' on wbq0-armhf-rb.debian.net.
Sun Mar 9 09:31:33 UTC 2025 I: Deleting $TMPDIR on wbq0-armhf-rb.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sat Mar 8 21:26:14 -12 2025
I: pbuilder-time-stamp: 1741512374
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: Copying source file
I: copying [pyensembl_2.3.13-2.dsc]
I: copying [./pyensembl_2.3.13.orig.tar.xz]
I: copying [./pyensembl_2.3.13-2.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./pyensembl_2.3.13-2.dsc: unsupported subcommand
dpkg-source: info: extracting pyensembl in pyensembl-2.3.13
dpkg-source: info: unpacking pyensembl_2.3.13.orig.tar.xz
dpkg-source: info: unpacking pyensembl_2.3.13-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying skip-benchmark.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/23648/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='armhf'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='armhf'
IFS='
'
INVOCATION_ID='abaae089bd104f4ab9c7ded342a46b3c'
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='23648'
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.MzrbFzWs/pbuilderrc_PuOM --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MzrbFzWs/b1 --logfile b1/build.log pyensembl_2.3.13-2.dsc'
SUDO_GID='113'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://10.0.0.15:3142/'
I: uname -a
Linux wbq0 6.1.0-31-armmp #1 SMP Debian 6.1.128-1 (2025-02-07) armv7l GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/23648/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: armhf
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), dh-sequence-python3, python3-setuptools, python3-all, python3-pandas, python3-numpy, python3-datacache, python3-serializable, python3-memoized-property, python3-gtfparse, python3-pytest
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19508 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-setuptools; however:
Package python3-setuptools is not installed.
pbuilder-satisfydepends-dummy depends on python3-all; however:
Package python3-all is not installed.
pbuilder-satisfydepends-dummy depends on python3-pandas; however:
Package python3-pandas is not installed.
pbuilder-satisfydepends-dummy depends on python3-numpy; however:
Package python3-numpy is not installed.
pbuilder-satisfydepends-dummy depends on python3-datacache; however:
Package python3-datacache is not installed.
pbuilder-satisfydepends-dummy depends on python3-serializable; however:
Package python3-serializable is not installed.
pbuilder-satisfydepends-dummy depends on python3-memoized-property; however:
Package python3-memoized-property is not installed.
pbuilder-satisfydepends-dummy depends on python3-gtfparse; however:
Package python3-gtfparse is not installed.
pbuilder-satisfydepends-dummy depends on python3-pytest; however:
Package python3-pytest 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} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} liblapack3{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} python3{a} python3-all{a} python3-autocommand{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-datacache{a} python3-dateutil{a} python3-gtfparse{a} python3-idna{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-memoized-property{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-pytest{a} python3-pytz{a} python3-requests{a} python3-serializable{a} python3-setuptools{a} python3-typechecks{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-urllib3{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx python3-bottleneck python3-bs4 python3-html5lib python3-jinja2 python3-lxml python3-matplotlib python3-numexpr python3-odf python3-openpyxl python3-pygments python3-scipy python3-tables wget
0 packages upgraded, 85 newly installed, 0 to remove and 0 not upgraded.
Need to get 42.8 MB of archives. After unpacking 177 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main armhf libpython3.13-minimal armhf 3.13.2-1 [845 kB]
Get: 2 http://deb.debian.org/debian unstable/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB]
Get: 3 http://deb.debian.org/debian unstable/main armhf python3.13-minimal armhf 3.13.2-1 [1842 kB]
Get: 4 http://deb.debian.org/debian unstable/main armhf python3-minimal armhf 3.13.2-2 [27.1 kB]
Get: 5 http://deb.debian.org/debian unstable/main armhf media-types all 13.0.0 [29.3 kB]
Get: 6 http://deb.debian.org/debian unstable/main armhf netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian unstable/main armhf tzdata all 2025a-2 [259 kB]
Get: 8 http://deb.debian.org/debian unstable/main armhf libffi8 armhf 3.4.7-1 [20.3 kB]
Get: 9 http://deb.debian.org/debian unstable/main armhf readline-common all 8.2-6 [69.4 kB]
Get: 10 http://deb.debian.org/debian unstable/main armhf libreadline8t64 armhf 8.2-6 [146 kB]
Get: 11 http://deb.debian.org/debian unstable/main armhf libpython3.13-stdlib armhf 3.13.2-1 [1853 kB]
Get: 12 http://deb.debian.org/debian unstable/main armhf python3.13 armhf 3.13.2-1 [745 kB]
Get: 13 http://deb.debian.org/debian unstable/main armhf libpython3-stdlib armhf 3.13.2-2 [10.1 kB]
Get: 14 http://deb.debian.org/debian unstable/main armhf python3 armhf 3.13.2-2 [28.1 kB]
Get: 15 http://deb.debian.org/debian unstable/main armhf python3-numpy-dev armhf 1:2.2.3+ds-4 [133 kB]
Get: 16 http://deb.debian.org/debian unstable/main armhf libblas3 armhf 3.12.1-2 [116 kB]
Get: 17 http://deb.debian.org/debian unstable/main armhf libgfortran5 armhf 14.2.0-17 [263 kB]
Get: 18 http://deb.debian.org/debian unstable/main armhf liblapack3 armhf 3.12.1-2 [1835 kB]
Get: 19 http://deb.debian.org/debian unstable/main armhf python3-numpy armhf 1:2.2.3+ds-4 [3477 kB]
Get: 20 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB]
Get: 21 http://deb.debian.org/debian unstable/main armhf openssl armhf 3.4.1-1 [1393 kB]
Get: 22 http://deb.debian.org/debian unstable/main armhf ca-certificates all 20241223 [164 kB]
Get: 23 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB]
Get: 24 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB]
Get: 25 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB]
Get: 26 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.23.1-1 [238 kB]
Get: 27 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB]
Get: 28 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-7 [1095 kB]
Get: 29 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.4-5 [84.9 kB]
Get: 30 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB]
Get: 31 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB]
Get: 32 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-7 [272 kB]
Get: 33 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB]
Get: 34 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 35 http://deb.debian.org/debian unstable/main armhf automake all 1:1.17-3 [862 kB]
Get: 36 http://deb.debian.org/debian unstable/main armhf autopoint all 0.23.1-1 [770 kB]
Get: 37 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 38 http://deb.debian.org/debian unstable/main armhf libtool all 2.5.4-4 [539 kB]
Get: 39 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 40 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 41 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 42 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 43 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB]
Get: 44 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB]
Get: 45 http://deb.debian.org/debian unstable/main armhf libunistring5 armhf 1.3-1 [444 kB]
Get: 46 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-6 [9086 kB]
Get: 47 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b2 [605 kB]
Get: 48 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.23.1-1 [1560 kB]
Get: 49 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 50 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 51 http://deb.debian.org/debian unstable/main armhf debhelper all 13.24.1 [920 kB]
Get: 52 http://deb.debian.org/debian unstable/main armhf dh-python all 6.20250308 [115 kB]
Get: 53 http://deb.debian.org/debian unstable/main armhf python3-all armhf 3.13.2-2 [1044 B]
Get: 54 http://deb.debian.org/debian unstable/main armhf python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 55 http://deb.debian.org/debian unstable/main armhf python3-certifi all 2025.1.31+ds-1 [9652 B]
Get: 56 http://deb.debian.org/debian unstable/main armhf python3-chardet all 5.2.0+dfsg-2 [108 kB]
Get: 57 http://deb.debian.org/debian unstable/main armhf python3-charset-normalizer armhf 3.4.1-1+b1 [118 kB]
Get: 58 http://deb.debian.org/debian unstable/main armhf python3-dateutil all 2.9.0-3 [79.3 kB]
Get: 59 http://deb.debian.org/debian unstable/main armhf python3-pytz all 2025.1-3 [150 kB]
Get: 60 http://deb.debian.org/debian unstable/main armhf python3-tz all 2025.1-3 [4004 B]
Get: 61 http://deb.debian.org/debian unstable/main armhf python3-pandas-lib armhf 2.2.3+dfsg-8+b1 [4141 kB]
Get: 62 http://deb.debian.org/debian unstable/main armhf python3-pandas all 2.2.3+dfsg-8 [3097 kB]
Get: 63 http://deb.debian.org/debian unstable/main armhf python3-platformdirs all 4.3.6-1 [16.6 kB]
Get: 64 http://deb.debian.org/debian unstable/main armhf python3-idna all 3.10-1 [42.0 kB]
Get: 65 http://deb.debian.org/debian unstable/main armhf python3-urllib3 all 2.3.0-1 [114 kB]
Get: 66 http://deb.debian.org/debian unstable/main armhf python3-requests all 2.32.3+dfsg-4 [72.1 kB]
Get: 67 http://deb.debian.org/debian unstable/main armhf python3-typechecks all 0.1.0+ds-4 [4580 B]
Get: 68 http://deb.debian.org/debian unstable/main armhf python3-datacache all 1.4.1-2 [12.9 kB]
Get: 69 http://deb.debian.org/debian unstable/main armhf python3-gtfparse all 1.3.0+ds-2 [10.2 kB]
Get: 70 http://deb.debian.org/debian unstable/main armhf python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 71 http://deb.debian.org/debian unstable/main armhf python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 72 http://deb.debian.org/debian unstable/main armhf python3-typeguard all 4.4.2-1 [37.3 kB]
Get: 73 http://deb.debian.org/debian unstable/main armhf python3-inflect all 7.3.1-2 [32.4 kB]
Get: 74 http://deb.debian.org/debian unstable/main armhf python3-iniconfig all 1.1.1-2 [6396 B]
Get: 75 http://deb.debian.org/debian unstable/main armhf python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 76 http://deb.debian.org/debian unstable/main armhf python3-pkg-resources all 75.8.0-1 [222 kB]
Get: 77 http://deb.debian.org/debian unstable/main armhf python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 78 http://deb.debian.org/debian unstable/main armhf python3-zipp all 3.21.0-1 [10.6 kB]
Get: 79 http://deb.debian.org/debian unstable/main armhf python3-setuptools all 75.8.0-1 [724 kB]
Get: 80 http://deb.debian.org/debian unstable/main armhf python3-jaraco.context all 6.0.1-1 [8276 B]
Get: 81 http://deb.debian.org/debian unstable/main armhf python3-memoized-property all 1.0.3-2 [5552 B]
Get: 82 http://deb.debian.org/debian unstable/main armhf python3-packaging all 24.2-1 [55.3 kB]
Get: 83 http://deb.debian.org/debian unstable/main armhf python3-pluggy all 1.5.0-1 [26.9 kB]
Get: 84 http://deb.debian.org/debian unstable/main armhf python3-pytest all 8.3.4-1 [250 kB]
Get: 85 http://deb.debian.org/debian unstable/main armhf python3-serializable all 0.4.1+ds-2 [8400 B]
Fetched 42.8 MB in 3s (12.3 MB/s)
Preconfiguring packages ...
Selecting previously unselected package libpython3.13-minimal:armhf.
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Current default time zone: 'Etc/UTC'
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Reading package lists...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/pyensembl-2.3.13/ && 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 > ../pyensembl_2.3.13-2_source.changes
dpkg-buildpackage: info: source package pyensembl
dpkg-buildpackage: info: source version 2.3.13-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Alexandre Detiste <tchet@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from pyensembl-2.3.13/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
debian/rules clean
dh clean --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/pyensembl-2.3.13'
dh_auto_clean
pybuild --clean -i python{version} -p 3.13
I: pybuild base:311: python3.13 setup.py clean
running clean
removing '/build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build' (and everything under it)
'build/bdist.linux-armv7l' does not exist -- can't clean it
'build/scripts-3.13' does not exist -- can't clean it
rm -rf .pybuild/
find . -name \*.pyc -exec rm {} \;
rm -f pyensembl.egg-info/SOURCES.txt pyensembl.egg-info/requires.txt
make[1]: Leaving directory '/build/reproducible-path/pyensembl-2.3.13'
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/pyensembl.substvars debian/files
rm -fr -- debian/pyensembl/ debian/tmp/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
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
pybuild --configure -i python{version} -p 3.13
I: pybuild base:311: python3.13 setup.py config
running config
dh_auto_build -O--buildsystem=pybuild
pybuild --build -i python{version} -p 3.13
I: pybuild base:311: /usr/bin/python3 setup.py build
running build
running build_py
creating /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/normalization.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/species.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/database.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/reference_name.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/ensembl_versions.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/search.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/transcript.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/version.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/locus.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/sequence_data.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/genome.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/ensembl_release.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/exon.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/__init__.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/shell.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/ensembl_url_templates.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/common.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/locus_with_genome.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/fasta.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/download_cache.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/gene.py -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/logging.conf -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl
copying pyensembl/../requirements.txt -> /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/..
dh_auto_test -O--buildsystem=pybuild
pybuild --test --test-pytest -i python{version} -p 3.13
I: pybuild base:311: cd /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build; python3.13 -m pytest -v -k 'not test_download_cache.py and not test_gene_ids.py and not test_gene_names.py and not test_gene_objects.py and not test_id_length.py and not test_search.py and not test_serialization.py and not test_transcript_ids.py and not test_transcript_objects.py and not test_contigs.py and not test_exon_id.py and not test_exon_object.py and not test_string_representation.py and not test_timings.py and not test_transcript_sequences.py and not test_transcript_support_level.py'
============================= test session starts ==============================
platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3.13
cachedir: .pytest_cache
rootdir: /build/reproducible-path/pyensembl-2.3.13
plugins: typeguard-4.4.2
collecting ... collected 126 items / 98 deselected / 28 selected
tests/test_ensembl_object_properties.py::test_human_reference_name PASSED [ 3%]
tests/test_locus.py::test_normalize_chromosome PASSED [ 7%]
tests/test_locus.py::test_locus_overlaps PASSED [ 10%]
tests/test_locus.py::test_locus_contains PASSED [ 14%]
tests/test_locus.py::test_position_offset PASSED [ 17%]
tests/test_locus.py::test_range_offset PASSED [ 21%]
tests/test_locus.py::test_locus_distance PASSED [ 25%]
tests/test_missing_genome_sources.py::test_transcript_fasta_only PASSED [ 28%]
tests/test_missing_genome_sources.py::test_protein_fasta_only PASSED [ 32%]
tests/test_missing_genome_sources.py::test_gtf_only PASSED [ 35%]
tests/test_missing_genome_sources.py::test_gtf_transcript_only PASSED [ 39%]
tests/test_missing_genome_sources.py::test_gtf_protein_only PASSED [ 42%]
tests/test_mouse.py::test_mouse_ENSMUSG00000017167 PASSED [ 46%]
tests/test_release_versions.py::test_version_too_old_1 PASSED [ 50%]
tests/test_release_versions.py::test_version_too_old_47 PASSED [ 53%]
tests/test_release_versions.py::test_version_is_not_numeric PASSED [ 57%]
tests/test_release_versions.py::test_version_is_none PASSED [ 60%]
tests/test_release_versions.py::test_max_ensembl_release PASSED [ 64%]
tests/test_release_versions.py::test_int_version PASSED [ 67%]
tests/test_release_versions.py::test_str_version PASSED [ 71%]
tests/test_sequence_data.py::test_sequence_type PASSED [ 75%]
tests/test_sequence_data.py::test_missing_sequence PASSED [ 78%]
tests/test_sequence_data.py::test_clear_cache PASSED [ 82%]
tests/test_shell.py::test_genome_selection_grch38 PASSED [ 85%]
tests/test_ucsc_gtf.py::test_ucsc_gencode_gtf PASSED [ 89%]
tests/test_ucsc_gtf.py::test_ucsc_gencode_genome PASSED [ 92%]
tests/test_ucsc_gtf.py::test_ucsc_refseq_gtf PASSED [ 96%]
tests/test_ucsc_gtf.py::test_ucsc_refseq_genome PASSED [100%]
=============================== warnings summary ===============================
pyensembl/shell.py:43
/build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/shell.py:43: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
import pkg_resources
pyensembl/shell.py:74
/build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/shell.py:74: DeprecationWarning: Nesting argument groups is deprecated.
release_group = root_group.add_argument_group()
pyensembl/shell.py:96
/build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/shell.py:96: DeprecationWarning: Nesting argument groups is deprecated.
path_group = root_group.add_argument_group()
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
================ 28 passed, 98 deselected, 3 warnings in 7.11s =================
rm -fr -- /tmp/dh-xdg-rundir-RVuR4S8C
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=pybuild
dh_prep -O--buildsystem=pybuild
rm -f -- debian/pyensembl.substvars
rm -fr -- debian/.debhelper/generated/pyensembl/ debian/pyensembl/ debian/tmp/
dh_auto_install --destdir=debian/pyensembl/ -O--buildsystem=pybuild
install -m0755 -d /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl
pybuild --install -i python{version} -p 3.13 --dest-dir=/build/reproducible-path/pyensembl-2.3.13/debian/pyensembl
I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl
running install
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:79: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!
********************************************************************************
Please avoid running ``setup.py`` directly.
Instead, use pypa/build, pypa/installer or other
standards-based tools.
See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
********************************************************************************
!!
self.initialize_options()
running build
running build_py
running install_lib
creating /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages
creating /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/normalization.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/species.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/database.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/reference_name.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/ensembl_versions.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/search.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/transcript.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/version.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/locus.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/sequence_data.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/genome.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/ensembl_release.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/exon.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__init__.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/shell.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/logging.conf -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/ensembl_url_templates.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/common.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/locus_with_genome.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/fasta.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/download_cache.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/gene.py -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl
creating /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/genome.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/gene.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/locus_with_genome.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/search.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/sequence_data.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/shell.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/download_cache.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/database.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/reference_name.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/ensembl_url_templates.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/version.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/exon.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/ensembl_versions.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/fasta.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/common.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/species.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/normalization.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/locus.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/transcript.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/pyensembl/__pycache__/ensembl_release.cpython-313.pyc -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__pycache__
copying /build/reproducible-path/pyensembl-2.3.13/.pybuild/cpython3_3.13_pyensembl/build/requirements.txt -> /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/normalization.py to normalization.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/species.py to species.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/database.py to database.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/reference_name.py to reference_name.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/ensembl_versions.py to ensembl_versions.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/search.py to search.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/transcript.py to transcript.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/version.py to version.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/locus.py to locus.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/sequence_data.py to sequence_data.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/genome.py to genome.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/ensembl_release.py to ensembl_release.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/exon.py to exon.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/__init__.py to __init__.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/shell.py to shell.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/ensembl_url_templates.py to ensembl_url_templates.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/common.py to common.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/locus_with_genome.py to locus_with_genome.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/fasta.py to fasta.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/download_cache.py to download_cache.cpython-313.pyc
byte-compiling /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl/gene.py to gene.cpython-313.pyc
running install_egg_info
running egg_info
creating pyensembl.egg-info
writing pyensembl.egg-info/PKG-INFO
writing dependency_links to pyensembl.egg-info/dependency_links.txt
writing entry points to pyensembl.egg-info/entry_points.txt
writing requirements to pyensembl.egg-info/requires.txt
writing top-level names to pyensembl.egg-info/top_level.txt
writing manifest file 'pyensembl.egg-info/SOURCES.txt'
reading manifest file 'pyensembl.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'pyensembl.egg-info/SOURCES.txt'
Copying pyensembl.egg-info to /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/lib/python3.13/dist-packages/pyensembl-2.3.13.egg-info
Skipping SOURCES.txt
running install_scripts
Installing pyensembl script to /build/reproducible-path/pyensembl-2.3.13/debian/pyensembl/usr/bin
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/pyensembl-2.3.13'
dh_install
find debian -name requirements.txt -delete
make[1]: Leaving directory '/build/reproducible-path/pyensembl-2.3.13'
dh_installdocs -O--buildsystem=pybuild
install -m0755 -d debian/pyensembl/usr/share/doc/pyensembl
install -p -m0644 debian/copyright debian/pyensembl/usr/share/doc/pyensembl/copyright
dh_installchangelogs -O--buildsystem=pybuild
install -m0755 -d debian/pyensembl/usr/share/doc/pyensembl
install -p -m0644 debian/.debhelper/generated/pyensembl/dh_installchangelogs.dch.trimmed debian/pyensembl/usr/share/doc/pyensembl/changelog.Debian
dh_installman -O--buildsystem=pybuild
install -m0755 -d debian/pyensembl/usr/share/man/man1/
install -p -m0644 ./debian/pyensembl.1 debian/pyensembl/usr/share/man/man1/pyensembl.1
man-recode --to-code UTF-8 --suffix .dh-new debian/pyensembl/usr/share/man/man1/pyensembl.1
mv debian/pyensembl/usr/share/man/man1/pyensembl.1.dh-new debian/pyensembl/usr/share/man/man1/pyensembl.1
chmod 0644 -- debian/pyensembl/usr/share/man/man1/pyensembl.1
dh_python3 -O--buildsystem=pybuild
D: dh_python3 dh_python3:180: version: 6.20250308
D: dh_python3 dh_python3:181: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild']
D: dh_python3 dh_python3:182: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=['--buildsystem=pybuild'])
D: dh_python3 dh_python3:183: supported Python versions: 3.13 (default=3.13)
D: dh_python3 debhelper:174: source=pyensembl, binary packages=['pyensembl']
D: dh_python3 dh_python3:205: processing package pyensembl...
D: dh_python3 fs:50: moving files from debian/pyensembl/usr/lib/python3.13/dist-packages to debian/pyensembl/usr/lib/python3/dist-packages/
D: dh_python3 fs:338: package pyensembl details = {'requires.txt': {'debian/pyensembl/usr/lib/python3/dist-packages/pyensembl-2.3.13.egg-info/requires.txt'}, 'egg-info': {'debian/pyensembl/usr/lib/python3/dist-packages/pyensembl-2.3.13.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': {/usr/bin/python3}, 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': set(), 'ext_no_version': set()}
D: dh_python3 depends:103: generating dependencies for package pyensembl
D: dh_python3 pydist:175: trying to find dependency for datacache<2.0.0,>=1.4.0 (python=None)
D: dh_python3 pydist:209: dependency: module seems to be installed
D: dh_python3 pydist:284: dependency: included in build-deps
D: dh_python3 pydist:175: trying to find dependency for gtfparse<3.0.0,>=2.5.0 (python=None)
D: dh_python3 pydist:209: dependency: module seems to be installed
D: dh_python3 pydist:284: dependency: included in build-deps
D: dh_python3 pydist:175: trying to find dependency for memoized-property>=1.0.2 (python=None)
D: dh_python3 pydist:209: dependency: module seems to be installed
D: dh_python3 pydist:284: dependency: included in build-deps
D: dh_python3 pydist:175: trying to find dependency for pylint<3.0.0,>=2.17.2 (python=None)
D: dh_python3 pydist:209: dependency: module seems to be installed
D: dh_python3 pydist:284: dependency: included in build-deps
D: dh_python3 pydist:175: trying to find dependency for serializable<1.0.0,>=0.2.1 (python=None)
D: dh_python3 pydist:209: dependency: module seems to be installed
D: dh_python3 pydist:284: dependency: included in build-deps
D: dh_python3 pydist:175: trying to find dependency for tinytimer<1.0.0,>=0.0.0 (python=None)
D: dh_python3 pydist:291: invoking dpkg -S *python3/*/[Tt][Ii][Nn][Yy][Tt][Ii][Mm][Ee][Rr]-?*.*-info
D: dh_python3 pydist:313: dpkg -S did not find package for tinytimer: dpkg-query: no path found matching pattern *python3/*/[Tt][Ii][Nn][Yy][Tt][Ii][Mm][Ee][Rr]-?*.*-info
I: dh_python3 pydist:316: Cannot find package that provides tinytimer. Please add package that provides it to Build-Depends or add "tinytimer python3-tinytimer" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info.
D: dh_python3 pydist:175: trying to find dependency for typechecks<1.0.0,>=0.0.2 (python=None)
D: dh_python3 pydist:209: dependency: module seems to be installed
D: dh_python3 pydist:284: dependency: included in build-deps
D: dh_python3 depends:253: D={'python3-gtfparse', 'python3-datacache', 'pylint', 'python3:any', 'python3-serializable', 'python3-memoized-property', 'python3-typechecks'}; R=[]; S=[]; E=[], B=[]; RT=[]
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
cd debian/pyensembl
chmod a-x usr/share/doc/pyensembl/changelog.Debian usr/share/man/man1/pyensembl.1
gzip -9nf usr/share/doc/pyensembl/changelog.Debian usr/share/man/man1/pyensembl.1
cd '/build/reproducible-path/pyensembl-2.3.13'
dh_fixperms -O--buildsystem=pybuild
find debian/pyensembl ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/pyensembl/usr/share/doc -type f -a -true -a ! -regex 'debian/pyensembl/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/pyensembl/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/pyensembl/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/pyensembl -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/pyensembl/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
find debian/pyensembl/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
dh_missing -O--buildsystem=pybuild
dh_installdeb -O--buildsystem=pybuild
install -m0755 -d debian/pyensembl/DEBIAN
printf '#!/bin/sh\nset -e\n' > debian/pyensembl/DEBIAN/postinst
cat debian/pyensembl.postinst.debhelper >> debian/pyensembl/DEBIAN/postinst
chmod 0755 -- debian/pyensembl/DEBIAN/postinst
printf '#!/bin/sh\nset -e\n' > debian/pyensembl/DEBIAN/prerm
cat debian/pyensembl.prerm.debhelper >> debian/pyensembl/DEBIAN/prerm
chmod 0755 -- debian/pyensembl/DEBIAN/prerm
dh_gencontrol -O--buildsystem=pybuild
install -m0755 -d debian/pyensembl/DEBIAN
echo misc:Depends= >> debian/pyensembl.substvars
echo misc:Pre-Depends= >> debian/pyensembl.substvars
dpkg-gencontrol -ppyensembl -ldebian/changelog -Tdebian/pyensembl.substvars -cdebian/control -Pdebian/pyensembl
chmod 0644 -- debian/pyensembl/DEBIAN/control
dh_md5sums -O--buildsystem=pybuild
install -m0755 -d debian/pyensembl/DEBIAN
cd debian/pyensembl >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/pyensembl/DEBIAN/md5sums
dh_builddeb -O--buildsystem=pybuild
dpkg-deb --root-owner-group --build debian/pyensembl ..
dpkg-deb: building package 'pyensembl' in '../pyensembl_2.3.13-2_all.deb'.
dpkg-genbuildinfo --build=binary -O../pyensembl_2.3.13-2_armhf.buildinfo
dpkg-genchanges --build=binary -O../pyensembl_2.3.13-2_armhf.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-source: info: using options from pyensembl-2.3.13/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original 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/23648 and its subdirectories
I: Current time: Sat Mar 8 21:31:28 -12 2025
I: pbuilder-time-stamp: 1741512688
Sun Mar 9 09:31:36 UTC 2025 I: 1st build successful. Starting 2nd build on remote node virt64a-armhf-rb.debian.net.
Sun Mar 9 09:31:36 UTC 2025 I: Preparing to do remote build '2' on virt64a-armhf-rb.debian.net.
Sun Mar 9 09:33:40 UTC 2025 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net.
Sun Mar 9 09:33:42 UTC 2025 I: pyensembl_2.3.13-2_armhf.changes:
Format: 1.8
Date: Sun, 16 Feb 2025 23:00:28 +0100
Source: pyensembl
Binary: pyensembl
Architecture: all
Version: 2.3.13-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Alexandre Detiste <tchet@debian.org>
Description:
pyensembl - installs data from the Ensembl genome database
Changes:
pyensembl (2.3.13-2) unstable; urgency=medium
.
* Team upload.
* Add explicit runtime dependency on python3-pkg-resources
Checksums-Sha1:
66d071ab2b72ae55230cc89326a22443f2f34271 36808 pyensembl_2.3.13-2_all.deb
4c3dc98567959f2a7a44bacadfd4983865dd37f5 6226 pyensembl_2.3.13-2_armhf.buildinfo
Checksums-Sha256:
6036bfc3ae682e276108702a27f2aac8826680aeb1f1415d3bb2997ea3be3590 36808 pyensembl_2.3.13-2_all.deb
2fd9e6b081c3c1222d26fe76e07b211cf2830cf08510a080671b8c9b527ccf9c 6226 pyensembl_2.3.13-2_armhf.buildinfo
Files:
1c97d458b729c041db0ca26827b95e12 36808 science optional pyensembl_2.3.13-2_all.deb
48aa7b4e8d3fd8c7540888131a8fd049 6226 science optional pyensembl_2.3.13-2_armhf.buildinfo
Sun Mar 9 09:33:43 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-armhf_10-7650.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.MzrbFzWs/pyensembl_2.3.13-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.MzrbFzWs/pyensembl_2.3.13-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.MzrbFzWs/pyensembl_2.3.13-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.MzrbFzWs/b1/pyensembl_2.3.13-2_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.MzrbFzWs/b2/pyensembl_2.3.13-2_armhf.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call diffoscope.comparators.binary.FilesystemFile
## main (total time: 0.003s)
0.003s 2 calls outputs
0.000s 1 call cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 222ms
CPU time consumed: 223ms
Sun Mar 9 09:33:43 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Sun Mar 9 09:33:43 UTC 2025 I: pyensembl from unstable built successfully and reproducibly on armhf.
Sun Mar 9 09:33:44 UTC 2025 I: Submitting .buildinfo files to external archives:
Sun Mar 9 09:33:44 UTC 2025 I: Submitting 8.0K b1/pyensembl_2.3.13-2_armhf.buildinfo.asc
Sun Mar 9 09:33:45 UTC 2025 I: Submitting 8.0K b2/pyensembl_2.3.13-2_armhf.buildinfo.asc
Sun Mar 9 09:33:46 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun Mar 9 09:33:46 UTC 2025 I: Done submitting .buildinfo files.
Sun Mar 9 09:33:46 UTC 2025 I: Removing signed pyensembl_2.3.13-2_armhf.buildinfo.asc files:
removed './b1/pyensembl_2.3.13-2_armhf.buildinfo.asc'
removed './b2/pyensembl_2.3.13-2_armhf.buildinfo.asc'