Thu Feb 27 15:45:28 UTC 2025 I: starting to build porechop/trixie/i386 on jenkins on '2025-02-27 15:45'
Thu Feb 27 15:45:28 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_5/52551/console.log
Thu Feb 27 15:45:28 UTC 2025 I: Downloading source for trixie/porechop=0.2.4+dfsg-6
--2025-02-27 15:45:28-- http://deb.debian.org/debian/pool/main/p/porechop/porechop_0.2.4%2bdfsg-6.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2215 (2.2K) [text/prs.lines.tag]
Saving to: ‘porechop_0.2.4+dfsg-6.dsc’
0K .. 100% 278M=0s
2025-02-27 15:45:28 (278 MB/s) - ‘porechop_0.2.4+dfsg-6.dsc’ saved [2215/2215]
Thu Feb 27 15:45:28 UTC 2025 I: porechop_0.2.4+dfsg-6.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: porechop
Binary: porechop
Architecture: any
Version: 0.2.4+dfsg-6
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Cédric Lood <cedric.lood@kuleuven.be>, Andreas Tille <tille@debian.org>
Homepage: https://rrwick.github.io/Porechop
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/porechop
Vcs-Git: https://salsa.debian.org/med-team/porechop.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), dh-python, libseqan2-dev, python3-dev, python3-setuptools
Package-List:
porechop deb science optional arch=any
Checksums-Sha1:
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bb290af32705362aa5ff264977de724eab70f86e 6152 porechop_0.2.4+dfsg-6.debian.tar.xz
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Files:
a09d363d707181eb1013200716142ad7 726312 porechop_0.2.4+dfsg.orig.tar.xz
81be161a3f63d898d8cbf0fab2d09398 6152 porechop_0.2.4+dfsg-6.debian.tar.xz
Dgit: 34a1fd15de707d4b2e997798036702b1f8a39647 debian archive/debian/0.2.4+dfsg-6 https://git.dgit.debian.org/porechop
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Thu Feb 27 15:45:28 UTC 2025 I: Checking whether the package is not for us
Thu Feb 27 15:45:29 UTC 2025 I: Starting 1st build on remote node ionos12-i386.debian.net.
Thu Feb 27 15:45:29 UTC 2025 I: Preparing to do remote build '1' on ionos12-i386.debian.net.
Thu Feb 27 15:47:31 UTC 2025 I: Deleting $TMPDIR on ionos12-i386.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Thu Feb 27 03:45:31 -12 2025
I: pbuilder-time-stamp: 1740671131
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
I: Copying source file
I: copying [porechop_0.2.4+dfsg-6.dsc]
I: copying [./porechop_0.2.4+dfsg.orig.tar.xz]
I: copying [./porechop_0.2.4+dfsg-6.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./porechop_0.2.4+dfsg-6.dsc: unsupported subcommand
dpkg-source: info: extracting porechop in porechop-0.2.4+dfsg
dpkg-source: info: unpacking porechop_0.2.4+dfsg.orig.tar.xz
dpkg-source: info: unpacking porechop_0.2.4+dfsg-6.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying add_python_interpreter_line.patch
dpkg-source: info: applying no_soname.patch
dpkg-source: info: applying define-all-attribute-in-clean.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/18215/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='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='7dce5851c38e4d3eb52affe71146c0e2'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
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='18215'
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.GZFxuX1f/pbuilderrc_jAox --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.GZFxuX1f/b1 --logfile b1/build.log porechop_0.2.4+dfsg-6.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://46.16.76.132:3128'
I: uname -a
Linux ionos12-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/18215/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), dh-python, libseqan2-dev, python3-dev, python3-setuptools
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19789 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on dh-python; however:
Package dh-python is not installed.
pbuilder-satisfydepends-dummy depends on libseqan2-dev; however:
Package libseqan2-dev is not installed.
pbuilder-satisfydepends-dummy depends on python3-dev; however:
Package python3-dev is not installed.
pbuilder-satisfydepends-dummy depends on python3-setuptools; however:
Package python3-setuptools 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} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libseqan2-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl javascript-common libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 67 newly installed, 0 to remove and 0 not upgraded.
Need to get 39.4 MB of archives. After unpacking 155 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main i386 libpython3.13-minimal i386 3.13.2-1 [859 kB]
Get: 2 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB]
Get: 3 http://deb.debian.org/debian trixie/main i386 python3.13-minimal i386 3.13.2-1 [2266 kB]
Get: 4 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.13.2-1 [27.1 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 media-types all 12.0.0 [28.9 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 tzdata all 2025a-2 [259 kB]
Get: 8 http://deb.debian.org/debian trixie/main i386 libffi8 i386 3.4.7-1 [21.4 kB]
Get: 9 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-6 [69.4 kB]
Get: 10 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-6 [173 kB]
Get: 11 http://deb.debian.org/debian trixie/main i386 libpython3.13-stdlib i386 3.13.2-1 [1985 kB]
Get: 12 http://deb.debian.org/debian trixie/main i386 python3.13 i386 3.13.2-1 [745 kB]
Get: 13 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.13.2-1 [10.0 kB]
Get: 14 http://deb.debian.org/debian trixie/main i386 python3 i386 3.13.2-1 [28.1 kB]
Get: 15 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 16 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 19 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.23.1-1 [245 kB]
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Get: 22 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.4-4 [96.4 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 24 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-5 [301 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 27 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 automake all 1:1.17-3 [862 kB]
Get: 29 http://deb.debian.org/debian trixie/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 30 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 31 http://deb.debian.org/debian trixie/main i386 libtool all 2.5.4-3 [539 kB]
Get: 32 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 33 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 34 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 35 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 36 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 37 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 38 http://deb.debian.org/debian trixie/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 39 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 40 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b2 [734 kB]
Get: 41 http://deb.debian.org/debian trixie/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 42 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 43 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 44 http://deb.debian.org/debian trixie/main i386 debhelper all 13.24.1 [920 kB]
Get: 45 http://deb.debian.org/debian trixie/main i386 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 46 http://deb.debian.org/debian trixie/main i386 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 47 http://deb.debian.org/debian trixie/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 48 http://deb.debian.org/debian trixie/main i386 python3-typeguard all 4.4.1-1 [37.0 kB]
Get: 49 http://deb.debian.org/debian trixie/main i386 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 50 http://deb.debian.org/debian trixie/main i386 python3-jaraco.context all 6.0.0-1 [7984 B]
Get: 51 http://deb.debian.org/debian trixie/main i386 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 52 http://deb.debian.org/debian trixie/main i386 python3-pkg-resources all 75.8.0-1 [222 kB]
Get: 53 http://deb.debian.org/debian trixie/main i386 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 54 http://deb.debian.org/debian trixie/main i386 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 55 http://deb.debian.org/debian trixie/main i386 python3-setuptools all 75.8.0-1 [724 kB]
Get: 56 http://deb.debian.org/debian trixie/main i386 dh-python all 6.20250108 [113 kB]
Get: 57 http://deb.debian.org/debian trixie/main i386 libexpat1-dev i386 2.6.4-1 [165 kB]
Get: 58 http://deb.debian.org/debian trixie/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 59 http://deb.debian.org/debian trixie/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 60 http://deb.debian.org/debian trixie/main i386 libjs-sphinxdoc all 8.1.3-5 [30.5 kB]
Get: 61 http://deb.debian.org/debian trixie/main i386 libpython3.13 i386 3.13.2-1 [2199 kB]
Get: 62 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Get: 63 http://deb.debian.org/debian trixie/main i386 libpython3.13-dev i386 3.13.2-1 [5181 kB]
Get: 64 http://deb.debian.org/debian trixie/main i386 libpython3-dev i386 3.13.2-1 [10.3 kB]
Get: 65 http://deb.debian.org/debian trixie/main i386 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB]
Get: 66 http://deb.debian.org/debian trixie/main i386 python3.13-dev i386 3.13.2-1 [505 kB]
Get: 67 http://deb.debian.org/debian trixie/main i386 python3-dev i386 3.13.2-1 [26.1 kB]
Fetched 39.4 MB in 1s (30.4 MB/s)
Preconfiguring packages ...
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Setting up libpython3.13-minimal:i386 (3.13.2-1) ...
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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/porechop-0.2.4+dfsg/ && 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 > ../porechop_0.2.4+dfsg-6_source.changes
dpkg-buildpackage: info: source package porechop
dpkg-buildpackage: info: source version 0.2.4+dfsg-6
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean --with python3 --buildsystem pybuild
dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:311: python3.13 setup.py clean
running clean
Deleting directory: /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build
dh_autoreconf_clean -O--buildsystem=pybuild
debian/rules override_dh_clean
make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg'
dh_clean
# Removing left .so files.
find . -name "*.so" -delete
make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg'
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:311: python3.13 setup.py config
running config
dh_auto_build -O--buildsystem=pybuild
I: pybuild base:311: /usr/bin/python3 setup.py build
running build
running build_py
creating /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop
copying porechop/adapters.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop
copying porechop/porechop.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop
copying porechop/nanopore_read.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop
copying porechop/version.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop
copying porechop/__init__.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop
copying porechop/misc.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop
copying porechop/cpp_function_wrappers.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop
Cleaning previous compilation: make clean
make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg'
rm -f porechop/src/alignment.o porechop/src/adapter_align.o
make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg'
Compiling Porechop: make -j 8
make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg'
g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/porechop-0.2.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o porechop/src/alignment.o porechop/src/alignment.cpp
g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/porechop-0.2.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o porechop/src/adapter_align.o porechop/src/adapter_align.cpp
g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/porechop-0.2.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -shared -o porechop/cpp_functions.so porechop/src/alignment.o porechop/src/adapter_align.o
make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg'
dh_auto_test -O--buildsystem=pybuild
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=pybuild
dh_prep -O--buildsystem=pybuild
dh_auto_install --destdir=debian/porechop/ -O--buildsystem=pybuild
I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop
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
Cleaning previous compilation: make clean
make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg'
rm -f porechop/src/alignment.o porechop/src/adapter_align.o
make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg'
Compiling Porechop: make -j 8
make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg'
g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/porechop-0.2.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o porechop/src/alignment.o porechop/src/alignment.cpp
g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/porechop-0.2.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o porechop/src/adapter_align.o porechop/src/adapter_align.cpp
g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/porechop-0.2.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -shared -o porechop/cpp_functions.so porechop/src/alignment.o porechop/src/adapter_align.o
make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg'
running install_lib
creating /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages
creating /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop
copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop/adapters.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop
copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop/porechop.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop
copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop/nanopore_read.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop
copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop/version.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop
copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop/__init__.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop
copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop/misc.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop
copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop/cpp_function_wrappers.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop
byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop/adapters.py to adapters.cpython-313.pyc
byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop/porechop.py to porechop.cpython-313.pyc
byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop/nanopore_read.py to nanopore_read.cpython-313.pyc
byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop/version.py to version.cpython-313.pyc
byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop/__init__.py to __init__.cpython-313.pyc
byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop/misc.py to misc.cpython-313.pyc
/usr/lib/python3.13/dist-packages/porechop/misc.py:261: SyntaxWarning: invalid escape sequence '\['
byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop/cpp_function_wrappers.py to cpp_function_wrappers.cpython-313.pyc
running install_egg_info
running egg_info
creating porechop.egg-info
writing porechop.egg-info/PKG-INFO
writing dependency_links to porechop.egg-info/dependency_links.txt
writing entry points to porechop.egg-info/entry_points.txt
writing top-level names to porechop.egg-info/top_level.txt
writing manifest file 'porechop.egg-info/SOURCES.txt'
reading manifest file 'porechop.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'porechop.egg-info/SOURCES.txt'
Copying porechop.egg-info to /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop-0.2.4.egg-info
Skipping SOURCES.txt
running install_scripts
Installing porechop script to /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/bin
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg'
dh_install
mv -v debian/porechop/usr/bin/porechop-runner.py debian/porechop/usr/bin/porechop
renamed 'debian/porechop/usr/bin/porechop-runner.py' -> 'debian/porechop/usr/bin/porechop'
make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg'
dh_installdocs -O--buildsystem=pybuild
dh_installchangelogs -O--buildsystem=pybuild
dh_installman -O--buildsystem=pybuild
debian/rules override_dh_python3
make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg'
dh_python3 --no-ext-rename
I: dh_python3 tools:113: replacing shebang in debian/porechop/usr/bin/porechop
make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg'
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 'porechop' in '../porechop_0.2.4+dfsg-6_i386.deb'.
dpkg-deb: building package 'porechop-dbgsym' in '../porechop-dbgsym_0.2.4+dfsg-6_i386.deb'.
dpkg-genbuildinfo --build=binary -O../porechop_0.2.4+dfsg-6_i386.buildinfo
dpkg-genchanges --build=binary -O../porechop_0.2.4+dfsg-6_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: 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/18215 and its subdirectories
I: Current time: Thu Feb 27 03:47:30 -12 2025
I: pbuilder-time-stamp: 1740671250
Thu Feb 27 15:47:31 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net.
Thu Feb 27 15:47:31 UTC 2025 I: Preparing to do remote build '2' on ionos6-i386.debian.net.
Thu Feb 27 15:48:23 UTC 2025 I: Deleting $TMPDIR on ionos6-i386.debian.net.
Thu Feb 27 15:48:24 UTC 2025 I: porechop_0.2.4+dfsg-6_i386.changes:
Format: 1.8
Date: Fri, 12 Jul 2024 23:49:53 +0200
Source: porechop
Binary: porechop porechop-dbgsym
Architecture: i386
Version: 0.2.4+dfsg-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
porechop - adapter trimmer for Oxford Nanopore reads
Closes: 1074677
Changes:
porechop (0.2.4+dfsg-6) unstable; urgency=medium
.
* Team upload.
* d/rules: remove the now broken workaround against setuptools 50 bug.
(Closes: #1074677)
Checksums-Sha1:
498ececf8442e7ca5a1652a293fa4e1aa3de4623 382456 porechop-dbgsym_0.2.4+dfsg-6_i386.deb
23a120820a3c4cb163c4d6dffe32c42d766d2bce 6083 porechop_0.2.4+dfsg-6_i386.buildinfo
40528e203729aa9b63a04507ef0cfcaf9e5e66d2 58528 porechop_0.2.4+dfsg-6_i386.deb
Checksums-Sha256:
800f543b3187cf81d033afdb42af95d67bf293917291833b072b4633376b37e4 382456 porechop-dbgsym_0.2.4+dfsg-6_i386.deb
673b2eb76788adc8b447e9b33878bdeb001d430ac80a79e68699b3e93c83afd5 6083 porechop_0.2.4+dfsg-6_i386.buildinfo
e6f3b7a444beee56624238981180016cf7f0fa7b7808616ce0e47000c382f02d 58528 porechop_0.2.4+dfsg-6_i386.deb
Files:
7f6a42a24dcf0974aac5d0aae17b88d2 382456 debug optional porechop-dbgsym_0.2.4+dfsg-6_i386.deb
11a4cb232a27c5e39b36c61aef3b0f43 6083 science optional porechop_0.2.4+dfsg-6_i386.buildinfo
c97ca6069ab4c9f6ea4984aaaf5a19cb 58528 science optional porechop_0.2.4+dfsg-6_i386.deb
Thu Feb 27 15:48:25 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-i386_5-52551.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.GZFxuX1f/porechop_0.2.4+dfsg-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.GZFxuX1f/porechop_0.2.4+dfsg-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.GZFxuX1f/porechop_0.2.4+dfsg-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.GZFxuX1f/b1/porechop_0.2.4+dfsg-6_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.GZFxuX1f/b2/porechop_0.2.4+dfsg-6_i386.changes
## close_archive (total time: 0.000s)
0.000s 8 calls diffoscope.comparators.deb.DebContainer
0.000s 18 calls diffoscope.comparators.xz.XzContainer
0.000s 12 calls diffoscope.comparators.tar.TarContainer
0.000s 6 calls diffoscope.comparators.deb.DebTarContainer
## command (total time: 3.358s)
1.542s 58 calls diff
1.064s 88 calls objdump
0.437s 438 calls readelf
0.194s 2 calls objcopy
0.112s 18 calls xz
0.008s 11 calls strings
0.001s 20 calls cmp (internal)
## compare_files (cumulative) (total time: 17.402s)
3.145s 1 call abc.DotChangesFile
3.130s 2 calls abc.DebFile
3.080s 4 calls abc.XzFile
2.919s 2 calls abc.DebDataTarFile
2.776s 1 call abc.ElfFile
2.036s 5 calls diffoscope.comparators.elf.ElfCodeSection
0.188s 13 calls diffoscope.comparators.elf.ElfSection
0.084s 2 calls abc.TarFile
0.019s 1 call abc.TextFile
0.013s 2 calls abc.Md5sumsFile
0.012s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection
## container_extract (total time: 0.159s)
0.114s 18 calls diffoscope.comparators.xz.XzContainer
0.023s 38 calls diffoscope.comparators.deb.DebTarContainer
0.012s 22 calls diffoscope.comparators.deb.DebContainer
0.010s 20 calls diffoscope.comparators.tar.TarContainer
## diff (total time: 0.779s)
0.779s 387 calls linediff
## has_same_content_as (total time: 0.004s)
0.001s 4 calls abc.Md5sumsFile
0.001s 6 calls abc.TextFile
0.000s 2 calls abc.DebDataTarFile
0.000s 4 calls abc.XzFile
0.000s 1 call diffoscope.comparators.binary.FilesystemFile
0.000s 2 calls abc.TarFile
0.000s 2 calls abc.DebFile
0.000s 1 call abc.ElfFile
0.000s 1 call abc.DotChangesFile
0.000s 1 call diffoscope.comparators.utils.libarchive.LibarchiveSymlink
0.000s 13 calls diffoscope.comparators.elf.ElfSection
0.000s 5 calls diffoscope.comparators.elf.ElfCodeSection
0.000s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection
## main (total time: 18.769s)
18.768s 2 calls outputs
0.001s 1 call cleanup
## open_archive (total time: 0.000s)
0.000s 18 calls diffoscope.comparators.xz.XzContainer
0.000s 12 calls diffoscope.comparators.tar.TarContainer
0.000s 8 calls diffoscope.comparators.deb.DebContainer
0.000s 6 calls diffoscope.comparators.deb.DebTarContainer
## output (total time: 15.238s)
15.154s 1 call html
0.055s 1 call text
0.029s 1 call json
## recognizes (total time: 0.197s)
0.096s 1674 calls diffoscope.comparators.utils.libarchive.LibarchiveMember
0.072s 780 calls diffoscope.comparators.utils.archive.ArchiveMember
0.019s 12 calls diffoscope.comparators.binary.FilesystemFile
0.010s 216 calls diffoscope.comparators.debian.DebControlMember
## specialize (total time: 0.450s)
0.450s 42 calls specialize
Finished with result: success
Main processes terminated with: code=exited/status=1
Service runtime: 19.144s
CPU time consumed: 19.702s
Thu Feb 27 15:48:45 UTC 2025 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate.
Thu Feb 27 15:48:45 UTC 2025 E: porechop failed to build reproducibly in trixie on i386.
Thu Feb 27 15:48:46 UTC 2025 I: Submitting .buildinfo files to external archives:
Thu Feb 27 15:48:46 UTC 2025 I: Submitting 8.0K b1/porechop_0.2.4+dfsg-6_i386.buildinfo.asc
Thu Feb 27 15:48:47 UTC 2025 I: Submitting 8.0K b2/porechop_0.2.4+dfsg-6_i386.buildinfo.asc
Thu Feb 27 15:48:48 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Thu Feb 27 15:48:48 UTC 2025 I: Done submitting .buildinfo files.
Thu Feb 27 15:48:48 UTC 2025 I: Removing signed porechop_0.2.4+dfsg-6_i386.buildinfo.asc files:
removed './b1/porechop_0.2.4+dfsg-6_i386.buildinfo.asc'
removed './b2/porechop_0.2.4+dfsg-6_i386.buildinfo.asc'