Thu Jan 23 00:20:11 UTC 2025 I: starting to build porechop/trixie/arm64 on jenkins on '2025-01-23 00:19'
Thu Jan 23 00:20:11 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_1/57101/console.log
Thu Jan 23 00:20:11 UTC 2025 I: Downloading source for trixie/porechop=0.2.4+dfsg-6
--2025-01-23 00:20:11-- 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% 352M=0s
2025-01-23 00:20:11 (352 MB/s) - ‘porechop_0.2.4+dfsg-6.dsc’ saved [2215/2215]
Thu Jan 23 00:20:11 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
Checksums-Sha256:
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4adf0600768b96d2efc1cda4c87031d01b09796b8da7cd09ccde621d3bd34807 6152 porechop_0.2.4+dfsg-6.debian.tar.xz
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 Jan 23 00:20:11 UTC 2025 I: Checking whether the package is not for us
Thu Jan 23 00:20:11 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net.
Thu Jan 23 00:20:11 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net.
Thu Jan 23 00:21:00 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Tue Feb 24 18:43:13 -12 2026
I: pbuilder-time-stamp: 1772001793
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: 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/11927/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='arm64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='arm64'
IFS='
'
INVOCATION_ID='93ede3dd2fd64771b792b9274a164be5'
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='11927'
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.yNnk20tm/pbuilderrc_vCFB --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.yNnk20tm/b1 --logfile b1/build.log porechop_0.2.4+dfsg-6.dsc'
SUDO_GID='109'
SUDO_UID='104'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://192.168.101.4:3128'
I: uname -a
Linux codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/11927/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: arm64
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 ... 19970 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} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libpipeline1{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} libseqan2-dev{a} libtirpc-common{a} libtirpc3t64{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} python3.12{a} python3.12-dev{a} python3.12-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 krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 76 newly installed, 0 to remove and 0 not upgraded.
Need to get 38.1 MB of archives. After unpacking 171 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.8-5 [810 kB]
Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB]
Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.8-5 [1934 kB]
Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.12.8-1 [26.9 kB]
Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB]
Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024b-6 [257 kB]
Get: 8 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB]
Get: 9 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB]
Get: 10 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB]
Get: 11 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB]
Get: 12 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B]
Get: 13 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB]
Get: 14 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB]
Get: 15 http://deb.debian.org/debian trixie/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 16 http://deb.debian.org/debian trixie/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB]
Get: 17 http://deb.debian.org/debian trixie/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB]
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Get: 20 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.8-5 [1904 kB]
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Get: 24 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB]
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Get: 35 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB]
Get: 36 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 37 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get: 38 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-4 [723 kB]
Get: 39 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.23 [90.6 kB]
Get: 40 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-2 [539 kB]
Get: 41 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 42 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 43 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 44 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 45 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 46 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 47 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB]
Get: 48 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB]
Get: 49 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB]
Get: 50 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-4 [1532 kB]
Get: 51 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 52 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 53 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.23 [919 kB]
Get: 54 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 55 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 56 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 57 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB]
Get: 58 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 59 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get: 60 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 61 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 75.6.0-1 [222 kB]
Get: 62 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 63 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 64 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 75.6.0-1 [720 kB]
Get: 65 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20250108 [113 kB]
Get: 66 http://deb.debian.org/debian trixie/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB]
Get: 67 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 68 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 69 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB]
Get: 70 http://deb.debian.org/debian trixie/main arm64 libpython3.12t64 arm64 3.12.8-5 [1985 kB]
Get: 71 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Get: 72 http://deb.debian.org/debian trixie/main arm64 libpython3.12-dev arm64 3.12.8-5 [4822 kB]
Get: 73 http://deb.debian.org/debian trixie/main arm64 libpython3-dev arm64 3.12.8-1 [10.1 kB]
Get: 74 http://deb.debian.org/debian trixie/main arm64 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB]
Get: 75 http://deb.debian.org/debian trixie/main arm64 python3.12-dev arm64 3.12.8-5 [506 kB]
Get: 76 http://deb.debian.org/debian trixie/main arm64 python3-dev arm64 3.12.8-1 [26.1 kB]
Fetched 38.1 MB in 0s (111 MB/s)
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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 arm64
debian/rules clean
dh clean --with python3 --buildsystem pybuild
dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:311: python3.12 setup.py clean
running clean
Deleting directory: /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/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: python3.12 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_3.12/build/porechop
copying porechop/porechop.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop
copying porechop/version.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop
copying porechop/nanopore_read.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop
copying porechop/misc.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop
copying porechop/cpp_function_wrappers.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop
copying porechop/adapters.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop
copying porechop/__init__.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!
********************************************************************************
Please avoid running ``setup.py`` directly.
Instead, use pypa/build, pypa/installer or other
standards-based tools.
See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
********************************************************************************
!!
self.initialize_options()
running build
running build_py
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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/python3.12/dist-packages
creating /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop
copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop/__init__.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop
copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop/adapters.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop
copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop/cpp_function_wrappers.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop
copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop/misc.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop
copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop/nanopore_read.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop
copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop/version.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop
copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.12/build/porechop/porechop.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop
byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop/adapters.py to adapters.cpython-312.pyc
byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop/cpp_function_wrappers.py to cpp_function_wrappers.cpython-312.pyc
byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop/misc.py to misc.cpython-312.pyc
/usr/lib/python3.12/dist-packages/porechop/misc.py:261: SyntaxWarning: invalid escape sequence '\['
byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop/nanopore_read.py to nanopore_read.cpython-312.pyc
byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop/version.py to version.cpython-312.pyc
byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.12/dist-packages/porechop/porechop.py to porechop.cpython-312.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/python3.12/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
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
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-dbgsym' in '../porechop-dbgsym_0.2.4+dfsg-6_arm64.deb'.
dpkg-deb: building package 'porechop' in '../porechop_0.2.4+dfsg-6_arm64.deb'.
dpkg-genbuildinfo --build=binary -O../porechop_0.2.4+dfsg-6_arm64.buildinfo
dpkg-genchanges --build=binary -O../porechop_0.2.4+dfsg-6_arm64.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/11927 and its subdirectories
I: Current time: Tue Feb 24 18:44:00 -12 2026
I: pbuilder-time-stamp: 1772001840
Thu Jan 23 00:21:01 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net.
Thu Jan 23 00:21:01 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net.
Thu Jan 23 00:21:56 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net.
Thu Jan 23 00:21:57 UTC 2025 I: porechop_0.2.4+dfsg-6_arm64.changes:
Format: 1.8
Date: Fri, 12 Jul 2024 23:49:53 +0200
Source: porechop
Binary: porechop porechop-dbgsym
Architecture: arm64
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:
ba8072df832f02df07eb057915273ead8fb2589b 379688 porechop-dbgsym_0.2.4+dfsg-6_arm64.deb
7e14f9bcd1258db191e56df8d39508eb1c35800b 6511 porechop_0.2.4+dfsg-6_arm64.buildinfo
582635907c93857bdf051076db0ac3f46768f02c 54136 porechop_0.2.4+dfsg-6_arm64.deb
Checksums-Sha256:
a7866853edaf81d2ba201e40efa90600dceb7ac6231c3cff5f7cfc9dd7354f08 379688 porechop-dbgsym_0.2.4+dfsg-6_arm64.deb
6ed33478b8c2d64f677ff856993cebf2665d9ca99615bbb22c0184691cc40680 6511 porechop_0.2.4+dfsg-6_arm64.buildinfo
3745c9a87faf0c5835616e2ed650da8a4a57ec498f0487a610b25cad7aa19cf6 54136 porechop_0.2.4+dfsg-6_arm64.deb
Files:
47069873158fc0c46894ea028c739801 379688 debug optional porechop-dbgsym_0.2.4+dfsg-6_arm64.deb
e9ca617b3762b1d1b7c1d996208892ab 6511 science optional porechop_0.2.4+dfsg-6_arm64.buildinfo
def650cdc23e89afe0b517b1aadf4430 54136 science optional porechop_0.2.4+dfsg-6_arm64.deb
Thu Jan 23 00:21:58 UTC 2025 I: diffoscope 285 will be used to compare the two builds:
Running as unit: rb-diffoscope-arm64_1-57101.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.yNnk20tm/porechop_0.2.4+dfsg-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.yNnk20tm/porechop_0.2.4+dfsg-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.yNnk20tm/porechop_0.2.4+dfsg-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.yNnk20tm/b1/porechop_0.2.4+dfsg-6_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.yNnk20tm/b2/porechop_0.2.4+dfsg-6_arm64.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: 0.330s)
0.330s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.017s)
0.017s 12 calls diffoscope.comparators.binary.FilesystemFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 623ms
CPU time consumed: 620ms
Thu Jan 23 00:21:59 UTC 2025 I: diffoscope 285 found no differences in the changes files, and a .buildinfo file also exists.
Thu Jan 23 00:21:59 UTC 2025 I: porechop from trixie built successfully and reproducibly on arm64.
Thu Jan 23 00:22:00 UTC 2025 I: Submitting .buildinfo files to external archives:
Thu Jan 23 00:22:00 UTC 2025 I: Submitting 8.0K b1/porechop_0.2.4+dfsg-6_arm64.buildinfo.asc
Thu Jan 23 00:22:01 UTC 2025 I: Submitting 8.0K b2/porechop_0.2.4+dfsg-6_arm64.buildinfo.asc
Thu Jan 23 00:22:02 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Thu Jan 23 00:22:02 UTC 2025 I: Done submitting .buildinfo files.
Thu Jan 23 00:22:02 UTC 2025 I: Removing signed porechop_0.2.4+dfsg-6_arm64.buildinfo.asc files:
removed './b1/porechop_0.2.4+dfsg-6_arm64.buildinfo.asc'
removed './b2/porechop_0.2.4+dfsg-6_arm64.buildinfo.asc'