Your message dated Fri, 06 Sep 2024 06:39:38 +0000
with message-id <e1smsd8-00awbg...@fasolo.debian.org>
and subject line Bug#1079439: fixed in python-biopython 1.83+dfsg1-4
has caused the Debian Bug report #1079439,
regarding python-biopython: autopkgtest stuck on riscv64
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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immediately.)
--
1079439: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1079439
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: python-biopython
Version: 1.83+dfsg1-3
Severity: important
I've been looking at why debci appears to be stuck on riscv64 for the
python-biopython package:
https://ci.debian.net/packages/p/python-biopython/testing/riscv64/
For that reason, I've been trying to reproduce it on the debian porter machine.
When trying to build the package manually, the build was stuck exactly
like on debci:
env DIALIGN2_DIR=/usr/share/dialign
EMBOSS_ROOT=/usr/lib/emboss
HOME=/home/siretart/python-biopython/.pybuild/cpython3_3.12/build/home
python3.12 run_tests.py --offline
Skipping any tests requiring internet access
Python version: 3.12.5 (main, Aug 7 2024, 13:49:14) [GCC 14.1.0]
Operating system: posix linux
test_Ace ... ok
test_Affy ... ok
test_AlignIO ... ok
test_AlignIO_ClustalIO ... ok
test_AlignIO_EmbossIO ... ok
test_AlignIO_FastaIO ... ok
test_AlignIO_MauveIO ... ok
test_AlignIO_PhylipIO ... ok
test_AlignIO_convert ... ok
test_AlignInfo ... ok
test_Align_Alignment ... ok
test_Align_a2m ... ok
test_Align_bed ... ok
test_Align_bigbed ... ok
test_Align_bigmaf ... ok
test_Align_bigpsl ... ok
test_Align_chain ... ok
test_Align_clustal ... ok
I managed to capture a process tree at the time it was stuck:
siretart@ricci:~$ pstree 3014984 -ac -St
dh /usr/bin/dh binary --with python3 --buildsystem=pybuild
└─rules -f debian/rules override_dh_auto_test
└─sh -c...
└─dh_auto_test /usr/bin/dh_auto_test -- --test --system=custom...
└─pybuild /usr/bin/pybuild --test -i python{version} -p 3.12
--test --system=custom...
└─sh -c...
└─python3.12 run_tests.py --offline
siretart 3014731 0.0 0.1 18980 17016 pts/2 S+ Aug22 0:00 |
\_ /usr/bin/perl /usr/bin/dpkg-buildpackage -b -us -uc
siretart 3014975 0.0 0.0 2200 1608 pts/2 S+ Aug22 0:00 |
\_ /usr/bin/make -f debian/rules binary
siretart 3014984 0.0 0.0 14148 11968 pts/2 S+ Aug22 0:00 |
\_ /usr/bin/perl /usr/bin/dh binary --with python3 --buildsystem=pybuild
siretart 3024296 0.0 0.0 2204 1400 pts/2 S+ Aug22 0:00 |
\_ /usr/bin/make -f debian/rules override_dh_auto_test
siretart 3024324 0.0 0.0 1980 1080 pts/2 S+ Aug22 0:00 |
\_ /bin/sh -c LC_ALL=C.UTF-8 dh_auto_test -- --test
--system=custom \ ?--test-args='set -e; \
siretart 3024325 0.0 0.0 18488 16268 pts/2 S+ Aug22 0:00 |
\_ /usr/bin/perl /usr/bin/dh_auto_test -- --test
--system=custom --test-args=set -e; \
siretart 3024333 0.0 0.0 20824 15860 pts/2 S+ Aug22 0:00 |
\_ /usr/bin/python3 /usr/bin/pybuild --test -i
python{version} -p 3.12 --test --system
siretart 3024336 0.0 0.0 1980 1160 pts/2 S+ Aug22 0:00 |
\_ /bin/sh -c set -e; \
mkdir -p /home/siretart/pytho
siretart 3024343 99.9 0.5 115704 97700 pts/2 R+ Aug22 801:57 |
\_ python3.12 run_tests.py --offline
This tells me that there is unlikely a single test that could be disabled get
the build unstuck. Rather, the issue seems triggered by the run_tests.py, and
might require a change to either run_tests.py [1] or the python interpreter on
riscv64?
[1]
https://sources.debian.org/src/python-biopython/1.83%2Bdfsg1-3/Tests/run_tests.py/
-- System Information:
Debian Release: trixie/sid
APT prefers testing
APT policy: (500, 'testing'), (50, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Kernel: Linux 6.10.4-amd64 (SMP w/8 CPU threads; PREEMPT)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
--- End Message ---
--- Begin Message ---
Source: python-biopython
Source-Version: 1.83+dfsg1-4
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
python-biopython, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1079...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated python-biopython
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 04 Sep 2024 21:44:05 +0200
Source: python-biopython
Architecture: source
Version: 1.83+dfsg1-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1079439
Changes:
python-biopython (1.83+dfsg1-4) unstable; urgency=medium
.
* skip-scipy-in-codonalign.patch: new: skip scipy tests on riscv64.
This patch is introduced to give some breath to Risc-V CI runners while
the core of the problem is investigated. (Closes: #1079439)
* d/rules: skip ncbi tools tests due to #1079439.
* d/rules: update list of excluded tests due to missing packages.
Checksums-Sha1:
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python-biopython_1.83+dfsg1-4.debian.tar.xz
Checksums-Sha256:
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--- End Message ---
