Your message dated Fri, 04 Jul 2025 08:49:13 +0000
with message-id <e1uxc6b-0050dj...@fasolo.debian.org>
and subject line Bug#1108309: fixed in mdanalysis 2.9.0-9
has caused the Debian Bug report #1108309,
regarding mdanalysis: FTBFS randomly: autobuilder hangs
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.
(NB: If you are a system administrator and have no idea what this
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immediately.)
--
1108309: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1108309
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:mdanalysis
Version: 2.9.0-8
Severity: serious
Tags: ftbfs trixie sid help
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_long_traj PASSED
[ 1%]
testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_updating_atomgroup
PASSED [ 1%]
testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_not_universe_atomgroup_error
PASSED [ 1%]
testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_DistanceMatrix_attr_warning
PASSED [ 1%]
testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_dihedral[client_Dihedral0]
PASSED [ 1%]
testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_dihedral_single_frame[client_Dihedral0]
PASSED [ 1%]
testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_atomgroup_list[client_Dihedral0]
PASSED [ 1%]
testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_enough_atoms[client_Dihedral0]
PASSED [ 1%]
testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_dihedral_attr_warning[client_Dihedral0]
E: Build killed with signal TERM after 30 minutes of inactivity
--------------------------------------------------------------------------------
Notes:
- The way it fails is not always the same. I've put a collection of different
build logs here:
https://people.debian.org/~sanvila/build-logs/202506/
- The build does not always fail, but the failure rate here is around 90%
(tested on systems
with 2 CPUs), which makes it not to be suitable for release. However, for some
reason,
the failure rate is only 20% on single-cpu systems, maybe this difference means
something.
- I believe, but I can't check anymore, that the failure rate raised a lot when
I switched
my autobuilders to trixie (i.e. when I started to use the kernel of trixie).
- This failure where the autobuilder hangs also happens on the buildds. Please
see:
https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=all&ver=2.9.0-3&stamp=1744942413&raw=0
https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=amd64&ver=2.9.0-7&stamp=1745409028&raw=0
https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=arm64&ver=2.9.0-6&stamp=1745371276&raw=0
https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=armel&ver=2.9.0-8&stamp=1747011477&raw=0
https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=i386&ver=2.9.0-2&stamp=1744893854&raw=0
https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=mips64el&ver=2.9.0-4&stamp=1745023633&raw=0
all of which end with a message like this:
E: Build killed with signal TERM after 150 minutes of inactivity
(In my build logs, I lowered the value to 30 minutes because I know that in
normal
circumstances the package should take a lot less than that).
- There are also similar failures (autobuilder hang) in the reproducible-builds
site:
https://tests.reproducible-builds.org/debian/rbuild/unstable/amd64/mdanalysis_2.9.0-8.rbuild.log.gz
https://tests.reproducible-builds.org/debian/logs/unstable/armhf/mdanalysis_2.8.0-4.build2.log.gz
- I have no idea of what's going on here, but as always, I can offer a VM to
reproduce
(contact me privately for details).
Thanks.
--- End Message ---
--- Begin Message ---
Source: mdanalysis
Source-Version: 2.9.0-9
Done: Drew Parsons <dpars...@debian.org>
We believe that the bug you reported is fixed in the latest version of
mdanalysis, 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 1108...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Drew Parsons <dpars...@debian.org> (supplier of updated mdanalysis 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: Fri, 04 Jul 2025 10:23:27 +0200
Source: mdanalysis
Architecture: source
Version: 2.9.0-9
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Closes: 1108309
Changes:
mdanalysis (2.9.0-9) unstable; urgency=medium
.
* debian/tests/control: mark mdanalysis with Restrictions: flaky.
mdanalysis tests are generally unreliable and fail often and
randomly. Closes: #1108309
* debian/tests: skip tests observed failing in debci
migration-reference runs:
test_dihedral_attr_warning test_AnalysisFromFunction
test_villin_unfolded test_rmsd_frames test_file_guess_hydrogens
test_gnm_run_step test_all_backends_give_correct_results
test_startframe test_hbond_analysis
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8e3e8bd85e0e76b4acadd9b14c5a9b26b9e47c5e 15888
mdanalysis_2.9.0-9_source.buildinfo
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mdanalysis_2.9.0-9.dsc
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Files:
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ef11611b1ccd68d2b0fa6b9de87f6592 13516 python optional
mdanalysis_2.9.0-9.debian.tar.xz
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mdanalysis_2.9.0-9_source.buildinfo
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--- End Message ---
