Your message dated Mon, 8 Jun 2026 01:01:11 +0200
with message-id <aiX4N6I_lsMd3Nc2@nuc>
and subject line mdanalysis: FTBFS randomly: autobuilder hangs
has caused the Debian Bug report #1108309,
regarding mdanalysis: FTBFS randomly: autobuilder hangs
to be marked as done.
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Bug report if necessary, and/or fix the problem forthwith.
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--
1108309: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1108309
Debian Bug Tracking System
Contact [email protected] 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 ---
This package used to fail 100% of the time in a reproducible way, but
at some point between 2026-05-24 and 2026-05-30, it started to work
again, and I have at least 30 successful builds after such date
without a single failure.
When I compare build logs, I see this difference:
-Setting up python3-scipy (1.16.3-4) ...
+Setting up python3-scipy (1.17.1-4) ...
I assume this was a bug in scipy after all, so I'm closing the bug.
Cc to Paul because of this note which Graham Inggs left in #1108997
when we requested a hint for trixie:
> I've added a skiptest hint for now. This will be fine for trixie.
> Please let elbrus know when the autopkgtests are properly fixed and
> can be enabled again.
So: If the autopkgtests are still disabled, I guess it would be ok to
reenable them again.
Thanks.
--- End Message ---
