Your message dated Sun, 12 Jul 2026 12:49:14 +0000
with message-id <[email protected]>
and subject line Bug#1140985: fixed in mdanalysis 2.10.0-4
has caused the Debian Bug report #1140985,
regarding mdanalysis: FTBFS: ERROR
testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupToTopology
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
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1140985: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1140985
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:mdanalysis
Version: 2.10.0-3
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, this package failed to build.
Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:
https://people.debian.org/~sanvila/build-logs/202606/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:mdanalysis, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --with sphinxdoc --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
debian/rules execute_after_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f .duecredit.p
rm -f package/MDAnalysis/authors.py
rm -f package/MDAnalysis/analysis/encore/clustering/affinityprop.c \
package/MDAnalysis/analysis/encore/cutils.c \
package/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c
\
package/MDAnalysis/coordinates/timestep.cpp \
package/MDAnalysis/lib/_augment.cpp \
package/MDAnalysis/lib/_cutil.cpp \
package/MDAnalysis/lib/c_distances.c \
package/MDAnalysis/lib/c_distances_openmp.c \
[... snipped ...]
writing output... [ 85%] documentation_pages/topology/PQRParser
writing output... [ 85%] documentation_pages/topology/PSFParser
writing output... [ 86%] documentation_pages/topology/TOPParser
writing output... [ 87%] documentation_pages/topology/TPRParser
writing output... [ 87%] documentation_pages/topology/TXYZParser
writing output... [ 88%] documentation_pages/topology/XYZParser
writing output... [ 88%] documentation_pages/topology/base
writing output... [ 89%] documentation_pages/topology/core
writing output... [ 89%] documentation_pages/topology/guessers
writing output... [ 90%] documentation_pages/topology/init
writing output... [ 91%] documentation_pages/topology/tables
writing output... [ 91%] documentation_pages/topology/tpr_util
writing output... [ 92%] documentation_pages/topology_modules
writing output... [ 92%] documentation_pages/trajectory_transformations
writing output... [ 93%] documentation_pages/transformations/base
writing output... [ 93%] documentation_pages/transformations/boxdimensions
writing output... [ 94%] documentation_pages/transformations/fit
writing output... [ 94%] documentation_pages/transformations/nojump
writing output... [ 95%] documentation_pages/transformations/positionaveraging
writing output... [ 96%] documentation_pages/transformations/rotate
writing output... [ 96%] documentation_pages/transformations/translate
writing output... [ 97%] documentation_pages/transformations/wrap
writing output... [ 97%] documentation_pages/units
writing output... [ 98%] documentation_pages/version
writing output... [ 98%] documentation_pages/visualization/streamlines
writing output... [ 99%] documentation_pages/visualization/streamlines_3D
writing output... [ 99%] documentation_pages/visualization_modules
writing output... [100%] index
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_mdanalysis/build/MDA
[too-long-redacted] eaderBase.n_frames [ref.python]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_mdanalysis/build/MDA
[too-long-redacted] eaderBase.n_frames [ref.python]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_mdanalysis/build/MDA
[too-long-redacted] eaderBase.n_frames [ref.python]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_mdanalysis/build/MDA
[too-long-redacted] eaderBase.n_frames [ref.python]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_mdanalysis/build/MDA
[too-long-redacted] eaderBase.n_frames [ref.python]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_mdanalysis/build/MDA
[too-long-redacted] eaderBase.n_frames [ref.python]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_mdanalysis/build/MDAnalysis/analysis/pca.py:docstring
of MDAnalysis.analysis.pca:81: WARNING: more than one target found for
cross-reference 'frames': MDAnalysis.analysis.base.AnalysisBase.frames,
MDAnalysis.analysis.base.AnalysisFromFunction.results.frames,
MDAnalysis.analysis.base.results.frames [ref.python]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_mdanalysis/build/MDAnalysis/converters/RDKitInferring.py:docstring
of MDAnalysis.converters.RDKitInferring.RDKitInferrer:1: WARNING: undefined
label: 'https://github.com/jensengroup/xyz2mol' [ref.ref]
WARNING: more than one target found for cross-reference 'type':
MDAnalysis.core.topologyobjects.TopologyObject.type,
MDAnalysis.topology.tpr.obj.Atoms.type [ref.python]
generating indices... genindex py-modindex done
highlighting module code... [ 1%] MDAnalysis.analysis.align
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MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod
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highlighting module code... [ 34%] MDAnalysis.coordinates.CRD
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highlighting module code... [ 38%] MDAnalysis.coordinates.GMS
highlighting module code... [ 38%] MDAnalysis.coordinates.GRO
highlighting module code... [ 39%] MDAnalysis.coordinates.GSD
highlighting module code... [ 39%] MDAnalysis.coordinates.H5MD
highlighting module code... [ 40%] MDAnalysis.coordinates.IMD
highlighting module code... [ 41%] MDAnalysis.coordinates.INPCRD
highlighting module code... [ 41%] MDAnalysis.coordinates.LAMMPS
highlighting module code... [ 42%] MDAnalysis.coordinates.MMTF
highlighting module code... [ 42%] MDAnalysis.coordinates.MOL2
highlighting module code... [ 43%] MDAnalysis.coordinates.NAMDBIN
highlighting module code... [ 44%] MDAnalysis.coordinates.PDB
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highlighting module code... [ 45%] MDAnalysis.coordinates.PQR
highlighting module code... [ 46%] MDAnalysis.coordinates.TNG
highlighting module code... [ 46%] MDAnalysis.coordinates.TPR
highlighting module code... [ 47%] MDAnalysis.coordinates.TRC
highlighting module code... [ 48%] MDAnalysis.coordinates.TRJ
highlighting module code... [ 48%] MDAnalysis.coordinates.TRR
highlighting module code... [ 49%] MDAnalysis.coordinates.TRZ
highlighting module code... [ 49%] MDAnalysis.coordinates.TXYZ
highlighting module code... [ 50%] MDAnalysis.coordinates.XDR
highlighting module code... [ 51%] MDAnalysis.coordinates.XTC
highlighting module code... [ 51%] MDAnalysis.coordinates.XYZ
highlighting module code... [ 52%] MDAnalysis.coordinates.base
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highlighting module code... [ 53%] MDAnalysis.coordinates.chemfiles
highlighting module code... [ 54%] MDAnalysis.coordinates.core
highlighting module code... [ 54%] MDAnalysis.coordinates.memory
highlighting module code... [ 55%] MDAnalysis.coordinates.null
highlighting module code... [ 56%] MDAnalysis.coordinates.timestep
highlighting module code... [ 56%] MDAnalysis.core._get_readers
highlighting module code... [ 57%] MDAnalysis.core.accessors
highlighting module code... [ 57%] MDAnalysis.core.groups
highlighting module code... [ 58%] MDAnalysis.core.selection
highlighting module code... [ 59%] MDAnalysis.core.topology
highlighting module code... [ 59%] MDAnalysis.core.topologyattrs
highlighting module code... [ 60%] MDAnalysis.core.topologyobjects
highlighting module code... [ 61%] MDAnalysis.core.universe
highlighting module code... [ 61%] MDAnalysis.exceptions
highlighting module code... [ 62%] MDAnalysis.guesser.base
highlighting module code... [ 62%] MDAnalysis.guesser.default_guesser
highlighting module code... [ 63%] MDAnalysis.guesser.tables
highlighting module code... [ 64%] MDAnalysis.lib.NeighborSearch
highlighting module code... [ 64%] MDAnalysis.lib._augment
highlighting module code... [ 65%] MDAnalysis.lib._cutil
highlighting module code... [ 66%] MDAnalysis.lib.correlations
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highlighting module code... [ 67%] MDAnalysis.lib.formats.libdcd
highlighting module code... [ 68%] MDAnalysis.lib.formats.libmdaxdr
highlighting module code... [ 68%] MDAnalysis.lib.log
highlighting module code... [ 69%] MDAnalysis.lib.mdamath
highlighting module code... [ 69%] MDAnalysis.lib.nsgrid
highlighting module code... [ 70%] MDAnalysis.lib.picklable_file_io
highlighting module code... [ 71%] MDAnalysis.lib.pkdtree
highlighting module code... [ 71%] MDAnalysis.lib.qcprot
highlighting module code... [ 72%] MDAnalysis.lib.transformations
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highlighting module code... [ 73%] MDAnalysis.selections
highlighting module code... [ 74%] MDAnalysis.selections.base
highlighting module code... [ 74%] MDAnalysis.selections.charmm
highlighting module code... [ 75%] MDAnalysis.selections.gromacs
highlighting module code... [ 76%] MDAnalysis.selections.jmol
highlighting module code... [ 76%] MDAnalysis.selections.pymol
highlighting module code... [ 77%] MDAnalysis.selections.vmd
highlighting module code... [ 78%] MDAnalysis.topology.CRDParser
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highlighting module code... [ 79%] MDAnalysis.topology.DMSParser
highlighting module code... [ 79%] MDAnalysis.topology.ExtendedPDBParser
highlighting module code... [ 80%] MDAnalysis.topology.FHIAIMSParser
highlighting module code... [ 81%] MDAnalysis.topology.GMSParser
highlighting module code... [ 81%] MDAnalysis.topology.GROParser
highlighting module code... [ 82%] MDAnalysis.topology.GSDParser
highlighting module code... [ 82%] MDAnalysis.topology.HoomdXMLParser
highlighting module code... [ 83%] MDAnalysis.topology.ITPParser
highlighting module code... [ 84%] MDAnalysis.topology.LAMMPSParser
highlighting module code... [ 84%] MDAnalysis.topology.MMTFParser
highlighting module code... [ 85%] MDAnalysis.topology.MOL2Parser
highlighting module code... [ 86%] MDAnalysis.topology.MinimalParser
highlighting module code... [ 86%] MDAnalysis.topology.PDBParser
highlighting module code... [ 87%] MDAnalysis.topology.PDBQTParser
highlighting module code... [ 88%] MDAnalysis.topology.PQRParser
highlighting module code... [ 88%] MDAnalysis.topology.PSFParser
highlighting module code... [ 89%] MDAnalysis.topology.TOPParser
highlighting module code... [ 89%] MDAnalysis.topology.TPRParser
highlighting module code... [ 90%] MDAnalysis.topology.TXYZParser
highlighting module code... [ 91%] MDAnalysis.topology.XYZParser
highlighting module code... [ 91%] MDAnalysis.topology.base
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highlighting module code... [ 99%] MDAnalysis.visualization.streamlines
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highlighting module code... [100%] builtins
writing additional pages... search opensearch done
copying images... [ 10%] images/rama_ref_plot.png
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dumping search index in English (code: en)... done
dumping object inventory... done
sphinx-sitemap: sitemap.xml was generated for URL https://docs.mdanalysis.org/
in /<<PKGBUILDDIR>>/.pybuild/html/sitemap.xml
build succeeded, 42 warnings.
The HTML pages are in ../../../.pybuild/html.
Build finished. The HTML pages are in /<<PKGBUILDDIR>>/.pybuild/html.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/package/doc/sphinx'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
py3versions: no X-Python3-Version in control file, using supported versions
set -e; \
for py in 3.13 3.14; do \
echo "=== testing with python$py ==="; \
pydir=`pybuild -p $py --system=distutils --print {build_dir}`; \
MPLBACKEND=agg PYTHONPATH=$pydir python$py -mpytest -v -k "not ( parallel or
multiprocess or openmp or gsd or GSD or test_distances or
test_all_import[.analysis.hole2] or journal.pcbi.1004568 )"
--disable-pytest-warnings testsuite; \
rm -rf $pydir/MDAnalysis/.hypothesis; \
rm -rf $pydir/MDAnalysis/.duecredit.p; \
done
=== testing with python3.13 ===
============================= test session starts ==============================
platform linux -- Python 3.13.14, pytest-9.1.1, pluggy-1.6.0 --
/usr/bin/python3.13
cachedir: .pytest_cache
hypothesis profile 'default'
rootdir: /<<PKGBUILDDIR>>/testsuite
configfile: pyproject.toml
plugins: hypothesis-6.152.4, typeguard-4.4.4
collecting ... collected 21496 items / 1 error / 3932 deselected / 6 skipped /
17564 selected
==================================== ERRORS ====================================
___________ ERROR collecting MDAnalysisTests/core/test_atomgroup.py ____________
MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupToTopology::test_VE: in
"parametrize" the number of names (1):
['btype']
must be equal to the number of values (4):
bond
=========================== short test summary info ============================
ERROR testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupToTopology
!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!
========== 6 skipped, 3932 deselected, 32 warnings, 1 error in 13.06s ==========
2026-06-28 04:57:03,072 [WARNING] DueCredit internal failure while running
<function DueSwitch.dump at 0x7f225f0eb420>: PermissionError(13, 'Permission
denied'). Please report to developers at
https://github.com/duecredit/duecredit/issues (utils.py:207)
DueCredit Report:
- Molecular simulation analysis library / MDAnalysis (v 2.10.0) [1, 2]
- Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.10.0) [3]
- DSSP algorithm description / MDAnalysis.analysis.dssp (v 2.10.0) [4]
- ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.10.0) [5]
- Hydrogen bond analysis implementation /
MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.10.0) [6]
- Hydrogen bonding autocorrelation time /
MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.10.0) [7]
- LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.10.0) [2]
- FCA fast correlation algorithm, Mean Squared Displacements with tidynamics
/ MDAnalysis.analysis.msd (v 2.10.0) [8, 9]
- QCProt implementation / MDAnalysis.lib.qcprot (v 2.10.0) [10, 11]
- Scientific tools library / numpy (v 2.4.6) [12]
2 packages cited
8 modules cited
0 functions cited
References
----------
[1] make[1]: *** [debian/rules:122: override_dh_auto_test] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:98: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit
status 2
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: mdanalysis
Source-Version: 2.10.0-4
Done: Drew Parsons <[email protected]>
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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Drew Parsons <[email protected]> (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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 12 Jul 2026 13:36:23 +0200
Source: mdanalysis
Architecture: source
Version: 2.10.0-4
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Drew Parsons <[email protected]>
Closes: 1121449 1140985
Changes:
mdanalysis (2.10.0-4) unstable; urgency=medium
.
* debian patch test_atomgroup_PR5401.patch applies upstream PR#5401
to fix test_VE parameters in test_atomgroup.py. Closes: #1140985
* remove installed doc files from the python package. Upstream placed
the doc dir in the package subdir, so they get installed as if
they're part of the python package. Closes: #1121449
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