#1140985 mdanalysis: FTBFS: ERROR testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupToTopology

Package:
src:mdanalysis
Source:
src:mdanalysis
Submitter:
Santiago Vila
Date:
2026-06-28 20:54:37 UTC
Severity:
normal
Tags:
#1140985#5
Date:
2026-06-28 20:51:21 UTC
From:
To:
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
highlighting module code... [  1%] MDAnalysis.analysis.atomicdistances
highlighting module code... [  2%] MDAnalysis.analysis.backends
highlighting module code... [  2%] MDAnalysis.analysis.base
highlighting module code... [  3%] MDAnalysis.analysis.bat
highlighting module code... [  4%] MDAnalysis.analysis.contacts
highlighting module code... [  4%] MDAnalysis.analysis.density
highlighting module code... [  5%] MDAnalysis.analysis.dielectric
highlighting module code... [  6%] MDAnalysis.analysis.diffusionmap
highlighting module code... [  6%] MDAnalysis.analysis.dihedrals
highlighting module code... [  7%] MDAnalysis.analysis.distances
highlighting module code... [  8%] MDAnalysis.analysis.dssp.dssp
highlighting module code... [  8%] MDAnalysis.analysis.dssp.pydssp_numpy
highlighting module code... [  9%] MDAnalysis.analysis.encore.bootstrap
highlighting module code... [  9%] MDAnalysis.analysis.encore.clustering.ClusterCollection
highlighting module code... [ 10%] MDAnalysis.analysis.encore.clustering.ClusteringMethod
highlighting module code... [ 11%] MDAnalysis.analysis.encore.clustering.affinityprop
highlighting module code... [ 11%] MDAnalysis.analysis.encore.clustering.cluster
highlighting module code... [ 12%] MDAnalysis.analysis.encore.confdistmatrix
highlighting module code... [ 12%] MDAnalysis.analysis.encore.covariance
highlighting module code... [ 13%] MDAnalysis.analysis.encore.cutils
highlighting module code... [ 14%] MDAnalysis.analysis.encore.dimensionality_reduction.DimensionalityReductionMethod
highlighting module code... [ 14%] MDAnalysis.analysis.encore.dimensionality_reduction.reduce_dimensionality
highlighting module code... [ 15%] MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed
highlighting module code... [ 16%] MDAnalysis.analysis.encore.similarity
highlighting module code... [ 16%] MDAnalysis.analysis.encore.utils
highlighting module code... [ 17%] MDAnalysis.analysis.gnm
highlighting module code... [ 18%] MDAnalysis.analysis.helix_analysis
highlighting module code... [ 18%] MDAnalysis.analysis.hydrogenbonds.hbond_analysis
highlighting module code... [ 19%] MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel
highlighting module code... [ 19%] MDAnalysis.analysis.hydrogenbonds.wbridge_analysis
highlighting module code... [ 20%] MDAnalysis.analysis.leaflet
highlighting module code... [ 21%] MDAnalysis.analysis.legacy.x3dna
highlighting module code... [ 21%] MDAnalysis.analysis.lineardensity
highlighting module code... [ 22%] MDAnalysis.analysis.msd
highlighting module code... [ 22%] MDAnalysis.analysis.nucleicacids
highlighting module code... [ 23%] MDAnalysis.analysis.nuclinfo
highlighting module code... [ 24%] MDAnalysis.analysis.pca
highlighting module code... [ 24%] MDAnalysis.analysis.polymer
highlighting module code... [ 25%] MDAnalysis.analysis.rdf
highlighting module code... [ 26%] MDAnalysis.analysis.results
highlighting module code... [ 26%] MDAnalysis.analysis.rms
highlighting module code... [ 27%] MDAnalysis.auxiliary.EDR
highlighting module code... [ 28%] MDAnalysis.auxiliary.XVG
highlighting module code... [ 28%] MDAnalysis.auxiliary.base
highlighting module code... [ 29%] MDAnalysis.auxiliary.core
highlighting module code... [ 29%] MDAnalysis.converters.OpenMM
highlighting module code... [ 30%] MDAnalysis.converters.OpenMMParser
highlighting module code... [ 31%] MDAnalysis.converters.ParmEd
highlighting module code... [ 31%] MDAnalysis.converters.ParmEdParser
highlighting module code... [ 32%] MDAnalysis.converters.RDKit
highlighting module code... [ 32%] MDAnalysis.converters.RDKitInferring
highlighting module code... [ 33%] MDAnalysis.converters.RDKitParser
highlighting module code... [ 34%] MDAnalysis.converters.base
highlighting module code... [ 34%] MDAnalysis.coordinates.CRD
highlighting module code... [ 35%] MDAnalysis.coordinates.DCD
highlighting module code... [ 36%] MDAnalysis.coordinates.DLPoly
highlighting module code... [ 36%] MDAnalysis.coordinates.DMS
highlighting module code... [ 37%] MDAnalysis.coordinates.FHIAIMS
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
highlighting module code... [ 44%] MDAnalysis.coordinates.PDBQT
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
highlighting module code... [ 52%] MDAnalysis.coordinates.chain
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
highlighting module code... [ 66%] MDAnalysis.lib.distances
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
highlighting module code... [ 72%] MDAnalysis.lib.util
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
highlighting module code... [ 78%] MDAnalysis.topology.DLPolyParser
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
highlighting module code... [ 92%] MDAnalysis.topology.tpr.obj
highlighting module code... [ 92%] MDAnalysis.topology.tpr.utils
highlighting module code... [ 93%] MDAnalysis.transformations.base
highlighting module code... [ 94%] MDAnalysis.transformations.boxdimensions
highlighting module code... [ 94%] MDAnalysis.transformations.fit
highlighting module code... [ 95%] MDAnalysis.transformations.nojump
highlighting module code... [ 96%] MDAnalysis.transformations.positionaveraging
highlighting module code... [ 96%] MDAnalysis.transformations.rotate
highlighting module code... [ 97%] MDAnalysis.transformations.translate
highlighting module code... [ 98%] MDAnalysis.transformations.wrap
highlighting module code... [ 98%] MDAnalysis.units
highlighting module code... [ 99%] MDAnalysis.visualization.streamlines
highlighting module code... [ 99%] MDAnalysis.visualization.streamlines_3D
highlighting module code... [100%] builtins

writing additional pages... search opensearch done
copying images... [ 10%] images/rama_ref_plot.png
copying images... [ 20%] images/janin_ref_plot.png
copying images... [ 30%] images/rama_demo_plot.png
copying images... [ 40%] images/janin_demo_plot.png
copying images... [ 50%] images/msd_demo_plot.png
copying images... [ 60%] images/AnalysisBase_parallel.png
copying images... [ 70%] images/parallelization_time.png
copying images... [ 80%] images/RSMD_plot.png
copying images... [ 90%] documentation_pages/visualization/testing_streamline.png
copying images... [100%] documentation_pages/visualization/test_streamplot_3D.png

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 ====================================