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... 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[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... 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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 --------------------------------------------------------------------------------
