Your message dated Mon, 27 Oct 2025 12:34:01 +0000
with message-id <[email protected]>
and subject line Bug#1118311: fixed in mdtraj 1.11.0-2
has caused the Debian Bug report #1118311,
regarding mdtraj: FTBFS: sphinx.errors.ExtensionError: Could not import
extension nbsphinx_link (exception: No module named
'docutils.utils.error_reporting')
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.)
--
1118311: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1118311
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:mdtraj
Version: 1.11.0-1
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/202510/
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:mdtraj, 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
pybuild --clean -i python{version} -p 3.13
I: pybuild base:311: python3.13 setup.py clean
Using built-in specs.
COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-linux-gnu/15/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debi
[too-long-redacted] n --enable-link-serialization=3
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 15.2.0 (Debian 15.2.0-4)
[... snipped ...]
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byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/hbond.py
to hbond.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/rg.py
to rg.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/thermodynamic_properties.py
to thermodynamic_properties.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/contact.py
to contact.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/internal.py
to internal.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/angle.py
to angle.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/dssp.py
to dssp.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/alignment.py
to alignment.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/rdf.py
to rdf.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/geometry/pi_stacking.py
to pi_stacking.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/__init__.py
to __init__.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/xtcreporter.py
to xtcreporter.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/dcdreporter.py
to dcdreporter.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/basereporter.py
to basereporter.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/hdf5reporter.py
to hdf5reporter.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/reporters/netcdfreporter.py
to netcdfreporter.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/netcdf.py
to netcdf.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/__init__.py
to __init__.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/gsd.py
to gsd.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/amberrst.py
to amberrst.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/openmmxml.py
to openmmxml.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/registry.py
to registry.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/lammpstrj.py
to lammpstrj.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/prmtop.py
to prmtop.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/gro.py
to gro.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/mdcrd.py
to mdcrd.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/arc.py
to arc.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/xyzfile.py
to xyzfile.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/mol2.py
to mol2.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/lh5.py
to lh5.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/__init__.py
to __init__.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/pdbstructure.py
to pdbstructure.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdb/pdbfile.py
to pdbfile.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/hdf5.py
to hdf5.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/hoomdxml.py
to hoomdxml.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx/__init__.py
to __init__.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx/pdbx.py
to pdbx.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx/PdbxContainers.py
to PdbxContainers.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx/PdbxReader.py
to PdbxReader.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/pdbx/pdbxfile.py
to pdbxfile.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/formats/psf.py
to psf.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/__init__.py
to __init__.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/rotation.py
to rotation.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/zipped.py
to zipped.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/singleton.py
to singleton.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/validation.py
to validation.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/__init__.py
to __init__.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/prefix.py
to prefix.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/constants.py
to constants.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/basedimension.py
to basedimension.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/unit.py
to unit.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/unit_operators.py
to unit_operators.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/standard_dimensions.py
to standard_dimensions.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/baseunit.py
to baseunit.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/mymatrix.py
to mymatrix.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/doctests.py
to doctests.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/unit_math.py
to unit_math.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/unit_definitions.py
to unit_definitions.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unit/quantity.py
to quantity.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/contextmanagers.py
to contextmanagers.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/unitcell.py
to unitcell.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/utils/delay_import.py
to delay_import.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/io.py
to io.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/_version.py
to _version.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/__init__.py
to __init__.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/docstrings.py
to docstrings.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/testing.py
to testing.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/testing/docscrape.py
to docscrape.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/mdinspect.py
to mdinspect.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/__init__.py
to __init__.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/scripts/mdconvert.py
to mdconvert.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/__init__.py
to __init__.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/scalar_couplings.py
to scalar_couplings.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/nmr/shift_wrappers.py
to shift_wrappers.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/__init__.py
to __init__.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/selection.py
to selection.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/trajectory.py
to trajectory.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/residue_names.py
to residue_names.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/topology.py
to topology.cpython-313.pyc
byte-compiling
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj/core/element.py
to element.cpython-313.pyc
running install_egg_info
running egg_info
creating mdtraj.egg-info
writing mdtraj.egg-info/PKG-INFO
writing dependency_links to mdtraj.egg-info/dependency_links.txt
writing entry points to mdtraj.egg-info/entry_points.txt
writing requirements to mdtraj.egg-info/requires.txt
writing top-level names to mdtraj.egg-info/top_level.txt
writing manifest file 'mdtraj.egg-info/SOURCES.txt'
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayscalars.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h
won't be automatically included in the manifest: the path must be relative
dependency
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ufuncobject.h
won't be automatically included in the manifest: the path must be relative
reading manifest file 'mdtraj.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching '__pycache__'
no previously-included directories found matching '*.pyc'
adding license file 'LICENSE'
writing manifest file 'mdtraj.egg-info/SOURCES.txt'
Copying mdtraj.egg-info to
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/lib/python3.13/dist-packages/mdtraj-1.11.0.egg-info
Skipping SOURCES.txt
running install_scripts
Installing mdconvert-mdtraj script to
/<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/bin
Installing mdinspect script to /<<PKGBUILDDIR>>/debian/python3-mdtraj/usr/bin
debian/rules execute_after_dh_auto_install-indep
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cp -a /<<PKGBUILDDIR>>/examples /<<PKGBUILDDIR>>/examples.orig
mkdir -p /<<PKGBUILDDIR>>/build/html/examples/iterload
ln -s /<<PKGBUILDDIR>>/examples/data
/<<PKGBUILDDIR>>/build/html/examples/iterload/data
sed "s|http://www.rcsb.org/pdb/files|/<<PKGBUILDDIR>>/debian/external|g" -i
/<<PKGBUILDDIR>>/examples/*.ipynb
PYTHONPATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_mdtraj/build \
MPLCONFIGDIR=/<<PKGBUILDDIR>>/build/matplotlib \
make -C docs BUILDDIR=/<<PKGBUILDDIR>>/build html
make[2]: Entering directory '/<<PKGBUILDDIR>>/docs'
sphinx-build -b html -d /<<PKGBUILDDIR>>/build/doctrees .
/<<PKGBUILDDIR>>/build/html
Running Sphinx v8.2.3
loading translations [en]... done
Extension error!
Versions
========
* Platform: linux;
(Linux-6.12.48+deb13-cloud-amd64-x86_64-with-glibc2.41)
* Python version: 3.13.9 (CPython)
* Sphinx version: 8.2.3
* Docutils version: 0.22.2
* Jinja2 version: 3.1.6
* Pygments version: 2.18.0
Last Messages
=============
None.
Loaded Extensions
=================
None.
Traceback
=========
File "/usr/lib/python3/dist-packages/sphinx/registry.py", line 544, in
load_extension
raise ExtensionError(
__('Could not import extension %s') % extname, err
) from err
sphinx.errors.ExtensionError: Could not import extension nbsphinx_link
(exception: No module named 'docutils.utils.error_reporting')
The full traceback has been saved in:
/tmp/sphinx-err-54wbhr8n.log
To report this error to the developers, please open an issue at
<https://github.com/sphinx-doc/sphinx/issues/>. Thanks!
Please also report this if it was a user error, so that a better error message
can be provided next time.
make[2]: *** [Makefile:53: html] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/docs'
make[1]: *** [debian/rules:42: execute_after_dh_auto_install-indep] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:13: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: mdtraj
Source-Version: 1.11.0-2
Done: Drew Parsons <[email protected]>
We believe that the bug you reported is fixed in the latest version of
mdtraj, 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 mdtraj 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])
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Hash: SHA512
Format: 1.8
Date: Mon, 27 Oct 2025 12:41:01 +0100
Source: mdtraj
Architecture: source
Version: 1.11.0-2
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Drew Parsons <[email protected]>
Closes: 1118311
Changes:
mdtraj (1.11.0-2) unstable; urgency=medium
.
* update debian patch drop_notebook_in_docs.patch to also drop
nbsphinx_link, which requires an obsolete docutils.
Remove Build-Depends: python3-nbsphinx-link.
See Bug#1118325. Closes: #1118311.
* Build-Depends: pybuild-plugin-pyproject to use pyproject.toml
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