Your message dated Tue, 21 Oct 2025 23:19:12 +0000
with message-id <[email protected]>
and subject line Bug#1114702: fixed in mdanalysis 2.10.0-1
has caused the Debian Bug report #1114702,
regarding mdanalysis: FTBFS with NumPy 2.3
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.
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--
1114702: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114702
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: mdanalysis
Version: 2.9.0-12
Severity: important
User: [email protected]
Usertags: numpy2.3
Tags: ftbfs, forky, sid
Dear maintainer,
During a test rebuild for NumPy 2.3, mdanalysis failed to rebuild.
Log Summary:
-------------------------------------------------------------------------------
[...]
In file included from
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5,
from MDAnalysis/lib/src/transformations/transformations.c:73:
MDAnalysis/lib/src/transformations/transformations.c: In function
‘PyConverter_DoubleArray’:
MDAnalysis/lib/src/transformations/transformations.c:778:53: error:
‘NPY_IN_ARRAY’ undeclared (first use in this function)
778 | *address = PyArray_FROM_OTF(object, NPY_DOUBLE, NPY_IN_ARRAY);
| ^~~~~~~~~~~~
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28:
note: in definition of macro ‘PyArray_FROM_OTF’
91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \
| ^~~~~
MDAnalysis/lib/src/transformations/transformations.c:778:53: note: each
undeclared identifier is reported only once for each function it appears in
778 | *address = PyArray_FROM_OTF(object, NPY_DOUBLE, NPY_IN_ARRAY);
| ^~~~~~~~~~~~
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28:
note: in definition of macro ‘PyArray_FROM_OTF’
91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \
| ^~~~~
MDAnalysis/lib/src/transformations/transformations.c: In function
‘PyConverter_AnyDoubleArray’:
MDAnalysis/lib/src/transformations/transformations.c:794:57: error:
‘NPY_ALIGNED’ undeclared (first use in this function); did you mean
‘Py_ALIGNED’?
794 | *address = PyArray_FROM_OTF(object, NPY_DOUBLE, NPY_ALIGNED);
| ^~~~~~~~~~~
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28:
note: in definition of macro ‘PyArray_FROM_OTF’
91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \
| ^~~~~
MDAnalysis/lib/src/transformations/transformations.c: In function
‘PyConverter_DoubleArrayOrNone’:
MDAnalysis/lib/src/transformations/transformations.c:811:57: error:
‘NPY_IN_ARRAY’ undeclared (first use in this function)
811 | *address = PyArray_FROM_OTF(object, NPY_DOUBLE, NPY_IN_ARRAY);
| ^~~~~~~~~~~~
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28:
note: in definition of macro ‘PyArray_FROM_OTF’
91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \
| ^~~~~
MDAnalysis/lib/src/transformations/transformations.c: In function
‘PyConverter_DoubleMatrix44’:
MDAnalysis/lib/src/transformations/transformations.c:826:53: error:
‘NPY_IN_ARRAY’ undeclared (first use in this function)
826 | *address = PyArray_FROM_OTF(object, NPY_DOUBLE, NPY_IN_ARRAY);
| ^~~~~~~~~~~~
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28:
note: in definition of macro ‘PyArray_FROM_OTF’
91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \
| ^~~~~
MDAnalysis/lib/src/transformations/transformations.c: In function
‘PyConverter_DoubleMatrix44Copy’:
MDAnalysis/lib/src/transformations/transformations.c:849:33: error:
‘NPY_ENSURECOPY’ undeclared (first use in this function)
849 | NPY_ENSURECOPY|NPY_IN_ARRAY);
| ^~~~~~~~~~~~~~
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28:
note: in definition of macro ‘PyArray_FROM_OTF’
91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \
| ^~~~~
MDAnalysis/lib/src/transformations/transformations.c:849:48: error:
‘NPY_IN_ARRAY’ undeclared (first use in this function)
849 | NPY_ENSURECOPY|NPY_IN_ARRAY);
| ^~~~~~~~~~~~
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28:
note: in definition of macro ‘PyArray_FROM_OTF’
91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \
| ^~~~~
MDAnalysis/lib/src/transformations/transformations.c: In function
‘PyConverter_DoubleVector3’:
MDAnalysis/lib/src/transformations/transformations.c:871:53: error:
‘NPY_IN_ARRAY’ undeclared (first use in this function)
871 | *address = PyArray_FROM_OTF(object, NPY_DOUBLE, NPY_IN_ARRAY);
| ^~~~~~~~~~~~
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28:
note: in definition of macro ‘PyArray_FROM_OTF’
91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \
| ^~~~~
MDAnalysis/lib/src/transformations/transformations.c: In function
‘PyConverter_DoubleVector4’:
MDAnalysis/lib/src/transformations/transformations.c:893:53: error:
‘NPY_IN_ARRAY’ undeclared (first use in this function)
893 | *address = PyArray_FROM_OTF(object, NPY_DOUBLE, NPY_IN_ARRAY);
| ^~~~~~~~~~~~
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28:
note: in definition of macro ‘PyArray_FROM_OTF’
91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \
| ^~~~~
MDAnalysis/lib/src/transformations/transformations.c: In function
‘PyConverter_DoubleVector4Copy’:
MDAnalysis/lib/src/transformations/transformations.c:916:33: error:
‘NPY_ENSURECOPY’ undeclared (first use in this function)
916 | NPY_ENSURECOPY|NPY_IN_ARRAY);
| ^~~~~~~~~~~~~~
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28:
note: in definition of macro ‘PyArray_FROM_OTF’
91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \
| ^~~~~
MDAnalysis/lib/src/transformations/transformations.c:916:48: error:
‘NPY_IN_ARRAY’ undeclared (first use in this function)
916 | NPY_ENSURECOPY|NPY_IN_ARRAY);
| ^~~~~~~~~~~~
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28:
note: in definition of macro ‘PyArray_FROM_OTF’
91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \
| ^~~~~
MDAnalysis/lib/src/transformations/transformations.c: In function
‘PyConverter_DoubleVector3OrNone’:
MDAnalysis/lib/src/transformations/transformations.c:941:57: error:
‘NPY_IN_ARRAY’ undeclared (first use in this function)
941 | *address = PyArray_FROM_OTF(object, NPY_DOUBLE, NPY_IN_ARRAY);
| ^~~~~~~~~~~~
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28:
note: in definition of macro ‘PyArray_FROM_OTF’
91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \
| ^~~~~
MDAnalysis/lib/src/transformations/transformations.c: In function
‘py_inverse_matrix’:
MDAnalysis/lib/src/transformations/transformations.c:3140:48: error:
‘NPY_IN_ARRAY’ undeclared (first use in this function)
3140 | NPY_IN_ARRAY);
| ^~~~~~~~~~~~
/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:91:28:
note: in definition of macro ‘PyArray_FROM_OTF’
91 | (((flags) & NPY_ARRAY_ENSURECOPY) ? \
| ^~~~~
error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
ERROR Backend subprocess exited when trying to invoke build_wheel
E: pybuild pybuild:389: build: plugin pyproject failed with: exit code=1:
python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir
/build/reproducible-path/mdanalysis-2.9.0/.pybuild/cpython3_3.13_mdanalysis
dh_auto_build: error: pybuild --build -i python{version} -p 3.13 returned exit
code 13
make: *** [debian/rules:100: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-09-08T03:01:04Z
-------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/debian/developers-roehling.numpy/artifact/2451787/
About the archive rebuild: The build was made on debusine.debian.net,
using sbuild.
You can find the build task here:
https://debusine.debian.net/debian/developers-roehling.numpy/work-request/163523/
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Cheers
Timo
--- End Message ---
--- Begin Message ---
Source: mdanalysis
Source-Version: 2.10.0-1
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: Wed, 22 Oct 2025 00:50:11 +0200
Source: mdanalysis
Architecture: source
Version: 2.10.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Drew Parsons <[email protected]>
Closes: 1114702
Changes:
mdanalysis (2.10.0-1) unstable; urgency=medium
.
* New upstream release
- supports numpy 2.3. Closes: #1114702
- Build-Depends-Indep: python3-sphinxcontrib.* for doc build:
applehelp, bibtex, devhelp, htmlhelp, qthelp, serializinghtml
* simplify debian/rules by removing nproc handling for tests
* Build-Depends: python3-numpy-dev (for dh_numpy3)
* debian patch docs_intersphinx_local.patch adds intersphinx links
to local documentation.
Build-Depends-Indep: python3-doc, python-gsd-doc, python-h5py-doc,
python-matplotlib-doc, python-numpy-doc, python-dask-doc,
python-scipy-doc, rdkit-doc
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Files:
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