[Debichem-devel] Bug#1114702: mdanalysis: FTBFS with NumPy 2.3
roehling at debian.org
roehling at debian.org
Mon Sep 8 20:44:19 BST 2025
Source: mdanalysis
Version: 2.9.0-12
Severity: important
User: debian-python at lists.debian.org
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
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