Bug#1081631: FTBFS with Python 3.13

Stefano Rivera stefanor at debian.org
Fri Sep 13 11:17:20 BST 2024 

Source: pyzoltan
Version: 1.0.1-9
Severity: serious
Tags: ftbfs
Justification: FTBFS

This package failed build from source when test-built.

The rebuild was part of a Python 3.13 rebuild, but it reproduces in a
pristine sid environment.

Log snippet:

creating build/temp.linux-aarch64-cpython-313/pyzoltan/core
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/trilinos -I/<<PKGBUILDDIR>>/pyzoltan/czoltan -I/usr/lib/python3/dist-packages/cyarray -I/usr/lib/python3/dist-packages/mpi4py/include -I/usr/include/python3.13 -c pyzoltan/core/zoltan.cpp -o build/temp.linux-aarch64-cpython-313/pyzoltan/core/zoltan.o -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from pyzoltan/core/zoltan.cpp:1291:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
pyzoltan/core/zoltan.cpp:2287:3: error: ‘MPI_Session’ does not name a type
 2287 |   MPI_Session ob_mpi;
      |   ^~~~~~~~~~~
error: command '/usr/bin/aarch64-linux-gnu-g++' failed with exit code 1
E: pybuild pybuild:389: build: plugin distutils failed with: exit code=1: /usr/bin/python3.13 setup.py build 
I: pybuild base:311: /usr/bin/python3 setup.py build 
----------------------------------------------------------------------
Using Zoltan from:
/usr/include/trilinos
/usr/lib
----------------------------------------------------------------------
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'setup_requres'
  warnings.warn(msg)
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan
copying pyzoltan/api.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan
copying pyzoltan/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core
copying pyzoltan/core/zoltan_utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core
copying pyzoltan/core/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/czoltan
copying pyzoltan/czoltan/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/czoltan
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/tools
copying pyzoltan/tools/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/tools
copying pyzoltan/tools/run_parallel_script.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/tools
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core/tests
copying pyzoltan/core/tests/zcomm.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core/tests
copying pyzoltan/core/tests/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core/tests
copying pyzoltan/core/tests/3d_partition.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core/tests
copying pyzoltan/core/tests/test_zoltan.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core/tests
copying pyzoltan/core/tests/geometric_partitioner.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core/tests
running egg_info
writing PyZoltan.egg-info/PKG-INFO
writing dependency_links to PyZoltan.egg-info/dependency_links.txt
writing requirements to PyZoltan.egg-info/requires.txt
writing top-level names to PyZoltan.egg-info/top_level.txt
reading manifest file 'PyZoltan.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'PyZoltan.egg-info/SOURCES.txt'
copying pyzoltan/core/__init__.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core
copying pyzoltan/core/msstdint.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core
copying pyzoltan/core/zoltan.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core
copying pyzoltan/core/zoltan_comm.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core
copying pyzoltan/core/zoltan_dd.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core
copying pyzoltan/czoltan/__init__.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/czoltan
copying pyzoltan/czoltan/czoltan.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/czoltan
copying pyzoltan/czoltan/czoltan_comm.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/czoltan
copying pyzoltan/czoltan/czoltan_config.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/czoltan
copying pyzoltan/czoltan/czoltan_dd.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/czoltan
copying pyzoltan/czoltan/czoltan_types.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/czoltan
copying pyzoltan/czoltan/mpi-compat.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/czoltan
copying pyzoltan/core/tests/mesh.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pyzoltan/build/pyzoltan/core/tests
running build_ext
building 'pyzoltan.core.zoltan' extension
creating build/temp.linux-aarch64-cpython-312
creating build/temp.linux-aarch64-cpython-312/pyzoltan
creating build/temp.linux-aarch64-cpython-312/pyzoltan/core
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/trilinos -I/<<PKGBUILDDIR>>/pyzoltan/czoltan -I/usr/lib/python3/dist-packages/cyarray -I/usr/lib/python3/dist-packages/mpi4py/include -I/usr/include/python3.12 -c pyzoltan/core/zoltan.cpp -o build/temp.linux-aarch64-cpython-312/pyzoltan/core/zoltan.o -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from pyzoltan/core/zoltan.cpp:1291:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
pyzoltan/core/zoltan.cpp:2287:3: error: ‘MPI_Session’ does not name a type
 2287 |   MPI_Session ob_mpi;
      |   ^~~~~~~~~~~
error: command '/usr/bin/aarch64-linux-gnu-g++' failed with exit code 1
E: pybuild pybuild:389: build: plugin distutils failed with: exit code=1: /usr/bin/python3 setup.py build 
dh_auto_build: error: pybuild --build -i python{version} -p "3.13 3.12" returned exit code 13
make: *** [debian/rules:14: binary-arch] Error 25
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2024-09-13T09:22:53Z


If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/artifact/709932/

This bug has been filed at "normal" severity, as we haven't started the
transition to add 3.13 as a supported version, yet. This will be raised to RC
as soon as that happens, hopefully well before trixie.

Thanks,

Stefano

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