Bug#1082098: pynfft FTBFS with Python 3.13

Stefano Rivera stefanor at debian.org
Wed Sep 18 10:56:17 BST 2024 

Source: pynfft
Version: 1.3.2-10
Severity: normal
User: debian-python at lists.debian.org
Usertags: python3.13

This package failed build from source when test-built against a version of
python3-defaults that includes 3.13 as a supported version.

To reproduce this issue, build against python3-defaults (python3-all-dev etc.)
from Debian experimental.

In this case, pynfft needs to get off cython3-legacy and build with a
modern cython that can support 3.13.

What's new in Python 3.13:
https://docs.python.org/3.13/whatsnew/3.13.html

Log snippet:

11733 |                 int ret = _PyLong_AsByteArray((PyLongObject *)v,
      |                           ^~~~~~~~~~~~~~~~~~~
/usr/include/python3.13/cpython/longobject.h:111:17: note: declared here
  111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v,
      |                 ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/pynfft/nfft.c: In function ‘__Pyx_PyInt_As_Py_intptr_t’:
/<<PKGBUILDDIR>>/pynfft/nfft.c:11929:27: error: too few arguments to function ‘_PyLong_AsByteArray’
11929 |                 int ret = _PyLong_AsByteArray((PyLongObject *)v,
      |                           ^~~~~~~~~~~~~~~~~~~
/usr/include/python3.13/cpython/longobject.h:111:17: note: declared here
  111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v,
      |                 ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/pynfft/nfft.c: In function ‘__Pyx_PyInt_As_unsigned_int’:
/<<PKGBUILDDIR>>/pynfft/nfft.c:12163:27: error: too few arguments to function ‘_PyLong_AsByteArray’
12163 |                 int ret = _PyLong_AsByteArray((PyLongObject *)v,
      |                           ^~~~~~~~~~~~~~~~~~~
/usr/include/python3.13/cpython/longobject.h:111:17: note: declared here
  111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v,
      |                 ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/pynfft/nfft.c: In function ‘__Pyx_PyInt_As_long’:
/<<PKGBUILDDIR>>/pynfft/nfft.c:12397:27: error: too few arguments to function ‘_PyLong_AsByteArray’
12397 |                 int ret = _PyLong_AsByteArray((PyLongObject *)v,
      |                           ^~~~~~~~~~~~~~~~~~~
/usr/include/python3.13/cpython/longobject.h:111:17: note: declared here
  111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v,
      |                 ^~~~~~~~~~~~~~~~~~~
error: command '/usr/bin/aarch64-linux-gnu-gcc' 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 
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pynfft/build/pynfft
copying pynfft/version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pynfft/build/pynfft
copying pynfft/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pynfft/build/pynfft
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pynfft/build/pynfft/tests
copying pynfft/tests/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pynfft/build/pynfft/tests
copying pynfft/tests/test_nfft.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pynfft/build/pynfft/tests
running build_ext
building 'pynfft.nfft' extension
creating build/temp.linux-aarch64-cpython-312
creating build/temp.linux-aarch64-cpython-312/build
creating build/temp.linux-aarch64-cpython-312/<<BUILDDIR>>
creating build/temp.linux-aarch64-cpython-312/<<PKGBUILDDIR>>
creating build/temp.linux-aarch64-cpython-312/<<PKGBUILDDIR>>/pynfft
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -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/python3.12 -c /<<PKGBUILDDIR>>/pynfft/nfft.c -o build/temp.linux-aarch64-cpython-312/<<PKGBUILDDIR>>/pynfft/nfft.o -O3 -fomit-frame-pointer -fstrict-aliasing -ffast-math
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 /<<PKGBUILDDIR>>/pynfft/nfft.c:789:
/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 " \
      |  ^~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/<<PKGBUILDDIR>>/pynfft/nfft.o -L/usr/lib/aarch64-linux-gnu -lnfft3_threads -lnfft3 -lfftw3_threads -lfftw3 -lm -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pynfft/build/pynfft/nfft.cpython-312-aarch64-linux-gnu.so
building 'pynfft.solver' extension
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -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/python3.12 -c /<<PKGBUILDDIR>>/pynfft/solver.c -o build/temp.linux-aarch64-cpython-312/<<PKGBUILDDIR>>/pynfft/solver.o -O3 -fomit-frame-pointer -fstrict-aliasing -ffast-math
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 /<<PKGBUILDDIR>>/pynfft/solver.c:787:
/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 " \
      |  ^~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/<<PKGBUILDDIR>>/pynfft/solver.o -L/usr/lib/aarch64-linux-gnu -lnfft3_threads -lnfft3 -lfftw3_threads -lfftw3 -lm -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pynfft/build/pynfft/solver.cpython-312-aarch64-linux-gnu.so
building 'pynfft.util' extension
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -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/python3.12 -c /<<PKGBUILDDIR>>/pynfft/util.c -o build/temp.linux-aarch64-cpython-312/<<PKGBUILDDIR>>/pynfft/util.o -O3 -fomit-frame-pointer -fstrict-aliasing -ffast-math
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 /<<PKGBUILDDIR>>/pynfft/util.c:787:
/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 " \
      |  ^~~~~~~
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/<<PKGBUILDDIR>>/pynfft/util.o -L/usr/lib/aarch64-linux-gnu -lnfft3_threads -lnfft3 -lfftw3_threads -lfftw3 -lm -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pynfft/build/pynfft/util.cpython-312-aarch64-linux-gnu.so
dh_auto_build: error: pybuild --build -i python{version} -p "3.13 3.12" returned exit code 13
make: *** [debian/rules:9: binary-arch] Error 25
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2024-09-18T08:33:40Z


If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/artifact/775269/

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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