[Debian-pan-maintainers] Bug#1118301: pynx: FTBFS: sphinx.errors.ExtensionError: Could not import extension nbsphinx_link (exception: No module named 'docutils.utils.error_reporting')

Santiago Vila sanvila at debian.org
Sat Oct 18 00:09:08 BST 2025 

Package: src:pynx
Version: 2025.1-2
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:pynx, so that this is still
visible in the BTS web page for this package.

Thanks.

--------------------------------------------------------------------------------
[...]
 debian/rules clean
dh clean --buildsystem=pybuild
   dh_auto_clean -O--buildsystem=pybuild
	pybuild --clean -i python{version} -p 3.13
	rm -rf .pybuild/
	find . -name \*.pyc -exec rm {} \;
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
	rm -f debian/debhelper-build-stamp
	rm -rf debian/.debhelper/
	rm -f -- debian/pynx.substvars debian/python3-pynx.substvars debian/python-pynx-doc.substvars debian/files
	rm -fr -- debian/pynx/ debian/tmp/ debian/python3-pynx/ debian/python-pynx-doc/
	find .  \( \( \
		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \

[... snipped ...]

adding 'pynx/ptycho/runner/__init__.py'
adding 'pynx/ptycho/runner/cristal.py'
adding 'pynx/ptycho/runner/cxi.py'
adding 'pynx/ptycho/runner/hermes.py'
adding 'pynx/ptycho/runner/id01.py'
adding 'pynx/ptycho/runner/id13.py'
adding 'pynx/ptycho/runner/id16a.py'
adding 'pynx/ptycho/runner/id16a_nfp.py'
adding 'pynx/ptycho/runner/nanomax.py'
adding 'pynx/ptycho/runner/nanoscopium.py'
adding 'pynx/ptycho/runner/p06.py'
adding 'pynx/ptycho/runner/parser.py'
adding 'pynx/ptycho/runner/ptypy.py'
adding 'pynx/ptycho/runner/runner.py'
adding 'pynx/ptycho/runner/simulation.py'
adding 'pynx/ptycho/runner/tps25a.py'
adding 'pynx/ptycho/runner/test/__init__.py'
adding 'pynx/ptycho/runner/test/test_runner.py'
adding 'pynx/ptycho/scripts/__init__.py'
adding 'pynx/ptycho/scripts/pynx_cristalpty.py'
adding 'pynx/ptycho/scripts/pynx_cxipty.py'
adding 'pynx/ptycho/scripts/pynx_hermespty.py'
adding 'pynx/ptycho/scripts/pynx_id01pty.py'
adding 'pynx/ptycho/scripts/pynx_id13pty.py'
adding 'pynx/ptycho/scripts/pynx_id16a_nfpty.py'
adding 'pynx/ptycho/scripts/pynx_id16apty.py'
adding 'pynx/ptycho/scripts/pynx_nanomaxpty.py'
adding 'pynx/ptycho/scripts/pynx_nanoscopiumpty.py'
adding 'pynx/ptycho/scripts/pynx_nfp2nxtomo.py'
adding 'pynx/ptycho/scripts/pynx_p06pty.py'
adding 'pynx/ptycho/scripts/pynx_ptycho_analysis.py'
adding 'pynx/ptycho/scripts/pynx_ptypy.py'
adding 'pynx/ptycho/scripts/pynx_simulationpty.py'
adding 'pynx/ptycho/scripts/pynx_tps25apty.py'
adding 'pynx/ptycho/test/__init__.py'
adding 'pynx/ptycho/test/test_ptycho.py'
adding 'pynx/scattering/__init__.py'
adding 'pynx/scattering/c_cpu.c'
adding 'pynx/scattering/cpu.cpython-313-x86_64-linux-gnu.so'
adding 'pynx/scattering/cpu.pyx'
adding 'pynx/scattering/detector.py'
adding 'pynx/scattering/fhkl.py'
adding 'pynx/scattering/fthomson.py'
adding 'pynx/scattering/gid.py'
adding 'pynx/scattering/sse_mathfun.h'
adding 'pynx/scattering/test/__init__.py'
adding 'pynx/scattering/test/test_scattering.py'
adding 'pynx/scripts/__init__.py'
adding 'pynx/scripts/pynx_info.py'
adding 'pynx/scripts/pynx_test.py'
adding 'pynx/test/__init__.py'
adding 'pynx/test/speed.py'
adding 'pynx/test/test_imports.py'
adding 'pynx/test/test_runner_datasets.py'
adding 'pynx/utils/__init__.py'
adding 'pynx/utils/_phase_cross_correlation.py'
adding 'pynx/utils/array.py'
adding 'pynx/utils/benchmark.py'
adding 'pynx/utils/correlation.py'
adding 'pynx/utils/fourier_shell_correlation.py'
adding 'pynx/utils/h5py.py'
adding 'pynx/utils/history.py'
adding 'pynx/utils/math.py'
adding 'pynx/utils/matplotlib.py'
adding 'pynx/utils/pattern.py'
adding 'pynx/utils/phase.py'
adding 'pynx/utils/phase_retrieval_transfer_function.py'
adding 'pynx/utils/plot_utils.py'
adding 'pynx/utils/registration.py'
adding 'pynx/utils/registration_cuda.py'
adding 'pynx/utils/rotation.py'
adding 'pynx/utils/string.py'
adding 'pynx/utils/time.py'
adding 'pynx/utils/vsnr_cuda.py'
adding 'pynx/utils/cuda/registration.cu'
adding 'pynx/utils/cuda/vsnr.cu'
adding 'pynx/utils/opencl/correlation.cl'
adding 'pynx/utils/opencl/std_dev_pair_elw.cl'
adding 'pynx/utils/scripts/__init__.py'
adding 'pynx/utils/scripts/pynx_resolution_FSC.py'
adding 'pynx/wavefront/__init__.py'
adding 'pynx/wavefront/cl_operator.py'
adding 'pynx/wavefront/cpu_operator.py'
adding 'pynx/wavefront/cu_operator.py'
adding 'pynx/wavefront/fresnel.py'
adding 'pynx/wavefront/fzp.py'
adding 'pynx/wavefront/operator.py'
adding 'pynx/wavefront/wavefront.py'
adding 'pynx/wavefront/cuda/mask_elw.cu'
adding 'pynx/wavefront/cuda/paganin_elw.cu'
adding 'pynx/wavefront/cuda/quad_phase_mult_elw.cu'
adding 'pynx/wavefront/opencl/mask_elw.cl'
adding 'pynx/wavefront/opencl/paganin_elw.cl'
adding 'pynx/wavefront/opencl/quad_phase_mult_elw.cl'
adding 'pynx/wavefront/test/__init__.py'
adding 'pynx/wavefront/test/test_wavefront.py'
adding 'pynx-2025.1.dist-info/licenses/LICENSE.txt'
adding 'pynx-2025.1.dist-info/METADATA'
adding 'pynx-2025.1.dist-info/WHEEL'
adding 'pynx-2025.1.dist-info/entry_points.txt'
adding 'pynx-2025.1.dist-info/top_level.txt'
adding 'pynx-2025.1.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
Successfully built pynx-2025.1-cp313-cp313-linux_x86_64.whl
I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 with "installer" module
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_test -- -s custom --test-args="PYTHONPATH={build_dir} {interpreter} pynx/scripts/pynx_test.py"
	pybuild --test -i python{version} -p 3.13 -s custom --test-args="PYTHONPATH={build_dir} {interpreter} pynx/scripts/pynx_test.py"
	rm -fr -- /tmp/dh-xdg-rundir-pcXIspiv
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   create-stamp debian/debhelper-build-stamp
   dh_testroot -O--buildsystem=pybuild
   dh_prep -O--buildsystem=pybuild
	rm -f -- debian/pynx.substvars debian/python3-pynx.substvars debian/python-pynx-doc.substvars
	rm -fr -- debian/.debhelper/generated/pynx/ debian/pynx/ debian/tmp/ debian/.debhelper/generated/python3-pynx/ debian/python3-pynx/ debian/.debhelper/generated/python-pynx-doc/ debian/python-pynx-doc/
   dh_auto_install -O--buildsystem=pybuild
	install -m0755 -d /<<PKGBUILDDIR>>/debian/tmp
	pybuild --install -i python{version} -p 3.13 --dest-dir=/<<PKGBUILDDIR>>/debian/tmp
I: pybuild plugin_pyproject:178: Copying package built for python3.13 to destdir
I: pybuild pybuild:334: rm -rf /<<PKGBUILDDIR>>/debian/python3-pynx/usr/bin/ /<<PKGBUILDDIR>>/debian/python3-pynx/usr/pynx/
	rm -f debian/pynx.debhelper.log debian/python-pynx-doc.debhelper.log debian/python3-pynx.debhelper.log
   debian/rules execute_after_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
python3 setup.py install_scripts -d debian/pynx/usr/bin
/usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!

        ********************************************************************************
        Requirements should be satisfied by a PEP 517 installer.
        If you are using pip, you can try `pip install --use-pep517`.
        ********************************************************************************

!!
  dist.fetch_build_eggs(dist.setup_requires)
/usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!

        ********************************************************************************
        Please consider removing the following classifiers in favor of a SPDX license expression:

        License :: License :: CEA CNRS Inria Logiciel Libre License B (CeCILL-B)

        See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
        ********************************************************************************

!!
  self._finalize_license_expression()
running install_scripts
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
running egg_info
writing PyNX.egg-info/PKG-INFO
writing dependency_links to PyNX.egg-info/dependency_links.txt
writing entry points to PyNX.egg-info/entry_points.txt
writing requirements to PyNX.egg-info/requires.txt
writing top-level names to PyNX.egg-info/top_level.txt
reading manifest file 'PyNX.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'pynx/ptycho/bragg/cuda/*.cu'
warning: no files found matching 'pynx/ptycho/bragg2d/cuda/*.cu'
adding license file 'LICENSE.txt'
writing manifest file 'PyNX.egg-info/SOURCES.txt'
Installing pynx-cdi-analysis script to debian/pynx/usr/bin
Installing pynx-cdi-analysis.py script to debian/pynx/usr/bin
Installing pynx-cdi-id01 script to debian/pynx/usr/bin
Installing pynx-cdi-id10 script to debian/pynx/usr/bin
Installing pynx-cdi-regrid script to debian/pynx/usr/bin
Installing pynx-cdi-regrid.py script to debian/pynx/usr/bin
Installing pynx-cdi-simulation script to debian/pynx/usr/bin
Installing pynx-cristalpty.py script to debian/pynx/usr/bin
Installing pynx-cxipty.py script to debian/pynx/usr/bin
Installing pynx-hermespty.py script to debian/pynx/usr/bin
Installing pynx-holotomo-id16b script to debian/pynx/usr/bin
Installing pynx-id01cdi.py script to debian/pynx/usr/bin
Installing pynx-id01pty.py script to debian/pynx/usr/bin
Installing pynx-id10cdi.py script to debian/pynx/usr/bin
Installing pynx-id13pty.py script to debian/pynx/usr/bin
Installing pynx-id16a-nfpty.py script to debian/pynx/usr/bin
Installing pynx-id16apty.py script to debian/pynx/usr/bin
Installing pynx-info script to debian/pynx/usr/bin
Installing pynx-info.py script to debian/pynx/usr/bin
Installing pynx-nanomaxpty.py script to debian/pynx/usr/bin
Installing pynx-nanoscopiumpty.py script to debian/pynx/usr/bin
Installing pynx-nfp2nxtomo script to debian/pynx/usr/bin
Installing pynx-ptycho-analysis script to debian/pynx/usr/bin
Installing pynx-ptycho-analysis.py script to debian/pynx/usr/bin
Installing pynx-ptycho-cristal script to debian/pynx/usr/bin
Installing pynx-ptycho-cxi script to debian/pynx/usr/bin
Installing pynx-ptycho-hermes script to debian/pynx/usr/bin
Installing pynx-ptycho-id01 script to debian/pynx/usr/bin
Installing pynx-ptycho-id13 script to debian/pynx/usr/bin
Installing pynx-ptycho-id16a script to debian/pynx/usr/bin
Installing pynx-ptycho-id16a-nf script to debian/pynx/usr/bin
Installing pynx-ptycho-nanomax script to debian/pynx/usr/bin
Installing pynx-ptycho-nanoscopium script to debian/pynx/usr/bin
Installing pynx-ptycho-p06 script to debian/pynx/usr/bin
Installing pynx-ptycho-ptypy script to debian/pynx/usr/bin
Installing pynx-ptycho-simulation script to debian/pynx/usr/bin
Installing pynx-ptycho-tps25a script to debian/pynx/usr/bin
Installing pynx-ptypy.py script to debian/pynx/usr/bin
Installing pynx-resolution-FSC.py script to debian/pynx/usr/bin
Installing pynx-resolution-fsc script to debian/pynx/usr/bin
Installing pynx-simulationpty.py script to debian/pynx/usr/bin
Installing pynx-test script to debian/pynx/usr/bin
Installing pynx-test.py script to debian/pynx/usr/bin
Installing pynx-tps25apty.py script to debian/pynx/usr/bin
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_installdocs -O--buildsystem=pybuild
	install -m0755 -d debian/pynx/usr/share/doc/pynx
	install -p -m0644 debian/copyright debian/pynx/usr/share/doc/pynx/copyright
	install -m0755 -d debian/python3-pynx/usr/share/doc/python3-pynx
	install -p -m0644 debian/copyright debian/python3-pynx/usr/share/doc/python3-pynx/copyright
	install -m0755 -d debian/python-pynx-doc/usr/share/doc/python-pynx-doc
	install -p -m0644 debian/copyright debian/python-pynx-doc/usr/share/doc/python-pynx-doc/copyright
   debian/rules override_dh_sphinxdoc
make[1]: Entering directory '/<<PKGBUILDDIR>>'
PYBUILD_SYSTEM=custom \
PYBUILD_BUILD_ARGS="cd doc && PYTHONPATH={build_dir} http_proxy='127.0.0.1:9' {interpreter} -m sphinx -N -bhtml . build/html" dh_auto_build  # HTML generator
	pybuild --build -i python{version} -p 3.13
I: pybuild base:311: cd doc && PYTHONPATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pynx/build http_proxy='127.0.0.1:9' python3.13 -m sphinx -N -bhtml . 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-gjexnyit.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.
E: pybuild pybuild:389: build: plugin custom failed with: exit code=2: cd doc && PYTHONPATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pynx/build http_proxy='127.0.0.1:9' python3.13 -m sphinx -N -bhtml . build/html
dh_auto_build: error: pybuild --build -i python{version} -p 3.13 returned exit code 13
make[1]: *** [debian/rules:33: override_dh_sphinxdoc] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:15: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------

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