[Debian-pan-maintainers] Bug#1116879: python-rosettasciio: FTBFS with the nocheck build profile

Tue Sep 30 15:54:05 BST 2025

Package: src:python-rosettasciio
Version: 0.7.1-2
Severity: important
Tags: forky sid ftbfs
User: debian-qa at lists.debian.org
Usertags: ftbfs-nocheck-profile

Dear maintainer:

During a rebuild of all packages in unstable using the nocheck build profile,
your package failed to build.

Below you will find how the build ends (probably the most relevant part,
but not necessarily). If required, the full build log is available here:

https://people.debian.org/~sanvila/build-logs/202509/

A wiki page discussing how to reproduce bugs in this category and
possible solutions is available here:

https://wiki.debian.org/qa.debian.org/FTBFS/Nocheck

(It's a wiki, so you are welcome to contribute)

[ Note: This is RC, but I will wait at least two weeks before raising
the severities, there are a lot of gcc-15 and CMake 4 bugs open now ].

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 could not 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:python-rosettasciio, 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

[... snipped ...]

copying build/lib/rsciio/emd/_emd_ncem.py -> build/bdist.linux-x86_64/wheel/./rsciio/emd
copying build/lib/rsciio/emd/_api.py -> build/bdist.linux-x86_64/wheel/./rsciio/emd
copying build/lib/rsciio/emd/_emd_velox.py -> build/bdist.linux-x86_64/wheel/./rsciio/emd
creating build/bdist.linux-x86_64/wheel/rsciio/renishaw
copying build/lib/rsciio/renishaw/__init__.py -> build/bdist.linux-x86_64/wheel/./rsciio/renishaw
copying build/lib/rsciio/renishaw/_api.py -> build/bdist.linux-x86_64/wheel/./rsciio/renishaw
copying build/lib/rsciio/_docstrings.py -> build/bdist.linux-x86_64/wheel/./rsciio
creating build/bdist.linux-x86_64/wheel/rsciio/trivista
copying build/lib/rsciio/trivista/__init__.py -> build/bdist.linux-x86_64/wheel/./rsciio/trivista
copying build/lib/rsciio/trivista/_api.py -> build/bdist.linux-x86_64/wheel/./rsciio/trivista
creating build/bdist.linux-x86_64/wheel/rsciio/semper
copying build/lib/rsciio/semper/__init__.py -> build/bdist.linux-x86_64/wheel/./rsciio/semper
copying build/lib/rsciio/semper/_api.py -> build/bdist.linux-x86_64/wheel/./rsciio/semper
creating build/bdist.linux-x86_64/wheel/rsciio/delmic
copying build/lib/rsciio/delmic/__init__.py -> build/bdist.linux-x86_64/wheel/./rsciio/delmic
copying build/lib/rsciio/delmic/_api.py -> build/bdist.linux-x86_64/wheel/./rsciio/delmic
creating build/bdist.linux-x86_64/wheel/rsciio/tia
copying build/lib/rsciio/tia/__init__.py -> build/bdist.linux-x86_64/wheel/./rsciio/tia
copying build/lib/rsciio/tia/_api.py -> build/bdist.linux-x86_64/wheel/./rsciio/tia
creating build/bdist.linux-x86_64/wheel/rsciio/ripple
copying build/lib/rsciio/ripple/__init__.py -> build/bdist.linux-x86_64/wheel/./rsciio/ripple
copying build/lib/rsciio/ripple/_api.py -> build/bdist.linux-x86_64/wheel/./rsciio/ripple
creating build/bdist.linux-x86_64/wheel/rsciio/phenom
copying build/lib/rsciio/phenom/__init__.py -> build/bdist.linux-x86_64/wheel/./rsciio/phenom
copying build/lib/rsciio/phenom/_api.py -> build/bdist.linux-x86_64/wheel/./rsciio/phenom
creating build/bdist.linux-x86_64/wheel/rsciio/hamamatsu
copying build/lib/rsciio/hamamatsu/__init__.py -> build/bdist.linux-x86_64/wheel/./rsciio/hamamatsu
copying build/lib/rsciio/hamamatsu/_api.py -> build/bdist.linux-x86_64/wheel/./rsciio/hamamatsu
creating build/bdist.linux-x86_64/wheel/rsciio/empad
copying build/lib/rsciio/empad/__init__.py -> build/bdist.linux-x86_64/wheel/./rsciio/empad
copying build/lib/rsciio/empad/_api.py -> build/bdist.linux-x86_64/wheel/./rsciio/empad
creating build/bdist.linux-x86_64/wheel/rsciio/mrc
copying build/lib/rsciio/mrc/__init__.py -> build/bdist.linux-x86_64/wheel/./rsciio/mrc
copying build/lib/rsciio/mrc/_api.py -> build/bdist.linux-x86_64/wheel/./rsciio/mrc
creating build/bdist.linux-x86_64/wheel/rsciio/bruker
copying build/lib/rsciio/bruker/__init__.py -> build/bdist.linux-x86_64/wheel/./rsciio/bruker
copying build/lib/rsciio/bruker/_api.py -> build/bdist.linux-x86_64/wheel/./rsciio/bruker
copying build/lib/rsciio/_logger.py -> build/bdist.linux-x86_64/wheel/./rsciio
creating build/bdist.linux-x86_64/wheel/rsciio/usid
copying build/lib/rsciio/usid/__init__.py -> build/bdist.linux-x86_64/wheel/./rsciio/usid
copying build/lib/rsciio/usid/_api.py -> build/bdist.linux-x86_64/wheel/./rsciio/usid
creating build/bdist.linux-x86_64/wheel/rsciio/quantumdetector
copying build/lib/rsciio/quantumdetector/__init__.py -> build/bdist.linux-x86_64/wheel/./rsciio/quantumdetector
copying build/lib/rsciio/quantumdetector/_api.py -> build/bdist.linux-x86_64/wheel/./rsciio/quantumdetector
creating build/bdist.linux-x86_64/wheel/rsciio/nexus
copying build/lib/rsciio/nexus/__init__.py -> build/bdist.linux-x86_64/wheel/./rsciio/nexus
copying build/lib/rsciio/nexus/_api.py -> build/bdist.linux-x86_64/wheel/./rsciio/nexus
copying build/lib/rsciio/_hierarchical.py -> build/bdist.linux-x86_64/wheel/./rsciio
creating build/bdist.linux-x86_64/wheel/rsciio/dens
copying build/lib/rsciio/dens/__init__.py -> build/bdist.linux-x86_64/wheel/./rsciio/dens
copying build/lib/rsciio/dens/_api.py -> build/bdist.linux-x86_64/wheel/./rsciio/dens
creating build/bdist.linux-x86_64/wheel/rsciio/protochips
copying build/lib/rsciio/protochips/__init__.py -> build/bdist.linux-x86_64/wheel/./rsciio/protochips
copying build/lib/rsciio/protochips/_api.py -> build/bdist.linux-x86_64/wheel/./rsciio/protochips
running install_egg_info
Copying rosettasciio.egg-info to build/bdist.linux-x86_64/wheel/./rosettasciio-0.0.0.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/rosettasciio-0.0.0.dist-info/WHEEL
creating '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_rosettasciio/.tmp-ozd0jhfj/rosettasciio-0.0.0-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'rosettasciio-0.0.0.dist-info/licenses/COPYING.txt'
adding 'rsciio/__init__.py'
adding 'rsciio/_docstrings.py'
adding 'rsciio/_hierarchical.py'
adding 'rsciio/_logger.py'
adding 'rsciio/blockfile/__init__.py'
adding 'rsciio/blockfile/_api.py'
adding 'rsciio/bruker/__init__.py'
adding 'rsciio/bruker/_api.py'
adding 'rsciio/delmic/__init__.py'
adding 'rsciio/delmic/_api.py'
adding 'rsciio/dens/__init__.py'
adding 'rsciio/dens/_api.py'
adding 'rsciio/digitalmicrograph/__init__.py'
adding 'rsciio/digitalmicrograph/_api.py'
adding 'rsciio/digitalsurf/__init__.py'
adding 'rsciio/digitalsurf/_api.py'
adding 'rsciio/edax/__init__.py'
adding 'rsciio/edax/_api.py'
adding 'rsciio/emd/__init__.py'
adding 'rsciio/emd/_api.py'
adding 'rsciio/emd/_emd_ncem.py'
adding 'rsciio/emd/_emd_velox.py'
adding 'rsciio/empad/__init__.py'
adding 'rsciio/empad/_api.py'
adding 'rsciio/hamamatsu/__init__.py'
adding 'rsciio/hamamatsu/_api.py'
adding 'rsciio/hspy/__init__.py'
adding 'rsciio/hspy/_api.py'
adding 'rsciio/image/__init__.py'
adding 'rsciio/image/_api.py'
adding 'rsciio/impulse/__init__.py'
adding 'rsciio/impulse/_api.py'
adding 'rsciio/jeol/__init__.py'
adding 'rsciio/jeol/_api.py'
adding 'rsciio/jobinyvon/__init__.py'
adding 'rsciio/jobinyvon/_api.py'
adding 'rsciio/mrc/__init__.py'
adding 'rsciio/mrc/_api.py'
adding 'rsciio/mrcz/__init__.py'
adding 'rsciio/mrcz/_api.py'
adding 'rsciio/msa/__init__.py'
adding 'rsciio/msa/_api.py'
adding 'rsciio/netcdf/__init__.py'
adding 'rsciio/netcdf/_api.py'
adding 'rsciio/nexus/__init__.py'
adding 'rsciio/nexus/_api.py'
adding 'rsciio/pantarhei/__init__.py'
adding 'rsciio/pantarhei/_api.py'
adding 'rsciio/phenom/__init__.py'
adding 'rsciio/phenom/_api.py'
adding 'rsciio/protochips/__init__.py'
adding 'rsciio/protochips/_api.py'
adding 'rsciio/quantumdetector/__init__.py'
adding 'rsciio/quantumdetector/_api.py'
adding 'rsciio/renishaw/__init__.py'
adding 'rsciio/renishaw/_api.py'
adding 'rsciio/ripple/__init__.py'
adding 'rsciio/ripple/_api.py'
adding 'rsciio/semper/__init__.py'
adding 'rsciio/semper/_api.py'
adding 'rsciio/tests/__init__.py'
adding 'rsciio/tests/conftest.py'
adding 'rsciio/tests/generate_dm_testing_files.py'
adding 'rsciio/tests/generate_renishaw_test_file.py'
adding 'rsciio/tests/registry.py'
adding 'rsciio/tests/registry_utils.py'
adding 'rsciio/tests/test_blockfile.py'
adding 'rsciio/tests/test_bruker.py'
adding 'rsciio/tests/test_de5.py'
adding 'rsciio/tests/test_delmic.py'
adding 'rsciio/tests/test_dens.py'
adding 'rsciio/tests/test_digitalmicrograph.py'
adding 'rsciio/tests/test_digitalsurf.py'
adding 'rsciio/tests/test_edax.py'
adding 'rsciio/tests/test_emd_ncem.py'
adding 'rsciio/tests/test_emd_prismatic.py'
adding 'rsciio/tests/test_emd_velox.py'
adding 'rsciio/tests/test_empad.py'
adding 'rsciio/tests/test_fei_stream_readers.py'
adding 'rsciio/tests/test_hamamatsu.py'
adding 'rsciio/tests/test_hspy.py'
adding 'rsciio/tests/test_image.py'
adding 'rsciio/tests/test_import.py'
adding 'rsciio/tests/test_impulse.py'
adding 'rsciio/tests/test_io.py'
adding 'rsciio/tests/test_jeol.py'
adding 'rsciio/tests/test_jobinyvon.py'
adding 'rsciio/tests/test_lazy_not_implemented.py'
adding 'rsciio/tests/test_mrc.py'
adding 'rsciio/tests/test_mrcz.py'
adding 'rsciio/tests/test_msa.py'
adding 'rsciio/tests/test_nexus.py'
adding 'rsciio/tests/test_pantarhei.py'
adding 'rsciio/tests/test_phenom.py'
adding 'rsciio/tests/test_protochips.py'
adding 'rsciio/tests/test_quantumdetector.py'
adding 'rsciio/tests/test_renishaw.py'
adding 'rsciio/tests/test_ripple.py'
adding 'rsciio/tests/test_semper.py'
adding 'rsciio/tests/test_set_log_level.py'
adding 'rsciio/tests/test_tia.py'
adding 'rsciio/tests/test_tiff.py'
adding 'rsciio/tests/test_trivista.py'
adding 'rsciio/tests/test_tvips.py'
adding 'rsciio/tests/test_usid.py'
adding 'rsciio/tests/test_zspy.py'
adding 'rsciio/tests/utils/__init__.py'
adding 'rsciio/tests/utils/test_rgbtools.py'
adding 'rsciio/tests/utils/test_utils.py'
adding 'rsciio/tia/__init__.py'
adding 'rsciio/tia/_api.py'
adding 'rsciio/tiff/__init__.py'
adding 'rsciio/tiff/_api.py'
adding 'rsciio/trivista/__init__.py'
adding 'rsciio/trivista/_api.py'
adding 'rsciio/tvips/__init__.py'
adding 'rsciio/tvips/_api.py'
adding 'rsciio/usid/__init__.py'
adding 'rsciio/usid/_api.py'
adding 'rsciio/utils/__init__.py'
adding 'rsciio/utils/array.py'
adding 'rsciio/utils/date_time_tools.py'
adding 'rsciio/utils/distributed.py'
adding 'rsciio/utils/elements.py'
adding 'rsciio/utils/exceptions.py'
adding 'rsciio/utils/fei_stream_readers.py'
adding 'rsciio/utils/hdf5.py'
adding 'rsciio/utils/image.py'
adding 'rsciio/utils/readfile.py'
adding 'rsciio/utils/rgb_tools.py'
adding 'rsciio/utils/skimage_exposure.py'
adding 'rsciio/utils/tests.py'
adding 'rsciio/utils/tools.py'
adding 'rsciio/zspy/__init__.py'
adding 'rsciio/zspy/_api.py'
adding 'rosettasciio-0.0.0.dist-info/METADATA'
adding 'rosettasciio-0.0.0.dist-info/WHEEL'
adding 'rosettasciio-0.0.0.dist-info/top_level.txt'
adding 'rosettasciio-0.0.0.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
Successfully built rosettasciio-0.0.0-py3-none-any.whl
I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 with "installer" module
   debian/rules execute_after_dh_auto_build-indep
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd doc && \
PYTHONPATH=/<<PKGBUILDDIR>> http_proxy='http://127.0.0.1:9/' https_proxy='https://127.0.0.1:9/' \
sphinx-build -N -E -T -b html . /<<PKGBUILDDIR>>/.pybuild/docs/html/
Running Sphinx v8.2.3

Configuration error!

Versions
========

* Platform:         linux; (Linux-6.12.48+deb13-cloud-amd64-x86_64-with-glibc2.41)
* Python version:   3.13.7 (CPython)
* Sphinx version:   8.2.3
* Docutils version: 0.21.2
* Jinja2 version:   3.1.6
* Pygments version: 2.18.0

Last Messages
=============

None.

Loaded Extensions
=================

None.

Traceback
=========

    Traceback (most recent call last):
      File "/usr/lib/python3/dist-packages/sphinx/config.py", line 601, in eval_config_file
        exec(code, namespace)  # NoQA: S102
        ~~~~^^^^^^^^^^^^^^^^^
      File "/<<PKGBUILDDIR>>/doc/conf.py", line 17, in <module>
        import numpydoc
    ModuleNotFoundError: No module named 'numpydoc'

    The above exception was the direct cause of the following exception:

    Traceback (most recent call last):
      File "/usr/lib/python3/dist-packages/sphinx/cmd/build.py", line 414, in build_main
        app = Sphinx(
            srcdir=args.sourcedir,
        ...<14 lines>...
            exception_on_warning=args.exception_on_warning,
        )
      File "/usr/lib/python3/dist-packages/sphinx/application.py", line 270, in __init__
        self.config = Config.read(self.confdir, confoverrides or {}, self.tags)
                      ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/usr/lib/python3/dist-packages/sphinx/config.py", line 357, in read
        namespace = eval_config_file(filename, tags)
      File "/usr/lib/python3/dist-packages/sphinx/config.py", line 616, in eval_config_file
        raise ConfigError(msg % traceback.format_exc()) from exc
    sphinx.errors.ConfigError: There is a programmable error in your configuration file:

    Traceback (most recent call last):
      File "/usr/lib/python3/dist-packages/sphinx/config.py", line 601, in eval_config_file
        exec(code, namespace)  # NoQA: S102
        ~~~~^^^^^^^^^^^^^^^^^
      File "/<<PKGBUILDDIR>>/doc/conf.py", line 17, in <module>
        import numpydoc
    ModuleNotFoundError: No module named 'numpydoc'

The full traceback has been saved in:
/tmp/sphinx-err-m_7dp7hy.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.
make[1]: *** [debian/rules:11: execute_after_dh_auto_build-indep] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:7: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------