[Debian-pan-maintainers] Bug#1127546: xraylarch: FTBFS: AttributeError: module 'collections' has no attribute 'MutableSet'
Santiago Vila
sanvila at debian.org
Mon Feb 9 18:06:10 GMT 2026
Package: src:xraylarch
Version: 0.9.81+ds1-3
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/202602/
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:xraylarch, 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 "3.14 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/python3-xraylarch.substvars debian/python-xraylarch-doc.substvars debian/files
rm -fr -- debian/python3-xraylarch/ debian/tmp/ debian/python-xraylarch-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 'larch/io/gse_xdiscan.py'
adding 'larch/io/hdf5group.py'
adding 'larch/io/mergegroups.py'
adding 'larch/io/nexus_xas.py'
adding 'larch/io/rixs_aps_gsecars.py'
adding 'larch/io/rixs_esrf_fame.py'
adding 'larch/io/rixs_esrf_id26.py'
adding 'larch/io/rixsdata.py'
adding 'larch/io/save_restore.py'
adding 'larch/io/specfile_reader.py'
adding 'larch/io/stepscan_file.py'
adding 'larch/io/tifffile.py'
adding 'larch/io/xafs_beamlines.py'
adding 'larch/io/xdi.py'
adding 'larch/io/xrd_hdf5.py'
adding 'larch/io/xrd_netcdf.py'
adding 'larch/io/xrf_netcdf.py'
adding 'larch/io/xsp3_hdf5.py'
adding 'larch/io/xas_data_source/__init__.py'
adding 'larch/io/xas_data_source/base.py'
adding 'larch/io/xas_data_source/hdf5_utils.py'
adding 'larch/io/xas_data_source/nexus.py'
adding 'larch/io/xas_data_source/read.py'
adding 'larch/io/xas_data_source/sources.py'
adding 'larch/io/xas_data_source/spec.py'
adding 'larch/math/__init__.py'
adding 'larch/math/convolution1D.py'
adding 'larch/math/deglitch.py'
adding 'larch/math/fitpeak.py'
adding 'larch/math/gridxyz.py'
adding 'larch/math/learn_regress.py'
adding 'larch/math/lincombo_fitting.py'
adding 'larch/math/lineshapes.py'
adding 'larch/math/normalization.py'
adding 'larch/math/pca.py'
adding 'larch/math/peaks.py'
adding 'larch/math/smoothing.py'
adding 'larch/math/spline.py'
adding 'larch/math/tomography.py'
adding 'larch/math/transformations.py'
adding 'larch/math/utils.py'
adding 'larch/plot/__init__.py'
adding 'larch/plot/bokeh_xafsplots.py'
adding 'larch/plot/plot_rixsdata.py'
adding 'larch/plot/plotly_xafsplots.py'
adding 'larch/qtlib/__init__.py'
adding 'larch/qtlib/console.py'
adding 'larch/qtlib/delegates.py'
adding 'larch/qtlib/items.py'
adding 'larch/qtlib/model.py'
adding 'larch/qtlib/plot1D.py'
adding 'larch/qtlib/plot2D.py'
adding 'larch/qtlib/plotarea.py'
adding 'larch/qtlib/view.py'
adding 'larch/qtrixs/__init__.py'
adding 'larch/qtrixs/application.py'
adding 'larch/qtrixs/items.py'
adding 'larch/qtrixs/model.py'
adding 'larch/qtrixs/plotrixs.py'
adding 'larch/qtrixs/profiletoolbar.py'
adding 'larch/qtrixs/view.py'
adding 'larch/qtrixs/window.py'
adding 'larch/utils/__init__.py'
adding 'larch/utils/debugtimer.py'
adding 'larch/utils/gformat.py'
adding 'larch/utils/jsonutils.py'
adding 'larch/utils/logging.py'
adding 'larch/utils/paths.py'
adding 'larch/utils/physical_constants.py'
adding 'larch/utils/shellutils.py'
adding 'larch/utils/show.py'
adding 'larch/utils/strutils.py'
adding 'larch/wxlib/__init__.py'
adding 'larch/wxlib/allow_idle_macosx.py'
adding 'larch/wxlib/athena_importer.py'
adding 'larch/wxlib/cif_browser.py'
adding 'larch/wxlib/columnframe.py'
adding 'larch/wxlib/feff_browser.py'
adding 'larch/wxlib/gui_utils.py'
adding 'larch/wxlib/inputhook.py'
adding 'larch/wxlib/larch_updater.py'
adding 'larch/wxlib/larchfilling.py'
adding 'larch/wxlib/larchframe.py'
adding 'larch/wxlib/parameter.py'
adding 'larch/wxlib/plotter.py'
adding 'larch/wxlib/readlinetextctrl.py'
adding 'larch/wxlib/reportframe.py'
adding 'larch/wxlib/specfile_importer.py'
adding 'larch/wxlib/structure2feff_browser.py'
adding 'larch/wxlib/xafsplots.py'
adding 'larch/wxlib/xas_importer.py'
adding 'larch/wxlib/xrfdisplay.py'
adding 'larch/wxlib/xrfdisplay_fitpeaks.py'
adding 'larch/wxlib/xrfdisplay_utils.py'
adding 'larch/wxmap/__init__.py'
adding 'larch/wxmap/gse_dtcorrect.py'
adding 'larch/wxmap/mapimageframe.py'
adding 'larch/wxmap/mapmathpanel.py'
adding 'larch/wxmap/maptomopanel.py'
adding 'larch/wxmap/mapviewer.py'
adding 'larch/wxmap/mapxrfpanel.py'
adding 'larch/wxxas/__init__.py'
adding 'larch/wxxas/config.py'
adding 'larch/wxxas/exafs_panel.py'
adding 'larch/wxxas/feffit_panel.py'
adding 'larch/wxxas/larix_app.py'
adding 'larch/wxxas/lincombo_panel.py'
adding 'larch/wxxas/pca_panel.py'
adding 'larch/wxxas/prepeak_panel.py'
adding 'larch/wxxas/regress_panel.py'
adding 'larch/wxxas/taskpanel.py'
adding 'larch/wxxas/xas_controller.py'
adding 'larch/wxxas/xas_dialogs.py'
adding 'larch/wxxas/xasgui.py'
adding 'larch/wxxas/xasnorm_panel.py'
adding 'larch/wxxas/xydata_panel.py'
adding 'larch/wxxrd/ImageControlsFrame.py'
adding 'larch/wxxrd/XRD2Dviewer.py'
adding 'larch/wxxrd/XRDCalibrationFrame.py'
adding 'larch/wxxrd/XRDMaskFrame.py'
adding 'larch/wxxrd/__init__.py'
adding 'larch/wxxrd/requirements.txt'
adding 'larch/wxxrd/xrd1d_display.py'
adding 'larch/xafs/__init__.py'
adding 'larch/xafs/autobk.py'
adding 'larch/xafs/cauchy_wavelet.py'
adding 'larch/xafs/deconvolve.py'
adding 'larch/xafs/diffkk.py'
adding 'larch/xafs/estimate_noise.py'
adding 'larch/xafs/feff8lpath.py'
adding 'larch/xafs/feffdat.py'
adding 'larch/xafs/feffit.py'
adding 'larch/xafs/feffrunner.py'
adding 'larch/xafs/feffutils.py'
adding 'larch/xafs/fluo.py'
adding 'larch/xafs/mback.py'
adding 'larch/xafs/pre_edge.py'
adding 'larch/xafs/prepeaks.py'
adding 'larch/xafs/rebin_xafs.py'
adding 'larch/xafs/sigma2_models.py'
adding 'larch/xafs/xafsft.py'
adding 'larch/xafs/xafsutils.py'
adding 'larch/xray/__init__.py'
adding 'larch/xray/background.py'
adding 'larch/xray/cromer_liberman.py'
adding 'larch/xrd/__init__.py'
adding 'larch/xrd/amcsd.py'
adding 'larch/xrd/amcsd_cif0.db'
adding 'larch/xrd/amcsd_cif1.db'
adding 'larch/xrd/amcsd_utils.py'
adding 'larch/xrd/cif2feff.py'
adding 'larch/xrd/cifdb.py'
adding 'larch/xrd/struct2xas.py'
adding 'larch/xrd/structure2feff.py'
adding 'larch/xrd/xrd.py'
adding 'larch/xrd/xrd_bgr.py'
adding 'larch/xrd/xrd_cif.py'
adding 'larch/xrd/xrd_files.py'
adding 'larch/xrd/xrd_fitting.py'
adding 'larch/xrd/xrd_pyFAI.py'
adding 'larch/xrd/xrd_tools.py'
adding 'larch/xrd/templates/fdmnes.tmpl'
adding 'larch/xrd/templates/feff_exafs.tmpl'
adding 'larch/xrf/__init__.py'
adding 'larch/xrf/deadtime.py'
adding 'larch/xrf/mca.py'
adding 'larch/xrf/roi.py'
adding 'larch/xrf/xrf_bgr.py'
adding 'larch/xrf/xrf_calib.py'
adding 'larch/xrf/xrf_model.py'
adding 'larch/xrf/xrf_peak.py'
adding 'larch/xrmmap/__init__.py'
adding 'larch/xrmmap/asciifiles.py'
adding 'larch/xrmmap/configfile.py'
adding 'larch/xrmmap/gsexrm_utils.py'
adding 'larch/xrmmap/xrm_mapfile.py'
adding 'larch/xsw/SimpleParratt.py'
adding 'larch/xsw/__init__.py'
adding 'larch/xsw/fluo_det.py'
adding 'larch/xsw/multilayer_film.py'
adding 'larch/xsw/plugins.txt'
adding 'xraylarch-0.9.81+ds1.dist-info/licenses/LICENSE'
adding 'xraylarch-0.9.81+ds1.dist-info/METADATA'
adding 'xraylarch-0.9.81+ds1.dist-info/WHEEL'
adding 'xraylarch-0.9.81+ds1.dist-info/entry_points.txt'
adding 'xraylarch-0.9.81+ds1.dist-info/top_level.txt'
adding 'xraylarch-0.9.81+ds1.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
Successfully built xraylarch-0.9.81+ds1-py3-none-any.whl
I: pybuild plugin_pyproject:168: Unpacking wheel built for python3.13 with "installer" module
debian/rules execute_after_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
I: pybuild base:384: echo /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_xraylarch/build
# generate the desktop files
cd /<<PKGBUILDDIR>>/debian; ./build-desktop
larch-cli.desktop
larch-gui.desktop
larch-larix.desktop
larch-xrfmap-viewer.desktop
larch-xrf-viewer.desktop
larch-xrd1d-viewer.desktop
# build the doc
env PYTHONPATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_xraylarch/build \
SPHINXBUILD="python3 -m sphinx" \
SPHINXOPTS="-D mathjax_path=MathJax.js" \
/usr/bin/make -C doc html
make[2]: Entering directory '/<<PKGBUILDDIR>>/doc'
cp sphinx/ext_mathjax.py extensions.py
sphinx-build -b html -d _build/doctrees . _build/html
Running Sphinx v8.2.3
mkdir -p failed for path /sbuild-nonexistent/.config/matplotlib: [Errno 13] Permission denied: '/sbuild-nonexistent'
Matplotlib created a temporary cache directory at /tmp/matplotlib-y_wgvyvs because there was an issue with the default path (/sbuild-nonexistent/.config/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
Configuration error!
Versions
========
* Platform: linux; (Linux-6.12.63+deb13-cloud-amd64-x86_64-with-glibc2.42)
* Python version: 3.13.12 (CPython)
* Sphinx version: 8.2.3
* Docutils version: 0.22.4
* Jinja2 version: 3.1.6
* Pygments version: 2.19.2
Last Messages
=============
None.
Loaded Extensions
=================
None.
Traceback
=========
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 63, in <module>
import larch
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_xraylarch/build/larch/__init__.py", line 37, in <module>
from .version import __date__, __version__, __release_version__
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_xraylarch/build/larch/version.py", line 14, in <module>
import urllib3
File "/usr/lib/python3/dist-packages/urllib3/__init__.py", line 15, in <module>
from ._base_connection import _TYPE_BODY
File "/usr/lib/python3/dist-packages/urllib3/_base_connection.py", line 5, in <module>
from .util.connection import _TYPE_SOCKET_OPTIONS
File "/usr/lib/python3/dist-packages/urllib3/util/__init__.py", line 5, in <module>
from .request import SKIP_HEADER, SKIPPABLE_HEADERS, make_headers
File "/usr/lib/python3/dist-packages/urllib3/util/request.py", line 37, in <module>
from backports import zstd as _unused_module_zstd # noqa: F401
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/doc/sphinx/ext/backports.py", line 255, in <module>
class OrderedSet(collections.MutableSet):
^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'collections' has no attribute 'MutableSet'
The full traceback has been saved in:
/tmp/sphinx-err-o5k9i6vs.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[2]: *** [Makefile:19: html] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc'
make[1]: *** [debian/rules:14: execute_after_dh_auto_build] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:8: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2
--------------------------------------------------------------------------------
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