Console Output
Skipping 195 KB..
Full Log[100%] Create "share/doc/6.0"
[100%] Built target brainvisa-cmake-usrdoc
[100%] Built target brainvisa-cmake-doc
[NbConvertApp] Writing 59249 bytes to /casa/host/src/capsul/master/doc/source/tutorial/capsul_tutorial.ipynb
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:24,057::INFO::Pipeline 'morphologist.capsul.fslnormalization.FSLNormalization' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.fslnormalization.FSLNormalization.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:24,063::INFO::Pipeline 'morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline.png'.
/casa/host/build/python/soma/config.py:docstring of soma.config.BRAINVISA_SHARE:1: WARNING: duplicate object description of soma.config.BRAINVISA_SHARE, other instance in api, use :no-index: for one of them
/casa/host/build/python/soma/controller/controller.py:docstring of soma.controller.controller.Controller.add_trait:1: WARNING: duplicate object description of soma.controller.controller.Controller.add_trait, other instance in api, use :no-index: for one of them
/casa/host/build/python/soma/controller/controller.py:docstring of soma.controller.controller.Controller.is_user_trait:1: WARNING: duplicate object description of soma.controller.controller.Controller.is_user_trait, other instance in api, use :no-index: for one of them
/casa/host/build/python/soma/controller/controller.py:docstring of soma.controller.controller.Controller.remove_trait:1: WARNING: duplicate object description of soma.controller.controller.Controller.remove_trait, other instance in api, use :no-index: for one of them
/casa/host/build/python/soma/controller/controller.py:docstring of soma.controller.controller.Controller.user_traits:1: WARNING: duplicate object description of soma.controller.controller.Controller.user_traits, other instance in api, use :no-index: for one of them
WARNING: autodoc: failed to import module 'crypt' from module 'soma'; the following exception was raised:
No module named 'Crypto'
/casa/host/build/python/soma/fom.py:docstring of soma.fom.AttributesToPaths.allowed_extensions_for_parameter:5: ERROR: Unexpected indentation.
/casa/host/build/python/soma/fom.py:docstring of soma.fom.AttributesToPaths.allowed_extensions_for_parameter:6: WARNING: Block quote ends without a blank line; unexpected unindent.
/casa/host/build/python/soma/mpfork.py:docstring of soma.mpfork.worker:4: ERROR: Unexpected indentation.
/casa/host/build/python/soma/mpfork.py:docstring of soma.mpfork.worker:5: WARNING: Block quote ends without a blank line; unexpected unindent.
looking for now-outdated files... none found
pickling environment... /casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:24,213::INFO::Pipeline 'morphologist.capsul.spmnormalization.SPMnormalizationPipeline' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.spmnormalization.SPMnormalizationPipeline.png'.
-- nbsphinx should work. --
Using Qt backend: PyQt6
source: /casa/host/src/capsul/master/doc/source
dest: /casa/host/build/share/doc/capsul-2.6
cwd: /casa/host/src/capsul/master/doc/source
exec: /usr/bin/python3 -m jupyter nbconvert --to notebook --output /casa/host/src/capsul/master/doc/source/tutorial/capsul_tutorial.ipynb /casa/host/src/capsul/master/doc/source/tutorial/capsul_tutorial.ipynb.in
loading pickled environment... /casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:24,322::INFO::Pipeline 'morphologist.capsul.axon.normalizationskullstripped.NormalizationSkullStripped' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.normalizationskullstripped.NormalizationSkullStripped.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:24,397::INFO::Pipeline 'morphologist.capsul.spmnormalization.SPMNormalization' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.spmnormalization.SPMNormalization.png'.
done
checking consistency... done
preparing documents... done
copying assets... copying static files... /casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:24,482::INFO::Pipeline 'morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline.png'.
done
copying extra files... done
done
[2Kwriting output... [ 50%] api
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:24,549::INFO::Pipeline 'morphologist.capsul.fslnormalization.FSLNormalization' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.fslnormalization.FSLNormalization.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:24,826::INFO::Pipeline 'morphologist.capsul.axon.normalizationskullstripped.NormalizationSkullStripped' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.normalizationskullstripped.NormalizationSkullStripped.png'.
done
loading intersphinx inventory from /casa/host/build/share/doc/soma-base-5.2/sphinx/objects.inv...
loading intersphinx inventory from /casa/host/build/share/doc/pyaims-5.2/sphinx/objects.inv...
WARNING: failed to reach any of the inventories with the following issues:
intersphinx inventory '/casa/host/build/share/doc/soma-base-5.2/sphinx/objects.inv' not fetchable due to <class 'FileNotFoundError'>: [Errno 2] No such file or directory: '/casa/host/build/share/doc/soma-base-5.2/sphinx/objects.inv'
loading intersphinx inventory from /casa/host/build/share/doc/pyanatomist-5.2/sphinx/objects.inv...
loading intersphinx inventory from /casa/host/build/share/doc/aimsdata-5.2/dev_doc/objects.inv...
WARNING: failed to reach any of the inventories with the following issues:
intersphinx inventory '/casa/host/build/share/doc/pyanatomist-5.2/sphinx/objects.inv' not fetchable due to <class 'FileNotFoundError'>: [Errno 2] No such file or directory: '/casa/host/build/share/doc/pyanatomist-5.2/sphinx/objects.inv'
loading intersphinx inventory from https://docs.python.org/3.12/objects.inv...
loading intersphinx inventory from https://numpy.org/doc/stable/objects.inv...
done
loading intersphinx inventory from /casa/host/build/share/doc/soma-base-5.3/sphinx/objects.inv...
loading intersphinx inventory from /casa/host/build/share/doc/soma-workflow-3.3/sphinx/objects.inv...
loading intersphinx inventory from https://docs.python.org/3.12/objects.inv...
loading intersphinx inventory from https://docs.enthought.com/traits/objects.inv...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:25,252::INFO::Pipeline 'morphologist.capsul.axon.brainorientation.BrainOrientation' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.brainorientation.BrainOrientation.png'.
libEGL warning: failed to open /dev/dri/card1: Permission denied
libEGL warning: failed to open /dev/dri/card1: Permission denied
libEGL warning: failed to open /dev/dri/card1: Permission denied
[autosummary] generating autosummary for: api/api.rst, api/attributes.rst, api/engine.rst, api/in_context.rst, api/index.rst, api/info.rst, api/pipeline.rst, api/plugins.rst, api/process.rst, api/qt_apps.rst, ..., api/subprocess.rst, api/utils.rst, documentation.rst, index.rst, installation.rst, status.rst, tutorial/capsul_tutorial.ipynb, user_guide_tree/advanced_usage.rst, user_guide_tree/index.rst, user_guide_tree/xml_spec.rst
The XKEYBOARD keymap compiler (xkbcomp) reports:
> Warning: Could not resolve keysym XF86CameraAccessEnable
> Warning: Could not resolve keysym XF86CameraAccessDisable
> Warning: Could not resolve keysym XF86CameraAccessToggle
> Warning: Could not resolve keysym XF86NextElement
> Warning: Could not resolve keysym XF86PreviousElement
> Warning: Could not resolve keysym XF86AutopilotEngageToggle
> Warning: Could not resolve keysym XF86MarkWaypoint
> Warning: Could not resolve keysym XF86Sos
> Warning: Could not resolve keysym XF86NavChart
> Warning: Could not resolve keysym XF86FishingChart
> Warning: Could not resolve keysym XF86SingleRangeRadar
> Warning: Could not resolve keysym XF86DualRangeRadar
> Warning: Could not resolve keysym XF86RadarOverlay
> Warning: Could not resolve keysym XF86TraditionalSonar
> Warning: Could not resolve keysym XF86ClearvuSonar
> Warning: Could not resolve keysym XF86SidevuSonar
> Warning: Could not resolve keysym XF86NavInfo
Errors from xkbcomp are not fatal to the X server
libEGL warning: failed to open /dev/dri/card1: Permission denied
libEGL warning: failed to open /dev/dri/card1: Permission denied
libEGL warning: failed to open /dev/dri/card1: Permission denied
The XKEYBOARD keymap compiler (xkbcomp) reports:
> Warning: Could not resolve keysym XF86CameraAccessEnable
> Warning: Could not resolve keysym XF86CameraAccessDisable
> Warning: Could not resolve keysym XF86CameraAccessToggle
> Warning: Could not resolve keysym XF86NextElement
> Warning: Could not resolve keysym XF86PreviousElement
> Warning: Could not resolve keysym XF86AutopilotEngageToggle
> Warning: Could not resolve keysym XF86MarkWaypoint
> Warning: Could not resolve keysym XF86Sos
> Warning: Could not resolve keysym XF86NavChart
> Warning: Could not resolve keysym XF86FishingChart
> Warning: Could not resolve keysym XF86SingleRangeRadar
> Warning: Could not resolve keysym XF86DualRangeRadar
> Warning: Could not resolve keysym XF86RadarOverlay
> Warning: Could not resolve keysym XF86TraditionalSonar
> Warning: Could not resolve keysym XF86ClearvuSonar
> Warning: Could not resolve keysym XF86SidevuSonar
> Warning: Could not resolve keysym XF86NavInfo
Errors from xkbcomp are not fatal to the X server
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-a-sac-ns-brainvisa'
libEGL warning: failed to open /dev/dri/card1: Permission denied
libEGL warning: failed to open /dev/dri/card1: Permission denied
libEGL warning: failed to open /dev/dri/card1: Permission denied
The XKEYBOARD keymap compiler (xkbcomp) reports:
> Warning: Could not resolve keysym XF86CameraAccessEnable
> Warning: Could not resolve keysym XF86CameraAccessDisable
> Warning: Could not resolve keysym XF86CameraAccessToggle
> Warning: Could not resolve keysym XF86NextElement
> Warning: Could not resolve keysym XF86PreviousElement
> Warning: Could not resolve keysym XF86AutopilotEngageToggle
> Warning: Could not resolve keysym XF86MarkWaypoint
> Warning: Could not resolve keysym XF86Sos
> Warning: Could not resolve keysym XF86NavChart
> Warning: Could not resolve keysym XF86FishingChart
> Warning: Could not resolve keysym XF86SingleRangeRadar
> Warning: Could not resolve keysym XF86DualRangeRadar
> Warning: Could not resolve keysym XF86RadarOverlay
> Warning: Could not resolve keysym XF86TraditionalSonar
> Warning: Could not resolve keysym XF86ClearvuSonar
> Warning: Could not resolve keysym XF86SidevuSonar
> Warning: Could not resolve keysym XF86NavInfo
Errors from xkbcomp are not fatal to the X server
[autosummary] generating autosummary for: index.rst, pyaims_aimsalgo.rst, pyaims_aimsalgo_examples.rst, pyaims_algo.rst, pyaims_api_aims.rst, pyaims_api_aimsalgo.rst, pyaims_examples.rst, pyaims_examples_advanced.rst, pyaims_highlevel.rst, pyaims_lowlevel.rst, pyaims_modules_api.rst, pyaims_tutorial.rst, pyaims_tutorial_nb.ipynb, volume_orientation.ipynb
[2Kwriting output... [100%] index
generating indices... genindex py-modindex done
[2Khighlighting module code... [ 3%] soma.application
[2Khighlighting module code... [ 5%] soma.archive
[2Khighlighting module code... [ 8%] soma.bufferandfile
[2Khighlighting module code... [ 11%] soma.config
[2Khighlighting module code... [ 14%] soma.controller.controller
[2Khighlighting module code... [ 16%] soma.debug
[2Khighlighting module code... [ 19%] soma.factory
[2Khighlighting module code... [ 22%] soma.fom
[2Khighlighting module code... [ 24%] soma.global_naming
[2Khighlighting module code... [ 27%] soma.html
[2Khighlighting module code... [ 30%] soma.importer
[2Khighlighting module code... [ 32%] soma.logging
[2Khighlighting module code... [ 35%] soma.minf.api
[2Khighlighting module code... [ 38%] soma.mpfork
[2Khighlighting module code... [ 41%] soma.notification
[2Khighlighting module code... [ 43%] soma.path
[2Khighlighting module code... [ 46%] soma.qimage2ndarray
[2Khighlighting module code... [ 49%] soma.qt_gui.controller_widget
[2Khighlighting module code... [ 51%] soma.qt_gui.io
[2Khighlighting module code... [ 54%] soma.qt_gui.qtThread
[2Khighlighting module code... [ 57%] soma.qt_gui.qt_backend
[2Khighlighting module code... [ 59%] soma.qt_gui.rangeSlider
[2Khighlighting module code... [ 62%] soma.qt_gui.timered_widgets
[2Khighlighting module code... [ 65%] soma.safemkdir
[2Khighlighting module code... [ 68%] soma.serialization
[2Khighlighting module code... [ 70%] soma.singleton
[2Khighlighting module code... [ 73%] soma.somatime
[2Khighlighting module code... [ 76%] soma.sorted_dictionary
[2Khighlighting module code... [ 78%] soma.sqlite_tools
[2Khighlighting module code... [ 81%] soma.stringtools
[2Khighlighting module code... [ 84%] soma.thread_calls
[2Khighlighting module code... [ 86%] soma.translation
[2Khighlighting module code... [ 89%] soma.utils.find_library
[2Khighlighting module code... [ 92%] soma.utils.functiontools
[2Khighlighting module code... [ 95%] soma.utils.loader
[2Khighlighting module code... [ 97%] soma.utils.weak_proxy
[2Khighlighting module code... [100%] soma.uuid
writing additional pages... search done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 11 warnings.
The HTML pages are in ../../share/doc/soma-base-5.3/sphinx.
building [mo]: targets for 0 po files that are out of date
writing output...
building [html]: targets for 0 source files that are out of date
updating environment: 0 added, 0 changed, 0 removed
reading sources...
looking for now-outdated files... none found
no targets are out of date.
build succeeded, 2 warnings.
The HTML pages are in ../../../../share/doc/pyaims-5.2/sphinx.
WARNING: Failed to import capsul.qt_apps.main_window.
Possible hints:
* ImportError: cannot import name 'QtWebKit' from 'soma.qt_gui.qt_backend' (/casa/host/build/python/soma/qt_gui/qt_backend.py)
* AttributeError: module 'capsul.qt_apps' has no attribute 'main_window'
Qt offscreen does not work.
Cannot allocate an OpenGL context. Using Xvfb if possible.
using DISPLAY=:3
VirtualGL found.
building [mo]: targets for 0 po files that are out of date
writing output...
building [html]: targets for 0 source files that are out of date
updating environment: 0 added, 0 changed, 0 removed
reading sources...
looking for now-outdated files... none found
no targets are out of date.
build succeeded, 1 warning.
The HTML pages are in ../../share/doc/axon-5.2/dev_doc.
libEGL warning: failed to open /dev/dri/card1: Permission denied
libEGL warning: failed to open /dev/dri/card1: Permission denied
libEGL warning: failed to open /dev/dri/card1: Permission denied
The XKEYBOARD keymap compiler (xkbcomp) reports:
> Warning: Could not resolve keysym XF86CameraAccessEnable
> Warning: Could not resolve keysym XF86CameraAccessDisable
> Warning: Could not resolve keysym XF86CameraAccessToggle
> Warning: Could not resolve keysym XF86NextElement
> Warning: Could not resolve keysym XF86PreviousElement
> Warning: Could not resolve keysym XF86AutopilotEngageToggle
> Warning: Could not resolve keysym XF86MarkWaypoint
> Warning: Could not resolve keysym XF86Sos
> Warning: Could not resolve keysym XF86NavChart
> Warning: Could not resolve keysym XF86FishingChart
> Warning: Could not resolve keysym XF86SingleRangeRadar
> Warning: Could not resolve keysym XF86DualRangeRadar
> Warning: Could not resolve keysym XF86RadarOverlay
> Warning: Could not resolve keysym XF86TraditionalSonar
> Warning: Could not resolve keysym XF86ClearvuSonar
> Warning: Could not resolve keysym XF86SidevuSonar
> Warning: Could not resolve keysym XF86NavInfo
Errors from xkbcomp are not fatal to the X server
[100%] Built target soma-base-sphinx
[100%] Create "share/doc/5.3"
[100%] Built target soma-base-devdoc
[100%] Built target soma-base-doc
/usr/lib/python3/dist-packages/sphinx_gallery/sphinx_compatibility.py:71: RemovedInSphinx80Warning: The alias 'sphinx.util.status_iterator' is deprecated, use 'sphinx.util.display.status_iterator' instead. Check CHANGES for Sphinx API modifications.
status_iterator = sphinx.util.status_iterator
WARNING: multiple files found for the document "auto_examples/activateaction": ['auto_examples/activateaction.ipynb', 'auto_examples/activateaction.rst', 'auto_examples/activateaction.py']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/activateaction.ipynb' for the build.
WARNING: multiple files found for the document "auto_examples/addMenuEntry": ['auto_examples/addMenuEntry.ipynb', 'auto_examples/addMenuEntry.rst', 'auto_examples/addMenuEntry.py']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/addMenuEntry.ipynb' for the build.
WARNING: multiple files found for the document "auto_examples/aimsvolumetest": ['auto_examples/aimsvolumetest.ipynb', 'auto_examples/aimsvolumetest.rst', 'auto_examples/aimsvolumetest.py.md5', 'auto_examples/aimsvolumetest.py']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/aimsvolumetest.ipynb' for the build.
WARNING: multiple files found for the document "auto_examples/anagraphannotate": ['auto_examples/anagraphannotate.ipynb', 'auto_examples/anagraphannotate.py', 'auto_examples/anagraphannotate.rst', 'auto_examples/anagraphannotate.py.md5']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/anagraphannotate.ipynb' for the build.
WARNING: multiple files found for the document "auto_examples/bvProcessSocket": ['auto_examples/bvProcessSocket.rst', 'auto_examples/bvProcessSocket.ipynb', 'auto_examples/bvProcessSocket.py']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/bvProcessSocket.ipynb' for the build.
WARNING: multiple files found for the document "auto_examples/control": ['auto_examples/control.ipynb', 'auto_examples/control.xpm', 'auto_examples/control.py', 'auto_examples/control.rst']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/control.ipynb' for the build.
WARNING: multiple files found for the document "auto_examples/customcommands": ['auto_examples/customcommands.py', 'auto_examples/customcommands.ipynb', 'auto_examples/customcommands.rst']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/customcommands.ipynb' for the build.
WARNING: multiple files found for the document "auto_examples/customopenglobject": ['auto_examples/customopenglobject.py.md5', 'auto_examples/customopenglobject.ipynb', 'auto_examples/customopenglobject.rst', 'auto_examples/customopenglobject.py']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/customopenglobject.ipynb' for the build.
WARNING: multiple files found for the document "auto_examples/ellipsoid": ['auto_examples/ellipsoid.rst', 'auto_examples/ellipsoid.py', 'auto_examples/ellipsoid.ipynb']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/ellipsoid.ipynb' for the build.
WARNING: multiple files found for the document "auto_examples/events": ['auto_examples/events.rst', 'auto_examples/events.py', 'auto_examples/events.ipynb']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/events.ipynb' for the build.
WARNING: multiple files found for the document "auto_examples/fusion": ['auto_examples/fusion.rst', 'auto_examples/fusion.py', 'auto_examples/fusion.ipynb']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/fusion.ipynb' for the build.
WARNING: multiple files found for the document "auto_examples/fusion3D": ['auto_examples/fusion3D.py', 'auto_examples/fusion3D.ipynb', 'auto_examples/fusion3D.py.md5', 'auto_examples/fusion3D.rst']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/fusion3D.ipynb' for the build.
WARNING: multiple files found for the document "auto_examples/graph": ['auto_examples/graph.ipynb', 'auto_examples/graph.py', 'auto_examples/graph.rst']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/graph.ipynb' for the build.
WARNING: multiple files found for the document "auto_examples/graph_building": ['auto_examples/graph_building.ipynb', 'auto_examples/graph_building.py.md5', 'auto_examples/graph_building.py', 'auto_examples/graph_building.rst']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/graph_building.ipynb' for the build.
WARNING: multiple files found for the document "auto_examples/meshtest": ['auto_examples/meshtest.py', 'auto_examples/meshtest.rst', 'auto_examples/meshtest.ipynb']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/meshtest.ipynb' for the build.
WARNING: multiple files found for the document "auto_examples/nomenclatureselection": ['auto_examples/nomenclatureselection.py', 'auto_examples/nomenclatureselection.ipynb', 'auto_examples/nomenclatureselection.rst', 'auto_examples/nomenclatureselection.py.md5']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/nomenclatureselection.ipynb' for the build.
WARNING: multiple files found for the document "auto_examples/selection": ['auto_examples/selection.ipynb', 'auto_examples/selection.rst', 'auto_examples/selection.py.md5', 'auto_examples/selection.py']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/selection.ipynb' for the build.
WARNING: multiple files found for the document "auto_examples/sphere": ['auto_examples/sphere.py', 'auto_examples/sphere.ipynb', 'auto_examples/sphere.rst']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/sphere.ipynb' for the build.
WARNING: multiple files found for the document "auto_examples/volumeMeasures": ['auto_examples/volumeMeasures.ipynb', 'auto_examples/volumeMeasures.rst', 'auto_examples/volumeMeasures.py']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/volumeMeasures.ipynb' for the build.
WARNING: multiple files found for the document "auto_examples/volumetest": ['auto_examples/volumetest.py.md5', 'auto_examples/volumetest.py', 'auto_examples/volumetest.rst', 'auto_examples/volumetest.ipynb']
Use '/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/sphinx/auto_examples/volumetest.ipynb' for the build.
Qt offscreen does not work.
Cannot allocate an OpenGL context. Using Xvfb if possible.
using DISPLAY=:2
VirtualGL found.
global modules: /casa/host/build/share/anatomist-5.2/python_plugins
home modules: /casa/home/.anatomist/python_plugins
loading module ana_image_math
loading module save_resampled
loading module modelGraphs
loading module volumepalettes
loading module valuesplotwindow
loading module gradientpalette
loading module histogram
loading module gltf_io
loading module foldsplit
loading module anacontrolmenu
loading module meshsplit
loading module paletteViewer
loading module simple_controls
loading module bundles_small_brains
loading module bundles_split_by_cortical_regions
loading module measure
loading module palettecontrols
loading module selection
loading module bsa_proba
loading module statsplotwindow
loading module profilewindow
loading module infowindow
all python modules loaded
Anatomist started.
loading intersphinx inventory from /casa/host/build/share/doc/soma-base-5.2/sphinx/objects.inv...
loading intersphinx inventory from https://docs.python.org/3.12/objects.inv...
WARNING: failed to reach any of the inventories with the following issues:
intersphinx inventory '/casa/host/build/share/doc/soma-base-5.2/sphinx/objects.inv' not fetchable due to <class 'FileNotFoundError'>: [Errno 2] No such file or directory: '/casa/host/build/share/doc/soma-base-5.2/sphinx/objects.inv'
[autosummary] generating autosummary for: ana_notebook.ipynb, auto_examples/activateaction.ipynb, auto_examples/addMenuEntry.ipynb, auto_examples/aimsvolumetest.ipynb, auto_examples/anagraphannotate.ipynb, auto_examples/bvProcessSocket.ipynb, auto_examples/control.ipynb, auto_examples/customcommands.ipynb, auto_examples/customopenglobject.ipynb, auto_examples/ellipsoid.ipynb, ..., pyanatomist_examples.rst, pyanatomist_headless.rst, pyanatomist_howto.rst, pyanatomist_notebook.rst, pyanatomist_pyaims_tutorial.rst, pyanatomist_socket.rst, pyanatomist_threaded.rst, pyanatomist_tutorial.rst, pyanatomist_tutorial_nb.ipynb, pyanatomist_wip.rst
WARNING: Failed to import capsul.qt_apps.pipeline_viewer_app.
Possible hints:
* ImportError: cannot import name 'QtWebKit' from 'soma.qt_gui.qt_backend' (/casa/host/build/python/soma/qt_gui/qt_backend.py)
* AttributeError: module 'capsul.qt_apps' has no attribute 'pipeline_viewer_app'
building [mo]: targets for 0 po files that are out of date
writing output...
building [html]: targets for 1 source files that are out of date
updating environment: 0 added, 2 changed, 0 removed
[2Kreading sources... [ 50%] api/qt_apps
[100%] Built target axon-sphinx
[100%] Create "share/doc/5.2"
[100%] Built target axon-devdoc
[2Kreading sources... [100%] tutorial/capsul_tutorial
WARNING: Failed to import anatomist.altas_viewer.
Possible hints:
* ModuleNotFoundError: No module named 'anatomist.altas_viewer'
* AttributeError: module 'anatomist' has no attribute 'altas_viewer'
WARNING: Failed to import anatomist.socket.api.
Possible hints:
* ImportError: cannot import name 'qApp' from 'PyQt6.Qt' (/usr/lib/python3/dist-packages/PyQt6/QtGui.abi3.so)
* AttributeError: module 'anatomist.socket' has no attribute 'api'
generating gallery...
Using Sphinx-Gallery to convert rst text blocks to markdown for .ipynb files.
[2Kgenerating gallery for auto_examples... [ 4%] volumetest.py
[2Kgenerating gallery for auto_examples... [ 9%] nomenclatureselection.py
[2Kgenerating gallery for auto_examples... [ 13%] graph.py
WARNING: /casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/examples/graph.py failed to execute correctly: Traceback (most recent call last):
File "/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/examples/graph.py", line 50, in <module>
if QtGui.qApp.startingUp():
^^^^^^^^^^
AttributeError: module 'PyQt6.QtGui' has no attribute 'qApp'
[2Kgenerating gallery for auto_examples... [ 17%] customcommands.py
[2Kgenerating gallery for auto_examples... [ 22%] events.py
[2Kgenerating gallery for auto_examples... [ 26%] addMenuEntry.py
[2Kgenerating gallery for auto_examples... [ 30%] fusion3D.py
[2Kgenerating gallery for auto_examples... [ 35%] selection.py
[2Kgenerating gallery for auto_examples... [ 39%] activateaction.py
[2Kgenerating gallery for auto_examples... [ 43%] graph_building.py
[2Kgenerating gallery for auto_examples... [ 48%] bvProcessSocket.py
[2Kgenerating gallery for auto_examples... [ 52%] aimsvolumetest.py
[2Kgenerating gallery for auto_examples... [ 57%] meshtest.py
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:32,380::INFO::Found '0' pipeline(s) in 'deepsulci.sulci_labeling.capsul'.
WARNING: /casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/examples/meshtest.py failed to execute correctly: Traceback (most recent call last):
File "/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/examples/meshtest.py", line 46, in <module>
from soma.qt_gui.qt_backend.QtGui import qApp
ImportError: cannot import name 'qApp' from 'PyQt6.QtGui' (/usr/lib/python3/dist-packages/PyQt6/QtGui.abi3.so)
[2Kgenerating gallery for auto_examples... [ 61%] sphere.py
[2Kgenerating gallery for auto_examples... [ 65%] fusion.py
[2Kgenerating gallery for auto_examples... [ 70%] ellipsoid.py
QOpenGLWidget is not supported on this platform.
QOpenGLWidget is not supported on this platform.
This plugin does not support propagateSizeHints()
This plugin does not support raise()
WARNING: /casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/examples/ellipsoid.py failed to execute correctly: Traceback (most recent call last):
File "/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/examples/ellipsoid.py", line 135, in <module>
QtGui.qApp.processEvents()
^^^^^^^^^^
AttributeError: module 'PyQt6.QtGui' has no attribute 'qApp'
[2Kgenerating gallery for auto_examples... [ 74%] control.py
WARNING: /casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/examples/control.py failed to execute correctly: Traceback (most recent call last):
File "/casa/host/src/anatomist/anatomist-gpl/master/pyanatomist/doc/examples/control.py", line 56, in <module>
if QtGui.qApp.startingUp() and 'IPython' not in sys.modules:
^^^^^^^^^^
AttributeError: module 'PyQt6.QtGui' has no attribute 'qApp'
[2Kgenerating gallery for auto_examples... [ 78%] anagraphannotate.py
[2Kgenerating gallery for auto_examples... [ 83%] customopenglobject.py
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:33,839::INFO::Pipeline 'morphologist.capsul.axon.sulcilabelling.SulciLabelling' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.sulcilabelling.SulciLabelling.png'.
[2Kgenerating gallery for auto_examples... [ 87%] volumeMeasures.py
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:33,852::INFO::Pipeline 'morphologist.capsul.axon.sulcilabelling.SulciLabelling' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.sulcilabelling.SulciLabelling.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:33,961::INFO::Pipeline 'morphologist.capsul.fslnormalization.FSLnormalizationPipeline' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.fslnormalization.FSLnormalizationPipeline.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:34,056::INFO::Pipeline 'morphologist.capsul.axon.normalization.Normalization' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.normalization.Normalization.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:34,058::INFO::Pipeline 'morphologist.capsul.axon.baladinnormalizationpipeline.BaladinNormalizationPipeline' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.baladinnormalizationpipeline.BaladinNormalizationPipeline.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:34,169::INFO::Pipeline 'morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline.png'.
[2Kgenerating gallery for auto_examples... [ 91%] anaevensimplerviewer.py
Process2 execution, a: 0.000000, b: blop
Process2 execution, a: 0.000000, b: yup
This plugin does not support propagateSizeHints()
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:35,182::INFO::Pipeline 'morphologist.capsul.axon.axonmorphologist.AxonMorphologist' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.axonmorphologist.AxonMorphologist.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:35,304::INFO::Pipeline 'morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline.png'.
QOpenGLWidget is not supported on this platform.
QOpenGLWidget is not supported on this platform.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:35,470::INFO::Pipeline 'morphologist.capsul.spmnormalization.SPMNormalization' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.spmnormalization.SPMNormalization.png'.
QOpenGLWidget is not supported on this platform.
QOpenGLWidget is not supported on this platform.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:35,575::INFO::Pipeline 'morphologist.capsul.axon.baladinnormalizationpipeline.BaladinNormalizationPipeline' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.baladinnormalizationpipeline.BaladinNormalizationPipeline.png'.
This plugin does not support propagateSizeHints()
This plugin does not support propagateSizeHints()
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:35,704::INFO::Pipeline 'morphologist.capsul.spmnormalization.SPMnormalizationPipeline' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.spmnormalization.SPMnormalizationPipeline.png'.
PyAnatomist Module present
PythonLauncher::runModules()
Multitexturing present
function glActiveTexture found.
function glClientActiveTexture found.
function glBlendEquation found.
function glTexImage3D found.
function glMultiTexCoord3f found.
function glBindFramebuffer found.
function glBindRenderbuffer found.
function glFramebufferTexture2D found.
function glGenFramebuffers found.
function glGenRenderbuffers found.
function glFramebufferRenderbuffer found.
function glRenderbufferStorage found.
function glCheckFramebufferStatus found.
function glDeleteRenderbuffers found.
function glDeleteFramebuffers found.
Number of texture units: 8
function glUniform1f found.
function glUniform1i found.
function glUniform4fv found.
function glGetUniformLocation found.
function glMultTransposeMatrixf found.
function glAttachShader found.
function glDetachShader found.
function glCompileShader found.
function glCreateProgram found.
function glCreateShader found.
function glDeleteProgram found.
function glDeleteShader found.
function glGetProgramiv found.
function glGetShaderiv found.
function glLinkProgram found.
function glShaderSource found.
function glUseProgram found.
GL_ARB_shadow present
GL_SGIX_shadow extension not available
GL_SGIX_depth_texture extension not available
GL_ARB_depth_texture extension present
GL_ARB_texture_cube_map extension present
GL_EXT_texture_cube_map extension present
Number of texture units: 8
QPainter::begin: Paint device returned engine == 0, type: 1
QPainter::setRenderHint: Painter must be active to set rendering hints
QPainter::setRenderHint: Painter must be active to set rendering hints
QPainter::worldTransform: Painter not active
QPainter::save: Painter not active
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:35,993::INFO::Pipeline 'morphologist.capsul.axon.brainorientation.BrainOrientation' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.brainorientation.BrainOrientation.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:36,107::INFO::Pipeline 'morphologist.capsul.fslnormalization.FSLnormalizationPipeline' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.fslnormalization.FSLnormalizationPipeline.png'.
[100%] Built target aims-free-sphinx
Segmentation fault (core dumped)
[100%] Built target anatomist-gpl-sphinx
[100%] Create "share/doc/5.2"
[100%] Create "share/doc/5.2"
[100%] Built target anatomist-gpl-devdoc
[100%] Built target aims-free-devdoc
Process2 execution, a: 0.000000, b: blop
[100%] Built target anatomist-gpl-doc
[100%] Built target aims-free-doc
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:47,356::INFO::Pipeline 'morphologist.capsul.morphologist.Morphologist' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.morphologist.Morphologist.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:47,600::INFO::Pipeline 'morphologist.capsul.axon.normalization.Normalization' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.normalization.Normalization.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:48,867::INFO::Pipeline 'morphologist.capsul.axon.axonmorphologist.AxonMorphologist' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.axonmorphologist.AxonMorphologist.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:48,990::INFO::Pipeline 'morphologist.capsul.axon.sulcilabellingspam.SulciLabellingSPAM' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.sulcilabellingspam.SulciLabellingSPAM.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:48,990::INFO::Summary: '14' files written for module 'capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:50,208::INFO::Pipeline 'morphologist.capsul.morphologist.Morphologist' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.morphologist.Morphologist.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:50,304::INFO::Pipeline 'morphologist.capsul.axon.sulcilabellingspam.SulciLabellingSPAM' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.sulcilabellingspam.SulciLabellingSPAM.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:58:50,304::INFO::Summary: '14' files written for module 'capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:50,349::INFO::Found '14' pipeline(s) in 'morphologist.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:50,349::INFO::Found '40' process(es) in 'morphologist.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:50,349::INFO::Processing pipeline 'morphologist.capsul.axon.axonmorphologist.AxonMorphologist'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:50,386::INFO::Found '0' pipeline(s) in 'deepsulci.sulci_labeling.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:50,386::INFO::Found '3' process(es) in 'deepsulci.sulci_labeling.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:50,387::INFO::Processing pipeline 'deepsulci.sulci_labeling.capsul.error_computation.ErrorComputation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:50,391::INFO::Processing pipeline 'deepsulci.sulci_labeling.capsul.labeling.SulciDeepLabeling'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:50,396::INFO::Processing pipeline 'deepsulci.sulci_labeling.capsul.training.SulciDeepTraining'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:50,398::INFO::Writing index at location '/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling/process/index.rst'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:50,398::INFO::process: '3' files written for module 'sulci_labeling' at location /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling/process.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:50,399::INFO::Writing module 'sulci_labeling' index at location '/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling/index.rst'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:50,399::INFO::Index: an index has been written for module 'sulci_labeling' at location /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:51,906::INFO::Found '14' pipeline(s) in 'morphologist.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:51,907::INFO::Found '40' process(es) in 'morphologist.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:51,907::INFO::Processing pipeline 'morphologist.capsul.axon.axonmorphologist.AxonMorphologist'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:59,539::INFO::Processing pipeline 'morphologist.capsul.axon.baladinnormalizationpipeline.BaladinNormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:59,557::INFO::Processing pipeline 'morphologist.capsul.axon.brainorientation.BrainOrientation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:59,725::INFO::Processing pipeline 'morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:59,750::INFO::Processing pipeline 'morphologist.capsul.axon.normalization.Normalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:58:59,866::INFO::Processing pipeline 'morphologist.capsul.axon.normalizationskullstripped.NormalizationSkullStripped'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:00,017::INFO::Processing pipeline 'morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:00,046::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabelling.SulciLabelling'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:59:00,085::ERROR::Traceback (most recent call last):
File "/casa/host/src/capsul/master/capsul/qt_apps/utils/find_pipelines.py", line 138, in find_pipeline_and_process
__import__(sub_sub_module_name)
File "/casa/host/build/python/deepsulci/pattern_classification/capsul/svm_training.py", line 8, in <module>
from ..method.svm import SVMPatternClassification
File "/casa/host/build/python/deepsulci/pattern_classification/method/svm.py", line 24, in <module>
import pcl
ModuleNotFoundError: No module named 'pcl'
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:59:00,085::ERROR::Can't load module deepsulci.pattern_classification.capsul.svm_training
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:59:00,088::ERROR::Traceback (most recent call last):
File "/casa/host/src/capsul/master/capsul/qt_apps/utils/find_pipelines.py", line 138, in find_pipeline_and_process
__import__(sub_sub_module_name)
File "/casa/host/build/python/deepsulci/pattern_classification/capsul/svm_labeling.py", line 7, in <module>
from ..method.svm import SVMPatternClassification
File "/casa/host/build/python/deepsulci/pattern_classification/method/svm.py", line 24, in <module>
import pcl
ModuleNotFoundError: No module named 'pcl'
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:59:00,088::ERROR::Can't load module deepsulci.pattern_classification.capsul.svm_labeling
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:00,100::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspam.SulciLabellingSPAM'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:00,126::INFO::Processing pipeline 'morphologist.capsul.fslnormalization.FSLNormalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:00,152::INFO::Processing pipeline 'morphologist.capsul.fslnormalization.FSLnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:00,190::INFO::Processing pipeline 'morphologist.capsul.morphologist.Morphologist'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-06-28 07:59:00,557::INFO::Found '0' pipeline(s) in 'deepsulci.pattern_classification.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:01,311::INFO::Processing pipeline 'morphologist.capsul.axon.baladinnormalizationpipeline.BaladinNormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:01,329::INFO::Processing pipeline 'morphologist.capsul.axon.brainorientation.BrainOrientation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:01,507::INFO::Processing pipeline 'morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:01,534::INFO::Processing pipeline 'morphologist.capsul.axon.normalization.Normalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:01,662::INFO::Processing pipeline 'morphologist.capsul.axon.normalizationskullstripped.NormalizationSkullStripped'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:01,826::INFO::Processing pipeline 'morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:01,871::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabelling.SulciLabelling'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:01,949::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspam.SulciLabellingSPAM'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:01,988::INFO::Processing pipeline 'morphologist.capsul.fslnormalization.FSLNormalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,018::INFO::Processing pipeline 'morphologist.capsul.fslnormalization.FSLnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,041::INFO::Processing pipeline 'morphologist.capsul.morphologist.Morphologist'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,169::INFO::Processing pipeline 'morphologist.capsul.spmnormalization.SPMNormalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,204::INFO::Processing pipeline 'morphologist.capsul.spmnormalization.SPMnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,233::INFO::Writing index at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/index.rst'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,234::INFO::pipeline: '14' files written for module 'capsul' at location /casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,234::INFO::Processing pipeline 'morphologist.capsul.axon.acpcorientation.AcpcOrientation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,238::INFO::Processing pipeline 'morphologist.capsul.axon.aimsconverter.AimsConverter'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,240::INFO::Processing pipeline 'morphologist.capsul.axon.baladinnormalizationtoaims.BaladinNormalizationToAims'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,241::INFO::Processing pipeline 'morphologist.capsul.axon.brainsegmentation.BrainSegmentation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,244::INFO::Processing pipeline 'morphologist.capsul.axon.brainvolumes.brainvolumes'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,247::INFO::Processing pipeline 'morphologist.capsul.axon.fslnormalizationtoaims.FSLnormalizationToAims'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,249::INFO::Processing pipeline 'morphologist.capsul.axon.greywhiteclassificationhemi.GreyWhiteClassificationHemi'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,251::INFO::Processing pipeline 'morphologist.capsul.axon.greywhitemesh.GreyWhiteMesh'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,252::INFO::Processing pipeline 'morphologist.capsul.axon.greywhitetopology.GreyWhiteTopology'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,253::INFO::Processing pipeline 'morphologist.capsul.axon.histoanalysis.HistoAnalysis'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,255::INFO::Processing pipeline 'morphologist.capsul.axon.importt1mri.ImportT1MRI'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,256::INFO::Processing pipeline 'morphologist.capsul.axon.morpho_report.morpho_report'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,259::INFO::Processing pipeline 'morphologist.capsul.axon.morphologistprocess.morphologistProcess'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,271::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_aimsmiregister.normalization_aimsmiregister'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,273::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_baladin.Normalization_Baladin'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,275::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_fsl_reinit.Normalization_FSL_reinit'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,276::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_spm_reinit.Normalization_SPM_reinit'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,278::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_t1_spm12_reinit.normalization_t1_spm12_reinit'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,280::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_t1_spm8_reinit.normalization_t1_spm8_reinit'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,282::INFO::Processing pipeline 'morphologist.capsul.axon.pialmesh.PialMesh'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,283::INFO::Processing pipeline 'morphologist.capsul.axon.reorientanatomy.ReorientAnatomy'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,285::INFO::Processing pipeline 'morphologist.capsul.axon.scalpmesh.ScalpMesh'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,287::INFO::Processing pipeline 'morphologist.capsul.axon.skullstripping.skullstripping'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,288::INFO::Processing pipeline 'morphologist.capsul.axon.splitbrain.SplitBrain'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,290::INFO::Processing pipeline 'morphologist.capsul.axon.spmsn3dtoaims.SPMsn3dToAims'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,292::INFO::Processing pipeline 'morphologist.capsul.axon.sulcigraph.SulciGraph'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,294::INFO::Processing pipeline 'morphologist.capsul.axon.sulcigraphmorphometrybysubject.sulcigraphmorphometrybysubject'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,296::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingann.SulciLabellingANN'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,298::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspamglobal.SulciLabellingSPAMGlobal'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,300::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspamlocal.SulciLabellingSPAMLocal'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,302::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspammarkov.SulciLabellingSPAMMarkov'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,304::INFO::Processing pipeline 'morphologist.capsul.axon.sulciskeleton.SulciSkeleton'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,305::INFO::Processing pipeline 'morphologist.capsul.axon.t1biascorrection.T1BiasCorrection'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,309::INFO::Processing pipeline 'morphologist.capsul.axon.talairachtransformation.TalairachTransformation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,310::INFO::Processing pipeline 'morphologist.capsul.axon.talairachtransformationfromnormalization.TalairachTransformationFromNormalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,312::INFO::Processing pipeline 'morphologist.capsul.import_t1_mri.ImportT1Mri'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,314::INFO::Processing pipeline 'morphologist.capsul.morphologist_simple.MorphologistSimple'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,326::INFO::Processing pipeline 'morphologist.capsul.morphologist_viewer.MorphologistView'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,329::INFO::Processing pipeline 'morphologist.capsul.sulci_manip.graph_pointcloud_label.GraphPointCloudLabel'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,330::INFO::Processing pipeline 'morphologist.capsul.talairachtransformationfromnormalization.TalairachTransformationFromNormalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,332::INFO::Writing index at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/process/index.rst'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,333::INFO::process: '40' files written for module 'capsul' at location /casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/process.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,333::INFO::Writing module 'capsul' index at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/index.rst'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:02,334::INFO::Index: an index has been written for module 'capsul' at location /casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,066::INFO::Processing pipeline 'morphologist.capsul.spmnormalization.SPMNormalization'...
WARNING: impossible to use version 2 of sip/Qt API.
generating CAPSUL processes docs...
['/usr/bin/python3', '-m', 'capsul.sphinxext.capsul_pipeline_rst', '-i', 'morphologist.capsul', '-o', '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist', '--schema']
loading pickled environment... /casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,100::INFO::Processing pipeline 'morphologist.capsul.spmnormalization.SPMnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,129::INFO::Writing index at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/pipeline/index.rst'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,130::INFO::pipeline: '14' files written for module 'capsul' at location /casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/pipeline.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,130::INFO::Processing pipeline 'morphologist.capsul.axon.acpcorientation.AcpcOrientation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,136::INFO::Processing pipeline 'morphologist.capsul.axon.aimsconverter.AimsConverter'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,138::INFO::Processing pipeline 'morphologist.capsul.axon.baladinnormalizationtoaims.BaladinNormalizationToAims'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,139::INFO::Processing pipeline 'morphologist.capsul.axon.brainsegmentation.BrainSegmentation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,142::INFO::Processing pipeline 'morphologist.capsul.axon.brainvolumes.brainvolumes'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,144::INFO::Processing pipeline 'morphologist.capsul.axon.fslnormalizationtoaims.FSLnormalizationToAims'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,145::INFO::Processing pipeline 'morphologist.capsul.axon.greywhiteclassificationhemi.GreyWhiteClassificationHemi'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,147::INFO::Processing pipeline 'morphologist.capsul.axon.greywhitemesh.GreyWhiteMesh'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,148::INFO::Processing pipeline 'morphologist.capsul.axon.greywhitetopology.GreyWhiteTopology'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,149::INFO::Processing pipeline 'morphologist.capsul.axon.histoanalysis.HistoAnalysis'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,151::INFO::Processing pipeline 'morphologist.capsul.axon.importt1mri.ImportT1MRI'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,152::INFO::Processing pipeline 'morphologist.capsul.axon.morpho_report.morpho_report'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,154::INFO::Processing pipeline 'morphologist.capsul.axon.morphologistprocess.morphologistProcess'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,166::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_aimsmiregister.normalization_aimsmiregister'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,167::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_baladin.Normalization_Baladin'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,168::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_fsl_reinit.Normalization_FSL_reinit'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,170::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_spm_reinit.Normalization_SPM_reinit'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,172::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_t1_spm12_reinit.normalization_t1_spm12_reinit'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,174::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_t1_spm8_reinit.normalization_t1_spm8_reinit'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,175::INFO::Processing pipeline 'morphologist.capsul.axon.pialmesh.PialMesh'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,177::INFO::Processing pipeline 'morphologist.capsul.axon.reorientanatomy.ReorientAnatomy'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,178::INFO::Processing pipeline 'morphologist.capsul.axon.scalpmesh.ScalpMesh'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,180::INFO::Processing pipeline 'morphologist.capsul.axon.skullstripping.skullstripping'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,181::INFO::Processing pipeline 'morphologist.capsul.axon.splitbrain.SplitBrain'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,183::INFO::Processing pipeline 'morphologist.capsul.axon.spmsn3dtoaims.SPMsn3dToAims'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,185::INFO::Processing pipeline 'morphologist.capsul.axon.sulcigraph.SulciGraph'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,187::INFO::Processing pipeline 'morphologist.capsul.axon.sulcigraphmorphometrybysubject.sulcigraphmorphometrybysubject'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,188::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingann.SulciLabellingANN'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,190::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspamglobal.SulciLabellingSPAMGlobal'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,192::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspamlocal.SulciLabellingSPAMLocal'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,194::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspammarkov.SulciLabellingSPAMMarkov'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,195::INFO::Processing pipeline 'morphologist.capsul.axon.sulciskeleton.SulciSkeleton'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,197::INFO::Processing pipeline 'morphologist.capsul.axon.t1biascorrection.T1BiasCorrection'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,200::INFO::Processing pipeline 'morphologist.capsul.axon.talairachtransformation.TalairachTransformation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:04,201::INFO::Processing pipeline 'morphologist.capsul.axon.talairachtransformationfromnormalization.TalairachTransformationFromNormalization'...
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done
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[autosummary] generating autosummary for: index.rst, process_docs/morphologist/capsul/index.rst, process_docs/morphologist/capsul/pipeline/index.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.axonmorphologist.AxonMorphologist.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.baladinnormalizationpipeline.BaladinNormalizationPipeline.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.brainorientation.BrainOrientation.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.normalization.Normalization.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.normalizationskullstripped.NormalizationSkullStripped.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline.rst, ..., process_docs/morphologist/capsul/process/morphologist.capsul.axon.sulciskeleton.SulciSkeleton.rst, process_docs/morphologist/capsul/process/morphologist.capsul.axon.t1biascorrection.T1BiasCorrection.rst, process_docs/morphologist/capsul/process/morphologist.capsul.axon.talairachtransformation.TalairachTransformation.rst, process_docs/morphologist/capsul/process/morphologist.capsul.axon.talairachtransformationfromnormalization.TalairachTransformationFromNormalization.rst, process_docs/morphologist/capsul/process/morphologist.capsul.import_t1_mri.ImportT1Mri.rst, process_docs/morphologist/capsul/process/morphologist.capsul.morphologist_simple.MorphologistSimple.rst, process_docs/morphologist/capsul/process/morphologist.capsul.morphologist_viewer.MorphologistView.rst, process_docs/morphologist/capsul/process/morphologist.capsul.sulci_manip.graph_pointcloud_label.GraphPointCloudLabel.rst, process_docs/morphologist/capsul/process/morphologist.capsul.talairachtransformationfromnormalization.TalairachTransformationFromNormalization.rst, sulpated.rst
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['/usr/bin/python3', '-m', 'capsul.sphinxext.capsul_pipeline_rst', '-i', 'morphologist.capsul', '-o', '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist', '--schema']
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[autosummary] generating autosummary for: index.rst, process_docs/morphologist/capsul/index.rst, process_docs/morphologist/capsul/pipeline/index.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.axonmorphologist.AxonMorphologist.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.baladinnormalizationpipeline.BaladinNormalizationPipeline.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.brainorientation.BrainOrientation.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.normalization.Normalization.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.normalizationskullstripped.NormalizationSkullStripped.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline.rst, ..., process_docs/morphologist/capsul/process/morphologist.capsul.axon.sulcilabellingspammarkov.SulciLabellingSPAMMarkov.rst, process_docs/morphologist/capsul/process/morphologist.capsul.axon.sulciskeleton.SulciSkeleton.rst, process_docs/morphologist/capsul/process/morphologist.capsul.axon.t1biascorrection.T1BiasCorrection.rst, process_docs/morphologist/capsul/process/morphologist.capsul.axon.talairachtransformation.TalairachTransformation.rst, process_docs/morphologist/capsul/process/morphologist.capsul.axon.talairachtransformationfromnormalization.TalairachTransformationFromNormalization.rst, process_docs/morphologist/capsul/process/morphologist.capsul.import_t1_mri.ImportT1Mri.rst, process_docs/morphologist/capsul/process/morphologist.capsul.morphologist_simple.MorphologistSimple.rst, process_docs/morphologist/capsul/process/morphologist.capsul.morphologist_viewer.MorphologistView.rst, process_docs/morphologist/capsul/process/morphologist.capsul.sulci_manip.graph_pointcloud_label.GraphPointCloudLabel.rst, process_docs/morphologist/capsul/process/morphologist.capsul.talairachtransformationfromnormalization.TalairachTransformationFromNormalization.rst
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/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline.rst:30: WARNING: duplicate label morphologist.capsul.axon.spmnormalizationpipeline.spmnormalizationpipeline_inputs, other instance in /casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.spmnormalization.SPMnormalizationPipeline.rst
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline.rst:70: WARNING: duplicate label morphologist.capsul.axon.spmnormalizationpipeline.spmnormalizationpipeline_outputs, other instance in /casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.spmnormalization.SPMnormalizationPipeline.rst
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.fslnormalization.FSLnormalizationPipeline.rst:30: WARNING: duplicate label morphologist.capsul.axon.fslnormalizationpipeline.fslnormalizationpipeline_inputs, other instance in /casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline.rst
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.fslnormalization.FSLnormalizationPipeline.rst:66: WARNING: duplicate label morphologist.capsul.axon.fslnormalizationpipeline.fslnormalizationpipeline_outputs, other instance in /casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline.rst
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.spmnormalization.SPMnormalizationPipeline.rst:30: WARNING: duplicate label morphologist.capsul.axon.spmnormalizationpipeline.spmnormalizationpipeline_inputs, other instance in /casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline.rst
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.spmnormalization.SPMnormalizationPipeline.rst:70: WARNING: duplicate label morphologist.capsul.axon.spmnormalizationpipeline.spmnormalizationpipeline_outputs, other instance in /casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline.rst
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The HTML pages are in ../../share/doc/morphologist-5.2/user_doc.
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build succeeded, 9 warnings.
The HTML pages are in ../../share/doc/morphologist-5.2/dev_doc.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:13,463::ERROR::Traceback (most recent call last):
File "/casa/host/src/capsul/master/capsul/qt_apps/utils/find_pipelines.py", line 138, in find_pipeline_and_process
__import__(sub_sub_module_name)
File "/casa/host/build/python/deepsulci/pattern_classification/capsul/svm_training.py", line 8, in <module>
from ..method.svm import SVMPatternClassification
File "/casa/host/build/python/deepsulci/pattern_classification/method/svm.py", line 24, in <module>
import pcl
ModuleNotFoundError: No module named 'pcl'
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:13,463::ERROR::Can't load module deepsulci.pattern_classification.capsul.svm_training
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:13,465::ERROR::Traceback (most recent call last):
File "/casa/host/src/capsul/master/capsul/qt_apps/utils/find_pipelines.py", line 138, in find_pipeline_and_process
__import__(sub_sub_module_name)
File "/casa/host/build/python/deepsulci/pattern_classification/capsul/svm_labeling.py", line 7, in <module>
from ..method.svm import SVMPatternClassification
File "/casa/host/build/python/deepsulci/pattern_classification/method/svm.py", line 24, in <module>
import pcl
ModuleNotFoundError: No module named 'pcl'
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:13,465::ERROR::Can't load module deepsulci.pattern_classification.capsul.svm_labeling
[100%] Built target morphologist-gpl-sphinx
[100%] Create "share/doc/5.2"
[100%] Built target morphologist-gpl-devdoc
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:13,945::INFO::Found '0' pipeline(s) in 'deepsulci.pattern_classification.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:13,945::INFO::Found '4' process(es) in 'deepsulci.pattern_classification.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:13,949::INFO::Processing pipeline 'deepsulci.pattern_classification.capsul.resnet_labeling.PatternDeepLabeling'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:13,951::INFO::Processing pipeline 'deepsulci.pattern_classification.capsul.resnet_training.PatternDeepTraining'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:13,954::INFO::Processing pipeline 'deepsulci.pattern_classification.capsul.snipe_labeling.PatternSnipeLabeling'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:13,955::INFO::Processing pipeline 'deepsulci.pattern_classification.capsul.snipe_training.PatternSnipeTraining'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:13,957::INFO::Writing index at location '/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/index.rst'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:13,958::INFO::process: '4' files written for module 'pattern_classification' at location /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:13,958::INFO::Writing module 'pattern_classification' index at location '/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/index.rst'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-06-28 07:59:13,958::INFO::Index: an index has been written for module 'pattern_classification' at location /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification.
[100%] Built target morphologist-gpl-doc
/usr/lib/python3/dist-packages/nbsphinx.py:1505: RuntimeWarning: You are using an unsupported version of pandoc (3.1.3).
Your version must be at least (1.12.1) but less than (3.0.0).
Refer to https://pandoc.org/installing.html.
Continuing with doubts...
nbconvert.utils.pandoc.check_pandoc_version()
WARNING: html_static_path entry '_static' does not exist
WARNING: impossible to use version 2 of sip/Qt API.
generating CAPSUL processes docs...
['/usr/bin/python3', '-m', 'capsul.sphinxext.capsul_pipeline_rst', '-i', 'deepsulci.sulci_labeling.capsul', '-o', '/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci', '--schema']
['/usr/bin/python3', '-m', 'capsul.sphinxext.capsul_pipeline_rst', '-i', 'deepsulci.pattern_classification.capsul', '-o', '/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci', '--schema']
loading pickled environment... done
loading intersphinx inventory from /casa/host/build/share/doc/soma-base-5.3/sphinx/objects.inv...
loading intersphinx inventory from /casa/host/build/share/doc/pyaims-5.2/sphinx/objects.inv...
loading intersphinx inventory from /casa/host/build/share/doc/pyanatomist-5.2/sphinx/objects.inv...
loading intersphinx inventory from /casa/host/build/share/doc/soma-workflow-3.3/sphinx/objects.inv...
WARNING: failed to reach any of the inventories with the following issues:
intersphinx inventory '/casa/host/build/share/doc/pyanatomist-5.2/sphinx/objects.inv' not fetchable due to <class 'FileNotFoundError'>: [Errno 2] No such file or directory: '/casa/host/build/share/doc/pyanatomist-5.2/sphinx/objects.inv'
loading intersphinx inventory from https://docs.python.org/3.12/objects.inv...
[autosummary] generating autosummary for: api.rst, index.rst, process_docs/deepsulci/pattern_classification/index.rst, process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.resnet_labeling.PatternDeepLabeling.rst, process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.resnet_training.PatternDeepTraining.rst, process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.snipe_labeling.PatternSnipeLabeling.rst, process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.snipe_training.PatternSnipeTraining.rst, process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.svm_labeling.PatternSVMLabeling.rst, process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.svm_training.PatternSVMTraining.rst, process_docs/deepsulci/pattern_classification/process/index.rst, process_docs/deepsulci/sulci_labeling/index.rst, process_docs/deepsulci/sulci_labeling/process/deepsulci.sulci_labeling.capsul.error_computation.ErrorComputation.rst, process_docs/deepsulci/sulci_labeling/process/deepsulci.sulci_labeling.capsul.labeling.SulciDeepLabeling.rst, process_docs/deepsulci/sulci_labeling/process/deepsulci.sulci_labeling.capsul.training.SulciDeepTraining.rst, process_docs/deepsulci/sulci_labeling/process/index.rst
/casa/host/src/capsul/master/doc/source/api/qt_apps.rst:5: WARNING: Could not import class or module 'capsul.qt_apps.main_window' specified for inheritance diagram
WARNING: autodoc: failed to import module 'main_window' from module 'capsul.qt_apps'; the following exception was raised:
cannot import name 'QtWebKit' from 'soma.qt_gui.qt_backend' (/casa/host/build/python/soma/qt_gui/qt_backend.py)
WARNING: autodoc: failed to import module 'pipeline_viewer_app' from module 'capsul.qt_apps'; the following exception was raised:
cannot import name 'QtWebKit' from 'soma.qt_gui.qt_backend' (/casa/host/build/python/soma/qt_gui/qt_backend.py)
/casa/host/src/capsul/master/doc/source/tutorial/capsul_tutorial.ipynb:1721: ERROR: Duplicate substitution definition name: "xml pipeline".
/casa/host/src/capsul/master/doc/source/tutorial/capsul_tutorial.ipynb:1722: ERROR: Duplicate substitution definition name: "xml pipeline controller".
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
copying assets... copying static files... done
copying extra files... done
done
[2Kwriting output... [ 20%] api/index
[2Kwriting output... [ 40%] api/qt_apps
[2Kwriting output... [ 60%] index
[2Kwriting output... [ 80%] tutorial/capsul_tutorial
WARNING: Failed to import deepsulci.pattern_classification.method.svm.
Possible hints:
* AttributeError: module 'deepsulci.pattern_classification.method' has no attribute 'svm'
* ModuleNotFoundError: No module named 'pcl'
pcl.registration missing !
building [mo]: targets for 0 po files that are out of date
writing output...
building [html]: targets for 11 source files that are out of date
updating environment: 0 added, 12 changed, 0 removed
[2Kreading sources... [ 8%] api
pcl.registration missing !
[2Kreading sources... [ 17%] process_docs/deepsulci/pattern_classification/index
[2Kreading sources... [ 25%] process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.resnet_labeling.PatternDeepLabeling
[2Kreading sources... [ 33%] process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.resnet_training.PatternDeepTraining
[2Kreading sources... [ 42%] process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.snipe_labeling.PatternSnipeLabeling
[2Kreading sources... [ 50%] process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.snipe_training.PatternSnipeTraining
[2Kreading sources... [ 58%] process_docs/deepsulci/pattern_classification/process/index
[2Kreading sources... [ 67%] process_docs/deepsulci/sulci_labeling/index
[2Kreading sources... [ 75%] process_docs/deepsulci/sulci_labeling/process/deepsulci.sulci_labeling.capsul.error_computation.ErrorComputation
[2Kreading sources... [ 83%] process_docs/deepsulci/sulci_labeling/process/deepsulci.sulci_labeling.capsul.labeling.SulciDeepLabeling
[2Kreading sources... [ 92%] process_docs/deepsulci/sulci_labeling/process/deepsulci.sulci_labeling.capsul.training.SulciDeepTraining
[2Kreading sources... [100%] process_docs/deepsulci/sulci_labeling/process/index
WARNING: autodoc: failed to import module 'svm' from module 'deepsulci.pattern_classification.method'; the following exception was raised:
No module named 'pcl'
/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/index.rst:23: CRITICAL: Problems with "include" directive path:
InputError: [Errno 2] No such file or directory: '../../../src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/pipeline/index.rst'.
/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/index.rst:21: WARNING: duplicate label pipelines, other instance in /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling/index.rst
/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/index.rst:26: WARNING: duplicate label buildingblocks, other instance in /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling/index.rst
/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.resnet_labeling.PatternDeepLabeling.rst:11: WARNING: duplicate label deepsulci.pattern_classification.capsul.resnet_labeling.patterndeeplabeling, other instance in /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.resnet_labeling.PatternDeepLabeling.rst
/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.resnet_labeling.PatternDeepLabeling.rst:32: WARNING: duplicate label inputs, other instance in /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling/process/deepsulci.sulci_labeling.capsul.training.SulciDeepTraining.rst
/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.resnet_labeling.PatternDeepLabeling.rst:47: WARNING: duplicate label outputs, other instance in /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling/process/deepsulci.sulci_labeling.capsul.training.SulciDeepTraining.rst
/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.resnet_training.PatternDeepTraining.rst:11: WARNING: duplicate label deepsulci.pattern_classification.capsul.resnet_training.patterndeeptraining, other instance in /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.resnet_training.PatternDeepTraining.rst
/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.resnet_training.PatternDeepTraining.rst:56: WARNING: duplicate label inputs, other instance in /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.resnet_labeling.PatternDeepLabeling.rst
/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.resnet_training.PatternDeepTraining.rst:84: WARNING: duplicate label outputs, other instance in /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.resnet_labeling.PatternDeepLabeling.rst
/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.snipe_labeling.PatternSnipeLabeling.rst:11: WARNING: duplicate label deepsulci.pattern_classification.capsul.snipe_labeling.patternsnipelabeling, other instance in /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.snipe_labeling.PatternSnipeLabeling.rst
/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.snipe_labeling.PatternSnipeLabeling.rst:33: WARNING: duplicate label inputs, other instance in /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.resnet_training.PatternDeepTraining.rst
/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.snipe_labeling.PatternSnipeLabeling.rst:53: WARNING: duplicate label outputs, other instance in /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.resnet_training.PatternDeepTraining.rst
/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.snipe_training.PatternSnipeTraining.rst:11: WARNING: duplicate label deepsulci.pattern_classification.capsul.snipe_training.patternsnipetraining, other instance in /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.snipe_training.PatternSnipeTraining.rst
/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.snipe_training.PatternSnipeTraining.rst:50: WARNING: duplicate label inputs, other instance in /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.snipe_labeling.PatternSnipeLabeling.rst
/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.snipe_training.PatternSnipeTraining.rst:74: WARNING: duplicate label outputs, other instance in /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/process/deepsulci.pattern_classification.capsul.snipe_labeling.PatternSnipeLabeling.rst
/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling/index.rst:23: CRITICAL: Problems with "include" directive path:
InputError: [Errno 2] No such file or directory: '../../../src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling/pipeline/index.rst'.
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/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling/process/deepsulci.sulci_labeling.capsul.labeling.SulciDeepLabeling.rst:11: WARNING: duplicate label deepsulci.sulci_labeling.capsul.labeling.sulcideeplabeling, other instance in /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling/process/deepsulci.sulci_labeling.capsul.labeling.SulciDeepLabeling.rst
/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling/process/deepsulci.sulci_labeling.capsul.labeling.SulciDeepLabeling.rst:36: WARNING: duplicate label inputs, other instance in /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling/process/deepsulci.sulci_labeling.capsul.error_computation.ErrorComputation.rst
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/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling/process/deepsulci.sulci_labeling.capsul.training.SulciDeepTraining.rst:11: WARNING: duplicate label deepsulci.sulci_labeling.capsul.training.sulcideeptraining, other instance in /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling/process/deepsulci.sulci_labeling.capsul.training.SulciDeepTraining.rst
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Finished: SUCCESS
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