Console Output
Skipping 194 KB..
Full Logwriting additional pages... search done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded.
The HTML pages are in ../../share/doc/brainvisa-cmake-6.0.
This plugin does not support propagateSizeHints()
[100%] Built target brainvisa-cmake-usrsphinx
[100%] Create "share/doc/6.0"
[100%] Built target brainvisa-cmake-usrdoc
[100%] Built target brainvisa-cmake-doc
/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looking for now-outdated files...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... done
checking consistency... done
preparing documents... /casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-07-28 06:13:47,665::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'.
done
copying assets... copying static files... /casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-07-28 06:13:47,695::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
copying extra files... done
done
[2Kwriting output... [ 50%] api
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-07-28 06:13:47,752::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::2025-07-28 06:13:47,803::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'.
[NbConvertApp] Converting notebook /casa/host/src/capsul/master/doc/source/tutorial/capsul_tutorial.ipynb.in to notebook
[NbConvertApp] Writing 59249 bytes to /casa/host/src/capsul/master/doc/source/tutorial/capsul_tutorial.ipynb
[2Kwriting output... [100%] index
generating indices... genindex -- 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... 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.
done
loading intersphinx inventory from /casa/host/build/share/doc/soma-base-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/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/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...
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
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
[100%] Built target soma-base-sphinx
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...
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: 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
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
[100%] Create "share/doc/5.3"
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-devdoc
[100%] Built target soma-base-doc
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'
/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'
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
[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 anatomist.altas_viewer.
Possible hints:
* AttributeError: module 'anatomist' has no attribute 'altas_viewer'
* ModuleNotFoundError: No module named 'anatomist.altas_viewer'
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'
[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
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 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.
[2Kbuilding [mo]: targets for 0 po files that are out of date
generating gallery for auto_examples... [ 4%] writing output... volumetest.py
building [html]: targets for 1 source files that are out of date
updating environment: [2Kgenerating gallery for auto_examples... [ 9%] nomenclatureselection.py
[2Kgenerating gallery for auto_examples... [ 13%] graph.py
0 added, 2 changed, 0 removed
[2Kreading sources... [ 50%] api/qt_apps
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
[100%] Built target axon-sphinx
[100%] Create "share/doc/5.2"
[100%] Built target axon-devdoc
[2Kreading sources... [100%] tutorial/capsul_tutorial
[2Kgenerating gallery for auto_examples... [ 52%] aimsvolumetest.py
[2Kgenerating gallery for auto_examples... [ 57%] meshtest.py
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
[2Kgenerating gallery for auto_examples... [ 87%] volumeMeasures.py
[2Kgenerating gallery for auto_examples... [ 91%] anaevensimplerviewer.py
This plugin does not support propagateSizeHints()
QOpenGLWidget is not supported on this platform.
QOpenGLWidget is not supported on this platform.
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 propagateSizeHints()
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::2025-07-28 06:13:54,242::INFO::Found '0' pipeline(s) in 'deepsulci.sulci_labeling.capsul'.
Segmentation fault (core dumped)
[100%] Built target anatomist-gpl-sphinx
[100%] Create "share/doc/5.2"
[100%] Built target anatomist-gpl-devdoc
[100%] Built target anatomist-gpl-doc
Process2 execution, a: 0.000000, b: blop
Process2 execution, a: 0.000000, b: yup
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-07-28 06:13:54,960::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'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-07-28 06:13:55,152::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::2025-07-28 06:13:55,274::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'.
Process2 execution, a: 0.000000, b: blop
[100%] Built target aims-free-sphinx
[100%] Create "share/doc/5.2"
[100%] Built target aims-free-devdoc
[100%] Built target aims-free-doc
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-07-28 06:14:00,657::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::2025-07-28 06:14:00,764::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'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-07-28 06:14:00,861::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'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-07-28 06:14:00,893::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::2025-07-28 06:14:00,980::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'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-07-28 06:14:01,507::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::2025-07-28 06:14:01,591::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::2025-07-28 06:14:01,632::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::2025-07-28 06:14:01,682::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::2025-07-28 06:14:01,735::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'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-07-28 06:14:01,828::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::2025-07-28 06:14:01,888::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::2025-07-28 06:14:01,930::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::2025-07-28 06:14:01,991::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_rst.py::2025-07-28 06:14:02,072::INFO::Found '0' pipeline(s) in 'deepsulci.sulci_labeling.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:02,073::INFO::Found '3' process(es) in 'deepsulci.sulci_labeling.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:02,073::INFO::Processing pipeline 'deepsulci.sulci_labeling.capsul.error_computation.ErrorComputation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:02,074::INFO::Processing pipeline 'deepsulci.sulci_labeling.capsul.labeling.SulciDeepLabeling'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:02,076::INFO::Processing pipeline 'deepsulci.sulci_labeling.capsul.training.SulciDeepTraining'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-07-28 06:14:02,077::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'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:02,077::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::2025-07-28 06:14:02,077::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::2025-07-28 06:14:02,077::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::2025-07-28 06:14:02,078::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_view.py::2025-07-28 06:14:02,132::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'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-07-28 06:14:02,189::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'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-07-28 06:14:02,271::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'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-07-28 06:14:02,271::INFO::Summary: '14' files written for module 'capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-07-28 06:14:02,276::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::2025-07-28 06:14:02,372::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::2025-07-28 06:14:02,545::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'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-07-28 06:14:02,545::INFO::Summary: '14' files written for module 'capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:03,359::INFO::Found '14' pipeline(s) in 'morphologist.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:03,359::INFO::Found '40' process(es) in 'morphologist.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:03,360::INFO::Processing pipeline 'morphologist.capsul.axon.axonmorphologist.AxonMorphologist'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:03,718::INFO::Found '14' pipeline(s) in 'morphologist.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:03,718::INFO::Found '40' process(es) in 'morphologist.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:03,719::INFO::Processing pipeline 'morphologist.capsul.axon.axonmorphologist.AxonMorphologist'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-07-28 06:14:07,439::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::2025-07-28 06:14:07,439::ERROR::Can't load module deepsulci.pattern_classification.capsul.svm_training
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-07-28 06:14:07,440::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::2025-07-28 06:14:07,440::ERROR::Can't load module deepsulci.pattern_classification.capsul.svm_labeling
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-07-28 06:14:07,641::INFO::Found '0' pipeline(s) in 'deepsulci.pattern_classification.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:07,953::INFO::Processing pipeline 'morphologist.capsul.axon.baladinnormalizationpipeline.BaladinNormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:07,961::INFO::Processing pipeline 'morphologist.capsul.axon.brainorientation.BrainOrientation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,035::INFO::Processing pipeline 'morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,046::INFO::Processing pipeline 'morphologist.capsul.axon.normalization.Normalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,097::INFO::Processing pipeline 'morphologist.capsul.axon.normalizationskullstripped.NormalizationSkullStripped'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,128::INFO::Processing pipeline 'morphologist.capsul.axon.baladinnormalizationpipeline.BaladinNormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,136::INFO::Processing pipeline 'morphologist.capsul.axon.brainorientation.BrainOrientation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,163::INFO::Processing pipeline 'morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,177::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabelling.SulciLabelling'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,207::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspam.SulciLabellingSPAM'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,208::INFO::Processing pipeline 'morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,219::INFO::Processing pipeline 'morphologist.capsul.axon.normalization.Normalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,222::INFO::Processing pipeline 'morphologist.capsul.fslnormalization.FSLNormalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,233::INFO::Processing pipeline 'morphologist.capsul.fslnormalization.FSLnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,243::INFO::Processing pipeline 'morphologist.capsul.morphologist.Morphologist'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,270::INFO::Processing pipeline 'morphologist.capsul.axon.normalizationskullstripped.NormalizationSkullStripped'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,337::INFO::Processing pipeline 'morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,350::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabelling.SulciLabelling'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,381::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspam.SulciLabellingSPAM'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,396::INFO::Processing pipeline 'morphologist.capsul.fslnormalization.FSLNormalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,408::INFO::Processing pipeline 'morphologist.capsul.fslnormalization.FSLnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:08,418::INFO::Processing pipeline 'morphologist.capsul.morphologist.Morphologist'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,102::INFO::Processing pipeline 'morphologist.capsul.spmnormalization.SPMNormalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,118::INFO::Processing pipeline 'morphologist.capsul.spmnormalization.SPMnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,132::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::2025-07-28 06:14:09,132::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::2025-07-28 06:14:09,132::INFO::Processing pipeline 'morphologist.capsul.axon.acpcorientation.AcpcOrientation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,133::INFO::Processing pipeline 'morphologist.capsul.axon.aimsconverter.AimsConverter'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,134::INFO::Processing pipeline 'morphologist.capsul.axon.baladinnormalizationtoaims.BaladinNormalizationToAims'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,135::INFO::Processing pipeline 'morphologist.capsul.axon.brainsegmentation.BrainSegmentation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,136::INFO::Processing pipeline 'morphologist.capsul.axon.brainvolumes.brainvolumes'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,137::INFO::Processing pipeline 'morphologist.capsul.axon.fslnormalizationtoaims.FSLnormalizationToAims'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,138::INFO::Processing pipeline 'morphologist.capsul.axon.greywhiteclassificationhemi.GreyWhiteClassificationHemi'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,139::INFO::Processing pipeline 'morphologist.capsul.axon.greywhitemesh.GreyWhiteMesh'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,139::INFO::Processing pipeline 'morphologist.capsul.axon.greywhitetopology.GreyWhiteTopology'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,140::INFO::Processing pipeline 'morphologist.capsul.axon.histoanalysis.HistoAnalysis'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,141::INFO::Processing pipeline 'morphologist.capsul.axon.importt1mri.ImportT1MRI'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,142::INFO::Processing pipeline 'morphologist.capsul.axon.morpho_report.morpho_report'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,143::INFO::Processing pipeline 'morphologist.capsul.axon.morphologistprocess.morphologistProcess'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,148::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_aimsmiregister.normalization_aimsmiregister'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,148::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_baladin.Normalization_Baladin'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,149::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_fsl_reinit.Normalization_FSL_reinit'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,150::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_spm_reinit.Normalization_SPM_reinit'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,151::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::2025-07-28 06:14:09,152::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::2025-07-28 06:14:09,153::INFO::Processing pipeline 'morphologist.capsul.axon.pialmesh.PialMesh'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,153::INFO::Processing pipeline 'morphologist.capsul.axon.reorientanatomy.ReorientAnatomy'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,154::INFO::Processing pipeline 'morphologist.capsul.axon.scalpmesh.ScalpMesh'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,155::INFO::Processing pipeline 'morphologist.capsul.axon.skullstripping.skullstripping'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,156::INFO::Processing pipeline 'morphologist.capsul.axon.splitbrain.SplitBrain'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,157::INFO::Processing pipeline 'morphologist.capsul.axon.spmsn3dtoaims.SPMsn3dToAims'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,157::INFO::Processing pipeline 'morphologist.capsul.axon.sulcigraph.SulciGraph'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,159::INFO::Processing pipeline 'morphologist.capsul.axon.sulcigraphmorphometrybysubject.sulcigraphmorphometrybysubject'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,159::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingann.SulciLabellingANN'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,160::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspamglobal.SulciLabellingSPAMGlobal'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,161::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspamlocal.SulciLabellingSPAMLocal'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,162::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspammarkov.SulciLabellingSPAMMarkov'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,163::INFO::Processing pipeline 'morphologist.capsul.axon.sulciskeleton.SulciSkeleton'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,164::INFO::Processing pipeline 'morphologist.capsul.axon.t1biascorrection.T1BiasCorrection'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,166::INFO::Processing pipeline 'morphologist.capsul.axon.talairachtransformation.TalairachTransformation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,166::INFO::Processing pipeline 'morphologist.capsul.axon.talairachtransformationfromnormalization.TalairachTransformationFromNormalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,167::INFO::Processing pipeline 'morphologist.capsul.import_t1_mri.ImportT1Mri'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,168::INFO::Processing pipeline 'morphologist.capsul.morphologist_simple.MorphologistSimple'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,173::INFO::Processing pipeline 'morphologist.capsul.morphologist_viewer.MorphologistView'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,174::INFO::Processing pipeline 'morphologist.capsul.sulci_manip.graph_pointcloud_label.GraphPointCloudLabel'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,174::INFO::Processing pipeline 'morphologist.capsul.talairachtransformationfromnormalization.TalairachTransformationFromNormalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,175::INFO::Writing index at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/process/index.rst'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,176::INFO::process: '40' files written for module 'capsul' at location /casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/process.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,176::INFO::Writing module 'capsul' index at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/index.rst'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,176::INFO::Index: an index has been written for module 'capsul' at location /casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,259::INFO::Processing pipeline 'morphologist.capsul.spmnormalization.SPMNormalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,276::INFO::Processing pipeline 'morphologist.capsul.spmnormalization.SPMnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,290::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::2025-07-28 06:14:09,291::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::2025-07-28 06:14:09,291::INFO::Processing pipeline 'morphologist.capsul.axon.acpcorientation.AcpcOrientation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,292::INFO::Processing pipeline 'morphologist.capsul.axon.aimsconverter.AimsConverter'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,293::INFO::Processing pipeline 'morphologist.capsul.axon.baladinnormalizationtoaims.BaladinNormalizationToAims'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,294::INFO::Processing pipeline 'morphologist.capsul.axon.brainsegmentation.BrainSegmentation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,295::INFO::Processing pipeline 'morphologist.capsul.axon.brainvolumes.brainvolumes'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,296::INFO::Processing pipeline 'morphologist.capsul.axon.fslnormalizationtoaims.FSLnormalizationToAims'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,297::INFO::Processing pipeline 'morphologist.capsul.axon.greywhiteclassificationhemi.GreyWhiteClassificationHemi'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,298::INFO::Processing pipeline 'morphologist.capsul.axon.greywhitemesh.GreyWhiteMesh'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,298::INFO::Processing pipeline 'morphologist.capsul.axon.greywhitetopology.GreyWhiteTopology'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,299::INFO::Processing pipeline 'morphologist.capsul.axon.histoanalysis.HistoAnalysis'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,300::INFO::Processing pipeline 'morphologist.capsul.axon.importt1mri.ImportT1MRI'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,301::INFO::Processing pipeline 'morphologist.capsul.axon.morpho_report.morpho_report'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,302::INFO::Processing pipeline 'morphologist.capsul.axon.morphologistprocess.morphologistProcess'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,307::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_aimsmiregister.normalization_aimsmiregister'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,308::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_baladin.Normalization_Baladin'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,309::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_fsl_reinit.Normalization_FSL_reinit'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,310::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_spm_reinit.Normalization_SPM_reinit'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,311::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::2025-07-28 06:14:09,311::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::2025-07-28 06:14:09,312::INFO::Processing pipeline 'morphologist.capsul.axon.pialmesh.PialMesh'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,313::INFO::Processing pipeline 'morphologist.capsul.axon.reorientanatomy.ReorientAnatomy'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,314::INFO::Processing pipeline 'morphologist.capsul.axon.scalpmesh.ScalpMesh'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,315::INFO::Processing pipeline 'morphologist.capsul.axon.skullstripping.skullstripping'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,316::INFO::Processing pipeline 'morphologist.capsul.axon.splitbrain.SplitBrain'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,317::INFO::Processing pipeline 'morphologist.capsul.axon.spmsn3dtoaims.SPMsn3dToAims'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,318::INFO::Processing pipeline 'morphologist.capsul.axon.sulcigraph.SulciGraph'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,319::INFO::Processing pipeline 'morphologist.capsul.axon.sulcigraphmorphometrybysubject.sulcigraphmorphometrybysubject'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,319::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingann.SulciLabellingANN'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,320::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspamglobal.SulciLabellingSPAMGlobal'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,321::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspamlocal.SulciLabellingSPAMLocal'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,322::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspammarkov.SulciLabellingSPAMMarkov'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,323::INFO::Processing pipeline 'morphologist.capsul.axon.sulciskeleton.SulciSkeleton'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,324::INFO::Processing pipeline 'morphologist.capsul.axon.t1biascorrection.T1BiasCorrection'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,326::INFO::Processing pipeline 'morphologist.capsul.axon.talairachtransformation.TalairachTransformation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,327::INFO::Processing pipeline 'morphologist.capsul.axon.talairachtransformationfromnormalization.TalairachTransformationFromNormalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,328::INFO::Processing pipeline 'morphologist.capsul.import_t1_mri.ImportT1Mri'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,328::INFO::Processing pipeline 'morphologist.capsul.morphologist_simple.MorphologistSimple'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,333::INFO::Processing pipeline 'morphologist.capsul.morphologist_viewer.MorphologistView'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,335::INFO::Processing pipeline 'morphologist.capsul.sulci_manip.graph_pointcloud_label.GraphPointCloudLabel'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,335::INFO::Processing pipeline 'morphologist.capsul.talairachtransformationfromnormalization.TalairachTransformationFromNormalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:09,336::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::2025-07-28 06:14:09,337::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::2025-07-28 06:14:09,337::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::2025-07-28 06:14:09,337::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.
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/dev_doc/process_docs/morphologist', '--schema']
loading pickled environment... 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... 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...
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 /casa/host/build/share/doc/soma-workflow-3.3/sphinx/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/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 doc/morphologist-ui-5.2/objects.inv...
WARNING: failed to reach any of the inventories with the following issues:
intersphinx inventory 'doc/morphologist-ui-5.2/objects.inv' not fetchable due to <class 'FileNotFoundError'>: [Errno 2] No such file or directory: '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/doc/morphologist-ui-5.2/objects.inv'
[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
building [mo]: targets for 0 po files that are out of date
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[2Kreading sources... [ 2%] process_docs/morphologist/capsul/index
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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
building [mo]: targets for 0 po files that are out of date
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[2Kreading sources... [ 2%] process_docs/morphologist/capsul/index
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/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_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/dev_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.spmnormalization.SPMnormalizationPipeline.rst
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_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/dev_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.spmnormalization.SPMnormalizationPipeline.rst
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_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/dev_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline.rst
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_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/dev_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline.rst
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_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/dev_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline.rst
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_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/dev_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline.rst
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/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.fslnormalizationpipeline.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.fslnormalization.FSLnormalizationPipeline.rst
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/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.fslnormalizationpipeline.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.fslnormalization.FSLnormalizationPipeline.rst
/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
checking consistency... /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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checking consistency... /casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/index.rst:10: WARNING: Citation [FISCHER2012] is not referenced.
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/index.rst:118: WARNING: Citation [PERROT2009] is not referenced.
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/index.rst:120: WARNING: Citation [PERROT2011] is not referenced.
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/index.rst:129: WARNING: Citation [TUCHOLKA2008] is not referenced.
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/index.rst:134: WARNING: Citation [KELLER2009] is not referenced.
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/index.rst:139: WARNING: Citation [VAROQUAUX2010] is not referenced.
done
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/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:13,854::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::2025-07-28 06:14:13,854::ERROR::Can't load module deepsulci.pattern_classification.capsul.svm_training
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:13,856::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::2025-07-28 06:14:13,856::ERROR::Can't load module deepsulci.pattern_classification.capsul.svm_labeling
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/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:14,096::INFO::Found '0' pipeline(s) in 'deepsulci.pattern_classification.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:14,097::INFO::Found '4' process(es) in 'deepsulci.pattern_classification.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:14,097::INFO::Processing pipeline 'deepsulci.pattern_classification.capsul.resnet_labeling.PatternDeepLabeling'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:14,098::INFO::Processing pipeline 'deepsulci.pattern_classification.capsul.resnet_training.PatternDeepTraining'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:14,100::INFO::Processing pipeline 'deepsulci.pattern_classification.capsul.snipe_labeling.PatternSnipeLabeling'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:14,100::INFO::Processing pipeline 'deepsulci.pattern_classification.capsul.snipe_training.PatternSnipeTraining'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-07-28 06:14:14,101::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::2025-07-28 06:14:14,102::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::2025-07-28 06:14:14,102::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::2025-07-28 06:14:14,102::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.
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...
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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 /casa/host/build/share/doc/soma-workflow-3.3/sphinx/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
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 !
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pcl.registration missing !
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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'.
/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling/index.rst:21: WARNING: duplicate label pipelines, other instance in /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/pattern_classification/index.rst
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build succeeded, 7 warnings.
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bv_maker summary:
OK step doc: /casa/host/build, started: 2025/07/28 06:13, stopped: 2025/07/28 06:14
All went good.
Finished: SUCCESS
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