FSLeyes hangs when starting #81
Comments
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Hi @hermancollin, I'm wondering if your desktop environment is using Wayland? What version of wxpython do you have installed? If you're using wayland, and have an older version of wxpython, you might be able to get things working by setting the Or, if you update to the latest version of wxpython (4.1.1), it should work under wayland without any extra configuration needed. |
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Hmm my desktop environment is KDE 5.82.0 / Plasma 5.21.5. Not sure about wayland. Anyway I saw that Also, I have the latest version of wxpython installed (4.1.1). Currently, I'm trying to install fsleyes in an isolated conda environment. Here is pip freezeabsl-py @ file:///tmp/build/80754af9/absl-py_1623861369333/work
alabaster==0.7.12
albumentations==0.3.0
argon2-cffi @ file:///tmp/build/80754af9/argon2-cffi_1613036642480/work
astor==0.8.1
async-generator==1.10
attrs @ file:///tmp/build/80754af9/attrs_1620827162558/work
Babel @ file:///home/conda/feedstock_root/build_artifacts/babel_1619719576210/work
backcall @ file:///home/ktietz/src/ci/backcall_1611930011877/work
bleach @ file:///tmp/build/80754af9/bleach_1626470256873/work
brotlipy==0.7.0
certifi==2021.5.30
cffi @ file:///tmp/build/80754af9/cffi_1625814693446/work
chardet @ file:///tmp/build/80754af9/chardet_1607706768982/work
cloudpickle @ file:///tmp/build/80754af9/cloudpickle_1598884132938/work
colorama @ file:///home/conda/feedstock_root/build_artifacts/colorama_1602866480661/work
contextlib2==0.6.0.post1
coverage @ file:///tmp/build/80754af9/coverage_1614614864940/work
cryptography @ file:///tmp/build/80754af9/cryptography_1616769182610/work
cycler==0.10.0
Cython @ file:///tmp/build/80754af9/cython_1626249882473/work
cytoolz==0.11.0
dask @ file:///tmp/build/80754af9/dask-core_1626066513842/work
decorator @ file:///tmp/build/80754af9/decorator_1621259047763/work
defusedxml @ file:///tmp/build/80754af9/defusedxml_1615228127516/work
docutils @ file:///home/conda/feedstock_root/build_artifacts/docutils_1618676240793/work
entrypoints==0.3
et-xmlfile==1.1.0
file-tree @ file:///home/conda/feedstock_root/build_artifacts/file-tree_1626714766742/work
file-tree-fsl @ file:///home/conda/feedstock_root/build_artifacts/file-tree-fsl_1618254561880/work
fsleyes @ file:///home/conda/feedstock_root/build_artifacts/fsleyes_1627037553776/work
fsleyes-props @ file:///home/conda/feedstock_root/build_artifacts/fsleyes-props_1619018550148/work
fsleyes-widgets @ file:///home/conda/feedstock_root/build_artifacts/fsleyes-widgets_1619035512156/work
fslpy @ file:///home/conda/feedstock_root/build_artifacts/fslpy_1624544149005/work
fsspec @ file:///tmp/build/80754af9/fsspec_1626383727127/work
gast @ file:///tmp/build/80754af9/gast_1625073243884/work
grpcio @ file:///tmp/build/80754af9/grpcio_1614883945333/work
h5py @ file:///home/conda/feedstock_root/build_artifacts/h5py_1617739440107/work
idna @ file:///home/linux1/recipes/ci/idna_1610986105248/work
imageio @ file:///home/conda/feedstock_root/build_artifacts/imageio_1594044661732/work
imagesize==1.2.0
imgaug @ file:///tmp/build/80754af9/imgaug_1605226543559/work
importlib-metadata @ file:///tmp/build/80754af9/importlib-metadata_1617877314848/work
indexed-gzip @ file:///home/conda/feedstock_root/build_artifacts/indexed_gzip_1621853443202/work
iniconfig @ file:///home/linux1/recipes/ci/iniconfig_1610983019677/work
ipykernel @ file:///tmp/build/80754af9/ipykernel_1596206598566/work/dist/ipykernel-5.3.4-py3-none-any.whl
ipython @ file:///tmp/build/80754af9/ipython_1617118429768/work
ipython-genutils @ file:///tmp/build/80754af9/ipython_genutils_1606773439826/work
ipywidgets @ file:///tmp/build/80754af9/ipywidgets_1610481889018/work
isodate==0.6.0
jdcal==1.4.1
jedi==0.17.0
Jinja2 @ file:///home/conda/feedstock_root/build_artifacts/jinja2_1612119311452/work
jsonschema @ file:///tmp/build/80754af9/jsonschema_1602607155483/work
jupyter @ file:///home/conda/feedstock_root/build_artifacts/jupyter_1611871908862/work
jupyter-client @ file:///tmp/build/80754af9/jupyter_client_1616770841739/work
jupyter-console @ file:///tmp/build/80754af9/jupyter_console_1616615302928/work
jupyter-core @ file:///tmp/build/80754af9/jupyter_core_1612213308260/work
jupyterlab-pygments @ file:///tmp/build/80754af9/jupyterlab_pygments_1601490720602/work
jupyterlab-widgets @ file:///tmp/build/80754af9/jupyterlab_widgets_1609884341231/work
Keras==2.3.1
Keras-Applications==1.0.8
Keras-Preprocessing @ file:///home/conda/feedstock_root/build_artifacts/keras-preprocessing_1610713559828/work
kiwisolver @ file:///tmp/build/80754af9/kiwisolver_1612282414123/work
locket==0.2.1
Mako @ file:///tmp/build/80754af9/mako_1610650590832/work
Markdown @ file:///tmp/build/80754af9/markdown_1614363832606/work
MarkupSafe @ file:///tmp/build/80754af9/markupsafe_1621528142364/work
matplotlib @ file:///tmp/build/80754af9/matplotlib-suite_1613407855456/work
mistune @ file:///tmp/build/80754af9/mistune_1594373098390/work
mkl-service==2.4.0
mock @ file:///tmp/build/80754af9/mock_1607622725907/work
more-itertools @ file:///tmp/build/80754af9/more-itertools_1622818384463/work
mpld3 @ file:///home/conda/feedstock_root/build_artifacts/mpld3_1624384796275/work
nbclient @ file:///tmp/build/80754af9/nbclient_1614364831625/work
nbconvert @ file:///tmp/build/80754af9/nbconvert_1624479062492/work
nbformat @ file:///tmp/build/80754af9/nbformat_1617383369282/work
nest-asyncio @ file:///tmp/build/80754af9/nest-asyncio_1613680548246/work
networkx @ file:///tmp/build/80754af9/networkx_1625827426685/work
nibabel @ file:///home/conda/feedstock_root/build_artifacts/nibabel_1606620997676/work
notebook @ file:///tmp/build/80754af9/notebook_1621523661196/work
numpy @ file:///home/conda/feedstock_root/build_artifacts/numpy_1624399863219/work
olefile==0.46
opencv-contrib-python==4.5.3.56
opencv-python-headless==4.5.3.56
openpyxl @ file:///home/conda/feedstock_root/build_artifacts/openpyxl_1615404969632/work
packaging @ file:///tmp/build/80754af9/packaging_1625611678980/work
pandas==1.3.0
pandocfilters @ file:///tmp/build/80754af9/pandocfilters_1605120451932/work
parse @ file:///home/conda/feedstock_root/build_artifacts/parse_1610612363844/work
parso @ file:///tmp/build/80754af9/parso_1617223946239/work
partd @ file:///tmp/build/80754af9/partd_1618000087440/work
pathlib2 @ file:///home/conda/feedstock_root/build_artifacts/pathlib2_1625503095928/work
pexpect @ file:///tmp/build/80754af9/pexpect_1605563209008/work
pickleshare @ file:///tmp/build/80754af9/pickleshare_1606932040724/work
Pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1625677823266/work
pluggy @ file:///tmp/build/80754af9/pluggy_1615976314111/work
prettytable @ file:///home/conda/feedstock_root/build_artifacts/prettytable_1614725168556/work
progressbar2 @ file:///home/conda/feedstock_root/build_artifacts/progressbar2_1599661727525/work
prometheus-client @ file:///tmp/build/80754af9/prometheus_client_1623189609245/work
prompt-toolkit @ file:///tmp/build/80754af9/prompt-toolkit_1616415428029/work
protobuf==3.8.0
ptyprocess @ file:///tmp/build/80754af9/ptyprocess_1609355006118/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl
py @ file:///tmp/build/80754af9/py_1607971587848/work
pycparser @ file:///tmp/build/80754af9/pycparser_1594388511720/work
pydicom @ file:///home/conda/feedstock_root/build_artifacts/pydicom_1607562682046/work
Pygments @ file:///tmp/build/80754af9/pygments_1621606182707/work
pygpu==0.7.6
PyOpenGL==3.1.5
pyOpenSSL @ file:///tmp/build/80754af9/pyopenssl_1608057966937/work
pyparsing @ file:///home/linux1/recipes/ci/pyparsing_1610983426697/work
Pypubsub==4.0.3
PyQt5==5.12.3
PyQt5-sip==4.19.18
PyQtChart==5.12
PyQtWebEngine==5.12.1
pyrsistent @ file:///tmp/build/80754af9/pyrsistent_1600141707582/work
PySocks @ file:///tmp/build/80754af9/pysocks_1594394576006/work
pytest==6.2.4
pytest-cov @ file:///home/conda/feedstock_root/build_artifacts/pytest-cov_1622651878478/work
python-dateutil @ file:///tmp/build/80754af9/python-dateutil_1626374649649/work
python-utils @ file:///home/conda/feedstock_root/build_artifacts/python-utils_1616867218381/work
pytz @ file:///tmp/build/80754af9/pytz_1612215392582/work
PyWavelets @ file:///tmp/build/80754af9/pywavelets_1601658308664/work
PyYAML==5.4.1
pyzmq==20.0.0
qtconsole @ file:///tmp/build/80754af9/qtconsole_1623278325812/work
QtPy==1.9.0
raven==6.10.0
requests @ file:///home/conda/feedstock_root/build_artifacts/requests_1608156231189/work
Rtree @ file:///home/conda/feedstock_root/build_artifacts/rtree_1626987839887/work
scikit-image==0.14.2
scikit-learn==0.19.2
scipy @ file:///home/conda/feedstock_root/build_artifacts/scipy_1624824869370/work
Send2Trash @ file:///tmp/build/80754af9/send2trash_1607525499227/work
Shapely @ file:///tmp/build/80754af9/shapely_1599817087478/work
six @ file:///tmp/build/80754af9/six_1623709665295/work
snowballstemmer @ file:///home/conda/feedstock_root/build_artifacts/snowballstemmer_1611270869511/work
Sphinx @ file:///home/conda/feedstock_root/build_artifacts/sphinx_1626290977112/work
sphinx-rtd-theme @ file:///home/conda/feedstock_root/build_artifacts/sphinx_rtd_theme_1617698677674/work
sphinxcontrib-applehelp==1.0.2
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp @ file:///home/conda/feedstock_root/build_artifacts/sphinxcontrib-htmlhelp_1621704829796/work
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml @ file:///home/conda/feedstock_root/build_artifacts/sphinxcontrib-serializinghtml_1621704833237/work
tabulate @ file:///home/conda/feedstock_root/build_artifacts/tabulate_1614001031686/work
tensorboard==1.13.1
tensorflow==1.13.1
tensorflow-estimator==1.13.0
termcolor==1.1.0
terminado==0.9.4
testpath @ file:///tmp/build/80754af9/testpath_1624638946665/work
Theano==1.0.2+2.gc449c86.dirty
toml @ file:///tmp/build/80754af9/toml_1616166611790/work
toolz @ file:///home/linux1/recipes/ci/toolz_1610987900194/work
tornado @ file:///tmp/build/80754af9/tornado_1606942283357/work
tqdm @ file:///home/conda/feedstock_root/build_artifacts/tqdm_1625664838498/work
traitlets @ file:///home/ktietz/src/ci/traitlets_1611929699868/work
trimesh @ file:///home/conda/feedstock_root/build_artifacts/trimesh_1626884538652/work
typing-extensions @ file:///tmp/build/80754af9/typing_extensions_1624965014186/work
urllib3 @ file:///tmp/build/80754af9/urllib3_1625084269274/work
wcwidth @ file:///tmp/build/80754af9/wcwidth_1593447189090/work
webencodings==0.5.1
Werkzeug @ file:///home/ktietz/src/ci/werkzeug_1611932622770/work
widgetsnbextension==3.5.1
wxnatpy==0.3.2
wxPython==4.1.1
xarray @ file:///home/conda/feedstock_root/build_artifacts/xarray_1627222030860/work
xnat @ file:///home/conda/feedstock_root/build_artifacts/xnat_1618825969432/work
zipp @ file:///tmp/build/80754af9/zipp_1625570634446/work |
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Did you install wxpython via conda-forge as well? The default behaviour of the conda-forge / pypi wxpython releases changed between 4.1.0 and 4.1.1 - 4.1.0 tries to interact with OpenGL via GLX, whereas 4.1.1 tries to interact with OpenGL via EGL. So if you are experiencing the error as reported (noting that the wxwidgets code pathway is hitting functions in At the moment, controlling whether wxPython/wxWidgets uses GLX or EGL to interface with OpenGL is a compile-time choice - there is a bit more information in this issue |
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Thanks you for your feedback @pauldmccarthy wxpython was installed via conda-forge as well. Still not sure how to fix the issue. |
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Would you be able to post the output of To create an isolated conda environment that just contains FSLeyes and wxPython should be as simple as: |
conda list |
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And what error do you get when running against 4.1.1? I can't see how you would get the reported error if you are using 4.1.1 |
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I get the reported error with 4.1.1: Interestingly, switching back to 4.1.0 and trying to launch fsleyes, I get additionnal informations and a "hard" crash (it crashed instead of hanging): If I launch fsleyes again, the program will hang. |
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Sorry, I made a mistake - there is actually another factor at play here, which is the version of GTK that the wxPython build was compiled against - all versions compiled against GTK2 will use GLX, whereas the versions compiled against GTK3 will use EGL. So both of the versions of wxpython that you have tried will be using GLX. Can we simpliffy things a bit? Instead of trying to run |
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Both glxgearsglxinfo |
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Sorry, I'm stumped. Do you get the same errors against both wxpython versions when running FSLeyes with the
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Unfortunately I get the same error with both wxpython versions and the At this point, should I try building wxpython from source? |
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I'm afraid you might have to, unless by chance one of the pre-built wheels at https://extras.wxpython.org/wxPython4/extras/linux/ is compatible with your system.. Building wxpython isn't too complicated, as long as you have all of the dependencies installed. I have a script for Ubuntu platforms, which should work against the |
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Hey there.
fsleyes hangs on startup on my side. I'm on linux 5.10.35-1-rt39-MANJARO. The team I work with have an older version of fsleyes (0.33.1) running inside a conda venv and everything works fine for them but I can't get it to work anymore. I tried installing the latest fsleyes version from conda-forge but still no luck. This is the error I got:
What do you guys think of this? Seems to be an issue with wxPython
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