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spyder-ide / spyder

Official repository for Spyder - The Scientific Python Development Environment
https://www.spyder-ide.org
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Spyder crashes on startup. Segmentation fault: fromIccProfile: failed minimal tag size sanity #22239

Open xaverm opened 2 weeks ago

xaverm commented 2 weeks ago

Spyder 5.5.5 does not start anymore. It crashes immediately after startup with two lines of err msg.:

fromIccProfile: failed minimal tag size sanity
Segmentation fault (core dumped)

Usually, when reporting, I list all of my config details here as from out of spyder - but as I wrote, it does not even start.

Any help please!?

xaverm commented 2 weeks ago

One additional comment: If I generate a new environment and only install spyder directly after that, Spyder will still generate fromIccProfile: failed minimal tag size sanity but it does not crash after that ...?

xaverm commented 2 weeks ago

Yet another comment: Setting up a new environment step-wise, the segfault of spyder happens after this conda install step

## Package Plan ##
  environment location: /home/xxxxx/.anaconda3/envs/sp
  added / updated specs:
    - mayavi

The following NEW packages will be INSTALLED:
  mayavi             conda-forge/linux-64::mayavi-4.8.2-py39hbf58f9e_3
  mesalib            conda-forge/linux-64::mesalib-24.1.3-h3ac77ca_0

The following packages will be DOWNGRADED:
  ffmpeg                             7.0.1-gpl_h3589c0a_102 --> 6.1.1-gpl_he2f97eb_114
  vtk                             9.3.1-qt_py39h1234567_200 --> 9.3.0-osmesa_py39h1234567_100
  vtk-base                        9.3.1-qt_py39h1234567_200 --> 9.3.0-osmesa_py39h1234567_100
  vtk-io-ffmpeg                   9.3.1-qt_py39h1234567_200 --> 9.3.0-osmesa_py39h1234567_100

Rolling back before that install, the segfault is gone again. Forcing a mayavi=4.8.1 install after that instead, there is no segfault. So maybe there is some issue with mayavi / mesalib / ffmpeg / vtk (?) This is about as far as my lame mileage gets me ...

Any help?

ccordoba12 commented 2 weeks ago

Hey @xaverm, thanks for reporting. The problem could be with VTK because I saw they're trying to transition to Qt6 and Spyder 5 is not ready for it.

My suggestion for you is to install Spyder in a different environment by running:

conda create -n spyder-env spyder python=3.11
conda activate spyder-env
spyder

Then you can connect that Spyder to your sp env by following the procedure described in our documentation:

http://docs.spyder-ide.org/current/faq.html#using-existing-environment

That would prevent the segfaults you're having and allow you to continue working with your current env.

xaverm commented 2 weeks ago

@ccordoba12 Thx. for getting back to me.

Ok. since the last revision without spyder segfaulting did have a vtk=9.2.6, I'll pin the environment to that version and will keep also mayavi=4.8.1 (which seems to force the qt update if updated by itself(?)). That seems to keep a running status, even if I do conda update --all after that and even if I stick with just one environment.

This is not really a mind-soothing situation ;-) ... anyway, are you guys having a rough plan when Spyder will cope with newer qt versions?

Edit: B.t.w.: Which are the recommended versions of the (many ... :-( ) qt packages that one should keep, such as to have spyder not get into trouble with them?

ccordoba12 commented 1 week ago

This is not really a mind-soothing situation ;-) ... anyway, are you guys having a rough plan when Spyder will cope with newer qt versions?

We should be able to support Qt6/PyQt6 next year. Spyder 6 will come with initial (but not default) support for it, but we still have to run our test suite against that version, which could take a couple of months to make it pass.

Edit: B.t.w.: Which are the recommended versions of the (many ... :-( ) qt packages that one should keep, such as to have spyder not get into trouble with them?

Spyder works best with PyQt5 5.15.

But I think you'd do much better by following my recommendation above, i.e. having Spyder in a separate env and connecting it to the envs you want to work with.

That would be much easier in Spyder 6 because we'll have a new submenu in the Consoles menu to open a console for any env you want.

ccordoba12 commented 1 week ago

One question for you @xaverm: is it ok to close this issue given that you managed to solve your problem?

NelsonUpenn commented 1 week ago

I run MacOS14.5 (latest). Today I downloaded and installed Anaconda. Then conda update --all Then conda list returns: spyder 5.5.1 py312hca03da5_3
(I will paste the entire listing below, but for now I will point out that vtk is not installed.) Then I asked at the command line for: spyder which gives the error:

The available OpenGL surface format was either not version 3.2 or higher or not a Core Profile. Chromium on macOS will fall back to software rendering in this case. Hardware acceleration and features such as WebGL will not be available. fromIccProfile: failed minimal tag size sanity /opt/anaconda3/bin/pythonw: line 3: 72922 Segmentation fault: 11 /opt/anaconda3/python.app/Contents/MacOS/python "$@"

I have no environments, just installed Anaconda out of the box.

This is disturbing. I did not quite follow the advice above, so could you offer a very explicit suggestion?

Thank you P Nelson =====FULL OUTPUT OF CONDA LIST $ conda list

packages in environment at /opt/anaconda3:

#

Name Version Build Channel

_anaconda_depends 2024.06 py312_openblas_2
abseil-cpp 20230802.0 h313beb8_2
aiobotocore 2.12.3 py312hca03da5_0
aiohttp 3.9.5 py312h80987f9_0
aioitertools 0.7.1 pyhd3eb1b0_0
aiosignal 1.2.0 pyhd3eb1b0_0
alabaster 0.7.16 py312hca03da5_0
altair 5.0.1 py312hca03da5_0
anaconda-anon-usage 0.4.4 py312hd6b623d_100
anaconda-catalogs 0.2.0 py312hca03da5_1
anaconda-client 1.12.3 py312hca03da5_0
anaconda-cloud-auth 0.5.1 py312hca03da5_0
anaconda-navigator 2.6.1 py312hca03da5_2
anaconda-project 0.11.1 py312hca03da5_0
annotated-types 0.6.0 py312hca03da5_0
anyio 4.2.0 py312hca03da5_0
aom 3.6.0 h313beb8_0
appdirs 1.4.4 pyhd3eb1b0_0
applaunchservices 0.3.0 py312hca03da5_0
appnope 0.1.3 py312hca03da5_1001
appscript 1.1.2 py312h80987f9_0
archspec 0.2.3 pyhd3eb1b0_0
argon2-cffi 21.3.0 pyhd3eb1b0_0
argon2-cffi-bindings 21.2.0 py312h80987f9_0
arrow 1.2.3 py312hca03da5_1
arrow-cpp 14.0.2 hc7aafb3_1
astroid 2.14.2 py312hca03da5_0
astropy 6.1.0 py312ha86b861_0
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asttokens 2.0.5 pyhd3eb1b0_0
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atomicwrites 1.4.0 py_0
attrs 23.1.0 py312hca03da5_0
automat 20.2.0 py_0
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aws-c-auth 0.6.19 h80987f9_0
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aws-c-compression 0.2.16 h80987f9_0
aws-c-event-stream 0.2.15 h313beb8_0
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c-ares 1.19.1 h80987f9_0
c-blosc2 2.12.0 h7df6c2f_0
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certifi 2024.7.4 py312hca03da5_0
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constantly 23.10.4 py312hca03da5_0
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cssselect 1.2.0 py312hca03da5_0
curl 8.7.1 h02f6b3c_0
cycler 0.11.0 pyhd3eb1b0_0
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dask-core 2024.5.0 py312hca03da5_0
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dav1d 1.2.1 h80987f9_0
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giflib 5.2.1 h80987f9_3
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hdf5 1.12.1 h05c076b_3
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hyperlink 21.0.0 pyhd3eb1b0_0
icu 73.1 h313beb8_0
idna 3.7 py312hca03da5_0
imagecodecs 2023.1.23 py312h75b721f_1
imageio 2.33.1 py312hca03da5_0
imagesize 1.4.1 py312hca03da5_0
imbalanced-learn 0.12.3 py312hca03da5_1
importlib-metadata 7.0.1 py312hca03da5_0
incremental 22.10.0 pyhd3eb1b0_0
inflection 0.5.1 py312hca03da5_1
iniconfig 1.1.1 pyhd3eb1b0_0
intake 0.7.0 py312hca03da5_0
intervaltree 3.1.0 pyhd3eb1b0_0
ipykernel 6.28.0 py312hca03da5_0
ipython 8.25.0 py312hca03da5_0
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ldid 2.1.5 h20b2a84_3
lerc 3.0 hc377ac9_0
libaec 1.0.4 hc377ac9_1
libarchive 3.6.2 h62fee54_3
libavif 0.11.1 h80987f9_0
libboost 1.82.0 h0bc93f9_2
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libclang 14.0.6 default_h1b80db6_1
libclang13 14.0.6 default_h24352ff_1
libcurl 8.7.1 h3e2b118_0
libcxx 14.0.6 h848a8c0_0
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libev 4.33 h1a28f6b_1
libevent 2.1.12 h02f6b3c_1
libffi 3.4.4 hca03da5_1
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libglib 2.78.4 h0a96307_0
libiconv 1.16 h80987f9_3
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libllvm14 14.0.6 h7ec7a93_3
libmamba 1.5.8 haeffa04_2
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libprotobuf 3.20.3 h514c7bf_0
libsodium 1.0.18 h1a28f6b_0
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nbformat 5.9.2 py312hca03da5_0
ncurses 6.4 h313beb8_0
nest-asyncio 1.6.0 py312hca03da5_0
networkx 3.3 py312hca03da5_0
nltk 3.8.1 py312hca03da5_0
notebook 7.0.8 py312hca03da5_2
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parsel 1.8.1 py312hca03da5_0
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patch 2.7.6 h1a28f6b_1001
pathspec 0.10.3 py312hca03da5_0
patsy 0.5.6 py312hca03da5_0
pcre2 10.42 hb066dcc_1
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pillow 10.4.0 py312h80987f9_0
pip 24.0 py312hca03da5_0
pkce 1.0.3 py312hca03da5_0
pkginfo 1.10.0 py312hca03da5_0
platformdirs 3.10.0 py312hca03da5_0
plotly 5.22.0 py312h989b03a_0
pluggy 1.0.0 py312hca03da5_1
ply 3.11 py312hca03da5_1
prometheus_client 0.14.1 py312hca03da5_0
prompt-toolkit 3.0.43 py312hca03da5_0
prompt_toolkit 3.0.43 hd3eb1b0_0
protego 0.1.16 py_0
protobuf 3.20.3 py312h313beb8_0
psutil 5.9.0 py312h80987f9_0
ptyprocess 0.7.0 pyhd3eb1b0_2
pure_eval 0.2.2 pyhd3eb1b0_0
py-cpuinfo 9.0.0 py312hca03da5_0
py-lief 0.12.3 py312h313beb8_0
pyarrow 14.0.2 py312h8604a13_0
pyasn1 0.4.8 pyhd3eb1b0_0
pyasn1-modules 0.2.8 py_0
pybind11-abi 5 hd3eb1b0_0
pycodestyle 2.11.1 py312hca03da5_0
pycosat 0.6.6 py312h80987f9_1
pycparser 2.21 pyhd3eb1b0_0
pyct 0.5.0 py312hca03da5_0
pycurl 7.45.2 py312h02f6b3c_1
pydantic 2.5.3 py312hca03da5_0
pydantic-core 2.14.6 py312hf0e4da2_0
pydeck 0.8.0 py312hca03da5_2
pydispatcher 2.0.5 py312hca03da5_3
pydocstyle 6.3.0 py312hca03da5_0
pyerfa 2.0.1.4 py312ha86b861_0
pyflakes 3.2.0 py312hca03da5_0
pygments 2.15.1 py312hca03da5_1
pyjwt 2.8.0 py312hca03da5_0
pylint 2.16.2 py312hca03da5_0
pylint-venv 3.0.3 py312hca03da5_0
pyls-spyder 0.4.0 pyhd3eb1b0_0
pyobjc-core 10.1 py312h80987f9_0
pyobjc-framework-cocoa 10.1 py312hb094c41_0
pyobjc-framework-coreservices 10.1 py312hdd8dd1f_0
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