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BUG: Launching cmpbidsappmanager v3.0.4 fails on Ubuntu #206

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milad7093 opened this issue Jul 26, 2022 · 4 comments · Fixed by #212 or #149
Closed

BUG: Launching cmpbidsappmanager v3.0.4 fails on Ubuntu #206

milad7093 opened this issue Jul 26, 2022 · 4 comments · Fixed by #212 or #149
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@sebastientourbier
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bug Something isn't working
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v3.1.0

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@milad7093
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milad7093 commented Jul 26, 2022 •
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Dear Sebastian

I tried to update the cmp3 to the latest version (v3.0.4) in another PC ( Ubuntu 18.04, 64 GB RAM) and followed all the installation steps. After completing the installation, There is an error when running the GUI as follow :

Connectome Mapper v3.0.4 - BIDS App Manager

Copyright (C) 2009-2022, Ecole Polytechnique Federale de Lausanne (EPFL) the University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland, and Contributors, All rights reserved.

.. INFO: Use qt (5.15.2) / pyqt5 (5.15.6) for graphical backend

Fatal Python error: Segmentation fault

Current thread 0x00007f0bb680d740 (most recent call first):
File "/home/sn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/traitsui/qt4/ui_base.py", line 321 in display_ui
File "/home/sn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/traitsui/qt4/ui_live.py", line 75 in _ui_dialog
File "/home/sn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/traitsui/qt4/ui_live.py", line 53 in ui_live
File "/home/sn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/traitsui/qt4/toolkit.py", line 173 in ui_live
File "/home/sn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/traitsui/ui.py", line 238 in ui
File "/home/sn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/traitsui/view.py", line 454 in ui
File "/home/sn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/traitsui/qt4/extra/qt_view.py", line 61 in ui
File "/home/sn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/traitsui/qt4/view_application.py", line 136 in init
File "/home/sn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/traitsui/qt4/view_application.py", line 94 in view_application
File "/home/sn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/traitsui/qt4/toolkit.py", line 243 in view_application
File "/home/sn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/traits/has_traits.py", line 2181 in configure_traits
File "/home/sn/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/cmp/cli/cmpbidsappmanager.py", line 160 in main
File "/home/sn/miniconda3/envs/py37cmp-gui/bin/cmpbidsappmanager", line 8 in
Segmentation fault (core dumped)

Do you have any suggestion on how to solve this error?

Thanks in advance to your helps,

Best regards,

-Milad
@sebastientourbier
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Dear Milad,

Checking at some forums such as https://bbs.archlinux.org/viewtopic.php?id=259275, it seems that this might be caused by conflicting versions of PyQt5 or Qt5. I suspect that mrtrix3 is installing its own version, which might conflict with the version installed explicitly in the conda/environment.yml:

connectomemapper3/conda/environment.yml

Line 25 in 2ce5619

- PyQt5==5.15.6

Please could you tell me what the output is when you enter in the terminal with the environment activated (py37cmp-gui)$ conda list?

I am gonna try to reproduce it on my end and compare the list of packages.

Best

@sebastientourbier sebastientourbier added the bug Something isn't working label Jul 27, 2022
@milad7093
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Dear Sebastian

Thanks for your answer. The command's outputs are as following:

(py37cmp-gui) sn@mph5:~$ conda list

packages in environment at /home/sn/miniconda3/envs/py37cmp-gui:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alabaster 0.7.12 py_0 conda-forge
alsa-lib 1.2.6.1 h7f98852_0 conda-forge
annexremote 1.6.0 pypi_0 pypi
appdirs 1.4.4 pypi_0 pypi
apscheduler 3.9.1 pypi_0 pypi
argcomplete 2.0.0 pypi_0 pypi
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py37h540881e_2 conda-forge
astor 0.8.1 pypi_0 pypi
atk-1.0 2.36.0 h3371d22_4 conda-forge
attr 2.5.1 h166bdaf_0 conda-forge
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
babel 2.10.3 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports-zoneinfo 0.2.1 pypi_0 pypi
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.11.1 pyha770c72_0 conda-forge
bids-validator 1.9.7 pypi_0 pypi
bleach 5.0.1 pyhd8ed1ab_0 conda-forge
blosc 1.21.1 h83bc5f7_3 conda-forge
boto 2.49.0 pypi_0 pypi
brotli 1.0.9 pypi_0 pypi
brotli-bin 1.0.9 h166bdaf_7 conda-forge
brotlipy 0.7.0 py37h540881e_1004 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2022.6.15 ha878542_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.16.0 ha61ee94_1011 conda-forge
certifi 2022.6.15 py37h89c1867_0 conda-forge
cffi 1.15.1 py37h43b0acd_0 conda-forge
chardet 5.0.0 pypi_0 pypi
charset-normalizer 2.1.0 pyhd8ed1ab_0 conda-forge
ci-info 0.2.0 pypi_0 pypi
citeproc-py 0.6.0 pypi_0 pypi
click 8.1.3 py37h89c1867_0 conda-forge
codecarbon 1.2.0 pypi_0 pypi
colorama 0.4.5 pyhd8ed1ab_0 conda-forge
commonmark 0.9.1 py_0 conda-forge
configparser 5.2.0 pypi_0 pypi
connectomemapper 3.0.4 pypi_0 pypi
cryptography 37.0.4 py37h38fbfac_0 conda-forge
cvxopt 1.3.0 py37h9b79bc5_1 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
dash 2.6.0 pypi_0 pypi
dash-bootstrap-components 0.13.1 pypi_0 pypi
dash-core-components 2.0.0 pypi_0 pypi
dash-html-components 2.0.0 pypi_0 pypi
dash-table 5.0.0 pypi_0 pypi
dataclasses 0.8 pyhc8e2a94_3 conda-forge
datalad 0.15.4 pypi_0 pypi
datalad-container 1.1.5 pypi_0 pypi
datalad-neuroimaging 0.3.1 pypi_0 pypi
dbus 1.13.6 h5008d03_3 conda-forge
dcm2niix 1.0.20211006 h924138e_0 conda-forge
debugpy 1.6.0 py37hd23a5d3_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
deprecated 1.2.13 pypi_0 pypi
dill 0.3.5.1 pyhd8ed1ab_0 conda-forge
dipy 1.3.0 py37ha21ca33_0 conda-forge
docopt 0.6.2 pypi_0 pypi
docutils 0.18.1 py37h89c1867_1 conda-forge
dsdp 5.8 hd9d9efa_1203 conda-forge
duecredit 0.9.1 pypi_0 pypi
elfutils 0.186 he364ef2_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
etelemetry 0.3.0 pypi_0 pypi
exifread 3.0.0 pypi_0 pypi
expat 2.4.8 h27087fc_0 conda-forge
fasteners 0.17.3 pypi_0 pypi
fftw 3.3.10 nompi_h77c792f_102 conda-forge
file-tree 1.0.0 pyhd8ed1ab_0 conda-forge
file-tree-fsl 0.2.1 pyhd8ed1ab_0 conda-forge
filelock 3.7.1 pypi_0 pypi
fire 0.4.0 pypi_0 pypi
flask 2.1.3 pypi_0 pypi
flask-compress 1.12 pypi_0 pypi
flit-core 3.7.1 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.0 h8e229c2_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.34.4 py37h540881e_0 conda-forge
formulaic 0.2.4 pypi_0 pypi
freetype 2.10.4 h0708190_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
fsleyes 1.3.3 py37h89c1867_1 conda-forge
fsleyes-props 1.7.3 pyhd8ed1ab_0 conda-forge
fsleyes-widgets 0.12.3 pyhd8ed1ab_0 conda-forge
fslpy 3.10.0 pyhd8ed1ab_0 conda-forge
future 0.18.2 py37h89c1867_5 conda-forge
gdk-pixbuf 2.42.8 hff1cb4f_0 conda-forge
gettext 0.19.8.1 h73d1719_1008 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
git-annex 8.20211123 nodep_h1234567_1 conda-forge
glib 2.72.1 h6239696_0 conda-forge
glib-tools 2.72.1 h6239696_0 conda-forge
glpk 4.65 h9202a9a_1004 conda-forge
gmp 6.2.1 h58526e2_0 conda-forge
gnutls 3.7.6 hf3e180e_5 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
graphviz 2.50.0 h5abf519_3 conda-forge
gsl 2.7 he838d99_0 conda-forge
gst-plugins-base 1.20.3 hf6a322e_0 conda-forge
gstreamer 1.20.3 hd4edc92_0 conda-forge
gtk2 2.24.33 h90689f9_2 conda-forge
gts 0.7.6 h64030ff_2 conda-forge
h5py 3.7.0 nompi_py37hc97082c_100 conda-forge
harfbuzz 4.4.1 hf9f4e7c_0 conda-forge
hdf5 1.12.1 nompi_h2386368_104 conda-forge
httpretty 1.1.4 pypi_0 pypi
humanize 4.2.3 pypi_0 pypi
icu 70.1 h27087fc_0 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
imagesize 1.4.1 pyhd8ed1ab_0 conda-forge
importlib-metadata 4.11.4 py37h89c1867_0 conda-forge
importlib_metadata 4.11.4 hd8ed1ab_0 conda-forge
importlib_resources 5.9.0 pyhd8ed1ab_0 conda-forge
indexed_gzip 1.6.4 py37he2e3b7d_1 conda-forge
interface-meta 1.3.0 pypi_0 pypi
ipykernel 6.15.1 pyh210e3f2_0 conda-forge
ipython 7.33.0 py37h89c1867_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
iso8601 1.0.2 pypi_0 pypi
isodate 0.6.1 pyhd8ed1ab_0 conda-forge
itsdangerous 2.1.2 pypi_0 pypi
jack 1.9.18 h8c3723f_1002 conda-forge
jedi 0.18.1 py37h89c1867_1 conda-forge
jeepney 0.8.0 pypi_0 pypi
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
joblib 1.1.0 pyhd8ed1ab_0 conda-forge
jpeg 9e h166bdaf_2 conda-forge
jsonschema 4.7.2 pyhd8ed1ab_0 conda-forge
jupyter_client 7.3.4 pyhd8ed1ab_0 conda-forge
jupyter_core 4.11.1 py37h89c1867_0 conda-forge
jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
keyring 23.7.0 pypi_0 pypi
keyrings-alt 4.1.1 pypi_0 pypi
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.4 py37h7cecad7_0 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libarchive 3.5.2 hb890918_3 conda-forge
libblas 3.9.0 15_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_7 conda-forge
libbrotlidec 1.0.9 h166bdaf_7 conda-forge
libbrotlienc 1.0.9 h166bdaf_7 conda-forge
libcap 2.64 ha37c62d_0 conda-forge
libcblas 3.9.0 15_linux64_openblas conda-forge
libclang 14.0.6 default_h2e3cab8_0 conda-forge
libclang13 14.0.6 default_h3a83d3e_0 conda-forge
libcups 2.3.3 hf5a7f15_1 conda-forge
libcurl 7.83.1 h7bff187_0 conda-forge
libdb 6.2.32 h9c3ff4c_0 conda-forge
libdeflate 1.12 h166bdaf_0 conda-forge
libdrm 2.4.112 h166bdaf_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libevent 2.1.10 h9b69904_4 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.3.4 h27087fc_0 conda-forge
libgcc-ng 12.1.0 h8d9b700_16 conda-forge
libgd 2.3.3 h18fbbfe_3 conda-forge
libgfortran-ng 12.1.0 h69a702a_16 conda-forge
libgfortran5 12.1.0 hdcd56e2_16 conda-forge
libglib 2.72.1 h2d90d5f_0 conda-forge
libglu 9.0.0 he1b5a44_1001 conda-forge
libgomp 12.1.0 h8d9b700_16 conda-forge
libiconv 1.16 h516909a_0 conda-forge
libidn2 2.3.3 h166bdaf_0 conda-forge
liblapack 3.9.0 15_linux64_openblas conda-forge
libllvm14 14.0.6 he0ac6c6_0 conda-forge
libmicrohttpd 0.9.75 h2603550_1 conda-forge
libnghttp2 1.47.0 h727a467_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.20 pthreads_h78a6416_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpciaccess 0.16 h516909a_0 conda-forge
libpng 1.6.37 h753d276_3 conda-forge
libpq 14.4 hd77ab85_0 conda-forge
librsvg 2.54.4 h7abd40a_0 conda-forge
libsndfile 1.0.31 h9c3ff4c_1 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libspatialindex 1.9.3 h9c3ff4c_4 conda-forge
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-ng 12.1.0 ha89aaad_16 conda-forge
libtasn1 4.18.0 h166bdaf_1 conda-forge
libtiff 4.4.0 hc85c160_1 conda-forge
libtool 2.4.6 h9c3ff4c_1008 conda-forge
libudev1 249 h166bdaf_4 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp 1.2.3 h522a892_1 conda-forge
libwebp-base 1.2.3 h166bdaf_2 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxkbcommon 1.0.3 he3ba5ed_0 conda-forge
libxml2 2.9.14 h22db469_3 conda-forge
libzlib 1.2.12 h166bdaf_2 conda-forge
lxml 4.9.1 pypi_0 pypi
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
lzo 2.10 h516909a_1000 conda-forge
markupsafe 2.1.1 py37h540881e_1 conda-forge
matplotlib-base 3.5.2 py37hc347a89_0 conda-forge
matplotlib-inline 0.1.3 pyhd8ed1ab_0 conda-forge
mesalib 21.2.5 h0e4506f_3 conda-forge
metis 5.1.0 h58526e2_1006 conda-forge
mistune 0.8.4 py37h5e8e339_1005 conda-forge
mne 0.24.1 pypi_0 pypi
mpfr 4.1.0 h9202a9a_1 conda-forge
mrtrix3 3.0.3 h2bc3f7f_0 mrtrix3
msgpack 1.0.4 pypi_0 pypi
multidict 6.0.2 pypi_0 pypi
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mutagen 1.45.1 pypi_0 pypi
mysql-common 8.0.29 haf5c9bc_1 conda-forge
mysql-libs 8.0.29 h28c427c_1 conda-forge
nbclient 0.6.6 pyhd8ed1ab_0 conda-forge
nbconvert 6.5.0 pyhd8ed1ab_0 conda-forge
nbconvert-core 6.5.0 pyhd8ed1ab_0 conda-forge
nbconvert-pandoc 6.5.0 pyhd8ed1ab_0 conda-forge
nbformat 5.4.0 pyhd8ed1ab_0 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
nest-asyncio 1.5.5 pyhd8ed1ab_0 conda-forge
nettle 3.8 hc379101_0 conda-forge
networkx 2.6.3 pypi_0 pypi
nibabel 3.2.2 pypi_0 pypi
nipype 1.8.0 pypi_0 pypi
nomkl 1.0 h5ca1d4c_0 conda-forge
nose 1.3.7 pypi_0 pypi
notebook 6.4.12 pyha770c72_0 conda-forge
nspr 4.32 h9c3ff4c_1 conda-forge
nss 3.78 h2350873_0 conda-forge
num2words 0.5.10 pypi_0 pypi
numexpr 2.8.3 py37h85a3170_100 conda-forge
numpy 1.21.6 py37h976b520_0 conda-forge
obspy 1.2.2 pypi_0 pypi
openjpeg 2.4.0 hb52868f_1 conda-forge
openssl 1.1.1q h166bdaf_0 conda-forge
p11-kit 0.24.1 hc5aa10d_0 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pandas 1.3.5 py37he8f5f7f_0 conda-forge
pandoc 2.18 ha770c72_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
pango 1.50.8 hbd2fdc8_0 conda-forge
parse 1.19.0 pyh44b312d_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
pathlib2 2.3.7.post1 py37h89c1867_1 conda-forge
patool 1.12 pypi_0 pypi
patsy 0.5.2 pypi_0 pypi
pcre 8.45 h9c3ff4c_0 conda-forge
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 9.2.0 py37h44f0d7a_0 conda-forge
pip 21.3.1 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
plotly 5.9.0 pypi_0 pypi
portaudio 19.6.0 h57a0ea0_5 conda-forge
progressbar2 4.0.0 pyhd8ed1ab_0 conda-forge
prometheus_client 0.14.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.30 pyha770c72_0 conda-forge
prov 2.0.0 pypi_0 pypi
psutil 5.9.1 py37h540881e_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pulseaudio 14.0 h7f54b18_8 conda-forge
py-cpuinfo 8.0.0 pypi_0 pypi
pybids 0.14.0 pypi_0 pypi
pycartool 0.1.1 pypi_0 pypi
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydicom 2.2.2 pypi_0 pypi
pydot 1.4.2 pypi_0 pypi
pyface 7.4.2 pypi_0 pypi
pygithub 1.55 pypi_0 pypi
pygments 2.12.0 pyhd8ed1ab_0 conda-forge
pyjwt 2.4.0 pypi_0 pypi
pynacl 1.5.0 pypi_0 pypi
pynvml 11.4.1 pypi_0 pypi
pyopengl 3.1.6 pyhd8ed1ab_1 conda-forge
pyopenssl 22.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 2.4.7 pyhd8ed1ab_1 conda-forge
pyperclip 1.8.2 pypi_0 pypi
pypubsub 4.0.3 py_0 conda-forge
pyqt5 5.15.6 pypi_0 pypi
pyqt5-qt5 5.15.2 pypi_0 pypi
pyqt5-sip 12.11.0 pypi_0 pypi
pyrsistent 0.18.1 py37h540881e_1 conda-forge
pysocks 1.7.1 py37h89c1867_5 conda-forge
pytables 3.7.0 py37h5dea08b_0 conda-forge
python 3.7.12 hb7a2778_100_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.16.1 pyhd8ed1ab_0 conda-forge
python-gitlab 3.6.0 pypi_0 pypi
python-utils 3.3.3 pyhd8ed1ab_0 conda-forge
python-xmp-toolkit 2.0.1 pypi_0 pypi
python_abi 3.7 2_cp37m conda-forge
pytz 2022.1 pyhd8ed1ab_0 conda-forge
pytz-deprecation-shim 0.1.0.post0 pypi_0 pypi
pyyaml 6.0 pypi_0 pypi
pyzmq 23.2.0 py37h0c0c2a8_0 conda-forge
qt 5.15.4 hf11cfaa_0 conda-forge
qt-main 5.15.4 ha5833f6_2 conda-forge
qt-webengine 5.15.4 hcbadb6c_3 conda-forge
rdflib 6.1.1 pypi_0 pypi
readline 8.1.2 h0f457ee_0 conda-forge
requests 2.28.1 pyhd8ed1ab_0 conda-forge
requests-ftp 0.3.1 pypi_0 pypi
requests-toolbelt 0.9.1 pypi_0 pypi
rich 12.5.1 pyhd8ed1ab_0 conda-forge
rtree 1.0.0 py37h0b55af0_1 conda-forge
scikit-learn 1.0.2 py37hf9e9bfc_0 conda-forge
scipy 1.7.3 py37hf2a6cf1_0 conda-forge
secretstorage 3.3.2 pypi_0 pypi
send2trash 1.8.0 pyhd8ed1ab_0 conda-forge
setuptools 59.8.0 py37h89c1867_1 conda-forge
simplejson 3.17.6 pypi_0 pypi
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.1.9 hbd366e4_1 conda-forge
snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge
sphinx 5.0.2 pyh6c4a22f_0 conda-forge
sphinx_rtd_theme 0.5.2 pyhd8ed1ab_0 conda-forge
sphinxcontrib-applehelp 1.0.2 py_0 conda-forge
sphinxcontrib-devhelp 1.0.2 py_0 conda-forge
sphinxcontrib-htmlhelp 2.0.0 pyhd8ed1ab_0 conda-forge
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
sphinxcontrib-qthelp 1.0.3 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge
sqlalchemy 1.3.24 pypi_0 pypi
sqlite 3.39.2 h4ff8645_0 conda-forge
statsmodels 0.13.1 pypi_0 pypi
suitesparse 5.10.1 h9e50725_1 conda-forge
tbb 2021.5.0 h924138e_1 conda-forge
tenacity 8.0.1 pypi_0 pypi
termcolor 1.1.0 pypi_0 pypi
terminado 0.15.0 py37h89c1867_0 conda-forge
textual 0.1.18 pyhd8ed1ab_1 conda-forge
threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge
tinycss2 1.1.1 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tornado 6.2 py37h540881e_0 conda-forge
tqdm 4.64.0 pypi_0 pypi
traitlets 5.3.0 pyhd8ed1ab_0 conda-forge
traits 6.3.2 pypi_0 pypi
traitsui 7.2.0 pypi_0 pypi
trimesh 3.12.8 pyh6c4a22f_0 conda-forge
typing-extensions 4.3.0 hd8ed1ab_0 conda-forge
typing_extensions 4.3.0 pyha770c72_0 conda-forge
tzdata 2022.1 pypi_0 pypi
tzlocal 4.2 pypi_0 pypi
unicodedata2 14.0.0 py37h540881e_1 conda-forge
urllib3 1.26.11 pyhd8ed1ab_0 conda-forge
vcrpy 4.2.0 pypi_0 pypi
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
werkzeug 2.2.0 pypi_0 pypi
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
whoosh 2.7.4 pypi_0 pypi
wrapt 1.14.1 pypi_0 pypi
wxnatpy 0.4.0 pyhd8ed1ab_0 conda-forge
wxpython 4.1.1 py37hecb6014_7 conda-forge
xarray 0.20.2 pyhd8ed1ab_0 conda-forge
xcb-util 0.4.0 h166bdaf_0 conda-forge
xcb-util-image 0.4.0 h166bdaf_0 conda-forge
xcb-util-keysyms 0.4.0 h166bdaf_0 conda-forge
xcb-util-renderutil 0.3.9 h166bdaf_0 conda-forge
xcb-util-wm 0.4.1 h166bdaf_0 conda-forge
xnat 0.4.2 pyhd8ed1ab_0 conda-forge
xorg-damageproto 1.2.1 h7f98852_1002 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-glproto 1.4.17 h7f98852_1002 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdamage 1.1.5 h7f98852_1 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxrandr 1.5.2 h7f98852_1 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-randrproto 1.5.0 h7f98852_1001 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-util-macros 1.19.3 h7f98852_0 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
yarl 1.7.2 pypi_0 pypi
zeromq 4.3.4 h9c3ff4c_1 conda-forge
zipp 3.8.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.12 h166bdaf_2 conda-forge
zstd 1.5.2 h8a70e8d_2 conda-forge

Best regards,

-Milad

@sebastientourbier
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sebastientourbier commented Jul 28, 2022 •
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Thanks Milad!

It seems there is some variations in the version that can explain why it raised the error on your ubuntu machine. What is surprising is that a similar environment in working on Mac (See similar issue #171)

i tried to install the environment in a VM with Ubuntu 20.04 that I already has using the version corresponding to the v3.0.4 release:

$ conda env create --debug -f environment.yml

which indeed failed to complete, with a different error, though. I did hang for some time with the following output and interrupted at some point with no error message 🤔:

DEBUG conda.resolve:solve(1401): Solve: maximize versions and builds of indirect dependencies.  Prefer arch over noarch where equivalent.
DEBUG conda.common._logic:_run_sat(600): Invoking SAT with clause count: 135167
DEBUG conda.common._logic:minimize(738): Final peak objective: 0
DEBUG conda.common._logic:_run_sat(600): Invoking SAT with clause count: 144935
DEBUG conda.common._logic:_run_sat(600): Invoking SAT with clause count: 135336
DEBUG conda.common._logic:_run_sat(600): Invoking SAT with clause count: 135910
DEBUG conda.common._logic:_run_sat(600): Invoking SAT with clause count: 136768
DEBUG conda.common._logic:_run_sat(600): Invoking SAT with clause count: 136199
DEBUG conda.common._logic:_run_sat(600): Invoking SAT with clause count: 136042
DEBUG conda.common._logic:_run_sat(600): Invoking SAT with clause count: 136105
DEBUG conda.common._logic:_run_sat(600): Invoking SAT with clause count: 136075
DEBUG conda.common._logic:_run_sat(600): Invoking SAT with clause count: 136042
DEBUG conda.common._logic:minimize(738): Final peak objective: 35

By investigating one by one each package of the environment, it seems that fsleyes is not happy with python=3.7 but the installation completed with python=3.9. I also modified the way Qt/PyQt is installed (now installed directly via conda and not pip) such that we are sure that all libraries are accessible and compatible.

In the end, I managed to complete the whole installation and launch the GUI.

Here is the content of my new environment.yml file:

name: py39cmp-gui

channels:
    - conda-forge
    - mrtrix3

dependencies:
    - python=3.9
    - pip=22.2
    - graphviz=2.50.0
    - dipy=1.3.0
    - fsleyes=1.3.3
    - indexed_gzip
    - mrtrix3=3.0.3
    - git-annex=10.20220724
    - qt=5.15.4
    - pyqt=5.15.4
    - pyqt5-sip=12.9.0

    - pip:
          - nibabel==3.2.2
          - numpy==1.21.6
          - matplotlib==3.5.2
          - configparser==5.2.0
          - nipype==1.8.0
          - traits==6.3.2
          - traitsui==7.2.0
          - duecredit==0.9.1
          - obspy==1.2.2
          - mne==0.24.1
          - datalad[full]==0.15.4
          - datalad-container==1.1.5
          - datalad-neuroimaging==0.3.1
          - pybids==0.14.0
          - statsmodels==0.13.1
          - networkx==2.6.3
          - pydicom==2.2.2
          - pycartool==0.1.1

Please could you test it on your side?
This would consist of:

  • Creating a new text file "environment.yml" where you copy the content above. Note that I changed the name of the environment to py39cmp-gui.

  • Installing the environment with conda:

    $ conda env create -f /path/to/your/new/environment.yml

  • Activating the py39cmp-gui environment and installing connectomemapper

    $ conda activate py39cmp-gui
(py39cmp-gui)$ pip install connectomemapper==3.0.4

  • Launch the GUI:

    $ cmpbidsappmanager

Let me know if this works, and I will proceed with a pull request that integrates the changes.

And if so, you can remove your old py37cmp-gui environment with the following command:

$ conda env remove -n py37cmp-gui

@sebastientourbier sebastientourbier self-assigned this Jul 28, 2022
@sebastientourbier sebastientourbier added this to the v3.1.0 milestone Jul 28, 2022
@sebastientourbier sebastientourbier changed the title Fatal Python error: Segmentation fault BUG: Launching cmpbidsappmanager v3.0.4 fails on Ubuntu Jul 28, 2022
sebastientourbier added a commit that referenced this issue Aug 10, 2022
@sebastientourbier
CONDA: Update conda environment with python 3.9 for GUI to solve #206
9eb4a8c
@sebastientourbier sebastientourbier mentioned this issue Aug 10, 2022
Merged
This was linked to pull requests Aug 10, 2022
FIX: Problem to launch cmpbidsappmanager in Ubuntu 18.04 #212
Merged
REL: v3.1.0 #149
Merged
@sebastientourbier sebastientourbier mentioned this issue Aug 10, 2022
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@milad7093
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Dear Sebastian

Sorry for delay in responding and thanks to your helps But the problem remains and I have some errors when trying to create the new py39cmp-gui environment.

Here are the errors:

mn@mn-HP-Z840-Workstation:~$ conda env create -f /home/mn/environment.yml
Collecting package metadata (repodata.json): \ WARNING conda.models.version:get_matcher(538): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 2., but conda is ignoring the . and treating it as 2
| WARNING conda.models.version:get_matcher(538): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 3.6., but conda is ignoring the . and treating it as 3.6
| WARNING conda.models.version:get_matcher(538): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1., but conda is ignoring the . and treating it as 1
done
Solving environment: done
Preparing transaction: done
Verifying transaction: done
Executing transaction: -
/
done
Installing pip dependencies: | Ran pip subprocess with arguments:
['/home/mn/miniconda3/envs/py39cmp-gui/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/mn/condaenv.f302r4ad.requirements.txt']
Pip subprocess output:
Collecting nibabel==3.2.2
Using cached nibabel-3.2.2-py3-none-any.whl (3.3 MB)
Collecting numpy==1.21.6
Using cached numpy-1.21.6-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
Requirement already satisfied: matplotlib==3.5.2 in ./miniconda3/envs/py39cmp-gui/lib/python3.9/site-packages (from -r /home/mn/condaenv.f302r4ad.requirements.txt (line 3)) (3.5.2)
Collecting configparser==5.2.0
Using cached configparser-5.2.0-py3-none-any.whl (19 kB)
Collecting nipype==1.8.0
Using cached nipype-1.8.0-py3-none-any.whl (3.2 MB)
Collecting traits==6.3.2
Using cached traits-6.3.2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (5.1 MB)
Collecting traitsui==7.2.0
Using cached traitsui-7.2.0-py3-none-any.whl
Collecting duecredit==0.9.1
Using cached duecredit-0.9.1-py3-none-any.whl (86 kB)
Collecting obspy==1.2.2
Using cached obspy-1.2.2.zip (24.7 MB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'error'

Pip subprocess error:
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [31 lines of output]
:48: DeprecationWarning:

    `numpy.distutils` is deprecated since NumPy 1.23.0, as a result
    of the deprecation of `distutils` itself. It will be removed for
    Python >= 3.12. For older Python versions it will remain present.
    It is recommended to use `setuptools < 60.0` for those Python versions.
    For more details, see:
      https://numpy.org/devdocs/reference/distutils_status_migration.html
  
  
  Traceback (most recent call last):
    File "/home/mn/miniconda3/envs/py39cmp-gui/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
      main()
    File "/home/mn/miniconda3/envs/py39cmp-gui/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
    File "/home/mn/miniconda3/envs/py39cmp-gui/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 130, in get_requires_for_build_wheel
      return hook(config_settings)
    File "/tmp/pip-build-env-vnwto_0t/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 337, in get_requires_for_build_wheel
      return self._get_build_requires(config_settings, requirements=['wheel'])
    File "/tmp/pip-build-env-vnwto_0t/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 319, in _get_build_requires
      self.run_setup()
    File "/tmp/pip-build-env-vnwto_0t/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 334, in run_setup
      exec(code, locals())
    File "<string>", line 48, in <module>
    File "/tmp/pip-build-env-vnwto_0t/overlay/lib/python3.9/site-packages/numpy/distutils/core.py", line 24, in <module>
      from numpy.distutils.command import config, config_compiler, \
    File "/tmp/pip-build-env-vnwto_0t/overlay/lib/python3.9/site-packages/numpy/distutils/command/config.py", line 19, in <module>
      from numpy.distutils.mingw32ccompiler import generate_manifest
    File "/tmp/pip-build-env-vnwto_0t/overlay/lib/python3.9/site-packages/numpy/distutils/mingw32ccompiler.py", line 28, in <module>
      from distutils.msvccompiler import get_build_version as get_build_msvc_version
  ModuleNotFoundError: No module named 'distutils.msvccompiler'
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

failed

CondaEnvException: Pip failed

I also tried to obtain outputs of "conda list -n py39cmp-gui" command. Here are the outputs:

(py39cmp-gui) mn@mn-HP-Z840-Workstation:~$ conda list -n py39cmp-gui

packages in environment at /home/mn/miniconda3/envs/py39cmp-gui:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alabaster 0.7.12 py_0 conda-forge
alsa-lib 1.2.6.1 h7f98852_0 conda-forge
aom 3.4.0 h27087fc_1 conda-forge
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py39hb9d737c_2 conda-forge
asttokens 2.0.5 pyhd8ed1ab_0 conda-forge
atk-1.0 2.36.0 h3371d22_4 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 22.1.0 pyh71513ae_1 conda-forge
babel 2.10.3 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.11.1 pyha770c72_0 conda-forge
bleach 5.0.1 pyhd8ed1ab_0 conda-forge
blosc 1.21.1 h83bc5f7_3 conda-forge
brotli 1.0.9 h166bdaf_7 conda-forge
brotli-bin 1.0.9 h166bdaf_7 conda-forge
brotlipy 0.7.0 py39hb9d737c_1004 conda-forge
brunsli 0.1 h9c3ff4c_0 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
c-blosc2 2.2.0 h7a311fb_0 conda-forge
ca-certificates 2022.6.15 ha878542_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.16.0 ha61ee94_1012 conda-forge
certifi 2022.6.15 py39hf3d152e_0 conda-forge
cffi 1.15.1 py39he91dace_0 conda-forge
cfitsio 4.1.0 hd9d235c_0 conda-forge
charls 2.3.4 h9c3ff4c_0 conda-forge
charset-normalizer 2.1.0 pyhd8ed1ab_0 conda-forge
click 8.1.3 py39hf3d152e_0 conda-forge
cloudpickle 2.1.0 pyhd8ed1ab_0 conda-forge
colorama 0.4.5 pyhd8ed1ab_0 conda-forge
commonmark 0.9.1 py_0 conda-forge
cryptography 37.0.4 py39hd97740a_0 conda-forge
curl 7.83.1 h7bff187_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cytoolz 0.12.0 py39hb9d737c_0 conda-forge
dask-core 2022.8.0 pyhd8ed1ab_0 conda-forge
dataclasses 0.8 pyhc8e2a94_3 conda-forge
dav1d 1.0.0 h166bdaf_1 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
dcm2niix 1.0.20220720 h924138e_0 conda-forge
debugpy 1.6.0 py39h5a03fae_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
dill 0.3.5.1 pyhd8ed1ab_0 conda-forge
dipy 1.3.0 py39h16ac069_1 conda-forge
docutils 0.19 py39hf3d152e_0 conda-forge
elfutils 0.186 he364ef2_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
executing 0.10.0 pyhd8ed1ab_0 conda-forge
expat 2.4.8 h27087fc_0 conda-forge
fftw 3.3.10 nompi_ha7695d1_103 conda-forge
file-tree 1.0.0 pyhd8ed1ab_0 conda-forge
file-tree-fsl 0.2.1 pyhd8ed1ab_0 conda-forge
flit-core 3.7.1 pyhd8ed1ab_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.0 h8e229c2_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.34.4 py39hb9d737c_0 conda-forge
freetype 2.10.4 hca18f0e_2 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
fsleyes 1.3.3 py39hf3d152e_1 conda-forge
fsleyes-props 1.7.3 pyhd8ed1ab_0 conda-forge
fsleyes-widgets 0.12.3 pyhd8ed1ab_0 conda-forge
fslpy 3.10.0 pyhd8ed1ab_0 conda-forge
fsspec 2022.7.1 pyhd8ed1ab_0 conda-forge
future 0.18.2 py39hf3d152e_5 conda-forge
gdk-pixbuf 2.42.8 hff1cb4f_0 conda-forge
gettext 0.19.8.1 h73d1719_1008 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
git 2.37.2 pl5321h36853c3_1 conda-forge
git-annex 10.20220724 alldep_hc98582e_100 conda-forge
glib 2.72.1 h6239696_0 conda-forge
glib-tools 2.72.1 h6239696_0 conda-forge
gmp 6.2.1 h58526e2_0 conda-forge
gnupg 2.3.3 h7853c96_0 conda-forge
gnutls 3.7.6 hf3e180e_5 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
graphviz 2.50.0 h5abf519_3 conda-forge
gst-plugins-base 1.20.3 hf6a322e_0 conda-forge
gstreamer 1.20.3 hd4edc92_0 conda-forge
gtk2 2.24.33 h90689f9_2 conda-forge
gts 0.7.6 h64030ff_2 conda-forge
h5py 3.7.0 nompi_py39hd51670d_101 conda-forge
harfbuzz 5.1.0 hf9f4e7c_0 conda-forge
hdf5 1.12.2 nompi_h2386368_100 conda-forge
icu 70.1 h27087fc_0 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
imagecodecs 2022.8.8 py39h6e07900_4 conda-forge
imageio 2.21.1 pyhfa7a67d_0 conda-forge
imagesize 1.4.1 pyhd8ed1ab_0 conda-forge
importlib-metadata 4.11.4 py39hf3d152e_0 conda-forge
importlib_resources 5.9.0 pyhd8ed1ab_0 conda-forge
indexed_gzip 1.6.13 py39hc217eb8_1 conda-forge
ipykernel 6.15.1 pyh210e3f2_0 conda-forge
ipython 8.4.0 py39hf3d152e_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
isodate 0.6.1 pyhd8ed1ab_0 conda-forge
jack 1.9.18 h8c3723f_1002 conda-forge
jedi 0.18.1 pyhd8ed1ab_2 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
joblib 1.1.0 pyhd8ed1ab_0 conda-forge
jpeg 9e h166bdaf_2 conda-forge
jsonschema 4.9.1 pyhd8ed1ab_0 conda-forge
jupyter_client 7.3.4 pyhd8ed1ab_0 conda-forge
jupyter_core 4.11.1 py39hf3d152e_0 conda-forge
jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
jxrlib 1.1 h7f98852_2 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.4 py39hf939315_0 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libaec 1.0.6 h9c3ff4c_0 conda-forge
libarchive 3.5.2 hb890918_3 conda-forge
libassuan 2.5.5 h9c3ff4c_0 conda-forge
libavif 0.10.1 h166bdaf_1 conda-forge
libblas 3.9.0 16_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_7 conda-forge
libbrotlidec 1.0.9 h166bdaf_7 conda-forge
libbrotlienc 1.0.9 h166bdaf_7 conda-forge
libcap 2.64 ha37c62d_0 conda-forge
libcblas 3.9.0 16_linux64_openblas conda-forge
libcbor 0.9.0 h9c3ff4c_0 conda-forge
libclang 14.0.6 default_h2e3cab8_0 conda-forge
libclang13 14.0.6 default_h3a83d3e_0 conda-forge
libcups 2.3.3 h3e49a29_2 conda-forge
libcurl 7.83.1 h7bff187_0 conda-forge
libdb 6.2.32 h9c3ff4c_0 conda-forge
libdeflate 1.13 h166bdaf_0 conda-forge
libdrm 2.4.112 h166bdaf_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libevent 2.1.10 h9b69904_4 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libfido2 1.11.0 h727a467_0 conda-forge
libflac 1.3.4 h27087fc_0 conda-forge
libgcc-ng 12.1.0 h8d9b700_16 conda-forge
libgcrypt 1.10.1 h166bdaf_0 conda-forge
libgd 2.3.3 h18fbbfe_3 conda-forge
libgfortran-ng 12.1.0 h69a702a_16 conda-forge
libgfortran5 12.1.0 hdcd56e2_16 conda-forge
libglib 2.72.1 h2d90d5f_0 conda-forge
libglu 9.0.0 he1b5a44_1001 conda-forge
libgomp 12.1.0 h8d9b700_16 conda-forge
libgpg-error 1.45 hc0c96e0_0 conda-forge
libiconv 1.16 h516909a_0 conda-forge
libidn2 2.3.3 h166bdaf_0 conda-forge
libksba 1.3.5 hf484d3e_1000 conda-forge
liblapack 3.9.0 16_linux64_openblas conda-forge
libllvm14 14.0.6 he0ac6c6_0 conda-forge
libmagic 5.39 h753d276_1 conda-forge
libmicrohttpd 0.9.75 h2603550_1 conda-forge
libnghttp2 1.47.0 hdcd2b5c_1 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.21 pthreads_h78a6416_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpciaccess 0.16 h516909a_0 conda-forge
libpng 1.6.37 h753d276_4 conda-forge
libpq 14.5 hd77ab85_0 conda-forge
librsvg 2.54.4 h7abd40a_0 conda-forge
libsndfile 1.0.31 h9c3ff4c_1 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libspatialindex 1.9.3 h9c3ff4c_4 conda-forge
libsqlite 3.39.2 h753d276_1 conda-forge
libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx-ng 12.1.0 ha89aaad_16 conda-forge
libtasn1 4.18.0 h166bdaf_1 conda-forge
libtiff 4.4.0 h0e0dad5_3 conda-forge
libtool 2.4.6 h9c3ff4c_1008 conda-forge
libudev1 249 h166bdaf_4 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp 1.2.4 h522a892_0 conda-forge
libwebp-base 1.2.4 h166bdaf_0 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxkbcommon 1.0.3 he3ba5ed_0 conda-forge
libxml2 2.9.14 h22db469_4 conda-forge
libxslt 1.1.35 h8affb1d_0 conda-forge
libzlib 1.2.12 h166bdaf_2 conda-forge
libzopfli 1.0.3 h9c3ff4c_0 conda-forge
locket 1.0.0 pyhd8ed1ab_0 conda-forge
lsof 4.89 h7f98852_1 conda-forge
lxml 4.9.1 py39hb9d737c_0 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
lzo 2.10 h516909a_1000 conda-forge
markupsafe 2.1.1 py39hb9d737c_1 conda-forge
matplotlib-base 3.5.2 py39h700656a_1 conda-forge
matplotlib-inline 0.1.3 pyhd8ed1ab_0 conda-forge
mesalib 21.2.5 h0e4506f_3 conda-forge
mistune 0.8.4 py39h3811e60_1005 conda-forge
mrtrix3 3.0.3 h2bc3f7f_0 mrtrix3
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 8.0.30 haf5c9bc_0 conda-forge
mysql-libs 8.0.30 h28c427c_0 conda-forge
nbclient 0.6.6 pyhd8ed1ab_0 conda-forge
nbconvert 6.5.3 pyhd8ed1ab_0 conda-forge
nbconvert-core 6.5.3 pyhd8ed1ab_0 conda-forge
nbconvert-pandoc 6.5.3 pyhd8ed1ab_0 conda-forge
nbformat 5.4.0 pyhd8ed1ab_0 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
nest-asyncio 1.5.5 pyhd8ed1ab_0 conda-forge
nettle 3.8.1 hc379101_1 conda-forge
networkx 2.8.5 pyhd8ed1ab_0 conda-forge
nibabel 4.0.1 pyhd8ed1ab_0 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
notebook 6.4.12 pyha770c72_0 conda-forge
npth 1.6 h27087fc_1001 conda-forge
nspr 4.32 h9c3ff4c_1 conda-forge
nss 3.78 h2350873_0 conda-forge
ntbtls 0.1.2 hdbcaa40_1000 conda-forge
numexpr 2.8.3 py39h194a79d_100 conda-forge
numpy 1.23.1 py39hba7629e_0 conda-forge
openjpeg 2.5.0 h7d73246_1 conda-forge
openssh 9.0p1 hf695f80_0 conda-forge
openssl 1.1.1q h166bdaf_0 conda-forge
p11-kit 0.24.1 hc5aa10d_0 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pandas 1.4.3 py39h1832856_0 conda-forge
pandoc 2.19 ha770c72_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
pango 1.50.9 hc4f8a73_0 conda-forge
parse 1.19.0 pyh44b312d_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
partd 1.3.0 pyhd8ed1ab_0 conda-forge
pathlib2 2.3.7.post1 py39hf3d152e_1 conda-forge
patsy 0.5.2 pyhd8ed1ab_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pcre2 10.37 hc3806b6_1 conda-forge
perl 5.32.1 2_h7f98852_perl5 conda-forge
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 9.2.0 py39hd5dbb17_2 conda-forge
pip 22.2.2 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge
popt 1.16 h0b475e3_2002 conda-forge
portaudio 19.6.0 h57a0ea0_5 conda-forge
progressbar2 4.0.0 pyhd8ed1ab_0 conda-forge
prometheus_client 0.14.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.30 pyha770c72_0 conda-forge
psutil 5.9.1 py39hb9d737c_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pulseaudio 14.0 h7f54b18_8 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydicom 2.3.0 pyh6c4a22f_0 conda-forge
pygments 2.12.0 pyhd8ed1ab_0 conda-forge
pyopengl 3.1.6 pyhd8ed1ab_1 conda-forge
pyopenssl 22.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 2.4.7 pyhd8ed1ab_1 conda-forge
pypubsub 4.0.3 py_0 conda-forge
pyqt 5.15.4 py39h18e9c17_1 conda-forge
pyqt5-sip 12.9.0 py39h5a03fae_1 conda-forge
pyrsistent 0.18.1 py39hb9d737c_1 conda-forge
pysocks 1.7.1 py39hf3d152e_5 conda-forge
pytables 3.7.0 py39hee6f8ba_2 conda-forge
python 3.9.13 h9a8a25e_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.16.1 pyhd8ed1ab_0 conda-forge
python-utils 3.3.3 pyhd8ed1ab_0 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytz 2022.2 pyhd8ed1ab_0 conda-forge
pywavelets 1.3.0 py39hd257fcd_1 conda-forge
pyyaml 6.0 py39hb9d737c_4 conda-forge
pyzmq 23.2.1 py39headdf64_0 conda-forge
qt 5.15.4 hf11cfaa_0 conda-forge
qt-main 5.15.4 ha5833f6_2 conda-forge
qt-webengine 5.15.4 hcbadb6c_3 conda-forge
readline 8.1.2 h0f457ee_0 conda-forge
requests 2.28.1 pyhd8ed1ab_0 conda-forge
rich 12.5.1 pyhd8ed1ab_0 conda-forge
rsync 3.2.3 hfa40b15_4 conda-forge
rtree 1.0.0 py39hb102c33_1 conda-forge
scikit-image 0.19.3 py39h1832856_1 conda-forge
scikit-learn 1.1.2 py39he5e8d7e_0 conda-forge
scipy 1.9.0 py39h8ba3f38_0 conda-forge
send2trash 1.8.0 pyhd8ed1ab_0 conda-forge
setuptools 64.0.3 py39hf3d152e_0 conda-forge
sip 6.5.1 py39he80948d_2 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.1.9 hbd366e4_1 conda-forge
snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge
sphinx 5.1.1 pyhd8ed1ab_1 conda-forge
sphinx_rtd_theme 0.5.2 pyhd8ed1ab_0 conda-forge
sphinxcontrib-applehelp 1.0.2 py_0 conda-forge
sphinxcontrib-devhelp 1.0.2 py_0 conda-forge
sphinxcontrib-htmlhelp 2.0.0 pyhd8ed1ab_0 conda-forge
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
sphinxcontrib-qthelp 1.0.3 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge
sqlite 3.39.2 h4ff8645_1 conda-forge
stack_data 0.4.0 pyhd8ed1ab_0 conda-forge
statsmodels 0.13.2 py39hd257fcd_0 conda-forge
terminado 0.15.0 py39hf3d152e_0 conda-forge
textual 0.1.18 pyhd8ed1ab_1 conda-forge
threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge
tifffile 2022.8.12 pyhd8ed1ab_0 conda-forge
tinycss2 1.1.1 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
toolz 0.12.0 pyhd8ed1ab_0 conda-forge
tornado 6.2 py39hb9d737c_0 conda-forge
tqdm 4.64.0 pyhd8ed1ab_0 conda-forge
traitlets 5.3.0 pyhd8ed1ab_0 conda-forge
trimesh 3.13.4 pyh6c4a22f_0 conda-forge
typing-extensions 4.3.0 hd8ed1ab_0 conda-forge
typing_extensions 4.3.0 pyha770c72_0 conda-forge
tzdata 2022b h191b570_0 conda-forge
unicodedata2 14.0.0 py39hb9d737c_1 conda-forge
urllib3 1.26.11 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
wxnatpy 0.4.0 pyhd8ed1ab_0 conda-forge
wxpython 4.1.1 py39hea8757a_7 conda-forge
xarray 2022.6.0 pyhd8ed1ab_1 conda-forge
xcb-util 0.4.0 h166bdaf_0 conda-forge
xcb-util-image 0.4.0 h166bdaf_0 conda-forge
xcb-util-keysyms 0.4.0 h166bdaf_0 conda-forge
xcb-util-renderutil 0.3.9 h166bdaf_0 conda-forge
xcb-util-wm 0.4.1 h166bdaf_0 conda-forge
xnat 0.4.2 pyhd8ed1ab_0 conda-forge
xorg-damageproto 1.2.1 h7f98852_1002 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-glproto 1.4.17 h7f98852_1002 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdamage 1.1.5 h7f98852_1 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxrandr 1.5.2 h7f98852_1 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-randrproto 1.5.0 h7f98852_1001 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-util-macros 1.19.3 h7f98852_0 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xxhash 0.8.0 h7f98852_3 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zeromq 4.3.4 h9c3ff4c_1 conda-forge
zfp 1.0.0 h27087fc_1 conda-forge
zipp 3.8.1 pyhd8ed1ab_0 conda-forge
zlib 1.2.12 h166bdaf_2 conda-forge
zlib-ng 2.0.6 h166bdaf_0 conda-forge
zstd 1.5.2 h8a70e8d_4 conda-forge

How can I solve this problem?

Thanks in advance to your helps

Best regards,

-Milad

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@milad7093 @sebastientourbier