Closed martuser closed 4 months ago
martuser
commented
11 months ago I've uninstalled Anaconda and installed the latest version to check if that could be the issue. Now, with the Anaconda3 version 2023.07-2 and conda version 23.7.2 , when following the README instructions, I still encounter the same error. The problem is that even though the error appears, it does display the GUI. However, when clicking on any cluster, the GUI crashes.
zm711
commented
11 months ago @martuser
Could you type:
conda listand copy the contents here inside of triple -tics (`) (so it formats nicely for me)
martuser
commented
11 months ago Thanks, Zach, for responding. Despite the error, there are times, rarely, when it has allowed me to work, but it's very slow. Usually, what tends to happen is that the GUI crashes. But the error is always there. Here is the information from 'conda list':
#
# Name Version Build Channel
_anaconda_depends 2023.07 py311_1
abseil-cpp 20211102.0 hd77b12b_0
aiobotocore 2.4.2 py311haa95532_0
aiofiles 22.1.0 py311haa95532_0
aiohttp 3.8.3 py311h2bbff1b_0
aioitertools 0.7.1 pyhd3eb1b0_0
aiosignal 1.2.0 pyhd3eb1b0_0
aiosqlite 0.18.0 py311haa95532_0
alabaster 0.7.12 pyhd3eb1b0_0
anaconda-catalogs 0.2.0 py311haa95532_0
anaconda-client 1.12.0 py311haa95532_0
anaconda-navigator 2.4.2 py311haa95532_0
anaconda-project 0.11.1 py311haa95532_0
anyio 3.5.0 py311haa95532_0
appdirs 1.4.4 pyhd3eb1b0_0
argon2-cffi 21.3.0 pyhd3eb1b0_0
argon2-cffi-bindings 21.2.0 py311h2bbff1b_0
arrow 1.2.3 py311haa95532_1
arrow-cpp 11.0.0 py311h308b814_0
astroid 2.14.2 py311haa95532_0
astropy 5.1 py311h5bb9823_0
asttokens 2.0.5 pyhd3eb1b0_0
async-timeout 4.0.2 py311haa95532_0
atomicwrites 1.4.0 py_0
attrs 22.1.0 py311haa95532_0
automat 20.2.0 py_0
autopep8 1.6.0 pyhd3eb1b0_1
aws-c-common 0.4.57 ha925a31_1
aws-c-event-stream 0.1.6 hd77b12b_5
aws-checksums 0.1.9 ha925a31_0
aws-sdk-cpp 1.8.185 hd77b12b_0
babel 2.11.0 py311haa95532_0
backcall 0.2.0 pyhd3eb1b0_0
backports 1.1 pyhd3eb1b0_0
backports.functools_lru_cache 1.6.4 pyhd3eb1b0_0
backports.tempfile 1.0 pyhd3eb1b0_1
backports.weakref 1.0.post1 py_1
bcrypt 3.2.0 py311h2bbff1b_1
beautifulsoup4 4.12.2 py311haa95532_0
binaryornot 0.4.4 pyhd3eb1b0_1
black 23.3.0 py311haa95532_0
blas 1.0 mkl
bleach 4.1.0 pyhd3eb1b0_0
blosc 1.21.3 h6c2663c_0
bokeh 3.2.1 py311h746a85d_0
boltons 23.0.0 py311haa95532_0
boost-cpp 1.73.0 h2bbff1b_12
boto3 1.24.28 py311haa95532_0
botocore 1.27.59 py311haa95532_0
bottleneck 1.3.5 py311h5bb9823_0
brotli 1.0.9 h2bbff1b_7
brotli-bin 1.0.9 h2bbff1b_7
brotlipy 0.7.0 py311h2bbff1b_1002
bzip2 1.0.8 he774522_0
c-ares 1.19.0 h2bbff1b_0
c-blosc2 2.8.0 hd77b12b_0
ca-certificates 2023.05.30 haa95532_0
certifi 2023.7.22 py311haa95532_0
cffi 1.15.1 py311h2bbff1b_3
cfitsio 3.470 h2bbff1b_7
chardet 4.0.0 py311haa95532_1003
charls 2.2.0 h6c2663c_0
charset-normalizer 2.0.4 pyhd3eb1b0_0
click 8.0.4 py311haa95532_0
cloudpickle 2.2.1 py311haa95532_0
clyent 1.2.2 py311haa95532_1
colorama 0.4.6 py311haa95532_0
colorcet 3.0.1 py311haa95532_0
comm 0.1.2 py311haa95532_0
conda 23.7.2 py311haa95532_0
conda-build 3.26.0 py311haa95532_0
conda-content-trust 0.1.1 pyhd3eb1b0_0
conda-index 0.2.3 py311haa95532_0
conda-libmamba-solver 23.5.0 py311haa95532_0
conda-pack 0.6.0 pyhd3eb1b0_0
conda-package-handling 2.2.0 py311haa95532_0
conda-package-streaming 0.9.0 py311haa95532_0
conda-repo-cli 1.0.41 py311haa95532_0
conda-token 0.4.0 pyhd3eb1b0_0
conda-verify 3.4.2 py_1
console_shortcut 0.1.1 4
constantly 15.1.0 py311haa95532_0
contourpy 1.0.5 py311h59b6b97_0
cookiecutter 1.7.3 pyhd3eb1b0_0
cryptography 41.0.2 py311h31511bf_0
cssselect 1.1.0 pyhd3eb1b0_0
curl 8.1.1 he2ea4bf_2
cycler 0.11.0 pyhd3eb1b0_0
cytoolz 0.12.0 py311h2bbff1b_0
daal4py 2023.1.1 py311h30df693_0
dal 2023.1.1 h59b6b97_48681
dask 2023.6.0 py311haa95532_0
dask-core 2023.6.0 py311haa95532_0
datashader 0.15.1 py311haa95532_0
datashape 0.5.4 py311haa95532_1
debugpy 1.6.7 py311hd77b12b_0
decorator 5.1.1 pyhd3eb1b0_0
defusedxml 0.7.1 pyhd3eb1b0_0
diff-match-patch 20200713 pyhd3eb1b0_0
dill 0.3.6 py311haa95532_0
distributed 2023.6.0 py311haa95532_0
docstring-to-markdown 0.11 py311haa95532_0
docutils 0.18.1 py311haa95532_3
entrypoints 0.4 py311haa95532_0
et_xmlfile 1.1.0 py311haa95532_0
executing 0.8.3 pyhd3eb1b0_0
filelock 3.9.0 py311haa95532_0
flake8 6.0.0 py311haa95532_0
flask 2.2.2 py311haa95532_0
fmt 9.1.0 h6d14046_0
fonttools 4.25.0 pyhd3eb1b0_0
freetype 2.12.1 ha860e81_0
frozenlist 1.3.3 py311h2bbff1b_0
fsspec 2023.3.0 py311haa95532_0
future 0.18.3 py311haa95532_0
gensim 4.3.0 py311heda8569_0
gflags 2.2.2 ha925a31_0
giflib 5.2.1 h8cc25b3_3
glib 2.69.1 h5dc1a3c_2
glob2 0.7 pyhd3eb1b0_0
glog 0.5.0 hd77b12b_0
greenlet 2.0.1 py311hd77b12b_0
gst-plugins-base 1.18.5 h9e645db_0
gstreamer 1.18.5 hd78058f_0
h5py 3.7.0 py311h259cc0e_0
hdf5 1.10.6 h1756f20_1
heapdict 1.0.1 pyhd3eb1b0_0
holoviews 1.17.0 py311haa95532_0
hvplot 0.8.4 py311haa95532_0
hyperlink 21.0.0 pyhd3eb1b0_0
icc_rt 2022.1.0 h6049295_2
icu 58.2 ha925a31_3
idna 3.4 py311haa95532_0
imagecodecs 2021.8.26 py311h94f204c_2
imageio 2.26.0 py311haa95532_0
imagesize 1.4.1 py311haa95532_0
imbalanced-learn 0.10.1 py311haa95532_1
importlib-metadata 6.0.0 py311haa95532_0
importlib_metadata 6.0.0 hd3eb1b0_0
incremental 21.3.0 pyhd3eb1b0_0
inflection 0.5.1 py311haa95532_0
iniconfig 1.1.1 pyhd3eb1b0_0
intake 0.6.8 py311haa95532_0
intel-openmp 2023.1.0 h59b6b97_46319
intervaltree 3.1.0 pyhd3eb1b0_0
ipykernel 6.19.2 py311h86cfffd_0
ipython 8.12.0 py311haa95532_0
ipython_genutils 0.2.0 pyhd3eb1b0_1
ipywidgets 8.0.4 py311haa95532_0
isort 5.9.3 pyhd3eb1b0_0
itemadapter 0.3.0 pyhd3eb1b0_0
itemloaders 1.0.4 pyhd3eb1b0_1
itsdangerous 2.0.1 pyhd3eb1b0_0
jaraco.classes 3.2.1 pyhd3eb1b0_0
jedi 0.18.1 py311haa95532_1
jellyfish 0.9.0 py311h2bbff1b_0
jinja2 3.1.2 py311haa95532_0
jinja2-time 0.2.0 pyhd3eb1b0_3
jmespath 0.10.0 pyhd3eb1b0_0
joblib 1.2.0 py311haa95532_0
jpeg 9e h2bbff1b_1
jq 1.6 haa95532_1
json5 0.9.6 pyhd3eb1b0_0
jsonpatch 1.32 pyhd3eb1b0_0
jsonpointer 2.1 pyhd3eb1b0_0
jsonschema 4.17.3 py311haa95532_0
jupyter 1.0.0 py311haa95532_8
jupyter_client 7.4.9 py311haa95532_0
jupyter_console 6.6.3 py311haa95532_0
jupyter_core 5.3.0 py311haa95532_0
jupyter_events 0.6.3 py311haa95532_0
jupyter_server 1.23.4 py311haa95532_0
jupyter_server_fileid 0.9.0 py311haa95532_0
jupyter_server_ydoc 0.8.0 py311haa95532_1
jupyter_ydoc 0.2.4 py311haa95532_0
jupyterlab 3.6.3 py311haa95532_0
jupyterlab_pygments 0.1.2 py_0
jupyterlab_server 2.22.0 py311haa95532_0
jupyterlab_widgets 3.0.5 py311haa95532_0
jxrlib 1.1 he774522_2
keyring 23.13.1 py311haa95532_0
kiwisolver 1.4.4 py311hd77b12b_0
krb5 1.19.4 h5b6d351_0
lazy-object-proxy 1.6.0 py311h2bbff1b_0
lazy_loader 0.2 py311haa95532_0
lcms2 2.12 h83e58a3_0
lerc 3.0 hd77b12b_0
libaec 1.0.4 h33f27b4_1
libarchive 3.6.2 h2033e3e_1
libboost 1.73.0 h6c2663c_12
libbrotlicommon 1.0.9 h2bbff1b_7
libbrotlidec 1.0.9 h2bbff1b_7
libbrotlienc 1.0.9 h2bbff1b_7
libclang 14.0.6 default_hb5a9fac_1
libclang13 14.0.6 default_h8e68704_1
libcurl 8.1.1 h86230a5_2
libdeflate 1.17 h2bbff1b_0
libevent 2.1.12 hcc03200_0
libffi 3.4.4 hd77b12b_0
libiconv 1.16 h2bbff1b_2
liblief 0.12.3 hd77b12b_0
libllvm14 14.0.6 h4157e71_3
libmamba 1.4.1 h214f63a_0
libmambapy 1.4.1 py311h214f63a_0
libogg 1.3.5 h2bbff1b_1
libpng 1.6.39 h8cc25b3_0
libprotobuf 3.20.3 h23ce68f_0
libsodium 1.0.18 h62dcd97_0
libsolv 0.7.22 h23ce68f_0
libspatialindex 1.9.3 h6c2663c_0
libssh2 1.10.0 hcd4344a_2
libthrift 0.15.0 he49ee6e_2
libtiff 4.5.0 h6c2663c_2
libvorbis 1.3.7 he774522_0
libwebp 1.2.4 hbc33d0d_1
libwebp-base 1.2.4 h2bbff1b_1
libxml2 2.10.3 h0ad7f3c_0
libxslt 1.1.37 h2bbff1b_0
libzopfli 1.0.3 ha925a31_0
linkify-it-py 2.0.0 py311haa95532_0
llvmlite 0.40.0 py311hf2fb9eb_0
locket 1.0.0 py311haa95532_0
lxml 4.9.2 py311h2bbff1b_0
lz4 4.3.2 py311h2bbff1b_0
lz4-c 1.9.4 h2bbff1b_0
lzo 2.10 he774522_2
m2-msys2-runtime 2.5.0.17080.65c939c 3
m2-patch 2.7.5 2
m2w64-libwinpthread-git 5.0.0.4634.697f757 2
markdown 3.4.1 py311haa95532_0
markdown-it-py 2.2.0 py311haa95532_1
markupsafe 2.1.1 py311h2bbff1b_0
matplotlib 3.7.1 py311haa95532_1
matplotlib-base 3.7.1 py311hf62ec03_1
matplotlib-inline 0.1.6 py311haa95532_0
mccabe 0.7.0 pyhd3eb1b0_0
mdit-py-plugins 0.3.0 py311haa95532_0
mdurl 0.1.0 py311haa95532_0
menuinst 1.4.19 py311h59b6b97_1
mistune 0.8.4 py311h2bbff1b_1000
mkl 2023.1.0 h8bd8f75_46356
mkl-service 2.4.0 py311h2bbff1b_1
mkl_fft 1.3.6 py311hf62ec03_1
mkl_random 1.2.2 py311hf62ec03_1
more-itertools 8.12.0 pyhd3eb1b0_0
mpmath 1.3.0 py311haa95532_0
msgpack-python 1.0.3 py311h59b6b97_0
msys2-conda-epoch 20160418 1
multidict 6.0.2 py311h2bbff1b_0
multipledispatch 0.6.0 py311haa95532_0
munkres 1.1.4 py_0
mypy_extensions 0.4.3 py311haa95532_1
navigator-updater 0.4.0 py311haa95532_0
nbclassic 0.5.5 py311haa95532_0
nbclient 0.5.13 py311haa95532_0
nbconvert 6.5.4 py311haa95532_0
nbformat 5.7.0 py311haa95532_0
nest-asyncio 1.5.6 py311haa95532_0
networkx 3.1 py311haa95532_0
nltk 3.8.1 py311haa95532_0
notebook 6.5.4 py311haa95532_1
notebook-shim 0.2.2 py311haa95532_0
numba 0.57.0 py311hf62ec03_0
numexpr 2.8.4 py311h1fcbade_1
numpy 1.24.3 py311hdab7c0b_1
numpy-base 1.24.3 py311hd01c5d8_1
numpydoc 1.5.0 py311haa95532_0
openjpeg 2.4.0 h4fc8c34_0
openpyxl 3.0.10 py311h2bbff1b_0
openssl 1.1.1u h2bbff1b_0
orc 1.7.4 h623e30f_1
packaging 23.0 py311haa95532_0
pandas 1.5.3 py311heda8569_0
pandocfilters 1.5.0 pyhd3eb1b0_0
panel 1.2.1 py311haa95532_0
param 1.13.0 py311haa95532_0
paramiko 2.8.1 pyhd3eb1b0_0
parsel 1.6.0 py311haa95532_0
parso 0.8.3 pyhd3eb1b0_0
partd 1.2.0 pyhd3eb1b0_1
pathlib 1.0.1 pyhd3eb1b0_1
pathspec 0.10.3 py311haa95532_0
patsy 0.5.3 py311haa95532_0
pcre 8.45 hd77b12b_0
pcre2 10.37 h0ff8eda_1
pep8 1.7.1 py311haa95532_1
pexpect 4.8.0 pyhd3eb1b0_3
pickleshare 0.7.5 pyhd3eb1b0_1003
pillow 9.4.0 py311hd77b12b_0
pip 23.2.1 py311haa95532_0
pkginfo 1.9.6 py311haa95532_0
platformdirs 2.5.2 py311haa95532_0
plotly 5.9.0 py311haa95532_0
pluggy 1.0.0 py311haa95532_1
ply 3.11 py311haa95532_0
pooch 1.4.0 pyhd3eb1b0_0
powershell_shortcut 0.0.1 3
poyo 0.5.0 pyhd3eb1b0_0
prometheus_client 0.14.1 py311haa95532_0
prompt-toolkit 3.0.36 py311haa95532_0
prompt_toolkit 3.0.36 hd3eb1b0_0
protego 0.1.16 py_0
psutil 5.9.0 py311h2bbff1b_0
ptyprocess 0.7.0 pyhd3eb1b0_2
pure_eval 0.2.2 pyhd3eb1b0_0
py-cpuinfo 8.0.0 pyhd3eb1b0_1
py-lief 0.12.3 py311hd77b12b_0
pyarrow 11.0.0 py311h8a3a540_0
pyasn1 0.4.8 pyhd3eb1b0_0
pyasn1-modules 0.2.8 py_0
pybind11-abi 4 hd3eb1b0_1
pycodestyle 2.10.0 py311haa95532_0
pycosat 0.6.4 py311h2bbff1b_0
pycparser 2.21 pyhd3eb1b0_0
pyct 0.5.0 py311haa95532_0
pycurl 7.45.2 py311hcd4344a_0
pydispatcher 2.0.5 py311haa95532_2
pydocstyle 6.3.0 py311haa95532_0
pyerfa 2.0.0 py311h2bbff1b_0
pyflakes 3.0.1 py311haa95532_0
pygments 2.15.1 py311haa95532_1
pyjwt 2.4.0 py311haa95532_0
pylint 2.16.2 py311haa95532_0
pylint-venv 2.3.0 py311haa95532_0
pyls-spyder 0.4.0 pyhd3eb1b0_0
pynacl 1.5.0 py311h8cc25b3_0
pyodbc 4.0.34 py311hd77b12b_0
pyopenssl 23.2.0 py311haa95532_0
pyparsing 3.0.9 py311haa95532_0
pyqt 5.15.7 py311hd77b12b_0
pyqt5-sip 12.11.0 py311hd77b12b_0
pyqtwebengine 5.15.7 py311hd77b12b_0
pyrsistent 0.18.0 py311h2bbff1b_0
pysocks 1.7.1 py311haa95532_0
pytables 3.8.0 py311ha4dc190_2
pytest 7.4.0 py311haa95532_0
python 3.11.4 h966fe2a_0
python-dateutil 2.8.2 pyhd3eb1b0_0
python-fastjsonschema 2.16.2 py311haa95532_0
python-json-logger 2.0.7 py311haa95532_0
python-libarchive-c 2.9 pyhd3eb1b0_1
python-lmdb 1.4.1 py311hd77b12b_0
python-lsp-black 1.2.1 py311haa95532_0
python-lsp-jsonrpc 1.0.0 pyhd3eb1b0_0
python-lsp-server 1.7.2 py311haa95532_0
python-slugify 5.0.2 pyhd3eb1b0_0
python-snappy 0.6.1 py311hd77b12b_0
pytoolconfig 1.2.5 py311haa95532_1
pytz 2022.7 py311haa95532_0
pyviz_comms 2.3.0 py311haa95532_0
pywavelets 1.4.1 py311h2bbff1b_0
pywin32 305 py311h2bbff1b_0
pywin32-ctypes 0.2.0 py311haa95532_1000
pywinpty 2.0.10 py311h5da7b33_0
pyyaml 6.0 py311h2bbff1b_1
pyzmq 23.2.0 py311hd77b12b_0
qdarkstyle 3.0.2 pyhd3eb1b0_0
qstylizer 0.2.2 py311haa95532_0
qt-main 5.15.2 he8e5bd7_8
qt-webengine 5.15.9 hb9a9bb5_5
qtawesome 1.2.2 py311haa95532_0
qtconsole 5.4.2 py311haa95532_0
qtpy 2.2.0 py311haa95532_0
qtwebkit 5.212 h2bbfb41_5
queuelib 1.5.0 py311haa95532_0
re2 2022.04.01 hd77b12b_0
regex 2022.7.9 py311h2bbff1b_0
reproc 14.2.4 hd77b12b_1
reproc-cpp 14.2.4 hd77b12b_1
requests 2.31.0 py311haa95532_0
requests-file 1.5.1 pyhd3eb1b0_0
requests-toolbelt 1.0.0 py311haa95532_0
rfc3339-validator 0.1.4 py311haa95532_0
rfc3986-validator 0.1.1 py311haa95532_0
rope 1.7.0 py311haa95532_0
rtree 1.0.1 py311h2eaa2aa_0
ruamel.yaml 0.17.21 py311h2bbff1b_0
ruamel_yaml 0.17.21 py311h2bbff1b_0
s3fs 2023.3.0 py311haa95532_0
s3transfer 0.6.0 py311haa95532_0
sacremoses 0.0.43 pyhd3eb1b0_0
scikit-image 0.20.0 py311h3513d60_0
scikit-learn 1.3.0 py311hf62ec03_0
scikit-learn-intelex 2023.1.1 py311haa95532_0
scipy 1.10.1 py311hc1ccb85_1
scrapy 2.8.0 py311haa95532_0
seaborn 0.12.2 py311haa95532_0
send2trash 1.8.0 pyhd3eb1b0_1
service_identity 18.1.0 pyhd3eb1b0_1
setuptools 68.0.0 py311haa95532_0
sip 6.6.2 py311hd77b12b_0
six 1.16.0 pyhd3eb1b0_1
smart_open 5.2.1 py311haa95532_0
snappy 1.1.9 h6c2663c_0
sniffio 1.2.0 py311haa95532_1
snowballstemmer 2.2.0 pyhd3eb1b0_0
sortedcontainers 2.4.0 pyhd3eb1b0_0
soupsieve 2.4 py311haa95532_0
sphinx 5.0.2 py311haa95532_0
sphinxcontrib-applehelp 1.0.2 pyhd3eb1b0_0
sphinxcontrib-devhelp 1.0.2 pyhd3eb1b0_0
sphinxcontrib-htmlhelp 2.0.0 pyhd3eb1b0_0
sphinxcontrib-jsmath 1.0.1 pyhd3eb1b0_0
sphinxcontrib-qthelp 1.0.3 pyhd3eb1b0_0
sphinxcontrib-serializinghtml 1.1.5 pyhd3eb1b0_0
spyder 5.4.3 py311haa95532_1
spyder-kernels 2.4.3 py311haa95532_0
sqlalchemy 1.4.39 py311h2bbff1b_0
sqlite 3.41.2 h2bbff1b_0
stack_data 0.2.0 pyhd3eb1b0_0
statsmodels 0.14.0 py311hd7041d2_0
sympy 1.11.1 py311haa95532_0
tabulate 0.8.10 py311haa95532_0
tbb 2021.8.0 h59b6b97_0
tbb4py 2021.8.0 py311h59b6b97_0
tblib 1.7.0 pyhd3eb1b0_0
tenacity 8.2.2 py311haa95532_0
terminado 0.17.1 py311haa95532_0
text-unidecode 1.3 pyhd3eb1b0_0
textdistance 4.2.1 pyhd3eb1b0_0
threadpoolctl 2.2.0 pyh0d69192_0
three-merge 0.1.1 pyhd3eb1b0_0
tifffile 2021.7.2 pyhd3eb1b0_2
tinycss2 1.2.1 py311haa95532_0
tk 8.6.12 h2bbff1b_0
tldextract 3.2.0 pyhd3eb1b0_0
toml 0.10.2 pyhd3eb1b0_0
tomlkit 0.11.1 py311haa95532_0
toolz 0.12.0 py311haa95532_0
tornado 6.3.2 py311h2bbff1b_0
tqdm 4.65.0 py311h746a85d_0
traitlets 5.7.1 py311haa95532_0
transformers 2.1.1 pyhd3eb1b0_0
twisted 22.10.0 py311h2bbff1b_0
twisted-iocpsupport 1.0.2 py311h2bbff1b_0
typing-extensions 4.7.1 py311haa95532_0
typing_extensions 4.7.1 py311haa95532_0
tzdata 2023c h04d1e81_0
uc-micro-py 1.0.1 py311haa95532_0
ujson 5.4.0 py311hd77b12b_0
unidecode 1.2.0 pyhd3eb1b0_0
urllib3 1.26.16 py311haa95532_0
utf8proc 2.6.1 h2bbff1b_0
vc 14.2 h21ff451_1
vs2015_runtime 14.27.29016 h5e58377_2
w3lib 1.21.0 pyhd3eb1b0_0
watchdog 2.1.6 py311haa95532_0
wcwidth 0.2.5 pyhd3eb1b0_0
webencodings 0.5.1 py311haa95532_1
websocket-client 0.58.0 py311haa95532_4
werkzeug 2.2.3 py311haa95532_0
whatthepatch 1.0.2 py311haa95532_0
wheel 0.38.4 py311haa95532_0
widgetsnbextension 4.0.5 py311haa95532_0
win_inet_pton 1.1.0 py311haa95532_0
winpty 0.4.3 4
wrapt 1.14.1 py311h2bbff1b_0
xarray 2023.6.0 py311haa95532_0
xlwings 0.29.1 py311haa95532_0
xyzservices 2022.9.0 py311haa95532_1
xz 5.4.2 h8cc25b3_0
y-py 0.5.9 py311hb6bf4ef_0
yaml 0.2.5 he774522_0
yaml-cpp 0.7.0 hd77b12b_1
yapf 0.31.0 pyhd3eb1b0_0
yarl 1.8.1 py311h2bbff1b_0
ypy-websocket 0.8.2 py311haa95532_0
zeromq 4.3.4 hd77b12b_0
zfp 0.5.5 hd77b12b_6
zict 2.2.0 py311haa95532_0
zipp 3.11.0 py311haa95532_0
zlib 1.2.13 h8cc25b3_0
zlib-ng 2.0.7 h2bbff1b_0
zope 1.0 py311haa95532_1
zope.interface 5.4.0 py311h2bbff1b_0
zstandard 0.19.0 py311h2bbff1b_0
zstd 1.5.5 hd43e919_0´´´@martuser,
I don't see phy. Is this your (base) or your (phy2) env?
Could you do the same inside of whatever env has phy installed?
martuser
commented
11 months ago Sorry, it was in base, here is in the env where phy is installed:
#
# Name Version Build Channel
abseil-cpp 20211102.0 hd77b12b_0
arrow-cpp 11.0.0 ha81ea56_2
asttokens 2.0.5 pyhd3eb1b0_0
aws-c-common 0.6.8 h2bbff1b_1
aws-c-event-stream 0.1.6 hd77b12b_6
aws-checksums 0.1.11 h2bbff1b_2
aws-sdk-cpp 1.8.185 hd77b12b_1
backcall 0.2.0 pyhd3eb1b0_0
blas 1.0 mkl
bokeh 3.3.0 py311h746a85d_0
boost-cpp 1.82.0 h59b6b97_2
bottleneck 1.3.5 py311h5bb9823_0
brotli 1.0.9 h2bbff1b_7
brotli-bin 1.0.9 h2bbff1b_7
brotlipy 0.7.0 py311h2bbff1b_1002
bzip2 1.0.8 he774522_0
c-ares 1.19.1 h2bbff1b_0
ca-certificates 2023.08.22 haa95532_0
certifi 2023.7.22 py311haa95532_0
cffi 1.15.1 py311h2bbff1b_3
charset-normalizer 2.0.4 pyhd3eb1b0_0
click 8.0.4 py311haa95532_0
cloudpickle 2.2.1 py311haa95532_0
colorama 0.4.6 py311haa95532_0
colorcet 3.0.1 pypi_0 pypi
comm 0.1.2 py311haa95532_0
contourpy 1.0.5 py311h59b6b97_0
cryptography 41.0.3 py311h89fc84f_0
cycler 0.11.0 pyhd3eb1b0_0
cython 3.0.0 py311h2bbff1b_0
cytoolz 0.12.0 py311h2bbff1b_0
dask 2023.6.0 py311haa95532_0
dask-core 2023.6.0 py311haa95532_0
debugpy 1.6.7 py311hd77b12b_0
decorator 5.1.1 pyhd3eb1b0_0
distributed 2023.6.0 py311haa95532_0
executing 0.8.3 pyhd3eb1b0_0
fonttools 4.25.0 pyhd3eb1b0_0
freetype 2.12.1 ha860e81_0
fsspec 2023.9.2 py311haa95532_0
gflags 2.2.2 ha925a31_0
ghp-import 2.1.0 pypi_0 pypi
giflib 5.2.1 h8cc25b3_3
git 2.40.1 haa95532_1
glib 2.69.1 h5dc1a3c_2
glog 0.5.0 hd77b12b_0
grpc-cpp 1.48.2 hfe90ff0_1
h5py 3.9.0 py311h4e0e482_0
hdf5 1.12.1 h51c971a_3
heapdict 1.0.1 pyhd3eb1b0_0
icc_rt 2022.1.0 h6049295_2
icu 58.2 ha925a31_3
idna 3.4 py311haa95532_0
importlib-metadata 6.0.0 py311haa95532_0
iniconfig 1.1.1 pyhd3eb1b0_0
intel-openmp 2023.1.0 h59b6b97_46319
ipykernel 6.25.0 py311h746a85d_0
ipython 8.15.0 py311haa95532_0
ipython_genutils 0.2.0 pyhd3eb1b0_1
jedi 0.18.1 py311haa95532_1
jinja2 3.1.2 py311haa95532_0
joblib 1.2.0 py311haa95532_0
jpeg 9e h2bbff1b_1
jupyter_client 8.1.0 py311haa95532_0
jupyter_core 5.3.0 py311haa95532_0
kiwisolver 1.4.4 py311hd77b12b_0
krb5 1.20.1 h5b6d351_0
lerc 3.0 hd77b12b_0
libboost 1.82.0 h3399ecb_2
libbrotlicommon 1.0.9 h2bbff1b_7
libbrotlidec 1.0.9 h2bbff1b_7
libbrotlienc 1.0.9 h2bbff1b_7
libclang 14.0.6 default_hb5a9fac_1
libclang13 14.0.6 default_h8e68704_1
libcurl 8.1.1 h86230a5_0
libdeflate 1.17 h2bbff1b_1
libevent 2.1.12 h56d1f94_1
libffi 3.4.4 hd77b12b_0
libiconv 1.16 h2bbff1b_2
libpng 1.6.39 h8cc25b3_0
libpq 12.15 h906ac69_1
libprotobuf 3.20.3 h23ce68f_0
libsodium 1.0.18 h62dcd97_0
libssh2 1.10.0 he2ea4bf_2
libthrift 0.15.0 h4364b78_2
libtiff 4.5.1 hd77b12b_0
libwebp 1.3.2 hbc33d0d_0
libwebp-base 1.3.2 h2bbff1b_0
libxml2 2.10.4 h0ad7f3c_1
libxslt 1.1.37 h2bbff1b_1
locket 1.0.0 py311haa95532_0
lz4 4.3.2 py311h2bbff1b_0
lz4-c 1.9.4 h2bbff1b_0
markdown 3.5 pypi_0 pypi
markupsafe 2.1.1 py311h2bbff1b_0
matplotlib 3.7.2 py311haa95532_0
matplotlib-base 3.7.2 py311hf62ec03_0
matplotlib-inline 0.1.6 py311haa95532_0
mergedeep 1.3.4 pypi_0 pypi
mkdocs 1.5.3 pypi_0 pypi
mkl 2023.1.0 h6b88ed4_46357
mkl-service 2.4.0 py311h2bbff1b_1
mkl_fft 1.3.8 py311h2bbff1b_0
mkl_random 1.2.4 py311h59b6b97_0
msgpack-python 1.0.3 py311h59b6b97_0
mtscomp 1.0.2 pypi_0 pypi
munkres 1.1.4 py_0
nest-asyncio 1.5.6 py311haa95532_0
numexpr 2.8.7 py311h1fcbade_0
numpy 1.26.0 py311hdab7c0b_0
numpy-base 1.26.0 py311hd01c5d8_0
openjpeg 2.4.0 h4fc8c34_0
openssl 3.0.11 h2bbff1b_2
orc 1.7.4 h623e30f_1
packaging 23.1 py311haa95532_0
pandas 2.1.1 py311hf62ec03_0
param 1.13.0 pypi_0 pypi
parso 0.8.3 pyhd3eb1b0_0
partd 1.4.0 py311haa95532_0
pathspec 0.11.2 pypi_0 pypi
pcre 8.45 hd77b12b_0
phy 2.0b5 pypi_0 pypi
phylib 2.4.3 pypi_0 pypi
pickleshare 0.7.5 pyhd3eb1b0_1003
pillow 10.0.1 py311h045eedc_0
pip 23.3 py311haa95532_0
platformdirs 3.10.0 py311haa95532_0
pluggy 1.0.0 py311haa95532_1
ply 3.11 py311haa95532_0
prompt-toolkit 3.0.36 py311haa95532_0
psutil 5.9.0 py311h2bbff1b_0
pure_eval 0.2.2 pyhd3eb1b0_0
pyarrow 11.0.0 py311h8a3a540_1
pycparser 2.21 pyhd3eb1b0_0
pyct 0.5.0 pypi_0 pypi
pygments 2.15.1 py311haa95532_1
pyopengl 3.1.1a1 py311haa95532_0
pyopenssl 23.2.0 py311haa95532_0
pyparsing 3.0.9 py311haa95532_0
pyqt 5.15.7 py311hd77b12b_0
pyqt5-sip 12.11.0 py311hd77b12b_0
pyqtwebengine 5.15.7 py311hd77b12b_0
pysocks 1.7.1 py311haa95532_0
pytest 7.4.0 py311haa95532_0
python 3.11.5 he1021f5_0
python-dateutil 2.8.2 pyhd3eb1b0_0
python-lmdb 1.4.1 py311hd77b12b_0
python-tzdata 2023.3 pyhd3eb1b0_0
pytz 2023.3.post1 py311haa95532_0
pywin32 305 py311h2bbff1b_0
pyyaml 6.0 py311h2bbff1b_1
pyyaml-env-tag 0.1 pypi_0 pypi
pyzmq 25.1.0 py311hd77b12b_0
qt-main 5.15.2 h879a1e9_9
qt-webengine 5.15.9 h5bd16bc_7
qtconsole 5.4.2 py311haa95532_0
qtpy 2.2.0 py311haa95532_0
qtwebkit 5.212 h2bbfb41_5
re2 2022.04.01 hd77b12b_0
requests 2.31.0 py311haa95532_0
responses 0.13.3 pyhd3eb1b0_0
scikit-learn 1.2.2 py311hd77b12b_1
scipy 1.11.3 py311hc1ccb85_0
setuptools 68.0.0 py311haa95532_0
sip 6.6.2 py311hd77b12b_0
six 1.16.0 pyhd3eb1b0_1
snappy 1.1.9 h6c2663c_0
sortedcontainers 2.4.0 pyhd3eb1b0_0
sqlite 3.41.2 h2bbff1b_0
stack_data 0.2.0 pyhd3eb1b0_0
tbb 2021.8.0 h59b6b97_0
tblib 1.7.0 pyhd3eb1b0_0
threadpoolctl 2.2.0 pyh0d69192_0
tk 8.6.12 h2bbff1b_0
toml 0.10.2 pyhd3eb1b0_0
toolz 0.12.0 py311haa95532_0
tornado 6.3.3 py311h2bbff1b_0
tqdm 4.66.1 pypi_0 pypi
traitlets 5.7.1 py311haa95532_0
tzdata 2023c h04d1e81_0
urllib3 1.26.16 py311haa95532_0
utf8proc 2.6.1 h2bbff1b_0
vc 14.2 h21ff451_1
vs2015_runtime 14.27.29016 h5e58377_2
watchdog 3.0.0 pypi_0 pypi
wcwidth 0.2.5 pyhd3eb1b0_0
wheel 0.41.2 py311haa95532_0
win_inet_pton 1.1.0 py311haa95532_0
xyzservices 2022.9.0 py311haa95532_1
xz 5.4.2 h8cc25b3_0
yaml 0.2.5 he774522_0
zeromq 4.3.4 hd77b12b_0
zict 3.0.0 py311haa95532_0
zipp 3.11.0 py311haa95532_0
zlib 1.2.13 h8cc25b3_0
zstd 1.5.5 hd43e919_0´´´cool thanks Marta.
One more thing. Could you copy the exact error that you are getting from the terminal/cmd prompt/? It would help if you run with debug so:
phy template-gui params.py --debugSo I can see the exact place where the error is occurring.
As long as you tested installing with the yaml as in #1218, then I need to see the specific error. If you haven't tried installing from the yaml, I would start with that.
martuser
commented
11 months ago This is the error using the environment that I currently have:
19:12:01.169 [D] __init__:68 Start capturing exceptions.
19:12:01.616 [W] model:603 Unreferenced clusters found in templates (generally not a problem)
19:12:01.932 [D] model:619 Loading spike clusters.
19:12:02.272 [W] model:625 Unreferenced clusters found in spike_clusters (generally not a problem)
19:12:02.592 [D] model:569 No channel shank file found.
19:12:02.593 [D] model:692 Loading templates.
19:12:02.676 [D] model:724 Templates are dense.
19:12:07.260 [W] model:667 Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed.
19:12:07.260 [D] model:730 Loading the whitening matrix.
19:12:07.264 [D] model:737 Loading the inverse of the whitening matrix.
19:12:07.284 [D] model:766 Loading features.
19:12:07.287 [D] model:781 Features are sparse.
19:12:07.288 [D] model:803 Loading template features.
19:12:07.290 [D] model:813 Template features are sparse.
19:12:07.292 [D] model:504 Load `cluster_Amplitude.tsv`.
19:12:07.298 [D] model:504 Load `cluster_ContamPct.tsv`.
19:12:07.394 [D] model:504 Load `cluster_group.tsv`.
19:12:07.395 [D] model:504 Load `cluster_KSLabel.tsv`.
19:12:08.062 [D] context:100 Initialize joblib cache dir at `F:\NP\LUX#75_NP-1_g0\kilosort2.5\.phy`.
19:12:08.062 [D] context:101 Reducing the size of the cache if needed.
19:12:08.194 [D] base:102 Add filter `high_pass`.
19:12:08.195 [D] config:31 Load config file `C:\Users\isaco\.phy\phy_config.py`.
19:12:08.196 [D] plugin:145 Loading 0 plugins.
19:12:08.196 [D] context:126 Load memcache for `phy.apps.base._get_mean_waveforms`.
19:12:08.223 [D] context:126 Load memcache for `phy.apps.base._get_mean_waveforms`.
19:12:08.248 [D] context:126 Load memcache for `phy.apps.base._get_template_waveforms`.
19:12:08.250 [D] context:126 Load memcache for `phy.apps.base.get_mean_spike_template_amplitudes`.
19:12:08.252 [D] context:126 Load memcache for `phy.apps.base.get_template_counts`.
19:12:08.266 [D] context:126 Load memcache for `phy.apps.base.get_template_for_cluster`.
19:12:08.282 [D] context:126 Load memcache for `phy.apps.template.gui.get_template_amplitude`.
19:12:08.296 [D] context:126 Load memcache for `phy.apps.base.get_cluster_amplitude`.
19:12:08.299 [D] context:126 Load memcache for `phy.apps.base.get_mean_firing_rate`.
19:12:08.302 [D] context:126 Load memcache for `phy.apps.base.get_best_channel`.
19:12:08.318 [D] context:126 Load memcache for `phy.apps.template.gui.get_best_channels`.
19:12:08.338 [D] context:126 Load memcache for `phy.apps.base.get_channel_shank`.
19:12:08.341 [D] context:126 Load memcache for `phy.apps.base.get_probe_depth`.
19:12:08.343 [D] context:126 Load memcache for `phy.apps.base.peak_channel_similarity`.
19:12:08.609 [D] context:185 Save data to `F:\NP\LUX#75_NP-1_g0\kilosort2.5\.phy\spikes_per_cluster.pkl`.
19:12:10.037 [D] gui:463 Creating GUI.
19:12:10.052 [D] state:46 Load C:\Users\isaco\.phy\TemplateGUI\state.json for GUIState.
19:12:10.054 [D] state:46 Load F:\NP\LUX#75_NP-1_g0\kilosort2.5\.phy\state.json for GUIState.
19:12:10.612 [D] gui:718 Add view ClusterView to GUI.
19:12:10.624 [D] gui:718 Add view SimilarityView to GUI.
19:12:10.670 [D] gui:718 Add view WaveformView to GUI.
19:12:10.675 [D] base:337 Set state for WaveformView.
19:12:10.689 [D] gui:718 Add view CorrelogramView to GUI.
19:12:10.692 [D] base:337 Set state for CorrelogramView.
19:12:10.709 [D] gui:718 Add view FeatureView to GUI.
19:12:10.711 [D] base:337 Set state for FeatureView.
19:12:10.735 [D] gui:718 Add view AmplitudeView to GUI.
19:12:10.738 [D] base:337 Set state for AmplitudeView.
19:12:10.761 [D] gui:718 Add view FiringRateView to GUI.
19:12:10.764 [D] base:337 Set state for FiringRateView.
19:12:11.556 [D] gui:718 Add view TraceView to GUI.
19:12:11.559 [D] base:337 Set state for TraceView.
19:12:11.560 [D] base:494 Set color scheme to random.
19:12:18.564 [D] base:1626 Adding default color schemes to TraceView.
19:12:22.318 [D] gui:718 Add view TemplateFeatureView to GUI.
19:12:22.320 [D] base:337 Set state for TemplateFeatureView.
19:12:22.541 [D] gui:519 Load the geometry state.
QMimeDatabase: Error loading internal MIME data
An error has been encountered at line 1 of <internal MIME data>: Premature end of document.:
19:12:23.936 [D] supervisor:817 Clusters selected: [180] (315) ´´´And this is the error using the environment from the yaml file in https://github.com/cortex-lab/phy/issues/1218:
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "C:\Users\isaco\.conda\envs\phy2\Scripts\phy.exe\__main__.py", line 4, in <module>
File "C:\Users\isaco\.conda\envs\phy2\Lib\site-packages\phy\__init__.py", line 21, in <module>
from .utils.config import load_master_config
File "C:\Users\isaco\.conda\envs\phy2\Lib\site-packages\phy\utils\__init__.py", line 8, in <module>
from .plugin import IPlugin, attach_plugins
File "C:\Users\isaco\.conda\envs\phy2\Lib\site-packages\phy\utils\plugin.py", line 14, in <module>
import imp
ModuleNotFoundError: No module named 'imp' ´´´Cool. That we can fix. So the issue is Python 3.12 just came out where they removed imp. So what you need to do is edit the yaml and say python=3.11 instead. Then try again with the yaml. I have a PR open to fix this issue, but I'm waiting for it to be merged. Can you try that and let me know if that works? (Or let me know if you want more explanation on ending the yaml.)
martuser
commented
11 months ago That's it! Thank you very much, Zach. I no longer have any errors, and the GUI is working! Here's what appears in debug mode:
19:56:11.602 [W] model:603 Unreferenced clusters found in templates (generally not a problem)
19:56:11.924 [D] model:619 Loading spike clusters.
19:56:12.310 [W] model:625 Unreferenced clusters found in spike_clusters (generally not a problem)
19:56:12.641 [D] model:569 No channel shank file found.
19:56:12.644 [D] model:692 Loading templates.
19:56:12.743 [D] model:724 Templates are dense.
19:56:17.356 [W] model:667 Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed.
19:56:17.356 [D] model:730 Loading the whitening matrix.
19:56:17.358 [D] model:737 Loading the inverse of the whitening matrix.
19:56:17.365 [D] model:766 Loading features.
19:56:17.366 [D] model:781 Features are sparse.
19:56:17.367 [D] model:803 Loading template features.
19:56:17.371 [D] model:813 Template features are sparse.
19:56:17.374 [D] model:504 Load `cluster_Amplitude.tsv`.
19:56:17.385 [D] model:504 Load `cluster_ContamPct.tsv`.
19:56:17.395 [D] model:504 Load `cluster_group.tsv`.
19:56:17.396 [D] model:504 Load `cluster_KSLabel.tsv`.
19:56:17.909 [D] context:100 Initialize joblib cache dir at `F:\NP\LUX#75_NP-1_g0\kilosort2.5\.phy`.
19:56:17.909 [D] context:101 Reducing the size of the cache if needed.
19:56:18.048 [D] base:102 Add filter `high_pass`.
19:56:18.050 [D] config:31 Load config file `C:\Users\isaco\.phy\phy_config.py`.
19:56:18.050 [D] plugin:145 Loading 0 plugins.
19:56:18.051 [D] context:126 Load memcache for `phy.apps.base._get_mean_waveforms`.
19:56:18.099 [D] context:126 Load memcache for `phy.apps.base._get_mean_waveforms`.
19:56:18.111 [D] context:126 Load memcache for `phy.apps.base._get_template_waveforms`.
19:56:18.112 [D] context:126 Load memcache for `phy.apps.base.get_mean_spike_template_amplitudes`.
19:56:18.112 [D] context:126 Load memcache for `phy.apps.base.get_template_counts`.
19:56:18.113 [D] context:126 Load memcache for `phy.apps.base.get_template_for_cluster`.
19:56:18.114 [D] context:126 Load memcache for `phy.apps.template.gui.get_template_amplitude`.
19:56:18.115 [D] context:126 Load memcache for `phy.apps.base.get_cluster_amplitude`.
19:56:18.116 [D] context:126 Load memcache for `phy.apps.base.get_mean_firing_rate`.
19:56:18.116 [D] context:126 Load memcache for `phy.apps.base.get_best_channel`.
19:56:18.117 [D] context:126 Load memcache for `phy.apps.template.gui.get_best_channels`.
19:56:18.120 [D] context:126 Load memcache for `phy.apps.base.get_channel_shank`.
19:56:18.120 [D] context:126 Load memcache for `phy.apps.base.get_probe_depth`.
19:56:18.121 [D] context:126 Load memcache for `phy.apps.base.peak_channel_similarity`.
19:56:18.695 [D] context:185 Save data to `F:\NP\LUX#75_NP-1_g0\kilosort2.5\.phy\spikes_per_cluster.pkl`.
19:56:19.668 [D] gui:463 Creating GUI.
19:56:19.680 [D] state:46 Load C:\Users\isaco\.phy\TemplateGUI\state.json for GUIState.
19:56:19.681 [D] state:46 Load F:\NP\LUX#75_NP-1_g0\kilosort2.5\.phy\state.json for GUIState.
19:56:20.168 [D] gui:718 Add view ClusterView to GUI.
19:56:20.189 [D] gui:718 Add view SimilarityView to GUI.
19:56:20.233 [D] gui:718 Add view WaveformView to GUI.
19:56:20.563 [D] base:337 Set state for WaveformView.
19:56:20.576 [D] gui:718 Add view CorrelogramView to GUI.
19:56:20.579 [D] base:337 Set state for CorrelogramView.
19:56:20.592 [D] gui:718 Add view FeatureView to GUI.
19:56:20.594 [D] base:337 Set state for FeatureView.
19:56:20.618 [D] gui:718 Add view AmplitudeView to GUI.
19:56:20.620 [D] base:337 Set state for AmplitudeView.
19:56:20.644 [D] gui:718 Add view FiringRateView to GUI.
19:56:20.646 [D] base:337 Set state for FiringRateView.
19:56:21.526 [D] gui:718 Add view TraceView to GUI.
19:56:21.529 [D] base:337 Set state for TraceView.
19:56:21.529 [D] base:494 Set color scheme to random.
19:56:28.463 [D] base:1626 Adding default color schemes to TraceView.
19:56:32.099 [D] gui:718 Add view TemplateFeatureView to GUI.
19:56:32.101 [D] base:337 Set state for TemplateFeatureView.
19:56:32.349 [D] gui:519 Load the geometry state.
19:56:33.711 [D] supervisor:817 Clusters selected: [180] (315)
19:58:50.172 [D] supervisor:817 Clusters selected: [41] (42) ´´´Happy it works. Best of luck Marta!
Cheers, Zach
Hi! I've checked issue 1212 and 1218 but I still have the same error. I've followed the exact instructions as its described in README. My OS is Windows 11 Pro for Workstations and conda version 4.10.3.
Thanks, Marta.