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flatironinstitute / CaImAn

Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
https://caiman.readthedocs.io
GNU General Public License v2.0
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Installation Issues #1399

Closed CeeLo closed 2 months ago

CeeLo commented 2 months ago

Hi, I've been having issues with installing Mesmerize-core. I have been following the instructions from the mesmerize-core to run the following: mamba create -n mescore -c conda-forge mesmerize-core and attempted to reinstall anaconda to see if it fixes the issue, but it did not do anything so far.

My computer information is: Operating System: MacOS Sonoma 14.5 Hardware Type: M1 chip, 16 GB RAM Python: 3.10.13

I have been getting the error message listed below. I'm not sure what the exact issue is in this case, I saw that there were issues with installing individual packages as well. What could I do to troubleshoot this?

Error Message: Traceback (most recent call last): File "/Users/cynthialo/anaconda3/lib/python3.10/site-packages/conda/exception_handler.py", line 18, in call return func(*args, *kwargs) File "/Users/cynthialo/anaconda3/lib/python3.10/site-packages/mamba/mamba.py", line 959, in exception_converter raise e File "/Users/cynthialo/anaconda3/lib/python3.10/site-packages/mamba/mamba.py", line 952, in exception_converter exit_code = _wrapped_main(args, **kwargs) File "/Users/cynthialo/anaconda3/lib/python3.10/site-packages/mamba/mamba.py", line 898, in _wrapped_main result = do_call(parsed_args, p) File "/Users/cynthialo/anaconda3/lib/python3.10/site-packages/mamba/mamba.py", line 767, in do_call exit_code = create(args, parser) File "/Users/cynthialo/anaconda3/lib/python3.10/site-packages/mamba/mamba.py", line 602, in create return install(args, parser, "create") File "/Users/cynthialo/anaconda3/lib/python3.10/site-packages/mamba/mamba.py", line 558, in install transaction.fetch_extract_packages() RuntimeError: Found incorrect download: libexpat. Aborting

$ /Users/cynthialo/anaconda3/bin/mamba create -n mescore -c conda-forge mesmerize-core

environment variables: CIO_TEST= CONDA_ALLOW_SOFTLINKS=false CONDA_DEFAULT_ENV=base CONDA_EXE=/Users/cynthialo/anaconda3/bin/conda CONDA_PREFIX=/Users/cynthialo/anaconda3 CONDA_PROMPT_MODIFIER=(base) CONDA_PYTHON_EXE=/Users/cynthialo/anaconda3/bin/python CONDA_ROOT=/Users/cynthialo/anaconda3 CONDA_SHLVL=1 CURL_CA_BUNDLE= INFOPATH=/opt/homebrew/share/info: LD_PRELOAD= MANPATH=/opt/homebrew/share/man:: PATH=/Users/cynthialo/anaconda3/bin:/Users/cynthialo/anaconda3/condabin:/op t/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App /usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cry ptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security .cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.c ryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/X11/bin:/Lib rary/Apple/usr/bin REQUESTS_CA_BUNDLE= SSL_CERT_FILE=

 active environment : base
active env location : /Users/cynthialo/anaconda3
        shell level : 1
   user config file : /Users/cynthialo/.condarc

populated config files : /Users/cynthialo/.condarc conda version : 24.7.1 conda-build version : 24.5.1 python version : 3.10.13.final.0 solver : classic virtual packages : archspec=1=m1 conda=24.7.1=0 osx=14.5=0 unix=0=0 base environment : /Users/cynthialo/anaconda3 (writable) conda av data dir : /Users/cynthialo/anaconda3/etc/conda conda av metadata url : None channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64 https://conda.anaconda.org/conda-forge/noarch https://conda.anaconda.org/bioconda/osx-arm64 https://conda.anaconda.org/bioconda/noarch https://repo.anaconda.com/pkgs/main/osx-arm64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/osx-arm64 https://repo.anaconda.com/pkgs/r/noarch package cache : /Users/cynthialo/anaconda3/pkgs /Users/cynthialo/.conda/pkgs envs directories : /Users/cynthialo/anaconda3/envs /Users/cynthialo/.conda/envs platform : osx-arm64 user-agent : conda/24.7.1 requests/2.32.3 CPython/3.10.13 Darwin/23.5.0 OSX/14.5 UID:GID : 501:20 netrc file : None offline mode : False

An unexpected error has occurred. Conda has prepared the above report. If you suspect this error is being caused by a malfunctioning plugin, consider using the --no-plugins option to turn off plugins.

Example: conda --no-plugins install

Alternatively, you can set the CONDA_NO_PLUGINS environment variable on the command line to run the command without plugins enabled.

Example: CONDA_NO_PLUGINS=true conda install

pgunn commented 2 months ago

I see you also filed an issue against mezmerise-core here: https://github.com/nel-lab/mesmerize-core/issues/313

Let's continue the conversation there.