nel-lab
Installation Issues
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. Do you have any advice on how 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
This seems not specific to mesmerize-core...are you able to install anything? For example can you run mamba create -n numpy -c conda-forge numpy?
It does seem like I can't install anything actually, numpy didn't work either. I tried uninstalling anaconda fully again just now, conda clean --all, and then mamba again - it took awhile but it did say it solved the environment, but then when I went to install mesmerize-core (or numpy), it threw the error below.
Would it likely be an issue with my mamba or anaconda?
Traceback (most recent call last):
File "/opt/anaconda3/bin/mamba", line 7, in <module>
from mamba.mamba import main
File "/opt/anaconda3/lib/python3.12/site-packages/mamba/mamba.py", line 44, in <module>
import libmambapy as api
File "/opt/anaconda3/lib/python3.12/site-packages/libmambapy/__init__.py", line 7, in <module>
raise e
File "/opt/anaconda3/lib/python3.12/site-packages/libmambapy/__init__.py", line 4, in <module>
from libmambapy.bindings import * # noqa: F401,F403
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ImportError: dlopen(/opt/anaconda3/lib/python3.12/site-packages/libmambapy/bindings.cpython-312-darwin.so, 0x0002): Library not loaded: @rpath/libarchive.13.dylib
Referenced from: <87BD792F-0587-3166-8AAF-20CF792B82F9> /opt/anaconda3/lib/libmamba.2.0.0.dylib
Reason: tried: '/opt/anaconda3/lib/libarchive.13.dylib' (no such file), '/opt/anaconda3/lib/python3.12/site-packages/libmambapy/../../../libarchive.13.dylib' (no such file), '/opt/anaconda3/lib/python3.12/site-packages/libmambapy/../../../libarchive.13.dylib' (no such file), '/opt/anaconda3/bin/../lib/libarchive.13.dylib' (no such file), '/opt/anaconda3/bin/../lib/libarchive.13.dylib' (no such file), '/usr/local/lib/libarchive.13.dylib' (no such file), '/usr/lib/libarchive.13.dylib' (no such file, not in dyld cache)
(base) cynthialo@Cynthias-MacBook-Pro-2 ~ %
I'm currently on vacation, but if you like when I get back (on the 4th) we can do a VC and see if we can figure it out live. Unless someone else solves it first.
One not of info you can add to this ticket that may let me solve it earlier would be to do a "conda env list" and paste the results in here; I have a few hunches that might explain it but we need more info
Thank you so much for your help! I think I managed to fix the mamba issue, as I've been able now to create the environment without any issues, but the verification step has not been working for me (mesmerize_core.version), it says it is not found. If you are able to jump on a VC after your vacation, I would really appreciate the help in getting mesmerize running on my computer!
AttributeError Traceback (most recent call last) Cell In[6], line 3 1 import mesmerize_core 2 print('import') ----> 3 mesmerize_core.version
AttributeError: module 'mesmerize_core' has no attribute 'version'
And here is the conda env list:
conda environments:
/Users/cynthialo/Library/Caches/org.R-project.R/R/basilisk/1.12.1/0
/Users/cynthialo/Library/Caches/org.R-project.R/R/basilisk/1.12.1/zellkonverter/1.10.1/zellkonverterAnnDataEnv-0.8.0
base * /opt/anaconda3 mescore /opt/anaconda3/envs/mescore
@CeeLo It may be that the formatting that github does is making those instructions less clear (or perhaps our communcation about them).
__version__ is meant to have double-underscores on both sides (github tends to format that with italics or bold I think). Can you check to see if mezmerize_core.__version__ has a value?
Oh yes, it does! Thank you, it says 0.4.0. Just one last question, I am trying to run through the example notebook, but it wasn't quite clear to me where to get/use the example data - does the download_demo() function download it, or am I missing a download somewhere?
Yes that function downloads the demo movie if you've run the caimanmanager step.
On Sun, Sep 1, 2024, 3:36 PM Cynthia @.***> wrote:
Oh yes, it does! Thank you, it says 0.4.0. Just one last question, I am trying to run through the example notebook, but it wasn't quite clear to me where to get/use the example data - does the download_demo() function download it, or am I missing a download somewhere?
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