Unable to load Seurat in R-studio (anaconda)

Hello,

I am running R studio through anaconda-navigator on a mac. I've installed Seurat but when trying to load it onto R-studio I get the following error message. Would someone be able to help me solve it?

Error: package or namespace load failed for ‘Seurat’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/opt/anaconda3/envs/Python/lib/R/library/Rtsne/libs/Rtsne.dylib':
  dlopen(/opt/anaconda3/envs/Python/lib/R/library/Rtsne/libs/Rtsne.dylib, 6): Library not loaded: @rpath/libopenblas.0.dylib
  Referenced from: /opt/anaconda3/envs/Python/lib/R/library/Rtsne/libs/Rtsne.dylib
  Reason: image not found

I should specify "Python" in the path above is an environment I made called Python. it doesnt refer to anything actually related to the language itself.

anaconda seurat r-studio anaconda-navigator

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written 6.7 years ago by V

1 answer

Try running conda install -c conda-forge openblas in the environment, because it looks like an openblas library is missing. Also, it's not a good idea to name your environments to match keywords, even if the casing is different.

Plus, conda environments don't play well with RStudio. Can you try running your command from the R command line launched with the environment active (conda activate Python; R)?

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written 6.7 years ago by Ram

Thank you very very much! This has solved my issue. Just had to install openblas by running the code you've typed and Seurat loaded just fine.

Thank you once again :)

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written 6.7 years ago by V

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work.

Upvote|Bookmark|Accept

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written 6.7 years ago by Ram

Thank you again, Im sorry but a slightly unrelated question to the above, if you happen to know. (on Mac), when launching jupyter lab through anaconda navigator, for some reason it can not go into "Documents". I can set cd to 'home' or any subfolder within home, but it will not set directory to any folder within documents. I've tried changing the ownership of 'Documents' from me to everyone to see if that would help but nothing happened. WOuld you know what is causing this ?

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written 6.7 years ago by V

Sorry, I use the conda command line. I don't know why a GUI cannot perform certain actions. If you were to try the command line, errors might be a little more verbose and easier to resolve.

The one thing I can say is to try using absolute paths, like /Users/V/ instead of $HOME/ or ~/.

I'd also recommend switching to miniconda from Anaconda. Leaner package managers are always better than bloated managers.

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written 6.7 years ago by Ram