problem with Giotto python environment about giotto HOT 5 CLOSED

Hi @orrzor, thanks for reaching out. Are you able to create the conda environment with anaconda3 as opposed to miniconda3? I am still looking at possible reasons for this but that is 1 thing I see that is different from our tutorial. Thanks!

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Hi @orrzor I'm amazed to see that even after a manual installation where all the modules have been installed, you still can not detect them.

One thing to try would be to reinstall the Giotto environment in a fresh R session without loading any other libraries or running any other code. You can simply do:

library(Giotto)  
installGiottoEnvironment(force_miniconda = TRUE, force_environment = TRUE)

This will force the reinstallation of miniconda and re-create the Giotto environment. It could be that the first time you created the Giotto environment the reticulate package was already used by another package and that could lead to problems.

Unfortunately I don't have a (working) linux machine at hand right now, but it does seems to work properly on our linux servers. Let us know if this worked.

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Hi Ruben, thanks for your help! I tried uninstalling and reinstalling Giotto, reticulate, and the giotto_env and was still getting the same error. After a lot of fiddling with reticulate, I found the issue with these specific python packages that weren't loading was due to the LD_LIBRARY_PATH environment variable. When importing modules with reticulate directly, I was seeing this error.

> import("leidenalg")
Error in py_module_import(module, convert = convert) : 
  ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/unix/orr/.local/share/r-miniconda/envs/giotto_env/lib/python3.6/site-packages/igraph/_igraph.cpython-36m-x86_64-linux-gnu.so)

and found I could fix this by running the following before starting my R from the terminal.

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/unix/orr/.local/share/r-miniconda/envs/giotto_env/lib

Now things work for me in the environment. So again, I think this is another reticulate issue, and may be worth highlighting on your installation instructions. Thanks again fro your help! Best- Orr

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Thanks @orrzor for letting us know how to fix this issue. I tried looking for an option that could work directly within R/Rstudio, but that doesn't seem to be trivial. We'll make sure to update our installation section with your suggestion in the next couple of days.
Thanks,
Ruben

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thank you Ruben! I'm excited to see what I get with the HMRF now that the technical issues (fingers crossed) are resolved. best, Orr

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