rargelaguet
commented
1 year ago Hi @xinhuiwang,
from what I can see in the output, you are installing the python dependencies using the default basilisk approach. Was there any error during the installation? Did you also try installing your own conda environemnt and then connecting R to the environment with reticulate?
P.S. Are you using the latest MOFA2 version? (1.8.0 if installed via Bioconductor)
I am running our data with the function "run_mofa(MOFAobject2,force=TRUE)"
I got the following error message:
_"Connecting to the mofapy2 package using basilisk. Set 'use_basilik' to FALSE if you prefer to manually set the python binary using 'reticulate'. Error in checkForRemoteErrors(lapply(cl, recvResult)) : one node produced an error: path[1]="/Users/username/Library/r-miniconda/envs/r-reticulate:/Users/username/Library/r-miniconda/envs/r-reticulate": No such file or directory In addition: Warning messages: 1: In run_mofa(MOFAobject2, use_basilisk = TRUE) : No output filename provided. Using /tmp/mofa20221205-125015.hdf5 to store the trained model. 2: In normalizePath(getPythonBinary(envpath)) : path[1]="/Users/username/Library/r-miniconda/envs/r-reticulate:/Users/username/Library/r-miniconda/envs/r-reticulate/bin/python": No such file or directory 3: In normalizePath(getPythonBinary(envpath)) : path[1]="/Users/username/Library/r-miniconda/envs/r-reticulate:/Users/username/Library/r-miniconda/envs/r-reticulate/bin/python": No such file or directory"
I reinstall the pyenv and the issue is still there.
When I check with "pyconfig()", I have the following messages: "python: /Users/username/Library/r-miniconda/envs/r-reticulate/bin/python libpython: /Users/username/Library/r-miniconda/envs/r-reticulate/lib/libpython3.8.dylib pythonhome: /Users/username/Library/r-miniconda/envs/r-reticulate:/Users/username/Library/r-miniconda/envs/r-reticulate version: 3.8.15 | packaged by conda-forge | (default, Nov 22 2022, 08:53:40) [Clang 14.0.6 ] numpy: /Users/username/Library/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/numpy numpyversion: 1.23.5"
Is there any idea with the problem?