module 'mofapy2' has no attribute 'run.entry_point'

[jiaqizhang0712]

I have been experimenting some errors to 'run_mofa', but I don't know what is going on after I tried all the solutions online:

> MOFAobject.trained <- run_mofa(MOFAobject, "./MOFA/model.hdf5", use_basilisk = TRUE)

Connecting to the mofapy2 package using basilisk. 
    Set 'use_basilisk' to FALSE if you prefer to manually set the python binary using 'reticulate'.
Error in py_get_attr(x, name, FALSE) : 
  AttributeError: module 'mofapy2' has no attribute 'run.entry_point'

I checked the packages list in the mofa_env, it seems everything went well.

> listPackages("./.cache/R/basilisk/1.12.1/MOFA2/1.10.0/mofa_env")
                           full         package
1                anndata==0.8.0         anndata
2        cached-property==1.5.2 cached-property
3             dtw-python==1.2.2      dtw-python
4                   h5py==3.6.0            h5py
5                 joblib==1.4.2          joblib
6                mofapy2==0.7.0         mofapy2
7                natsort==8.4.0         natsort
8                 numpy==1.23.1           numpy
9               packaging==24.2       packaging
10                pandas==1.4.3          pandas
11                  pip==24.3.1             pip
12 python-dateutil==2.9.0.post0 python-dateutil
13                 pytz==2024.2            pytz
14          scikit-learn==1.1.1    scikit-learn
15                 scipy==1.8.1           scipy
16           setuptools==75.6.0      setuptools
17                  six==1.17.0             six
18         threadpoolctl==3.5.0   threadpoolctl
19                wheel==0.45.1           wheel

I've restarted the R sessions many times as the methods online, but it still doesn't work.

[SColson82]

I encountered this issue as well.

I found that the environment location was in $HOME/.cache/R/basilisk/1.12.0/MOFA2/1.12.1/mofa_env/.

The file $HOME/.cache/R/basilisk/1.12.0/MOFA2/1.12.1/mofa_env/lib/python3.10/site-packages/mofapy2/__init__.py had the following:

from .version import __version__
from .config import *

To this, I added a 3rd line:

from mofapy2.run.entry_point import *

Once that was complete I was able to move on, but encountered another error:

Error: ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by $HOME/.cache/R/basilisk/1.12.0/MOFA2/1.12.1/mofa_env/lib/python3.10/site-packages/scipy/linalg/_matfuncs_sqrtm_triu.cpython-310-x86_64-linux-gnu.so)

The fix to this was to add the location of libstdc++.so.6 in the conda environment to the LD_LIBRARY_PATH:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/.cache/R/basilisk/1.12.0/MOFA2/1.12.1/mofa_env/lib

After these changes, I was able to complete the run. I'm not saying this is the only or best fix but maybe it works for others until someone more knowledgeable comes along!