leiden
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install dependencies error
This is possibly related to a previous issue (https://github.com/TomKellyGenetics/leiden/issues/20). I recently tried to use the CRAN version of leiden (0.4.3). Upon loading, I see the following:
> library(leiden)
using environment: r-reticulate
conda environment r-reticulate installed
install dependencies (yes/no)?yes
yes
using environment: r-reticulate
/path/miniconda3/envs/r-reticulate/lib/python3.8/site-packages/numba/core/types/__init__.py:108: FutureWarning: In the future `np.long` will be defined as the corresponding NumPy scalar.
long_ = _make_signed(np.long)
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /path/miniconda3/envs/r-reticulate/envs/r-reticulate
added / updated specs:
- python
All the dependencies are actually installed. I think part of the problem may be that reticulate::py_module_available("umap")
should be reticulate::py_module_available("umap-learn")
in leiden.R
.
When it tries to install the dependencies, it does it in a new sub-environment (notice the path in the message).