Install gseapy in R PackagesNotFoundError

Question

I would like to run gseapy in rstudio as I need to perform some pathway analysis using GSEA_InContext. This is what I have:

library(reticulate)
use_condaenv('/home/user/.local/share/r-miniconda/envs/r-reticulate')
conda_install("r-reticulate", "gseapy")

However, it throws me error as:

'/home/user/.local/share/r-miniconda/bin/conda' 'install' '--yes' '--name' 'r-reticulate' '-c' 'conda-forge' 'gseapy'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - gseapy
Current channels:

  - https://conda.anaconda.org/conda-forge/linux-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.


Error: one or more Python packages failed to install [error code 1]

How can I solve this issue?

Asked By: Nmgh

||

Source

Answer 1

Bioinformatics tools are generally hosted on Bioconda, and that includes gseapy. In the future, please search Anaconda.org to find Conda package builds.

To install with reticulate, would be something like

conda_install("gseapy", channel=c('conda-forge', 'bioconda', 'defaults')

I don’t think you should be also installing r-reticulate (an R package) in the Python environment. Personally, I’ve found keeping environments granular (task-based) and not mixing Python and R in the same environment leads to a smoother user experience.

Answered By: merv

Install gseapy in R PackagesNotFoundError

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