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ndcn / omicser

The NDCN omics browser app for browsing and sharing general omics data.
https://ndcn.github.io/omicser
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conda_install fails with CRAN version of reticulate #157

Closed bnovotny closed 2 years ago

bnovotny commented 2 years ago

Describe the bug During installation on Windows 10, conda_install fails: 

WARNING: pip is configured with locations that require TLS/SSL, however the ssl module in Python is not available.
ERROR: Could not find a version that satisfies the requirement scanpy[leiden] (from versions: none)
ERROR: No matching distribution found for scanpy[leiden]

Problem is solved by installing the dev version of reticulate: remotes::install_github("rstudio/reticulate"). This has been noted previously: https://github.com/rstudio/tensorflow/issues/491

Although this is a reticulate problem I think it would be helpful to note in the omicser documentation.

To Reproduce Steps to reproduce the behavior:

  1. Install reticulate on Windows 10 using install.packages("reticulate")
  2. Create the conda environment as described here https://ndcn.github.io/omicser/articles/01_installation.html
  3. Installation is failing at 
    reticulate::conda_install(envname=OMICSER_PYTHON,
                      channel = "conda-forge",
                      pip = TRUE,
                      packages =  packages )

Desktop (please complete the following information):

ricoderks commented 2 years ago

When I set up the Windows 10 test environment I did not have this problem. I checked and the reticulate version from CRAN is now 1.23. This version was released 3 days ago. Looks like this is fixed now, but maybe we should leave it open for a while just to be sure.

bnovotny commented 2 years ago

Sure enough, I installed 1.23 from source and no more issues on my end. Thanks!

ergonyc commented 2 years ago

Looks like the CRAN update fully solves this.