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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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conda install issue -- submit package to conda-forge? #479

Closed ssobt closed 1 year ago

ssobt commented 1 year ago

Hi,

Thank you for taking the time to actively update and maintain this package.

I'm trying to install the package into a conda environment using: mamba install -c bioconda bioconductor-infercnv

and I get the following error: nothing provides r-rjags needed by bioconductor-infercnv-1.0.3-r36_0

The same error occurs regardless of if the package is put into a new or an existing conda environment. Unfortunately bioconda doesn't contain all of the dependencies (like rjags) needed for InferCNV requiring channel mixing b/w bioconda and conda-forge which doesn't end up working out well (I've tried). Would it be possible to sync InferCNV to the conda-forge channel to prevent this error?

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (1.0.0) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

     active environment : None
            shell level : 0
       user config file : /home/ssobti/.condarc
 populated config files : /home/ssobti/.condarc
          conda version : 4.12.0
    conda-build version : not installed
         python version : 3.9.13.final.0
       virtual packages : __linux=5.15.0=0
                          __glibc=2.35=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/ssobti/miniconda3  (writable)
      conda av data dir : /home/ssobti/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : 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
          package cache : /home/ssobti/miniconda3/pkgs
                          /home/ssobti/.conda/pkgs
       envs directories : /home/ssobti/miniconda3/envs
                          /home/ssobti/.conda/envs
               platform : linux-64
             user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.13 Linux/5.15.0-50-generic ubuntu/22.04.1 glibc/2.35
                UID:GID : 1011:1013
             netrc file : None
           offline mode : False

Thanks!

EDIT: This error was due to the conda env build file (.yml) containing packages pinned to r-3.3. Package installs beautifully using a fresh conda env with r-base and r-essentials.