![]() never ever run conda install ever again after the first time unless you absolutely have to (occasionally I've had to install pacakge like ncurses from conda-forge before installing anything else, but thats rare),ģ). make sure the full path to the conda install directory is not too long, because it gets hard-coded into the shebang lines in a lot of the installed files and shebang lines have a size limit of ~127 characters usually Ģ). be careful if conda tries to update itself and/or its included Python versions because sometimes this can cause conda to break itself, if that happens then be sure to include args with conda install to lock versions of conda itself and/or Pythonġb). install all the R packages you need up front with a single conda install command without specifying library versions, then let conda pick compatible libraries, then note which versions it chose, then delete the entire conda install and start over with a new fresh conda installation and run conda install again while specifying the exact versions of libraries you want based on the list conda chose for you,ġa). use a fresh new conda installation for each project, dont try to manage multiple conda env's in a single conda installation, you can download Miniconda from here:, yes this wastes some disk space but it saves you a lot of headachesġ). I have never found R and R lib installation in conda to be particularly difficult as long as you follow some of these steps & precautionsĠ). (DISCLAIMER: some of the steps described here explicitly go against the official conda installation & usage instructions beginners should follow the official guides instead before trying any of these steps, and fully understand what these steps are doing before trying them out) Packages such as ComplexHeatMap packages and Cairo can not be installed. So it is still not a very good way of installing R. Note: You can not update R-packages installed through r-essentials especially rcurl. If (!requireNamespace("BiocManager", quietly = TRUE)) # Open R and install BiocManager and select a mirror to install the packages from. Mamba install -c conda-forge r-essentials Mamba create -n R -c conda-forge r-base -y Installing R # installing Mamba for fasta downloading of packages in condaĬonda install mamba -n base -c conda-forge -y & chmod +x miniconda.sh & bash miniconda.sh -b -p minicondaĮxport PATH=$base_dir/miniconda/bin:$PATHĮcho -e "$base_dir/miniconda/etc/profile.d/conda.sh" > ~/.profile ![]() So same rstudio can run on multiple R versions by switching between different R environments in conda.Īlso making a separate R environment is desirable to keep it safe from unintentional upgrade/downgrade of r-base (some tools come with their own r-base version and downgrades r-base).įinally use mamba for quickly installing r packages and resolving dependencies issues. In case if you want to use studio, just activate your R environment in conda and whichever r-base version is available in that environment, studio will pick it up. So here are new steps to install R.Īlso r-studio available on the Anaconda package site downgrades the r-base from 4.0.3 to 3.6 version so I no longer suggest installing r-studio that way. With time as my knowledge improved, I learned that conda-forge is more reliable than installing from private repositories as it is tested and reviewed thoroughly by the Conda team. I invite others to share their experience because installation of R has been a challenge. Maintain a separate file and keep the installation commands saved to use them if the R needs to be reinstalled.
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