Installing R Packages from GitHub

R packages can be installed from GitHub, and these can be troublesome in terms of their dependencies as they are less community tested. This example shows installation of the TwoSampleMR package from GitHub, with an explanation of why some packages are manually installed.

Note if you are trying to install a package and you get stream of error messages, the first thing to try it to install those packages in mamba with "r-" prepended as below in step 3.

If you haven't already, follow the setup mamba instructions to get mamba working.

1. Log on to an interactive alma session and move somewhere sensible on scratch

   ssh username@alma.icr.ac.uk
   srun --pty --mem=10GB -c 1 -t 30:00:00 -p interactive bash
   cd /data/scratch/somewhere/sensible
   

2. Create and activate a virtual environment

   mamba create --name mamba-TwoSampleMR -c bioconda r-tidyverse r-remotes r-base=4.3
   mamba activate mamba-TwoSampleMR
   

3. Manually install some packages in a dependency safe way

   mamba install r-meta
   mamba install r-nloptr
   mamba install r-lme4
   

4. Install custom package

   R -e 'remotes::install_github("MRCIEU/TwoSampleMR")'