How to install a R package into Sandbox?
Step 1:
Go to alphabetical list of all cran r-project packages at cran web page
Step 2:
Find your R package and click the package name to open the package page. For example, Reticulate package
Step 3:
Load the package to your local machine (from Package source line, red arrow in Figure 1)
Fig 1)
Step 4:
Check if all dependences (green arrow) are already in your Sandbox
Step 5:
Open RStudio and type
ListOfPackages = library()$results[,1]
Step 6:
Then go through all dependences (indicated by green arrow in Figure 1) to check if they are already found.
'Name_of_package' %in% ListOfPackages
Example: 'Matrix' %in% ListOfPackages
Step 7:
If the package is found, R returns TRUE. If not, R returns FALSE.
Step 8:
If dependences are not found load them to your local machine as well.
Step 9:
After you have R packages you need on your local machine, load them to FinnGen green bucked by follow uploading instructions in section “How to upload to your own IVM via /finngen/green”.
Step 10:
Install your packages. In Sandbox RStudio console or in R type
install.packages("/finngen/green/reticulate_1.20.tar.gz ", 'path/to_your_gnu_library_folder', repos = NULL, type="source")
Step 11:
You can check the name and path of your gnu library folder with your file manager. It is something like /home/ivm/R/x86_64-pc-linux-gnu-library/4.1.
Step 12:
That’s it. You can now call your library in R / RStudio as usual, e.g. at the console: library(reticulate)
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