Reference R package location when loading on mox

[yaaminiv]

I'm running this methylKit script on mox and I keep running into the following errors when loading all my packages:

I know I installed these packages, so I think they're not being installed from their actual location? BiocManager, devtools, and dplyr are in the /gscratch/srlab/rpackages/ directory:

methylKit is installed in /gscratch/home/yaaminiv/R/x86_64-pc-linux-gnu-library/3.6/:

Is there a way to reference the package's location when loading the package with require()?

[kubu4]

Try setting the library path in an R environment file.

Check the contents of your .Renviron file:

cat ~/.Renviron

This will show you if there's already a set library location. If that file doesn't exist, create it and then add this to it:

R_LIBS="/gscratch/home/yaaminiv/R/"

I'm not entirely sure if that will be recursive or not. You may have to update it to be:

R_LIBS="/gscratch/home/yaaminiv/R/x86_64-pc-linux-gnu-library/3.6/"

[kubu4]

Ugh, sorry, just realized you have packages in two different locations!

If you want to load a specific package from a specific location, you can use this example:

library(mypkg, lib.loc = "/gscratch/home/yaaminiv/R/x86_64-pc-linux-gnu-library/3.6/")

[yaaminiv]

sweet! that argument exists for require() too. I made the following changes:

# Load packages

require(devtools, lib.loc = "/gscratch/srlab/rpackages/")
require(BiocManager, lib.loc = "/gscratch/srlab/rpackages/")
require(methylKit, lib.loc = "/gscratch/home/yaaminiv/R/x86_64-pc-linux-gnu-library/3.6/")
require(dplyr, lib.loc = "/gscratch/srlab/rpackages/")
sessionInfo()

my script isn't running yet, but I will update this discussion once it starts to run.

[kubu4]

Excellent! Looks like script is still running after ~3mins... That's a good sign!