Installing R Package on Mox

[aspencoyle]

Hi!

I'm trying to install a package (specifically pheatmap) onto Mox. I'm trying to use it in the manual module creation script that Laura made - my computer just doesn't have the memory for it.

I loaded R version 3.6.0, ran install.packages("pheatmap"), and then started up the interactive RStudio session and ran library(pheatmap, lib.loc = "/gscratch/srlab/afcoyle/rpackages/")

This returned Error: package or namespace load failed for ‘pheatmap’: package ‘pheatmap’ was installed before R 4.0.0: please re-install it

I then tried to re-download the package using R version 4.0.5 (as described in Yaamini's discussion post here). However, when trying to install using `install.packages("pheatmap", lib="gscratch/srlab/afcoyle/rpackages"), it returned

Warning in install.packages("pheatmap", lib = "gscratch/srlab/afcoyle/rpackages") : lib = "gscratch/srlab/afcoyle/rpackages"' is not writable

I ignored and it returned

The downloaded source packages are in
        '/tmp/RtmpePJGqF/downloaded_packages'
Warning messages:
1: In install.packages("pheatmap", lib = "gscratch/srlab/afcoyle/rpackages") :
  installation of package 'rlang' had non-zero exit status
2: In install.packages("pheatmap", lib = "gscratch/srlab/afcoyle/rpackages") :
  installation of package 'lifecycle' had non-zero exit status
3: In install.packages("pheatmap", lib = "gscratch/srlab/afcoyle/rpackages") :
  installation of package 'scales' had non-zero exit status
4: In install.packages("pheatmap", lib = "gscratch/srlab/afcoyle/rpackages") :
  installation of package 'pheatmap' had non-zero exit status

When I then tried to load using library(pheatmap, lib.loc = "/tmp/RtmpePJGqF/downloaded_packages") it just returned Error in library(pheatmap, lib.loc = "/tmp/RtmpePJGqF/downloaded_packages") : no library trees found in 'lib.loc'

Any advice for how to load this dang package?

[kubu4]

At a minimum, you'll have to install all those other packages that returned errors first, then install pheatmap.

[aspencoyle]

I tried installing those individually, and couldn't install any of them either - all returned some variation of Warning message: In install.packages("rlang", lib = "/gscratch/srlab/afcoyle/rpackages") : installation of package 'rlang' had non-zero exit status

[kubu4]

Didn't notice this part before:

Warning in install.packages("pheatmap", lib = "gscratch/srlab/afcoyle/rpackages") : lib = "gscratch/srlab/afcoyle/rpackages"' is not writable

Try changing permissions on that directory so it's writable.

[kubu4]

Thanks. It's a compiler error. You'll probably need to load a compiler module before trying again. Use module avail to list all modules. See if you can find one that looks like it will match the gnu99 stuff...

I'll try to look in a bit to provide more guidance.

[aspencoyle]

Gotcha, thanks! I just checked, and can't see any modules that match anything close to gnu99.

Also just to give some background, I'm trying to load this package so I can use it in Rstudio on Mox , and remember that early on, you installed the DESeq2 and WGCNA packages for me for that purpose. If that's different from what I've been doing, can you share the method you used to do that?

[kubu4]

Yes, you should be updating (or building a new) Singularity container! Instructions are in Handbook.

[yaaminiv]

Yes, you should be updating (or building a new) Singularity container! Instructions are in Handbook.

FYI I wanted to do something similar to install R packages bsseq and DSS for use on the R Studio server, and building a new Singularity container worked for me!

[aspencoyle]

I did that and it worked perfectly - thanks so much!