Arkansas High Performace Computing Center [hpcwiki]

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=== R ===

The "R" statistical/programming package is installed on the clusters.  The greatest number of add-on packages are installed in the 4.0.2 version.  Also included are older saved versions, newer 4.1.0 and R 4.2.2 and slightly modified Microsoft R Open 4.0.2 [[https://web.archive.org/web/20200808203121/https://analyttica.com/microsoft-r-or-open-source-r-which-suits-you-the-best/]].

<code>
module load gcc/9.3.1 mkl/19.0.5 R/4.2.2
</code>
"gcc" module may be omitted unless you are adding R packages (see below).  Substitute R/4.1.0 or MR/4.0.2 as desired for those versions.  You can also add rstudio if you want the gui.  This is best run through a portal (via interactive-apps Desktop or Rstudio GUI).
<code>
module load gcc/9.3.1 mkl/19.0.5 R/4.2.2 rstudio
</code>

If you need a new R package, you can ask hpc-support to add it to the central installation, or you can add your own packages as demonstrated below for the package "broman".  R is not as prone to conflicts as Python, so most packages can be added to the central installation without issues.  Another way to create a custom installation is using [[python|conda]], which would be better if you see conflicts with standard ''R''. It will, however, install many thousands of files in your home.

For this simple installation, before starting, create files ~/.Rprofile and ~/.Renviron as shown, plus  the R library directories (changing full version 4.2.2 to 4.2 in this example) and any of the other R environment variables you may want to set [[https://rstats.wtf/r-startup.html|rstats.wtf]].   

<code>
pinnacle-l4:feynman:$ cat .Rprofile
options(repos = c(CRAN = "https://mirrors.nics.utk.edu/cran"))
pinnacle-l4:feynman:$ cat .Renviron
R_LIBS_USER=~/R/%p/%v
pinnacle-l4:feynman:$ cd;mkdir -p R
pinnacle-l4:feynman:$ mkdir -p R/x86_64-pc-linux-gnu
pinnacle-l4:feynman:$ mkdir -p R/x86_64-pc-linux-gnu/4.2
</code>

With those files in place you can install any R package yourself. Some redundant text output below has been omitted. 

<code>
pinnacle-l4:feynman:$ module load gcc/9.3.1 mkl/19.0.5 R/4.2.2
pinnacle-l4:feynman:$ R
R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

[Previously saved workspace restored]

> install.packages("broman")
Installing package into ‘/scrfs/storage/feynman/home/R/x86_64-pc-linux-gnu/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://mirrors.nics.utk.edu/cran/src/contrib/broman_0.76.tar.gz'
Content type 'application/x-gzip' length 79834 bytes (77 KB)
==================================================
downloaded 77 KB

* installing *source* package ‘broman’ ...
** package ‘broman’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/share/apps/R/R-4.0.2/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c R_init.c -o R_init.o
gcc -I"/share/apps/R/R-4.0.2/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c compare_rows.c -o compare_rows.o
gcc -I"/share/apps/R/R-4.0.2/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c count_close.c -o count_close.o
gcc -I"/share/apps/R/R-4.0.2/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c normalize.c -o normalize.o
gcc -I"/share/apps/R/R-4.0.2/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c runningmean.c -o runningmean.o
gcc -shared -L/share/apps/R/R-4.0.2/lib64/R/lib -L/usr/local/lib64 -o broman.so R_init.o compare_rows.o count_close.o normalize.o runningmean.o -L/share/apps/R/R-4.0.2/lib64/R/lib -lR
installing to /scrfs/storage/feynman/home/R/x86_64-pc-linux-gnu/4.0/00LOCK-broman/00new/broman/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (broman)

The downloaded source packages are in
	‘/tmp/RtmpRuxu78/downloaded_packages’
> quit()
Save workspace image? [y/n/c]: n
pinnacle-l4:feynman:$

</code>
Arkansas High Performace Computing Center [hpcwiki]

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