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--- r [2021/12/14 18:20]
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+++ r [2022/12/07 16:08]
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 === R ===
-The "R" statistical/programming package is installed on the clusters.  Most add-on packages are in the 4.0.2 version.  Also included are slightly newer 4.1.0 and slightly modified Microsoft R 4.0.2, plus older saved versions.
+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 slightly newer 4.1.0 and R 4.2.2 and slightly modified Microsoft R Open 4.0.2, plus older saved versions.  See [[https://www.analyttica.com/microsoft-r-or-open-source-r-which-suits-you-the-best/|R vs. Microsoft R]].
 <code>
-module load gcc/7.3.1 mkl/19.0.4 R/4.0.2
+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 most easily run through a portal.
+<code>
+module load gcc/9.3.1 mkl/19.0.5 R/4.2.2 rstudio
 </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.
-If you need a new R package, you can ask support to add it to the central installation, or you can add your own packages as shown 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 custome installation is using [[python|conda]], which would be better if you see conflicts, at the cost of installing thousands of files.
+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.
-Before starting, create files ~/.Rprofile and ~/.Renviron as shown, plus other variables you may need.  See [[https://rstats.wtf/r-startup.html|rstats.wtf]].   Some redundant text output has been omitted.
+For this simple installation, before starting, create files ~/.Rprofile and ~/.Renviron as shown, plus other variables you may want to set.  See [[https://rstats.wtf/r-startup.html|rstats.wtf]].   Some redundant text output has been omitted.
+The files ~/.Rprofile and ~/.Renviron should look like this. Also create ``mkdir -p`` the R library directories as shown with the major version of R that you are using (changing 4.2.2 to 4.2 in this case).
 <code>
 pinnacle-l4:feynman:$ cat .Rprofile
@@ Line 17: / Line 21: @@
 pinnacle-l4:feynman:$ cat .Renviron
 R_LIBS_USER=~/R/%p/%v
-pinnacle-l4:feynman:$ module load gcc/7.3.1 mkl/19.0.4 R/4.0.2
+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.  Your packages will be installed into
+a directory in your /home directory.  In this example '/scrfs/storage/feynman/home/R/x86_64-pc-linux-gnu/4.2':
+<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)
-R version 4.0.2 (2020-06-22) -- "Taking Off Again"
 [Previously saved workspace restored]

Arkansas High Performace Computing Center [hpcwiki]

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