R on ARC

General

Text mode interactive shell

When you start R usual way you get into interactive R shell where you can type commands and get the results back. Like this:

$ module load R/3.6.2
$ R

R version 3.6.2 (2019-12-12) -- "Dark and Stormy Night"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
....
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.info()
                              sysname                               release 
                              "Linux"              "3.10.0-1127.el7.x86_64" 
                              version                              nodename 
"#1 SMP Tue Mar 31 23:36:51 UTC 2020"                                 "arc" 
                              machine                                 login 
                             "x86_64"                            "drozmano" 
                                 user                        effective_user 
                           "drozmano"                            "drozmano" 

> quit()
$

Running R scripts from the command line

In order to run R scripts / programs on ARC as jobs you have to pre-record the commands you want in a text file, for example test.R, and run it as a script non-interactively.

test.R:

cwd = getwd()
cat(" Current Directory: ", cwd, "\n")

t = Sys.time()
cat("      Current time: ", format(t), "\n")

u = Sys.info()["user"]
cat("         User name: ", u, "\n")

There are three ways to run an R script.

From standard input

An R script can be sent to the standard input of the R interactive shell. This is similar to typing the commands in R:

$ R --no-save < test.R

R version 3.6.2 (2019-12-12) -- "Dark and Stormy Night"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> cwd = getwd()
> cat(" Current Directory: ", cwd, "\n")
 Current Directory:  /global/software/src/r/tests 
> 
> t = Sys.time()
> cat("      Current time: ", format(t), "\n")
      Current time:  2020-05-07 15:16:12 
> 
> u = Sys.info()["user"]
> cat("         User name: ", u, "\n")
         User name:  drozmano 
> 
> 

After executing all the commands from the script, R terminates. Note that both the commands and the printed output are shown.

Using CMD BATCH command

An R script can be passed as an argument to the "R CMD BATCH" command. The output does not go to the screen, but is saved to the .Rout file:

$ R CMD BATCH test.R

$ ls -l
-rw-r--r-- 1 drozmano drozmano  176 May  7 15:03 test.R
-rw-r--r-- 1 drozmano drozmano 1121 May  7 15:19 test.Rout

To see the output use the cat or less commands:

$ cat test.Rout

R version 3.6.2 (2019-12-12) -- "Dark and Stormy Night"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> cwd = getwd()
> cat(" Current Directory: ", cwd, "\n")
 Current Directory:  /global/software/src/r/tests 
> 
> t = Sys.time()
> cat("      Current time: ", format(t), "\n")
      Current time:  2020-05-07 15:19:07 
> 
> u = Sys.info()["user"]
> cat("         User name: ", u, "\n")
         User name:  drozmano 
> 
> 
> proc.time()
   user  system elapsed 
  0.219   0.079   0.369 

The output if very similar to the first way, but contains some additional timing information. Again, both the commands and the output are shown.

Using Rscript version of R

Probably the best non-interactive way to run an R script is to use a special non-interactive version of R, Rscript:

$ Rscript test.R
 Current Directory:  /global/software/src/r/tests 
      Current time:  2020-05-07 15:22:17 
         User name:  drozmano 

In this case R does not print any extra information, and only explicitly printed values are shown in the output, the commands themselves are not printed.

Using R on ARC

Like other calculations on ARC systems, R scripts and programs are run by submitting an appropriate script for batch scheduling using the sbatch command. For more information about submitting jobs, see Running jobs article.

R modules

Currently there are several software modules on ARC that provide different versions of R. The versions differ in the release date.

You can see them using the module command:

$ module avail R

----------- /global/software/Modules/3.2.10/modulefiles ---------
R/3.5.3 
R/3.6.2

In addition,

• Module biobuilds/2017.11 provides R v.3.4.2.
• Module bioconda/2018.11 provides R v.3.4.1.

These modules are designed with bioinformatics applications in mind and have a number of specialized R packages preinstalled.

Installed R packages

When installing a new R version, the following packages are typically installed at the same time.

arules          purrr           xaringan        glue            covr            lintr                   
reprex          reticulate      utf8            promises        devtools        cluster         
dbscan          epiR            epitools        glasso          Hmisc           irr             
mi              RSQLite         foreign         openxlsx        dplyr           tidyr           
stringr         stringi         lubridate       ggplot2         ggvis           rgl             
htmlwidgets     googleVis       car             lme4            nlme            mgcv    
randomForest    multcomp        vcd             glmnet          survival        caret           
shiny           rmarkdown       xtable          sp              maptools        maps            
ggmap           zoo             xts             quantmod        Rcpp            data.table              
XML             jsonlite        httr            RcppArmadillo   manipulate      proto           
dichromat       reshape2        mice            rpart           party           caret           
randomForest    nnet            e1071           kernlab         neuralnet       rnn             
h2o             RSNNS           tensorflow      keras           infer           janitor         
DataExplorer    sparklyr        drake           DALEX           raster          gpclib           

# BioConductor 
BiocManager
GenomicFeatures
AnnotationDbi
DESeq
DESeq2
MAST
FEM
DEGseq
EBSeq
DRIMSeq
SGSeqRNASeqR

If you want to use a specific R package with a centrally installed R you can check if it has already been installed before attempting installing it:

$ module load R/3.6.2 

$ R
R version 3.6.2 (2019-12-12) -- "Dark and Stormy Night"
....
Type 'q()' to quit R.

> is.installed <- function(mypkg)is.element(mypkg, installed.packages()[,1])

> is.installed("FEM")
[1] TRUE

> is.installed("e1071")
[1] TRUE

> is.installed("rgdal")
[1] FALSE