I have a problem when running R scripts on a Unix cluster as a batch job. The issue is when trying to load libraries in the environment, R cannot find the library. I'll give you an example. I'll use a basic R script names sess.R:
print(.libPaths())
library("gtools")
print(sessionInfo())
If I just run this script from the command line using the command:
$ Rscript sess.R
I get the following output:
[1] "/usr/lib64/R/library" "/usr/share/R/library"
R version 3.2.3 (2015-12-10)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.6 (Final)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets base
other attached packages:
[1] gtools_3.5.0
The library "gtools" is correctly loaded, script is working. however if I write a simple batch job (I will include in the job a couple of optional parameters including an error and output file) like:
#!/bin/bash
#SBATCH --output=sess.out
#SBATCH --error=sess.err
Rscript sess.R
The job fails after a second. The two output files I get are of course sess.out and sess.err. Sess.out contains the library directory:
[1] "/usr/lib64/R/library" "/usr/share/R/library"
which seem to be the same as when running Rscript from the command line, so no error there. However there is no printing of the Info Session since the script has been terminated. The sess.err file contains the following error:
Error in library("gtools") : there is no package called ‘gtools’
Execution halted
There, it seems like R cannot find gtools in this situation, even if the library path is the same... Am I missing something? Is there an error I don't see somewhere? Or is it a problems of cluster settings?
