I have a severe problem with R at the moment - I call R-scripts from a cluster and use PBS-Arrays in order to use them. Hence, I can formulate a parameter "args" that I define when using qsub.
Everything works out fine until the very last line of the script. Here, a result file should be written, the name of the file is then dependent on args to make the array parts differentiable.
I receive the following error message: "saveRDS(Res,paste0("LBFGS_Ob4_Stand_Test",as.numeric(args[2]),"_Broad.rds")))" Execution halted
This makes zero sense! The third parenthesis you see at the end of the code line is not even written in the script... when I arrays of let's say 5 parts, frequently two will randomly finish successfully, while the rest cancels with this message. I have no idea what is going on.
Here is an example code for my R script (massively reduced):
setwd("/someFolder")
args <- commandArgs(TRUE) # allows the handing over of the array parameter when using qsub
set.seed(as.numeric(args[2])) # usage example for the array parameter (it is always index 2)
Res=matrix(0,1,1) # just as a random example
saveRDS(Res,paste0("LBFGS_Ob4_Stand_Test",as.numeric(args[2]),"_Broad.rds"))
When I define args locally and execute, everything works out fine. This is really infuriating - does anyone have a clue?
Also this is a typical qsub-command I use for the call:
qsub -t 1-5 -l cput=200:00:00 Example.sh
-t defines the array parameter. So here I call the script 5 times and args[2] takes the values from 1 to 5.