I have the following bash script trying to run it in Linux but I receive an error message that line 31: Rscript: command not found
. Can you please give me an advice if where I am wrong?
#!/bin/bash
#PBS -S /bin/bash
#PBS -N garunsmodel
#PBS -l mem=10g
#PBS -l walltime=02:00:00
#PBS -A improvingherds
#PBS -m ae
nodeDir=`mktemp -d /tmp/phuong.XXXXX`
cp -r /group/dairy/phuongho/garuns $nodeDir
cd $nodeDir
cd garuns
module load gcc vle // this is to load vle platform
rm -rf out
mkdir out
#In garuns.vpz. The output file path has to be changed.
#to an absolute path that's available on the node the script is running.
XXX=`pwd`
sed -i "s|/group/dairy/phuongho/garuns/out|$XXX/out/|" exp/garuns.vpz
Rscript R/repetability.R
DATE=`date +%Y%m%d-%H%M%S`
mkdir "/group/dairy/phuongho/job.$DATE"
cp -r out "/group/dairy/phuongho/job.$DATE"
When I tried to access manually to tmp/phuong.XXXXX/garuns
then run R, it worked just fine.
Best Answer
If R has already been installed, it could be that the
PATH
variable picks up the wrongRScript
? Check withwhich RScript
In this case try
export PATH=/path/to/alternate/r/bin:$PATH
Or try brute-forcing by giving the absolute path when referencingRScript
, e.g.~/R-3.2.5_patched/bin/RScript/R/repetability.R