On 18.03.2012 05:47, Lorenzo Cattarino wrote:
Hi R users,
Working from a PC, I am trying to install the spatstat package on a Unix
cluster. I created the following PBS file to send a job array:
#!/bin/bash -ue
#PBS -m ae
#PBS -M my email
#PBS -J 1-45
#PBS -A my username
#PBS -N job name
#PBS -l resources
#PBS -l walltime
cd $PBS_O_WORKDIR
module load R/2.14.1
R CMD INSTALL -l /path/to/library spatstat
This command installs *a* source package from the current subdirectory
spatstat.
If there is no such directory containing the sources, it won't work.
Either provide the gzipped tarball and give its name or use
install.packages("spatstat") within an R script.
It makes sense to install it outside the parallel processing into a
common directory and just use it in parallel (It is not entirely clear
to me if you are really running the installation on all nodes).
Uwe Ligges
R CMD BATCH /path/to/folder/Script_$PBS_ARRAY_INDEX.R
Obviosuly I failed to understand pag 19 of the R admin manual because I keep
getting the following error message:
Warning: invalid package ‘spatstat’
Error: ERROR: no packages specified
I'd appreciate if you can point me in the right direction
Thanks
Lorenzo
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