Hi,

We have been running DEXSeq on our linux cluster.  To submit jobs to compute nodes we generate a shell script that calls on R to run a file that contains all of the commands to complete the DEXSeq analysis.  The command file has been tested on the cluster through an interactive session using R and works fine within R.  However, when we evoke Rscript to run at the command line or in a shell script we get the following error:
------------------------------------------------------------------------
$Rscript /path/to/DEXSeq_script.R

$ cat DEXseq.e136397
Loading required package: Biobase

Welcome to Bioconductor

 Vignettes contain introductory material. To view, type
 'browseVignettes()'. To cite Bioconductor, see
 'citation("Biobase")' and for packages 'citation("pkgname")'.

Execution halted
--------------------------------------------------------------------------
I would appreciate any thoughts as to why the Rscript approach fails to run DEXSeq from the command line.

Note that we have worked around this problem by running R in an interactive job through Screen on the cluster and this has been a good solution.

Thank you!

best wishes,
Chris


Christopher Gregg, PhD.
Assistant Professor, Neurobiology and Anatomy
Adjunct Professor, Human Genetics
323 Wintrobe Bldg 530
University of Utah, School of Medicine
20 North 1900 East, 401 MREB
Salt Lake City, Utah 84132-3401

phone: (801) 581-8212
fax: (801) 585-9736
------------------------------------
Gregg Lab Website: www.neuro.utah.edu/labs/gregg/index.html<http://www.neuro.utah.edu/labs/gregg/index.html>



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