I checked the idrPlotWrapper.sh file and it just renames the two *.sav files to idrPlot-uri.sav and idrPlot-em.sav prior to running the R script on them.

Running batch-consistency-plot.r manually on the two files gives this cryptic output:

null device

but a idrPlot-plot.ps file is actually written. The next step of idrPlotWrapper.sh invokes ps2pdf on it and it works just fine if I run it manually.

Thus it should not be an R problem.


Il 06/12/13 16:15, Björn Grüning ha scritto:

my guess is that some previous steps failed and the assumed tempfile was
not created. That can have many different reasons, probably some R
dependencies are missing. Try to run the generated commandline from your
terminal and catch more error messages.



recently I installed the idr_package from the Galaxy tool-shed but the
tool IDR-plot does not work for my Galaxy instance.

This is the error message:

GPL Ghostscript 8.70: **** Could not open temporary file
**** Unable to open the initial device, quitting.
mv: cannot stat `./idrPlot-plot.pdf': No such file or directory

It seems it doesn't find an expected temporary file. Does anybody have

Many thanks

Federico Zambelli, Ph.D.
Bioinformatics, Evolution and Comparative Genomics Lab
Dept. of Biosciences
University of Milano - Italy

What can be asserted without proof can be dismissed without proof.
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