From efg at stowers-institute.org  Thu Sep 27 21:53:47 2007
From: efg at stowers-institute.org (Earl F. Glynn)
Date: Thu, 27 Sep 2007 14:53:47 -0500
Subject: [Rd] R "capabilities" on a cluster node
Message-ID: <fdh1od$sor$1@sea.gmane.org>

R version 2.5.1 (2007-06-27)

I' running some simple R jobs via the  Sun Grid Engine on our Linux cluster 
in preparation for some bigger ones.

I checked R's capabilities on the cluster nodes (after failing to create a 
png file) and am getting the following warning message:
[Run on a cluster node using qrsh:]



> capabilities()

    jpeg      png    tcltk      X11 http/ftp  sockets   libxml     fifo

   FALSE    FALSE    FALSE    FALSE     TRUE     TRUE     TRUE     TRUE

  cledit    iconv      NLS  profmem

    TRUE     TRUE     TRUE    FALSE

Warning message:

unable to load shared library 
'/n/site/inst/Linux-i686/bioinfo/R/2.5.1/lib/R/modules//R_X11.so':

  libSM.so.6: cannot open shared object file: No such file or directory in: 
capabilities()





Is the double slash (//) in the path above a bug in how we've configured R 
here (the /n/site/inst/ directory is shared but is platform specific), or a 
bug in how the capabilities command works?  The file does exist if the 
double slash in the path had not caused the warning above.






How can one programmatically get the info from ?Devices, which appears to be 
dynamic based on one's system?  Is it safe to assume that pdf's or 
postscript files are always available in R since they're not listed in 
capabilities and seem to be shown everywhere under ?Devices ?





Part of the ?Devices output on a cluster node says this:



   The following devices will be available if R was compiled to use

     them:



        *  'X11' The graphics driver for the X11 Window system



        *  'png' PNG bitmap device



        *  'jpeg' JPEG bitmap device



We can just recompile to get png or jpeg support?  Are X11 libraries used on 
cluster nodes while running "headless"?  Can I create pngs or jpegs without 
X11?



Thanks for any advice about this.



efg



Earl F. Glynn

Scientific Programmer
Stowers Institute for Medical Research



[Rd] R "capabilities" on a cluster node
Earl F. Glynn