[Rd] R "capabilities" on a cluster node

From: Earl F. Glynn <efg_at_stowers-institute.org>
Date: Thu, 27 Sep 2007 14:53:47 -0500


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:

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



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