The double '//' is harmless. What you are failing at is that your R-build-host has the system X11 runtime libraries (libSM.so.6 and friends) while your execution hosts don't have them, and R_X11.so depends on the system X11 libraries which R cannot find on the execution hosts.
So - ask your grid engine administrator to install the X11 runtime libraries on the grid nodes, or ask him/her to build a special version of R which doesn't depend on X11. (the former is the recommended approach, but your admins may think the latter suit their policies). Yes, pdf/ps are always available. (they are just save-to-file devices using R's own pdf/ps writing code). The png/jpeg situation are similar to but separate from X11. On the R build host, you need both the development headers (libpng-devel, libjpeg-devel, libX11-devel & other libX*-devel packages for redhat systems) as well as the runtime libraries (libpng, libjpeg, libX*) to build R with each of the support for these 3. On the execution hosts, you need just the runtime libraries. The reason why you are missing jpeg/png is probably because your build host doesn't have the headers. (it is relatively rare not to have jpeg/png runtime, but the headers are normally not installed). We (used to?) have a similiar situation on our sun grid - my desktop R can do png but our cluster grid R cannot. (ghostscript and a few other software can convert ps/pdf to png so it is not a big loss, just a minor inconvenience). Earl F. Glynn wrote: > 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 > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
