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Question: Running R without X11?
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10.0 years ago by
Amy Johnson40
Amy Johnson40 wrote:
modified 10.0 years ago by ALok170 • written 10.0 years ago by Amy Johnson40
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10.0 years ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:
Hi Amy, Our build system here in Seattle faces the same problem: it needs to run 'R CMD build' and 'R CMD check' non-interactively on all the BioC packages. Running these commands will execute the code that is in the vignettes and in the example section of the man pages of every package. For some packages that means that they will try to connect to an X server. One solution to this is to start the X virtual server (Xvfb) and then define the DISPLAY environment variable. From the Bourne shell (bash): PID= Xvfb :$PID -screen 0 800x600x16 & xvfb_pid=$! export DISPLAY=:$PID.0 Then your batch R scripts will be able to connect to this virtual server. That means that the above commands must be executed early enough so that your R scripts actually see the DISPLAY variable in their environment. When you are done, shutdown the X virtual server with: kill$xvfb_pid Hope this helps, H. Amy Johnson wrote: > Hi, I'm trying to run batch R scripts that is triggered online with PHP code: > > exec(R --no-save -q < myscript.r > output.txt 2>&1); > > However, as there are some R libraries, e.g. qvalue, webbioc needs X11 > (tcltk) loaded, I got the following errors: > > Loading Tcl/Tk interface ... Error in dyn.load(file, DLLpath = DLLpath, ...) > : > unable to load shared library > '/usr/local/lib/R/library/tcltk/libs/tcltk.so': > /usr/lib/libXft.so.2: undefined symbol: FT_GlyphSlot_Embolden > Error : .onLoad failed in 'loadNamespace' for 'tcltk' > Error: package/namespace load failed for 'tcltk' > Execution halted > > I have no problem to run the script on the shell when X11 is lauched. How do > I launch X11 before running R scripts in batch from the web? Is there a way > to avoid loading tcltk when loading R libraries like qvalue and webbioc? As > far as I remember, the old versions of qvalue and webbioc do not require > tcltk. > > Thanks > > Amy. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
0
10.0 years ago by
ALok170
ALok170 wrote:

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