[R] Qsub - unable to open connection to X11 display

[Bernd Jagla]

That is great, bitmap works.

Now I have the problem that the gray levels are too bright. I tried using
col="black" in the hist function, but that only fills the bars. The tick
marks etc are all in a fainting gray... Any idea on how to get those
darker???

Thanks again,

Bernd

|-----Original Message-----
|From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu]
|Sent: Monday, October 29, 2007 1:26 PM
|To: Duncan Murdoch
|Cc: Bernd Jagla; r-help at r-project.org
|Subject: Re: [R] Qsub - unable to open connection to X11 display
|
|But doesn't it suffice to replace png() by bitmap()?
|b
|
|On Oct 29, 2007, at 12:47 PM, Duncan Murdoch wrote:
|
|> On 10/29/2007 12:06 PM, Bernd Jagla wrote:
|>> Hi there,
|>>
|>>
|>>
|>> I want to run an R script on a cluster with qsub. Obviously I
|>> don't want to
|>> display any X window, but I want use png() or something else to
|>> write out
|>> images.
|>>
|>> Unfortunately I get the following error message:
|>>
|>>
|>>
|>>> png(filename = " ALL.png", width = 480, height = 480, pointsize =
|>>> 12, bg =
|>> "white", res = NA)
|>>
|>> Error in X11(paste("png::", filename, sep = ""), width, height,
|>> pointsize,
|>> :
|>>
|>>         unable to start device PNG
|>>
|>> In addition: Warning message:
|>>
|>> unable to open connection to X11 display ''
|>>
|>> Execution halted
|>>
|>>
|>>
|>> When X11 is working everything works fine.
|>>
|>>
|>>
|>> Is there a way to make this work without X11?
|>>
|>>
|>>
|>> Or, how would I simulate an X11 environment (including the correct
|>> DISPLAY
|>> variable) on a cluster node?
|>
|> Xvfb is the usual trick to fake an X11 environment without a display.
|> (It's a "virtual frame buffer" X server.)  I don't know if PNG works
|> with it or not.
|>
|> Duncan Murdoch
|>>
|>>
|>>
|>> I appreciate any comments or suggestions.
|>>
|>>
|>>
|>> Thanks,
|>>
|>>
|>>
|>> Bernd
|>>
|>>
|>> 	[[alternative HTML version deleted]]
|>>
|>> ______________________________________________
|>> R-help at r-project.org mailing list
|>> https://stat.ethz.ch/mailman/listinfo/r-help
|>> PLEASE do read the posting guide http://www.R-project.org/posting-
|>> guide.html
|>> and provide commented, minimal, self-contained, reproducible code.
|>
|> ______________________________________________
|> R-help at r-project.org mailing list
|> https://stat.ethz.ch/mailman/listinfo/r-help
|> PLEASE do read the posting guide http://www.R-project.org/posting-
|> guide.html
|> and provide commented, minimal, self-contained, reproducible code.