[R] jpeg in batch mode
Prof Brian Ripley
ripley at stats.ox.ac.uk
Thu Feb 21 22:29:47 CET 2008
On Thu, 21 Feb 2008, Elizabeth Purdom wrote:
> I am running some commands in batch on a server that I SSH into; some of
> the commands call jpeg(). If I continue to stay signed on (with my
> xwindows working on my machine) then the jpeg() command works (with a
> single caveat, below). If I leave it and sign off (with a nohup command
> in front of my BATCH) then jpeg gives me an error like this:
> Error in X11(paste("jpeg::", quality, ":", filename, sep = ""), width, :
> unable to start device JPEG
> In addition: Warning message:
> could not open JPEG file xyz.jpeg
> I don't have this problem with pdf(); but the images I want to draw are
> really massive in terms of the number of points/images so they take
> forever to open in adobe (as well as being HUGE) so I'd like them in
> jpeg. Can I get around this somehow? I saw other people posted similar
> problems, but saw no solutions.
Well, this is documented and there are solutions even on the jpeg() help
page and mamy more in the archives. Basically
1) Use a Xvfb X server
2) Use bitmap()
3) Use an alternative such as GDD or Cairo (but for me those do a poor job
on symbol fonts).
The good news is that R 2.7.0 will have a better solution, producing JPEGs
without using X11.
> R-2.6.0, GNU/Linux
> My caveat from above about the jpeg working as long as I'm signed on:
> one time I got the mysterious error:
> Error in jpeg("~/batch5Effect/ProbPbsets_summaryHeatmaps%03d.jpeg",
> height = 1200, :
> X11 fatal IO error: please save work and shut down R
> Even though it had just correctly done this same basic command a few
> lines back. I redid it (without changing anything that I was aware of)
> and it worked fine. So I don't think it's related.
That's an X11 problem, not an R problem.
> R-help at r-project.org mailing list
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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