Thank you both. I use R on linux both remotely (over CGI) and I log in using Exceed from windows. The problem occurs over both. I don't run Xvfb (though I can do as I have done in the past). I have root priveleges so I will look and see what the settings are, though I don't think my pet sys/admin will have changed the defaults....
________________________________ From: [EMAIL PROTECTED] on behalf of Paul Gilbert Sent: Mon 15/10/2007 10:13 PM To: r-help@r-project.org Subject: Re: [R] Error: X11 cannot allocate additional graphics colours. (This could be fixed, it has not happened to me in a long time, but I will mention it mainly because it is not something you are likely to think of.) It used to be that the X colours might be defined by the first application that needed them, so if the systems administrator happened to start up X and mozilla on the server, especially if the server had limited graphics, then that could potentially cause this problem. I never really understood why it would be like this, so probably it is fixed. (This was not an R bug.) Paul Marc Schwartz wrote: > This is not a X server version issue. > > There are Linux system (not R) display settings that will dictate the > number of simultaneous colors that can be displayed. This will be > dependent upon the display resolution defined and the amount of video > RAM on the graphics card. The higher the display resolution the more > video memory it takes since you have more pixels. The more colors you > want to display simultaneously, the more memory per pixel it takes. > > Those concepts, BTW, are the same on Windows and OS X. > > So if you are running directly on the RHEL system, check the display > setting to be sure that it is set for a sufficient number of colors. > This would be an administrative task requiring root privilege. Ideally, > you want so-called TrueColor or "Millions of Colors" to be set. This > requires a pixel depth of 24 bpp or 32 bpp, depending upon VRAM > available. > > On the other hand, if you are connected remotely to the RHEL server, > using ssh and Xvfb on a server that is not running X, then you will need > to adjust (or have the SysAdmin adjust) the -pixdepths setting on the > RHEL server. This controls the 'bpp' available on the server. > > See 'man Xvfb' for more information for the latter scenario. > > HTH, > > Marc Schwartz > > On Mon, 2007-10-15 at 20:53 +0100, michael watson (IAH-C) wrote: >> Thanks for the response... >> >> My confusion about plot stems from the fact I am plotting 82 points >> with 82 colours, so surely all colours get plotted? >> >> As for updating X, I recently installed the latest version of XFree86 >> for my version of linux, RHEL 4. >> >> As for Brian's e-mail you quoted, I do try and look at things like >> that, but I don't know what arguments he refers to: >> >> "Run the X11 device with the arguments stated" >> >> Which arguments, and how do I run my X11 device with them? >> >> I've pretty much had this problem with every version of R on linux, >> all the way from SuSe 8.2 to SuSe 9.2, through to RHEL3 and now RHEL4 >> - I always have this problem. >> >> Perhaps you could tell me which version of X you use to generate 1000 >> colours without getting the error message? I'm sorry, but what i >> would really love is someone to say "RHEL4? Aha , you need to install >> X version foo, available from http://www.foo.com/bar.rpm...) >> >> -----Original Message----- >> From: Charles C. Berry [mailto:[EMAIL PROTECTED] >> Sent: Mon 15/10/2007 7:54 PM >> To: michael watson (IAH-C) >> Cc: r-help@r-project.org >> Subject: Re: [R] Error: X11 cannot allocate additional graphics colours. >> >> >> You knew this? >> >> http://tolstoy.newcastle.edu.au/R/e2/help/06/09/0640.html >> >> I cannot replicate your error. I use n <- 1000 on R-2.6.0, and it still >> works. >> >> >> Only a guess, but maybe your X setup is out of date. Maybe an update would >> help? >> >> As for why axis triggers this, axis uses all the colors, but image only >> uses (something like) those that fall into the bins shown here: >> >> hist( mat, breaks=n ) >> >> >> >> As you see there are usually some empty bins and those colors do not get >> rendered till axis() does its thing. >> >> Chuck >> >> On Mon, 15 Oct 2007, michael watson (IAH-C) wrote: >> >>> Dear All >>> >>> Another one I have touched on before with a much older OS and version. >>> >>> My sessionInfo() is: >>>> sessionInfo() >>> R version 2.5.1 (2007-06-27) >>> i686-redhat-linux-gnu >>> >>> locale: >>> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.U >>> TF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF- >>> 8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_ID >>> ENTIFICATION=C >>> >>> attached base packages: >>> [1] "stats" "graphics" "grDevices" "utils" "datasets" >>> "methods" >>> [7] "base" >>> >>> other attached packages: >>> DetectiV >>> "1.1" >>> >>> I'm getting the following error message when plotting a quite complex >>> graph: >>> >>> Error in axis(side = 2, at = c(min[i] - sptl, max[i] + sptl), labels = >>> NA, : >>> Error: X11 cannot allocate additional graphics colours. >>> Consider using X11 with colortype="pseudo.cube" or "gray". >>> >>> The problem is I only get it under certain circumstances. I have some >>> quite convoluted test code: >>> >>> n <- 82 >>> mat <- matrix(rnorm(n*10), ncol=n) >>> fcolors <- terrain.colors(n) >>> image(z=mat, axes=FALSE) >>> oneis <- 1 / ncol(mat) >>> sptl <- oneis / 3 >>> max <- 1:n * oneis >>> min <- c(0, max[1:length(max)-1]) >>> for (i in 1:n) { >>> axis(side=2, at=c(min[i]-sptl,max[i]+sptl), labels=NA, line=0.9, >>> lwd=3, lty=1, tick=TRUE, tck=0, col=fcolors[i],lend=2) >>> } >>> >>> Now, this code works without error on values of n up to and including >>> 81, but produces the error when it is 82: >>> >>> Error in axis(side = 2, at = c(min[i] - sptl, max[i] + sptl), labels = >>> NA, : >>> Error: X11 cannot allocate additional graphics colours. >>> Consider using X11 with colortype="pseudo.cube" or "gray". >>> >>> The issue I have with it is that if I do a normal plot operation, I >>> don't get the error! >>> >>> n <- 82 >>> fcolors <- terrain.colors(n) >>> plot(1:n,1:n, col=fcolors) >>> >>> Here the plot works, there are no errors and the colours come out fine. >>> But when I use the axis command, in the more complex code above, I get >>> an error. >>> >>> The real question I want to know is how can I enable R (or my OS) to >>> plot a greater number of colours? I can plot 820 colours on R under >>> windows, probably more, I just plucked 820 out of the air. I'm guessing >>> this is because my windows graphics card can produce that many colours, >>> whereas on linux I am limited by what x-windows can produce, but there >>> must be some way of increasing the number of colours I can plot using R >>> under linux...? >>> >>> Many thanks >>> Mick >>> >>> The information contained in this message may be =\ co...{{dropped:20}} >> ______________________________________________ >> R-help@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@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. ==================================================================================== La version française suit le texte anglais. ------------------------------------------------------------------------------------ This email may contain privileged and/or confidential in...{{dropped:26}} ______________________________________________ R-help@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@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.
