Thank you for all your responses. For the font problem, all I need is someone to tell me *which* font libraries I need to install. I can seek local help from my Sys Admin, only they will just ask "Which fonts would you like to install?" and I will be back at square one.
Yesterday, I installed these fonts: http://download.savannah.nongnu.org/releases/freefont/freefont-ttf-20060126.tar.gz And then I installed these fonts: http://www.cl.cam.ac.uk/~mgk25/download/ucs-fonts.tar.gz I know the font problem is on the server as when I run a script on the server itself, the fonts do not appear. The CGI I was referring to is apache and perl on the server, connecting using http and internet explorer to port 80. I realise this is mostly an X/linux problem, but R is looking for some fonts and not finding them and R-help is the only place that I can find out *which* fonts it's looking for. -----Original Message----- From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Sent: 16 October 2007 07:29 To: michael watson (IAH-C) Cc: Paul Gilbert; r-help@r-project.org Subject: Re: [R] Error: X11 cannot allocate additional graphics colours. On Mon, 15 Oct 2007, michael watson (IAH-C) wrote: > 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. The latter may explain the font problem: it is a crucial fact. The X server is running on the Windows box, not on RHEL4, so it is the Exceed settings that count. The penultimate time I tried this, Exceed had no iso10646 fonts. I did update Exceed a couple of months ago, and it found some which worked for ASCII but practically nothing else. I don't know what you mean by 'over CGI'. Some scenarios for running remotely run the X server on the client but most run it on the server: the latter may well have limited bit depth by default, as e.g. Xvfb and rdesktop too. I would be seeking local help on the system setup rather than asking on R-help about X11 issues. > > 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. > -- Brian D. Ripley, [EMAIL PROTECTED] 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 ______________________________________________ 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.
