[R] Error: X11 cannot allocate additional graphics colours.

Mon Oct 15 23:21:50 CEST 2007

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: r-help-bounces at r-project.org on behalf of Paul Gilbert
Sent: Mon 15/10/2007 10:13 PM
To: r-help at 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:cberry at tajo.ucsd.edu]
>> Sent: Mon 15/10/2007 7:54 PM
>> To: michael watson (IAH-C)
>> Cc: r-help at 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}}
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>
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