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.
