R help - Feb 2005 - [Rdev] any way to generate "bitmap" (tif, jpeg, png etc) files in R CMD BATCH

On Fri, 25 Feb 2005, Oleg Sklyar wrote:
> Hi Community,
>
> here is the problem, Linux problem (reported to work on Windows). I need to
> generate graphical output in any of bitmap format under the 'R CMD
BATCH'.
> Whereas the script generating png-s works perfectly in the R session, such 
> things as X11, png and jpeg are not usable in BATCH (they cannot be
switched
> on by --gui-X11 etc) and X11 is prompted to be required for png.
FAQ 7.19 How do I produce PNG graphics in batch mode?

 	-thomas

Please do consult the posting guide and not post to multiple lists.

On Fri, 25 Feb 2005, Oleg Sklyar wrote:
> here is the problem, Linux problem (reported to work on Windows). I need to
> generate graphical output in any of bitmap format under the 'R CMD
BATCH'.
> Whereas the script generating png-s works perfectly in the R session, such 
> things as X11, png and jpeg are not usable in BATCH (they cannot be
switched
> on by --gui-X11 etc) and X11 is prompted to be required for png. At the
same
BATCH is just a script, effectively to do

R --save--restore --save --no-readline < infile > outfile 2>&1

and in earlier versions includes --gui=none.  So if you are running BATCH 
with access to an X server (unusual), you can just use the above.
> time, such things as postscript and pdf, which are generally X-independent 
> work fine. The problem is that as a result I need something previewable in 
> the web browser: png, jpeg. Any suggestions how to proceed?
See also ?bitmap, linked from the help page for png().

-- 
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

Hi Community,

here is the problem, Linux problem (reported to work on Windows). I need 
to generate graphical output in any of bitmap format under the 'R CMD 
BATCH'. Whereas the script generating png-s works perfectly in the R 
session, such things as X11, png and jpeg are not usable in BATCH (they 
cannot be switched on by --gui-X11 etc) and X11 is prompted to be 
required for png. At the same time, such things as postscript and pdf, 
which are generally X-independent work fine. The problem is that as a 
result I need something previewable in the web browser: png, jpeg. Any 
suggestions how to proceed? Generally I could use command line linux 
tools to convert from almost any bitmpa format to the required png or 
jpeg, but it would be nicer to have them as direct R output.

Kind regards
Oleg

-- 
Dr Oleg Sklyar
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, CB10 1SD
England
phone/fax  +44(0)1223 49 4478/4468
e-mail osklyar@ebi.ac.uk

On Fri, 25 Feb 2005, Oleg Sklyar wrote:
> Hi Community,
> 
Use a virtual framebuffer - an example of an earlier question about this 
on the list is:

http://finzi.psych.upenn.edu/R/Rhelp02a/archive/15988.html

(the searchable archives have lots of good tips)
> here is the problem, Linux problem (reported to work on Windows). I need 
> to generate graphical output in any of bitmap format under the 'R CMD 
> BATCH'. Whereas the script generating png-s works perfectly in the R 
> session, such things as X11, png and jpeg are not usable in BATCH (they 
> cannot be switched on by --gui-X11 etc) and X11 is prompted to be 
> required for png. At the same time, such things as postscript and pdf, 
> which are generally X-independent work fine. The problem is that as a 
> result I need something previewable in the web browser: png, jpeg. Any 
> suggestions how to proceed? Generally I could use command line linux 
> tools to convert from almost any bitmpa format to the required png or 
> jpeg, but it would be nicer to have them as direct R output.
> 
> Kind regards
> Oleg
> 
> 
-- 
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Breiviksveien 40, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 93 93
e-mail: Roger.Bivand@nhh.no

On Feb 25, 2005, at 10:05 AM, Oleg Sklyar wrote:
> here is the problem, Linux problem (reported to work on Windows). I 
> need to generate graphical output in any of bitmap format under the 'R 
> CMD BATCH'. Whereas the script generating png-s works perfectly in the 
> R session, such things as X11, png and jpeg are not usable in BATCH
There are other ways, but if you have (or can install) libgd and 
freetype, you may consider using the GDD device - it can produce jpeg, 
png and gif on unix w/o the need of X11. The nice thing about it is 
speed (it doesn't use any external process) and that it uses 
anti-aliasing of both text and lines. It was designed specifically for 
graphics-on-demand on web servers.

Currenly GDD is not on CRAN (yet), but you can get it from
http://www.rosuda.org/R/nightly/
Just make sure that you have libgd and freetype (if you any problems or 
suggestions, please drop me a line).

There are other methods, too, like the bitmap device, which uses gs 
(AFAICS), or you can run virtual X11 to satisfy the devices that 
require X11.

Cheers,
Simon

Oleg, 

Please do not cross-post between r-devel and r-help. It is considered bad
taste. 

On 25 February 2005 at 15:05, Oleg Sklyar wrote:
| Hi Community,
| 
| here is the problem, Linux problem (reported to work on Windows). I need 
| to generate graphical output in any of bitmap format under the 'R CMD 
| BATCH'. Whereas the script generating png-s works perfectly in the R 
| session, such things as X11, png and jpeg are not usable in BATCH (they 
| cannot be switched on by --gui-X11 etc) and X11 is prompted to be 
| required for png. At the same time, such things as postscript and pdf, 
| which are generally X-independent work fine. The problem is that as a 
| result I need something previewable in the web browser: png, jpeg. Any 
| suggestions how to proceed? Generally I could use command line linux 
| tools to convert from almost any bitmpa format to the required png or 
| jpeg, but it would be nicer to have them as direct R output.

This is a FAQ, see

http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-do-I-produce-PNG-graphics-in-batch-mode_003f

and, say, "?bitmap" in R.

Hth, Dirk

-- 
Better to have an approximate answer to the right question than a precise 
answer to the wrong question.  --  John Tukey as quoted by John Chambers