[Bioc-devel] PNG Graphics overwrite problem on MacOSX

[Kasper Daniel Hansen]

Is this only for PNG are does this also seems weird when you use, say, pdf() on OS X?

It is hard to say, but it seems that the title is not just overplotting, but two different texts overplotted.  Are you explicitly drawing the title several times and for the other platforms the text just gets positioned exactly on top of each other, or are you sure you are only drawing the text once (this is impossible to tell from your snippet)?  For the 2nd and 3rd png the title is not only overplotted, but seems to be two different sets of text (note the presence of "1" in the title).  

Kasper


On Jan 11, 2010, at 6:44 AM, Steffen Neumann wrote:

> Hi,
> 
> we're developers of http://bioconductor.org/packages/bioc/html/xcms.html
> and by now more than one user has reported a problem 
> with PNG graphics created by xcms *on MacOSX only*.
> 
> Some examples can be seen at:
> Correct: http://dl.dropbox.com/u/814697/001.png
> Broken: http://dl.dropbox.com/u/814697/002.png
> Broken: http://dl.dropbox.com/u/814697/003.png
> 
> As you see, axis and main title are overdrawn for the 2nd and 4rd plot.
> whereas the actual plot content is fine.
> 
> The graphics are created with approx. the following code snippet:
> 
> plot.xcmsEIC <- function(x, ...) {
>   # Create one plot for each grp
>   for (i in grpidx) {
>        plot(0, 0, type = "n", 
>             main = paste("Extracted ...:", object at mzrange[i,1],
>                          "-", object at mzrange[i,2], "m/z"))
>        points(pts[i], type = "l")
>   } 
> }
> 
> and called via 
> 
>            png(file.path(eicdir, "%003d.png"), width = w, height = h)
>            plot(eics, object, rtrange = eicwidth)
>            dev.off()
> 
> Questions: 
> 1) Has anyone seen such an effect before ? On system configuration is
> described below. 
> 2) Is there a way to see the vignettes created 
> on pit/pelham ?
> 
> Yours,
> Steffen
> 
> On Fri, 2010-01-08 at 20:42 +0100, GUILLOU Claude wrote:
>> I confirm this problem observed by Daniel on the EIC png images.
>> Actually It it was on my Macbook that Steffen observed that problem
> last July.
>> In the mean time we installed XCMS on both Linux and windows machines
> where this bug does not appear.
>> As regards the Mac I could not find a fix. In fact  I hoped that
> installation of Snow Leopard ,  full reinstallation with latest R
> release version  R 2.10.0 GUI 1.30 Leopard build 64-bit of last october
> together with the  latest XCMS package might solve the problem.
> 
> 
> 
> 
> 
> -- 
> IPB Halle                    AG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann          http://www.IPB-Halle.DE
> Weinberg 3                   http://msbi.bic-gh.de
> 06120 Halle                  Tel. +49 (0) 345 5582 - 1470
>                                  +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
> 
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