[Bioc-devel] PNG Graphics overwrite problem on MacOSX

Steffen Neumann sneumann at ipb-halle.de
Mon Jan 11 12:44:07 CET 2010


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)

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 ?


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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