[Bioc-devel] reproducible quartz only PNG Graphics overwrite problem on MacOSX

[Kasper Daniel Hansen]

There is clearly a bug in the quartz driver for png I would say (although when you report it you might want to be careful about where you claim the bug to be since it is not clear that the bug is in R - it could be the rendering code).  I also think that there seems to be a funny issue for type = "cairo" since one can see a difference between the box and the axis line - but that could again be a rendering issue, not an R issue (it would still be nice if it was worked around).  The reproducible example is very nice.

You need to report this to either R-devel or R-sig-mac or to the bug report system.

I would refrain from hardcoding type = "Xlib" in your package code, but that is just my opinion.

Kasper

On Jan 11, 2010, at 14:33 PM, Neumann, Steffen wrote:

> Hi,
> 
> I think this qualifies either as a Bug 
> in the Quartz png() driver, of abuse of plot(0,0, type="n")
> beyond what is specified. See below for the test script.
> 
> Yours,
> Steffen
> 
> -----Original Message-----
> From:	owner-xcms at scripps.edu on behalf of GUILLOU Claude
> Sent:	Mon 1/11/2010 20:04
> To:	xcms at scripps.edu
> Cc:	
> Subject:	Re: EIC png creation problem with diffreport
> 
> Hi Steffen,
> 
> on my Mac test_cairo_plot00x.png and test_Xlib_plot00x.png have the same
> size (4KB) and seem almost identical.
> 
> test_quartz_plot001.png is 16K starts as well as  test_quartz_plot002.png,
> but test_quartz_plot003.png is 20K.
> The overlap of both x and y axes starts with test_quartz_plot002.png.
> 
> Although Cairo and Xlib png outputs look similar, Xlib seem cleaner: the
> segment between the extreme ticks show some overlap but the scale remain
> correct.
> Do you want me to send the images?
> 
> Obviously it seems in our case  we should impose to use type  ="Xlib" for
> X11 display as explained in the png() R documentation.
> 
> Thanks a lot for this hint. That was really annoying. I will correct my
> scripts accordingly and return to the pleasure of using my Macbook for data
> processing :-)
> 
> Claude
> 
> 2010/1/11 Steffen Neumann <sneumann at ipb-halle.de>
> 
>> Hi Claude and Daniel,
>> 
>> could you two Mac guys do me a favor and try the script below ?
>> 
>> It will create 3*3=9 plots, please look at e.g. the *003.png variants
>> and check for our problem. Also check the file sizes
>> between the subtypes, e.g. on Linux test_quartz_plot003.png
>> and test_Xlib_plot003.png have the same size/are identical.
>> 
>> Thanks for your time.
>> 
>> Yours,
>> Steffen
> 
> capabilities("png")
> 
> for (subtype in c("cairo", "Xlib", "quartz")) {
> png(filename=paste("test",subtype,"plot%003d.png", sep="_"),
>     width = 640, height = 480, type=subtype)
> for (i in c(1,2,3)) {
>   plot(0,0, type="n", main=i,
>        xlim=c(-1 + 0.1*i, +1 + 0.1*i),
>        ylim=c(-1 + 0.1*i, +1 + 0.1*i),
>        xlab="xlab",ylab="ylab")
>   points(0.1*i, 0.1*i , col=i)
>   Sys.sleep(1)
> }
> dev.off()
> }
> 
> 
>> 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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