[Bioc-devel] XCMS in BioC 2.3 [Was: BioC 2.3 release: please commit bug fixes]

[Steffen Neumann]

On Sat, 2008-10-18 at 08:50 -0700, hpages at fhcrc.org wrote:
> Hi developpers,
Hi Herve,

I know you're currently extremely busy getting the BioC release
out of the door. At the end of the mail I have the request 
to set xcms on MacOS to "unsupported" for the upcoming release.

Thanks for fixing a bug in xcmsSet.R:xcmsBoxPlot(),
we currently still have an issue with this function on MacOS: 

http://bioconductor.org/checkResults/2.3/bioc-LATEST/xcms/pitt-buildsrc.html
	Last Changed Rev: 34729 / Revision: 34773
	Error: QuartzBitmap_Output - unable to open file 'example_box/402.png'

The graphic file is only opened for write, and this works fine on e.g. i386:

	ls -l xcms.Rcheck/inst/doc/example_box/402.png 
	-rw-r--r-- sneumann 2451 2008-10-21 20:25 xcms.Rcheck/inst/doc/example_box/402.png

Since I don't have any Mac experience, I am unsure what might be special 
about the Quartz Device, or (less likely) whether this is a symptom 
of R-2.8.0 beta on pitt. Google is no help either, the three hits are 
the error message in the R-SVN repo and our own build report :-(

	http://www.google.de/search?q=Error%3A+QuartzBitmap_Output

Right now  I tried to add a dev.off() call, which seems to have been missing:

	r34799 | s.neumann | 2008-10-21 20:53:31 +0200 (Tue, 21 Oct 2008) | 1 line
	Added missing dev.off(), fixing MacOS now ?

and maybe Quartz is more sensitive to such omissions.

Just to be sure I also removed some tree plotting in the xcmsMSn.Rnw vignette,
which might (?) have caused a bus error with the Rgraphviz call that 
otherwise works fine on the other arches.

Because it is unlikely that we get all MacOS issues fixed in time, 
I'd like to ask for xcms on MacOS to be set to "unsupported", 
so that it can proceed into the BioC-2.3 release.

Yours,
Steffen