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

Patrick Aboyoun paboyoun at fhcrc.org
Tue Oct 21 21:28:41 CEST 2008

Your efforts weren't in vain. I just tried xcms on pitt (Mac OS X build machine) with the fixes you made and the package built and checked without issue. We'll be able to release xcms in all three package types (source, Windows binary, and Mac OS X binary).


Steffen Neumann wrote:
> 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
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