[Bioc-devel] XCMS in BioC 2.3 [Was: BioC 2.3 release: please commit bug fixes]
sneumann at ipb-halle.de
Tue Oct 21 21:00:28 CEST 2008
On Sat, 2008-10-18 at 08:50 -0700, hpages at fhcrc.org wrote:
> Hi developpers,
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:
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 :-(
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.
More information about the Bioc-devel