[BioC] Bioconductor's qvalue package not working on Macs!

[Wolfgang Huber]

Josh,

the qvalue package and in particular the code you list below works 
perfectly well (the GUI opens and responds) on the machine I have just 
tested it with (OS X 10.8.1 (12B19)). Perhaps your installation of R is 
broken?

 > sessionInfo()
R Under development (unstable) (2012-09-18 r60759)
Platform: x86_64-apple-darwin12.1.0/x86_64 (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] qvalue_1.31.0        BiocInstaller_1.5.12 fortunes_1.5-0

loaded via a namespace (and not attached):
[1] tcltk_2.16.0 tools_2.16.0

PS in·duc·tion; noun, the inference of a general statement from a finite 
set of examples.

	Best wishes
	Wolfgang
	

Sep/18/12 10:29 PM, Josh B scripsit:
> Dear listserv members,
>
> I have discovered that the qvalue package no longer works on Macs, at
> least those running OS X Lion or Mountain Lion. I have tried multiple
> different machines, and in each case, the qvalue package fails to
> load properly and R crashes when I attempt to use the "qvalue()"
> command.
>
> Is there something I am doing wrong, or can someone verify that I am
> right? This is a serious problem for me.
>
> Here is the exact code I am running (please note that changing the
> Bioconductor mirror does NOT help):
>
> Source("http://bioconductor.org/biocLite.R") biocLite("qvalue") #this
> generates many indecipherable warnings library(qvalue) #now this part
> coming up here is the specific part that causes the crash:
>
> qvalue() #boom, that's it, R shuts down. #Please note that changing
> the Bioconductor mirror does not help:
>
> chooseBioCmirror() #choose whichever mirror you like
>
> Source("http://bioconductor.org/biocLite.R") biocLite("qvalue")
> #again, many indecipherable warnings library(qvalue) qvalue() #boom,
> R shuts down again, same as before
>
> If you run my code, above, you will find this exact same problem on
> ANY Mac running OSX Lion or Mountain Lion. But is there any way to
> get qvalue working on my Mac? I very much need it.
>
> Thank you in advance!
>
> Sincerely, Josh Banta, Ph.D
>
> Assistant Professor Department of Biology The University of Texas at
> Tyler Tyler, TX 75799 Tel: (903) 565-5655
> http://plantevolutionaryecology.org
>

-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber