Dear Ben (and others who responded),

I figured out my problem! I did not have the Tcl/Tk libraries installed. They used to be included as part of the OS X installation, but now they are not. So now they must be installed separately.

For others who encounter my problem:
First download the *signed* version of the latest R installation package. Then, if you look very carefully at the same screen where you downloaded the latest R installation package, you'll see the following text: "This package only contains the R framework, 32-bit GUI (R.app) and 64-bit GUI (R64.app). For Tcl/Tk libraries (needed if you want to use tcltk) and GNU Fortran (needed if you want to compile packages from sources that contain FORTRAN code) please see the tools directory." Click on the link in that text to download the package containing the Tcl/Tk libraries, and then install the package.

Voila! It will work!

I thank all of you who took the time to respond to my query. You got me pointed in the right direction. Your feedback was vital.

Sincerely,
Josh


________________________________
 From: Benilton Carvalho <beniltoncarvalho@gmail.com>
To: Wolfgang Huber <whuber@embl.de> 
Cc: bioconductor@r-project.org 
Sent: Wednesday, September 19, 2012 4:52 AM
[[elided Yahoo spam]]

Idem for a machine on 10.6.8 running the latest stable R release.

> sessionInfo()
R version 2.15.1 Patched (2012-09-03 r60555)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] qvalue_1.30.0       RColorBrewer_1.0-5  BiocInstaller_1.4.7

loaded via a namespace (and not attached):
[1] tcltk_2.15.1 tools_2.15.1


On 19 September 2012 07:47, Wolfgang Huber <whuber@embl.de> wrote:
> 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.
>>
[[elided Yahoo spam]]
>>
>> 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
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor

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