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

[Benilton Carvalho]

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 at 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.
>>
>> 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
>
>
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