[BioC] Bioconductor's qvalue package not working on Macs!
beniltoncarvalho at gmail.com
Wed Sep 19 11:52:04 CEST 2012
Idem for a machine on 10.6.8 running the latest stable R release.
R version 2.15.1 Patched (2012-09-03 r60555)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
attached base packages:
 stats graphics grDevices datasets utils methods base
other attached packages:
 qvalue_1.30.0 RColorBrewer_1.0-5 BiocInstaller_1.4.7
loaded via a namespace (and not attached):
 tcltk_2.15.1 tools_2.15.1
On 19 September 2012 07:47, Wolfgang Huber <whuber at embl.de> wrote:
> 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?
> R Under development (unstable) (2012-09-18 r60759)
> Platform: x86_64-apple-darwin12.1.0/x86_64 (64-bit)
>  C
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  qvalue_1.31.0 BiocInstaller_1.5.12 fortunes_1.5-0
> loaded via a namespace (and not attached):
>  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
> 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()"
>> 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
> Best wishes
> Wolfgang Huber
> Bioconductor mailing list
> Bioconductor at r-project.org
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