Dear Wolfgang,

Thank you for your reply. 

This is very strange! I cannot get qvalue to work on any of three different Macs (running either OSX Mountain Lion or Lion.) The error messages are the same on all three machines, even after I uninstall R and re-install.

Here is the full output from my session, including the crash:

> source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.4.7, ?biocLite for help
> biocLite("qvalue")
BioC_mirror: http://bioconductor.org
Using R version 2.15, BiocInstaller version 1.4.7.
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15
Installing package(s) 'qvalue'
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15
trying URL 'http://www.bioconductor.org/packages/2.10/bioc/bin/macosx/leopard/contrib/2.15/qvalue_1.30.0.tgz'
Content type 'application/x-gzip' length 553875 bytes (540 Kb)
opened URL
==================================================
downloaded 540 Kb


The downloaded binary packages are in
/var/folders/yx/wxbjjl592j775_b0fgrdry440000gn/T//RtmpG3UNv7/downloaded_packages
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15
> library(qvalue)
Loading Tcl/Tk interface ...
 *** caught segfault ***
address 0x70000000c, cause 'memory not mapped'

Traceback:
 1: sys.parent()
 2: sys.function(sys.parent())
 3: formals(sys.function(sys.parent()))
 4: match.arg(encoding)
 5: match(match.arg(encoding), c("", "bytes", "UTF-8"))
 6: textConnection("rval", "w", local = TRUE)
 7: capture.output(print(args(sessionInfo)))
 8: paste(capture.output(print(args(sessionInfo))), collapse = "")
 9: gsub("\\s+", " ", paste(capture.output(print(args(sessionInfo))),     collapse = ""))
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        msg <- conditionMessage(e)        sm <- strsplit(msg, "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && identical(getOption("show.error.messages"),         TRUE)) {        cat(msg, file = stderr())      
  .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
14: try(gsub("\\s+", " ", paste(capture.output(print(args(sessionInfo))),     collapse = "")), silent = TRUE)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

> sessionInfo()


________________________________
 From: Wolfgang Huber <whuber@embl.de>
To: bioconductor@r-project.org 
Sent: Wednesday, September 19, 2012 1:47 AM
[[elided Yahoo spam]]

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

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