[BioC] qvalue package hangs R

[Peter Langfelder]

I have seen this happen a few times - in the cases I have seen, the
culprit was an oudated Tcl/Tk library (system library, not R package).
Did you recently update your OS? If so, you may want to search for an
update for the Tcl/Tk library to match your OS version.

HTH,

Peter

On Tue, Nov 6, 2012 at 9:33 PM, Silav Bremos <silavb at yahoo.com> wrote:
> Dear list members
> I am getting the error shown below after installing the package qvalue and calling library(qvalue).
> On another machine doing the same thing made R unresponsive and I had to force quit.
> Both times I started R, installed the package and called the library.
> I used iMac, Mac OS X, version 10.7.5
> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> Can anyone suggest a solution?
>
> Silav
>
> --------------------------------
>
>> biocLite("qvalue")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> Installing package(s) 'qvalue'
> trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/macosx/leopard/contrib/2.15/qvalue_1.32.0.tgz'
> Content type 'application/x-gzip' length 553570 bytes (540 Kb)
> opened URL
> ==================================================
> downloaded 540 Kb
>
> The downloaded binary packages are in .....
>>
>> library(qvalue)
> Loading Tcl/Tk interface ...
>>
>>
>  *** caught segfault ***
> address 0x0, cause 'unknown'
>
> 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()
> Selection:
>         [[alternative HTML version deleted]]
>
>
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