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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/leop
ard/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:
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