[R-SIG-Mac] *** caught segfault *** cause 'memory not mapped'

[peter dalgaard]

Looks like an internal bug, but I can't reproduce it using Snow Leopard.
Most likely, the problem sits in the GUI interface R.app.

Some issues have been fixed recently in R.app, so you might try getting it from r.research.att.com and installing it. 

See if the issue disappears. If not, I think we need a little more precise information: Are you loading Rcmdr in the R GUI, then typing into the console (not the Rcmdr script window)? Does the same thing happen if you run R in a terminal? Do you have Rcmdr itself working properly?

On Feb 17, 2013, at 10:33 , Vanni Rovera wrote:

> Hi there,
> 
> I'm running the Mac OS X version 10.7.5, Processor 2.8 Ghz Intel Core i7,
> Memory 4GB 1333 MHz DDR3, and the software is up to date. I get R 2.15.2
> GUI 1.53 Leopard build 64-bit (6335), up to date too. Nevertheless I get a
> strange error when I try to use the R function plotMeans() in the package
> Rcmdr. More precisely, I digit the string 'plotMeans' in the R console, but
> when I add the parenthesis '(' I obtain what follows:
> 
> *** caught segfault ***
> address 0x1000080, 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(plotMeans)))
> 8: paste(capture.output(print(args(plotMeans))), collapse = "")
> 9: gsub("\\s+", " ", paste(capture.output(print(args(plotMeans))),
> 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(plotMeans))),
> 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
> 
>> plotMeans()
> Selection:
> 
> What is this? I tried to write the complete string
> 'plotMeans(dependent_var,independent_var)' and then to paste it in the R
> console, but never changes: I obtain the same error, only with a random
> different address (see the second line of the error). I also tried to
> uninstall the package Rcmdr and then to reinstall it, but again never
> changed.
> 
> I'm not skilled with computer and software issues, I only argued that this
> involves the segmentation of the memory, but I know nothing about this
> technical informatics topics. I don't know how to do. I tried to search
> some online solutions through forums, but I didn't find any help other than
> "check your software is up to date" or "try to uninstall and then reinstall
> your R". If possible, I would prefer some 'constructive' solution as I get
> R for a long time, and uninstalling it I will loose all the packages I
> installed in time.
> 
> Thank you in advance for any help or suggestion,
> Vanni Rovera
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com