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

[peter dalgaard]

On Feb 17, 2013, at 17:01 , Vanni Rovera wrote:

> I tried with the R.app GUI you suggested, but nothing has changed.
> 
> I try to answer to your questions: I always work directly in the R console, typing the commands and then pressing the Enter key. I never use scripts. Now I tried to write a script using the dataset persproject. The script was as follows:
> 
> attach(persproject)
> library(Rcmdr)
> plotMeans(Recall,Dosage)
> 
> When I selected 'Execute' R went down and remained like frozen. I had to force quit. If instead I type directly in the R console I obtain the following:
> 
> > attach(persproject)
> > library(Rcmdr)
> Carico il pacchetto richiesto: car
> Carico il pacchetto richiesto: MASS
> Carico il pacchetto richiesto: nnet
> Loading Tcl/Tk interface ... 
> > plotMeans(
> 


I can't reproduce this on 10.7.5/R 2.15.2. The only thing I can spot is that I have

> library(Rcmdr)
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Loading required package: car
Loading required package: MASS
Loading required package: nnet

where you seem to be missing the tcltk bit.

Otherwise, it could be something in the Italian translations, or maybe there is something with the persproject data set that you are not telling us. Or there could be a problem with your Tcl/Tk libraries.

Did you try starting R from a terminal? (As in Launchpad -> Utilities -> Terminal, then type R at the prompt).


> and here, when I type '(', the *** caught segfault*** error appears. Moreover I tried some other function of the Rcmdr package, and all of them produce the same error. It always appears when I open the parenthesis '('. I specify that some days ago I uninstalled the package Rcmdr and try to reinstall it, downloading it from a different CRAN mirror; but nothing has changed.
> 
> On Sun, Feb 17, 2013 at 4:21 PM, peter dalgaard <pdalgd at gmail.com> wrote:
> 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]]
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> --
> 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
> 
> 
> 
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> 
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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