[R-SIG-Mac] *** caught segfault *** cause 'memory not mapped'
Simon Urbanek
simon.urbanek at r-project.org
Sat Feb 23 14:38:57 CET 2013
On Feb 23, 2013, at 8:24 AM, Vanni Rovera wrote:
> Hi Simon,
>
> I think I have some issue with the tcltk package. If I try to follow your instructions I obtain the following:
>
> > library(tcltk)
> Loading Tcl/Tk interface ...
> >
>
> It doesn't say 'done' after the three points. If then I try to load some other package, I obtain the caugh segfault error.
>
> If instead I try to open the Package Manager I see that the tcltk package has the status 'not loaded'. Then I click on it and the status 'loaded' appears, but R get frozen. It try continuously to load something for some second, and then it get frozen. The only way is to force quit.
>
> Moreover I tried to get Tcl/Tk from this source:
>
> http://www.tcl.tk/software/tcltk/download.html
>
That's not the right place, please install tcltk from CRAN:
http://cran.r-project.org/bin/macosx/tools/tcltk-8.5.5-x11.dmg
Also you make sure you have installed X11 -- I think you mentioned Lion so that would be from
http://xquartz.macosforge.org
Cheers,
Simon
> but I understand nothing, I am not able to install it on my pc, the read me files are incomprehensible to me, too much technical, and they say nothing about installation.
>
> Do you know how to do?
>
> Thank you,
> Vanni
>
> On Tue, Feb 19, 2013 at 11:00 PM, Simon Urbanek <simon.urbanek at r-project.org> wrote:
>
> On Feb 19, 2013, at 4:44 PM, Vanni Rovera wrote:
>
> > Dear Dr. Dalgaard,
> >
> > your suggestion seems to be enlightening. I tried to install the tcltk
> > package and I obtained a very strange thing. I have done the following:
> >
> >> install.packages("tcltk",dependencies=T)
> > --- Please select a CRAN mirror for use in this session ---
> > Warning message:
> > package Œtcltk‚ is not available (for R version 2.15.2)
> >
> > Thus the error seems to be due to the lacking of this package. I tried with
> > two different CRAN mirrors, but the result is the same. Do you know why it
> > says the package is not available?
> >
>
> Because it's part of R, not a separate package on CRAN. It's already installed when you installed R -- just type
> library(tcltk)
>
> Cheers,
> Simon
>
>
>
> > In each case let me say: many thanks!
> >
> > On Mon, Feb 18, 2013 at 1:18 PM, peter dalgaard <pdalgd at gmail.com> wrote:
> >
> >>
> >> 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
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>
> >> --
> >> 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
> >>
> >>
> >
> > [[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
>
>
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