[R-SIG-Mac] *** caught segfault *** cause 'memory not mapped'
Simon Urbanek
simon.urbanek at r-project.org
Tue Feb 19 23:00:51 CET 2013
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]]
>
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