[R-SIG-Mac] Mac GUI for 2.9.0 alpha and Rgraphviz
Simon Urbanek
simon.urbanek at r-project.org
Mon Mar 23 21:44:29 CET 2009
On Mar 23, 2009, at 15:18 , William Revelle wrote:
> Kasper,
>
> At 9:39 AM -0700 3/23/09, Kasper Daniel Hansen wrote:
>> What do you mean by "running R.app directly from the X11 window"?
>
> My naming mistake. I was running R itself from the X11 window.
>>
>> We would also like to get some details on what version of Rgraphviz
>> you are using as well as what version of Graphviz you are using and
>> how you installed the two versions? graphvizVersion() might be
>> useful. It might also be useful to update to the latest version of
>> Rgraphviz in the devel branch of Bioconductor, it has version
>> 1.21.9 and install it from source.
>
>> graphvizVersion()
> [1] "2.20.3"
>
> I installed it by hand. Copying it over from the R2.8.1 library
> into the 2.9.0 (alpha) library.
That won't work. The paths to libR are entirely different - you have
to re-compile between R 2.8.x and R 2.9.x.
Cheers,
S
>
> I did that because the R Gui that I downloaded yesterday (and again
> this morning) does not seem to allow me to use the package installer
> or manager)
> (error message:
> Error: could not find function "browse.pkgs"
> Error: could not find function "package.manager"
>
>
> For R in X11 the sessionInfo shows
>> sessionInfo()
> R version 2.9.0 alpha (2009-03-22 r48193)
> i386-apple-darwin8.11.1
>
> locale:
> C
>
> attached base packages:
> [1] grid stats graphics grDevices utils datasets
> methods [8] base
> other attached packages:
> [1] MASS_7.2-46 Rgraphviz_1.20.0 graph_1.20.0
> [4] GPArotation_2008.05-1 psych_1.0-67
> loaded via a namespace (and not attached):
> [1] cluster_1.11.12 tools_2.9.0
> For R.app (GUI) the sessionInfo() is
>
>> sessionInfo()
> R version 2.9.0 alpha (2009-03-22 r48193)
> i386-apple-darwin8.11.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
> other attached packages:
> [1] psych_1.0-67
>>
> The Gui is
> R.app GUI 1.28-devel (5355 Leopard build 32-bit), S.Urbanek &
> S.M.Iacus, © R Foundation for Statistical Computing, 2008
>
> Best,
>
> Bill
>
>>
>> Kasper
>>
>>
>> On Mar 23, 2009, at 6:52 , William Revelle wrote:
>>
>>> Dear Simon and other Mac Gui developers,
>>>
>>> I have been testing the psych package for 2.9.0 and have found an
>>> unrelated problem with the GUI when it is interacting with
>>> Rgraphviz.
>>>
>>> If I run R.app directly from the X11 window, I can load and run
>>> Rgraphviz with no problem.
>>>
>>> But, when I try loading the Rgraphviz package by
>>>> library(Rgraphviz) , the Gui crashes;
>>>
>>> *** caught segfault ***
>>> address 0x656c7574, cause 'memory not mapped'
>>>
>>> Traceback:
>>> 1: .Call("Rgraphviz_init", PACKAGE = "Rgraphviz")
>>> 2: fun(...)
>>> 3: doTryCatch(return(expr), name, parentenv, handler)
>>> 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>>> 5: tryCatchList(expr, classes, parentenv, handlers)
>>> 6: 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]] if (14L + nchar(dcall, type =
>>> "w") + nchar(sm[1L], type = "w") > LONG) prefix <-
>>> paste(prefix, "\n ", sep = "") } else prefix <- "Error : "
>>> msg <- paste(prefix, conditionMessage(e), "\n", sep =
>>> "") .Internal(seterrmessage(msg[1L])) if (!silent &&
>>> identical(getOption("show.error.messages"), TRUE)) { cat(msg, file
>>> = stderr()) .Internal(printDeferredWarnings()) }
>>> invisible(structure(msg, class = "try-error"))})
>>> 7: try({ fun(...) NULL})
>>> 8: runHook(".onLoad", package, env, package.lib, package)
>>> 9: loadNamespace(package, c(which.lib.loc, lib.loc), keep.source =
>>> keep.source)
>>> 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]] if (14L + nchar(dcall, type =
>>> "w") + nchar(sm[1L], type = "w") > LONG) prefix <-
>>> paste(prefix, "\n ", sep = "") } else prefix <- "Error : "
>>> msg <- paste(prefix, conditionMessage(e), "\n", sep =
>>> "") .Internal(seterrmessage(msg[1L])) if (!silent &&
>>> identical(getOption("show.error.messages"), TRUE)) { cat(msg, file
>>> = stderr()) .Internal(printDeferredWarnings()) }
>>> invisible(structure(msg, class = "try-error"))})
>>> 14: try({ ns <- loadNamespace(package, c(which.lib.loc,
>>> lib.loc), keep.source = keep.source) dataPath <-
>>> file.path(which.lib.loc, package, "data") env <-
>>> attachNamespace(ns, pos = pos, dataPath = dataPath)})
>>> 15: library(Rgraphviz)
>>>
>>> my sessionInfo is
>>>
>>> R version 2.9.0 alpha (2009-03-21 r48181)
>>> i386-apple-darwin8.11.1
>>>
>>> locale:
>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>> other attached packages:
>>> [1] psych_1.0-67
>>>
>>> R 2.8.1 GUI 1.27 Tiger build 32-bit (5372)
>>>
>>>
>>> (I have the identical problem with
>>> R.app GUI 1.28-devel (5355 Leopard build 32-bit),)
>>>
>>> In that this does not happen in the R.app itself, but with the Mac
>>> Gui, I am reporting it here.
>>>
>>> Thanks again for the wonderful GUI. My students who use PCs are
>>> very jealous.
>>>
>>> Bill
>>>
>>>
>>>
>>> --
>>> William Revelle http://personality-project.org/revelle.html
>>> Professor http://personality-project.org/personality.html
>>> Department of Psychology http://www.wcas.northwestern.edu/psych/
>>> Northwestern University http://www.northwestern.edu/
>>> Attend ISSID/ARP:2009 http://issid.org/issid.2009/
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
>
> --
> William Revelle http://personality-project.org/revelle.html
> Professor http://personality-project.org/personality.html
> Department of Psychology http://www.wcas.northwestern.edu/psych/
> Northwestern University http://www.northwestern.edu/
> Attend ISSID/ARP:2009 http://issid.org/issid.2009/
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
>
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