[R-SIG-Mac] Mac GUI for 2.9.0 alpha and Rgraphviz

William Revelle lists at revelle.net
Mon Mar 23 20:18:17 CET 2009


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.
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/



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