What do you mean by "running R.app directly 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.
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/
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