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
[email protected]
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
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
