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installation problems GTK+ package

Hi all,

I just tried to install metaXCMS on my new Mac (OSX 10.8.3, R3.0.0). I did however not succeed. I followed the installation guidelines given on the scripps website. I guess it has something to do with the loading of the GTK+ package: after installing this package after loading the cairodevice, other packages in R keep on asking to install the GTK+ package and metaXCMS does not install. This is what I get:


'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so, 6): Library not loaded: /Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so
  Reason: image not found
trying URL 'http://r.research.att.com/libs/GTK_2.18.5-X11.pkg'
Content type 'text/plain' length 59914166 bytes (57.1 Mb)
opened URL
=================================================
downloaded 57.1 Mb

Learn more about GTK+ at http://www.gtk.org
If the package still does not load, please ensure that GTK+ is installed and that it is on your PATH environment variable
IN ANY CASE, RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN
starting httpd help server ... done
Loading required package: sp
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RGtk2/libs/RGtk2.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RGtk2/libs/RGtk2.so, 6): Library not loaded: /Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RGtk2/libs/RGtk2.so
  Reason: image not found
In addition: Warning message:
In fun(libname, pkgname) :
  Failed to load cairoDevice, attempting to install itError in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so, 6): Library not loaded: /Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so
  Reason: image not found

Learn more about GTK+ at http://www.gtk.org
If the package still does not load, please ensure that GTK+ is installed and that it is on your PATH environment variable
IN ANY CASE, RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN
Loading required package: xlsxjars
Loading required package: rJava
* installing *source* package ‘metaXCMS’ ...
** R
** inst
** preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so, 6): Library not loaded: /Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so
  Reason: image not found
Warning in fun(libname, pkgname) :
  Failed to load cairoDevice, attempting to install itError in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so, 6): Library not loaded: /Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so
  Reason: image not found

Please install GTK+ from http://r.research.att.com/libs/GTK_2.18.5-X11.pkg
If the package still does not load, please ensure that GTK+ is installed and that it is on your PATH environment variable
IN ANY CASE, RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RGtk2/libs/RGtk2.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RGtk2/libs/RGtk2.so, 6): Library not loaded: /Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RGtk2/libs/RGtk2.so
  Reason: image not found
Warning: Failed to load RGtk2 dynamic library, attempting to install it.
Please install GTK+ from http://r.research.att.com/libs/GTK_2.18.5-X11.pkg
If the package still does not load, please ensure that GTK+ is installed and that it is on your PATH environment variable
IN ANY CASE, RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so, 6): Library not loaded: /Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so
  Reason: image not found
Warning in fun(libname, pkgname) :
  Failed to load cairoDevice, attempting to install itError in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so, 6): Library not loaded: /Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/cairoDevice/libs/cairoDevice.so
  Reason: image not found

Please install GTK+ from http://r.research.att.com/libs/GTK_2.18.5-X11.pkg
If the package still does not load, please ensure that GTK+ is installed and that it is on your PATH environment variable
IN ANY CASE, RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RGtk2/libs/RGtk2.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RGtk2/libs/RGtk2.so, 6): Library not loaded: /Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RGtk2/libs/RGtk2.so
  Reason: image not found
Warning: Failed to load RGtk2 dynamic library, attempting to install it.
Please install GTK+ from http://r.research.att.com/libs/GTK_2.18.5-X11.pkg
If the package still does not load, please ensure that GTK+ is installed and that it is on your PATH environment variable
IN ANY CASE, RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN
Error : .onAttach failed in attachNamespace() for 'metaXCMS', details:
  call: .Call(name, ..., PACKAGE = PACKAGE)
  error: "S_gtk_window_new" not available for .Call() for package "RGtk2"
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/metaXCMS’
 

Thanks,
Koen

Re: installation problems GTK+ package

Reply #1
Did you install GTK+ from http://r.research.att.com/libs/GTK_2.18.5-X11.pkg ?

Also make sure that the cairoDevice package is installed.

you need to be able to load the packages
Code: [Select]
library(cairoDevice)
library(RGtk2)

Re: installation problems GTK+ package

Reply #2
Hi Ralf,
I got around the problem of R repeatedly asking for the installation of GTK+. It turned out to be a version problem: On OSX 10.8.3 you need the GTK_2.24.17-X11 package (not the GTK 2.18.5-X11 that automatically loads. I still do not succeed in installing metaXCMS. It tends to install, as I just see a flash of metaXCMS, but this window quickly disappears after opening, generating in the following error message:

Loading required package: sp
* installing *source* package ‘metaXCMS’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
sh: line 1:  775 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --slave 2>&1 < /var/folders/0s/ym2z5zqs7n301k1l1zvpb4dr0000gp/T//Rtmp6EkMJr/file3053799c556


 *** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
 1: .Call(name, ..., PACKAGE = PACKAGE)
 2: .RGtkCall("S_gtk_main_iteration", PACKAGE = "RGtk2")
 3: gtkMainIteration()
 4: gtkWait()
 5: metaxcms()
 6: fun(libname, pkgname)
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch(fun(libname, pkgname), error = identity)
11: runHook(".onAttach", ns, dirname(nspath), nsname)
12: attachNamespace(ns, pos = pos, deps)
13: doTryCatch(return(expr), name, parentenv, handler)
14: tryCatchOne(expr, names, parentenv, handlers[[1L]])
15: tryCatchList(expr, classes, parentenv, handlers)
16: 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))})
17: try({    ns <- loadNamespace(package, c(which.lib.loc, lib.loc))    env <- attachNamespace(ns, pos = pos, deps)})
18: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)
19: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
20: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/metaXCMS’

,    character.only = TRUE, logical.return = TRUE))
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: 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))})
25: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,    character.only = TRUE, logical.return = TRUE)))
26: tools:::.test_load_package("metaXCMS", "/Library/Frameworks/R.framework/Versions/3.0/Resources/library")
aborting ...


Any idea what is going wrong here?

Thanks,
Koen

Re: installation problems GTK+ package

Reply #3
R is crashing with a segfault when trying to run GTK.
I guess I would try to completely remove GTK+ and RGtk and then reinstall, maybe even on on a new R installation.
If that doesn't help you would need to contact the maintainer of the RGtk2 package.

We also have an alpha-release of the online version of metaXCMS available if you want to try it I can give you some details via PM.