Error in as.GType(type) : Cannot convert RGtkBuilder to GType

[Vanslyke Jason - jvansl]

Hi rattle-users,

 

We are trying to get rattle successfully installed on a Linux, RHEL 5 server.

 

Server OS:

Red Hat Enterprise Linux Server release 5.6 (Tikanga)

Linux gcstat1.corp.acxiom.net 2.6.18-238.9.1.el5 #1 SMP Fri Mar 18 12:42:39 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux

 

Config Details:

Server is behind a firewall with NO internet access.

We load R packages from a local mirror.

 

GTK install:

$ rpm -qa | grep -i gtk

pygtk2-2.10.1-12.el5

gtk+-1.2.10-56.el5

usermode-gtk-1.88-3.el5.2

pygtk2-libglade-2.10.1-12.el5

gtk2-devel-2.10.4-21.el5_7.7

authconfig-gtk-5.3.21-6.el5

gtk2-2.10.4-21.el5_7.7

gtk+-devel-1.2.10-56.el5

 

 

In R:

R version 2.13.2 (2011-09-30)

Copyright (C) 2011 The R Foundation for Statistical Computing

ISBN 3-900051-07-0

Platform: x86_64-unknown-linux-gnu (64-bit)

 

> library("rattle")

Rattle: A free graphical interface for data mining with R.

Version 2.6.13 Copyright (c) 2006-2011 Togaware Pty Ltd.

Type 'rattle()' to shake, rattle, and roll your data.

> rattle()

Error in as.GType(type) : Cannot convert RGtkBuilder to GType

 

Inconsistently, we also get this feedback with both library(“RGtk2”) and library("rattle"):

R session is headless; GTK+ not initialized.

 

And, probably of note too, this last message occurred on the RGtk2 package install.

 

Any ideas about how to fix this would be greatly appreciated?

 

Thx, Jason

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[Graham Williams]

Hi Jason,

My first thought is that the version of gtk installed looks too old, and that leads to the GtkBuilder error (which did not exist in the older gtk).

Is there any option to upgrade to a newer version of gtk on RHEL?

Alternatively, an older version of Rattle may work (http://cran.r-project.org/src/contrib/Archive/rattle). Not sure off hand which version might be worth trying - will try to check.

Regards,
Graham

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[Vanslyke Jason - jvansl]

Hi Graham,

 

Thank you for taking time to consider our dilemma!

 

Please correct me if I’m wrong but it is my understanding that it is the RGtk2 package that builds the interface with GTK? If that is true, then if we go to the CRAN page for RGtk2 it spec’s out the following:

SystemRequirements: Cairo (>= 1.0.0), ATK (>= 1.10.0), Pango (>= 1.10.0), GTK+ (>= 2.8.0), GLib (>= 2.8.0)

We have GTK v2.10 installed

 

What I suspect, though, is that my view of how this all works is way too simplistic. I’ve forwarded your email to our Senior Sys Admin Engineer to see if it is possible to upgrade GTK to a newer version level.

 

Thx, Jason

[Graham Williams]

It is probably the use of GtkBuilder by Rattle that is the issue. The old method of using libglade to build GUIs has been superseded by GtkBuilder in the GTK library, and GtkBiulder does not exist in older versions of GTK. Rattle used to use libglade but now uses GtkBuilder.

Regards,
Graham

[Harris Dimitriou]

So is there any way to get past this? I've been searching for a couple of days now and i'm desperate.
My rattleInfo() shows:

> rattleInfo()
Rattle: version 2.6.18 cran 2.6.18
R: version 2.15.0 (2012-03-30) (Revision 58871)

Sysname: Linux
Release: 2.6.18-308.4.1.el5
Version: #1 SMP Tue Apr 17 17:08:00 EDT 2012
Nodename: productrdev
Machine: x86_64
Login: unknown
User: hdimitriou
Effective_user: hdimitriou

Installed Dependencies
RGtk2: version 2.20.24
foreign: version 0.8-49
gWidgetsRGtk2: version 0.0-81
Matrix: version 1.0-6
nnet: version 7.3-1
RGtk2Extras: version 0.5.0
rpart: version 3.1-52
survival: version 2.36-14

That was 10 packages.

Regards,
Graham

Regards,
Graham

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[Harris Dimitriou]

So what can we do to get past this? I've been looking for a solution some days now and i'm desperate..

My rattleInfo() shows:

> rattleInfo()
Rattle: version 2.6.18 cran 2.6.18
R: version 2.15.0 (2012-03-30) (Revision 58871)

Sysname: Linux
Release: 2.6.18-308.4.1.el5
Version: #1 SMP Tue Apr 17 17:08:00 EDT 2012
Nodename: productrdev
Machine: x86_64
Login: unknown
User: hdimitriou
Effective_user: hdimitriou

Installed Dependencies
RGtk2: version 2.20.24
foreign: version 0.8-49
gWidgetsRGtk2: version 0.0-81
Matrix: version 1.0-6
nnet: version 7.3-1
RGtk2Extras: version 0.5.0
rpart: version 3.1-52
survival: version 2.36-14

That was 10 packages.

On Saturday, March 3, 2012 8:37:04 PM UTC+2, Graham Williams wrote:

[Harris Dimitriou]

Is there any update on this issue? How can we get past it?

On Saturday, March 3, 2012 8:37:04 PM UTC+2, Graham Williams wrote:

It is probably the use of GtkBuilder by Rattle that is the issue. The old method of using libglade to build GUIs has been superseded by GtkBuilder in the GTK library, and GtkBiulder does not exist in older versions of GTK. Rattle used to use libglade but now uses GtkBuilder.

Regards,
Graham

On 4 March 2012 03:27, Vanslyke Jason - jvansl  wrote:

Hi Graham,

 

Thank you for taking time to consider our dilemma!

 

Please correct me if I’m wrong but it is my understanding that it is the RGtk2 package that builds the interface with GTK? If that is true, then if we go to the CRAN page for RGtk2 it spec’s out the following:

SystemRequirements: Cairo (>= 1.0.0), ATK (>= 1.10.0), Pango (>= 1.10.0), GTK+ (>= 2.8.0), GLib (>= 2.8.0)

We have GTK v2.10 installed

 

What I suspect, though, is that my view of how this all works is way too simplistic. I’ve forwarded your email to our Senior Sys Admin Engineer to see if it is possible to upgrade GTK to a newer version level.

 

Thx, Jason

 

[Graham Williams]

According to http://rattle.togaware.com/rattle-install-troubleshooting.html
this will often be displayed if you have not restarted R after
installing the GTK+ libraries. It will also be displayed if the GTK+
libraries (which are installed separately to R itself) have not been
installed. Have you check both of these issues?

Regards,
Graham

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[Harris Dimitriou]

Hello Graham,

I really am desperate on this matter, as I have spent countless hours trying to compile GTK libraries without success.

I admit i'm not the most experienced linx-user, however since i need to install RStudio Server,  got to put it on linux.

My best option for my company is Centos 5. 

If I try to install using 'yum install' i end up getting " Error in as.GType(type) : Cannot convert RGtkBuilder to GType".
In order to install RGtk2 package, one must have GTK+ thus, it's not possible not having installed the GTK+ libraries.

As for restarting R, the only way I know to do this is to "q()" or sign out from RStudio. Still, I get the same error.

Do you know if it's possible to make rattle work on linux? I bet it is - how can one achieve this? Whenever I try to install using packages I end up to this error and I can't get past it. Does rattle->rgtk2 need a specific version of GTK+ I can find as a package to install in a linux distribution?

Can you tell me which versions of the dependencies you have on a working linux distributions and if you made it work using packages or just 'configure/make/make install'?

Regards,

Harris Dimitriou

[Graham Williams]

Hi Harris,

Rattle is developed under Linux and many users of Rattle use Linux.
So, yes, it runs under Linux. It works right out of the box on Ubuntu
which uses Gnome by default and hence the Gtk+ libraries are there and
just needs r-base and r-cran-rgtk2 to be installed and all the
dependencies get installed. Similarly Debian. I know many Red Hat
users also and I have set it up for some labs using Centos. So there
is hope!

If you have a choice of OS and you know little of Linux, I would
suggest Ubuntu 12.04 as the best option.

The best thing to diagnose is to try some non-R packages using Gtk -
ggobi or even just gedit might be a start.

In R, load "library(RGtk2)" to make sure that is installed.

Under RStudio, make sure you Quit from R using the File menu.

Try R from an terminal, like the gnome-terminal. Run R from the shell,
then try rattle.

As noted, I've seen the error you are getting when R can't find the
Gtk libraries so I think the clue has to be in that somehow?

Regards,
Graham

[Harris Dimitriou]

Graham,

I made it work on Ubuntu, however I wonder:

Since i'm working on RStudio Server, if I do "rattle()" from a remote server, the rattle window appears on the Ubuntu installation, however the person who is connected via browser to RStudio cannot see it. 

Is this normal? Does this mean that one can't use rattle under RStudio *Server* ?

Regards,

Harris Dimitriou

[Graham Williams]

RStudio Server can only display things it specifically is programmed
to capture, not any general windows that open up on the server side.
You can't run rattle (or any other X windows app) remotely unless you
install an X server on your client machine (which is probably already
running X if the client is Linux, but you need to install an X server
if your client is Windows).

Regards,
Graham

[Harris Dimitriou]

Hello Graham,

Even though i have managed to make rattle work on Ubuntu, I still fail to do so on Centos. I still get the same error "Error in as.GType(type) : Cannot convert RGtkBuilder to GType"

I don't know what else to try - this time my installation did not involve any ./configure , make etc. My only prob was that I got this error "pkgIndex.tcl: too many nested evaluations (infinite loop?)" that had my console stuck on an infinite loop and i had to kill the process.

> rattleInfo()
Rattle: version 2.6.18 cran 2.6.18
R: version 2.15.0 (2012-03-30) (Revision 58871)

Sysname: Linux
Release: 2.6.18-308.4.1.el5
Version: #1 SMP Tue Apr 17 17:08:00 EDT 2012
Nodename: localhost.localdomain
Machine: x86_64
Login: unknown
User: hdimitriou
Effective_user: hdimitriou

Installed Dependencies
RGtk2: version 2.20.24
pmml: version 1.2.30
bitops: version 1.0-4.1
colorspace: version 1.1-1
ada: version 2.0-2
amap: version 0.8-7
arules: version 1.0-8
arulesViz: version 0.1-5
biclust: version 1.0.1
cairoDevice: version 2.19
cba: version 0.2-9
descr: version 0.9.7
doBy: version 4.5-3
e1071: version 1.6
ellipse: version 0.3-7
fEcofin: version 290.76
fBasics: version 2160.81
foreign: version 0.8-50
fpc: version 2.0-3
gdata: version 2.8.2
gplots: version 2.10.1
gtools: version 2.6.2
gWidgetsRGtk2: version 0.0-81
Hmisc: version 3.9-3
kernlab: version 0.9-14
latticist: version 0.9-44
Matrix: version 1.0-6
mice: version 2.12
network: version 1.7-1
nnet: version 7.3-1
odfWeave: version 0.7.17
party: version 1.0-2
playwith: version 0.9-53
psych: version 1.2.4
randomForest: version 4.6-6
RColorBrewer: version 1.0-5
reshape: version 0.8.4
RGtk2Extras: version 0.5.0
ROCR: version 1.0-4
rpart: version 3.1-52
rpart.plot: version 1.2-2
RSvgDevice: version 0.6.4.1
survival: version 2.36-14
timeDate: version 2160.95
verification: version 1.32
weightedKmeans: version 1.2.0
XML: version 3.9-4

That was 49 packages.

I have read about path and zlib on windows, but i don't know if this can be related to Centos 5 as well.
I'd be grateful if you can provide me with any more hints on the issue.

Regards,
Harris Dimitriou

[Graham Williams]

Could this be the issue noted on: http://rattle.togaware.com/rattle-install-troubleshooting.html

Error in as.GType(type) : Cannot convert RGtkBuilder to GType

This will often be displayed if you have not restarted R after installing the GTK+ libraries. It will also be displayed if the GTK+ libraries (which are installed separately to R itself) have not been installed. On MS/Windows this can also occur if there are conflicts in your PATH, such as when there are multiple GTK+ libraries found in your PATH and you are running R32 but it finds GTK64 first.

Graham Williams

http://togaware.com

On 14 March 2013 04:53, Dani <dani...@gmail.com> wrote:

Dear Rattle-user and Graham Williams,

I've installed Rattle on my macs, no problem, and just love the beautiful package and book Graham Williams put together. 

Now, I must make it available to my users in a computing facility, and install rattle in a big machine running Scientific Linux.

After surfing the web for a week, looking for answers, I beg for your help in how to manage the problem with the error: "Error in as.GType(type) : Cannot convert RGtkBuilder to GType"

1. RGtk2 installs fine, either not specifying paths or doing setenv PATH "${PATH}:${GTK_PATH}", where GTK_PATH = /usr/lib/gtk-2.0/2.10.0/

2. I've checked the package and run the test below. The version should not be a problem according to instructions that say anything >=2.8 should work

> require('RGtk2')

Loading required package: RGtk2

> boundGTKVersion() >= "2.12.0"

[1] FALSE

> boundGTKVersion()            

[1] '2.10.4

3. when i start rattle(), i get the Error in as.GType(type) : Cannot convert RGtkBuilder to GType

Other info that may help to understand the problem:

R version 2.15.2 (2012-10-26) -- "Trick or Treat"

Installed Dependencies

RGtk2: version 2.20.25

pmml: version 1.2.34

bitops: version 1.0-5

colorspace: version 1.2-1

ada: version 2.0-3

amap: version 0.8-7

arules: version 1.0-12

biclust: version 1.0.1 upgrade available 1.0.2

cairoDevice: version 2.19

cba: version 0.2-11

descr: version 1.0.1

doBy: version 4.5-5

e1071: version 1.6-1

ellipse: version 0.3-7

fBasics: version 2160.85

foreign: version 0.8-52

fpc: version 2.1-5

gdata: version 2.12.0

ggplot2: version 0.9.3.1

gplots: version 2.11.0

gtools: version 2.7.0

gWidgetsRGtk2: version 0.0-81

hmeasure: version 1.0

Hmisc: version 3.10-1

kernlab: version 0.9-16

latticist: version 0.9-44

Matrix: version 1.0-11

mice: version 2.13

network: version 1.7-1.1

nnet: version 7.3-5

odfWeave: version 0.8.2

party: version 1.0-6

psych: version 1.3.2

randomForest: version 4.6-7

RColorBrewer: version 1.0-5

reshape: version 0.8.4

RGtk2Extras: version 0.6.1

ROCR: version 1.0-4

rpart: version 4.1-0

rpart.plot: version 1.4-3

survival: version 2.37-4

timeDate: version 2160.97

verification: version 1.35

weightedKmeans: version 1.2.0

XML: version 3.95-0.1 upgrade available 3.95-0.2

Your help is super appreciated. thanks, Dani

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[Dani]

Thanks Graham for your response, and the link to common issues. The problem persists, and I did took care of restarting R, even the machine at this point. The machine runs Scientific Linux, rattle installation went all the way through, 

1) Checked the following and they are oka

Cairo (>= 1.0.0) 

ATK (>= 1.10.0) 

Pango (>= 1.10)  

GTK+ (>= 2.10.0)  

GLib (>= 2.10.0) 

2) installed RGtk2 separately successfully, then installed Rattle (only rJava and RWeka failed), then closed R, than came back and the following persists:

>require('rattle')

>rattle()

Error in as.GType(type) : Cannot convert RGtkBuilder to GType

3) Further details from rattleInfo below ***NOTICE that RGtk2 can be loaded with no problems:

> rattle()

Error in as.GType(type) : Cannot convert RGtkBuilder to GType

> require('RGtk2')

> rattleInfo()

Rattle: version 2.6.26 r77 cran 2.6.26

R: version 2.15.2 (2012-10-26) (Revision 61015)

Sysname: Linux

Release: 2.6.18-238.12.1.el5.xxxx

Version: #1 SMP Mon Jul 11 16:15:58 PDT 2011

Nodename: cvrsvc03

Machine: x86_64

Login: ushizima

User: ushizima

Effective_user: ushizima

Installed Dependencies

RGtk2: version 2.20.25

pmml: version 1.2.34

bitops: version 1.0-5

colorspace: version 1.2-1

ada: version 2.0-3

amap: version 0.8-7

arules: version 1.0-12

arulesViz: version 0.1-5

biclust: version 1.0.1 upgrade available 1.0.2

cairoDevice: version 2.19

cba: version 0.2-11

Deducer: version 0.7-6

descr: version 1.0.1

doBy: version 4.5-5 upgrade available 4.5-6

e1071: version 1.6-1

ellipse: version 0.3-7

fBasics: version 2160.85

foreign: version 0.8-52 upgrade available 0.8-53

fpc: version 2.1-5

gdata: version 2.12.0

ggdendro: version 0.1-12

ggplot2: version 0.9.3.1

gplots: version 2.11.0

gtools: version 2.7.0

gWidgetsRGtk2: version 0.0-81

hmeasure: version 1.0

Hmisc: version 3.10-1

kernlab: version 0.9-16 upgrade available 0.9-17

latticist: version 0.9-44

Matrix: version 1.0-11

mice: version 2.13 upgrade available 2.14

network: version 1.7-1.1

nnet: version 7.3-5 upgrade available 7.3-6

odfWeave: version 0.8.2

party: version 1.0-6

playwith: version 0.9-54

psych: version 1.3.2

randomForest: version 4.6-7

RColorBrewer: version 1.0-5

reshape: version 0.8.4

RGtk2Extras: version 0.6.1

ROCR: version 1.0-4

rpart: version 4.1-0 upgrade available 4.1-1

rpart.plot: version 1.4-3

Snowball: version 0.0-9

survival: version 2.37-4

timeDate: version 2160.97

verification: version 1.35

weightedKmeans: version 1.2.0

XML: version 3.95-0.1 upgrade available 3.96-0.2

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--------------

Best regards,

Dani

"The first to apologize is the BRAVEST, the first to forgive is the STRONGEST, and the first to forget is the HAPPIEST." 

P.I.Q.

[Graham Williams]

Hi Dani,

I think the problem is that your GTK 2.10.0 is too old (that is actually quite old). Checking my Ubutnu systems I have:

$ dpkg -s libgtk2.0-0 | grep '^Version'

Version: 2.24.13-0ubuntu2

Graham Williams

http://togaware.com

[Graham Williams]

Thanks for the posts re Rattle and RGtk2 on Mac OS/X. Please report the R and Rattle version (output of rattleInfo()). The latest release is Version 2.6.27 r100:

> install.packages("rattle", repos="http://rattle.togaware.com", type="source")

Also something to try:

> library(rattle)

> crv$rattleUI <- "rattle_macosx.ui"

> rattle()

or 

> library(rattle)

> crv$rattleUI <- "rattle.ui"

> rattle()

It is not yet clear where the problem is (not having access to Mac OS/X does not help the debugging...)

Rattle itself does not install GTK+ but relies on RGtk2 for that - Rattle calls on RGtk2 to be installed which in turn installs GTK+.

Could the problem be that there are multiple versions of GTK installed? Perhaps try removing all GTK installations and then reinstall the latest.

Also, I would be keen to know if the following works:

Graham Williams

http://togaware.com

On 8 April 2013 05:37, Jeff <jmst...@gmail.com> wrote:

On Mac-OS there seems to be a mismatch between the version of GTK+ (namely 2.18.5) that is installed by Rattle versus the version that RGtk2 is actually looking for. Look at this diagnostic:

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 

I've bolded the version of the GTK framework that is being sought. When I go to that directory, there is version 2.18.X11 that was dutifully installed by Rattle, and there is no other version for Rattle to work with. 

[Graham Williams]

Thanks Julian. It seems that the rattle GUI is working for you once you downgraded R. Could the problem be the data you are trying to load? Can you load for example the rattle supplied CSV files?

On 11/04/2013 11:56 AM, "Julian" <julian...@gmail.com> wrote:

Hi Graham,

I'm having the same problem as others in this thread -- unable to get Rattle working after upgrading to R 3.0, even after I then downgraded (tried 2.15.3 and then 2.11.0).

I did my best to start from scratch, i.e. uninstalling GTK files from /library/frameworks, and uninstalling other R versions, but no luck.

I'm able to open Rattle, albeit with a bunch of errors in the background, the first of which is:

Apr 10 16:56:47 Julian-Himess-MacBook-Pro.local R[5825] <Error>: CGContextSetFont: invalid context 0x0

But when I try to open a dataset, I get the following error:

An error occured in the following command:

crs$dataset <- read.csv("file:///Users/julian/Documents/00IRPS/Q62013/Big Data/Datasets/ToyotaCorolla.xls", na.strings=c(".", "NA", "", "?"), strip.white=TRUE, encoding="UTF-8"). 

The error message was:

Error in make.names(col.names, unique = TRUE) : 

  invalid multibyte string at '<d0><cf> ࡱ<1a><e1>'

Any ideas?

Thanks for your help,

Julian

On Monday, April 8, 2013 3:59:34 PM UTC-7, Connie wrote:

I would like to try uninstalling GTK, what would be the best way to do that? I downgraded back to R 2.15-something and it works now, but would like to update R to the latest version. 

On Friday, March 2, 2012 7:59:31 AM UTC-8, Vanslyke Jason - jvansl wrote:

--

[David Winsemius]

On Apr 10, 2013, at 7:47 PM, timeitself wrote:

It is not working yet.

I tried reinstalling GTK, removing RGtk2 and Rattle and reinstalling them. Nothing.

As Jeff mentioned, the problem seems to be in the library pointed in 6): Library not loaded: /Library/Frameworks/GTK+.framework/Versions/2.24.X11/Resources/lib/libgtk-x11-2.0.0.dylib

There is no ...\Versions/2.24.X11 but ...\Versions/2.18.X11

Any idea on how to fix it?

There is a binary at the att.research website:

http://r.research.att.com/libs/GTK_2.24.17-X11.pkg

-- 

David.

Thanks!

David Winsemius

Alameda, CA, USA

[David Winsemius]

(Jumping ahead it appears rattle is expecting to be run in an i386 environment. I wonder if that is even possible in R 3.0.0?)


I have installed the newer version (2.24) of the binary RGtk+ package from the att website. I have downloaded the Mac binary for RGtk2 and in a Terminal session run:

R CMD INSTALL /Users/davidwinsemius/RGtk2_2.20.25.tgz # no error and RGtk2 will load

I then ran:

install.packages("rattle", repos="http://rattle.togaware.com", type="source") # from a GUI session of R 3.0.0 RC

> library(rattle)

Rattle: A free graphical interface for data mining with R.

Version 2.6.27 r100 Copyright (c) 2006-2013 Togaware Pty Ltd.

Type 'rattle()' to shake, rattle, and roll your data.

> crv$rattleUI <- "rattle_macosx.ui"
> rattle()

*** caught segfault ***
address 0x0, cause 'unknown'

Traceback:
1: match(objects(i, all.names = TRUE), ob, nomatch = 0L)
2: checkConflicts(value)
3: attach(NULL, pos = pos, name = attname)
4: attachNamespace(ns, pos = pos, deps)
5: doTryCatch(return(expr), name, parentenv, handler)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: tryCatchList(expr, classes, parentenv, handlers)
8: 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))})
9: try({ ns <- loadNamespace(package, c(which.lib.loc, lib.loc)) env <- attachNamespace(ns, pos = pos, deps)})
10: library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, warn.conflicts = warn.conflicts, quietly = quietly)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch(library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, warn.conflicts = warn.conflicts, quietly = quietly), error = function(e) e)
15: require(XML, quietly = TRUE)
16: loadTooltips()
17: rattle()

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: I picked 3

I had gotten several other similar segfaults on trying to run rattle before this one.

Restarting R:

> library(RGtk2) # to show that RGtk2 could be loaded
> sessionInfo()
R version 3.0.0 RC (2013-03-31 r62463)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grDevices datasets splines graphics utils stats methods base

other attached packages:
[1] RGtk2_2.20.25 rms_3.6-3 Hmisc_3.10-1 survival_2.37-4 sos_1.3-5
[6] brew_1.0-6 lattice_0.20-15

loaded via a namespace (and not attached):
[1] cluster_1.14.4 colorspace_1.2-1 dichromat_2.0-0 digest_0.6.3
[5] ggplot2_0.9.3.1 grid_3.0.0 gtable_0.1.2 labeling_0.1
[9] MASS_7.3-26 munsell_0.4 plyr_1.8 proto_0.3-10
[13] RColorBrewer_1.0-5 reshape2_1.2.2 scales_0.2.3 stringr_0.6.2

> rattleInfo()
Rattle: version 2.6.27 r100 cran 2.6.26
R: version 3.0.0 RC (2013-03-31 r62463) (Revision 62463)

Sysname: Darwin
Release: 10.8.0
Version: Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386
Nodename: david-winsemiuss-mac-pro.local
Machine: i386 # this look wrong. I am in an R64 session.
Login: davidwinsemius
User: davidwinsemius
Effective_user: davidwinsemius

Installed Dependencies
RGtk2: version 2.20.25
pmml: version 1.2.34
bitops: version 1.0-5
colorspace: version 1.2-1
ada: version 2.0-3
amap: version 0.8-7

arules: version 1.0-12 upgrade available 1.0-13
arulesViz: version 0.1-5
biclust: version 1.0.2

cairoDevice: version 2.19
cba: version 0.2-11
Deducer: version 0.7-6
descr: version 1.0.1
doBy: version 4.5-5 upgrade available 4.5-6
e1071: version 1.6-1
ellipse: version 0.3-7
fBasics: version 2160.85

foreign: version 0.8-53

fpc: version 2.1-5
gdata: version 2.12.0
ggdendro: version 0.1-12
ggplot2: version 0.9.3.1
gplots: version 2.11.0

gtools: version 2.7.0 upgrade available 2.7.1

gWidgetsRGtk2: version 0.0-81
hmeasure: version 1.0
Hmisc: version 3.10-1

kernlab: version 0.9-17
latticist: version 0.9-44
Matrix: version 1.0-12
mice: version 2.13 upgrade available 2.15
network: version 1.7-1.1 upgrade available 1.7.2
nnet: version 7.3-6

odfWeave: version 0.8.2
party: version 1.0-6
playwith: version 0.9-54
psych: version 1.3.2
randomForest: version 4.6-7
RColorBrewer: version 1.0-5
reshape: version 0.8.4
RGtk2Extras: version 0.6.1
ROCR: version 1.0-4

RODBC: version 1.3-6
rpart: version 4.1-1
rpart.plot: version 1.4-3
Snowball: version 0.0-8 upgrade available 0.0-9

survival: version 2.37-4
timeDate: version 2160.97
verification: version 1.35
weightedKmeans: version 1.2.0

XML: version 3.95-0.2

That was 57 packages.

Update the packages with either of the following commands:

> install.packages(c("arules", "doBy", "gtools", "mice", "network", "Snowball"))

> install.packages(rattleInfo())

Alternatively update all installed packages:

> update.packages()



I had earlier added the newer GTK+ path to my $PATH:

david-winsemiuss-mac-pro:~ davidwinsemius$ echo $PATH
/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/ImageMagick/bin:/usr/X11/bin:/usr/X11R6/bin:/Library/Frameworks/GTK+.framework/Versions/2.24.X11
david-winsemiuss-mac-pro:~ davidwinsemius$


--
David

On Apr 7, 2013, at 1:02 PM, Graham Williams wrote:

> Thanks for the posts re Rattle and RGtk2 on Mac OS/X. Please report the R and Rattle version (output of rattleInfo()). The latest release is Version 2.6.27 r100:
>
> > install.packages("rattle", repos="http://rattle.togaware.com", type="source")
>
> Also something to try:
>
> > library(rattle)
> > crv$rattleUI <- "rattle_macosx.ui"
> > rattle()
>
> or
>
> > library(rattle)
> > crv$rattleUI <- "rattle.ui"
> > rattle()
>
> It is not yet clear where the problem is (not having access to Mac OS/X does not help the debugging...)
>
> Rattle itself does not install GTK+ but relies on RGtk2 for that - Rattle calls on RGtk2 to be installed which in turn installs GTK+.
>
> Could the problem be that there are multiple versions of GTK installed? Perhaps try removing all GTK installations and then reinstall the latest.
>
> Also, I would be keen to know if the following works:
>
> Graham Williams
> http://togaware.com
>
>
> On 8 April 2013 05:37, Jeff <jmst...@gmail.com> wrote:
> On Mac-OS there seems to be a mismatch between the version of GTK+ (namely 2.18.5) that is installed by Rattle versus the version that RGtk2 is actually looking for. Look at this diagnostic:
>
> 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
>
> I've bolded the version of the GTK framework that is being sought. When I go to that directory, there is version 2.18.X11 that was dutifully installed by Rattle, and there is no other version for Rattle to work with.
>
> --

>