Entering edit mode
Hi Angel,
As Sean says, it helps you more if you provide sessionInfo() output.
I have been writing some notes recently for people who have had this sort of
problem with limmaGUI or affylmGUI. An extract from these notes is shown below:
************************************************
Tcl/Tk issues with R and limmaGUI and affylmGUI.
================================================
First a note on Terminology:
----------------------------
I use "Tcl/Tk" to refer to the Tool Command Language/Tool Kit package of
software that is installed on the current operating system.
I use "tcltk" to refer to the R package that can be installed into the R
installation which allows R to interface to the Tcl/TK language.
Advice about the Linux OS should probably apply to several other versions of
unix, however Mac OSX is referred to separately.
Tcl/Tk needs to be installed on your OS if you wish to use limmaGUI and
affylmGUI. In fact Tcl/Tk has many packages written for it and to be precise,
the particular Tcl/Tk packages that are called by R packages must be installed
into Tcl/Tk on your computer.
Tcl/Tk packages maybe installed in /usr/lib or /usr/local/lib. For eg. On my
Linux computer, Tktable2.9 is in /usr/lib/ and the BWidget package is located in
/usr/local/lib/.
Tcl/Tk packages on my Linux box use the X11 windowing system.
For MS Windows systems, ActiveState Tcl can be installed in C:\Tcl\bin and
C:\Tcl\bin should be in the path. ActiveState Tcl/Tk uses the MS Windowing
system and does not need an X11 server.
ActiveState Tcl/Tk is available from:
http://www.activestate.com/Products/ActiveTcl/
For Mac OSX, The Tcl/Tk libraries that use the Mac Native Windowing system are
installed on a standard installation of Mac OSX, usually in
MacHDname/System/Library/Tcl. However limmaGUI and affylmGUI do not use these
and require the Tcl/Tk libraries that are linked into the X11 windowing system.
Tcl/Tk for X11 is distributed with R and is installed during the installation of
R for Mac OSX, usually into /usr/local/lib. Tcl/Tk for X11 can be installed
separately if it wasn't installed with R.
R and Tcl/Tk and X11.
=====================
If an R package is going to use Tcl/Tk then the interface package tcltk must be
installed into R. (It is installed with a standard install of R).
If an R package uses Tcl/Tk then Tcl/Tk must be installed on the OS before the R
package can be installed into R. Also the X Server should be running on Mac OSX
and Linux when these packages are installed, which is normal for Linux, but not
for Mac OSX.
On Linux and Mac OSX you will need to have an X11 server running and you will
needed to have defined your DISPLAY environment variable. This can be done in a
bash shell using a command like this:
export DISPLAY=localhost:0
or if your are displaying on another computer, it maybe, for example:
export DISPLAY=pc512.mydomain.edu.au:0
One of these commands should be in your .bashrc file (or equivalent for other
shells). Check the value of your DISPLAY variable on your unix/Mac OSX computer
using
echo $DISPLAY
assuming you are using a bash shell.
Tktable and BWidget:
====================
These two Tcl/Tk packages are needed by affylmGUI and limmaGUI for their
functionality.
BWidget
-------
BWidget is a package written entirely in the tcl scripting language (ie. it is
all text files) and hence is not compiled. Consequently it is the same on any
platform and should be in the Tcl/Tk auto_path.
On my MS Windows computer the bwidget1.7 folder is located in C:\Tcl\lib.
On my Mac OSX computer the folder BWidget-1.7.0 is located in /usr/local/lib.
On my Linux computer, the directory BWidget-1.7.0 is in /usr/local/lib.
To find where these files (if at all), are installed on unix based computers(
including Mac OSX), use the command:
%find / -name "BWi*" -print 2>/dev/null
(Use man on the find command for more detail).
This will list all files on your computer (that you have permission to read) for
files beginning with "BWi".
Tktable
-------
Tktable has some code written in C and hence is a compiled package. It therefore
is different for each type of CPU and OS.
On my MS Windows computer, the "Tktable2.9" directory is located in
"C:\Tcl\lib". It contains the dynamic link library "Tktable29.dll".
On my Mac OSX computer (PPC G4 CPU, OSX 10.4.8) the folder "Tktable2.9" is
located in "/usr/local/lib". The folder "Tktable2.9" contains a dynamic library
called "libTktable2.9.dylib". It is 136,708 bytes in size. This file is
available from:
http://bioinf.wehi.edu.au/affylmGUI/Tktable2.9MacOSX_X11.ppc.zip.
The dynamic library suitable for an Intel based Mac is 143312 bytes in size.
This version is needed for the recently released Intel duo core based Macs. This
file is available from:
http://bioinf.wehi.edu.au/affylmGUI/Tktable2.9MacOSX_X11.intel.tar.gz.
On my unix server (i686 i386 GNU/Linux) the "Tktable2.9" folder is in
"/usr/lib". It contains a "libTktable2.9.so" shared object file. This would be
created when the package was installed from source files.
Note that the *.tcl files on the Mac OSX versions of TkTable2.9 are different
(slightly) from the MS Windows versions of these files. For example,
pkgIndex.tcl refers to the dynamic link library by name, which differs from Mac
to Windows.
Note also that the *.tcl files on the Mac OSX versions of TkTable2.9 are
different (slightly) from the Linux versions of these files. For example,
pkgIndex.tcl refers to the dynamic link library by name, which differs from Mac
to Linux.
To find if these files, are installed on unix based computers(including Mac
OSX), use the command:
%find / -name "Tkt*" -print 2>/dev/null
(Use man on the find command for more detail).
This will list all files on your computer (that you have permission to read) for
files beginning with "Tkt".
************************************************
Hope this helps.
PS. I've made an educated guess with one or two of the statements above about
Linux and MacOSX, if others, more knowledgeable than I, see anything I should
correct, would you please email me and I'll publish my complete note soon on the
list,
cheers,
Keith
Angel Reyes wrote:
> Hello,
>
> I am getting the following message when I try to run The R Project
for
> Statistical Computing.
>
> Cannot find Tcl/TK pckage "Bwidget" limmaGUI cannot continue.
>
> How can I correct this.
>
>
> Thank You
> Angel L. Reyes
> Senior Computer Support Specialist
> Information Technology
> 212-327-8984
>
> [[alternative HTML version deleted]]
>
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