[BioC] affylmGUI problem with tkcmd

[Wonjong Moon]

I downgraded R 2.4 to 2.3.1 The problem that affylmGUI halted
disappeared. 
I pasted sessionInfo().
Thank you

Wonjong.
------------------------------------------------------------------------
-----------------------------
> library(affylmGUI)
Loading required package: limma
Loading required package: tcltk
Loading required package: affy
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: affyio
Warning message:
'tkcmd' is deprecated.
Use 'tcl' instead.
See help("Deprecated") 
Warning messages:
1: 'tkcmd' is deprecated.
Use 'tcl' instead.
See help("Deprecated") 
2: 'tkcmd' is deprecated.
Use 'tcl' instead.
See help("Deprecated") 

ActiveTcl was found in the Windows Registry (for LOCAL_MACHINE),
installed in
C:\Tcl
This directory will be added to the Tcl search path to enable affylmGUI
to find the Tktable and BWidget extensions.

To begin, type affylmGUI() or use the pull-down menu.

Searching for user-defined affylmGUI commands in
C:/PROGRA~1/R/R-23~1.1/library/affylmGUI/etc ...

Attaching package: 'affylmGUI'


        The following object(s) are masked from package:limma :

         changeLog limmaUsersGuide 

Warning messages:
1: 'tkcmd' is deprecated.
Use 'tcl' instead.
See help("Deprecated") 
2: 'tkcmd' is deprecated.
Use 'tcl' instead.
See help("Deprecated") 
> sessionInfo()
Version 2.3.1 (2006-06-01) 
i386-pc-mingw32 

attached base packages:
[1] "tools"     "tcltk"     "methods"   "stats"     "graphics"
"grDevices"
[7] "utils"     "datasets"  "base"     

other attached packages:
affylmGUI      affy    affyio   Biobase     limma 
  "1.5.4"  "1.10.0"   "1.0.0"  "1.10.1"  "2.7.10" 
> 

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

Message: 10
Date: Mon, 18 Dec 2006 12:57:45 -0800
From: "Wonjong Moon" <wonjong.moon at sbri.org>
Subject: [BioC]  affylmGUI problem with tkcmd
To: <bioconductor at stat.math.ethz.ch>
Message-ID: <A0697D4AA169824A898C69FA2C96FFDE36E8CD at mail01.sbri.org>
Content-Type: text/plain;	charset="us-ascii"

I am using affylmGUI with R2.4.
I have the following error
tkcmd is defunct. Use tcl instead. See help ("Defunct")
After this error, AffylmGUI had no response. I had to quit R.
How can I solve this problem?
Thank you.

Wonjong.



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

Message: 11
Date: Mon, 18 Dec 2006 13:28:50 -0800
From: Seth Falcon <sfalcon at fhcrc.org>
Subject: Re: [BioC] affylmGUI problem with tkcmd
To: bioconductor at stat.math.ethz.ch
Message-ID: <m2fybczyel.fsf at ziti.local>
Content-Type: text/plain; charset=us-ascii

"Wonjong Moon" <wonjong.moon at sbri.org> writes:

> I am using affylmGUI with R2.4.

Please send us the output from sessionInfo().  This will tell us
exactly which version of R 2.4 you have along with which version of
affylmGUI you have installed.

I suspect that your software is out of date.

+ seth