[BioC] affylmGUI problem with tkcmd

[Keith Satterley]

Hi Wonjong,

affylmGUI 1.8.0 was released with R2.4.0 and it does not use tkcmd.
tkcmd was deprecated in <R2.4.0 and made defunct(ie does not work anymore) in 
R2.4.0 and above.

Use biocLite to update affylmGUI and you should have a problem anymore with 
affylmGUI and R2.4.0,

cheers,

Keith


Wonjong Moon wrote:
>  
> 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
> 
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