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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor