Problems encountered using affy in R
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@maryelogueucdie-204
Last seen 7.1 years ago
Hello everyone, I am new to R. I have downloaded R 1.6.2 from CRAN. Then I followed the instructions on the bioconductor website for windows (I'm using windows 2000 professional) and typed in getBioC(libName="affy"). I answered yes to download XML version >= 0.92-2. It then said that the following packages were not updated: annotate, genefilter, geneplotter, edd, ROC, multtest, affy. vsn, Biobase, tkWidgets. I then installed affy using the install package option in R. I then loaded affy by typing library(affy) and tried to read in some files by typing affyfiles <- ReadAffy (widget=T). It gave the following message: Loading required package: tkWidgets Loading required package: tcltk Error in firstlib(which.lib.loc, package): TCD_library is not set Error in eval(expr, envir, enclos): tcl/tk package 'tcltk' not available -- forget about 'tkWidgets'! I don't know what to do now so your help would be very much appreciated. Regards, Mary Logue Mary Logue, Department of Biochemistry, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4
Biobase annotate genefilter multtest ROC tkWidgets affy vsn Biobase annotate genefilter • 716 views
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@rafael-a-irizarry-205
Last seen 7.1 years ago
from the email archive: >From merk@ibe.med.uni-muenchen.de Tue Mar 4 09:17:04 2003 Date: Tue, 04 Mar 2003 13:54:53 +0100 From: Sylvia Merk <merk@ibe.med.uni-muenchen.de> To: bioconductor@stat.math.ethz.ch Subject: [BioC] Re: memory problem with Affy Hi Philippe, for your tkWidgets-Problem: A few weeks ago I had the same problem. I installed ActiveTcl8.3.5.0 to c:\Tcl Then I set the environment variable TCL_LIBRARY to the path C:\Tcl\lib\tcl8.3 After that tkWidgets worked. greetings, sylvia _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor On Wed, 5 Mar 2003 mary.e.logue@ucd.ie wrote: > Hello everyone, > > I am new to R. I have downloaded R 1.6.2 from CRAN. Then I followed > the instructions on the bioconductor website for windows (I'm using > windows 2000 professional) and typed in getBioC(libName="affy"). I > answered yes to download XML version >= 0.92-2. It then said that the > following packages were not updated: annotate, genefilter, geneplotter, > edd, ROC, multtest, affy. vsn, Biobase, tkWidgets. > > I then installed affy using the install package option in R. > > I then loaded affy by typing library(affy) and tried to read in some files > by typing affyfiles <- ReadAffy (widget=T). It gave the following > message: > > Loading required package: tkWidgets > Loading required package: tcltk > Error in firstlib(which.lib.loc, package): > TCD_library is not set > Error in eval(expr, envir, enclos): tcl/tk package 'tcltk' not available -- > forget about 'tkWidgets'! > > > I don't know what to do now so your help would be very much > appreciated. > > Regards, > > Mary Logue > > > Mary Logue, > Department of Biochemistry, > Conway Institute of Biomolecular and Biomedical Research, > University College Dublin, > Belfield, > Dublin 4 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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@vincent-j-carey-jr-4
Last seen 3 days ago
United States
> by typing affyfiles <- ReadAffy (widget=T). It gave the following > message: > > Loading required package: tkWidgets > Loading required package: tcltk > Error in firstlib(which.lib.loc, package): > TCD_library is not set Good description of setup, but the error is more likely TCL_LIBRARY is not set This means that your environment variable that identifies the location of the Tcl/Tk distribution is not properly set. If you can find your Tcl/Tk distribution (or install one) and use the cascade (from windows start button) Settings/Control Panel/System/Advanced/Environment Variables to set the variable and then re-start R you will probably get better results. For a typical installation C:\Tcl\lib is the correct value. Newer versions of R1.7.0 for windows will come with Tcl/Tk bundled in so that this problem should go away in the relatively near future.
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