[BioC] tcltk problems

Vsevolod (Simon) Ilyushchenko simonf at cshl.edu
Wed Apr 13 17:26:15 CEST 2005

Seth Falcon wrote on 04/13/2005 10:31 AM:
> Hi Simon,
> "Vsevolod (Simon) Ilyushchenko" <simonf at cshl.edu> writes:
>>After installing R-2.0.1 and reinstalling bioconductor I've started 
>>having problems with tcltk (below).
> Can you report what you get, in R, for capabilities()?
> If tcltk is FALSE, then the issue is related to your new R install.
> You may need to have the tcl-dev and tk-dev (guessing names) rpms
> installed as well before intalling the R rpm.  This would at least be
> true if you wanted to build R from source.

Thanks, Seth - tcltk was FALSE, and installing the RPMs did the trick. I 
did not have to have the tcl/tk packages before (I compile R on a 
machine without them, but use R on other machines where they are present).

I ran into another issue, though: Ruuid was not installed (it's required 
by graph and Rgraphviz). When I tried to reinstall it manually, I got this:

 > getBioC("Ruuid")
Running getBioC version 1.2.69....
If you encounter problems, first make sure that
you are running the latest version of getBioC()
which can be found at: www.bioconductor.org/getBioC.R

Please direct any concerns or questions to bioconductor at stat.math.ethz.ch.

Error in getBioC("Ruuid") :
default:        targets affy, cdna and exprs.
exprs:          packages Biobase, annotate, genefilter, geneploter, edd,
                 ROC, multtest, pamr vsn, and limma.
affy:           packages affy, affydata, annaffy, affyPLM, makecdfenv,
                 and matchprobes plus 'exprs'.
cdna:           packages marray, vsn, plus 'exprs'.
prog:           packages graph, hexbin, externalVector.
graph:          packages graph, Rgraphviz, RBGL
widgets:        packages tkWidgets, widgetTools, DynDoc.
design:         packages daMA and factDesign
externalData:   package externalVector.
database:       AnnBuilder, SAGElyzer, Rdbi and RdbiPgSQL.
analyses:       packages Biobase, ctc, daMA, edd, factDesign,
                 genefilter, geneplotter, globaltest, gpls, limma,
                 RMAGEML, multtest, pamr, wvalue, ROC, siggenes and 
annotation:     packages annotate, AnnBuilder, humanLLMappings
                 KEGG, GO, SNPtools, makecdfenv and ontoTools.
proteomics:     packages gpls, PROcess and apComplex.
arrayCGH:       packages aCGH, DNAcopy, repeated, and rmutil.
all:            All of the Bioconductor packages


Simon (Vsevolod ILyushchenko)   simonf at cshl.edu

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