[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:
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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