Seth Falcon wrote on 04/13/2005 10:31 AM: > Hi Simon, > > "Vsevolod (Simon) Ilyushchenko" <simonf@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@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 splicegear. 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 Thanks, Simon -- Simon (Vsevolod ILyushchenko) simonf@cshl.edu http://www.simonf.com Terrorism is a tactic and so to declare war on terrorism is equivalent to Roosevelt's declaring war on blitzkrieg. Zbigniew Brzezinski, U.S. national security advisor, 1977-81

>>>getBioC("Ruuid") > > > getBioC isn't that smart. Try the following instead: > > library(reposTools) > install.packages2("Ruuid") Thanks again. I was missing the glib-devel RPM. Simon -- Simon (Vsevolod ILyushchenko) simonf@cshl.edu http://www.simonf.com Terrorism is a tactic and so to declare war on terrorism is equivalent to Roosevelt's declaring war on blitzkrieg. Zbigniew Brzezinski, U.S. national security advisor, 1977-81