Question: problems with getBioC() and getBioC(develOK=TRUE) on R 2.0.0
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gravatar for rgentleman
15.2 years ago by
rgentleman5.5k
United States
rgentleman5.5k wrote:
Yes, and it is rather unfortunate, but actually well documented. Please, if you want to use Bioconductor with R 2.0.0 you *must* use the devel branch, or you can use R 1.9.1 with the release branch. The next release is a few weeks away, but there is a necessary lag between R releases and BioC releases. Robert On Wed, Oct 13, 2004 at 10:28:50AM +0200, Goeman, J.J. (MSTAT) wrote: > Hi, > > I'm trying to install Bioconductor on R 2.0.0 (windows version). I get some > strange errors > > I first try the release version: > > > source("http://www.bioconductor.org/getBioC.R") > > getBioC() > Running getBioC version 1.2.65.... > 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. > > [1] "Installing reposTools ..." > Loading required package: reposTools > Error in library(package, character.only = TRUE, logical = TRUE, > warn.conflicts = warn.conflicts, : > 'reposTools' is not a valid package -- installed < 2.0.0? > > Maybe I shouldn't use the release version on 2.0.0? Then I try the > developmental version: > > > getBioC(develOK=TRUE) > Running getBioC version 1.2.65.... > 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. > > [1] "Installing reposTools ..." > Loading required package: reposTools > Loading required package: tools > [1] "Test:" > NULL > Error in getBioC(develOK = TRUE) : > 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: packages externalVector and rhdf5. > 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 Bio > > > Here's my version info: > > version > _ > platform i386-pc-mingw32 > arch i386 > os mingw32 > system i386, mingw32 > status > major 2 > minor 0.0 > year 2004 > month 10 > day 04 > language R > > What's wrong? > > Kind regards, > > Jelle Goeman > > http://www.math.leidenuniv.nl/~jgoeman > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+
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