[BioC] problems with getBioC() and getBioC(develOK=TRUE) on R 2.0.0

[Robert Gentleman]

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 at 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 at 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 at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor

-- 
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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B20                            |
| Harvard School of Public Health  email: rgentlem at jimmy.harvard.edu        |
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