[BioC] Errors w/ getBioC(develOK =TRUE) with R2.0 devel

[Matthew Hannah]

I still can't update my developmental packages, even on a fresh install,
any help? Have other people got R2.0 devel, BioC devel on win2k??

Thanks,
Matt


<<<<<<<<<<<<<<<<

Jeff,

I've just downloaded and installed the latest r devel as advised, but
still get exactly the same error message when I try get BioC. So there
must be something else wrong.

I also tried installing R devel in new directory and updating packages
from scratch but no luck.

Plain getBioC() seems to work correctly so must be something with the
develOK... any more ideas?

Cheers,
Matt

Full error -

> source("http://www.bioconductor.org/getBioC.R")
> 
> getBioC(develOK=TRUE)
Running getBioC version 1.2.64....
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.
<https://stat.ethz.ch/mailman/listinfo/bioconductor> 

Loading required package: reposTools 
Loading required package: tools 
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
> traceback()
2: stop(packNameOutput())
1: getBioC(develOK = TRUE)






> -----Original Message-----
> From: Jeff Gentry [mailto:HYPERLINK
"https://stat.ethz.ch/mailman/listinfo/bioconductor"jgentry at
jimmy.harvard.edu <mailto:HYPERLINK> ] 
> Sent: Mittwoch, 1. September 2004 16:10
> To: Matthew Hannah
> Subject: RE: !SPAM? RE: [BioC] Errors w/ getBioC()
> 
> > yes, as in my fist post R 2.0 devel (first release). I 
> understood you 
> > needed to in order to use the devel BioC, or was that only 
> towards the 
> > end of R1.9? When I get time I'll update. Last time I checked c. 1 
> > month ago - the R devel was still the same version. I'll 
> check again.
> 
> R-devel changes constantly.  The version number it lists (in this case
> 2.0) is merely the version number of the next official 
> release - going by version number (again, 2.0) means very 
> little when tracking R-devel ... for instance using an 
> R-devel from 2 weeks ago gives you a radically different 
> version of R then the R-devel from today, despite both of 
> them being listed as "R-2.0".
> 
> Since BioC-devel tracks R-devel, sometimes when things change 
> radically in R-devel, things will need ot change radically in 
> various packages in BioC to compensate for that ... thus the 
> problem you encountered.
> 
> -J
> 
> 
>