[Bioc-devel] BioC Release 2.0 REMINDER

Seth Falcon sfalcon at fhcrc.org
Tue Apr 10 15:25:21 CEST 2007

Hi Martin,

Martin Maechler <maechler at stat.math.ethz.ch> writes:
> I wonder however, why
>   biocLite(.)  or biocinstalll(.)

biocinstall is an implementation detail (perhaps we should hide it
better) and should never be called directly.

> do only partially work for me.
> I get
>   Running biocinstall version 2.0.3 with R version 2.5.0 (currently in alpha)
>   Your version of R requires version 2.0 of Bioconductor (currently in alpha too).
>   Will install the following packages:
>    [1] "affy"        "affydata"    "affyPLM"     "annaffy"     "annotate"   
>    [6] "Biobase"     "Biostrings"  "DynDoc"      "gcrma"       "genefilter" 
>   [11] "geneplotter" "hgu95av2"    "limma"       "marray"      "matchprobes"
>   [16] "multtest"    "ROC"         "vsn"         "xtable"     
>   Please wait...
>   Warning: unable to access index for repository http://bioconductor.org/packages/2.0/bioc/src/contrib
>   Warning: unable to access index for repository http://bioconductor.org/packages/2.0/data/annotation/src/contrib
>   ...............
> and in the end nothing is installed.
> Maybe you need to update the index file there,
> or was I supposed not to use biocinstall() for alpha/beta
> testing ?

Can you verify that you can connect to the bioconductor.org website?
biocLite worked for me on the 8th (from Switzerland, even) and seems
to be working for me this morning in Seattle.

It would also help to know what getOption("pkgType") says for you.

Can others confirm difficulty using biocLite?


+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center

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