[BioC] biocLite() does not accept 'lib.loc' for updating

[Dan Tenenbaum]

Hi Martin,

On Mon, Mar 19, 2012 at 2:27 AM, Martin Maechler
<maechler at stat.math.ethz.ch> wrote:
> For updating bioconductor,
>
> we recommend
>
>   biocLite(character(), ask=FALSE)
>
> However, when I (have several versions of R and bioconductor and)
> keep my bioconductor packages in a specific library not first in
> my .libPaths(),
> I want to specify   ' lib.loc = <my-bioc-library> '
>
> but that works {via "..."} only for else { ... } clause in
> biocLite(),
> not for the first one :
>
>> biocLite
> function (pkgs = c("Biobase", "IRanges", "AnnotationDbi"), suppressUpdates = FALSE,
>    suppressAutoUpdate = FALSE, ask = TRUE, ...)
> {
>    svnRev <- as.integer(R.Version()$`svn rev`)
>    if (svnRev < 55733)
>        .stop("R-2.14 r55733 or newer required.")
>    if (!suppressAutoUpdate && !bioconductorPackageIsCurrent()) {
>        on.exit(updateBioconductorPackage(pkgs, ask = ask, suppressUpdates = suppressUpdates,
>            ...))
>    }
>    else {
>        biocLiteInstall(pkgs, ask = ask, suppressUpdates = suppressUpdates,
>            ...)
>    }
> }
> <environment: namespace:BiocInstaller>
>
>> maintainer("BiocInstaller")
> [1] "Biocore Team c/o BioC user list\n<bioconductor at stat.math.ethz.ch>"
>>
>
> --------
>
> Thank you for fixing/workaround/..

This is fixed in BiocInstaller 1.3.8, which will be available tomorrow.
Dan


>
> Martin
>
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