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

Martin Maechler maechler at stat.math.ethz.ch
Mon Mar 19 10:27:02 CET 2012


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/..

Martin



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