Oh, sorry, my mistake, it's still hanging with "testing if packages can be
loaded".
However, after starting R with R --vanilla, I can install Biobase without
problems. I guess there is something wrong with my .Rprofile, let me post
it here for your examination:

history = function(max.show = 25, reverse = FALSE, filter = TRUE, pattern,
...)
{
    file1 <- tempfile("Rrawhist")
    savehistory(file1)
    rawhist <- readLines(file1)
    unlink(file1)

    # the modification to stock
    if (filter)
      rawhist <- rawhist[cumsum(rle(rawhist)$lengths)]
    # end of modification

    if (!missing(pattern))
        rawhist <- unique(grep(pattern, rawhist, value = TRUE,
            ...))
    nlines <- length(rawhist)
    if (nlines) {
        inds <- max(1, nlines - max.show):nlines
        if (reverse)
            inds <- rev(inds)
    }
    else inds <- integer()
    file2 <- tempfile("hist")
    writeLines(rawhist[inds], file2)
    file.show(file2, title = "R History", delete.file = TRUE)
}


options(papersize="a4")
options(editor="vim")
# options(pager="internal")
# R interactive prompt
options(prompt="R>")
options(continue="    ")
# to prefer Compiled HTML
# help options(chmhelp=TRUE)
# to prefer HTML help
# options(htmlhelp=TRUE)
options(tab.width = 4)
options(width = 80)
options(graphics.record=TRUE)
# If you would like to forbid conversion of strings into factors,
# uncomment the following line
options(stringsAsFactors=FALSE)
options(max.print=1000)
# number of digits to display
options(digits=5)
# traceback when error occurs
options(error=traceback)

# set default CRAN repo
r = getOption('repos')
r["CRAN"] = "http://cran-mirror.cs.uu.nl"
options(repos=r)
rm(r)

if(interactive()){
}

.First <- function(){
}

.Last <- function(){
    savehistory()
}




Best regards,

Kaiyin ZHONG
------------------------------
Forensic Molecular Biology, Erasmus MC
k.zhong@erasmusmc.nl
kindlychung@gmail.com


On Tue, Jun 25, 2013 at 6:55 PM, Kaiyin Zhong (Victor Chung) <
k.zhong@erasmusmc.nl> wrote:

>
> On Tue, Jun 25, 2013 at 6:46 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:
>
>> source("http://bioconductor.org/biocLite.R")
>>
>
> ​Problem solved after applying update to some packages, having not idea
> why it worked. My system is Ubuntu 12.04.
>
>
>
> Best regards,
>
> Kaiyin ZHONG
> ------------------------------
> Forensic Molecular Biology, Erasmus MC
> k.zhong@erasmusmc.nl
> kindlychung@gmail.com
>

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