[BioC] installing the bioconductor package in R 3.0

[Dan Tenenbaum]

On Tue, Jun 25, 2013 at 10:04 AM, Kaiyin Zhong (Victor Chung)
<k.zhong at erasmusmc.nl> wrote:
> 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:
>

Without needing to look at your .Rprofile I can tell you there is
something wrong with it, since installing packages works with
--vanilla.

I'm not sure what the problem is; maybe the CRAN mirror you've chosen is down?
You can try with a fresh (empty) .Rprofile and add one line/function
at a time and see where it breaks.

Dan


> 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 at erasmusmc.nl
> kindlychung at gmail.com
>
>
> On Tue, Jun 25, 2013 at 6:55 PM, Kaiyin Zhong (Victor Chung) <
> k.zhong at erasmusmc.nl> wrote:
>
>>
>> On Tue, Jun 25, 2013 at 6:46 PM, Dan Tenenbaum <dtenenba at 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 at erasmusmc.nl
>> kindlychung at gmail.com
>>
>
>         [[alternative HTML version deleted]]
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor