[BioC] installing the bioconductor package in R 3.0

[Dan Tenenbaum]

On Tue, Jun 25, 2013 at 8:27 AM, Kaiyin Zhong (Victor Chung)
<k.zhong at erasmusmc.nl> wrote:
> I am having some trouble installing the bioconductor package in R, it is
> hanging at the "testing if installed packages can be loaded" part
>
>     source("http://bioconductor.org/biocLite.R")
>     #Installing package into ‘/homexxx/lib/R’
>     #(as ‘lib’ is unspecified)
>     #trying URL
> 'http://www.bioconductor.org/packages/2.12/bioc/src/contrib/BiocInstaller_1.10.2.tar.gz'
>     #Content type 'application/x-gzip' length 13424 bytes (13 Kb)
>     #opened URL
>     #==================================================
>     #downloaded 13 Kb
>     #
>     #* installing *source* package ‘BiocInstaller’ ...
>     #** R
>     #** inst
>     #** preparing package for lazy loading
>     #** help
>     #*** installing help indices
>     #** building package indices
>     #** testing if installed package can be loaded
>     #^C
>     #No traceback available
>     #* removing ‘/home/xxx/lib/R/BiocInstaller’
>     #
>     #The downloaded source packages are in
>     #        ‘/tmp/Rtmpb2nVhP/downloaded_packages’
>     #'biocLite.R' failed to install 'BiocInstaller', use
>     #  'install.packages("BiocInstaller",
>     #  repos="http://www.bioconductor.org/packages/2.12/bioc")'
>
>  Here is R version:
>
> R --version
> R version 3.0.1 (2013-05-16) -- "Good Sport"Copyright (C) 2013 The R
> Foundation for Statistical ComputingPlatform: x86_64-pc-linux-gnu
> (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.You are
> welcome to redistribute it under the terms of the
> GNU General Public License versions 2 or 3.For more information about
> these matters see
> http://www.gnu.org/licenses/.
>
>
> I also tried install.packages("BiocInstaller", repos="
> http://www.bioconductor.org/packages/2.12/bioc") as indicated in the error
> message, but no luck there either.
>

The BiocInstaller package installs itself automatically; what happens
if you try and install a different package; for example:

source("http://bioconductor.org/biocLite.R")
biocLite("Biobase")

?

Dan


> Best regards,
>
> Kaiyin ZHONG
> ------------------------------
> Forensic Molecular Biology, Erasmus MC
> k.zhong at erasmusmc.nl
> kindlychung at gmail.com
>
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>
>
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