[BioC] Installing bioconductor from behind a firewall

[Jose Duarte]

I've come across this problem in the past to install BioC in our linux
cluster (in a private network). The best solution I found was mirroring
the whole www.bioconductor.org web site with wget and changing the
pointer for www.bioconductor.org to the internal mirrored server.

Of course this is useful if what you want to install is most of the
packages of BioC (as we did here). This way you don't have to worry
about dependencies or other issues you might come across by scripting
your own installation of BioC with "R CMD install". 

Hope this helps

Jose


On Mon, 2004-08-16 at 15:35, James MacDonald wrote:
> You can download all the packages you are interested in at
> www.bioconductor.org, and then install using R CMD install.
> 
> Best,
> 
> Jim
> 
> 
> 
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> 
> >>> Michael Hoffman <hoffman at ebi.ac.uk> 08/13/04 10:59AM >>>
> I have been trying to install Bioconductor on a HP alpha running OSF1
> from behind a firewall that blocks outgoing port 80 and have had
> little success. We are required to use an HTTP proxy for all of our
> outgoing requests.
> 
> Using getBioC() with method="wget" does not work because getBioC()
> tries to get many files using url() instead of download.file(), and so
> the specified method is not used.
> 
> Is there an easy way to download the packages ahead of time and
> install them without needing an Internet connection during the install
> process?