[BioC] Repository for Bioconductor annotation packages

[Daniel Gatti]

"James W. MacDonald" wrote:
>>biocLite installs in the R library directory on the server.  
> 
> 
> That's not true. biocLite() is simply a wrapper to install.packages() 
> that among other things sets the correct repositories to iterate 
> through. All you have to do is pass a lib argument and it will install 
> wherever you want, just like install.packages().
> 
>  > biocLite("affy", lib="C:/Documents and Settings/dd1/Desktop/test")
> Running getBioC version 0.1.6 with R version 2.3.0
> Running biocinstall version 1.8.4 with R version 2.3.0
> Your version of R requires version 1.8 of Bioconductor.
> trying URL 
> 'http://bioconductor.org/packages/1.8/bioc/bin/windows/contrib/2.3/affy_1.10.0.zip'
> Content type 'application/zip' length 2230953 bytes
> opened URL
> downloaded 2178Kb
> 
> package 'affy' successfully unpacked and MD5 sums checked
> 
> The downloaded packages are in
>          C:\Documents and Settings\dd1\Local 
> Settings\Temp\RtmpM8Sbqb\downloaded_packages
> updating HTML package descriptions
>  > dir("C:/Documents and Settings/dd1/Desktop/test")
> [1] "affy"

Got it.  Thanks.  I had never noticed that biocLite() took any arguments 
other than the packages to install.  The advantage of using biodLite() 
is that it gave me a more meanigful error message.  Whereas 
install.packages() just said "can't find repository", biocLite() said 
that it couldn't communicate on http:port 80.  This led me to enquire 
with the system admins for the server and they infomred me that they 
block port 80.  So now I know the root of the problem.

http://bioconductor.org/packages/1.8/data/annotation/ is the correct 
directory for the annotation files.  And I can download them on another 
machine into my UNIX home directory and then install from zip files.

Thanks to all!
Dan