[BioC] Repository for Bioconductor annotation packages
dmgatti at email.unc.edu
Sun Jul 16 13:57:46 CEST 2006
"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
> 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
> updating HTML package descriptions
> > dir("C:/Documents and Settings/dd1/Desktop/test")
>  "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!
More information about the Bioconductor