R help - Jul 2003 - using getBioC()

Hello,
    I am trying to install R/Bioconductor on a G4 Mac running OS X.  I 
have successfully installed R so that a command window opens, but 
installation of the downloaded Bioconductor package is giving me 
trouble.  After copying/pasting the Bioconductor installation script 
in to the window and typing getBioC(), I get the following error 
message.

"Error in getBioC():  R not currently configured to allow HTTP 
connections, which is required for getBioC to work properly."

   Any suggestions would be greatly appreciated.

Sincerely,

Carol Foster


-- 
Carol M. Foster, Ph.D.
Postdoctoral Research Associate
Department of Genetics, Development, and Cell Biology
353 Bessey Hall
Iowa State University
Ames, Iowa  50011  USA
Phone: (515) 294-3509, Fax: (515) 294-1337
Email: cmfoster at iastate.edu

There was a post in the Bioconductor mailing list regarding the same
error message:

https://stat.ethz.ch/pipermail/bioconductor/2003-February/000854.html

One possible solution mentioned there was to remove the line in
getBioC() that checks the capabilities. Since it seems likely that you
do have access to http from your machine, even if the R version doesn't
know that, then you could try saving the script to a local file, edit it
to change the line that reads:

http <- as.logical(capabilities(what="http/ftp"))

to:
##http <- as.logical(capabilities(what="http/ftp"))
http <- TRUE

then source your local copy of the file, and finally try re-running the
function.

I don't understand why the capability would be detected as FALSE. I
built my version on Linux, but never made any explicit selection of the
capability. I do see some other items listed by the capabilities()
function that I did configure. (It wouldn't be some oddity of the Mac OS
would it?...)

Anyway, I hope this helps.

Cheers,

Bill Barnard

On Tue, 2003-07-22 at 16:43, Carol Foster wrote:
> Hello,
>     I am trying to install R/Bioconductor on a G4 Mac running OS X.  I 
> have successfully installed R so that a command window opens, but 
> installation of the downloaded Bioconductor package is giving me 
> trouble.  After copying/pasting the Bioconductor installation script 
> in to the window and typing getBioC(), I get the following error 
> message.
> 
> "Error in getBioC():  R not currently configured to allow HTTP 
> connections, which is required for getBioC to work properly."
> 
>    Any suggestions would be greatly appreciated.
> 
> Sincerely,
> 
> Carol Foster
>