downloading an entire repository (was Re: [BioC] (no subject))

Adaikalavan Ramasamy ramasamy at
Fri Apr 8 13:34:12 CEST 2005

1) Please use an informative subject line

2) Please search the appropriate FAQ and the mailing archives. The link
that you provide (which does not exist) is for R not BioConductor. The
correct documentation and section can be found at . Next, you can naively
simply do a "wget" on the links given here recursively and extract the
packages you need.

3) I feel this is a better option than above. On an interactive
terminal, try the following :

 z <- repositories()
 # now enter 2 for BioConductor Release 1.5 Source repository
 download.packages2( repEntry=z, destDir="/tmp" )

and hopefully they should be in the /tmp/ directory.

On aside, I do not fully understand why the BioConductor core recommends
on using getBioC.R script from the web instead of hard-coding it into R
but I guess it is because the field is quite dynamic and they want the
changes to be reflected immediately.

Regards, Adai

On Thu, 2005-04-07 at 11:16 -0400, Howard Schumacher wrote:
> Morning everyone.
> I don't know how many of you there are, so to those of you that have 
> n opart in the following matter, I apologize for the intrusion.
> I'm supporting a user who would like to use Bioconductor R in a lab 
> environment.  Your site says "users are encouraged to use getBioC to 
> obtain, install and update their packages".  No thanks.  It doesn't 
> save bandwidth or shorten the download time.  getBioC is also an 
> impairment to using one's admin console, and eliminates any 
> possibility of performing the installation off-line if needs be.
> I'd prefer a web link for "all" packages.  There is no such web link 
> though.  The FAQ didn't explain why.  The 
> page was not 
> available.
> I'd appreciate the link in any form, published or unpublished.
> thanks a mil,
> h

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