downloading an entire repository (was Re: [BioC] (no subject))
ramasamy at cancer.org.uk
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
http://www.bioconductor.org/faq.html#downloading . 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.
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
> http://cran.r-project.org/bin/macosx/RAqua-FAQ.html page was not
> I'd appreciate the link in any form, published or unpublished.
> thanks a mil,
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