[BioC] biocLite to install a local binary sourced package for mac

[Martin Morgan]

Hi Weiwei,

(For those stumbling across this thread: the strongly recommended way
to install Bioconductor packages is described on the bioconductor web
page; generally, do NOT install from a manually downloaded file,
unless you want to make life more complicated than it needs to be).

To install a package from disk, use install.packages with
repos=NULL. See the help pages of install.packages for details, and
perhaps the source code for biocLite and biocinstall, both downloaded
when you source('http://bioconductor.org/biocLite.R').

'Automatically unzip' is a configuration issue with the software used
to download the file from the internet, e.g., your web browser
automatically processing files with a .tgz extension. Configure your
software not to do this.

I think it's not a good idea to ask what to do with a .tgz file that
has been expanded -- you might be able to use 'install.packages' or
the command line R CMD INSTALL, or perhaps zip it back up using
standard tools ('tar' in your case), and the success of these methods
might depend on the content of the package (e.g., compiled C code,
versus lazy loaded data, vs, ...) the operating system, etc. In the
end you'll spend more time figuring out and confirming that you've
done the right thing than you will by downloading the files again. You
might investigate download.packages and its 'type' option as a way of
creating a snapshot of the appropriate files.

Martin

"Weiwei Shi" <helprhelp at gmail.com> writes:

> Hi,
> I am working from China and the internet from home is really slow; I cannot
> use biocLite("hgu133a") to install the package. I knew maybe I could install
> it from downloaded one; but the menu for biocLite function is not very clear
> on how to proceed.
>
> btw, when I use mac to download the package, it automatically unzip it. How
> could I make it into .tgz again? I assume biocLite only install .tgz file,
> right?
>
> thanks.
>
> -- 
> Weiwei Shi, Ph.D
> Research Scientist
> GeneGO, Inc.
>
> "Did you always know?"
> "No, I did not. But I believed..."
> ---Matrix III
>
> 	[[alternative HTML version deleted]]
>
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-- 
Dr. Martin Morgan, PhD
Computational Biology Shared Resource Director
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793