[Bioc-devel] Complete download of Bioconductor 1.8

[Seth Falcon]

"Claudio Lottaz" <Claudio.Lottaz at molgen.mpg.de> writes:
> Hi all,
>
> I am responsible for the installation of Bioconductor at our institute.
> I found it helpful to download all packages from the Bioconductor repository
> and then install from local copies. I did this for release 1.7 using the
> reposTools package. In the current reposTools package, no repositories for
> release 1.8 have been added (when using repositories()).

reposTools has been deprecated.  The 1.8 release repositories are not
available in reposTools format.

> Is this, because the 1.8 repositories now have standard format as announced
> earlier?
> And how would I go about downloading all packages in Bioconductor
> repositories?

Yes, all Bioc package repositories are normal CRAN-style repositories.
To get the current complete list of Bioc repositories:

library("Biobase")
biocReposList()
allp <- available.packages(contriburl=contrib.url(biocReposList()))

However, this includes all of CRAN, all annotation and experiment
packages, etc.

For just the software packages:

softwarePkgs <- available.packages(contrib.url(biocReposList()["bioc"]))

Then you can use download.packages:

download.packages(rownames(softwarePkgs), "destdir", repos=biocReposList()["bioc"])

Also, you might be interested in these instructions:
http://www.bioconductor.org/download/mirrors/mirror-howto.html

-- 
+ seth