[Bioc-devel] Complete download of Bioconductor 1.8
sfalcon at fhcrc.org
Fri Apr 28 17:18:21 CEST 2006
"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
> And how would I go about downloading all packages in Bioconductor
Yes, all Bioc package repositories are normal CRAN-style repositories.
To get the current complete list of Bioc repositories:
allp <- available.packages(contriburl=contrib.url(biocReposList()))
However, this includes all of CRAN, all annotation and experiment
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:
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