"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