[Bioc-devel] building R and bioconductor

Berri, Stefano sberri at illumina.com
Tue Apr 28 17:50:13 CEST 2015


I need a very reproducible way of creating a R builds with a series of CRAN and Bioconductor packages.

I want to be able to download a specific version or R, a specific version of all packages and then install them in the right order (to make sure every package has the dependencies at installation time). I do not want to use install.packages or biocLite because they are not very transparent/reproducible
I have done it for R-3.0.2, but it has been rather slow and boring (Try installing a package, see the complaint, go into a working installation, load the package an figure out the version of all the related packages). 

I am wondering if there is an automated way, or a repository, to recursively retrieve all the package versions required in a certain version of R.

I am also looking into easybuild (http://easybuild.readthedocs.org/en/latest/), and, also there, knowing the exact path to all the packages in the right order seem crucial.

how do install.packages or biocLite know what version is required and where it is located?

Thanks a lot


More information about the Bioc-devel mailing list