[Bioc-devel] building R and bioconductor
lg390 at cam.ac.uk
Tue Apr 28 19:36:36 CEST 2015
On 28 April 2015 16:50, Berri, Stefano wrote:
> 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.
Using biocLite, you will get the specific package versions required for
your R version. If you want more control, I think packrat [1,2] from
RStudio or this paper  by Gabe Becker et al. might helpful.
You might also consider rolling out your own docker image.
> 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
> how do install.packages or biocLite know what version is required and
> where it is located?
The locations are defined by getOption("repos") and biocinstallRepos()
respectively. In the latter case, these will also depend on the version
Hope this helps.
> Thanks a lot
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