[Bioc-devel] building R and bioconductor

[Laurent Gatto]

Dear Stefano,

On 28 April 2015 16:50, Berri, Stefano wrote:

> Hi.
>
> 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 [3] by Gabe Becker et al. might helpful.

  [1] https://rstudio.github.io/packrat/
  [2] https://github.com/rstudio/packrat
  [3] http://arxiv.org/abs/1501.02284
  
You might also consider rolling out your own docker image.

  [4] http://bioconductor.org/help/docker/

> 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?

The locations are defined by getOption("repos") and biocinstallRepos()
respectively. In the latter case, these will also depend on the version
of R. 

Hope this helps.

Best wishes,

Laurent

> Thanks a lot
>
> Stefano
>
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