[Bioc-devel] bioc pkgs depending on packages that are only in github?

Michael Lawrence lawrence.michael at gene.com
Sat Nov 8 17:53:30 CET 2014

On Sat, Nov 8, 2014 at 8:01 AM, Vincent Carey <stvjc at channing.harvard.edu>

> our guidelines state
> Packages you depend on must be available via Bioconductor or CRAN; users
> and the automated build system have no way to install packages from other
> sources.
> with increased utility of devtools/install_github perhaps we can relax
> this?
> is it a can of worms we don't want to open?
Gabe Becker is finishing up a framework that generalizes the notion of
package repositories such that packages can be distributed over multiple
sources, including traditional repositories and SCM systems like Github. If
Bioconductor were to maintain a manifest, then our generalized installation
machinery would be able to install everything in a dependency-aware manner
(install_github can only resolve dependencies located in repositories).
BiocInstaller could wrap it. The manifest system is a prototype for
something that could end up in R itself.

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