Use BiocInstaller repositories if installing a Bioconductor package

[jimhester]

If the user specified repositories take precedence over the default
Bioconductor repositories.

This allows one to use install_github() with Bioconductor packages and have the dependencies work like any other package. e.g.

install_github("Bioconductor-mirror/S4Vectors")

[PeteHaitch]

Very happy to see this being worked on! (And sorry I haven't made any progress myself)

One question, Jim: are you proposing that dependencies that are from the Bioconductor devel branch are installed from the Bioconductor-mirror github repo rather than using BiocInstaller::useDevel(TRUE); BiocInstaller::biocLite("pkg")? The issue I see there is that those packages available from the Bioconductor-mirror repo aren't guaranteed to pass R CMD build/check since they haven't been run through the BioC build system. Apologies if I've misunderstood.

[jimhester]

@PeteHaitch The dependencies work with this patch the same way they do with biocLite(), they pull from the BiocInstaller::biocinstallRepos(), so it will only be packages that have successfully passed through the Bioconductor build system, not from the git mirrors.

[PeteHaitch]

Awesome! I thought so (given the code) but your example confused me. Cheers.

[hadley]

Could you please add a bullet to NEWS?

[jimhester]

Done 406f3dd

[hadley]

Thanks!