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Use BiocInstaller repositories if installing a Bioconductor package #895

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merged 2 commits into from Sep 2, 2015

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jimhester commented Aug 13, 2015

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")
Use BiocInstaller repositories if installing a Bioconductor package
If the user specified repositories take precedence over the default
Bioconductor repositories.

@jimhester jimhester referenced this pull request Aug 20, 2015

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Add Travis-CI support #5

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PeteHaitch commented Aug 21, 2015

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.

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jimhester commented Aug 21, 2015

@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.

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PeteHaitch commented Aug 23, 2015

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

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hadley commented Sep 2, 2015

Could you please add a bullet to NEWS?

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jimhester commented Sep 2, 2015

Done 406f3dd

hadley added a commit that referenced this pull request Sep 2, 2015

Merge pull request #895 from jimhester/bioc_depends
Use BiocInstaller repositories if installing a Bioconductor package

@hadley hadley merged commit ecf945a into r-lib:master Sep 2, 2015

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hadley commented Sep 2, 2015

Thanks!

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