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DesiQuintans / librarian

Install, Update, Load Packages from CRAN, Bioconductor, and GitHub in One Step.
GNU General Public License v3.0
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Known API change: biocLite transitioning to BiocManager #8

Closed DesiQuintans closed 5 years ago

DesiQuintans commented 6 years ago

For now (2018-11-15), librarian uses biocLite to install and update Bioconductor packages. This is still working, and the Bioconductor team have not indicated that this will change.

But it's important to a) stay on top of API changes, and b) provide BiocManager's features to librarian users. librarian will therefore transition to BiocManager too.

See: https://twitter.com/biologeek/status/1060445010770964481
See: https://bioconductor.org/install/#why-biocmanagerinstall

DesiQuintans commented 5 years ago

In the process of doing my checks for CRAN submission I found that BiocManager does not support R 3.4.x releases. This could be a problem because I was trying to maintain R-oldrelease compatibility because I care about my users haha. There are two paths from here:

  1. Roll back to biocLite, keeping that until there is a new minor release of R. At that point, R-current will become R-oldrelease and a BiocManager will exist for it.
  2. Somehow only import BiocManager if the R version is > 3.5.0 (Suggests?), and include a check in shelf() that runs either biocLite or BiocManager depending on the R version.
DesiQuintans commented 5 years ago

This hasn't come up as an issue in the last 5 months, so I will mark this transition as done.