Bioconductor
installing a local package with BiocManager?
Unless I've missed something, you have to use an alternative like devtools::install('.', dependencies=TRUE, build_vignettes=TRUE, repos = BiocManager::repositories()) to install a local package normally or in Dockerfiles, taking us away from BiocManager as our one-and-only package manager. Could you either implement a local package installer, or document the recommended approach? Here's an example in the wild that could be a recommended approach. Note, it does not use the github remotes installation because it is meant to also run from alternative git branches.
https://github.com/seandavi/BuildABiocWorkshop/blob/3161063ee879720f866ba109048247906dea5a93/Dockerfile#L9
I would rather document an alternative approach, since installing locally is not consistent with bioconductor best practices. PR welcome but I won't write one.
How do you install and test when developing locally - with install.packages or devtools::install?
My gut reaction here is that the best practice is for a package to start its life in github. Then BiocManager can install it.
Personally I use devtools::load_all() etc leading naturally to ::check(); if i actually install the package it's usually from the command line R CMD INSTALL . so that I don't get anything unexpected from a devtools installation. Also there is no need to install package dependencies, other than via BiocManager::install()during the development process.
Good to know; my thought is that version control should commence as soon as possible.