[Bioc-devel] BiocInstaller: next generation

Aaron Lun @lun @ending from wehi@edu@@u
Thu May 10 01:05:03 CEST 2018

This all sounds pretty reasonable to me. The ability to choose the
version in install() is nice, especially if we can easily flip between
versions in different install locations. I presume that
version="release" will be the default?

As for the names - BiocManager seems the most sober of the lot. And
thematically appropriate - you might have an orchestra and conductor,
but you still need a manager to get everyone paid, fed and on the stage.


Martin Morgan wrote:
> Developers --
> A preliminary heads-up and request for comments.
> Almost since project inception, we've used the commands
>   source("https://bioconductor.org/biocLite.R")
>   biocLite(pkgs)
> to install packages. This poses security risks (e.g., typos in the
> url) and deviates from standard R package installation procedures.
> We'd like to move to a different system where a base package, call it
> 'BiocManager', is installed from CRAN and used to install Bioconductor
> packages
>   if (!"BiocManager" %in% rownames(installed.packages()))
>       install.packages("BiocManager")
>   BiocManager::install(pkgs)
> This establishes a secure chain from user R session to Bioconductor
> package installation. It is also more consistent with base R package
> installation procedures.
> BiocManager exposes four functions
>   - install() or update packages
>   - version() version of Bioconductor in use
>   - valid() are all Bioconductor packages from the same Bioconductor
> version?
>   - repositories() url location for Bioconductor version-specific
> repositories
> install() behaves like biocLite(), using the most current version of
> Bioconductor for the version of R in use. It stores this state using a
> Bioconductor package 'BiocVersion', which is nothing more than a
> sentinel for the version in use. One can also 'use devel' or a
> particular version of Bioconductor (consistent with the version of R)
> with
>   BiocManager::install(version = "3.8")   # or the synonym "devel"
> We intend to phase this in over several release cycles, and to
> continue to support the traditional biocLite() route for versions
> before BiocManager becomes available.
> We also intend to change the overall versioning of 'Bioconductor'
> itself, where releases are always even (3.8, 3.10, 3.12, ...) and
> 'devel' always odd.
> Obviously this is a large change, eventually requiring updates to many
> locations on our web site and individual vignettes.
> Of course the key question is the name of the 'BiocManager' package.
> It cannot easily be 'BiocInstaller', because of the differences in way
> CRAN and Bioconductor version packages. Some possible names are
> '
> BiocInstall::install()
> BiocPackages::install()
> BiocManager
> BiocMaestro
> Your comments are welcome...
> Martin
> This email message may contain legally privileged and/or...{{dropped:2}}
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