[Bioc-devel] BiocInstaller: next generation

Lluís Revilla llui@@revill@ @ending from gm@il@com
Fri May 11 09:33:00 CEST 2018

Dear Bioconductor team,

Bioconductor packages can be installed via install.packages when they are a
dependency of another package if there is in the DESCRIPTION file a
"biocViews:" section (see https://github.com/r-lib/devtools/issues/700#
issuecomment-235127291) .
I don't know how install.packages handles these packages in Bioconductor
but would it be possible to use this trick to directly install the packages
in Bioconductor?

What will happen with BiocInstaller package? The package has the same
description and purpose of the proposed new package.
Wouldn't be better to move this new functionality to BiocInstaller and move
it to CRAN?



On 10 May 2018 at 00:11, Martin Morgan <martin.morgan at roswellpark.org>

> 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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