[Bioc-devel] BiocManager now on CRAN

Marcel Ramos M@rcel@R@mo@ @ending from ro@wellp@rk@org
Wed Jun 20 18:23:51 CEST 2018

Dear bioc-devs,

A month ago we notified you about our "next generation" changes to

Thanks to all beta testers and those who provided feedback and
suggestions for a new package name.

I am pleased to inform you that BiocManager is now on CRAN:

As mentioned in our last email, you can now install BiocManager using:


Action Item:

   -   Please modify the vignettes in your bioc-devel packages to
reflect the use of BiocManager

After the next couple of weeks or so, we will be identifying packages in
bioc-devel (3.8) that still
mention BiocInstaller / biocLite.

Best regards,

Bioconductor Core Team
Roswell Park Cancer Institute
Dept. of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263

On 05/09/2018 06:11 PM, 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}}
> _______________________________________________
> Bioc-devel using r-project.org mailing list
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