[Bioc-devel] BiocManager now on CRAN

[Marcel Ramos]

Dear bioc-devs,


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

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:
https://cran.r-project.org/web/packages/BiocManager/index.html


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

```
install.packages("BiocManager")
BiocManager::install("YourPackageNameHere")
```

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,
Marcel

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
>
>
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>
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