[Bioc-devel] BiocManager now on CRAN

[Joris Meys]

Dear Marcel,

A big thanks to you and the entire bioconductor team. I will spread the
word among my colleagues. I also noticed that the installation instructions
aren't adapted yet on the bioconductor site (
https://www.bioconductor.org/install/). Probably I'm just rushing here and
you are working on it, but I thought to inform you anyway as our courses
link to that website for official installation instructions.

Cheers
Joris

On Wed, Jun 20, 2018 at 6:23 PM, Marcel Ramos <Marcel.Ramos using roswellpark.org>
wrote:

> 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
> >
> >
> > This email message may contain legally privileged and/or...{{dropped:2}}
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> This email message may contain legally privileged and/or...{{dropped:4}}
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
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