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@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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
