On 05/09/2018 07:05 PM, Aaron Lun wrote:
This all sounds pretty reasonable to me. The ability to choose the version in install() is nice, especially if we can easily flip between versions in different install locations. I presume that version="release" will be the default?
I actually have some reservation about introducing the 'release' synonym -- telling a user on April 30 that they should use 'release' and then again on May 2 that they should use 'release', but to mean two different versions of Bioconductor seems confusing to me. Also the notion that a more-or-less casual user will get into Bioconducor enough to grok the whole release / devel cycle seems somehow presumptuous. Of course developers are a more sophisticated lot, and the notion of a 'devel' branch is central to Bioconductor's approach to version management...
Martin
As for the names - BiocManager seems the most sober of the lot. And thematically appropriate - you might have an orchestra and conductor, but you still need a manager to get everyone paid, fed and on the stage. -Aaron 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_______________________________________________ The information in this email is confidential and inte...{{dropped:12}}
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