Hi, On Wed, 2018-05-09 at 18:11 -0400, Martin Morgan wrote: > > ... > - version() version of Bioconductor in use > - valid() are all Bioconductor packages from the same > Bioconductor > version?
I'd like to challenge the concept of the release and the pretty strong term valid(). I think BioC is the only R package repository that has the release concept, and this is good to have a consistent well tested environment of packages for a given R version. It is also great to pick the most recent package version within a release for installation, but that also prevents installing a package newer than the one tied to the R version at hand. But R already has the concept of versioned dependencies, so in theory we wouldn't /need/ the release concept. I'd like to suggest to make it easier to shoot yourself into the foot by installing less tested combinations of R and BioC packages, and to support installing BiocManager::install(X, version=0.8.15) BiocManager::install(X, release=3.8) BiocManager::install(X, release=devel) i.e. a package from a given BioC release, or a specific version of a package, regardless from which release it comes. The valid() is a bit unspecific name, what is probably meant here is BiocManager::tainted(), which indicates that packages come from different BioC versions, and all hell might break loose and it'll eat your kittens. This also means that Package developers would ask for the tainted() status in bug reports, and (c|sh)ould refuse help for unsupported combination. It also means that packagers would have to be more careful with the versioned dependencies, and supply minimal versions. If they give a versioned dependency on the Biobase, they essentially forbid installing on old BioC releases, which would be fine. Just my 2c, Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel