On Sat, Nov 8, 2014 at 12:22 PM, Martin Morgan <mtmor...@fredhutch.org> wrote:
> On 11/08/2014 08:53 AM, Michael Lawrence wrote: > >> On Sat, Nov 8, 2014 at 8:01 AM, Vincent Carey <st...@channing.harvard.edu >> > >> wrote: >> >> our guidelines state >>> >>> Packages you depend on must be available via Bioconductor or CRAN; users >>> and the automated build system have no way to install packages from other >>> sources. >>> >>> with increased utility of devtools/install_github perhaps we can relax >>> this? >>> >>> is it a can of worms we don't want to open? >>> >>> >>> Gabe Becker is finishing up a framework that generalizes the notion of >> package repositories such that packages can be distributed over multiple >> sources, including traditional repositories and SCM systems like Github. >> If >> Bioconductor were to maintain a manifest, then our generalized >> installation >> > > Probably you mean a manifest in a different sense, but in case not I'll > mention > > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/ > Rpacks/bioc_3.1.manifest > > and friends. > > Gabe's manifest is a list of packages, but it also points to package locations and, optionally, versions. > machinery would be able to install everything in a dependency-aware manner >> (install_github can only resolve dependencies located in repositories). >> > > > Managing dependencies seems like an important and necessary advance, but I > don't think sufficient for Bioc purposes? E.g., both CRAN and Bioconductor > at some level take control of package sources, so the source is available > even after the developer has (usually casually) lost interest in the useful > resource they are providing. Likewise the 'quality assurance' provided by > build and check (on change for CRAN, nightly for Bioc) across platforms and > against current versions, and the manual maintenance activities of both the > CRAN and Bioc teams (e.g., identifying the root cause of problems exhibited > by package A as a change or deficiency in package B). > > There is a tension between the desire for validation and the pace of science. Our goal is to enable the user to choose his or her comfort zone. Gabe's switchr/GRAN framework makes it relatively easy to deploy a manifest as a traditional, validated repository. It will even pull from github or other SCM with each build (I think it just checks for a version bump, but that might be configurable). Of course, this means the user has the skills and resources necessary to deploy such a repository. The Bioconductor project certainly would though, so some sort of validated approach would definitely be preferable. > Certainly it will be interesting to see Gabe's mature product. > > Martin > > > BiocInstaller could wrap it. The manifest system is a prototype for >> something that could end up in R itself. >> >> >> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >>> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
