[Bioc-devel] bioc pkgs depending on packages that are only in github?
On Sat, Nov 8, 2014 at 12:22 PM, Martin Morgan <mtmorgan at fredhutch.org> wrote:
On 11/08/2014 08:53 AM, Michael Lawrence wrote:
On Sat, Nov 8, 2014 at 8:01 AM, Vincent Carey <stvjc at 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.
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