Really, people who distribute their packages solely through github are making it convenient for the developers and doing a lot of potential harm to users. When you use install_github, there is no real concept of versioning, of whether the package succeed building or passes checks on various platforms (which is pretty important for example for anything with C(++) code). What we have in Bioconductor is so much better for the end user, and so much better for reproducible research. On top of this, as Tim says, we have some additional QC checks.
It does seem that CRAN these days are very hard to deal with, and I am happy that I don't have packages in that repository. The Bioc way (interfacing the repository with source code version control), which allows much more rapid pushing of fixes to users (assuming they use devel), seems uniformly better in my opinion. I can understand why package authors may be fed up with CRAN, but by just putting packages on github they also signal (in my opinion) that they are not willing to go the last mile and make their code release quality. As everyone knows, actually writing a vignette, making sure the code passes check on all platforms, having man pages etc etc. can be some amount of tedious work, but it really does make the end experience uniformly better. There is clearly a trend towards just putting things up on github and not bothering with submitting to a repository. That is - in my opinion - a trend towards inferior quality. And importantly, as I see it, it does not support reproducible research. Best, Kasper On Sat, Nov 8, 2014 at 11:53 AM, Michael Lawrence <lawrence.mich...@gene.com > 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 > machinery would be able to install everything in a dependency-aware manner > (install_github can only resolve dependencies located in repositories). > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
