[Bioc-devel] bioc pkgs depending on packages that are only in github?

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Sat Nov 8 19:40:41 CET 2014

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.


On Sat, Nov 8, 2014 at 11:53 AM, Michael Lawrence <lawrence.michael at gene.com
> 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
> 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 at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
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