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

Martin Morgan mtmorgan at fredhutch.org
Sat Nov 8 21:12:22 CET 2014

On 11/08/2014 08:01 AM, Vincent Carey 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?

Presence on git hub today doesn't imply any commitment to ongoing availability, 
and does not provide even nominal assurance that the package builds and installs 
across the major platforms. It also doesn't have formal requirements for passing 
R CMD check or meeting the higher documentation standards of Biocondcutor, and 
there are no guarantees about basic programming best practices (e.g., consistent 
version numbering across releases).  (Of course many individual github resources 
are well maintained and documented, and are cross-platform compatible.) So for 
these reasons it seems like the bar for dependencies should remain at least 
approximately where it is -- CRAN or Bioc packages.


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