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

[Martin Morgan]

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.

> 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).

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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