Message-ID: <CAOQ5NycxKi6m1=+U9We8DF=mMF1AC16JaAzc1uG2UV2kmOGEMw@mail.gmail.com>
Date: 2014-11-08T16:53:30Z
From: Michael Lawrence
Subject: [Bioc-devel] bioc pkgs depending on packages that are only in github?
In-Reply-To: <CAANT7+UYtqQJ84hwQwhmcrMyX7x81iwRdr6_d_YfpFtxAJZ5Hg@mail.gmail.com>
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.
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