[Bioc-devel] Meta-information about bioc and bioc-package releases

Dan Tenenbaum dtenenba at fredhutch.org
Wed May 27 19:47:05 CEST 2015

----- Original Message -----
> From: "Gabe Becker" <becker.gabe at gene.com>
> To: bioc-devel at r-project.org
> Cc: "csardi gabor" <csardi.gabor at gmail.com>
> Sent: Wednesday, May 27, 2015 10:31:43 AM
> Subject: [Bioc-devel] Meta-information about bioc and bioc-package releases
> Hey all,
> I've been wondering if bioc could offer a way to query information
> about
> itself similar - though not necessarily identical -  to what Gabor
> Csardi's
> (cc'ed) crandb offers http://www.r-pkg.org/services#api
> <http://www.r-pkg.org/services#api>
> Basically, I would really like two things, in increasing order of
> difficulty:
> #1: A webservice to easily determine the Bioc release version
> associated
> with a particular version of R.
> R knows how to do this itself, but it doesn't share the wealth
> (function
> not exported) so I can't get at that without a NOTE which blocks
> submission
> to CRAN.

Here's a web service to do this:

 curl -u readonly:readonly https://hedgehog.fhcrc.org/bioconductor/trunk/bioconductor.org/config.yaml

This returns a yaml file containing a list/hash called "r_ver_for_bioc_ver". It also contains the current release ("release_version") and devel ("devel_version") of Bioconductor. Putting this information together you should be able to 
determine what you want. 

> Note that I explicitly do not want to require or depend on the
> presence of
> BiocInstaller. Depending on BiocInstaller would prevent switchr from
> allowing context switching between Bioc versions, which is a major
> use-case
> for the software.
> Something as simple as a web service which accepts an R version
> string and
> spits out the Bioc release number would be sufficient, though a way
> to get
> the full repo URLs would be a nice bonus
> #2: A crandb-like database of Bioc package version releases.
> The queries that I would specifically like, in the context of
> reproducibility with my switchr package, are:
>    - Which exact package versions were available on a specific date
>    - Start and end dates for a given release of bioc
>    - What date was a specific package version first released, and the
>    span
>    dates it was available via (a) repo
>    - Dependency and reverse dependency information for each release
>    of each
>    package
>    - Given a package version, the smallest set of packages necessary
>    to
>    install the package, and the versions of those dependencies that
>    were
>    concurrent with the initial release, midpoint, and last moment
>    before being
>    superceded for the package in question. (crandb does not offer
>    this; I can
>    do it with many seperate calls, but it seems like the computation
>    should be
>    server-side for this). Peferably with or without including
>    Suggests.
>    Depending on implementation this could be completely or partially
>    pre-computed for efficiency.
>    - A mapping from package versions in repositories to SVN branch
>    and
>    commit, if possible.
>    - Possibly other stuff crandb tracks.
> Would one or both of these be possible?
> I looked at using the crandb code directly, but it pulls from
> <cranmirror>/src/contrib/Meta/archive.rds to get all of this
> information,
> and that file either doesn't exist or isn't readable in the Bioc
> repositories.  If we were to change that, I think a lot of what
> crandb
> offers would come nearly for free, the only work being adding things
> that
> crandb doesn't offer (the tree-shaking and version to svn mapping,
> for
> example).

I'm not sure how the Meta/archive.rds file is generated; do you know?

As for the other requests, we'll need to discuss this stuff internally before responding further.


> Best
> ~G
> --
> Gabriel Becker, Ph.D
> Computational Biologist
> Genentech Research
> 	[[alternative HTML version deleted]]
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