GNU bug report logs - #39885
Bioconductor URI, fallback and time-machine

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: bug-guix <at> gnu.org, Tobias Geerinckx-Rice <me <at> tobias.gr>,
 Ricardo Wurmus <rekado <at> elephly.net>
Subject: Bioconductor URI, fallback and time-machine
Date: Tue, 3 Mar 2020 16:59:03 +0100

[Message part 1 (text/plain, inline)]

Dear,

Currently, the URI scheme (see 'bioconductor-uri' in
guix/build-system/r.scm) is:

 https://bioconductor.org/packages/release/data/<type-url-part>/src/contrib/<upstream-name>-<version>.tar.gz

which leads to 2 issues:

 1. when Bioconductor updates their release, some package versions are
updated too, and so, the upstream return 404.
 2. for this reason 1., the "guix time-machine" is broken for all the
Bioconductor packages, at least if Berlin or SWH does not have a
substitute; which is not expected for 'annotation' packages.

However, the Bioconductor archive still serves the old release, i.e.,

https://bioconductor.org/packages/3.x/data/<type-url-part>/src/contrib/<upstream-name>-<version>.tar.gz


The ways to fix the both issues are:

 a) Add the Bioconductor release (known at packaging time) to all the
packages; provide as argument to 'bioconductor-uri'.
 b) Add more URLs to fallback.

As discussed on IRC, Tobias seems more inclined with the option a) and
I am more in favour of option b.

Attached, a quick patch showing the option b).


Please also consider #36805 which was never merged or closed.
 http://issues.guix.gnu.org/issue/36805


All the best,
simon

[0001-build-system-r-Use-Bioconductor-old-releases-to-fall.patch (text/x-patch, attachment)]

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