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bug#39885: Bioconductor URI, fallback and time-machine

From: zimoun
Subject: bug#39885: Bioconductor URI, fallback and time-machine
Date: Tue, 3 Mar 2020 16:59:03 +0100


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


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.,


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.

All the best,

Attachment: 0001-build-system-r-Use-Bioconductor-old-releases-to-fall.patch
Description: Text Data

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