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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 |
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
Description: Text Data
- bug#39885: Bioconductor URI, fallback and time-machine,
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