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bug#39885: Bioconductor URI, fallback and time-machine
From: |
zimoun |
Subject: |
bug#39885: Bioconductor URI, fallback and time-machine |
Date: |
Wed, 24 Jun 2020 13:07:13 +0200 |
Dear,
The time-machine is broken for some BioConductor packages.. For an
example, consider the package "r-genomegraphs" which has been removed
from the BioConductor in 3.11 release.
(Well, now the issue is mitigated because ci.guix.gnu.org serves a lot
of upstream substitutes but ci.guix.gnu.org could be down. Other
said, we should use the upstream resources where they are available.)
Concretely, there are 2 issues:
a) What to do for the removed packages? For 3.11, the list is there
[1]. Do we keep them in gnu/packages/bioconductor.scm but then
'bioconductor-uri' needs some tweaks? Or do we transfer them to the
channel guix-past (for example)?
b) The fallback URI in guix/build-system/r.scm(bioconductor-uri)
added by commit c586f427b4831b9b492e5b900b2226e898b8fcfa is not
correct, if I do not misread:
--8<---------------cut here---------------start------------->8---
"https://bioconductor.org/packages/3.10/bioc/src/contrib/Archive/GenomeGraphs_1.46.0.tar.gz"
404 "Not Found"
--8<---------------cut here---------------end--------------->8---
The correct seems to be (without Archive):
https://bioconductor.org/packages/3.10/bioc/src/contrib/GenomeGraphs_1.46.0.tar.gz
All the best,
simon
1:
https://bioconductor.org/news/bioc_3_11_release/#deprecated-and-defunct-packages
- bug#39885: Bioconductor URI, fallback and time-machine,
zimoun <=