From: zimoun <zimon.toutoune@gmail.com>
To: 39885@debbugs.gnu.org, Tobias Geerinckx-Rice <me@tobias.gr>,
Ricardo Wurmus <rekado@elephly.net>
Subject: bug#39885: Bioconductor URI, fallback and time-machine
Date: Wed, 24 Jun 2020 13:07:13 +0200 [thread overview]
Message-ID: <CAJ3okZ1Xwd-2WArzNus3xE_KOayDdXPp+ku1SxYBon4Zm0qQQg@mail.gmail.com> (raw)
In-Reply-To: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@mail.gmail.com>
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
next prev parent reply other threads:[~2020-06-24 11:12 UTC|newest]
Thread overview: 31+ messages / expand[flat|nested] mbox.gz Atom feed top
2020-03-03 15:59 bug#39885: Bioconductor URI, fallback and time-machine zimoun
2020-03-23 21:20 ` Ricardo Wurmus
2020-05-21 23:29 ` zimoun
2020-06-24 11:07 ` zimoun [this message]
2020-06-28 20:14 ` Ludovic Courtès
2020-06-29 17:36 ` zimoun
2020-06-29 20:42 ` Ludovic Courtès
2020-11-19 14:22 ` zimoun
2021-11-22 19:48 ` zimoun
2022-07-18 16:03 ` zimoun
2022-07-18 16:21 ` Ricardo Wurmus
2022-08-10 18:25 ` Ricardo Wurmus
2022-08-10 19:44 ` Maxime Devos
2022-08-10 19:48 ` Maxime Devos
2022-09-09 17:23 ` zimoun
2024-01-08 15:07 ` Ludovic Courtès
2024-01-08 15:34 ` Ricardo Wurmus
2024-01-11 16:11 ` Simon Tournier
2023-12-22 13:40 ` bug#39885: Bioconductor tarballs are not archived Ludovic Courtès
2024-01-08 9:09 ` Simon Tournier
2024-01-08 15:02 ` Ludovic Courtès
2024-01-10 12:41 ` Ricardo Wurmus
2024-01-10 15:23 ` Simon Tournier
2024-01-19 15:46 ` Timothy Sample
2024-01-23 9:10 ` Ludovic Courtès
2024-02-14 15:23 ` Simon Tournier
2024-02-16 16:14 ` Timothy Sample
2024-02-19 16:50 ` Simon Tournier
2024-02-21 18:16 ` Timothy Sample
2023-12-22 20:57 ` bug#39885: Bioconductor URI, fallback and time-machine Ludovic Courtès
2024-01-02 9:20 ` Simon Tournier
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