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

From: zimoun <[email-masked]>
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