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
