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charset="UTF-8" X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Spam-Score: -1.0 (-) X-BeenThere: bug-guix@gnu.org List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: bug-guix-bounces+larch=yhetil.org@gnu.org Sender: "bug-Guix" X-Scanner: scn0 Authentication-Results: aspmx1.migadu.com; dkim=fail (rsa verify failed) header.d=gmail.com header.s=20161025 header.b=XxlfNeoX; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of bug-guix-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=bug-guix-bounces@gnu.org X-Spam-Score: 0.09 X-TUID: qC9V7zofRSIa 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