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Thu, 19 Nov 2020 06:22:12 -0800 (PST) From: zimoun References: Date: Thu, 19 Nov 2020 15:22:11 +0100 In-Reply-To: (zimoun's message of "Tue, 3 Mar 2020 16:59:03 +0100") Message-ID: <87r1ope8a4.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable 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: ns3122888.ip-94-23-21.eu Authentication-Results: aspmx1.migadu.com; dkim=fail (headers rsa verify failed) header.d=gmail.com header.s=20161025 header.b=geXsceiP; 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: IptFdLtKktvb Hi, Some explanations of the issue are provided here: Since we are currently updating to 3.12, maybe it is the occasion to fix the issue. See option a) below. On Tue, 03 Mar 2020 at 16:59, zimoun wrote: > Currently, the URI scheme (see 'bioconductor-uri' in > guix/build-system/r.scm) is: > > https://bioconductor.org/packages/release/data//src/contr= ib/-.tar.gz > > which leads to 2 issues: > > 1. when Bioconductor updates their release, some package versions are > updated too, and so, the upstream return 404. > > 2. for this reason 1., the "guix time-machine" is broken for all the > Bioconductor packages, at least if Berlin or SWH does not have a > substitute; which is not expected for 'annotation' packages. An example of this issue is for example: --8<---------------cut here---------------start------------->8--- $ guix time-machine --commit=3Daee183e -- import cran -a bioconductor CATAL= YST -r Updating channel 'guix' from Git repository at 'https://git.savannah.gnu.or= g/git/guix.git'... Starting download of /tmp/guix-file.Nxajqh >From https://bioconductor.org/packages/release/bioc/src/contrib/CATALYST_1.= 12.2.tar.gz... download failed "https://bioconductor.org/packages/release/bioc/src/contrib= /CATALYST_1.12.2.tar.gz" 404 "Not Found" failed to download "/tmp/guix-file.Nxajqh" from "https://bioconductor.org/p= ackages/release/bioc/src/contrib/CATALYST_1.12.2.tar.gz" error: failed to retrieve package information from "https://cran.r-project.= org/web/packages/CATALYST/DESCRIPTION": 404 ("Not Found") Backtrace: 4 (primitive-load "/home/simon/.cache/guix/inferiors/vznc=E2=80= =A6") In guix/ui.scm: 2117:12 3 (run-guix-command _ . _) In guix/scripts/import.scm: 120:11 2 (guix-import . _) In srfi/srfi-1.scm: 586:17 1 (map1 (#f)) In guix/import/utils.scm: 258:2 0 (package->definition _) guix/import/utils.scm:258:2: In procedure package->definition: Throw to key `match-error' with args `("match" "no matching pattern" #f)'. --8<---------------cut here---------------end--------------->8--- Aside the ugly backtrace which is tracked by #44115, the main issue is because Bioconductor updated to 3.12 and Guix is still at 3.11. Concretely, the issue is that =E2=80=99release=E2=80=99 in the URL: now refers to 3.12 (because Bioconductor update) and Guix still think it is 3.11 (because Guix has not yet updated; work-in-progress). And CATALYST in 3.12 is at version 1.14.0 against 1.12.2 for 3.11. Therefore, the conflict and the error. It means that while: (define %bioconductor-version "3.11") is not updated to 3.12, all the Bioconductor packages are broken; in the meaning not buildable from source. > a) Add the Bioconductor release (known at packaging time) to all the > packages; provide as argument to 'bioconductor-uri'. > b) Add more URLs to fallback, e.g.: > > https://bioconductor.org/packages/release/data//src/contri= b/-.tar.gz > https://bioconductor.org/packages/3.11/data//src/contrib/<= upstream-name>-.tar.gz > > Attached, a quick patch showing the option b). Then each time we update Bioconductor, we add an URL to the list. > As discussed on IRC, Tobias seems more inclined with the option a) and > I am more in favour of option b. Tobias and Ricardo are in favor for a) (see this thread). Which means a lot of work IMHO, i.e., add 3.11 as arguments and then 3.12 to all the Bioconductor packages and fix the importer, IIUC; while b) means do nothing except merge the proposed patch (possibly re-worked). Just to note that only the task to group in bioconductor.scm all the Bioconductor packages scattered here and there is still not done, I think option a) is not doable by hand =E2=80=93 I do not volunteer! :-) Els= e, any suggestion to script the task instead? Since I am more in favor of b), I am less motivated to fix the a). ;-) But I am motivated to fix the issue at hand. :-) Other option c) is to switch all the Bioconductor to git-fetch instead of url-fetch. I have not checked yet how could be the transition. > Please also consider #36805 which was never merged or closed. > http://issues.guix.gnu.org/issue/36805 This patch could help for option a). WDYT? All the best, simon