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Tue, 12 Apr 2022 09:25:56 -0700 (PDT) From: zimoun References: <868rsf23th.fsf@gmail.com> <874k2zzj9p.fsf@elephly.net> Date: Tue, 12 Apr 2022 18:25:51 +0200 In-Reply-To: <874k2zzj9p.fsf@elephly.net> (Ricardo Wurmus's message of "Mon, 11 Apr 2022 18:15:39 +0200") Message-ID: <87ilre5kvk.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: bug-guix@gnu.org List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: 54787@debbugs.gnu.org Errors-To: bug-guix-bounces+larch=yhetil.org@gnu.org Sender: "bug-Guix" X-Migadu-Flow: FLOW_IN X-Migadu-To: larch@yhetil.org X-Migadu-Country: US ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1649780843; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; 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spf=pass (aspmx1.migadu.com: domain of "bug-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="bug-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 5.94 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=NpTyHHqH; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "bug-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="bug-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 7A2DEB913 X-Spam-Score: 5.94 X-Migadu-Scanner: scn1.migadu.com X-TUID: aT2uWzSRmUNv Hi Ricardo, On lun., 11 avril 2022 at 18:15, Ricardo Wurmus wrote: > zimoun writes: > >> $ guix import cran -a bioconductor CHETAH >> guix import: warning: failed to retrieve package information from >> https://cran.r-project.org/web/packages/CHETAH/DESCRIPTION: 404 (Not Fou= nd) >> guix import: error: failed to download description for package 'CHETAH' >> >> The reason is because there is no source package. Only the Git source >> repo. > > We should finally switch to fetching the sources from Git. I wonder why > we haven=E2=80=99t done this earlier. Because, maybe, we have just finished the janitor work cleaning the files cran.scm, bioconductor.scm and bioinformatics.scm. :-) > I guess we should do this gradually to avoid mass updates, so perhaps we > should introduce bioconductor-git-reference and switch over packages one > by one. First, note that annotations do not have Git repo; at least not always, e.g., Second, if we go for something like: --8<---------------cut here---------------start------------->8--- (define* (bioconductor-git-reference name #:optional (release %bioconductor-version)) "Return a for the R package archive on Bioconductor for t= he RELEASE corresponding to NAME." (git-reference (url (string-append %bioconductor-git-url name)) (commit (string-append "RELEASE_" (string-replace-substring %bioconductor-version "." "_"))))) --8<---------------cut here---------------end--------------->8--- then, it raises the question: import/cran.scm or build-system/r.scm ? i.e., do we put a module dependency against (guix git-download) for the r-build-system or not? TeXLive already has a dependency to svn-download, so why not. Well, I am also in favor to break the API and move %bioconductor-version and %bioconductor-url to (guix build-system r). WDYT? It would simplify some things (#36805 and #39885), I guess. Third, the adjustments of the importer require a large cup of coffee. Back to CHETAH, note that guix import cran -a git htpps://git.bioconductor.org/CHETAH works but it points to master instead of RELEASE_3_14. Well, I am not very familiar with the Bioconductor workflow for their release. Last, using this in gnu/packages/bioconductor.scm, --8<---------------cut here---------------start------------->8--- (define-public r-chetah (package (name "r-chetah") (version "1.11.2") (source (origin (method git-fetch) (uri (bioconductor-git-reference "CHETAH")) (file-name (git-file-name name version)) (sha256 (base32 "021v5831zqdy4pirfsb35kbnz8kmz4lxqc4cwi55qgd6r081xlgh")))) (properties `((upstream-name . "CHETAH"))) (build-system r-build-system) (propagated-inputs (list r-biodist r-corrplot r-cowplot r-dendextend r-ggplot2 r-gplots r-pheatmap r-plotly r-reshape2 r-s4vectors r-shiny r-singlecellexperiment r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://git.bioconductor.org/packages/CHETAH") (synopsis "Fast and accurate scRNA-seq cell type identification") (description "CHETAH (CHaracterization of cEll Types Aided by Hierarchical classifi= cation) is an accurate, selective and fast scRNA-seq classifier. Classification is gu= ided by a reference dataset, preferentially also a scRNA-seq dataset. By hierarchical clustering of the reference data, CHETAH creates a classificat= ion tree that enables a step-wise, top-to-bottom classification. Using a novel stopping rule, CHETAH classifies the input cells to the cell types of the references and to \"intermediate types\": more general classifications that= ended in an intermediate node of the tree.") (license #f))) --8<---------------cut here---------------end--------------->8--- it just builds with, ./pre-inst-env guix build r-chetah WDYT? Cheers, simon