From unknown Sat Jun 21 10:35:46 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#55120 <55120@debbugs.gnu.org> To: bug#55120 <55120@debbugs.gnu.org> Subject: Status: =?UTF-8?Q?=E2=80=9Cguix?= import =?UTF-8?Q?cran=E2=80=9D?= fails for some git repositories Reply-To: bug#55120 <55120@debbugs.gnu.org> Date: Sat, 21 Jun 2025 17:35:46 +0000 retitle 55120 =E2=80=9Cguix import cran=E2=80=9D fails for some git reposit= ories reassign 55120 guix submitter 55120 Ricardo Wurmus severity 55120 normal thanks From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 26 02:44:28 2022 Received: (at submit) by debbugs.gnu.org; 26 Apr 2022 06:44:28 +0000 Received: from localhost ([127.0.0.1]:36665 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njEw0-0006RA-4V for submit@debbugs.gnu.org; Tue, 26 Apr 2022 02:44:28 -0400 Received: from lists.gnu.org ([209.51.188.17]:33546) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njEvz-0006R3-1r for submit@debbugs.gnu.org; Tue, 26 Apr 2022 02:44:27 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:40624) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njEvy-0000CY-Q8 for bug-guix@gnu.org; Tue, 26 Apr 2022 02:44:26 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21133) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njEvw-0005H4-IC for bug-guix@gnu.org; Tue, 26 Apr 2022 02:44:26 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1650955461; cv=none; d=zohomail.com; s=zohoarc; b=IUzRMwG5j0wq/iDHPw2chUtK16/3oo1DxaOXCj34z4DKycQ/73Gbgrv+RBavjFltPFxmNTR2u2aC0Uz0+ssIWOcTTRYfl6Iygh+L8pD3mKrLhspnjHKQ/tXIQZJltTS26GEbuImhj6Y+ptMGEZ3g/4aMyIP68CgeAMg7IGRF2J0= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1650955461; h=Content-Type:Content-Transfer-Encoding:Date:From:MIME-Version:Message-ID:Subject:To; bh=mzmXU6eDKpX1VaCx6zQ0J0rcz8IYfdrmwGWo/zQhzcE=; b=e2aSFtHs9K9yvWhNCjVft8y5qPbVrj+FMlBeuap1LpsnVHKtlHB6iBU7Gf1gF9wEp3g5v8OKnRwashg5P7DKgKxmjeA7EUdDps7WtoXtRacAgg6tbJ6zTBLk665jLl7Dv2azMQHAkNi/etNyHdEsojaTVvEz9B9HoaKImIPEFiQ= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1650955461; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To:Cc; bh=mzmXU6eDKpX1VaCx6zQ0J0rcz8IYfdrmwGWo/zQhzcE=; b=SwJRai9MGH/NecKUJ0oHFWC211+pHk2Uc8jmfXqMKBiBQNhsrigB9uZO/PKHUT/P 8ShScflSjs2Gv6qTyYdQyD1HbpdlNjd2vD9q3s/kGCqSq57uReKhsChZhs6ANpke/r/ w9E1mkJ32miZ9kWLNbVrXksEjhq7G7wJClZ1W+1I= Received: from localhost (56-111-142-46.pool.kielnet.net [46.142.111.56]) by mx.zohomail.com with SMTPS id 1650955457975264.2368535929104; Mon, 25 Apr 2022 23:44:17 -0700 (PDT) User-agent: mu4e 1.6.10; emacs 28.0.50 From: Ricardo Wurmus To: bug-guix@gnu.org Subject: =?utf-8?Q?=E2=80=9Cguix?= import =?utf-8?Q?cran=E2=80=9D?= fails for some git repositories Date: Tue, 26 Apr 2022 08:42:01 +0200 X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <878rrs739d.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External Received-SPF: pass client-ip=136.143.188.51; envelope-from=rekado@elephly.net; helo=sender4-of-o51.zoho.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) Importing an R package from Git fails: --8<---------------cut here---------------start------------->8--- $ guix import cran -a git -r https://github.com/RubD/Giotto/ Backtrace: In guix/ui.scm: 1347:6 19 (guix-import-cran . _) In ice-9/boot-9.scm: 1752:10 18 (with-exception-handler _ _ #:unwind? _ #:unwind-for-type _) In guix/scripts/import/cran.scm: 108:31 17 (_) In guix/import/utils.scm: 507:27 16 (recursive-import _ #:repo->guix-package _ #:guix-name _ #:ver= sion _ #:repo _) 497:33 15 (lookup-node "https://github.com/RubD/Giotto/" #f) In guix/memoization.scm: 98:0 14 (mproc "https://github.com/RubD/Giotto/" #:version #f #:repo g= it) In unknown file: 13 (_ #= # (this is nothing)) In guix/import/cran.scm: 596:24 12 (_ "https://github.com/RubD/Giotto/" #:repo _ #:version _) 296:25 11 (fetch-description _ "https://github.com/RubD/Giotto/" _) In guix/memoization.scm: 98:0 10 (mproc "https://github.com/RubD/Giotto/" #:method git) In unknown file: 9 (_ #= # (this is nothing)) In ice-9/boot-9.scm: 1752:10 8 (with-exception-handler _ _ #:unwind? _ #:unwind-for-type _) In guix/store.scm: 658:37 7 (thunk) In guix/git.scm: 550:8 6 (latest-repository-commit # "https://github.com/RubD/Giotto/" #:recursive? _ #:log-port _ # =E2=80= =A6) 279:4 5 (update-cached-checkout _ #:ref _ #:recursive? _ #:check-out? = _ #:starting-commit _ #:log-port _ #:cache-directory _) 232:18 4 (resolve _) In git/reference.scm: 60:8 3 (_ _ _) In git/bindings.scm: 77:2 2 (raise-git-error _) In ice-9/boot-9.scm: 1685:16 1 (raise-exception _ #:continuable? _) 1685:16 0 (raise-exception _ #:continuable? _) ice-9/boot-9.scm:1685:16: In procedure raise-exception: Git error: reference 'refs/remotes/origin/HEAD' not found --8<---------------cut here---------------end--------------->8--- --=20 Ricardo From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 26 08:27:02 2022 Received: (at 55120) by debbugs.gnu.org; 26 Apr 2022 12:27:02 +0000 Received: from localhost ([127.0.0.1]:37360 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKHV-0002IN-9X for submit@debbugs.gnu.org; Tue, 26 Apr 2022 08:27:02 -0400 Received: from mail-pl1-f179.google.com ([209.85.214.179]:38491) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njKHS-0002I1-Rp for 55120@debbugs.gnu.org; Tue, 26 Apr 2022 08:26:59 -0400 Received: by mail-pl1-f179.google.com with SMTP id n18so30056226plg.5 for <55120@debbugs.gnu.org>; Tue, 26 Apr 2022 05:26:58 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc:content-transfer-encoding; bh=kht0ok8e62iIuD/zTIjF5MUOQ8Ffmh+hHI/LY5veVPE=; b=ShJsREq5x8VwbArLEYwATx9SCSZC7oc4RcMP6H/SHB+tCITw/nHGr144Ik47v9aF1Q AtwofDA9UZSWdTP2/jDwnT800Bd5k5UxznZLU24bwq6kx5admgXZ2d/JNfkKPou5UhzM Q8NU60NHFaoAkM1pEUz3u+LXInZiuXsnuD+7PjH8bWQBgYVG+d2U7Cdaw95KLGrbMGLn qwp0MfA552IiPcm4pP0vr1MTqP8AgSNxupmaNE7fDu666yr3rc0xaTgG3zH1rVxAUFJz wun2MtTdE/wpv+XyMur28rSUx6mwYyMazARBJZJUwq91L4RkJqvy3NDUrsW9o6S891U7 WbPA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc:content-transfer-encoding; bh=kht0ok8e62iIuD/zTIjF5MUOQ8Ffmh+hHI/LY5veVPE=; b=4wWU4Ufpj0gNzHMpaLM8/xHyrTGO1+WVoncH/GHuLHrpNjUd9pbEJwGg84PYW0LlMX XBS9n3Ai3cchakP1L6JzP8XEIGa6nJ5no1KRj/ufDGx9fln39GqucvmXJox3OUQ5MfNy QE9lEHEZoVyhQTBSxPvQsMFN/FbJYuUtKrtTPLVKpUIKCemot43dPOCyFzHHFN+3FTuX GwEEyFDj/4JQY1/PUYnEhI1wGt+F7Nim4yYVk9P25SmAjOaU+6PDCwPlTPNZJlqfTSIx lC37kWrFLnJCTu8c3INPj1NfA/nRGFnrAM2PSOzD0S5kyotKRUz8/zL5EvudlTrBdWu8 dZSQ== X-Gm-Message-State: AOAM5312+ahYqnIJ3ob17WpPnCx0v1RrNNOAWJoUkruU+gRkqlZUU1FW 1zpx7Xr+khOao5644/gkpP90DfrjcTQl1sAjLcTYYit5CZ8= X-Google-Smtp-Source: ABdhPJzmnnl/4/pjtls8o0eQ2xoc+9JCTxSzcrY7sQYwVxNG2bxKEh1gj5RnJv+Rd1RUb5c8uC+s6EY3poTnltog2a4= X-Received: by 2002:a17:902:ea4f:b0:158:5013:1403 with SMTP id r15-20020a170902ea4f00b0015850131403mr22933634plg.75.1650976012867; Tue, 26 Apr 2022 05:26:52 -0700 (PDT) MIME-Version: 1.0 References: <878rrs739d.fsf@elephly.net> In-Reply-To: <878rrs739d.fsf@elephly.net> From: zimoun Date: Tue, 26 Apr 2022 14:26:41 +0200 Message-ID: Subject: =?UTF-8?Q?Re=3A_bug=2355120=3A_=E2=80=9Cguix_import_cran=E2=80=9D_fails_for_some?= =?UTF-8?Q?_git_repositories?= To: Ricardo Wurmus Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 55120 Cc: 55120@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi Ricardo, It works for me from my desktop machine behind the strong network of the University. And it also fails from my laptop at home. Maybe it comes from GitHub and our way to connect overthere. I do not know. --8<---------------cut here---------------start------------->8--- $ guix import cran -a git https://github.com/RubD/Giotto/ -r Starting download of /tmp/guix-file.wKIOEz >From http://cran.r-project.org/src/contrib/dbscan_1.1-10.tar.gz... =E2=80=A6-10.tar.gz 2.2MiB 3.6MiB/s 00:01 [#############= #####] 100.0% Starting download of /tmp/guix-file.zTh09D >From https://bioconductor.org/packages/release/bioc/src/contrib/lfa_1.24.0.= tar.gz... =E2=80=A6.0.tar.gz 284KiB 46.9MiB/s 00:00 [#############= #####] 100.0% Starting download of /tmp/guix-file.wx30kh >From https://bioconductor.org/packages/release/bioc/src/contrib/lfa_1.24.0.= tar.gz... =E2=80=A6.0.tar.gz 284KiB 55.6MiB/s 00:00 [#############= #####] 100.0% (define-public r-lfa (package (name "r-lfa") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lfa" version)) (sha256 (base32 "02b90xjb2lfm86hbsdrvzpv20pijnq78ibz4dwjzqd9v4xhia3wr")))= ) (properties `((upstream-name . "lfa"))) (build-system r-build-system) (propagated-inputs (list r-corpcor)) (native-inputs (list r-knitr)) (home-page "https://github.com/StoreyLab/lfa") (synopsis "Logistic Factor Analysis for Categorical Data") (description "LFA is a method for a PCA analogue on Binomial data via estimation of latent structure in the natural parameter.") (license gpl3))) (define-public r-dbscan (package (name "r-dbscan") (version "1.1-10") (source (origin (method url-fetch) (uri (cran-uri "dbscan" version)) (sha256 (base32 "1h8x1v9kk5zmw5qd575cyr16yz8l226lsaq71n079l4i8crcrzg1")))= ) (properties `((upstream-name . "dbscan"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/mhahsler/dbscan") (synopsis "Density-Based Spatial Clustering of Applications with Noise (DBSCAN) and Related Algorithms") (description "This package provides a fast reimplementation of several density-bas= ed algorithms of the DBSCAN family. Includes the clustering algorithms DBSCAN (density-based spatial clustering of applications with noise) and HDBSCAN (hierarchical DBSCAN), the ordering algorithm OPTICS (ordering points to identify the clustering structure), shared nearest neighbor clustering, and= the outlier detection algorithms LOF (local outlier factor) and GLOSH (global-l= ocal outlier score from hierarchies). The implementations use the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided. Hahsler= , Piekenbrock and Doran (2019) .") (license gpl2+))) (define-public r-giotto (let ((commit "68d7390dce87223cac11d4d8f31705fe0144d011") (revision "1")) (package (name "r-giotto") (version (git-version "1.1.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/RubD/Giotto/") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "0mv60khc05wrxzr4ir6cirn7dpqvgwan5hm00lmafsyalr51nf5i")= ))) (properties `((upstream-name . "Giotto"))) (build-system r-build-system) (propagated-inputs (list r-clusterr r-complexheatmap r-cowplot r-data-table r-dbscan r-deldir r-farver r-fitdistrplus r-ggdendro r-ggplot2 r-ggraph r-ggrepel r-igraph r-irlba r-lfa r-limma r-magick r-magrittr r-matrix r-matrixstats r-plotly r-qvalue r-r-utils r-rcolorbrewer r-rcpp r-reshape2 r-reticulate r-rfast r-rlang r-rtsne r-scales r-uwot)) (native-inputs (list r-knitr)) (home-page "https://github.com/RubD/Giotto/") (synopsis "Spatial Single-Cell Transcriptomics Toolbox") (description "Toolbox to process, analyze and visualize spatial single-cell expression data.") (license #f)))) --8<---------------cut here---------------end--------------->8--- Cheers, simon From debbugs-submit-bounces@debbugs.gnu.org Wed Dec 28 13:23:53 2022 Received: (at 55120-done) by debbugs.gnu.org; 28 Dec 2022 18:23:53 +0000 Received: from localhost ([127.0.0.1]:58630 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pAb5l-0007QT-0Y for submit@debbugs.gnu.org; Wed, 28 Dec 2022 13:23:53 -0500 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21186) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pAb5i-0007QJ-1F for 55120-done@debbugs.gnu.org; Wed, 28 Dec 2022 13:23:51 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1672251826; cv=none; d=zohomail.com; s=zohoarc; b=eXne1PsqYLa0OEqvx94Nmy3IC3JHQzZ3WMnRYPPOw3/505mEFp/MEMeowEkjl6S2E9sbJIcJe/6P3tNd3lgA0AHszkQhGFltmLGGTMdFlyK8Prs/TkeROb814PPi5rDLETaYxP4fVeY/vLaMrSL+ypA+vfc3aFn5wRg4eFm4sR0= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1672251826; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=vkTSCMVMARBJ8+6V7PR6aEQH3j6n5J3j65p2+z1NZO8=; b=Mp4s7UNY+sZBN38NbYtL4aSHDuvy0F0P03dLq5YG7f+ZfXYvKdlhF4ZzVCGVnB3LHG7gAfEipxY7hdz+TUnzzYBZlKLP3Xj04dZzk6HaRdexCVpSout4ejQXkY84RU2vTOzB31Hvwzj3SKqNu9UzW3DdS/Vxj1VG76ZNDP5EQXM= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1672251826; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=vkTSCMVMARBJ8+6V7PR6aEQH3j6n5J3j65p2+z1NZO8=; b=UksY+3sHxtmd000F0n0NS59LVa9rPNuBBsCqCW2Z+5cSjBNALzCo+IQsXLb/zixC rndqzL7WlMfikMIAx1XNYbTTA5eNVQql9XEY2NPER5hc2CLvMK/cLJTAGjXFMgqbg6c 9lZjGjcIUV2AaVWMaF8+3fPftqBd9fNU+pDqKzGg= Received: from localhost (i5E862CB7.versanet.de [94.134.44.183]) by mx.zohomail.com with SMTPS id 1672251826397217.49030839514467; Wed, 28 Dec 2022 10:23:46 -0800 (PST) User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus To: 55120-done@debbugs.gnu.org Subject: =?utf-8?Q?=E2=80=9Cguix?= import =?utf-8?Q?cran=E2=80=9D?= fails for some git repositories Date: Wed, 28 Dec 2022 19:22:36 +0100 X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87mt779ykx.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 55120-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) This has been fixed in the meantime. If you still have this problem you may need to remove your git checkout cache in ~/.cache/guix/checkouts. -- Ricardo From unknown Sat Jun 21 10:35:46 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Thu, 26 Jan 2023 12:24:04 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator