From unknown Sat Aug 16 21:01:00 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#61097] [PATCH] gnu: Add r-castor. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 27 Jan 2023 15:06:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 61097 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61097@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.167483195823229 (code B ref -1); Fri, 27 Jan 2023 15:06:02 +0000 Received: (at submit) by debbugs.gnu.org; 27 Jan 2023 15:05:58 +0000 Received: from localhost ([127.0.0.1]:38242 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pLQIf-00062b-T2 for submit@debbugs.gnu.org; Fri, 27 Jan 2023 10:05:58 -0500 Received: from lists.gnu.org ([209.51.188.17]:56896) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pLQIc-00062R-LT for submit@debbugs.gnu.org; Fri, 27 Jan 2023 10:05:56 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pLQIc-0003sp-9G for guix-patches@gnu.org; Fri, 27 Jan 2023 10:05:54 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pLQIY-0004rI-9o for guix-patches@gnu.org; Fri, 27 Jan 2023 10:05:54 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1674831929; x=1676646330; bh=yR4ZjddZ/0spLiH yAVuZw9/9ZAMFiQVJtbeBPhDJ/Rw=; b=IZ0Xvm0L3jJIftvKKNSEagz5U0S0Tz2 rdkAENFOAGiiRzuT7lRV97dOujv8QnDPeP/H9hKUUnhqWYiFN4OsCCtE0ASVzwo/ +qSMVNyzrloBdE6AYi2UM8NZC0CAIlSOYfqMg8FgSgDGYjAEeNm1ynoLbOn9+lQ1 nEfe8pFiIDV8= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 69DB8A0524 for ; Fri, 27 Jan 2023 16:05:29 +0100 (CET) Received: from localhost.localdomain (10.84.128.74) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.17; Fri, 27 Jan 2023 16:05:28 +0100 From: Navid Afkhami Date: Fri, 27 Jan 2023 16:05:17 +0100 Message-ID: <20230127150517.33849-1-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [10.84.128.74] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27412.000 X-TM-AS-Result: No-10-0.480600-5.000000 X-TMASE-MatchedRID: GQw6Xh/XS6X/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOU8ftiyKjZrRjx 55n/478OoK9M8rNZd7SpAHLwSiW7QpT6aKfZ6tn9a87CDXaKRVJITEcvqjcF4EJZ5MDd4/kU5wM PMqdPNSx+CxzcGwLNWDdXvUUlUc7GjCdeLVo6OBizdz0FxOSzHLEPn6mTzpGcjpvD0UdCUNwpzW EpqR83WRDGJu1g7pgtElOOOz3JPpijxYyRBa/qJUl4W8WVUOR/9xS3mVzWUuAojN1lLei7RSjos msRelswCnx7T6kteE9PcmRc+loXpVC0oCDPBfysvBGlMg3nj9DBVY4Zi/dzLNCRVyzhs88BeTWn SrIpo03LMoz9JPXm11koJqWxWZxCNZA9irUk5qtj27eUrb9iufzsdE1PQouS X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.480600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27412.000 X-TM-SNTS-SMTP: E0A7ED4C554AA958E84504A1F593FF99567F8D9F7438AF5C2C0E97F074B2E11B2002:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=a2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 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_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -2.3 (--) 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: -3.3 (---) * gnu/packages/cran.scm (r-castor): New variable. --- gnu/packages/cran.scm | 28 +++++++++++++++++++++++++++- 1 file changed, 27 insertions(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dce349890a..51c9230156 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -35,7 +35,7 @@ ;;; Copyright © 2020 Aniket Patil ;;; Copyright © 2021 Marcel Schilling ;;; Copyright © 2021 Guillaume Le Vaillant -;;; Copyright © 2022 Navid Afkhami +;;; Copyright © 2022,2023 Navid Afkhami ;;; Copyright © 2022 Greg Hogan ;;; ;;; This file is part of GNU Guix. @@ -256,6 +256,32 @@ (define-public r-cachem automatically pruning objects to maintain the constraints.") (license license:expat))) +(define-public r-castor + (package + (name "r-castor") + (version "1.7.6") + (source (origin + (method url-fetch) + (uri (cran-uri "castor" version)) + (sha256 + (base32 + "1qbndwmzzpkzgiah0hgid9z5f9iv2j53d515bjcci1591gx1fk36")))) + (properties `((upstream-name . "castor"))) + (build-system r-build-system) + (propagated-inputs (list r-matrix r-naturalsort r-rcpp r-rspectra)) + (home-page "https://cran.r-project.org/package=castor") + (synopsis "Efficient phylogenetics on large trees") + (description + "This tool analyses on massive phylogenies comprising up to millions of tips. +Functions include pruning, rerooting, calculation of most-recent +common ancestors, calculating distances from the tree root and calculating +pairwise distances. In addition, This tool takes care of Calculation of +phylogenetic signal and mean trait depth (trait conservatism), ancestral state +reconstruction and hidden character prediction of discrete characters, simulating +and fitting models of trait evolution, fitting and simulating diversification +models, dating trees, comparing trees, and reading/writing trees in Newick format.") + (license license:gpl2+))) + (define-public r-collections (package (name "r-collections") -- 2.34.1 From unknown Sat Aug 16 21:01:00 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Navid Afkhami Subject: bug#61097: closed ([PATCH] gnu: Add r-castor.) Message-ID: References: <87k017bxna.fsf@elephly.net> <20230127150517.33849-1-navid.afkhami@mdc-berlin.de> X-Gnu-PR-Message: they-closed 61097 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 61097@debbugs.gnu.org Date: Fri, 27 Jan 2023 19:12:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1674846722-15834-1" This is a multi-part message in MIME format... ------------=_1674846722-15834-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #61097: [PATCH] gnu: Add r-castor. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 61097@debbugs.gnu.org. --=20 61097: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D61097 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1674846722-15834-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 61097-done) by debbugs.gnu.org; 27 Jan 2023 19:11:52 +0000 Received: from localhost ([127.0.0.1]:38501 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pLU8e-000471-DO for submit@debbugs.gnu.org; Fri, 27 Jan 2023 14:11:52 -0500 Received: from sender3-of-o57.zoho.com ([136.143.184.57]:21748) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pLU8a-00046r-MO for 61097-done@debbugs.gnu.org; Fri, 27 Jan 2023 14:11:50 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1674846706; cv=none; d=zohomail.com; s=zohoarc; b=UNkRryg0ueIiaiMVN8vZkZNAjEeYoQKDEBkW+rHOeHGaKSCv5zsKcHBIou6t4daxNpYuE3ICAnCoZJ7YZSk3QWklUGGuS+nTvoGhHZMwt6pkfRTqRmkHiVroGV8U4QK/LWxFPOrY4GCopCaOgGFDTbQg+2ZK0UR5mwHpcWV8igI= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1674846706; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=/tsbLiiSDN9eoHYFSVVdrKdE13fldLzUu8+v6AwnNJ4=; b=DBAQkgtjwvdmZUOQrXcdohCzUmbcRB12+WkxcZ240wLnmSInPqMmfvxuKFuXST/DQm7oKJzZ4kqltHi0UT0wa8ccGsGMvCCzp2vQFiQnnoh7sic2vnxALZvSzFLXg40riGIZls5FwAMtSmoSXghUfVk5shpDo2JVajT2bnobY3I= 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=1674846706; 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=/tsbLiiSDN9eoHYFSVVdrKdE13fldLzUu8+v6AwnNJ4=; b=QrL33R9IheEK3YwozATF6s6UfiDvRLq0Y46g5tc+C4hmNVK0tcId5HHapBE0B76O R4KqJhTCQ9Zq+c/sXHXmN/+EmvFVeENSLawG4UUElvJzZ0F6O7G4QB34tMNgywUx6po FgYtvdyVkDSx56HkBsxoza4Qh3pXH4Q5RugVwZEM= Received: from localhost (196-108-142-46.pool.kielnet.net [46.142.108.196]) by mx.zohomail.com with SMTPS id 1674846700540306.9026500351663; Fri, 27 Jan 2023 11:11:40 -0800 (PST) User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus To: 61097-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-castor. Date: Fri, 27 Jan 2023 20:10:56 +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: <87k017bxna.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 61097-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 (-) Applied with commit 5ebbedea5803fcee3d99eb15bacca838bf4c124d, thank you! -- Ricardo ------------=_1674846722-15834-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 27 Jan 2023 15:05:58 +0000 Received: from localhost ([127.0.0.1]:38242 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pLQIf-00062b-T2 for submit@debbugs.gnu.org; Fri, 27 Jan 2023 10:05:58 -0500 Received: from lists.gnu.org ([209.51.188.17]:56896) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pLQIc-00062R-LT for submit@debbugs.gnu.org; Fri, 27 Jan 2023 10:05:56 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pLQIc-0003sp-9G for guix-patches@gnu.org; Fri, 27 Jan 2023 10:05:54 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pLQIY-0004rI-9o for guix-patches@gnu.org; Fri, 27 Jan 2023 10:05:54 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1674831929; x=1676646330; bh=yR4ZjddZ/0spLiH yAVuZw9/9ZAMFiQVJtbeBPhDJ/Rw=; b=IZ0Xvm0L3jJIftvKKNSEagz5U0S0Tz2 rdkAENFOAGiiRzuT7lRV97dOujv8QnDPeP/H9hKUUnhqWYiFN4OsCCtE0ASVzwo/ +qSMVNyzrloBdE6AYi2UM8NZC0CAIlSOYfqMg8FgSgDGYjAEeNm1ynoLbOn9+lQ1 nEfe8pFiIDV8= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 69DB8A0524 for ; Fri, 27 Jan 2023 16:05:29 +0100 (CET) Received: from localhost.localdomain (10.84.128.74) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.17; Fri, 27 Jan 2023 16:05:28 +0100 From: Navid Afkhami To: Subject: [PATCH] gnu: Add r-castor. Date: Fri, 27 Jan 2023 16:05:17 +0100 Message-ID: <20230127150517.33849-1-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [10.84.128.74] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27412.000 X-TM-AS-Result: No-10-0.480600-5.000000 X-TMASE-MatchedRID: GQw6Xh/XS6X/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOU8ftiyKjZrRjx 55n/478OoK9M8rNZd7SpAHLwSiW7QpT6aKfZ6tn9a87CDXaKRVJITEcvqjcF4EJZ5MDd4/kU5wM PMqdPNSx+CxzcGwLNWDdXvUUlUc7GjCdeLVo6OBizdz0FxOSzHLEPn6mTzpGcjpvD0UdCUNwpzW EpqR83WRDGJu1g7pgtElOOOz3JPpijxYyRBa/qJUl4W8WVUOR/9xS3mVzWUuAojN1lLei7RSjos msRelswCnx7T6kteE9PcmRc+loXpVC0oCDPBfysvBGlMg3nj9DBVY4Zi/dzLNCRVyzhs88BeTWn SrIpo03LMoz9JPXm11koJqWxWZxCNZA9irUk5qtj27eUrb9iufzsdE1PQouS X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.480600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27412.000 X-TM-SNTS-SMTP: E0A7ED4C554AA958E84504A1F593FF99567F8D9F7438AF5C2C0E97F074B2E11B2002:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=a2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 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_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -2.3 (--) 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: -3.3 (---) * gnu/packages/cran.scm (r-castor): New variable. --- gnu/packages/cran.scm | 28 +++++++++++++++++++++++++++- 1 file changed, 27 insertions(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dce349890a..51c9230156 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -35,7 +35,7 @@ ;;; Copyright © 2020 Aniket Patil ;;; Copyright © 2021 Marcel Schilling ;;; Copyright © 2021 Guillaume Le Vaillant -;;; Copyright © 2022 Navid Afkhami +;;; Copyright © 2022,2023 Navid Afkhami ;;; Copyright © 2022 Greg Hogan ;;; ;;; This file is part of GNU Guix. @@ -256,6 +256,32 @@ (define-public r-cachem automatically pruning objects to maintain the constraints.") (license license:expat))) +(define-public r-castor + (package + (name "r-castor") + (version "1.7.6") + (source (origin + (method url-fetch) + (uri (cran-uri "castor" version)) + (sha256 + (base32 + "1qbndwmzzpkzgiah0hgid9z5f9iv2j53d515bjcci1591gx1fk36")))) + (properties `((upstream-name . "castor"))) + (build-system r-build-system) + (propagated-inputs (list r-matrix r-naturalsort r-rcpp r-rspectra)) + (home-page "https://cran.r-project.org/package=castor") + (synopsis "Efficient phylogenetics on large trees") + (description + "This tool analyses on massive phylogenies comprising up to millions of tips. +Functions include pruning, rerooting, calculation of most-recent +common ancestors, calculating distances from the tree root and calculating +pairwise distances. In addition, This tool takes care of Calculation of +phylogenetic signal and mean trait depth (trait conservatism), ancestral state +reconstruction and hidden character prediction of discrete characters, simulating +and fitting models of trait evolution, fitting and simulating diversification +models, dating trees, comparing trees, and reading/writing trees in Newick format.") + (license license:gpl2+))) + (define-public r-collections (package (name "r-collections") -- 2.34.1 ------------=_1674846722-15834-1--