From unknown Fri Jun 20 19:54:33 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#73025] [PATCH] gnu: Add r-pairwiseadonis. 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Change-Id: Idf7ad9efa3625bb60663f421ec79d0a69170e4dd --- gnu/packages/bioinformatics.scm | 50 ++++++++++++++++++++++++++++++++- 1 file changed, 49 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4653360792..0206ebe1a3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11,7 +11,7 @@ ;;; Copyright © 2017, 2021, 2022, 2024 Arun Isaac ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Gábor Boskovits -;;; Copyright © 2018-2023 Mădălin Ionel Patrașcu +;;; Copyright © 2018-2024 Mădălin Ionel Patrașcu ;;; Copyright © 2019, 2020, 2021, 2023 Maxim Cournoyer ;;; Copyright © 2019 Brian Leung ;;; Copyright © 2019 Brett Gilio @@ -13155,6 +13155,54 @@ (define-public r-pairadise (propagated-inputs (list r-doparallel r-foreach r-iterators r-nloptr)) (license license:expat))) +(define-public r-pairwiseadonis + ;; There is no tag for version 0.4.1, nor is there a release archive. + (let ((commit "cb190f7668a0c82c0b0853927db239e7b9ec3e83") + (revision "1")) + (package + (name "r-pairwiseadonis") + ;; The versioning scheme of this package is inconsistent, with versions + ;; progressing from 0.21 to 0.3 and then to 0.4.1, which does not follow + ;; a standard numerical order or convention (e.g., semantic versioning). + (version (git-version "0.4.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pmartinezarbizu/pairwiseAdonis") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "11hl6qqmr5vns476921802y0qmb46i1jf0rf7xfkyswlh6xkcl99")))) + (properties `((upstream-name . "pairwiseAdonis"))) + (build-system r-build-system) + (arguments + (list + #:phases + ;; Move into the subdirectory containing the R package files + '(modify-phases %standard-phases + (add-after 'unpack 'move-to-subdir + (lambda _ (chdir "pairwiseAdonis")))))) + (propagated-inputs + (list r-cluster + r-permute + r-vegan)) + (synopsis "Pairwise multilevel comparison using adonis") + (description + "This package implements two functions: +@itemize +@item @code{pairwise.adonis} is a wrapper function for multilevel pairwise +comparison using adonis2 from package vegan. The function returns adjusted +p-values using @code{p.adjust()}. It does not accept interaction between factors +neither strata. +@item @code{pairwise.adonis2} accepts a model formula like in adonis from vegan. +You can use interactions between factors and define strata to constrain +permutations. For pairwise comparison a list of unique pairwise combination of +factors is produced. +@end itemize") + (home-page "https://github.com/pmartinezarbizu/pairwiseAdonis") + (license license:gpl2+)))) + (define-public pardre (package (name "pardre") base-commit: 7fa9df431e9423e2b79c8c520de1d0ef7aed910d -- 2.45.2 From unknown Fri Jun 20 19:54:33 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: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Subject: bug#73025: closed (Close) Message-ID: References: X-Gnu-PR-Message: they-closed 73025 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 73025@debbugs.gnu.org Date: Sat, 21 Sep 2024 07:28:03 +0000 Content-Type: multipart/mixed; boundary="----------=_1726903683-17414-1" This is a multi-part message in MIME format... ------------=_1726903683-17414-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #73025: [PATCH] gnu: Add r-pairwiseadonis. 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 73025@debbugs.gnu.org. --=20 73025: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D73025 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1726903683-17414-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 73025-done) by debbugs.gnu.org; 21 Sep 2024 07:27:50 +0000 Received: from localhost ([127.0.0.1]:36961 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sruWz-0004W4-Ly for submit@debbugs.gnu.org; Sat, 21 Sep 2024 03:27:49 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:53728) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sruWx-0004Vh-FJ; Sat, 21 Sep 2024 03:27:47 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 1B81F3CA; Sat, 21 Sep 2024 09:27:21 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id ytNwJuG1wbBb; Sat, 21 Sep 2024 09:27:20 +0200 (CEST) Received: from jurong (unknown [IPv6:2001:861:c4:f2f0::c64]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 8D270332; Sat, 21 Sep 2024 09:27:20 +0200 (CEST) Date: Sat, 21 Sep 2024 09:27:18 +0200 From: Andreas Enge To: 73025-done@debbugs.gnu.org, 73017-done@debbugs.gnu.org Subject: Close Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 73025-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 (-) Pushed, thanks! Andreas ------------=_1726903683-17414-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 4 Sep 2024 11:47:10 +0000 Received: from localhost ([127.0.0.1]:33710 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sloTd-0006vH-Tq for submit@debbugs.gnu.org; Wed, 04 Sep 2024 07:47:10 -0400 Received: from lists.gnu.org ([209.51.188.17]:41884) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sloTb-0006v8-8C for submit@debbugs.gnu.org; Wed, 04 Sep 2024 07:47:08 -0400 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 1sloSY-0006ZH-0x for guix-patches@gnu.org; Wed, 04 Sep 2024 07:46:02 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sloSS-0006AB-73 for guix-patches@gnu.org; Wed, 04 Sep 2024 07:46:00 -0400 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=1725449972; x=1727264373; bh=LPMV5uQks+MFlJG OPRVwIKNeLJ/iUIWVE/Tmoh1EHA4=; b=TF4qCaclyg4ehvlrF5CRkZyMJA6IL5M 2Y+VU9I+WpvNRNkAXid5Cui3Qhy8r9ouBxXSC/D/zFtgebsS1e1Ty0/x9vCF2Kny 4FH0QjOq6DqPY8cgGLotKeme9e8Lb00b6ouHiC0u3EtbHXs7OuPpK83KmQP+mAyl r+OisRDN0uVg= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 409BE1601D5 for ; Wed, 4 Sep 2024 13:39:32 +0200 (CEST) Received: from cl-akalin11.mdc-berlin.net (141.80.219.20) 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 15.2.1544.11; Wed, 4 Sep 2024 13:39:31 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-pairwiseadonis. Date: Wed, 4 Sep 2024 13:37:40 +0200 Message-ID: X-Mailer: git-send-email 2.45.2 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.219.20] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3152-9.1.2019-28640.007 X-TM-AS-Result: No-10--3.702000-5.000000 X-TMASE-MatchedRID: huMMtcahIlBYhP20o6vOMFY9XYa1m8xAJ3y+iqiko29rIVA3IGfCC6DE DQa+uiKUQpP6/vBOuJO+ZX5NgfjmnAnNYZr04T6RkeKjJDBQ5DpR3UkpERYmZK3tRi3BwhSzE83 tqeQrbIbcVgld+UcaEg6tmPhDRPB72LCsQMUxaolgFLgE7TxyQ1/SKo1alLC4ixGjypoW7ac/u5 gb+XjzzW/lCyzZ5/9zcwoQmcDvcnyU8+AkVynQBGy53dw2JHQmdXI+BffqLuQ2v41fguYI5e+dp uWEKnR/x0ulmXsvhgH59xqSiQVT0PArB6nbKtYX0PrEu9fgzgi59u66wM4v4nIpRBPj43vPVc6o xg15iGbpCnPgkxvrgAlRHKqdgWoj2k5RhlnTpfjDFkiary56Z4VgVvW8uI0CA+hfHLpPyedsv1s AtwiKT8tRnvFfq98bS9zgHsvoUe/Fg79k2EbyJbTnVnv1JP77sGTvZJmllrz/PhPL0kApH8kjm+ elEcbI X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.702000-5.000000 X-TMASE-Version: SMEX-14.0.0.3152-9.1.2019-28640.007 X-TM-SNTS-SMTP: 76CD4C1B24EA75BD4A129C0AFA1794A625496655FA3ABBB3E5DE29A6572D9AFF2000:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=b2062.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, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) 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: -2.4 (--) * gnu/packages/bioinformatics.scm (r-pairwiseadonis): New variable. Change-Id: Idf7ad9efa3625bb60663f421ec79d0a69170e4dd --- gnu/packages/bioinformatics.scm | 50 ++++++++++++++++++++++++++++++++- 1 file changed, 49 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4653360792..0206ebe1a3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11,7 +11,7 @@ ;;; Copyright © 2017, 2021, 2022, 2024 Arun Isaac ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Gábor Boskovits -;;; Copyright © 2018-2023 Mădălin Ionel Patrașcu +;;; Copyright © 2018-2024 Mădălin Ionel Patrașcu ;;; Copyright © 2019, 2020, 2021, 2023 Maxim Cournoyer ;;; Copyright © 2019 Brian Leung ;;; Copyright © 2019 Brett Gilio @@ -13155,6 +13155,54 @@ (define-public r-pairadise (propagated-inputs (list r-doparallel r-foreach r-iterators r-nloptr)) (license license:expat))) +(define-public r-pairwiseadonis + ;; There is no tag for version 0.4.1, nor is there a release archive. + (let ((commit "cb190f7668a0c82c0b0853927db239e7b9ec3e83") + (revision "1")) + (package + (name "r-pairwiseadonis") + ;; The versioning scheme of this package is inconsistent, with versions + ;; progressing from 0.21 to 0.3 and then to 0.4.1, which does not follow + ;; a standard numerical order or convention (e.g., semantic versioning). + (version (git-version "0.4.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pmartinezarbizu/pairwiseAdonis") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "11hl6qqmr5vns476921802y0qmb46i1jf0rf7xfkyswlh6xkcl99")))) + (properties `((upstream-name . "pairwiseAdonis"))) + (build-system r-build-system) + (arguments + (list + #:phases + ;; Move into the subdirectory containing the R package files + '(modify-phases %standard-phases + (add-after 'unpack 'move-to-subdir + (lambda _ (chdir "pairwiseAdonis")))))) + (propagated-inputs + (list r-cluster + r-permute + r-vegan)) + (synopsis "Pairwise multilevel comparison using adonis") + (description + "This package implements two functions: +@itemize +@item @code{pairwise.adonis} is a wrapper function for multilevel pairwise +comparison using adonis2 from package vegan. The function returns adjusted +p-values using @code{p.adjust()}. It does not accept interaction between factors +neither strata. +@item @code{pairwise.adonis2} accepts a model formula like in adonis from vegan. +You can use interactions between factors and define strata to constrain +permutations. For pairwise comparison a list of unique pairwise combination of +factors is produced. +@end itemize") + (home-page "https://github.com/pmartinezarbizu/pairwiseAdonis") + (license license:gpl2+)))) + (define-public pardre (package (name "pardre") base-commit: 7fa9df431e9423e2b79c8c520de1d0ef7aed910d -- 2.45.2 ------------=_1726903683-17414-1--