From unknown Wed Jun 18 23:04:39 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#58511 <58511@debbugs.gnu.org> To: bug#58511 <58511@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add r-tximportdata. X-Debbugs-Cc: rekado@elephly.net Reply-To: bug#58511 <58511@debbugs.gnu.org> Date: Thu, 19 Jun 2025 06:04:39 +0000 retitle 58511 [PATCH] gnu: Add r-tximportdata. X-Debbugs-Cc: rekado@elephly= .net reassign 58511 guix-patches submitter 58511 M=C4=83d=C4=83lin Ionel Patra=C8=99cu severity 58511 normal tag 58511 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Fri Oct 14 07:12:43 2022 Received: (at submit) by debbugs.gnu.org; 14 Oct 2022 11:12:43 +0000 Received: from localhost ([127.0.0.1]:35923 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ojIcM-0005Ue-N4 for submit@debbugs.gnu.org; Fri, 14 Oct 2022 07:12:43 -0400 Received: from lists.gnu.org ([209.51.188.17]:45562) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ojIcL-0005UX-Gh for submit@debbugs.gnu.org; Fri, 14 Oct 2022 07:12:41 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:56600) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ojIcL-0006fX-17 for guix-patches@gnu.org; Fri, 14 Oct 2022 07:12:41 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:47109) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ojIcH-0007Hk-LN for guix-patches@gnu.org; Fri, 14 Oct 2022 07:12:40 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1665745949; x=1667560350; bh=cnBgPQK8Uck0gLK kukyD4sw3Zgb1fkAJX7DsWEX/EzE=; b=Kawix76hGhQhXLWlgpPszEPvVaKAlqo CmoqJnf1cGrVo36t+V+MCunXHPWJKWOfd/kFzvCCXqJ1QywcTCh2Q00uG0XZvKNb xZuxM87EussY9h3hN8a/iYfgBmdOo37QkJLaK9zcZ7RkOjZKykIDGxvYiKT8QfRs 7AP/UflDR5Ss= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 6F61330038E for ; Fri, 14 Oct 2022 13:12:29 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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 15.1.2507.12; Fri, 14 Oct 2022 13:12:28 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-tximportdata. X-Debbugs-Cc: rekado@elephly.net Date: Fri, 14 Oct 2022 13:12:16 +0200 Message-ID: <20221014111216.1389-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.3 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27200.007 X-TM-AS-Result: No-10--4.547400-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCxSHjB5Y+o5ZMay5jJvrxqMycO hvTXTlouSkIUZyUQUJ1365UWdO2/F0N7DjAdxZNTi8zVgXoAltuJ5hXsnxp7jC24oEZ6SpSl2+n EixMccdpFOlJCK/1ftAYOAIXRfir7ZyBslBmRlcMKIeBxEtwDlPDrTewFEoV7qR2uAT/IAeD/5Y ZwkJxZdhRUxmmdaWXSDfVvgmJtrvJ3L8i8NnELX0r6EbbNJLyTcUke23u350xU7OJY7bdPeD9iv /sJMsVc7Oyi/ulxQeKUgZdIaXg4f X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.547400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27200.007 X-TM-SNTS-SMTP: C92AA5C6CCD7F35779EE265A49FD19016B4B4FE8E603A37DFF96B61C496B49E92002:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=c2062.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: -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/bioconductor.scm (r-tximportdata): New variable. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ecb60f2e24..bfb773672b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1605,6 +1605,30 @@ (define-public r-tcgabiolinksgui-data TCGAbiolinksGUI package.") (license license:gpl3))) +(define-public r-tximportdata + (package + (name "r-tximportdata") + (version "1.24.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "tximportData" version + 'experiment)) + (sha256 + (base32 + "0mgbwpybg2xd6x1ijrflmjh5w63qz6ylnzszbbyp437n618m7riy")))) + (properties `((upstream-name . "tximportData"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/tximportData") + (synopsis "Data for the tximport package") + (description + "This package provides the output of running various transcript abundance +quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The +quantifiers were @code{Cufflinks}, @code{RSEM}, @code{kallisto}, @code{Salmon} +and @code{Sailfish}. @code{alevin} example output is also included.") + (license license:gpl2+))) + + ;;; Packages base-commit: 10d429f2fce321d8285684503094694ec3979865 -- 2.37.3 From debbugs-submit-bounces@debbugs.gnu.org Thu Oct 27 09:24:48 2022 Received: (at 58511-done) by debbugs.gnu.org; 27 Oct 2022 13:24:48 +0000 Received: from localhost ([127.0.0.1]:56460 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oo2sJ-0002ZR-VN for submit@debbugs.gnu.org; Thu, 27 Oct 2022 09:24:48 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21114) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oo2sH-0002ZI-55 for 58511-done@debbugs.gnu.org; Thu, 27 Oct 2022 09:24:46 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1666877083; cv=none; d=zohomail.com; s=zohoarc; b=al7GHPpoMD3Mk9lf1lXLGd1nKGgBYL+PqK0OYqr5fwjP46O3ymOIkQhzlI3YCdLUT4VIwBsK6W7xneJ/Tj8Oea4SrcFLrdqsTo/NW3cYUKQvt6v/GACLVgSGmRCUI2n6LYng8v7F5eJKCBzo9ewBQ7b60bSgvb1Jnt8VmKM2YCw= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1666877083; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=jy8Ka3x/jqcjVVE54keDwxlqwnnwuIHi1Ps2q8S6KaU=; b=E3CEkghsfU8Xtp4WZa1vUSWmHGI9F1m6m3ZsxpIIG1asFhKM6Ex5GwZVGsbsHlWAfFKhY4nyyJdQYJGPTAcpA/d3JEjGSOKJhVdjnX0Jwx3k8OmxvXHThHg6IpPeMWeJuJ9a109sibRwjOTLJtfc7DqVcISwSYG4y6knmdpy1ec= 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=1666877083; 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=jy8Ka3x/jqcjVVE54keDwxlqwnnwuIHi1Ps2q8S6KaU=; b=K9LqhTmC4VEmJf7JAX2c/yVNSZkuqqbdVpJ0FOdjh3Ml3mv1ZADzFpayfuZPHGVI Sr9NmbGBCDkpbzzsSvwZNmBC1DOJNFXMxcpnXLg8lwXOlXd5Qf04GFdvF1AtvOI/JDa Fdp/n1cg9Bd/9sIdT0a0F+Mx9QbXOIH6Fc+84Zdg= Received: from localhost (151-110-142-46.pool.kielnet.net [46.142.110.151]) by mx.zohomail.com with SMTPS id 1666877081646890.8831561709264; Thu, 27 Oct 2022 06:24:41 -0700 (PDT) User-agent: mu4e 1.8.9; emacs 28.1 From: Ricardo Wurmus To: 58511-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-tximportdata. 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