From unknown Wed Aug 20 01:21:38 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#61250] [PATCH 1/3] gnu: Add r-viper. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 03 Feb 2023 12:20:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 61250 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61250@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.16754267694963 (code B ref -1); Fri, 03 Feb 2023 12:20:01 +0000 Received: (at submit) by debbugs.gnu.org; 3 Feb 2023 12:19:29 +0000 Received: from localhost ([127.0.0.1]:36658 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNv2O-0001Hu-I6 for submit@debbugs.gnu.org; Fri, 03 Feb 2023 07:19:28 -0500 Received: from lists.gnu.org ([209.51.188.17]:39724) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNv2M-0001Hk-2Q for submit@debbugs.gnu.org; Fri, 03 Feb 2023 07:19:27 -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 1pNv2K-0005Xk-JR for guix-patches@gnu.org; Fri, 03 Feb 2023 07:19:24 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pNv2I-0005p5-A6 for guix-patches@gnu.org; Fri, 03 Feb 2023 07:19:24 -0500 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=1675426749; x=1677241150; bh=yXMCYYaKRkcpM8P enon+bzc41XnrJnjp7pfBmpmFWWs=; b=AwxynC8ZP7d0gm/Oj6WWloOYhGMeVXA /3ai8pdLSw71LinqK1LLvlmHWeUtTc4xNWVbEWAi76XLaAW48T7DlocPcwLaoOkK z9pwFd3FFiuZbO0kjYaIXDt2VjS6W2ixdy+DS0P4JHxHNNJZ9g2vSi1BBLMT2qU3 4wJ3CQtISYEw= 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 2205F30046A for ; Fri, 3 Feb 2023 13:19:06 +0100 (CET) Received: from localhost.localdomain (10.84.128.45) 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, 3 Feb 2023 13:19:05 +0100 From: Navid Afkhami Date: Fri, 3 Feb 2023 13:18:52 +0100 Message-ID: <20230203121854.95308-1-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [10.84.128.45] 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-14.0.0.3092-9.0.1002-27424.007 X-TM-AS-Result: No-10-2.372600-5.000000 X-TMASE-MatchedRID: 4r2MyAYFTnf/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEMwD q5LCkpMyRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v9AKgfO6jacGaY5ZGw7wyeHvSr X73EbCvzF+KCpGE37CJsoi2XrUn/J8m+hzBStantdY+ZoWiLIm8K21zBg2Klf+gmVy5VdZkmfrd mIETRVJ87q+UfprFy0Z/QAh+OcADEdfRFpwHjBvzmcRWGv0Z11+KPePv/jwUtPGwBtlzRKvdyNs TVQr6HGarvaEx2RCcooQg4MrLBPLqN8mCVfMdDqzFFXNLNe3bF/6uEw9r+ytQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-2.372600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27424.007 X-TM-SNTS-SMTP: C8F6CBFBE2B4DB989EA6D0CD98E8BBCE891A3EAA3FAAA7DAEB1AA67237822D292002:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=Navid.Afkhami@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: -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/bioconductor.scm (r-viper): New variable. --- gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 711b988e7f..aeef6f4106 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8307,6 +8307,27 @@ (define-public r-variantannotation coding changes and predict coding outcomes.") (license license:artistic2.0))) +(define-public r-viper + (package + (name "r-viper") + (version "1.32.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "viper" version)) + (sha256 + (base32 + "11i2q9nakh534nx2l736id7k1yqhk7jpg32sbfl4vrnh398q86h6")))) + (properties `((upstream-name . "viper"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-e1071 r-kernsmooth r-mixtools)) + (home-page "https://bioconductor.org/packages/viper") + (synopsis + "Virtual inference of protein-activity by enriched regulon analysis") + (description + "Inference of protein activity from gene expression data. +Including the VIPER and msVIPER algorithms") + (license license:gpl2+))) + (define-public r-vsn (package (name "r-vsn") -- 2.34.1 From unknown Wed Aug 20 01:21:38 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#61250: closed ([PATCH 1/3] gnu: Add r-viper.) Message-ID: References: <87ilgi92c2.fsf@elephly.net> <20230203121854.95308-1-navid.afkhami@mdc-berlin.de> X-Gnu-PR-Message: they-closed 61250 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 61250@debbugs.gnu.org Date: Fri, 03 Feb 2023 15:50:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1675439402-14377-1" This is a multi-part message in MIME format... ------------=_1675439402-14377-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #61250: [PATCH 1/3] gnu: Add r-viper. 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 61250@debbugs.gnu.org. --=20 61250: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D61250 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1675439402-14377-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 61250-done) by debbugs.gnu.org; 3 Feb 2023 15:49:18 +0000 Received: from localhost ([127.0.0.1]:39809 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNyJO-0003if-Ur for submit@debbugs.gnu.org; Fri, 03 Feb 2023 10:49:18 -0500 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21159) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNyJI-0003iQ-MO for 61250-done@debbugs.gnu.org; Fri, 03 Feb 2023 10:49:13 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1675439346; cv=none; d=zohomail.com; s=zohoarc; b=JhWgVbqEJaPbWc7uzTmfMjWZHmGrOgq5JAfTirXzXidtJ76P4KQ/oMcNrmNUMRjnxpJnWULcsts3TQ19XfxnXHJVFnKe63oVlZLsJXgWNfQPSa7vb9KceYJYMRoTOsZgRDKxXNdKL3wlYjsISTN9vCrG9q3/2DaExoSdn3ZkcCs= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1675439346; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=u+dcL/eCrkKHozUnL09bgjopTsPKS4zpPYdgU3NWb4s=; b=FOSfH5gq2zOaFRHHV46Hx7bnRJHY/irDA1p7Dk9PQ1djPZ36viI1VFyymbd/NoiiqR3sgxcis2oJTn3R1FPUQs9dKEneCYf5jvHiWrdzHlrCtSHDMbYnP8vYETEy1tejRC0vvDYCWhgvAJ/AeEyrKrspKvkgDGfP/7isCgPEycE= 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=1675439346; 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=u+dcL/eCrkKHozUnL09bgjopTsPKS4zpPYdgU3NWb4s=; b=XmOnT4IwxqWPHEf9Njx4iQacbQNsMXWr1409lO0uNWA9+uCnTjbUX7+1I6B1TAb9 I+sU4eGx9AbnzLHuDzAw2gixzRMx9t+OGM8vMT+oMlB18IiXikwZ7bpfVCs6WQRXG2x MEYUIE7kEi4wDPluFc8PbNpX612iuCmLeyKaG6KE= Received: from localhost (i5E862D0C.versanet.de [94.134.45.12]) by mx.zohomail.com with SMTPS id 1675439344645312.03422799073553; Fri, 3 Feb 2023 07:49:04 -0800 (PST) User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus To: 61250-done@debbugs.gnu.org Subject: [PATCH 1/3] gnu: Add r-viper. Date: Fri, 03 Feb 2023 16:47:28 +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: <87ilgi92c2.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 61250-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 (-) Unfortunately, we cannot add this to Guix. The license says: c. You agree that You will only use the Program and Documentation for non-commercial internal academic or educational research purposes only. You will not (i) reproduce or copy the Program (ii) use, or cause or permit the use of, the Program in whole or in part for any purpose other than as permitted under this License; (iii) distribute, sell, lease, license or otherwise make the Program available to a third party outside Your organization; or (iv) reverse engineer, decompile, or disassemble the Program. I have instead added the package to guix-science-nonfree. -- Ricardo ------------=_1675439402-14377-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 3 Feb 2023 12:19:29 +0000 Received: from localhost ([127.0.0.1]:36658 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNv2O-0001Hu-I6 for submit@debbugs.gnu.org; Fri, 03 Feb 2023 07:19:28 -0500 Received: from lists.gnu.org ([209.51.188.17]:39724) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNv2M-0001Hk-2Q for submit@debbugs.gnu.org; Fri, 03 Feb 2023 07:19:27 -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 1pNv2K-0005Xk-JR for guix-patches@gnu.org; Fri, 03 Feb 2023 07:19:24 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pNv2I-0005p5-A6 for guix-patches@gnu.org; Fri, 03 Feb 2023 07:19:24 -0500 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=1675426749; x=1677241150; bh=yXMCYYaKRkcpM8P enon+bzc41XnrJnjp7pfBmpmFWWs=; b=AwxynC8ZP7d0gm/Oj6WWloOYhGMeVXA /3ai8pdLSw71LinqK1LLvlmHWeUtTc4xNWVbEWAi76XLaAW48T7DlocPcwLaoOkK z9pwFd3FFiuZbO0kjYaIXDt2VjS6W2ixdy+DS0P4JHxHNNJZ9g2vSi1BBLMT2qU3 4wJ3CQtISYEw= 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 2205F30046A for ; Fri, 3 Feb 2023 13:19:06 +0100 (CET) Received: from localhost.localdomain (10.84.128.45) 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, 3 Feb 2023 13:19:05 +0100 From: Navid Afkhami To: Subject: [PATCH 1/3] gnu: Add r-viper. Date: Fri, 3 Feb 2023 13:18:52 +0100 Message-ID: <20230203121854.95308-1-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [10.84.128.45] 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-14.0.0.3092-9.0.1002-27424.007 X-TM-AS-Result: No-10-2.372600-5.000000 X-TMASE-MatchedRID: 4r2MyAYFTnf/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEMwD q5LCkpMyRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v9AKgfO6jacGaY5ZGw7wyeHvSr X73EbCvzF+KCpGE37CJsoi2XrUn/J8m+hzBStantdY+ZoWiLIm8K21zBg2Klf+gmVy5VdZkmfrd mIETRVJ87q+UfprFy0Z/QAh+OcADEdfRFpwHjBvzmcRWGv0Z11+KPePv/jwUtPGwBtlzRKvdyNs TVQr6HGarvaEx2RCcooQg4MrLBPLqN8mCVfMdDqzFFXNLNe3bF/6uEw9r+ytQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-2.372600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27424.007 X-TM-SNTS-SMTP: C8F6CBFBE2B4DB989EA6D0CD98E8BBCE891A3EAA3FAAA7DAEB1AA67237822D292002:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=Navid.Afkhami@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: -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/bioconductor.scm (r-viper): New variable. --- gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 711b988e7f..aeef6f4106 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8307,6 +8307,27 @@ (define-public r-variantannotation coding changes and predict coding outcomes.") (license license:artistic2.0))) +(define-public r-viper + (package + (name "r-viper") + (version "1.32.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "viper" version)) + (sha256 + (base32 + "11i2q9nakh534nx2l736id7k1yqhk7jpg32sbfl4vrnh398q86h6")))) + (properties `((upstream-name . "viper"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-e1071 r-kernsmooth r-mixtools)) + (home-page "https://bioconductor.org/packages/viper") + (synopsis + "Virtual inference of protein-activity by enriched regulon analysis") + (description + "Inference of protein activity from gene expression data. +Including the VIPER and msVIPER algorithms") + (license license:gpl2+))) + (define-public r-vsn (package (name "r-vsn") -- 2.34.1 ------------=_1675439402-14377-1--