From unknown Sat Jun 21 10:42:51 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#54897] [PATCH] gnu: Add r-acde. Resent-From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 12 Apr 2022 22:32:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 54897 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 54897@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.164980267719012 (code B ref -1); Tue, 12 Apr 2022 22:32:01 +0000 Received: (at submit) by debbugs.gnu.org; 12 Apr 2022 22:31:17 +0000 Received: from localhost ([127.0.0.1]:50521 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1neP2a-0004wa-OG for submit@debbugs.gnu.org; Tue, 12 Apr 2022 18:31:16 -0400 Received: from lists.gnu.org ([209.51.188.17]:45180) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1neP2Y-0004wR-Q8 for submit@debbugs.gnu.org; Tue, 12 Apr 2022 18:31:15 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:39122) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1neP2Y-0001jO-KI for guix-patches@gnu.org; Tue, 12 Apr 2022 18:31:14 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:57943) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1neP2V-0001vZ-KZ for guix-patches@gnu.org; Tue, 12 Apr 2022 18:31:13 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id C2077160153 for ; Wed, 13 Apr 2022 00:31:07 +0200 (CEST) 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:received:received; s=mdc; t=1649802667; x=1651617068; bh=5i5320O5hB2P+Ar37jFrbymwftmp2uRkVyxBDWsPbWM=; b=lV2cZBzIAKi8 UqB7qP7ABxOunAjm51MUY3gO7aK5VvCjVKizVLnAw4E7I7eUSS/J/kUeBiewVj93 6cm4WOKwGzLKcGbdrnR1KZD/3dKFhPOerjeFq3N6bRNKyQ+XYWcsSxtMR8BXNi1H xl6RcjXbN6AEuGODiawEQt2H9sD0h1c= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id 77sc5AGybxKC for ; Wed, 13 Apr 2022 00:31:07 +0200 (CEST) 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 for ; Wed, 13 Apr 2022 00:31:06 +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 15.1.2375.24; Wed, 13 Apr 2022 00:31:06 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Wed, 13 Apr 2022 00:30:47 +0200 Message-ID: <20220412223047.9620-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.34.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1000-26830.003 X-TM-AS-Result: No-10--3.138900-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkyStUSqCaVPsZ8zsjIitoJnVTWWiNp+v/M6O3vXX/Za6Y5ZGw7wyeHNBL YK2KW3iIiqfmvD3r0Gvd70oiE2G0nrWL/xQJnm46rm7DrUlmNkIAy6p60ZV62fJ5/bZ6npdjKay T/BQTiGlxbwYSOR4POLTPUBLeBpBc342yLO18mKnpSOJv5kUYoh1oNp38qE0H/G75DAYp9piC8V xFsWpbpXCMv7Ki4hei8bfzpakBmnt+h8u/BEfb4tOdWe/Uk/vuwZO9kmaWWvP8+E8vSQCkfySOb 56URxsg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.138900-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1000-26830.003 X-TM-SNTS-SMTP: 8AE5EFDB9EBD2C6A547EDDAEE66DAD2B710BE9A4CA58494E566BCD7EDCE0FDAF2000: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-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-acde): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 803437a033..87cbbb24fc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11642,6 +11642,31 @@ (define-public r-universalmotif motifs, and others.") (license license:gpl3))) +(define-public r-acde + (package + (name "r-acde") + (version "1.24.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "acde" version)) + (sha256 + (base32 + "13ks87am73m3bjn9ljapxml2a9cxdpgv9flwvly8aqmi3ndxyqi6")))) + (properties `((upstream-name . "acde"))) + (build-system r-build-system) + (propagated-inputs (list r-boot)) + (home-page "https://bioconductor.org/packages/acde") + (synopsis + "Identification of differentially expressed genes with artificial components") + (description + "This package provides a multivariate inferential analysis method for +detecting differentially expressed genes in gene expression data. It uses +artificial components, close to the data's principal components but with an +exact interpretation in terms of differential genetic expression, to identify +differentially expressed genes while controlling the @dfn{false discovery rate} +(FDR).") + (license license:gpl3))) + ;; This is a CRAN package, but it depends on Bioconductor packages, so we put ;; it here. (define-public r-activedriverwgs -- 2.34.0 From unknown Sat Jun 21 10:42:51 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#54897: closed ([PATCH] gnu: Add r-acde.) Message-ID: References: <87a6cnx69c.fsf@elephly.net> <20220412223047.9620-1-madalinionel.patrascu@mdc-berlin.de> X-Gnu-PR-Message: they-closed 54897 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 54897@debbugs.gnu.org Date: Thu, 14 Apr 2022 11:19:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1649935142-22911-1" This is a multi-part message in MIME format... ------------=_1649935142-22911-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #54897: [PATCH] gnu: Add r-acde. 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 54897@debbugs.gnu.org. --=20 54897: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D54897 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1649935142-22911-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 54897-done) by debbugs.gnu.org; 14 Apr 2022 11:18:47 +0000 Received: from localhost ([127.0.0.1]:55425 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nexUt-0005x2-2T for submit@debbugs.gnu.org; Thu, 14 Apr 2022 07:18:47 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21109) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nexUr-0005wu-QX for 54897-done@debbugs.gnu.org; Thu, 14 Apr 2022 07:18:46 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1649935123; cv=none; d=zohomail.com; s=zohoarc; b=IXYD3JeKmIlLooOs+FWB16uRhje6rparDCrscClNV/fPWeDOf2m/nRL0N3agodOwYOPM2KKP9UxjZ/aT9UzGW+oZcN6rD3gPn4CXnyVpMIOpGwlSIknlkOlOZlubrVlJ0ufSkfeOjjlWFNVZVRJavK7Nge+pIvW+dKH2sFNnvv0= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1649935123; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=VG1LAp/EGbsdBwo79AT5alOgM25zAG9b1t+IIDa4dWU=; b=iYF5rgpQ9HDdVoZZC3QyslEujOC0G1G1K8p8Qqz71+zuvTxK61oApWz4ZqG57N4p1YpMMraO68/nVSMVvGtTzUwqj9KbGsziUkOcpesPr5wvLLzsXe1MaRtQoHm3adczQ7iN61+cwd8a7PPz4AsJlBsz69QM149VpM/qWyx6pP0= 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=1649935123; 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=VG1LAp/EGbsdBwo79AT5alOgM25zAG9b1t+IIDa4dWU=; b=Qvc42K8uz8dUq1lko7xZWbNbqBNR0kI/pzZOR9T47BDhBCx5R3AuLtmtj/f0gKeM T6R90Odl2ZR/oNUhP/cSEMfAH1IWwJ1X+L80kheB4AmjLTpYtxPqClYLl7IIY/gMipW M5mxh79TfqAIRfTPrj5wH2MqzUS9FwWmJv897rWs= Received: from localhost (152-108-142-46.pool.kielnet.net [46.142.108.152]) by mx.zohomail.com with SMTPS id 1649935122205587.1278276493165; Thu, 14 Apr 2022 04:18:42 -0700 (PDT) User-agent: mu4e 1.6.10; emacs 28.0.50 From: Ricardo Wurmus To: 54897-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-acde. Date: Thu, 14 Apr 2022 13:18:27 +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: <87a6cnx69c.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 54897-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, thanks! -- Ricardo ------------=_1649935142-22911-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 12 Apr 2022 22:31:17 +0000 Received: from localhost ([127.0.0.1]:50521 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1neP2a-0004wa-OG for submit@debbugs.gnu.org; Tue, 12 Apr 2022 18:31:16 -0400 Received: from lists.gnu.org ([209.51.188.17]:45180) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1neP2Y-0004wR-Q8 for submit@debbugs.gnu.org; Tue, 12 Apr 2022 18:31:15 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:39122) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1neP2Y-0001jO-KI for guix-patches@gnu.org; Tue, 12 Apr 2022 18:31:14 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:57943) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1neP2V-0001vZ-KZ for guix-patches@gnu.org; Tue, 12 Apr 2022 18:31:13 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id C2077160153 for ; Wed, 13 Apr 2022 00:31:07 +0200 (CEST) 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:received:received; s=mdc; t=1649802667; x=1651617068; bh=5i5320O5hB2P+Ar37jFrbymwftmp2uRkVyxBDWsPbWM=; b=lV2cZBzIAKi8 UqB7qP7ABxOunAjm51MUY3gO7aK5VvCjVKizVLnAw4E7I7eUSS/J/kUeBiewVj93 6cm4WOKwGzLKcGbdrnR1KZD/3dKFhPOerjeFq3N6bRNKyQ+XYWcsSxtMR8BXNi1H xl6RcjXbN6AEuGODiawEQt2H9sD0h1c= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id 77sc5AGybxKC for ; Wed, 13 Apr 2022 00:31:07 +0200 (CEST) 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 for ; Wed, 13 Apr 2022 00:31:06 +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 15.1.2375.24; Wed, 13 Apr 2022 00:31:06 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-acde. Date: Wed, 13 Apr 2022 00:30:47 +0200 Message-ID: <20220412223047.9620-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.34.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1000-26830.003 X-TM-AS-Result: No-10--3.138900-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkyStUSqCaVPsZ8zsjIitoJnVTWWiNp+v/M6O3vXX/Za6Y5ZGw7wyeHNBL YK2KW3iIiqfmvD3r0Gvd70oiE2G0nrWL/xQJnm46rm7DrUlmNkIAy6p60ZV62fJ5/bZ6npdjKay T/BQTiGlxbwYSOR4POLTPUBLeBpBc342yLO18mKnpSOJv5kUYoh1oNp38qE0H/G75DAYp9piC8V xFsWpbpXCMv7Ki4hei8bfzpakBmnt+h8u/BEfb4tOdWe/Uk/vuwZO9kmaWWvP8+E8vSQCkfySOb 56URxsg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.138900-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1000-26830.003 X-TM-SNTS-SMTP: 8AE5EFDB9EBD2C6A547EDDAEE66DAD2B710BE9A4CA58494E566BCD7EDCE0FDAF2000: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/bioconductor.scm (r-acde): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 803437a033..87cbbb24fc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11642,6 +11642,31 @@ (define-public r-universalmotif motifs, and others.") (license license:gpl3))) +(define-public r-acde + (package + (name "r-acde") + (version "1.24.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "acde" version)) + (sha256 + (base32 + "13ks87am73m3bjn9ljapxml2a9cxdpgv9flwvly8aqmi3ndxyqi6")))) + (properties `((upstream-name . "acde"))) + (build-system r-build-system) + (propagated-inputs (list r-boot)) + (home-page "https://bioconductor.org/packages/acde") + (synopsis + "Identification of differentially expressed genes with artificial components") + (description + "This package provides a multivariate inferential analysis method for +detecting differentially expressed genes in gene expression data. It uses +artificial components, close to the data's principal components but with an +exact interpretation in terms of differential genetic expression, to identify +differentially expressed genes while controlling the @dfn{false discovery rate} +(FDR).") + (license license:gpl3))) + ;; This is a CRAN package, but it depends on Bioconductor packages, so we put ;; it here. (define-public r-activedriverwgs -- 2.34.0 ------------=_1649935142-22911-1--