From unknown Sun Jun 22 17:18:34 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#56040] [PATCH] gnu: Add r-antiprofiles. Resent-From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Fri, 17 Jun 2022 14:25:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 56040 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 56040@debbugs.gnu.org Cc: rekado@elephly.net X-Debbugs-Original-To: X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by submit@debbugs.gnu.org id=B.165547589419693 (code B ref -1); Fri, 17 Jun 2022 14:25:01 +0000 Received: (at submit) by debbugs.gnu.org; 17 Jun 2022 14:24:54 +0000 Received: from localhost ([127.0.0.1]:46554 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o2Cu4-00057X-Go for submit@debbugs.gnu.org; Fri, 17 Jun 2022 10:24:54 -0400 Received: from lists.gnu.org ([209.51.188.17]:54456) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o2Ctp-00057D-Qp for submit@debbugs.gnu.org; Fri, 17 Jun 2022 10:24:50 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:58268) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o2Ctp-00088W-BS for guix-patches@gnu.org; Fri, 17 Jun 2022 10:24:37 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:39961) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o2Ctm-0005gc-Qn for guix-patches@gnu.org; Fri, 17 Jun 2022 10:24:36 -0400 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id DEA2CA0327 for ; Fri, 17 Jun 2022 16:24:30 +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=1655475870; x=1657290271; bh=ZVJ07CoilqX8ZohEFlB1WawqB0rxk5QVHl5GDsL/NAM=; b=lXuoqQYfl3hr 47G4u4kcJ9eF6WPvgl6vmOqIKOekifHRCVsX68stL3S/8MVyNjT0hTjYfrDjNKKS SKMRJiH0YFSgXLC/E5W17qZB41R6rKqk0aYzNg/ov1mRxF3wyH/RKJGb0wKzZgYS WXcv60YFU9bjKiV0BZsc/pA/MPg5eeo= Received: from a2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-han.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id HVqrPlbAWvyF for ; Fri, 17 Jun 2022 16:24:30 +0200 (CEST) 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 for ; Fri, 17 Jun 2022 16:24:29 +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 15.1.2507.9; Fri, 17 Jun 2022 16:24:29 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Fri, 17 Jun 2022 16:24:15 +0200 Message-ID: <20220617142415.11554-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] 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-14.0.0.3092-9.0.1002-26960.007 X-TM-AS-Result: No-10--2.252500-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcMu0i9VlgrN6hF4zyLyne+ATJDl9FKHbrn7fZJfDdCIXPo1 c6H9DbojwkwY92nLGuXj0Sbso8/33llDiuV7LjH+Bk2IeIQvz59F5qVUCGhwT+HExX0Q1Y9dNyl ek8JXQTeGsZX0q3FpiOhAZQXEXXZuTvHzGcGqiIKrm7DrUlmNkIAy6p60ZV62yA7duzCw6dLdB/ CxWTRRu3aDLLDbFMGF48un0VfXCJZECtSPjjb9Xnq3Zr7okXZ5UIQm7FkwYM8Y9GG1gqxAitb1c WmhTtHyt4NN/fLxUVa/nDgj5jZlxjHQApLYo4zsx6Xh3Vy4y2+O91s7FwLn8xC2a7GIAOqG8ody TXpQo3UZHwBcdw5+Mg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.252500-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26960.007 X-TM-SNTS-SMTP: 39303BC30F2559BC72FABB7F5DA910FFB6AE83A2702FE6716A8B8369CA4F54AA2002:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=MadalinIonel.Patrascu@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, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) 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 (--) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..1eacd863de 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2029,6 +2029,32 @@ (define-public r-aneufinder sequencing data.") (license license:artistic2.0))) +(define-public r-antiprofiles + (package + (name "r-antiprofiles") + (version "1.36.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "antiProfiles" version)) + (sha256 + (base32 + "1277kg5xpyb2yriyjy18p437q5lj22h4al7z7pygkzxzywxv9g40")))) + (properties `((upstream-name . "antiProfiles"))) + (build-system r-build-system) + (propagated-inputs + (list r-locfit + r-matrixstats)) + (home-page "https://github.com/HCBravoLab/antiProfiles") + (synopsis "Implementation of gene expression anti-profiles") + (description + "This package implements the gene expression anti-profiles method. +Anti-profiles are a new approach for developing cancer genomic signatures that +specifically take advantage of gene expression heterogeneity. They explicitly +model increased gene expression variability in cancer to define robust and +reproducible gene expression signatures capable of accurately distinguishing +tumor samples from healthy controls.") + (license license:artistic2.0))) + (define-public r-biocversion (package (name "r-biocversion") base-commit: d6bd483cd53cedc8da39fcc6c419f7241080ed21 -- 2.36.1 From unknown Sun Jun 22 17:18:34 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#56040: closed (Re: [bug#56040] [PATCH] gnu: Add r-antiprofiles.) Message-ID: References: <87wncx6xy1.fsf@elephly.net> <20220617142415.11554-1-madalinionel.patrascu@mdc-berlin.de> X-Gnu-PR-Message: they-closed 56040 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 56040@debbugs.gnu.org Date: Fri, 01 Jul 2022 08:27:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1656664022-4795-1" This is a multi-part message in MIME format... ------------=_1656664022-4795-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #56040: [PATCH] gnu: Add r-antiprofiles. 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 56040@debbugs.gnu.org. --=20 56040: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D56040 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1656664022-4795-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 56040-done) by debbugs.gnu.org; 1 Jul 2022 08:26:25 +0000 Received: from localhost ([127.0.0.1]:36192 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o7Byr-0001ET-9A for submit@debbugs.gnu.org; Fri, 01 Jul 2022 04:26:25 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21005) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o7Byp-0001EI-5i for 56040-done@debbugs.gnu.org; Fri, 01 Jul 2022 04:26:24 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1656663980; cv=none; d=zohomail.com; s=zohoarc; b=gAC8nvQutg1IJT/tX2pWsHqn5KugCd07dkIrBdRO4W4c9K8wOIlMfbxrAKX7byOGZDa/8JTGuKy64VH2LpBavM16roe/ZwRmR/1Cv3BnBllVu+DwYMFOpAB8cVJNYwwzBpiyFwZ7rF2cDUEOw7bgFIHNqhS6o+n5HmB6G9zJdD4= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1656663980; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=fb1SS1lNUKQNSvnHXPCgbwhD0JeJcPX3yWpWGeSzyqI=; b=Ul8cPh3Wxg842Run3CPCKE+i8TJBdtH6WJFmWJ4m58kGsOQ4FYu75hvvhERNMMeTkWB20z60TsnKIdBQmx1isdpL94q050GOevkFk4Z1bhAxXNNkvU30moobdR8GD0/Jb0mNIY26YdbjxmGkMrCd9EaW1C7oG/OXEhxQLvwHT2Y= 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=1656663980; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=fb1SS1lNUKQNSvnHXPCgbwhD0JeJcPX3yWpWGeSzyqI=; b=TxYPAtwYPeULKAWfZaXVrxl/VvEW4n4GI2eLfTU8uoSwYidQXg1a8eXa5ivqS8x1 d7AnRrSA2FQaekY8nOjOqA2ro7bQxjlJGy8EH9eP8xycFr3EWJBmsms5LYZWh49nVhj XPqciwzpudZ3Rtp9gbuWBb/AN0DXfMJav0+c48oo= Received: from localhost (72-109-142-46.pool.kielnet.net [46.142.109.72]) by mx.zohomail.com with SMTPS id 1656663976928160.41535650174706; Fri, 1 Jul 2022 01:26:16 -0700 (PDT) References: <20220617142415.11554-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.6.11; emacs 28.1 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#56040] [PATCH] gnu: Add r-antiprofiles. Date: Fri, 01 Jul 2022 10:25:59 +0200 In-reply-to: <20220617142415.11554-1-madalinionel.patrascu@mdc-berlin.de> 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: <87wncx6xy1.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 56040-done Cc: 56040-done@debbugs.gnu.org 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 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm > index 1e87b190c2..1eacd863de 100644 > --- a/gnu/packages/bioconductor.scm > +++ b/gnu/packages/bioconductor.scm > @@ -2029,6 +2029,32 @@ (define-public r-aneufinder > sequencing data.") > (license license:artistic2.0))) >=20=20 > +(define-public r-antiprofiles Thanks. I applied it with a commit message. --=20 Ricardo ------------=_1656664022-4795-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 17 Jun 2022 14:24:54 +0000 Received: from localhost ([127.0.0.1]:46554 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o2Cu4-00057X-Go for submit@debbugs.gnu.org; Fri, 17 Jun 2022 10:24:54 -0400 Received: from lists.gnu.org ([209.51.188.17]:54456) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o2Ctp-00057D-Qp for submit@debbugs.gnu.org; Fri, 17 Jun 2022 10:24:50 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:58268) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o2Ctp-00088W-BS for guix-patches@gnu.org; Fri, 17 Jun 2022 10:24:37 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:39961) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o2Ctm-0005gc-Qn for guix-patches@gnu.org; Fri, 17 Jun 2022 10:24:36 -0400 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id DEA2CA0327 for ; Fri, 17 Jun 2022 16:24:30 +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=1655475870; x=1657290271; bh=ZVJ07CoilqX8ZohEFlB1WawqB0rxk5QVHl5GDsL/NAM=; b=lXuoqQYfl3hr 47G4u4kcJ9eF6WPvgl6vmOqIKOekifHRCVsX68stL3S/8MVyNjT0hTjYfrDjNKKS SKMRJiH0YFSgXLC/E5W17qZB41R6rKqk0aYzNg/ov1mRxF3wyH/RKJGb0wKzZgYS WXcv60YFU9bjKiV0BZsc/pA/MPg5eeo= Received: from a2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-han.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id HVqrPlbAWvyF for ; Fri, 17 Jun 2022 16:24:30 +0200 (CEST) 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 for ; Fri, 17 Jun 2022 16:24:29 +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 15.1.2507.9; Fri, 17 Jun 2022 16:24:29 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-antiprofiles. Date: Fri, 17 Jun 2022 16:24:15 +0200 Message-ID: <20220617142415.11554-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] 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-14.0.0.3092-9.0.1002-26960.007 X-TM-AS-Result: No-10--2.252500-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcMu0i9VlgrN6hF4zyLyne+ATJDl9FKHbrn7fZJfDdCIXPo1 c6H9DbojwkwY92nLGuXj0Sbso8/33llDiuV7LjH+Bk2IeIQvz59F5qVUCGhwT+HExX0Q1Y9dNyl ek8JXQTeGsZX0q3FpiOhAZQXEXXZuTvHzGcGqiIKrm7DrUlmNkIAy6p60ZV62yA7duzCw6dLdB/ CxWTRRu3aDLLDbFMGF48un0VfXCJZECtSPjjb9Xnq3Zr7okXZ5UIQm7FkwYM8Y9GG1gqxAitb1c WmhTtHyt4NN/fLxUVa/nDgj5jZlxjHQApLYo4zsx6Xh3Vy4y2+O91s7FwLn8xC2a7GIAOqG8ody TXpQo3UZHwBcdw5+Mg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.252500-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26960.007 X-TM-SNTS-SMTP: 39303BC30F2559BC72FABB7F5DA910FFB6AE83A2702FE6716A8B8369CA4F54AA2002:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=MadalinIonel.Patrascu@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, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) 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 (--) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..1eacd863de 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2029,6 +2029,32 @@ (define-public r-aneufinder sequencing data.") (license license:artistic2.0))) +(define-public r-antiprofiles + (package + (name "r-antiprofiles") + (version "1.36.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "antiProfiles" version)) + (sha256 + (base32 + "1277kg5xpyb2yriyjy18p437q5lj22h4al7z7pygkzxzywxv9g40")))) + (properties `((upstream-name . "antiProfiles"))) + (build-system r-build-system) + (propagated-inputs + (list r-locfit + r-matrixstats)) + (home-page "https://github.com/HCBravoLab/antiProfiles") + (synopsis "Implementation of gene expression anti-profiles") + (description + "This package implements the gene expression anti-profiles method. +Anti-profiles are a new approach for developing cancer genomic signatures that +specifically take advantage of gene expression heterogeneity. They explicitly +model increased gene expression variability in cancer to define robust and +reproducible gene expression signatures capable of accurately distinguishing +tumor samples from healthy controls.") + (license license:artistic2.0))) + (define-public r-biocversion (package (name "r-biocversion") base-commit: d6bd483cd53cedc8da39fcc6c419f7241080ed21 -- 2.36.1 ------------=_1656664022-4795-1--