From unknown Sat Jun 21 12:30:48 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#55148] [PATCH] gnu: Add r-agilp. 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Wed, 27 Apr 2022 14:50:28 +0200 (CEST) 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 for ; Wed, 27 Apr 2022 14:50:27 +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, 27 Apr 2022 14:50:27 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Wed, 27 Apr 2022 14:50:15 +0200 Message-ID: <20220427125015.27456-1-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-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-14.0.0.3092-9.0.1000-26858.007 X-TM-AS-Result: No-10--1.108400-5.000000 X-TMASE-MatchedRID: DIEPoA0d9jz/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEJw6 tnDgS/8FRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8XjfR3d0weRiDGLLbElle9Vcq n6yxxpJJBPQd6lWNwpO0srDIOZE4B1L8/uaw/imEGTYh4hC/Pn0Rw107cERT7OhR0VsdhRrC2Cb ZwsD5I10MOHpHyM+8Uvt8QObnSdjd8UU8TClOmYSwjpa51oXxrTSz0JdEAJbQvfU/riSJXkcnDo b0105aLkpCFGclEFCe1Yo1HZ6kAVoJYxfHyi9oJ4vM1YF6AJbbCCfuIMF6xLcK21zBg2KlfvG0V HndRxgIjKzhiN6R+I7v7pMLJ5G3wd+CAWjOfCnAebX72LdEKEpg3Gb/nj3JLtQ+5ywmBumZ6Tav UTOXCWArcdqjh0JdP+QWccNjKu1YoQg4MrLBPLqN8mCVfMdDqzFFXNLNe3bF/6uEw9r+ytQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.108400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1000-26858.007 X-TM-SNTS-SMTP: B02A460E66A5D7FF10B1FA4AB0CC4006F8B459C22FAF5B3CA4EEC7049CACBAC62000: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, 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-agilp): New variable. --- gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 67ee6079c6..c0d874b423 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1664,6 +1664,50 @@ (define-public r-adamgui the @code{GFAGpathUi} function.") (license license:gpl2+))) +(define-public r-agilp + (package + (name "r-agilp") + (version "3.26.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "agilp" version)) + (sha256 + (base32 + "02cyc2y4v3y16zlrnax2c96b2qfxj6b2j37ps4g2gdqgas08n9xp")))) + (properties `((upstream-name . "agilp"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/agilp") + (synopsis "Processing of Agilent expression array") + (description + "This package @code{agilp} was developed to provide a pipeline for the +low-level analysis of gene expression microarray data, primarily focused on the +Agilent platform, but which also provides utilities which may be useful for +other platforms. @code{Agilp} implements functions like: +@itemize +@item +@code{AAProcess}: extracts raw expression data from Agilent expression array +scanner files; +@item +@code{filenamex}: a file name listing utility; +@item +@code{Baseline}: constructs a file with the mean of each probe from a set of raw +expression array data files +@item +@code{Loader}: selects a set of processed array files from directory according +to criteria from a template file; +@item +@code{AALoess}: normalises a set of gene expression data files using @code{LOESS} +against a reference data set; +@item +@code{IDswop}: maps expression data across different bioinformatic identifiers; +@item +@code{Equaliser}: trims a set of gene expression data files to include only the +set of identifiers common to all files. +@end itemize") + ;; Some files are under GPLv2+ but the combined work is released under the + ;; GPLv3. + (license license:gpl3))) + (define-public r-aneufinder (package (name "r-aneufinder") base-commit: 4fb6ef6636acd7608889639c1b2e492517256f76 -- 2.34.0 From unknown Sat Jun 21 12:30:48 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#55148: closed (Re: [bug#55148] [PATCH] gnu: Add r-agilp.) Message-ID: References: <8735hy4mn8.fsf@elephly.net> <20220427125015.27456-1-madalinionel.patrascu@mdc-berlin.de> X-Gnu-PR-Message: they-closed 55148 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 55148@debbugs.gnu.org Date: Wed, 27 Apr 2022 14:39:01 +0000 Content-Type: multipart/mixed; boundary="----------=_1651070341-15492-1" This is a multi-part message in MIME format... ------------=_1651070341-15492-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #55148: [PATCH] gnu: Add r-agilp. 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 55148@debbugs.gnu.org. --=20 55148: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D55148 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1651070341-15492-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 55148-done) by debbugs.gnu.org; 27 Apr 2022 14:38:30 +0000 Received: from localhost ([127.0.0.1]:43902 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njioH-000416-NL for submit@debbugs.gnu.org; Wed, 27 Apr 2022 10:38:29 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21063) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njioF-00040u-00 for 55148-done@debbugs.gnu.org; Wed, 27 Apr 2022 10:38:28 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1651070303; cv=none; d=zohomail.com; s=zohoarc; b=BIvFd8U7eV0IhiB0dGRIlCd5thqY3Xeb/Rl/pFC4iRgEf8MW1BbXEisN4KuKCFKJOEbc6TG0DUiUcfvgzldy44DTQlkvQ3SrdHwnT3YNFRpwACQSNgHIoMGn/usuzEjkQ87Tbt2NQzhxOjyFeZUL+RJ578f1bd2ZI1WcTmZEqQI= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1651070303; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=lQWZzcH++wipjetiCd15g+dtnhOXb9I3/KMwQX/X51o=; b=cRnm/KvNeGmb8r+brMYuXKpGUcILvG/PjtiXKfzMPAdILVfmOF7huezsLM2gSeiwubJJKqGMbeU3PCMpF1Dr4b40Eo7u++WTH3V2AwRxyYvZQnIwSmn6305m/8xECqh5wD8CQByL2xzTiQ+HQaCXDFcgRbi7ik52QbmllEpOtDA= 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=1651070303; 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=lQWZzcH++wipjetiCd15g+dtnhOXb9I3/KMwQX/X51o=; b=UTbadYPrX41qm0zOLqaOlH/RYdFRmMREy7UpyiXwAG+QtcTOAtOzzJBVAd3vpLbX 4dj4cYdO0DDoeGulyZvTfw0+6pughUrCQePBtjwsgD8Flz15YjUeda/PLZIp+cORt10 xvKFC7jv0alsk1YJQnF30mfID/LHvyPT/sLb4C2A= Received: from localhost (56-111-142-46.pool.kielnet.net [46.142.111.56]) by mx.zohomail.com with SMTPS id 1651070301733821.9632147283056; Wed, 27 Apr 2022 07:38:21 -0700 (PDT) References: <20220427125015.27456-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.6.10; emacs 28.0.50 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#55148] [PATCH] gnu: Add r-agilp. Date: Wed, 27 Apr 2022 16:36:42 +0200 In-reply-to: <20220427125015.27456-1-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: <8735hy4mn8.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: 55148-done Cc: 55148-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: > * gnu/packages/bioconductor.scm (r-agilp): New variable. Thank you. I applied it after trimming the description, because all that detail was probably a little much. --=20 Ricardo ------------=_1651070341-15492-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 27 Apr 2022 12:50:38 +0000 Received: from localhost ([127.0.0.1]:41505 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njh7u-0000BG-35 for submit@debbugs.gnu.org; Wed, 27 Apr 2022 08:50:38 -0400 Received: from lists.gnu.org ([209.51.188.17]:51718) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1njh7r-0000B8-Vx for submit@debbugs.gnu.org; Wed, 27 Apr 2022 08:50:36 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:33650) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njh7r-0007yv-JO for guix-patches@gnu.org; Wed, 27 Apr 2022 08:50:35 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:40513) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1njh7o-0007ri-KE for guix-patches@gnu.org; Wed, 27 Apr 2022 08:50:34 -0400 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id AF3B030012A for ; Wed, 27 Apr 2022 14:50:28 +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=1651063828; x=1652878229; bh=HR4SoNkz2V7Wk2yLrKVa97A1tgSPwVMroOAGNmla5DA=; b=jA6kXIl5f0f5 ilCAC6wuZRg40JvFXuFN5r3Dxe0HpsJA514h1sNsK+n1E3TVfuglp/O0MXbQAJbx B/Hhsn+WN5DrxYPPFB9q6boFHG2bkXuUOU1o/dpEJbXUi+dAulv7xb6zB7leyzzH wHfzk2CY+WYVQ0H2WOXYDJfPL2pF7Hk= Received: from c2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-erl.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id bdwepijCecC4 for ; Wed, 27 Apr 2022 14:50:28 +0200 (CEST) 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 for ; Wed, 27 Apr 2022 14:50:27 +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, 27 Apr 2022 14:50:27 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-agilp. Date: Wed, 27 Apr 2022 14:50:15 +0200 Message-ID: <20220427125015.27456-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.34.0 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-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-14.0.0.3092-9.0.1000-26858.007 X-TM-AS-Result: No-10--1.108400-5.000000 X-TMASE-MatchedRID: DIEPoA0d9jz/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEJw6 tnDgS/8FRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8XjfR3d0weRiDGLLbElle9Vcq n6yxxpJJBPQd6lWNwpO0srDIOZE4B1L8/uaw/imEGTYh4hC/Pn0Rw107cERT7OhR0VsdhRrC2Cb ZwsD5I10MOHpHyM+8Uvt8QObnSdjd8UU8TClOmYSwjpa51oXxrTSz0JdEAJbQvfU/riSJXkcnDo b0105aLkpCFGclEFCe1Yo1HZ6kAVoJYxfHyi9oJ4vM1YF6AJbbCCfuIMF6xLcK21zBg2KlfvG0V HndRxgIjKzhiN6R+I7v7pMLJ5G3wd+CAWjOfCnAebX72LdEKEpg3Gb/nj3JLtQ+5ywmBumZ6Tav UTOXCWArcdqjh0JdP+QWccNjKu1YoQg4MrLBPLqN8mCVfMdDqzFFXNLNe3bF/6uEw9r+ytQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.108400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1000-26858.007 X-TM-SNTS-SMTP: B02A460E66A5D7FF10B1FA4AB0CC4006F8B459C22FAF5B3CA4EEC7049CACBAC62000: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, 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-agilp): New variable. --- gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 67ee6079c6..c0d874b423 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1664,6 +1664,50 @@ (define-public r-adamgui the @code{GFAGpathUi} function.") (license license:gpl2+))) +(define-public r-agilp + (package + (name "r-agilp") + (version "3.26.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "agilp" version)) + (sha256 + (base32 + "02cyc2y4v3y16zlrnax2c96b2qfxj6b2j37ps4g2gdqgas08n9xp")))) + (properties `((upstream-name . "agilp"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/agilp") + (synopsis "Processing of Agilent expression array") + (description + "This package @code{agilp} was developed to provide a pipeline for the +low-level analysis of gene expression microarray data, primarily focused on the +Agilent platform, but which also provides utilities which may be useful for +other platforms. @code{Agilp} implements functions like: +@itemize +@item +@code{AAProcess}: extracts raw expression data from Agilent expression array +scanner files; +@item +@code{filenamex}: a file name listing utility; +@item +@code{Baseline}: constructs a file with the mean of each probe from a set of raw +expression array data files +@item +@code{Loader}: selects a set of processed array files from directory according +to criteria from a template file; +@item +@code{AALoess}: normalises a set of gene expression data files using @code{LOESS} +against a reference data set; +@item +@code{IDswop}: maps expression data across different bioinformatic identifiers; +@item +@code{Equaliser}: trims a set of gene expression data files to include only the +set of identifiers common to all files. +@end itemize") + ;; Some files are under GPLv2+ but the combined work is released under the + ;; GPLv3. + (license license:gpl3))) + (define-public r-aneufinder (package (name "r-aneufinder") base-commit: 4fb6ef6636acd7608889639c1b2e492517256f76 -- 2.34.0 ------------=_1651070341-15492-1--