From unknown Sun Jun 22 11:36:11 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#56039] [PATCH] gnu: Add r-annmap. 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 14:07:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 56039 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 56039@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.16554747809746 (code B ref -1); Fri, 17 Jun 2022 14:07:02 +0000 Received: (at submit) by debbugs.gnu.org; 17 Jun 2022 14:06:20 +0000 Received: from localhost ([127.0.0.1]:46541 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o2Cc7-0002X8-UE for submit@debbugs.gnu.org; Fri, 17 Jun 2022 10:06:20 -0400 Received: from lists.gnu.org ([209.51.188.17]:42772) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o2Cc5-0002Wx-Rx for submit@debbugs.gnu.org; Fri, 17 Jun 2022 10:06:18 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:53592) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o2Cc5-0007VN-Du for guix-patches@gnu.org; Fri, 17 Jun 2022 10:06:17 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:33229) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o2Cc2-0008BF-Ik for guix-patches@gnu.org; Fri, 17 Jun 2022 10:06:16 -0400 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id B9892A0327 for ; Fri, 17 Jun 2022 16:06:10 +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=1655474769; x=1657289170; bh=aYpJhWxohSeGrLOhsYb0MKCFCViH7CVrtNEOtvJpIsw=; b=cp+g0ZzNj3fr sD0OPZM/Lj5lR54oGTQPvZatGEwbAETV4flhWlnrqnLmu2Oc57JODYxSjLbgfyg7 02M1UDcd1tBFRxAMDjDKj4KngI94qhJ7FxdtWqvnTAuZZ+J2hWe39dK4W1f02Gjb U3EocUA/U2tTdtTviIe/zsH43bw24a4= 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 Us4dCe9PI8dW for ; Fri, 17 Jun 2022 16:06:09 +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 16:06:09 +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 16:06:09 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Fri, 17 Jun 2022 16:05:58 +0200 Message-ID: <20220617140558.10555-1-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--10.429400-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJMu0i9VlgrN6hF4zyLyne+ATJDl9FKHbrn7fZJfDdCIXPo1 c6H9Dboj+l1YtaXbEaEDAE8BxKGooC/33TWoSUH6Xke6tLU6lcJ4mYJHAxGkc6Y5ZGw7wyeHj8o aNv1+cAozt/CCoNZd9/V58hdT3FI3ygR7McnOqmXGL//8mlodAz5//buCv56OlwV2iaAfSWcURS Scn+QSXt0H8LFZNFG73Yq8RVaZivWJG3urFSFxc4pNDpt2csPVMlbgABNnuP2kZ8EL1ntx3HCqg wqiNmlK X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--10.429400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26960.007 X-TM-SNTS-SMTP: 31805067AFEBED84085B45363625CEA0F957B2841221CF3088F27F760A17B6F72002: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: -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 (--) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..5b74118974 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2029,6 +2029,40 @@ (define-public r-aneufinder sequencing data.") (license license:artistic2.0))) +(define-public r-annmap + (package + (name "r-annmap") + (version "1.38.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "annmap" version)) + (sha256 + (base32 + "0ywqbb8jia7rrkzcsf6a11kqf8dnx96z8n8xw7067mahycykbixv")))) + (properties `((upstream-name . "annmap"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-dbi + r-digest + r-genefilter + r-genomicranges + r-iranges + r-lattice + r-rmysql + r-rsamtools)) + (home-page "https://github.com/cruk-mi/annmap") + (synopsis + "Genome annotation and visualisation for Affymetrix arrays and NGS analysis") + (description + "This package @code{annmap} provides annotation mappings for Affymetrix exon +arrays and coordinate based queries to support deep sequencing data analysis. +Database access is hidden behind the API which provides a set of functions such +as @code{genesInRange()}, @code{geneToExon()}, @code{exonDetails()}, etc. +Functions to plot gene architecture and BAM file data are also provided.") + (license license:gpl2))) + (define-public r-biocversion (package (name "r-biocversion") base-commit: d6bd483cd53cedc8da39fcc6c419f7241080ed21 -- 2.36.1 From unknown Sun Jun 22 11:36:11 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#56039: closed (Re: [bug#56039] [PATCH] gnu: Add r-annmap.) Message-ID: References: <871qv58cj4.fsf@elephly.net> <20220617140558.10555-1-madalinionel.patrascu@mdc-berlin.de> X-Gnu-PR-Message: they-closed 56039 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 56039@debbugs.gnu.org Date: Fri, 01 Jul 2022 08:26:03 +0000 Content-Type: multipart/mixed; boundary="----------=_1656663963-4662-1" This is a multi-part message in MIME format... ------------=_1656663963-4662-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #56039: [PATCH] gnu: Add r-annmap. 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 56039@debbugs.gnu.org. --=20 56039: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D56039 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1656663963-4662-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 56039-done) by debbugs.gnu.org; 1 Jul 2022 08:26:01 +0000 Received: from localhost ([127.0.0.1]:36177 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o7ByT-0001CR-0N for submit@debbugs.gnu.org; Fri, 01 Jul 2022 04:26:01 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21087) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o7ByR-0001CI-8G for 56039-done@debbugs.gnu.org; Fri, 01 Jul 2022 04:25:59 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1656663956; cv=none; d=zohomail.com; s=zohoarc; b=mvaaZDesxko+zH1ADbxVoC6voCM2VEalLIS58rq+Fi/SVRzPBiK9gEpMprBStYgOoLe/eVAP+hVxuUt9jpCagFrZ+gJoDmGZAGmDCxJcreUdu1iKUYeMXD+e8b1hBpr28K3MK/hJylHBqhMl1/bivRyofwpuWb9z0WWDi5BmmsY= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1656663956; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=hhpK1ZFUOvJ69lh7bGj2yzehfaeeqAf7NRx8xPKsaX8=; b=IVegn+SMjb0TkpLTzvwV+U2Lw4OH8pWlXfApgjtOV/hRZHr/GMB7fNu2Bn4KKcR7V2CVuWtBoCSB2nTIG/wuSQUCibzwlrXYpeJnlKUTwGHuYMSPjUTiDojWXxb578o49mMb9INkgDb3ISETfc4grVJ8yLcPf8SVt/qYCtXqf60= 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=1656663956; 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=hhpK1ZFUOvJ69lh7bGj2yzehfaeeqAf7NRx8xPKsaX8=; b=T/RxEW5+QncaF9bromXi7CmoFxpj7rdF+zJq7uh9wvQDqjNUe0MLu4E425jqa8b+ yDY2wtuL5ozZZu/zUuUXNEOkxblbEm0NDFNGzTAcgtSqJlOVk4m7gvF7VhVQ7+G+JhS pDCcEquErzbrEUFcNR2ud0B+lvBz78opHC348Afk= Received: from localhost (72-109-142-46.pool.kielnet.net [46.142.109.72]) by mx.zohomail.com with SMTPS id 1656663953592514.7614358352556; Fri, 1 Jul 2022 01:25:53 -0700 (PDT) References: <20220617140558.10555-1-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#56039] [PATCH] gnu: Add r-annmap. Date: Fri, 01 Jul 2022 10:25:37 +0200 In-reply-to: <20220617140558.10555-1-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: <871qv58cj4.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: 56039-done Cc: 56039-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..5b74118974 100644 > --- a/gnu/packages/bioconductor.scm > +++ b/gnu/packages/bioconductor.scm > @@ -2029,6 +2029,40 @@ (define-public r-aneufinder > sequencing data.") > (license license:artistic2.0))) >=20=20 > +(define-public r-annmap Thanks. I applied it with a commit message. --=20 Ricardo ------------=_1656663963-4662-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 17 Jun 2022 14:06:20 +0000 Received: from localhost ([127.0.0.1]:46541 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o2Cc7-0002X8-UE for submit@debbugs.gnu.org; Fri, 17 Jun 2022 10:06:20 -0400 Received: from lists.gnu.org ([209.51.188.17]:42772) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o2Cc5-0002Wx-Rx for submit@debbugs.gnu.org; Fri, 17 Jun 2022 10:06:18 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:53592) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o2Cc5-0007VN-Du for guix-patches@gnu.org; Fri, 17 Jun 2022 10:06:17 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:33229) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o2Cc2-0008BF-Ik for guix-patches@gnu.org; Fri, 17 Jun 2022 10:06:16 -0400 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id B9892A0327 for ; Fri, 17 Jun 2022 16:06:10 +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=1655474769; x=1657289170; bh=aYpJhWxohSeGrLOhsYb0MKCFCViH7CVrtNEOtvJpIsw=; b=cp+g0ZzNj3fr sD0OPZM/Lj5lR54oGTQPvZatGEwbAETV4flhWlnrqnLmu2Oc57JODYxSjLbgfyg7 02M1UDcd1tBFRxAMDjDKj4KngI94qhJ7FxdtWqvnTAuZZ+J2hWe39dK4W1f02Gjb U3EocUA/U2tTdtTviIe/zsH43bw24a4= 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 Us4dCe9PI8dW for ; Fri, 17 Jun 2022 16:06:09 +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 16:06:09 +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 16:06:09 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-annmap. Date: Fri, 17 Jun 2022 16:05:58 +0200 Message-ID: <20220617140558.10555-1-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--10.429400-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJMu0i9VlgrN6hF4zyLyne+ATJDl9FKHbrn7fZJfDdCIXPo1 c6H9Dboj+l1YtaXbEaEDAE8BxKGooC/33TWoSUH6Xke6tLU6lcJ4mYJHAxGkc6Y5ZGw7wyeHj8o aNv1+cAozt/CCoNZd9/V58hdT3FI3ygR7McnOqmXGL//8mlodAz5//buCv56OlwV2iaAfSWcURS Scn+QSXt0H8LFZNFG73Yq8RVaZivWJG3urFSFxc4pNDpt2csPVMlbgABNnuP2kZ8EL1ntx3HCqg wqiNmlK X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--10.429400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26960.007 X-TM-SNTS-SMTP: 31805067AFEBED84085B45363625CEA0F957B2841221CF3088F27F760A17B6F72002: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: -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 (--) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..5b74118974 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2029,6 +2029,40 @@ (define-public r-aneufinder sequencing data.") (license license:artistic2.0))) +(define-public r-annmap + (package + (name "r-annmap") + (version "1.38.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "annmap" version)) + (sha256 + (base32 + "0ywqbb8jia7rrkzcsf6a11kqf8dnx96z8n8xw7067mahycykbixv")))) + (properties `((upstream-name . "annmap"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-dbi + r-digest + r-genefilter + r-genomicranges + r-iranges + r-lattice + r-rmysql + r-rsamtools)) + (home-page "https://github.com/cruk-mi/annmap") + (synopsis + "Genome annotation and visualisation for Affymetrix arrays and NGS analysis") + (description + "This package @code{annmap} provides annotation mappings for Affymetrix exon +arrays and coordinate based queries to support deep sequencing data analysis. +Database access is hidden behind the API which provides a set of functions such +as @code{genesInRange()}, @code{geneToExon()}, @code{exonDetails()}, etc. +Functions to plot gene architecture and BAM file data are also provided.") + (license license:gpl2))) + (define-public r-biocversion (package (name "r-biocversion") base-commit: d6bd483cd53cedc8da39fcc6c419f7241080ed21 -- 2.36.1 ------------=_1656663963-4662-1--