From unknown Sun Jun 15 01:08:51 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#51511] [PATCH] gnu: Add r-xmapbridge. 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Sat, 30 Oct 2021 16:20:49 +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; Sat, 30 Oct 2021 16:20:49 +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 15.1.2308.15; Sat, 30 Oct 2021 16:20:49 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Sat, 30 Oct 2021 16:20:35 +0200 Message-ID: <20211030142035.25460-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.33.0 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-14.0.0.3092-8.6.1018-26500.000 X-TM-AS-Result: No-10--5.710600-8.000000 X-TMASE-MatchedRID: OhoAOyintKAsaaYlMvaOHAPZZctd3P4BC//1TMV5chPIFck3f6fvyNN0 iv48FC5C7IvvzMgzLKZbRMZywJ4kaMjZGpIBeHfelknuuADbyTTiRe0jkfeQlWFe9xWMc71y2Lg EVfggSljFCmRbyZuc35u2AnZz+7oImo2ZG/E7i3Pnh6rB4tZovsWLeiJW8Z+pPHMAbjuhwd93cS 3nQXHauRXTAropxEmVAdXPD0156qEUt79wf2J8qcuQbFwklcWl3WFaxVW7M2hL1bsQnKxbl+YmA qNpt2KuUq6CDvN7P1XRL37QbokInmmMP8rZmFyK3QqJN4m15UHrixWWWJYrHx8TzIzimOwPD16O IL8FA90vM/mydp5vVCq2rl3dzGQ1l3+bAt/YFVQ5mqHKcoPzr6PXLpVbsZ65eDhsC4sV2eHYrJ5 D/YJJ/0uFvzEYSdV+ X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.710600-8.000000 X-TMASE-Version: SMEX-14.0.0.3092-8.6.1018-26500.000 X-TM-SNTS-SMTP: 165C3895F60334F9809E4E94409216A609E42B906793395202B92A47CF9D9B0B2000: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 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-xmapbridge): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 90a0e1f288..24ab4897d5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4627,6 +4627,33 @@ (define-public r-vsn and specific in detecting differential transcription.") (license license:artistic2.0))) +(define-public r-xmapbridge + (package + (name "r-xmapbridge") + (version "1.52.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "xmapbridge" version)) + (sha256 + (base32 "1zsqhisbq6f9qgw9f0a6ixxh635h3qm17117yfns5nnfw73ndlgi")))) + (properties `((upstream-name . "xmapbridge"))) + (build-system r-build-system) + (home-page "https://git.bioconductor.org/packages/xmapbridge") + (synopsis "Display numeric data in the web based genome browser X:MAP") + (description + "The package @code{r-xmapBridge} can plot graphs in the X:Map genome +browser. X:Map uses the Google Maps API to provide a scrollable view of the +genome. It supports a number of species, and can be accessed at +http://xmap.picr.man.ac.uk. This package exports plotting files in a suitable +format. Graph plotting in R is done using calls to the functions +@code{xmap.plot} and @code{xmap.points}, which have parameters that aim to be +similar to those used by the standard plot methods in R. These result in data +being written to a set of files (in a specific directory structure) that +contain the data to be displayed, as well as some additional meta-data +describing each of the graphs.") + (license license:lgpl3))) + (define-public r-xvector (package (name "r-xvector") -- 2.33.0 From unknown Sun Jun 15 01:08:51 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#51511: closed (Re: [PATCH] gnu: Add r-xmapbridge.) Message-ID: References: <87a6hqoru0.fsf@elephly.net> <20211030142035.25460-1-madalinionel.patrascu@mdc-berlin.de> X-Gnu-PR-Message: they-closed 51511 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 51511@debbugs.gnu.org Date: Sat, 27 Nov 2021 09:46:01 +0000 Content-Type: multipart/mixed; boundary="----------=_1638006361-15642-1" This is a multi-part message in MIME format... ------------=_1638006361-15642-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #51511: [PATCH] gnu: Add r-xmapbridge. 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 51511@debbugs.gnu.org. --=20 51511: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D51511 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1638006361-15642-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 51511-done) by debbugs.gnu.org; 27 Nov 2021 09:45:05 +0000 Received: from localhost ([127.0.0.1]:32972 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mquGW-000430-UZ for submit@debbugs.gnu.org; Sat, 27 Nov 2021 04:45:05 -0500 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21138) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mquGU-00042p-BU for 51511-done@debbugs.gnu.org; Sat, 27 Nov 2021 04:45:03 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1638006300; cv=none; d=zohomail.com; s=zohoarc; b=kxyztuqLxUkxWW3lJHOH5Y5TQntKLSeSlB7WilUSSmH1FJCOSTedYoEsmFP9MNiYKckKYvmvCa1jmk2DmaiupPqVJUpQT5eJpt7oe+xaIhXlenqrXyKQnb9S9JqOBZ2lGEDtPrzQgpZs04U15yV0gxrm1aulOHB1sme7JBHFP64= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1638006300; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=bgbCSDZrHF90mrB54EJoCnZuIpjxbQuDYylHHR/VVQY=; b=QWfl3EYSOGRqHhyvkvNRzRy1hbqOinINaxZ9upYWxRvL/HNFDfgA4OxL9OXcxeYHlY9Ono4abMEEzNz+EI5erdKw3mZxaXAdHnba0UV1Qo4nHUUxQh1kxQy0cSRdwwNfQB132wjrg0WRz3jPG34pglMntGhbcfcZoJNnayq9+vo= 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=1638006300; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; bh=bgbCSDZrHF90mrB54EJoCnZuIpjxbQuDYylHHR/VVQY=; b=KdGOh5uPELn0zQIJndvf8odQ3lhwifyIbg5ubvB6LpnwjonkaB8x8hq3iX+Jz7Xs 3/V0LWjGq819Ov2rKHJAAqQaDVjWW1EgBW55pD9RonymfYTGs32CPRmq0pno6zIP7N2 EX1f1Oj/U2hWuGfO8OB+FJyM+RFLcnogYtO+Sin8= Received: from localhost (p4fd5a75b.dip0.t-ipconnect.de [79.213.167.91]) by mx.zohomail.com with SMTPS id 1638006298255607.858291636385; Sat, 27 Nov 2021 01:44:58 -0800 (PST) References: <20211030142035.25460-1-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: [PATCH] gnu: Add r-xmapbridge. Date: Sat, 27 Nov 2021 10:44:34 +0100 In-reply-to: <20211030142035.25460-1-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: <87a6hqoru0.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 51511-done Cc: 51511-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 = =20 writes: > * gnu/packages/bioconductor.scm (r-xmapbridge): New variable. Applied, thank you! --=20 Ricardo ------------=_1638006361-15642-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 30 Oct 2021 14:21:08 +0000 Received: from localhost ([127.0.0.1]:58095 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mgpEJ-00034A-IV for submit@debbugs.gnu.org; Sat, 30 Oct 2021 10:21:07 -0400 Received: from lists.gnu.org ([209.51.188.17]:57966) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mgpEI-000342-4K for submit@debbugs.gnu.org; Sat, 30 Oct 2021 10:21:06 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:59528) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mgpEH-0002c0-VH for guix-patches@gnu.org; Sat, 30 Oct 2021 10:21:05 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:35787) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mgpEE-0005mL-SH for guix-patches@gnu.org; Sat, 30 Oct 2021 10:21:05 -0400 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id 33C3CA0142; Sat, 30 Oct 2021 16:20:50 +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=1635603649; x=1637418050; bh=3i4M9YmMtanqFyeraANUpP/lN8CgYXijb8c3Xgnqq48=; b=MAo3MBC7EVct ZYIXZrbv1rogf0EVpWMqt7FZzS5iCFl1LMxrS3thgWGurvwULIIG/6ndCDtOwyhS Cl+Tx7QyruVbRg6vzCnaNJamH1LOE7GU9qy1SSVPEdTpdySrs75/VU46NlNTjhYQ 3jnVI9u8AcYIa9dW7Lulx2vgytIJx04= 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 JiJo-cljGVPO; Sat, 30 Oct 2021 16:20:49 +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; Sat, 30 Oct 2021 16:20:49 +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 15.1.2308.15; Sat, 30 Oct 2021 16:20:49 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-xmapbridge. Date: Sat, 30 Oct 2021 16:20:35 +0200 Message-ID: <20211030142035.25460-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.33.0 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-14.0.0.3092-8.6.1018-26500.000 X-TM-AS-Result: No-10--5.710600-8.000000 X-TMASE-MatchedRID: OhoAOyintKAsaaYlMvaOHAPZZctd3P4BC//1TMV5chPIFck3f6fvyNN0 iv48FC5C7IvvzMgzLKZbRMZywJ4kaMjZGpIBeHfelknuuADbyTTiRe0jkfeQlWFe9xWMc71y2Lg EVfggSljFCmRbyZuc35u2AnZz+7oImo2ZG/E7i3Pnh6rB4tZovsWLeiJW8Z+pPHMAbjuhwd93cS 3nQXHauRXTAropxEmVAdXPD0156qEUt79wf2J8qcuQbFwklcWl3WFaxVW7M2hL1bsQnKxbl+YmA qNpt2KuUq6CDvN7P1XRL37QbokInmmMP8rZmFyK3QqJN4m15UHrixWWWJYrHx8TzIzimOwPD16O IL8FA90vM/mydp5vVCq2rl3dzGQ1l3+bAt/YFVQ5mqHKcoPzr6PXLpVbsZ65eDhsC4sV2eHYrJ5 D/YJJ/0uFvzEYSdV+ X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.710600-8.000000 X-TMASE-Version: SMEX-14.0.0.3092-8.6.1018-26500.000 X-TM-SNTS-SMTP: 165C3895F60334F9809E4E94409216A609E42B906793395202B92A47CF9D9B0B2000: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 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit Cc: rekado@elephly.net, =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= 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-xmapbridge): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 90a0e1f288..24ab4897d5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4627,6 +4627,33 @@ (define-public r-vsn and specific in detecting differential transcription.") (license license:artistic2.0))) +(define-public r-xmapbridge + (package + (name "r-xmapbridge") + (version "1.52.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "xmapbridge" version)) + (sha256 + (base32 "1zsqhisbq6f9qgw9f0a6ixxh635h3qm17117yfns5nnfw73ndlgi")))) + (properties `((upstream-name . "xmapbridge"))) + (build-system r-build-system) + (home-page "https://git.bioconductor.org/packages/xmapbridge") + (synopsis "Display numeric data in the web based genome browser X:MAP") + (description + "The package @code{r-xmapBridge} can plot graphs in the X:Map genome +browser. X:Map uses the Google Maps API to provide a scrollable view of the +genome. It supports a number of species, and can be accessed at +http://xmap.picr.man.ac.uk. This package exports plotting files in a suitable +format. Graph plotting in R is done using calls to the functions +@code{xmap.plot} and @code{xmap.points}, which have parameters that aim to be +similar to those used by the standard plot methods in R. These result in data +being written to a set of files (in a specific directory structure) that +contain the data to be displayed, as well as some additional meta-data +describing each of the graphs.") + (license license:lgpl3))) + (define-public r-xvector (package (name "r-xvector") -- 2.33.0 ------------=_1638006361-15642-1--