From unknown Wed Jun 18 23:12:51 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#46937 <46937@debbugs.gnu.org> To: bug#46937 <46937@debbugs.gnu.org> Subject: Status: (no subject) Reply-To: bug#46937 <46937@debbugs.gnu.org> Date: Thu, 19 Jun 2025 06:12:51 +0000 retitle 46937 (no subject) reassign 46937 guix-patches submitter 46937 M=C4=83d=C4=83lin Ionel Patra=C8=99cu severity 46937 normal thanks From debbugs-submit-bounces@debbugs.gnu.org Thu Mar 04 20:18:44 2021 Received: (at submit) by debbugs.gnu.org; 5 Mar 2021 01:18:44 +0000 Received: from localhost ([127.0.0.1]:60660 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHz76-0005Yg-Ix for submit@debbugs.gnu.org; Thu, 04 Mar 2021 20:18:44 -0500 Received: from lists.gnu.org ([209.51.188.17]:50788) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHz74-0005YX-Gc for submit@debbugs.gnu.org; Thu, 04 Mar 2021 20:18:43 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:37272) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lHz73-0002ck-3v for guix-patches@gnu.org; Thu, 04 Mar 2021 20:18:41 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:50903) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lHz6x-0006OC-UI for guix-patches@gnu.org; Thu, 04 Mar 2021 20:18:40 -0500 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 06B2930014B for ; Fri, 5 Mar 2021 02:18:18 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-language:content-transfer-encoding:content-type :content-type:mime-version:user-agent:date:date:message-id:from :from:received:received:received; s=mdc; t=1614907097; x= 1616721498; bh=frcCV1k9oG9oKj3dpUqdJg1PxRT2RSN/XKdLCPjaYaY=; b=i zV2mGUBnDrAPlDNcXr5VdEFuy4fXLY8+RUS4MgnyfIG6YMclHTT9hIeCxMhFGqqv 8hW3uhLMlfPB7bkqePM0Lk5wYppNHhtAiwzwvMEmkmDMWd3WAm3VO9EHAoPtbsY2 2lZiOJaQt/gK8CTgAYM5ZwxAeGktquem5pNC1sPbKs= 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 NeTGtC-sYWHK for ; Fri, 5 Mar 2021 02:18:17 +0100 (CET) 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 ; Fri, 5 Mar 2021 02:18:17 +0100 (CET) Received: from [192.168.1.220] (31.18.50.167) 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 15.1.2176.2; Fri, 5 Mar 2021 02:18:17 +0100 To: From: =?UTF-8?B?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= Message-ID: <10231918-e505-c813-7573-b7e8f9fb4eee@mdc-berlin.de> Date: Fri, 5 Mar 2021 02:18:16 +0100 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.10.0 MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8"; format=flowed Content-Transfer-Encoding: 7bit Content-Language: en-US X-Originating-IP: [31.18.50.167] 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-14.0.0.3080-8.6.1012-26010.004 X-TM-AS-Result: No-10-2.373600-8.000000 X-TMASE-MatchedRID: zNHEZVbO6+CYN/UYLI7XqOLzNWBegCW2RYvisGWbbS/ITICTZKCMNexJ beH3K4ldgPn1rCdWbriK1w/mwA00Qd0H8LFZNFG73Yq8RVaZivV4OXlDu6jxLpvOJThWZQ3kbSv Uj/BK7J9DE2SiozhChZlMspqOq0CS X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-2.373600-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26010.004 X-TM-SNTS-SMTP: 8865B1FF740AE561123EFB7B40419EEB39680F2B028D3999F74B1E3A58BF73762000: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: 18 X-Spam_score: 1.8 X-Spam_bar: + X-Spam_report: (1.8 / 5.0 requ) BAYES_00=-1.9, BODY_EMPTY=0.673, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, EMPTY_MESSAGE=2.32, MISSING_SUBJECT=1.799, PYZOR_CHECK=1.392, RCVD_IN_DNSWL_MED=-2.3, RCVD_IN_MSPIKE_H4=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=no autolearn_force=no X-Spam_action: no action X-Spam-Score: 3.6 (+++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: Content analysis details: (3.6 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -2.3 RCVD_IN_DNSWL_MED RBL: Sender listed at https://www.dnswl.org/, medium trust [209.51.188.17 listed in list.dnswl.org] 0.9 SPF_FAIL SPF: sender does not match SPF record (fail) [SPF failed: Please see http://www.openspf.org/Why?s=mfrom; id=madalinionel.patrascu%40mdc-berlin.de; ip=209.51.188.17; r=debbugs.gnu.org] -0.0 SPF_HELO_PASS SPF: HELO matches SPF record 0.0 RCVD_IN_MSPIKE_H3 RBL: Good reputation (+3) [209.51.188.17 listed in wl.mailspike.net] 1.8 MISSING_SUBJECT Missing Subject: header 0.2 NO_SUBJECT Extra score for no subject 2.3 EMPTY_MESSAGE Message appears to have no textual parts and no Subject: text 0.0 RCVD_IN_MSPIKE_WL Mailspike good senders 0.7 BODY_EMPTY No body text in message 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: 2.6 (++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: Content analysis details: (2.6 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -2.3 RCVD_IN_DNSWL_MED RBL: Sender listed at https://www.dnswl.org/, medium trust [209.51.188.17 listed in list.dnswl.org] 0.0 RCVD_IN_MSPIKE_H3 RBL: Good reputation (+3) [209.51.188.17 listed in wl.mailspike.net] 0.9 SPF_FAIL SPF: sender does not match SPF record (fail) [SPF failed: Please see http://www.openspf.org/Why?s=mfrom;id=madalinionel.patrascu%40mdc-berlin.de;ip=209.51.188.17;r=debbugs.gnu.org] -0.0 SPF_HELO_PASS SPF: HELO matches SPF record -1.0 MAILING_LIST_MULTI Multiple indicators imply a widely-seen list manager 1.8 MISSING_SUBJECT Missing Subject: header 0.2 NO_SUBJECT Extra score for no subject 2.3 EMPTY_MESSAGE Message appears to have no textual parts and no Subject: text 0.0 RCVD_IN_MSPIKE_WL Mailspike good senders 0.7 BODY_EMPTY No body text in message From debbugs-submit-bounces@debbugs.gnu.org Thu Mar 04 20:21:05 2021 Received: (at 46937) by debbugs.gnu.org; 5 Mar 2021 01:21:05 +0000 Received: from localhost ([127.0.0.1]:60665 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHz9H-0005cU-Uc for submit@debbugs.gnu.org; Thu, 04 Mar 2021 20:21:05 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:42485) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHz9G-0005cG-3P for 46937@debbugs.gnu.org; Thu, 04 Mar 2021 20:20:59 -0500 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id 8810BA0106; Fri, 5 Mar 2021 02:20:51 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1614907251; x=1616721652; bh=aquJyikfqBhZq9jut4QuVOzVF/lUcV+iquINoE1W45o=; b=V8HrZ9QT4KEc urnKvQ7blxpB5orBl5P8UIlrUU8MS0dVd9pJ5M70PHPcuXtwoGpq2oJZqscTZD/z /ky9/zASeDAdhvuYAHcaasKax1ss9GwrN+8OiJhgbEusAalmhlRHUqaScwmkG9dW eDnoDuyh0XrfEdqICqlZJJ51zOJ60SE= 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 26v_mG1kuARa; Fri, 5 Mar 2021 02:20:51 +0100 (CET) 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; Fri, 5 Mar 2021 02:20:50 +0100 (CET) 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 15.1.2176.2; Fri, 5 Mar 2021 02:20:50 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <46937@debbugs.gnu.org> Subject: [PATCH 1/3] gnu: Add r-rcppthread. Date: Fri, 5 Mar 2021 02:20:37 +0100 Message-ID: <20210305012039.15219-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.30.1 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit 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-14.0.0.3080-8.6.1012-26010.004 X-TM-AS-Result: No-10--0.250400-8.000000 X-TMASE-MatchedRID: xPvPRJicGCTRtBxlwMMWfD8Ckw9b/GFeTJDl9FKHbrmv/7fHaEp6EzjO 5tmKyhZMSzp4xfbpblOO/Rcr1vttxSq+GZ9ZHxIhUYXhMajr0x53G1bsm5zfjMZygq/CPmro86z su81iFU5bHRirBBg/NFWlox17XqhAzqLACWuCC/JqZ6OipRp3el3n+beqvEXMuSti1BoHqPaCKF cSai97mZ7AIF9am+V3ElOOOz3JPpijxYyRBa/qJQOkBnb8H8GWjaPj0W1qn0TKayT/BQTiGqeHo idXaPIyqZvZRUGhneYRQvcpZUt1dH9HSDNLSMM0ExgAmZ8Sn7R3N24RYd07/GC/bVYA02ceyc7i v4Y3JnB5iOIDigzu3uWrs/+5064veFv61dDRnYf0c5qUjgqLKvYlQeU3xrH0XtGJm2N/3yI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.250400-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26010.004 X-TM-SNTS-SMTP: 20CE7B09A3935E6FB973884493800944716B67D4077E1F4C416147516C9E87452000:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 46937 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: -3.3 (---) * gnu/packages/cran.scm (r-rcppthread): New variable. --- gnu/packages/cran.scm | 23 ++++++++++++++++++++++- 1 file changed, 22 insertions(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1d574b9768..4ac4b4cae1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11,7 +11,7 @@ ;;; Copyright © 2018 Sandeep Subramanian ;;; Copyright © 2018 Charlie Ritter ;;; Copyright © 2018 Konrad Hinsen -;;; Copyright © 2018, 2020 Mădălin Ionel Patrașcu +;;; Copyright © 2018, 2020, 2021 Mădălin Ionel Patrașcu ;;; Copyright © 2018 Laura Lazzati ;;; Copyright © 2018 Leo Famulari ;;; Copyright © 2018 Marius Bakke @@ -2668,6 +2668,27 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see @code{citation(\"Rcpp\")} for details on these last two.") (license license:gpl2+))) +(define-public r-rcppthread + (package + (name "r-rcppthread") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "RcppThread" version)) + (sha256 + (base32 + "1xfcxrny779kgknlvnc4j02ifprnakndnkhx8bhy50d39vp4hjjl")))) + (properties `((upstream-name . "RcppThread"))) + (build-system r-build-system) + (home-page + "https://github.com/tnagler/RcppThread") + (synopsis "R threading in C++") + (description + "This package provides a C++11-style thread class and thread pool that can +safely be interrupted from R.") + (license license:expat))) + (define-public r-bindr (package (name "r-bindr") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Thu Mar 04 20:21:08 2021 Received: (at 46937) by debbugs.gnu.org; 5 Mar 2021 01:21:08 +0000 Received: from localhost ([127.0.0.1]:60668 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHz9Q-0005dS-9N for submit@debbugs.gnu.org; Thu, 04 Mar 2021 20:21:08 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:47605) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHz9N-0005cW-Qg for 46937@debbugs.gnu.org; Thu, 04 Mar 2021 20:21:06 -0500 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 9995116011B; Fri, 5 Mar 2021 02:20:59 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received:received:received; s=mdc; t= 1614907259; x=1616721660; bh=N0aMjs0YAqYMrHJ9JsRrnwWAL7Ka5GerCkZ rwcMHcgY=; b=aszju8YGDAzJVsje7MTYhUbrT/ao9DJFqM8TDnndpOygFXU6Rmm iC1Vvq8XK2oODjzBGluQXcwXr+k7vQ5YoU3zNMFkUyvrG1q7DrI5ZKg9JW6zYXTz pAVhkxxeXrIJLr+HVa9ubcqzK33/DTStZaW8oin/5P9kOG+xNbdF8LDM= 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 B9u_4Xuh87qY; Fri, 5 Mar 2021 02:20:59 +0100 (CET) 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; Fri, 5 Mar 2021 02:20:59 +0100 (CET) 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 15.1.2176.2; Fri, 5 Mar 2021 02:20:58 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <46937@debbugs.gnu.org> Subject: [PATCH 2/3] gnu: Add r-universalmotif. Date: Fri, 5 Mar 2021 02:20:38 +0100 Message-ID: <20210305012039.15219-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210305012039.15219-1-madalinionel.patrascu@mdc-berlin.de> References: <20210305012039.15219-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit 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-14.0.0.3080-8.6.1012-26010.004 X-TM-AS-Result: No-10--4.104600-8.000000 X-TMASE-MatchedRID: FTxIpntvkVXRtBxlwMMWfD8Ckw9b/GFeTJDl9FKHbrnvrj2fROADidSQ QZwCn1OrWGH5wVAlhqF58gNAZ71WHYjRwo/Cjf7ifOaYwP8dcX5IvK4LrXs1aTcQcUZK1ILgedg e6osRC6g37vLQSViJKPharoQvMIWZUriXxFmUkHwBnSWdyp4eob/I3arxTrvirFjA6CZN1k3ukJ QjHbvwOZh97xQuugnjLb6XLHjqIvT7lPrMqaVmF4vqrlGw2G/k/BBU1WQWNfKYeMTPaAHLLWnNr fyaFzoAj8WQoLb8C5uhu8LBW5hICTpB6vA8GIIRXA16ExwD56wB/ULfnyF0r6BWLBsfseG+OZss O+6krjjF+KCpGE37CJsoi2XrUn/JmTDwp0zM3zoqtq5d3cxkNRqXnrxrKCOXrDM22rSqua19EeG YUYJeLIDDQrkx7TtWS9wbvUevNHux4fwawh+QBlPqmZ4ScCB+ssF9BB5AQNDRmi5vpEJjMwYiFV GJeB5u6Mfa6qKy6iI+O46LdUapZwroQfh7NkPlxUbkcyBaCqh+3BndfXUhXQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.104600-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26010.004 X-TM-SNTS-SMTP: 09E6BB5DB9BEEA4E9E08D2520D447126E88819EED59B06C8C337265C2C5D82542000:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 46937 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: -3.3 (---) * gnu/packages/bioconductor.scm (r-universalmotif): New variable. --- gnu/packages/bioconductor.scm | 53 ++++++++++++++++++++++++++++++++++- 1 file changed, 52 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a4d97fad65..55a9b07509 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020 Simon Tournier ;;; Copyright © 2020 Peter Lo -;;; Copyright © 2020 Mădălin Ionel Patrașcu +;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Jakub Kądziołka ;;; ;;; This file is part of GNU Guix. @@ -7435,6 +7435,57 @@ data. This modified test allows for testing differential expression in qPCR data.") (license license:gpl2+))) +(define-public r-universalmotif + (package + (name "r-universalmotif") + (version "1.8.3") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "universalmotif" version)) + (sha256 + (base32 + "1ys2kbayc1rzv8nzi60208yfslm4kzynndfg7vw2n0c30dvzycrc")))) + (properties + `((upstream-name . "universalmotif"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-link + (lambda _ + (substitute* "src/Makevars" + (("/usr/bin/strip") (which "strip"))) + #t))))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-ggplot2" ,r-ggplot2) + ("r-ggseqlogo" ,r-ggseqlogo) + ("r-iranges" ,r-iranges) + ("r-mass" ,r-mass) + ("r-rcpp" ,r-rcpp) + ("r-rcppthread" ,r-rcppthread) + ("r-rdpack" ,r-rdpack) + ("r-rlang" ,r-rlang) + ("r-s4vectors" ,r-s4vectors) + ("r-yaml" ,r-yaml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page + "https://bioconductor.org/packages/universalmotif/") + (synopsis + "Specific structures importer, modifier, and exporter for R") + (description + "This package allows importing most common @dfn{specific structure} +(motif) types into R for use by functions provided by other Bioconductor +motif-related packages. Motifs can be exported into most major motif formats +from various classes as defined by other Bioconductor packages. A suite of +motif and sequence manipulation and analysis functions are included, including +enrichment, comparison, P-value calculation, shuffling, trimming, higher-order +motifs, and others.") + (license license:gpl3))) + ;; This is a CRAN package, but it depends on Bioconductor packages, so we put ;; it here. (define-public r-activedriverwgs -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Thu Mar 04 20:21:13 2021 Received: (at 46937) by debbugs.gnu.org; 5 Mar 2021 01:21:14 +0000 Received: from localhost ([127.0.0.1]:60671 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHz9V-0005dk-Kj for submit@debbugs.gnu.org; Thu, 04 Mar 2021 20:21:13 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:60835) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHz9T-0005dK-MY for 46937@debbugs.gnu.org; Thu, 04 Mar 2021 20:21:12 -0500 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id CB7DE3000DE; Fri, 5 Mar 2021 02:21:05 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received:received:received; s=mdc; t= 1614907265; x=1616721666; bh=If8Ji49LgH5sbIR7EXedEs3PUFtJ+vAGxQB KorBTh4I=; b=NVrc/J9IJ3qPLaPRt0qiXl5dscm9UsyDoTAF7w0oIJv685qYuyW cXeNV+Xa1i++p/MHtPzWgmHw1PW1KFLvZZpXRodjs6x14cShYhO1+19cOZ6zshPJ EQfMUhhL33+NjI/TLdnSkA2aglv4KJQwwOp1tyzwBVIpOeG84gD8sFlI= 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 VISoKwoyooWp; Fri, 5 Mar 2021 02:21:05 +0100 (CET) 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; Fri, 5 Mar 2021 02:21:05 +0100 (CET) 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 15.1.2176.2; Fri, 5 Mar 2021 02:21:04 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <46937@debbugs.gnu.org> Subject: [PATCH 3/3] gnu: Add r-circrnaprofiler. Date: Fri, 5 Mar 2021 02:20:39 +0100 Message-ID: <20210305012039.15219-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210305012039.15219-1-madalinionel.patrascu@mdc-berlin.de> References: <20210305012039.15219-1-madalinionel.patrascu@mdc-berlin.de> 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-14.0.0.3080-8.6.1012-26010.004 X-TM-AS-Result: No-10--3.693300-8.000000 X-TMASE-MatchedRID: qYH9YzLp+XssaaYlMvaOHAPZZctd3P4BlwT0XposETUIP8WG05jq8Abo TDS3zulAkzpHopPQfRr9E3D6X+2jHW2x/ChgpGE+TT9ZveSPAxX4qCLIu0mtIPj/xqm3b+MoP4x DpnkWHW8c3dYpQhN0IYHDDaAVX9kI8T3ZGQTX60nRSfdpjZZR7lF5adRR2Ej1tSlhqC3qPOh2Pq BW66jvyVbRH5B/+lqLUw3F1+6WUPyhznSgFQVXH6ubsOtSWY2QgDLqnrRlXrZ8nn9tnqel2MprJ P8FBOIab3/xwmHh63msfUuHRu7UH8o0m4F7lG1Jq7PhR+u3KVM0bb4LD/gftvfRVd2xp0GrUok9 zSnsZir26sKykYIkfL0ZBgLRyUHz+Bepavj7kpF4W/rV0NGdh/RzmpSOCosq9iVB5TfGsfRe0Ym bY3/fIg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.693300-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26010.004 X-TM-SNTS-SMTP: 8B6D5D5A91A402B4F6FDFBD7C01B739A2BECB42538212C7EA11445D4338671F62000:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 46937 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: -3.3 (---) * gnu/packages/bioconductor.scm (r-circrnaprofiler): New variable. --- gnu/packages/bioconductor.scm | 53 +++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 55a9b07509..2da2be6ae3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6810,6 +6810,59 @@ accessibility data.") ,@(alist-delete "r-monocle" (package-propagated-inputs r-cicero))))))) +(define-public r-circrnaprofiler + (package + (name "r-circrnaprofiler") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "circRNAprofiler" version)) + (sha256 + (base32 + "1rwpl9a5p5242aiapik0vf4ywqh7m6phzl8z8qmzcy0imbx7mpbn")))) + (properties + `((upstream-name . "circRNAprofiler"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationhub" ,r-annotationhub) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-deseq2" ,r-deseq2) + ("r-dplyr" ,r-dplyr) + ("r-edger" ,r-edger) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-gwascat" ,r-gwascat) + ("r-iranges" ,r-iranges) + ("r-magrittr" ,r-magrittr) + ("r-r-utils" ,r-r-utils) + ("r-readr" ,r-readr) + ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-seqinr" ,r-seqinr) + ("r-stringi" ,r-stringi) + ("r-stringr" ,r-stringr) + ("r-universalmotif" ,r-universalmotif))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page + "https://github.com/Aufiero/circRNAprofiler") + (synopsis + "Computational framework for the downstream analysis of circular RNA's") + (description + "@code{r-circrnaprofiler} is a computational framework for a comprehensive +in silico analysis of @dfn{circular RNA} (circRNAs). This computational +framework allows to combine and analyze circRNAs previously detected by +multiple publicly available annotation-based circRNA detection tools. It +covers different aspects of circRNAs analysis from differential expression +analysis, evolutionary conservation, biogenesis to functional analysis.") + (license license:gpl3))) + (define-public r-cistopic (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950") (revision "0")) -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 05 10:21:41 2021 Received: (at 46937-done) by debbugs.gnu.org; 5 Mar 2021 15:21:41 +0000 Received: from localhost ([127.0.0.1]:35157 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lICGq-00040Y-SY for submit@debbugs.gnu.org; Fri, 05 Mar 2021 10:21:41 -0500 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21146) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lICGp-00040Q-He for 46937-done@debbugs.gnu.org; Fri, 05 Mar 2021 10:21:40 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1614957696; cv=none; d=zohomail.com; s=zohoarc; b=UFFFpFTn5WchozAxJ7wTXHlndJDG8sP7PgeUnZqid7SgVvXsjahwet6VZKa1oWmrMVA1+b/Bh7+ibnheflV8OOaAzRVFqnrTZ9n3n9aGgAIk/grRwdS8qZjS2V7VSB4kuEt2L10QBvRvJHmaB4nPtzJMCikPjm6onfpmew6L4fk= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1614957696; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=z7cyOr+sRNmnIwh/Oxc2Ru1U5yVzuzm7QgJIOKcb59Y=; b=igSzjwxC51+gwbiVZMplmgfghiHnaT8jUvNLdriDwrROjujfK9hViFUSkujj0WnXOeZD4Y/FW8CxtkTulGVGqJ5IIlqrk7r4hVB63WzyL3yG+tsIXep5MvbYCdEx4xJK8FDz+5LiRiaH8UQpuErSQbsLR2Bo8u7dT0BrEfsEaVE= 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= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1614957696; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; bh=z7cyOr+sRNmnIwh/Oxc2Ru1U5yVzuzm7QgJIOKcb59Y=; b=ZbPPU4qKW59froKS6U7XYzt1po9lHRFNSne6R4E6nQyeudi/6ClkR2Ltvn+QuTNo aXq8ti4b7rxTb6LGvqFCBH1cMOdG3niYIo7f7JG+k+J7VObpJzxc/SyJ2e3j6VNnUHC YXrslZ7v7EEQVfohzNmWp2CKx4rvNKG7FA73Fh6k= Received: from localhost (p54ad4c23.dip0.t-ipconnect.de [84.173.76.35]) by mx.zohomail.com with SMTPS id 1614957693143495.9576801801651; Fri, 5 Mar 2021 07:21:33 -0800 (PST) References: <20210305012039.15219-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.4.14; emacs 27.1 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [PATCH 1/3] gnu: Add r-rcppthread. In-reply-to: <20210305012039.15219-1-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 Date: Fri, 05 Mar 2021 16:21:29 +0100 Message-ID: <87ft19tyme.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: 46937-done Cc: 46937-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/cran.scm (r-rcppthread): New variable. [=E2=80=A6] > * gnu/packages/bioconductor.scm (r-universalmotif): New variable. [=E2=80= =A6] > * gnu/packages/bioconductor.scm (r-circrnaprofiler): New variable. Applied with minor changes: we no longer end phases with #t. Thank you! --=20 Ricardo From unknown Wed Jun 18 23:12:51 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Sat, 03 Apr 2021 11:24:06 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator