From patchwork Sat Mar 25 17:45:55 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 48679 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 9E63F16FE7; Sat, 25 Mar 2023 17:48:01 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=DKIM_INVALID,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 9601616D87 for ; Sat, 25 Mar 2023 17:48:00 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pg7yy-00051Z-46; Sat, 25 Mar 2023 13:47:12 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pg7yq-0004zR-Me for guix-patches@gnu.org; Sat, 25 Mar 2023 13:47:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pg7yq-0005nn-E1 for guix-patches@gnu.org; Sat, 25 Mar 2023 13:47:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pg7yp-00087y-9i; Sat, 25 Mar 2023 13:47:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#62441] [PATCH 4/4] gnu: Add r-ctrdata. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Sat, 25 Mar 2023 17:47:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 62441 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <62441@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 62441-submit@debbugs.gnu.org id=B62441.167976640431189 (code B ref 62441); Sat, 25 Mar 2023 17:47:03 +0000 Received: (at 62441) by debbugs.gnu.org; 25 Mar 2023 17:46:44 +0000 Received: from localhost ([127.0.0.1]:43418 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pg7yW-00086z-9m for submit@debbugs.gnu.org; Sat, 25 Mar 2023 13:46:44 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:59757) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pg7yK-00085w-HV for 62441@debbugs.gnu.org; Sat, 25 Mar 2023 13:46:33 -0400 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; s=mdc; t=1679766386; x=1681580787; bh=lKxij0GKexrq5jyvTIGWeispF7hGWuEkJgEAzGd2WOk=; b=BoncWdrbkmtp BL6+OJQrvmCZ3GOuhGIIqLQvGq0klDCLbV2F4NbM0PzgpTlnZTN5jXqgRBnG1CfW wk580k35R0+yOb/0dtWYv0MEMnXxwfZ6JXWItq0ItdKCfR1m/8m9IEke0k5Yd+wb /LbMHfhZZNd2YFIssPNi92M/c9sKJIA= 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 id 9BB3C16014E for <62441@debbugs.gnu.org>; Sat, 25 Mar 2023 18:46:26 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.23; Sat, 25 Mar 2023 18:46:21 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 25 Mar 2023 18:45:55 +0100 Message-ID: <20230325174555.837323-4-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230325174555.837323-1-madalinionel.patrascu@mdc-berlin.de> References: <20230325174555.837323-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27526.001 X-TM-AS-Result: No-10-3.500300-5.000000 X-TMASE-MatchedRID: ZAkTtSyZ7B7/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEPVS VC7uYV8ESQyRa2QqiAppuUdAUcH4tSq+GZ9ZHxIhuW77/y896siFzNNPDc6umBHfiujuTbedBO6 2kWcWGBhu4z/YYEdR45bpyCR4N2Viq2NInS93zS9oMLOoNHsM9rLZpUHs8KMVpz4V9BzQ0RpwuO Ip1++GNwWy+slqkucq38BVk5/okjyLBhscdVmCC4FhphRl/QgVN5dqZcIK7VgCHZkKE/8Uqp6ba /D5x6cp4vM1YF6AJbbY2hczJbMEQgtuKBGekqUpOlxBO2IcOBYFPVJaadF6GoKXCgPaz4KMCxLZ 5MCYylxqJ3jSe0KrrSQTUdsZa70Jjxkh99Y595kohu0bpV5Ex0MP4oSvXW48/gL0Zxhzykd+3Bn dfXUhXQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-3.500300-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27526.001 X-TM-SNTS-SMTP: 3A90914720C714FACA7E7756E67FA6AB47DD8D5AC4456D49C027E0B764512CCD2002:F X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/cran.scm (r-ctrdata): New variable. --- gnu/packages/cran.scm | 46 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9b314bae43..6e70dd134a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -97,6 +97,7 @@ (define-module (gnu packages cran) #:use-module (gnu packages pcre) #:use-module (gnu packages pdf) #:use-module (gnu packages perl) + #:use-module (gnu packages php) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pulseaudio) ;libsndfile #:use-module (gnu packages protobuf) @@ -396,6 +397,51 @@ (define-public r-cplm comparison tool involving zero-inflated and highly skewed distributions.") (license license:gpl2+))) +(define-public r-ctrdata + (package + (name "r-ctrdata") + (version "1.11.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ctrdata" version)) + (sha256 + (base32 "076v3bll8s6m61wcbwgrgrm34g0wa7gsc90mbwxwap1xfxyzjjsg")))) + (properties `((upstream-name . "ctrdata"))) + (build-system r-build-system) + (inputs + (list coreutils + perl + php + sed)) + (propagated-inputs + (list r-clipr + r-curl + r-dplyr + r-httr + r-jsonlite + r-lubridate + r-nodbi + r-rvest + r-stringi + r-xml2)) + (native-inputs (list r-r-rsp)) + (home-page "https://cran.r-project.org/package=ctrdata") + (synopsis "Retrieve and analyze clinical trials in public registers") + (description + "This package provides a system for querying, retrieving and analyzing +protocol- and results-related information on clinical trials from three public +registers, the @acronym{EUCTR, European Union Clinical Trials Register} @url{ +https://www.clinicaltrialsregister.eu/}, @acronym{CTGOV, ClinicalTrials.gov} +@url{https://clinicaltrials.gov/} and the @acronym{ISRCTN, International Clinical +Trials Registry Platform} @url{https://www.isrctn.com/}. Trial information is +downloaded, converted and stored in a database. Functions are included to +identify deduplicated records, to easily find and extract variables (fields) of +interest even from complex nesting as used by the registers, and to update +previous queries. The package can be used for meta-analysis and trend-analysis +of the design and conduct as well as for results of clinical trials.") + (license license:expat))) + (define-public r-ctrialsgov (package (name "r-ctrialsgov")