From patchwork Tue Jan 17 13:18:22 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: 46224 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 65C7E27BBE9; Tue, 17 Jan 2023 13:19:41 +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=-3.7 required=5.0 tests=BAYES_00,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 BB4A927BBE9 for ; Tue, 17 Jan 2023 13:19:40 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pHls7-0002y1-D1; Tue, 17 Jan 2023 08:19:27 -0500 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 1pHlrj-0002v9-Mz for guix-patches@gnu.org; Tue, 17 Jan 2023 08:19:08 -0500 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 1pHlrj-000821-Em for guix-patches@gnu.org; Tue, 17 Jan 2023 08:19:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pHlri-0007dd-U1; Tue, 17 Jan 2023 08:19:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60878] [PATCH 1/2] gnu: Add r-rapiclient. References: <74d154b3c447432ebf531d0fb7415d91@mdc-berlin.de> In-Reply-To: <74d154b3c447432ebf531d0fb7415d91@mdc-berlin.de> 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: Tue, 17 Jan 2023 13:19:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60878 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <60878@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 60878-submit@debbugs.gnu.org id=B60878.167396153329336 (code B ref 60878); Tue, 17 Jan 2023 13:19:02 +0000 Received: (at 60878) by debbugs.gnu.org; 17 Jan 2023 13:18:53 +0000 Received: from localhost ([127.0.0.1]:36102 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHlrY-0007d1-U8 for submit@debbugs.gnu.org; Tue, 17 Jan 2023 08:18:53 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:35143) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHlrT-0007cb-2e for 60878@debbugs.gnu.org; Tue, 17 Jan 2023 08:18:51 -0500 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; s=mdc; t=1673961519; x=1675775920; bh=9HEUyGCRG236PO0 oDPK89KDq0NmzxYFGXvjaFBYIe2I=; b=NIKWarE9lpHTzLEIhtM2sG2hGb9OurE kMfRfar3+WxVEAv5bTh/8wpyGS95JDz7vDmKmBXHTs4Q3N//j7hjMHUkBh+YThJb ddefas0Er1FjlFPxIrJaYMd58CSFkXJyTzaAtbHWDSDwIjm1xpBsDxmLubzd0p35 BVVQBE8DT1M0= 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 A7DAD1600C9 for <60878@debbugs.gnu.org>; Tue, 17 Jan 2023 14:18:39 +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 15.1.2507.17; Tue, 17 Jan 2023 14:18:38 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Tue, 17 Jan 2023 14:18:22 +0100 Message-ID: <20230117131823.55318-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.38.1 MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27390.007 X-TM-AS-Result: No-10--5.148400-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPODy7 zxidHhYpGJHAl8RgcXAZijt1cgK90C/33TWoSUH6194/5X9VfCxb4dXBMpIkhofgjpBknTuRhi9 5Kz020gaGsZX0q3FpiOhAZQXEXXZuTvHzGcGqiIKrm7DrUlmNkIAy6p60ZV62yA7duzCw6dLdB/ CxWTRRu92KvEVWmYr1Z+GTZVEYn1U8Z9ddASknsQwaeoGAu0/N6LImcCHnwJE9cEchZrDWLw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.148400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27390.007 X-TM-SNTS-SMTP: 6D3B7E8AEFE54E882FB05B1742B2E63E98F561E64803EBBBB7349B0DC30B601C2002: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-rapiclient): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) base-commit: 29efa2791dafb042ca8ace77bcf8538fb404d492 diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3fcbd3b9f6..1914c9d85a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -10252,6 +10252,30 @@ (define-public r-collapsibletree the source data frame.") (license license:gpl3+))) +(define-public r-rapiclient + (package + (name "r-rapiclient") + (version "0.1.3") + (source (origin + (method url-fetch) + (uri (cran-uri "rapiclient" version)) + (sha256 + (base32 + "1pm4kdga2nz1cpmchdb0ad8gr3bqfm84b1kl32cyc0x3x5rr2syz")))) + (properties `((upstream-name . "rapiclient"))) + (build-system r-build-system) + (propagated-inputs + (list r-httr + r-jsonlite + r-yaml)) + (home-page "https://github.com/bergant/rapiclient") + (synopsis "Dynamic OpenAPI/Swagger client") + (description + "This package access services specified in OpenAPI (formerly Swagger) format. +It is not a code generator. The client is generated dynamically as a list of R +functions.") + (license license:expat))) + (define-public r-rappdirs (package (name "r-rappdirs") From patchwork Tue Jan 17 13:18:23 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: 46223 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 364BF27BBE9; Tue, 17 Jan 2023 13:19:38 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=unavailable 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 D591427BBEB for ; Tue, 17 Jan 2023 13:19:35 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pHls1-0002xY-HB; Tue, 17 Jan 2023 08:19:21 -0500 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 1pHlrj-0002v8-6j for guix-patches@gnu.org; Tue, 17 Jan 2023 08:19:07 -0500 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 1pHlri-00081p-SV for guix-patches@gnu.org; Tue, 17 Jan 2023 08:19:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pHlri-0007dU-I6; Tue, 17 Jan 2023 08:19:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60878] [PATCH 2/2] gnu: Add r-anvil. 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: Tue, 17 Jan 2023 13:19:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60878 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <60878@debbugs.gnu.org> Cc: rekado@elephly.net X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by 60878-submit@debbugs.gnu.org id=B60878.167396153329330 (code B ref 60878); Tue, 17 Jan 2023 13:19:02 +0000 Received: (at 60878) by debbugs.gnu.org; 17 Jan 2023 13:18:53 +0000 Received: from localhost ([127.0.0.1]:36100 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHlrY-0007cz-IF for submit@debbugs.gnu.org; Tue, 17 Jan 2023 08:18:52 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:52249) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHlrT-0007cd-5m for 60878@debbugs.gnu.org; Tue, 17 Jan 2023 08:18:50 -0500 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=1673961520; x=1675775921; bh=eHj94x3kMsRAK8p/bm7RYVHWNvAIk+x23fYr7Lh9vYg=; b=bPrLV9X5MIgC Tw0sY+G43omga7a5/x4M/kzDOc4GpYkYdJMlO+WjHaT1vcF8F/vV0rHVtqqaaRF4 pIPBUnETYAaz4GKR355tm+jXFNbwXBJA2K6wI1UhdJkyBBvtkyOKlz38EW6xeLIs E6BnqsnJ1t1YRnvj0/uxjC5Ghp4pea8= 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 A1A1216010D for <60878@debbugs.gnu.org>; Tue, 17 Jan 2023 14:18:40 +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 15.1.2507.17; Tue, 17 Jan 2023 14:18:39 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Tue, 17 Jan 2023 14:18:23 +0100 Message-ID: <20230117131823.55318-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.38.1 In-Reply-To: <20230117131823.55318-1-madalinionel.patrascu@mdc-berlin.de> References: <20230117131823.55318-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] 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-14.0.0.3092-9.0.1002-27390.007 X-TM-AS-Result: No-10--4.747400-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJO6ZW5Sc5wvHgrcxrzwsv5uwTlc9CcHMZerwqxtE531VNnf JrUSEbFD+7QmOJudfuPuNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIG1/OiWPM9c7cmM mAcpqutOjKgB/G5ipU7juWvhUjDfwe1Ws2JcOmw4vYlQ7uxD3/IqPnoYdELInlwV2iaAfSWcURS Scn+QSXt0H8LFZNFG7doMssNsUwYUF728hd3d10CP6v829Hz134Owm3fCfdbyvv860WmvahfKLo beqpxNhdExmvumdxe20ZxsO5qzAaMNzuez3p1Lww0e9zy7qCqzHpeHdXLjLb473WzsXAufzELZr sYgA6obyh3JNelCjdRkfAFx3Dn4y X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.747400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27390.007 X-TM-SNTS-SMTP: 5F93AB33F5B9F3FCC468CBC1A172B12BF2E9886881DF7AF5664897A09146E7CC2002: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/bioconductor.scm (r-anvil): New variable. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ca236bcf75..35aed4b62c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2443,6 +2443,47 @@ (define-public r-animalcules to understand their data better and discover new insights.") (license license:artistic2.0))) +(define-public r-anvil + (package + (name "r-anvil") + (version "1.10.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AnVIL" version)) + (sha256 + (base32 + "0iqsffkrxv28g9cddx2w05f2dbscwxhh6bpizwa8xaxhvn5bcpsv")))) + (properties `((upstream-name . "AnVIL"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocmanager + r-dplyr + r-dt + r-futile-logger + r-htmltools + r-httr + r-jsonlite + r-miniui + r-rapiclient + r-rlang + r-shiny + r-tibble + r-tidyr + r-tidyselect)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AnVIL") + (synopsis "Provides access to AnVIL, Terra, Leonardo and other projects") + (description + "The AnVIL is a cloud computing resource developed in part by the National +Human Genome Research Institute. The AnVIL package provides end-user and developer +functionality. For the end-user, AnVIL provides fast binary package installation, +utitlities for working with Terra/AnVIL table and data resources, and convenient +functions for file movement to and from Google cloud storage. For developers, +AnVIL provides programatic access to the Terra, Leonardo, Rawls, Dockstore, and +Gen3 RESTful programming interface, including helper functions to transform JSON +responses to formats more amenable to manipulation in R.") + (license license:artistic2.0))) + (define-public r-aldex2 (package (name "r-aldex2")