From patchwork Fri May 21 20:26:11 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29502 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 500B227BC81; Fri, 21 May 2021 21:33:57 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H4, RCVD_IN_MSPIKE_WL,SPF_HELO_PASS,T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id C672127BC78 for ; Fri, 21 May 2021 21:33:56 +0100 (BST) Received: from localhost ([::1]:47984 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBqG-00054I-1f for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:33:56 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52658) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBkq-0005Ra-OU for guix-patches@gnu.org; Fri, 21 May 2021 16:28:20 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54527) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBkq-000352-FA for guix-patches@gnu.org; Fri, 21 May 2021 16:28:20 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBkq-0000Qi-Bc for guix-patches@gnu.org; Fri, 21 May 2021 16:28:20 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 39/50] gnu: r-rhtslib: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:20 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 48575 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 48575@debbugs.gnu.org Cc: zimoun Received: via spool by 48575-submit@debbugs.gnu.org id=B48575.16216288641288 (code B ref 48575); Fri, 21 May 2021 20:28:20 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:44 +0000 Received: from localhost ([127.0.0.1]:37793 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBkF-0000Kc-Ha for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:43 -0400 Received: from mail-wm1-f45.google.com ([209.85.128.45]:43638) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjW-0000Bo-95 for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:14 -0400 Received: by mail-wm1-f45.google.com with SMTP id z85-20020a1c7e580000b029017a76f3afbaso5254968wmc.2 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:58 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=GjjPXYSiS+BefP9e4AIkdMmcWJKldfr6UalG2dfVP6s=; b=IpZA3Y3QYDciZj7vTgUT4b1bzMSXUSP+Ke2VqEs1z08NOi5r5MHzYuk9rjUY9bpQ6I KlCgjOSAE238DA604C58BSDm2RyxLX2W60CAgxwDpeos02silOl/F7P8RjieQftxG1BB VH0I/M+miWa51cEBAifmX5MLErS700u6lXjsLmk6HMdRk+uTaUlPHTWzoCyGw37a4ylj QAKLvk7L5wwuj3tEbsmXZZWgxmKbqg/N4lJTizxEKwscpmjdACz6LXd3wCpKfibZZEbX iCz0r6/4fSJNRTQr+WwbdeuclbqBnAravPhPN/vW7Emn2VNEXbWxtyR9lB8/IB9YyrKN Nz4A== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=GjjPXYSiS+BefP9e4AIkdMmcWJKldfr6UalG2dfVP6s=; b=LT54YxYANVjQV9tl4I0cBl0qZ8fNGztrVE1yVSG02WrVbwa9w/6I3+Hvgilk+AS5pe 5A79zbVNEmfSPNom9MUSnCZRbSbcM1welVTf17hITdufjIdbmh9ennJW6erzGhkKAxhW s47Qot9mXhP02U/w+QeAzzIuYP97BXUdHoHeU+2vlUEw2e0KqHEEYdT0LkiAvsTdfvYc tIjUIFi6c0uHUiWdMDDJwjFbnisjFL5aTNh1aRcPtkNeFzyidl9dmALlQp3IlEI8L5EO EQtBLjQL+u6axMe+kWuCkfBCHbX3FPw3yt0mHW/HQJ7xqRecLol5eGEktq0lRq58MJMG sRWg== X-Gm-Message-State: AOAM532br2PGTG+R9mfs5Ms5ibTvu6AvYXQbwEj9ysGcMb89PCPVSndN iYNwQ/QwKUNghuvlCONcLwnA8A6uC5g= X-Google-Smtp-Source: ABdhPJzLjzXDb1UoO675KkZBTK7z8LhPM0txLA6N551d06bm83FC97rw1kM3gKeuEf4Nc71jP1bR8Q== X-Received: by 2002:a1c:7fd0:: with SMTP id a199mr10226636wmd.161.1621628812804; Fri, 21 May 2021 13:26:52 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.52 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:52 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:26:11 +0200 Message-Id: <20210521202622.26591-39-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (r-rhtslib): Move from here... * gnu/packages/bioconductor.scm (r-rhtslib): ...to here. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 32 insertions(+), 31 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e720d7bf6a..8e78a2a0ca 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -39,6 +39,7 @@ #:use-module (gnu packages boost) #:use-module (gnu packages cran) #:use-module (gnu packages compression) + #:use-module (gnu packages curl) #:use-module (gnu packages gcc) #:use-module (gnu packages graph) #:use-module (gnu packages graphviz) @@ -2832,6 +2833,37 @@ Enrichment Analysis} (GSEA).") the Human Protein Atlas project.") (license license:artistic2.0))) +(define-public r-rhtslib + (package + (name "r-rhtslib") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Rhtslib" version)) + (sha256 + (base32 + "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4")))) + (properties `((upstream-name . "Rhtslib"))) + (build-system r-build-system) + ;; Without this a temporary directory ends up in the Rhtslib.so binary, + ;; which makes R abort the build. + (arguments '(#:configure-flags '("--no-staged-install"))) + (propagated-inputs + `(("curl" ,curl) + ("zlib" ,zlib) ; packages using rhtslib need to link with zlib + ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) + (home-page "https://github.com/nhayden/Rhtslib") + (synopsis "High-throughput sequencing library as an R package") + (description + "This package provides the HTSlib C library for high-throughput +nucleotide sequence analysis. The package is primarily useful to developers +of other R packages who wish to make use of HTSlib.") + (license license:lgpl2.0+))) + (define-public r-impute (package (name "r-impute") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 39c437f4a2..586efcf21e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7872,37 +7872,6 @@ including VCF header and contents in RDF and JSON.") secondary structure and comparative analysis in R.") (license license:gpl3+))) -(define-public r-rhtslib - (package - (name "r-rhtslib") - (version "1.22.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "Rhtslib" version)) - (sha256 - (base32 - "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4")))) - (properties `((upstream-name . "Rhtslib"))) - (build-system r-build-system) - ;; Without this a temporary directory ends up in the Rhtslib.so binary, - ;; which makes R abort the build. - (arguments '(#:configure-flags '("--no-staged-install"))) - (propagated-inputs - `(("curl" ,curl) - ("zlib" ,zlib) ; packages using rhtslib need to link with zlib - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) - (home-page "https://github.com/nhayden/Rhtslib") - (synopsis "High-throughput sequencing library as an R package") - (description - "This package provides the HTSlib C library for high-throughput -nucleotide sequence analysis. The package is primarily useful to developers -of other R packages who wish to make use of HTSlib.") - (license license:lgpl2.0+))) - (define-public r-bamsignals (package (name "r-bamsignals")