From patchwork Fri May 21 20:26:05 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29499 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 35DAF27BC83; Fri, 21 May 2021 21:33:49 +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 A7D7D27BC78 for ; Fri, 21 May 2021 21:33:48 +0100 (BST) Received: from localhost ([::1]:47444 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBq7-0004fh-T2 for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:33:47 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52564) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBkk-0004wy-27 for guix-patches@gnu.org; Fri, 21 May 2021 16:28:14 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54510) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBkj-00031K-Pv for guix-patches@gnu.org; Fri, 21 May 2021 16:28:13 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBkj-0000Oh-L4 for guix-patches@gnu.org; Fri, 21 May 2021 16:28:13 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 33/50] gnu: r-mzr: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:13 +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=B48575.16216288541156 (code B ref 48575); Fri, 21 May 2021 20:28:13 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:34 +0000 Received: from localhost ([127.0.0.1]:37759 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk5-0000IU-Bc for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:33 -0400 Received: from mail-wr1-f45.google.com ([209.85.221.45]:45892) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjT-0000B3-No for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:56 -0400 Received: by mail-wr1-f45.google.com with SMTP id x7so2594125wrt.12 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:55 -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=3bzLoBL+wfpmWr0LO51TWODHnKj4fRH43j3EeZGVyqA=; b=OcdUIhqNLFA46MNhI3BQFJKRENNXus6y0Xy4+RMHkG/dRJzM8NTl+k30ik192bC4Eu IoLaF0UEjjJ4Q2rk9RdKfLKNbI7dUDvdg4DLgH2DzzekW2/rMm2R3LyGBOTlg+wl5GDl kjOk+/tZghhjMfxJwLDDw57T36RMXUM+DKgUdJoKAAKM9bkJt2nshrNL2hL6UybuZsd1 o6+gV++eW6DkaZnU7c87FNCic8RXP6CY8810MSX0irz3qBSMxCgf4cb/xHAqO6j5/98N GN2DXAaHE/aKhvvZXfqHWB8NE+tS2W7aC3Z5lUes7WWtF1fiTqJ2QN0UsFz6TkKe0kzE 7R7Q== 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=3bzLoBL+wfpmWr0LO51TWODHnKj4fRH43j3EeZGVyqA=; b=X1EFnPA/rTJhN8fhTvC8AU8v86oKg7UvykpD/Z8nUoFmzGZO1q8816/K5ip2fQTfRZ 1Qp2fa7sqto7dLc2TzUyXYpxChrhDRGCBdXIllJD8rjx6ERv0qr+kneOD6PzVSRrOVmN V/0RxfJCpDBJqacNds3KikOv3chhOc0Zo2QXuuUsCwmBYXwevOcGa1kYQ6e0HUhJCVSU 910OVxz8ec/38gjhStmJpBA+849PkadrV8FXEWF084tS58X5Ugw+Dv/pQSzxW+Rkc3hM ZPMd7D+gR4yrfL+1zHeqS2V4KdpUKXJg4u74u8MjcuE9Enq8bwxhlpH+aYTSWyJcMLsy Ui+g== X-Gm-Message-State: AOAM532bFGG1kh1MUS/tOeqx0woe/knx3dZ8eI5r+OTB1l3UQqUMA967 rGUu8g+17lnAbMwF3rjO94v3xllK2eg= X-Google-Smtp-Source: ABdhPJx+XoGDCyubWXKYbZ30aj4R3eACs4zoiTIcPbqrbHELVlxm1Z/+0SpTy6N8tKHyRrq6HOJmBQ== X-Received: by 2002:adf:f7cf:: with SMTP id a15mr11037611wrq.184.1621628810140; Fri, 21 May 2021 13:26:50 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.49 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:49 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:26:05 +0200 Message-Id: <20210521202622.26591-33-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-mzr): Move from here... * gnu/packages/bioconductor.scm (r-mzr): ...to here. --- gnu/packages/bioconductor.scm | 62 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 61 -------------------------------- 2 files changed, 62 insertions(+), 61 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7e86af7d21..5ceffd7b4d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -36,6 +36,7 @@ #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) + #:use-module (gnu packages boost) #:use-module (gnu packages cran) #:use-module (gnu packages compression) #:use-module (gnu packages gcc) @@ -3051,6 +3052,67 @@ mzIdentML files with the drawback of having less pretty output than a vendor specific parser.") (license license:gpl2+))) +(define-public r-mzr + (package + (name "r-mzr") + (version "2.24.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mzR" version)) + (sha256 + (base32 + "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "src/boost") + #t)))) + (properties `((upstream-name . "mzR"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-boost + (lambda _ + (substitute* "src/Makevars" + (("\\./boost/libs.*") "") + ;; This is to avoid having a plain directory on the list of + ;; libraries to link. + (("\\(RHDF5_LIBS\\)" match) + (string-append match "/libhdf5.a")) + (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ") + (("\\ARCH_OBJS=" line) + (string-append line + "\nBOOST_LIBS=-lboost_system -lboost_regex \ +-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) + #t))))) + (inputs + `(;; Our default boost package won't work here, unfortunately, even with + ;; mzR version 2.24.1. + ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources + ("zlib" ,zlib))) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-ncdf4" ,r-ncdf4) + ("r-protgenerics" ,r-protgenerics) + ("r-rcpp" ,r-rcpp) + ("r-rhdf5lib" ,r-rhdf5lib) + ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/sneumann/mzR/") + (synopsis "Parser for mass spectrometry data files") + (description + "The mzR package provides a unified API to the common file formats and +parsers available for mass spectrometry data. It comes with a wrapper for the +ISB random access parser for mass spectrometry mzXML, mzData and mzML files. +The package contains the original code written by the ISB, and a subset of the +proteowizard library for mzML and mzIdentML. The netCDF reading code has +previously been used in XCMS.") + (license license:artistic2.0))) + (define-public r-organismdbi (package (name "r-organismdbi") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index baef88cd2e..a6321a179a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8873,67 +8873,6 @@ trait.") proteomics packages.") (license license:artistic2.0))) -(define-public r-mzr - (package - (name "r-mzr") - (version "2.24.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "mzR" version)) - (sha256 - (base32 - "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg")) - (modules '((guix build utils))) - (snippet - '(begin - (delete-file-recursively "src/boost") - #t)))) - (properties `((upstream-name . "mzR"))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-system-boost - (lambda _ - (substitute* "src/Makevars" - (("\\./boost/libs.*") "") - ;; This is to avoid having a plain directory on the list of - ;; libraries to link. - (("\\(RHDF5_LIBS\\)" match) - (string-append match "/libhdf5.a")) - (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ") - (("\\ARCH_OBJS=" line) - (string-append line - "\nBOOST_LIBS=-lboost_system -lboost_regex \ --lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) - #t))))) - (inputs - `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.24.1. - ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources - ("zlib" ,zlib))) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-ncdf4" ,r-ncdf4) - ("r-protgenerics" ,r-protgenerics) - ("r-rcpp" ,r-rcpp) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/sneumann/mzR/") - (synopsis "Parser for mass spectrometry data files") - (description - "The mzR package provides a unified API to the common file formats and -parsers available for mass spectrometry data. It comes with a wrapper for the -ISB random access parser for mass spectrometry mzXML, mzData and mzML files. -The package contains the original code written by the ISB, and a subset of the -proteowizard library for mzML and mzIdentML. The netCDF reading code has -previously been used in XCMS.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2"))