From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp0 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id 6M0rD82dX1/tAgAA0tVLHw (envelope-from ) for ; Mon, 14 Sep 2020 16:43:57 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp0 with LMTPS id 8GqCCc2dX19rGwAA1q6Kng (envelope-from ) for ; Mon, 14 Sep 2020 16:43:57 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id B3EE9940878 for ; Mon, 14 Sep 2020 16:43:56 +0000 (UTC) Received: from localhost ([::1]:41672 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kHra7-0005iZ-OJ for larch@yhetil.org; Mon, 14 Sep 2020 12:43:55 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:55228) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kHr2R-0004XA-2D for guix-patches@gnu.org; Mon, 14 Sep 2020 12:09:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:44459) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kHr2Q-0002fK-P3 for guix-patches@gnu.org; Mon, 14 Sep 2020 12:09:06 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1kHr2Q-0008VF-Kw for guix-patches@gnu.org; Mon, 14 Sep 2020 12:09:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#43400] [PATCH 09/12] gnu: r-rhdf5lib: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 14 Sep 2020 16:09:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 43400 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 43400@debbugs.gnu.org Cc: zimoun Received: via spool by 43400-submit@debbugs.gnu.org id=B43400.160009970432555 (code B ref 43400); Mon, 14 Sep 2020 16:09:06 +0000 Received: (at 43400) by debbugs.gnu.org; 14 Sep 2020 16:08:24 +0000 Received: from localhost ([127.0.0.1]:55994 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1j-0008T1-Or for submit@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:24 -0400 Received: from mail-wm1-f44.google.com ([209.85.128.44]:35455) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kHr1S-0008QB-Ir for 43400@debbugs.gnu.org; Mon, 14 Sep 2020 12:08:10 -0400 Received: by mail-wm1-f44.google.com with SMTP id y15so635862wmi.0 for <43400@debbugs.gnu.org>; Mon, 14 Sep 2020 09:08:06 -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=Yaf+qkABzTAsimJvzt6Vmu8oDVZ3zYmNV6OyFMBKM1U=; b=F5QWRcePWNMmKPk/bUNey/Ma5dnX8se7Sy2DUw9jAyJ5nSWpTJn55YcfFo2UgmKRfa 16riQfFUEiGMXzw5Jy9KsjN4noVTkGYcdBMlun4XiSun9JF9dzB9ASX5WVpbcj+3NSNM mVaHA170LH6/jQS61s0fzyuBtdjBrkbiP6b/TtW01PO26hQetnF8f3d14x7YR7xhdrL1 P96If4j8GcfhQYzP3jh49BG6Dos3xNeZx0esUB833B/NfCRwviGXI0iMWAiCl5BwWBaw zpyCkvX+dA6cVmExyRzXDNDVj8h3Uj8hxq1GaPCyGAcII2AnhKXPd8PrsnD4KY4g5jhQ 3EFQ== 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=Yaf+qkABzTAsimJvzt6Vmu8oDVZ3zYmNV6OyFMBKM1U=; b=hqDOoZwsO5IJvUzndYbCfa/fATS8iQh+LJKvITJx4SV0g90vPoUT5ZHFoH70JI97j4 TgQjLYD9BRD8NEff85X+9nElKbenJxdgShe+tqP1ZxFr2vxJXRnbdhYDCU2KkPXJSXwn nawq81nfsC5ZeE14dmNVJhdgFZs27Zy6zczyFlDg8nlgh8KwMy+TOUsxakJDOg0vURPv RA6Y501noWKh8+QV8qEgpRPhRl5qGvmwuaI0W8kY+eXD6WIpZ4aXtv4Uih+8fe51lFn0 I0bLGR1+tOFqlryMjUToa71Xu2RatCrG9yFMR49gwmk7+O8gfU4bUwgePRp6qeYxTt9z 28Tg== X-Gm-Message-State: AOAM531N7c1+VhGJLIjiVF4MdRI2qo1+UObvP3OohzvhZmQ56+kjVh7+ htok3GR86Ga8eAcV34GEiDVg2XbBMiE= X-Google-Smtp-Source: ABdhPJzvSXuK5nUyVTz6+vlpyvfrBdnv7AmiRODMoMdtuCcbe6ORmi4v2VpEBWYptXKlsvreYbZ03A== X-Received: by 2002:a1c:b388:: with SMTP id c130mr73979wmf.175.1600099680664; Mon, 14 Sep 2020 09:08:00 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id s5sm22012851wrm.33.2020.09.14.09.08.00 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 14 Sep 2020 09:08:00 -0700 (PDT) From: zimoun Date: Mon, 14 Sep 2020 18:07:44 +0200 Message-Id: <20200914160747.8983-9-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.28.0 In-Reply-To: <20200914160747.8983-1-zimon.toutoune@gmail.com> References: <20200914160747.8983-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Spam-Score: -1.0 (-) X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Scanner: scn0 Authentication-Results: aspmx1.migadu.com; dkim=fail (rsa verify failed) header.d=gmail.com header.s=20161025 header.b=F5QWRceP; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Spam-Score: 0.09 X-TUID: l+TuparqeGMr * gnu/packages/bioinformatics.scm (r-rhdf5lib): Move from here... * gnu/packages/bioconductor.scm (r-rhdf5lib): ...to here. --- gnu/packages/bioconductor.scm | 83 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 82 -------------------------------- 2 files changed, 83 insertions(+), 82 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0ecb460bc4..0e63c486ee 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2019 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020 Mădălin Ionel Patrașcu +;;; Copyright © 2020 Jakub Kądziołka ;;; ;;; This file is part of GNU Guix. ;;; @@ -8336,6 +8337,88 @@ routines.") objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-rhdf5lib + (package + (name "r-rhdf5lib") + (version "1.10.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Rhdf5lib" version)) + (sha256 + (base32 + "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete bundled binaries + (delete-file-recursively "src/wininclude/") + (delete-file-recursively "src/winlib-4.9.3/") + (delete-file-recursively "src/winlib-8.3.0/") + (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz") + #t)))) + (properties `((upstream-name . "Rhdf5lib"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'do-not-use-bundled-hdf5 + (lambda* (#:key inputs #:allow-other-keys) + (for-each delete-file '("configure" "configure.ac")) + ;; Do not make other packages link with the proprietary libsz. + (substitute* "R/zzz.R" + ((" \"%s/libsz.a\"") "")) + (with-directory-excursion "src" + (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) + (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) + "hdf5") + ;; Remove timestamp and host system information to make + ;; the build reproducible. + (substitute* "hdf5/src/libhdf5.settings.in" + (("Configured on: @CONFIG_DATE@") + "Configured on: Guix") + (("Uname information:.*") + "Uname information: Linux\n") + ;; Remove unnecessary store reference. + (("C Compiler:.*") + "C Compiler: GCC\n")) + (rename-file "Makevars.in" "Makevars") + (substitute* "Makevars" + (("@ZLIB_LIB@") "-lz") + (("@ZLIB_INCLUDE@") "") + (("HDF5_CXX_LIB=.*") + (string-append "HDF5_CXX_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n")) + (("HDF5_LIB=.*") + (string-append "HDF5_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n")) + (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") + (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") + (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n") + (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n") + (("HDF5_HL_LIB=.*") + (string-append "HDF5_HL_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n")) + (("HDF5_HL_CXX_LIB=.*") + (string-append "HDF5_HL_CXX_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n")) + ;; szip is non-free software + (("cp \"\\$\\{SZIP_LIB\\}.*") "") + (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))) + #t))))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("hdf5" ,hdf5-1.10))) + (native-inputs + `(("hdf5-source" ,(package-source hdf5-1.10)) + ("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/Rhdf5lib") + (synopsis "HDF5 library as an R package") + (description "This package provides C and C++ HDF5 libraries for use in R +packages.") + (license license:artistic2.0))) + (define-public r-beachmat (package (name "r-beachmat") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a84d19727c..8bd42c9429 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10684,88 +10684,6 @@ access and manipulation of HDF5 datasets. It supports delayed operations and block processing.") (license license:artistic2.0))) -(define-public r-rhdf5lib - (package - (name "r-rhdf5lib") - (version "1.10.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "Rhdf5lib" version)) - (sha256 - (base32 - "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Delete bundled binaries - (delete-file-recursively "src/wininclude/") - (delete-file-recursively "src/winlib-4.9.3/") - (delete-file-recursively "src/winlib-8.3.0/") - (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz") - #t)))) - (properties `((upstream-name . "Rhdf5lib"))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'do-not-use-bundled-hdf5 - (lambda* (#:key inputs #:allow-other-keys) - (for-each delete-file '("configure" "configure.ac")) - ;; Do not make other packages link with the proprietary libsz. - (substitute* "R/zzz.R" - ((" \"%s/libsz.a\"") "")) - (with-directory-excursion "src" - (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) - (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) - "hdf5") - ;; Remove timestamp and host system information to make - ;; the build reproducible. - (substitute* "hdf5/src/libhdf5.settings.in" - (("Configured on: @CONFIG_DATE@") - "Configured on: Guix") - (("Uname information:.*") - "Uname information: Linux\n") - ;; Remove unnecessary store reference. - (("C Compiler:.*") - "C Compiler: GCC\n")) - (rename-file "Makevars.in" "Makevars") - (substitute* "Makevars" - (("@ZLIB_LIB@") "-lz") - (("@ZLIB_INCLUDE@") "") - (("HDF5_CXX_LIB=.*") - (string-append "HDF5_CXX_LIB=" - (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n")) - (("HDF5_LIB=.*") - (string-append "HDF5_LIB=" - (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n")) - (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") - (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") - (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n") - (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n") - (("HDF5_HL_LIB=.*") - (string-append "HDF5_HL_LIB=" - (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n")) - (("HDF5_HL_CXX_LIB=.*") - (string-append "HDF5_HL_CXX_LIB=" - (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n")) - ;; szip is non-free software - (("cp \"\\$\\{SZIP_LIB\\}.*") "") - (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))) - #t))))) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("hdf5" ,hdf5-1.10))) - (native-inputs - `(("hdf5-source" ,(package-source hdf5-1.10)) - ("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/Rhdf5lib") - (synopsis "HDF5 library as an R package") - (description "This package provides C and C++ HDF5 libraries for use in R -packages.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.28.0