From patchwork Tue Nov 5 18:19:54 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 15973 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 3F4AB176D5; Tue, 5 Nov 2019 18:24:23 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,FREEMAIL_FROM, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id AC1B0176D4 for ; Tue, 5 Nov 2019 18:24:22 +0000 (GMT) Received: from localhost ([::1]:47260 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iS3V8-0003bY-1V for patchwork@mira.cbaines.net; Tue, 05 Nov 2019 13:24:22 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:54948) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iS3Rv-0000B9-F1 for guix-patches@gnu.org; Tue, 05 Nov 2019 13:21:04 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iS3Ru-0001TN-0g for guix-patches@gnu.org; Tue, 05 Nov 2019 13:21:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:58469) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iS3Rt-0001TD-T6 for guix-patches@gnu.org; Tue, 05 Nov 2019 13:21:01 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1iS3Rt-0005OR-Np for guix-patches@gnu.org; Tue, 05 Nov 2019 13:21:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#37988] [PATCH v3 3/6] gnu: Add r-rprotobuflib. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 05 Nov 2019 18:21:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 37988 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 37988@debbugs.gnu.org Cc: zimoun Received: via spool by 37988-submit@debbugs.gnu.org id=B37988.157297800820647 (code B ref 37988); Tue, 05 Nov 2019 18:21:01 +0000 Received: (at 37988) by debbugs.gnu.org; 5 Nov 2019 18:20:08 +0000 Received: from localhost ([127.0.0.1]:39057 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iS3R0-0005Mt-0v for submit@debbugs.gnu.org; Tue, 05 Nov 2019 13:20:06 -0500 Received: from mail-wr1-f42.google.com ([209.85.221.42]:37340) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iS3Qx-0005M8-Jd for 37988@debbugs.gnu.org; Tue, 05 Nov 2019 13:20:04 -0500 Received: by mail-wr1-f42.google.com with SMTP id t1so16666608wrv.4 for <37988@debbugs.gnu.org>; Tue, 05 Nov 2019 10:20:03 -0800 (PST) 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=D9hXoHnqI4wIlwZ6yrF/KI6ZimwfshrfxxJ8+Z8P1DI=; b=scxagQw9neWGQ2bSccWu9B9SbwZm67HrRfigePgDKR9IgWXoBCjrowNa3wPpsyyUHc X/f6KHUvcl+7PQlGIz1c0ZS6pKzfZO+UW5jc4Hq0DHy+IyaowuhIylPuAh0Mtf7OaYTO kQbgNl6mQGDIJYMqM3aUD5OK6jnXRFIYnw7CZEfhGh23PPDOed5POG0RG/Y4x3OxMc/5 e5lF4ZaZISbQLnsx1M7aiGTZixZsqrhPdS1ndADvbZgRhMNoQ0DJN6YN7dc2wmq1Vwk7 wJFxTQ0rily42YmYSN0gVqcRz1RyGQOlr8ZwgCSCOMwcKOqYPUqb+6Bbutr6/Ir/KDn0 XGGg== 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=D9hXoHnqI4wIlwZ6yrF/KI6ZimwfshrfxxJ8+Z8P1DI=; b=lo/XeXG7JynDwivHrH6HZ0qn70sImwAr4qavM9qo5WvXU2d+OtqIwVmmgbCywRlTQW KoF7K96rove8CbE4WgyoEn0Qne7OCPGyafiICEdnwEcbRQVSyQTK7PiwplXQzxi4N358 k/1m2iIU7wZGYgPaR+hVqmLBqpRxkEBJssS/8aZxX2zTj1rAfYLrzTNgmhZS5AaiRC8x 2zTK3V5j0wBFynCIeAmc6hInakhPS005cRedAUd3XkwzVtcjn/37+eR1hKGgLO3Ga3BI Xzd90erMsVHPsDrjQya7YgAuTC7zvNnSv/M7SjoS0XXPGSGzoNpM5YYWEMJd134Wwf9g 9gbg== X-Gm-Message-State: APjAAAUM2XkUkTSsdN1f1g34arqkYDeyo+fDhKzEA+mQcayMIulOGrFy jpMQ27pfD1Wh2gGtVm1cSAxhV71f X-Google-Smtp-Source: APXvYqwl4Zpf6wsbr1TsdZNRsxTo/JO85kPtiBra41+GvR/PEFf0FTNW4AZpGRjtY98Hpf0y+gtloA== X-Received: by 2002:adf:df81:: with SMTP id z1mr28576348wrl.278.1572977997488; Tue, 05 Nov 2019 10:19:57 -0800 (PST) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id y15sm8304033wrh.94.2019.11.05.10.19.56 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 05 Nov 2019 10:19:56 -0800 (PST) From: zimoun Date: Tue, 5 Nov 2019 19:19:54 +0100 Message-Id: <20191105181954.26339-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.23.0 In-Reply-To: <8736fah38i.fsf@elephly.net> References: <8736fah38i.fsf@elephly.net> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 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/bioconductor.scm (r-rprotobuflib): New variable. * gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch: New file. --- gnu/packages/bioconductor.scm | 31 ++++++++++ .../r-rprotobuflib-unbundle-dependency.patch | 57 +++++++++++++++++++ 2 files changed, 88 insertions(+) create mode 100644 gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 92e5d3ec0b..801e52245b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -38,6 +38,7 @@ #:use-module (gnu packages netpbm) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages protobuf) #:use-module (gnu packages statistics) #:use-module (gnu packages web) #:use-module (srfi srfi-1)) @@ -6166,3 +6167,33 @@ data.") (synopsis "Visualization for flow cytometry data") (description "This package provides visualization tools for flow cytometry data.") (license license:artistic2.0))) + +(define-public r-rprotobuflib + (package + (name "r-rprotobuflib") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RProtoBufLib" version)) + (sha256 + (base32 + "1vhwxw7281n5wpg30ik3m1gwarfmj4b8cqxdvj0sck44yx24lphg")) + ;; Remove bundled binaries: + ;; src/win/lib/{i386,x64}/libprotobuf.a + (modules '((guix build utils))) + (snippet '(begin + (delete-file-recursively "src/win") + #t)) + (patches + (search-patches "r-rprotobuflib-unbundle-dependency.patch")))) + (properties + `((upstream-name . "RProtoBufLib"))) + (build-system r-build-system) + (propagated-inputs + `(("protobuf-2" ,protobuf-2))) + (home-page "https://bioconductor.org/packages/RProtoBufLib") + (synopsis "C++ headers and static libraries of Protocol buffers") + (description "This package provides the headers and static library of +Protocol buffers for other R packages to compile and link against.") + (license license:bsd-3))) diff --git a/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch b/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch new file mode 100644 index 0000000000..c26b6c7e0f --- /dev/null +++ b/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch @@ -0,0 +1,57 @@ +diff --git a/configure b/configure +index 7edae5f..eff2489 100755 +--- a/configure ++++ b/configure +@@ -2856,39 +2856,6 @@ ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ex + ac_compiler_gnu=$ac_cv_cxx_compiler_gnu + + +-#untar the lib +-BASEPBNAME="protobuf-2.6.0" +-PBTGZNAME=${BASEPBNAME}.tgz +-cd src +-if test -d ./${BASEPBNAME}; then +- echo 'found ' $BASEPBNAME ' header sources and tar archive;using what is there.' +-else +- echo "untarring protobuf ..."; +- gunzip -dc ${PBTGZNAME} | tar xf -; +-fi; +- +-#run this bootstrap script to update all the gnu auto build files (e.g. automake symlinked fils (e.g. ./compile), alocal.m4,etc... ) +-cd ${BASEPBNAME} +-#./autogen.sh +-#automake --add-missing #do this because the old Autoconf (e.g. 2.13) may not handle this in autoreconf +-#mv m4/lt~obsolete.m4 m4/lt-obsolete.m4 # R CMD check gives warning about ~ character in filename +-cd .. +- +-echo "building protobuf..."; +-PBBUILD=$(pwd)/pb_build +-if test -d ${PBBUILD}; then +- echo 'found ' $PBBUILD ' ;using what is there.' +-else +- mkdir ${PBBUILD} +-fi; +- +-cd ${BASEPBNAME}; +-./configure --enable-static=yes --with-pic=yes --enable-shared=no --prefix="${PBBUILD}" --libdir="${PBBUILD}/lib" CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CC="${CC}" CFLAGS="${CFLAGS}" +-$MAKE install +- +-cd ../../ +- +- + + + ac_config_files="$ac_config_files src/Makevars" +diff --git a/src/Makevars.in b/src/Makevars.in +index 63803fb..575d507 100644 +--- a/src/Makevars.in ++++ b/src/Makevars.in +@@ -10,9 +10,6 @@ all: copying + + #copy hdf5 library headers to package include + copying: $(GS_LIB) +- mkdir -p "${USER_INCLUDE}" +- cp -r @PBBUILD@/include/google ${USER_INCLUDE} + mkdir -p "${USER_LIB_DIR}" +- cp @PBBUILD@/lib/* ${USER_LIB_DIR} + cp $(GS_LIB) ${USER_LIB_DIR}/GatingSet.pb.o