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Tue, 05 Nov 2019 10:29:33 -0800 (PST) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id f6sm23348281wrm.61.2019.11.05.10.29.32 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 05 Nov 2019 10:29:32 -0800 (PST) From: zimoun Date: Tue, 5 Nov 2019 19:29:31 +0100 Message-Id: <20191105182931.27048-1-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/local.mk | 2 + gnu/packages/bioconductor.scm | 31 ++++++++++ .../r-rprotobuflib-unbundle-dependency.patch | 57 +++++++++++++++++++ 3 files changed, 90 insertions(+) create mode 100644 gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch diff --git a/gnu/local.mk b/gnu/local.mk index 5b81791542..178c8b903f 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -22,6 +22,7 @@ # Copyright © 2018 Maxim Cournoyer # Copyright © 2019 Guillaume Le Vaillant # Copyright © 2019 John Soo +# Copyright © 2019 Simon Tournier # # This file is part of GNU Guix. # @@ -1295,6 +1296,7 @@ dist_patch_DATA = \ %D%/packages/patches/quagga-reproducible-build.patch \ %D%/packages/patches/quickswitch-fix-dmenu-check.patch \ %D%/packages/patches/qtwebkit-pbutils-include.patch \ + %D%/packages/patches/r-rprotobuflib-unbundle-dependency.patch \ %D%/packages/patches/randomjungle-disable-static-build.patch \ %D%/packages/patches/rapicorn-isnan.patch \ %D%/packages/patches/rapidjson-gcc-compat.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