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diff --git a/RProtoBufLib/R/build.R b/RProtoBufLib/R/build.R
index 6086972..3470cd7 100644
--- a/RProtoBufLib/R/build.R
+++ b/RProtoBufLib/R/build.R
@@ -35,75 +35,5 @@ pbCxxFlags <- function() {
# Return the linker flags requried for pb on this platform
pbLdFlags <- function() {
- lite = FALSE
- # on Windows and Solaris we need to explicitly link against pb.dll
- if ((Sys.info()['sysname'] %in% c("Windows", "SunOS")) && !isSparc()) {
- suffix <- ifelse(lite, "-lite", "")
- pb <- pbLibPath(suffix)
- gs <- gsLibPath()
-# res <- asBuildPath(pb)
- res <- paste(asBuildPath(gs), " -L", asBuildPath(dirname(pb)), " -lprotobuf ", sep = "")
- } else {
- res <- ""
- }
- # if(all)
- # res <- paste(res, gslibs)
- res
-}
-
-# Determine the platform-specific path to the pb library
-pbLibPath <- function(suffix = "") {
- sysname <- Sys.info()['sysname']
- pbSupported <- list(
- "Darwin" = paste("libprotobuf", suffix, ".dylib", sep = ""),
- "Linux" = paste("libprotobuf", suffix, ".so", sep = ""),
- "Windows" = paste("libprotobuf", suffix, ".a", sep = ""),
- "SunOS" = paste("libprotobuf", suffix, ".so", sep = "")
- )
- # browser()
- if ((sysname %in% names(pbSupported)) && !isSparc()) {
- libDir <- "lib/"
- if (sysname == "Windows")
- libDir <- paste(libDir, .Platform$r_arch, "/", sep="")
- system.file(paste(libDir, pbSupported[[sysname]], sep = ""),
- package = "RProtoBufLib")
- } else {
- NULL
- }
-}
-
-gsLibPath <- function(suffix = "") {
- sysname <- Sys.info()['sysname']
- pbSupported <- list(
- "Darwin" = paste("libGatingSet.pb", suffix, ".dylib", sep = ""),
- "Linux" = paste("libGatingSet.pb", suffix, ".so", sep = ""),
- "Windows" = paste("GatingSet.pb", suffix, ".o", sep = ""),
- "SunOS" = paste("libGatingSet.pb", suffix, ".so", sep = "")
- )
- # browser()
- if ((sysname %in% names(pbSupported)) && !isSparc()) {
- libDir <- "lib/"
- if (sysname == "Windows")
- libDir <- paste(libDir, .Platform$r_arch, "/", sep="")
- system.file(paste(libDir, pbSupported[[sysname]], sep = ""),
- package = "RProtoBufLib")
- } else {
- NULL
- }
-}
-
-isSparc <- function() {
- Sys.info()['sysname'] == "SunOS" && Sys.info()[["machine"]] != "i86pc"
-}
-
-# Helper function to ape the behavior of the R build system
-# when providing paths to libraries
-asBuildPath <- function(path) {
- if (.Platform$OS.type == "windows") {
- path <- normalizePath(path)
- if (grepl(' ', path, fixed=TRUE))
- path <- utils::shortPathName(path)
- path <- gsub("\\\\", "/", path)
- }
- return(path)
+ "-lGatingSet.pb -lprotobuf"
}
diff --git a/RProtoBufLib/R/hooks.R a/RProtoBufLib/R/hooks.R
deleted file mode 100644
index b5857a8..0000000
--- a/RProtoBufLib/R/hooks.R
+++ /dev/null
@@ -1,37 +0,0 @@
-
-dllInfo <- NULL
-
-.onLoad <- function(libname, pkgname) {
-
- # load pb and pbmalloc on supported platforms
- pb <- pbLibPath()
- if (!is.null(pb)&&Sys.info()['sysname']!="Windows") {
- if (!file.exists(pb)) {
- warning(paste("libprotobuf library", pb, "not found."))
- } else {
- dllInfo <<- dyn.load(pb, local = FALSE, now = TRUE)
- }
- }
-
- gs <- gsLibPath()
- if (!is.null(gs)&&Sys.info()['sysname']!="Windows") {
- if (!file.exists(gs)) {
- warning(paste("libGatingSet.pb library", gs, "not found."))
- } else {
- dllInfo <<- c(dllInfo, dyn.load(gs, local = FALSE, now = TRUE))
- }
- }
-
-}
-
-.onUnload <- function(libpath) {
-
- # unload the package library
- # library.dynam.unload("RProtoBufLib", libpath)
-
- # unload dll if we loaded it
- for(dll in dllInfo)
- if (!is.null(dll))
- dyn.unload(dll[["path"]])
-
-}
diff --git a/RProtoBufLib/configure.ac b/RProtoBufLib/configure.ac
index b9b4a26..950c043 100644
--- a/RProtoBufLib/configure.ac
+++ b/RProtoBufLib/configure.ac
@@ -24,41 +24,5 @@ AC_LANG(C++)
AC_PROG_CC
AC_PROG_CXX
-#untar the lib
-BASEPBNAME="protobuf-3.8.0"
-PBTGZNAME=${BASEPBNAME}.tar.gz
-cd src
-if test -d ./${BASEPBNAME}; then
- echo 'found ' $BASEPBNAME ' header sources and tar archive;using what is there.'
-else
- echo "untarring protobuf ...";
- gzip -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 ${BASEPBNAME};
-./configure --enable-static=no --with-pic=yes --enable-shared=yes --prefix="${PBBUILD}" --libdir="${PBBUILD}/lib" CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CC="${CC}" CFLAGS="${CFLAGS}"
-$MAKE install
-
-cd ../../
-
-
-
-AC_SUBST(PBBUILD)
AC_CONFIG_FILES([src/Makevars])
AC_OUTPUT
-
diff --git a/RProtoBufLib/inst/include/generate_pb_code.sh b/RProtoBufLib/inst/include/generate_pb_code.sh
index 2a8361f..f34860e 100644
--- a/RProtoBufLib/inst/include/generate_pb_code.sh
+++ b/RProtoBufLib/inst/include/generate_pb_code.sh
@@ -1,6 +1,4 @@
-#generate pb code (using bundled pb library to ensure to consistency of boilerplate code generation)
-export LD_LIBRARY_PATH=../../src/pb_build/lib/
-../../src/pb_build/bin/protoc --cpp_out=cytolib/ GatingSet.proto
+protoc --cpp_out=cytolib/ GatingSet.proto
#move the source to src
mv cytolib/GatingSet.pb.cc ../../src/GatingSet_pb_lib/
#update the include path to header
diff --git a/RProtoBufLib/src/Makevars.in b/RProtoBufLib/src/Makevars.in
index fb5da6f..8b569ad 100644
--- a/RProtoBufLib/src/Makevars.in
+++ b/RProtoBufLib/src/Makevars.in
@@ -1,18 +1,18 @@
-CXX_STD = CXX11
-PKG_CPPFLAGS =-I../inst/include/ -I@PBBUILD@/include/
+CXX_STD = CXX17
+PKG_CPPFLAGS =-I../inst/include/
#expose headers in installed package include folder
USER_INCLUDE = ${R_PACKAGE_DIR}/include
USER_LIB_DIR = ${R_PACKAGE_DIR}/lib${R_ARCH}/
#expose compiled object of GatingSet pb API for cytolib to link to
-GS_LIB=libGatingSet.pb${DYLIB_EXT}
+GS_LIB := libGatingSet.pb.so.$(SOVER)
GS_LIB_DIR = GatingSet_pb_lib
-all: copying
+all: $(GS_LIB) $(SHLIB)
-$(GS_LIB):
- ${SHLIB_CXXLD} ${SHLIB_CXXLDFLAGS} ${CXXPICFLAGS} ${PKG_CPPFLAGS} -o ${GS_LIB_DIR}/${GS_LIB} ${GS_LIB_DIR}/GatingSet.pb.cc
+$(GS_LIB): $(GS_LIB_DIR)/GatingSet.pb.o
+ $(SHLIB_CXXLD) $(SHLIB_CXXLDFLAGS) $(LDFLAGS) -Wl,-soname=$(GS_LIB) -o $@ $^ -lprotobuf
#copy hdf5 library headers to package include
@@ -22,4 +22,3 @@ copying: $(GS_LIB)
mkdir -p "${USER_LIB_DIR}"
cp @PBBUILD@/lib/libprotobuf* ${USER_LIB_DIR}
cp ${GS_LIB_DIR}/$(GS_LIB) ${USER_LIB_DIR}/${GS_LIB}
-
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