From e865d69d529133e0ca5ed3ce7965781a9bb681b1 Mon Sep 17 00:00:00 2001
From: mikejiang <wjiang2@fhcrc.org>
Date: Thu, 28 Feb 2019 16:33:16 -0800
Subject: [PATCH] build GatingSet.pb as shared lib. fix #7

---
 R/build.R       | 28 ++++++++++++++++++++++++----
 R/hooks.R       | 19 ++++++++++++++-----
 src/Makevars.in | 10 +++++++---
 3 files changed, 45 insertions(+), 12 deletions(-)

diff --git a/R/build.R b/R/build.R
index 2da5ba4..900bc04 100644
--- a/R/build.R
+++ b/R/build.R
@@ -37,16 +37,17 @@ pbCxxFlags <- function() {
 
 # Return the linker flags requried for pb on this platform
 pbLdFlags <- function(all = TRUE) {
-	gslibs <- system.file(file.path("lib", "GatingSet.pb.o"), package = "RProtoBufLib")
+# gslibs <- system.file(file.path("lib", "GatingSet.pb.o"), package = "RProtoBufLib")
    # on Windows and Solaris we need to explicitly link against pb.dll
    if ((Sys.info()['sysname'] %in% c("Windows", "SunOS")) && !isSparc()) {
       pb <- pbLibPath()
-      res <- paste("-L", asBuildPath(dirname(pb)), " -lprotobuf", sep = "")
+      gs <- gsLibPath()
+      res <- paste("-L", asBuildPath(dirname(pb)), asBuildPath(dirname(gs)), " -lprotobuf -lGatingSet.pb", sep = "")
    } else {
      res <- ""
    }
-	if(all)
-	  res <- paste(res, gslibs)
+	# if(all)
+	  # res <- paste(res, gslibs)
 	res
 }
 
@@ -70,6 +71,25 @@ pbLibPath <- function(suffix = "") {
       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("libGatingSet.pb", suffix, ".dll", 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"
diff --git a/R/hooks.R b/R/hooks.R
index 8ef76ec..443e18c 100644
--- a/R/hooks.R
+++ b/R/hooks.R
@@ -7,12 +7,20 @@ dllInfo <- NULL
    pb <- pbLibPath()
    if (!is.null(pb)) {
       if (!file.exists(pb)) {
-         warning(paste("pb library", pb, "not found."))
+         warning(paste("libprotobuf library", pb, "not found."))
       } else {
          dllInfo <<- dyn.load(pb, local = FALSE, now = TRUE)
       }
    }
-    
+   gs <- gsLibPath()
+   if (!is.null(gs)) {
+     if (!file.exists(gs)) {
+       warning(paste("libGatingSet.pb library", gs, "not found."))
+     } else {
+       dllInfo <<- c(dllInfo, dyn.load(gs, local = FALSE, now = TRUE))
+     }
+   }
+   
    # load the package library
    # library.dynam("RProtoBufLib", pkgname, libname)
    
@@ -23,7 +31,8 @@ dllInfo <- NULL
    # unload the package library
    # library.dynam.unload("RProtoBufLib", libpath)
    
-   # unload pb if we loaded it
-   if (!is.null(dllInfo))
-      dyn.unload(dllInfo[["path"]])
+   # unload dll if we loaded it
+  for(dll in dllInfo)
+   if (!is.null(dll))
+      dyn.unload(dll[["path"]])
 }
diff --git a/src/Makevars.in b/src/Makevars.in
index 63803fb..dce35c9 100644
--- a/src/Makevars.in
+++ b/src/Makevars.in
@@ -4,15 +4,19 @@ 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 = GatingSet_pb_lib/GatingSet.pb.o
+GS_LIB=libGatingSet.pb${SHLIB_EXT}
+GS_LIB_DIR = GatingSet_pb_lib
 
 all: copying  
-	
+
+$(GS_LIB):
+	${SHLIB_CXXLD} ${SHLIB_CXXLDFLAGS} ${CXXPICFLAGS} ${PKG_CPPFLAGS} -o ${GS_LIB_DIR}/${GS_LIB} ${GS_LIB_DIR}/GatingSet.pb.cc
+	 	
 #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
+	cp ${GS_LIB_DIR}/$(GS_LIB) ${USER_LIB_DIR}/${GS_LIB}