Merge pull request #155 from Intel-HLS/osxcross_compile

Fixes for cross-compilation

Author: kgururaj

CMakeLists.txt

@@ -305,8 +305,7 @@ if(BUILD_JAVA)
         OUTPUT ${GENOMICSDB_MAVEN_BUILD_DIR}/genomicsdb-${GENOMICSDB_RELEASE_VERSION}.jar ${GENOMICSDB_MAVEN_BUILD_DIR}/genomicsdb-${GENOMICSDB_RELEASE_VERSION}-jar-with-dependencies.jar
         COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/pom.xml ${CMAKE_BINARY_DIR}/pom.xml
         COMMAND mvn versions:set ${MAVEN_QUIET_ARGS} -DnewVersion=${GENOMICSDB_RELEASE_VERSION} ${MAVEN_PROFILE}
-        COMMAND mvn package -DskipTests
-          ${MAVEN_ARGS}
+        COMMAND mvn package -DskipTests ${MAVEN_ARGS}
         DEPENDS tiledbgenomicsdb ${JAVA_SCALA_SOURCES} pom.xml
         WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
     install(FILES ${GENOMICSDB_MAVEN_BUILD_DIR}/genomicsdb-${GENOMICSDB_RELEASE_VERSION}.jar ${GENOMICSDB_MAVEN_BUILD_DIR}/genomicsdb-${GENOMICSDB_RELEASE_VERSION}-jar-with-dependencies.jar DESTINATION bin)
@@ -326,6 +325,18 @@ if(BUILD_JAVA)
         INCLUDE_JARS ${GENOMICSDB_MAVEN_BUILD_DIR}/genomicsdb-${GENOMICSDB_RELEASE_VERSION}-jar-with-dependencies.jar
         OUTPUT_DIR ${GENOMICSDB_MAVEN_BUILD_DIR})
 
+    #Deploy to Maven central
+    #Cannot specify the jars in the DEPENDS clause. CMake manual specifies, quoting:
+    #"Do not list the output in more than one independent target that may build in parallel or
+    #the two instances of the rule may conflict"
+    #Jars are already listed as dependencies in the add_jar command (-examples)
+    #So, use the examples target as a dependency for this target
+    add_custom_target(mvn_central_deploy
+        COMMAND mvn ${MAVEN_ARGS} deploy
+        COMMENT "Deploy to Maven central"
+    )
+    add_dependencies(mvn_central_deploy genomicsdb-${GENOMICSDB_RELEASE_VERSION}-examples)
+
     add_test(NAME CI_tests
         COMMAND /usr/bin/python ${CMAKE_SOURCE_DIR}/tests/run.py
         ${CMAKE_BINARY_DIR}

cmake/Modules/FindProtobufWrapper.cmake

@@ -11,7 +11,7 @@ else()
 endif()
 include(FindPackageHandleStandardArgs)
 find_package_handle_standard_args(Protobuf "Could not find Protobuf headers and/or libraries\n${DEFAULT_MSG}" PROTOBUF_INCLUDE_DIRS PROTOBUF_LIBRARIES)
-find_program(PROTOBUF_PROTOC_EXECUTABLE NAMES protoc PATHS "${PROTOBUF_LIBRARY}" "${PROTOBUF_LIBRARY}/bin")
+find_program(PROTOBUF_PROTOC_EXECUTABLE NAMES protoc PATHS "${PROTOBUF_PROTOC_EXECUTABLE}" "${PROTOBUF_LIBRARY}" "${PROTOBUF_LIBRARY}/bin")
 if(PROTOBUF_FOUND)
     set(PROTOBUF_LIBRARY ${PROTOBUF_LIBRARIES})
     set(PROTOBUF_INCLUDE_DIR ${PROTOBUF_INCLUDE_DIRS})

cmake/Modules/FindRapidJSON.cmake

@@ -10,6 +10,6 @@ if(RAPIDJSON_INCLUDE_DIR)
     unset(RAPIDJSON_INCLUDE_DIR CACHE)
 endif()
 find_path(RAPIDJSON_INCLUDE_DIR NAMES rapidjson/rapidjson.h HINTS "${RAPIDJSON_INCLUDE_DIR_HINT}"
-    PATHS "${CMAKE_SOURCE_DIR}/dependencies/RapidJSON/include")
+    PATHS "${CMAKE_SOURCE_DIR}/dependencies/RapidJSON/include" CMAKE_FIND_ROOT_PATH_BOTH)
 include(FindPackageHandleStandardArgs)
 find_package_handle_standard_args(RapidJSON "Could not find RapidJSON header: rapidjson/rapidjson.h - specify the variable RAPIDJSON_INCLUDE_DIR to point to the directory <RapidJSON>/include" RAPIDJSON_INCLUDE_DIR)

cmake/Modules/FindTileDB.cmake

@@ -44,6 +44,11 @@ if(TILEDB_SOURCE_DIR)
     list(APPEND TILEDB_CMAKE_ARGS "-DUSE_OPENMP:BOOL=${TILEDB_USE_OPENMP}")
     list(APPEND TILEDB_CMAKE_ARGS "-DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_INSTALL_PREFIX}")
 
+    if(CMAKE_TOOLCHAIN_FILE)
+        list(APPEND TILEDB_CMAKE_ARGS "-DCMAKE_FIND_ROOT_PATH:PATH=${CMAKE_FIND_ROOT_PATH}")
+        list(APPEND TILEDB_CMAKE_ARGS "-DCMAKE_TOOLCHAIN_FILE:PATH=${CMAKE_TOOLCHAIN_FILE}")
+    endif()
+
     #Build as external project
     include(ExternalProject)
     ExternalProject_Add(

cmake/Modules/Findhtslib.cmake

@@ -15,21 +15,28 @@ if(HTSLIB_SOURCE_DIR)
     if(APPLE AND BUILD_DISTRIBUTABLE_LIBRARY)
         set(HTSLIB_EXTRA_CFLAGS -mmacosx-version-min=${CMAKE_OSX_DEPLOYMENT_TARGET})
     endif()
+    #Cross compiling for MacOSX
+    if((NOT (CMAKE_SYSTEM_NAME STREQUAL CMAKE_HOST_SYSTEM_NAME)) AND APPLE)
+        set(HTSLIB_OSXCROSS_COMPILE_FLAGS LIBS=${OSXCROSS_LIBS} CPPFLAGS=${OSXCROSS_CPPFLAGS} --host=${CMAKE_SYSTEM_PROCESSOR}-${CMAKE_SYSTEM})
+    endif()
     ExternalProject_Add(
         htslib
         DOWNLOAD_COMMAND ""
         SOURCE_DIR "${HTSLIB_SOURCE_DIR}"
         UPDATE_COMMAND "autoreconf"
         PATCH_COMMAND ""
         CONFIGURE_COMMAND ${HTSLIB_SOURCE_DIR}/configure CFLAGS=${HTSLIB_${CMAKE_BUILD_TYPE}_CFLAGS} LDFLAGS=${HTSLIB_${CMAKE_BUILD_TYPE}_LDFLAGS}
-                --disable-lzma --disable-bz2 --disable-libcurl
+            CC=${CMAKE_C_COMPILER} AR=${CMAKE_AR} RANLIB=${CMAKE_RANLIB}
+            ${HTSLIB_OSXCROSS_COMPILE_FLAGS}
+            --disable-lzma --disable-bz2 --disable-libcurl
         BUILD_COMMAND ${CMAKE_COMMAND} -E make_directory cram
             COMMAND ${CMAKE_COMMAND} -E make_directory test
             COMMAND $(MAKE) -f ${HTSLIB_SOURCE_DIR}/Makefile VPATH=${HTSLIB_SOURCE_DIR} SOURCE_DIR=${HTSLIB_SOURCE_DIR}
+            AR=${CMAKE_AR}
         #BUILD_IN_SOURCE 1
         INSTALL_COMMAND ""
         )
-    find_path(HTSLIB_INCLUDE_DIR NAMES htslib/vcf.h HINTS "${HTSLIB_SOURCE_DIR}")
+    find_path(HTSLIB_INCLUDE_DIR NAMES htslib/vcf.h HINTS "${HTSLIB_SOURCE_DIR}" CMAKE_FIND_ROOT_PATH_BOTH)
     ExternalProject_Get_Property(htslib BINARY_DIR)
     set(HTSLIB_DIR_IN_BUILD_DIR "${BINARY_DIR}")
     set(HTSLIB_LIBRARY "${BINARY_DIR}/libhts.a")