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Author: Andreas Tille <tille@debian.org>
Last-Update: Tue, 28 Nov 2017 10:37:22 +0100
Description: Use Debian packaged hdf5
--- a/gatb-core/thirdparty/CMakeLists.txt
+++ b/gatb-core/thirdparty/CMakeLists.txt
@@ -5,6 +5,8 @@
#SET (HDF5_ENABLE_THREADSAFE ON)
#SET (H5_HAVE_THREADSAFE 1)
+FIND_PACKAGE(HDF5 COMPONENTS C REQUIRED)
+
########## MOMENTARY DEACTIVATED => CRASH ON MACOS TO BE INVESTIGATED ##########
SET (HDF5_BUILD_TOOLS ON CACHE BOOL "Build HDF5 Tools")
#SET (CMAKE_EXE_LINKER_FLAGS "-lpthread -lz")
@@ -16,9 +18,9 @@ SET (HDF5_EXTERNALLY_CONFIGURED ON)
SET (HDF5_INSTALL_BIN_DIR bin)
SET (HDF5_INSTALL_LIB_DIR lib)
-SET (HDF5_INSTALL_INCLUDE_DIR ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5)
-SET (HDF5_INSTALL_DATA_DIR ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE})
-SET (HDF5_INSTALL_CMAKE_DIR ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE})
+SET (HDF5_INSTALL_INCLUDE_DIR /usr/include/${CMAKE_BUILD_TYPE}/hdf5)
+SET (HDF5_INSTALL_DATA_DIR /usr/share/${CMAKE_BUILD_TYPE})
+SET (HDF5_INSTALL_CMAKE_DIR /usr/share/${CMAKE_BUILD_TYPE})
IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
SET (HDF5_EXPORTED_TARGETS "gatb-hdf5")
@@ -32,23 +34,6 @@ ENDIF()
set (COMPILE_DEFINITIONS "${COMPILE_DEFINITIONS} -w")
add_definitions (${COMPILE_DEFINITIONS})
-# add HDF5 generation
-ADD_SUBDIRECTORY (hdf5)
-
-# We add a custom target for copying header files.
-add_custom_target (hdf5_postbuild ALL)
-
-# We build the output directory
-add_custom_command (TARGET hdf5_postbuild POST_BUILD COMMAND ${CMAKE_COMMAND} -E make_directory ${HDF5_INSTALL_INCLUDE_DIR})
-
-# We define all the header files to be copied
-file (GLOB headerfiles ${PROJECT_SOURCE_DIR}/thirdparty/hdf5/src/*.h ${PROJECT_BINARY_DIR}/thirdparty/hdf5/H5pubconf.h)
-
-# We copy each header file
-foreach (header ${headerfiles})
- add_custom_command (TARGET hdf5_postbuild POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy_if_different ${header} ${HDF5_INSTALL_INCLUDE_DIR} )
-endforeach()
-
# include other smaller libraries (json, Boophf)
add_custom_target (thirdparty_copy ALL)
@@ -63,7 +48,5 @@ add_custom_command (TARGET thirdparty_co
# INSTALL
################################################################################
IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
- INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5 DESTINATION include)
- INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/json DESTINATION include)
INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/BooPHF DESTINATION include)
ENDIF ()
--- a/gatb-core/CMakeLists.txt
+++ b/gatb-core/CMakeLists.txt
@@ -99,7 +99,7 @@ endif()
# GENERAL DEFINITIONS
################################################################################
set (LIBRARY_COMPILE_DEFINITIONS "-std=c++11")
-set (LIB_COMPILE_WARNINGS "-Wall -Wno-unused-function -Wno-format -Wno-unknown-pragmas") # last one is exclusively for BooPHF
+set (LIB_COMPILE_WARNINGS "-Wall -Wno-unused-function -Wno-unknown-pragmas") # last one is exclusively for BooPHF
if (CMAKE_BUILD_TYPE STREQUAL "Debug")
set (debug 1)
@@ -211,16 +211,23 @@ set (gatb-core-flags ${LIBRARY_COMPILE_D
set (gatb-core-includes ${PROJECT_BINARY_DIR}/include ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE} ${PROJECT_SOURCE_DIR}/src ${PROJECT_SOURCE_DIR}/thirdparty ${gatb-core-extra-libraries-inc})
# We define the libraries used for linking binary based on gatb core
-set (gatb-core-libraries gatbcore-static dl pthread z hdf5 ${gatb-core-extra-libraries})
+set (gatb-core-libraries gatbcore-static dl pthread z ${gatb-core-extra-libraries})
# We define the directory where to find cmake helpers
set (gatb-core-cmake ${CMAKE_MODULE_PATH})
-# NOTE... we have to duplicate the variables for the other scopes (in particular for sub directories)
-set (gatb-core-flags ${gatb-core-flags} PARENT_SCOPE)
-set (gatb-core-includes ${gatb-core-includes} PARENT_SCOPE)
-set (gatb-core-libraries ${gatb-core-libraries} PARENT_SCOPE)
-set (gatb-core-cmake ${gatb-core-cmake} PARENT_SCOPE)
+################################################################################
+# DEPENDENCIES
+################################################################################
+# we must be sure that hdf5 is built and installed before building gatb-core
+find_package(HDF5 REQUIRED)
+include_directories(${HDF5_INCLUDE_DIRS})
+# Not sure what exact programs will need these libraries
+# see https://lists.debian.org/debian-mentors/2017/11/msg00227.html
+# target_link_libraries(name_of_program_or_library ${HDF5_LIBRARIES})
+set (gatb-core-libraries ${gatb-core-libraries} ${HDF5_LIBRARIES})
+MESSAGE(STATUS HDF5_LIBRARIES="${HDF5_LIBRARIES}")
+
################################################################################
# LIBRARY GENERATION
@@ -253,11 +260,13 @@ ENDIF()
################################################################################
ADD_SUBDIRECTORY(thirdparty)
-################################################################################
-# DEPENDENCIES
-################################################################################
-# we must be sure that hdf5 is built and installed before building gatb-core
-ADD_DEPENDENCIES (gatbcore-static hdf5 hdf5_postbuild)
+
+# NOTE... we have to duplicate the variables for the other scopes (in particular for sub directories)
+set (gatb-core-flags ${gatb-core-flags} PARENT_SCOPE)
+set (gatb-core-includes ${gatb-core-includes} PARENT_SCOPE)
+set (gatb-core-libraries ${gatb-core-libraries} PARENT_SCOPE)
+set (gatb-core-cmake ${gatb-core-cmake} PARENT_SCOPE)
+
################################################################################
# DOCUMENTATION GENERATION
@@ -288,7 +297,7 @@ IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUD
INSTALL (FILES ${PROJECT_SOURCE_DIR}/doc/misc/README.txt DESTINATION . OPTIONAL)
INSTALL (FILES ${PROJECT_SOURCE_DIR}/LICENCE DESTINATION . OPTIONAL)
INSTALL (FILES ${PROJECT_SOURCE_DIR}/THIRDPARTIES.md DESTINATION . OPTIONAL)
- INSTALL (DIRECTORY ${PROJECT_SOURCE_DIR}/thirdparty/boost DESTINATION ./include)
+# INSTALL (DIRECTORY ${PROJECT_SOURCE_DIR}/thirdparty/boost DESTINATION ./include)
ENDIF()
################################################################################
|
