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Subject: use HDF5 lib in Debian
Description: use Debian libs instead of embedded one
Author: Olivier Sallou <osallou@debian.org>
Last-Updated: 2014-08-18
Forwarded: no
--- a/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/LargeInt.hpp
+++ b/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/LargeInt.hpp
@@ -35,7 +35,7 @@
#include <stdint.h>
#include <algorithm>
#include <iostream>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
#include <gatb/system/api/Exception.hpp>
#include <gatb/tools/math/NativeInt64.hpp>
--- a/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
+++ b/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
@@ -40,7 +40,7 @@
#include <string>
#include <vector>
#include <stdarg.h>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
/********************************************************************************/
namespace gatb {
--- a/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
+++ b/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
@@ -32,7 +32,7 @@
#include <gatb/tools/storage/impl/CollectionHDF5.hpp>
#include <gatb/system/impl/System.hpp>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
#include <typeinfo>
/********************************************************************************/
--- a/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt128.hpp
+++ b/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt128.hpp
@@ -33,7 +33,7 @@
/********************************************************************************/
#include <iostream>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
#include <gatb/system/api/types.hpp>
#include <gatb/tools/misc/api/Abundance.hpp>
--- a/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt16.hpp
+++ b/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt16.hpp
@@ -31,7 +31,7 @@
#include <iostream>
#include <gatb/system/api/types.hpp>
#include <gatb/tools/misc/api/Abundance.hpp>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
/********************************************************************************/
namespace gatb {
--- a/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt64.hpp
+++ b/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt64.hpp
@@ -31,7 +31,7 @@
#include <iostream>
#include <gatb/system/api/types.hpp>
#include <gatb/tools/misc/api/Abundance.hpp>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
extern const unsigned char revcomp_4NT[];
extern const unsigned char comp_NT [];
--- a/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt8.hpp
+++ b/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt8.hpp
@@ -31,7 +31,7 @@
#include <iostream>
#include <gatb/system/api/types.hpp>
#include <gatb/tools/misc/api/Abundance.hpp>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
/********************************************************************************/
namespace gatb {
--- a/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
+++ b/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
@@ -27,7 +27,7 @@
#define _GATB_CORE_TOOLS_MISC_IHISTOGRAM_HPP_
#include <gatb/system/api/ISmartPointer.hpp>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
/********************************************************************************/
namespace gatb {
--- a/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
+++ b/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
@@ -31,7 +31,7 @@
/********************************************************************************/
#include <sys/types.h>
-#include <hdf5/hdf5.h>
+#include <hdf5.h>
/********************************************************************************/
namespace gatb {
--- a/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/CMakeLists.txt
+++ b/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/CMakeLists.txt
@@ -2,47 +2,6 @@
# HDF5 GENERATION
################################################################################
-SET (HDF5_ENABLE_THREADSAFE ON)
-
-########## 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")
-
-SET (HDF5_EXTERNALLY_CONFIGURED ON)
-
-#SET (HDF5_INSTALL_BIN_DIR ${PROJECT_BINARY_DIR}/bin/${CMAKE_BUILD_TYPE})
-#SET (HDF5_INSTALL_LIB_DIR ${PROJECT_BINARY_DIR}/lib/${CMAKE_BUILD_TYPE})
-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})
-
-IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
- SET (HDF5_EXPORTED_TARGETS "gatb-hdf5")
-ENDIF()
-
-# We don't want warnings from HDF5 compilation
-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()
################################################################################
# EMPHF GENERATION
@@ -82,7 +41,6 @@ ENDIF() # WITH_MPHF
# INSTALL
################################################################################
IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
- INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5 DESTINATION include)
IF (DEFINED WITH_MPHF)
INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/emphf DESTINATION include)
ENDIF()
--- a/mapsembler2_extremities/thirdparty/gatb-core/CMakeLists.txt
+++ b/mapsembler2_extremities/thirdparty/gatb-core/CMakeLists.txt
@@ -217,7 +217,7 @@ 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)
+ADD_DEPENDENCIES (gatbcore-static hdf5)
IF (DEFINED WITH_MPHF)
ADD_DEPENDENCIES(gatbcore-static emphf_copyasis)
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