Author: osallou Date: 2014-09-19 11:56:20 +0000 (Fri, 19 Sep 2014) New Revision: 18073
Added: trunk/packages/mapsembler2/trunk/debian/patches/skip_mphe Modified: trunk/packages/mapsembler2/trunk/debian/changelog trunk/packages/mapsembler2/trunk/debian/patches/add_hardening trunk/packages/mapsembler2/trunk/debian/patches/run_pipeline trunk/packages/mapsembler2/trunk/debian/patches/series trunk/packages/mapsembler2/trunk/debian/patches/use_debian_libs trunk/packages/mapsembler2/trunk/debian/rules Log: prepare next release 2.2.3, coming soon with fixes for compilation Modified: trunk/packages/mapsembler2/trunk/debian/changelog =================================================================== --- trunk/packages/mapsembler2/trunk/debian/changelog 2014-09-18 20:13:02 UTC (rev 18072) +++ trunk/packages/mapsembler2/trunk/debian/changelog 2014-09-19 11:56:20 UTC (rev 18073) @@ -1,3 +1,10 @@ +mapsembler2 (2.2.3+dfsg-1) UNRELEASED; urgency=medium + + * New upstream release - No yet public release, coming soon + * Fix some compilation issues + + -- Olivier Sallou <[email protected]> Fri, 19 Sep 2014 13:41:47 +0200 + mapsembler2 (2.2.1+dfsg-3) unstable; urgency=medium [Gilles Filippini <[email protected]> ] Modified: trunk/packages/mapsembler2/trunk/debian/patches/add_hardening =================================================================== --- trunk/packages/mapsembler2/trunk/debian/patches/add_hardening 2014-09-18 20:13:02 UTC (rev 18072) +++ trunk/packages/mapsembler2/trunk/debian/patches/add_hardening 2014-09-19 11:56:20 UTC (rev 18073) @@ -3,65 +3,63 @@ Author: Olivier Sallou <[email protected]> Last-Updated: 2014-08-18 Forwarded: no -Index: mapsembler2_pipeline/kissreads/Makefile -=================================================================== ---- mapsembler2_pipeline.orig/kissreads/Makefile -+++ mapsembler2_pipeline/kissreads/Makefile -@@ -20,10 +20,14 @@ CC =gcc +--- a/kissreads/Makefile ++++ b/kissreads/Makefile +@@ -20,11 +20,16 @@ # optimized flags - #CFLAGS=-Wall -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@!ยง --CFLAGS= -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@! -+#CFLAGS= -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@! + #CFLAGS=-Wall -O3 -L/../thirdparty/zlib/build/ -lz +-CFLAGS= -O3 -L../thirdparty/zlib/build/ -lz ++CFLAGS= -O3 -lz CFLAGS+=$(MYFLAGS) - #LDFLAGS+=-Wall -lm -O3 -lz -DOMP -fopenmp#-fopenmp --LDFLAGS+= -lm -O3 -lz -DOMP -fopenmp#-fopenmp -+#LDFLAGS+= -lm -O3 -lz -DOMP -fopenmp#-fopenmp + + #LDFLAGS+=-Wall -lm -O3 -L../thirdparty/zlib/build/ -lz +-LDFLAGS+= -lm -O3 -L../thirdparty/zlib/build/ -lz ++LDFLAGS+= -lm -O3 -lz + +CPPFLAGS += $(shell dpkg-buildflags --get CPPFLAGS) +CFLAGS += $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O3 -lz +LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS) -lm -O3 -lz ++ ## debug flags - -Index: mapsembler2_pipeline/kissreads_graph/makefile -=================================================================== ---- mapsembler2_pipeline.orig/kissreads_graph/makefile -+++ mapsembler2_pipeline/kissreads_graph/makefile -@@ -4,6 +4,9 @@ EXEC=kissreads_graph - #Loader.cpp CFLAGS= -g -lz -std=c++11 -DMINIA_IS_IN_PARENT_FOLDER - #Loader.cpp - CFLAGS= -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER + #CFLAGS +=-Wall -g -lz -fopenmp +--- a/kissreads_graph/makefile ++++ b/kissreads_graph/makefile +@@ -6,6 +6,9 @@ + #CFLAGS= -g -L../thirdparty/zlib/build -lz -std=c++11 -DMINIA_IS_IN_PARENT_FOLDER + #CFLAGS= -g -L../thirdparty/zlib/build -lz -DMINIA_IS_IN_PARENT_FOLDER + CFLAGS+= -D_FILE_OFFSET_BITS=64 +CPPFLAGS=$(shell dpkg-buildflags --get CPPFLAGS) -+CFLAGS += $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER ++CFLAGS += $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER -D_FILE_OFFSET_BITS=64 +LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS) - #CFLAGS= -g -lz -DMINIA_IS_IN_PARENT_FOLDER SRC=block_allocator.cpp DeBruijnGraph.cpp Fragment.cpp json.cpp read_coherence_mapsembler/libchash.cpp read_coherence_mapsembler/couple.cpp read_coherence_mapsembler/misc_tools.cpp read_coherence_mapsembler/read_groups.cpp read_coherence_mapsembler/consensus_common.cpp read_coherence_mapsembler/list.cpp read_coherence_mapsembler/read_coherence.cpp read_coherence_mapsembler/interface_libchash.cpp commons.cpp ../minia/Kmer.cpp ../minia/Bank.cpp Loader.cpp ReadMapper.cpp OBJ= $(SRC:.cpp=.o) -@@ -48,7 +51,7 @@ endif all: $(EXEC) +@@ -49,7 +52,7 @@ + all: $(EXEC) kissreads_graph: $(OBJ) KissReadsGraph.cpp - $(CC) -o $@ $^ $(CFLAGS) + $(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS) %.o: %.cpp %.h - $(CC) -lz -o $@ -c $< $(CFLAGS) -Index: mapsembler2_pipeline/mapsembler2_extend/makefile -=================================================================== ---- mapsembler2_pipeline.orig/mapsembler2_extend/makefile -+++ mapsembler2_pipeline/mapsembler2_extend/makefile -@@ -3,6 +3,9 @@ EXEC=mapsembler_extend - #CFLAGS= -O4 -lz --std=gnu++0x - #CFLAGS= -g -lz -DMINIA_IS_IN_PARENT_FOLDER - CFLAGS= -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER + $(CC) -o $@ -c $< $(CFLAGS) +--- a/mapsembler2_extend/makefile ++++ b/mapsembler2_extend/makefile +@@ -51,6 +51,11 @@ + endif + endif + +CPPFLAGS=$(shell dpkg-buildflags --get CPPFLAGS) -+CFLAGS += $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER ++CFLAGS += $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) +LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS) - #CFLAGS= -g -lz --std=gnu++0x -DMINIA_IS_IN_PARENT_FOLDER - #CFLAGS= -g -lz -DMINIA_IS_IN_PARENT_FOLDER ++ ++ SRC=../minia/Pool.cpp ../minia/Bank.cpp ../minia/Bloom.cpp ../minia/Hash16.cpp ../minia/Terminator.cpp ../minia/Kmer.cpp ../minia/Traversal.cpp ../minia/LinearCounter.cpp ../minia/Set.cpp ../minia/Utils.cpp ../minia/SortingCount.cpp ../minia/Debloom.cpp ../minia/OAHash.cpp commons.cpp IterativeExtensions.cpp Fragment_Bank.cpp Fragment.cpp GraphOutput.cpp -@@ -49,7 +52,7 @@ all: $(EXEC) + OBJ= $(SRC:.cpp=.o) + all: $(EXEC) +@@ -105,7 +110,7 @@ mapsembler_extend: $(OBJ) $(OBJ2) mapsembler_extend.cpp #mapsembler: $(OBJ) $(OBJ2) test.cpp @@ -69,12 +67,10 @@ + $(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS) %.o: %.cpp %.h - $(CC) -lz -o $@ -c $< $(CFLAGS) -Index: mapsembler2_pipeline/mapsembler2_extremities/CMakeLists.txt -=================================================================== ---- mapsembler2_pipeline.orig/mapsembler2_extremities/CMakeLists.txt -+++ mapsembler2_pipeline/mapsembler2_extremities/CMakeLists.txt -@@ -2,6 +2,7 @@ project(mapsembler2_extremities) + $(CC) -o $@ -c $< $(CFLAGS) +--- a/mapsembler2_extremities/CMakeLists.txt ++++ b/mapsembler2_extremities/CMakeLists.txt +@@ -2,6 +2,7 @@ cmake_minimum_required(VERSION 2.6) Modified: trunk/packages/mapsembler2/trunk/debian/patches/run_pipeline =================================================================== --- trunk/packages/mapsembler2/trunk/debian/patches/run_pipeline 2014-09-18 20:13:02 UTC (rev 18072) +++ trunk/packages/mapsembler2/trunk/debian/patches/run_pipeline 2014-09-19 11:56:20 UTC (rev 18073) @@ -3,11 +3,9 @@ Description: use tools in path instead of local dirs as upstream Last-Updated: 2014-08-20 Forwarded: no -Index: mapsembler2_pipeline/run_mapsembler2_pipeline.sh -=================================================================== ---- mapsembler2_pipeline.orig/run_mapsembler2_pipeline.sh -+++ mapsembler2_pipeline/run_mapsembler2_pipeline.sh -@@ -16,7 +16,7 @@ t=0 +--- a/run_mapsembler2_pipeline.sh ++++ b/run_mapsembler2_pipeline.sh +@@ -16,7 +16,7 @@ f=1 #kind of process (search mode 1=Breadth and 2=Depth) x=40 #node length limit y=10000 #graph depth limit @@ -16,7 +14,7 @@ ####################################################################### #################### END HEADER ####################### ####################################################################### -@@ -211,20 +211,20 @@ fi +@@ -211,20 +211,20 @@ if [ $t -gt 2 ] then echo -e "\n" @@ -43,7 +41,7 @@ exit fi -@@ -232,11 +232,11 @@ $PATH_TOOLS\kissreads_graph $prefix_resu +@@ -232,11 +232,11 @@ else echo -e "\n" Modified: trunk/packages/mapsembler2/trunk/debian/patches/series =================================================================== --- trunk/packages/mapsembler2/trunk/debian/patches/series 2014-09-18 20:13:02 UTC (rev 18072) +++ trunk/packages/mapsembler2/trunk/debian/patches/series 2014-09-19 11:56:20 UTC (rev 18073) @@ -1,3 +1,4 @@ use_debian_libs +run_pipeline add_hardening -run_pipeline +skip_mphe Added: trunk/packages/mapsembler2/trunk/debian/patches/skip_mphe =================================================================== --- trunk/packages/mapsembler2/trunk/debian/patches/skip_mphe (rev 0) +++ trunk/packages/mapsembler2/trunk/debian/patches/skip_mphe 2014-09-19 11:56:20 UTC (rev 18073) @@ -0,0 +1,16 @@ +Subject: skip embedded mphe +Description: mphe uses sse which is not available on all archs + Disable in makefile the use of this lib as not mandatory +Author: Olivier Sallou +Last-Updated: 2014-09-19 +Forwarded: no +--- a/mapsembler2_extremities/thirdparty/gatb-core/CMakeLists.txt ++++ b/mapsembler2_extremities/thirdparty/gatb-core/CMakeLists.txt +@@ -118,6 +118,7 @@ + set (LIBRARY_COMPILE_DEFINITIONS "${LIBRARY_COMPILE_DEFINITIONS} -DWITH_LAMBDA_EXPRESSION ${CXX_STD_VERSION}") + endif() + ++set (use_mphf 0) + if (use_mphf) + set (LIBRARY_COMPILE_DEFINITIONS "${LIBRARY_COMPILE_DEFINITIONS} -DWITH_MPHF ") + message ("-------------------------------------------------------------------------------------") Modified: trunk/packages/mapsembler2/trunk/debian/patches/use_debian_libs =================================================================== --- trunk/packages/mapsembler2/trunk/debian/patches/use_debian_libs 2014-09-18 20:13:02 UTC (rev 18072) +++ trunk/packages/mapsembler2/trunk/debian/patches/use_debian_libs 2014-09-19 11:56:20 UTC (rev 18073) @@ -3,82 +3,8 @@ Author: Olivier Sallou <[email protected]> Last-Updated: 2014-08-18 Forwarded: no -Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/CMakeLists.txt -=================================================================== ---- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/CMakeLists.txt -+++ mapsembler2_pipeline/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 -@@ -77,6 +36,5 @@ endforeach() - # 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}/emphf DESTINATION include) - ENDIF () -Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/CMakeLists.txt -=================================================================== ---- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/CMakeLists.txt -+++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/CMakeLists.txt -@@ -173,7 +173,7 @@ 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 emphf_copyasis) -+ADD_DEPENDENCIES (gatbcore-static hdf5 emphf_copyasis) - - - ################################################################################ -Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/LargeInt.hpp -=================================================================== ---- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/LargeInt.hpp -+++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/LargeInt.hpp +--- 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> @@ -88,10 +14,8 @@ #include <gatb/system/api/Exception.hpp> #include <gatb/tools/math/NativeInt64.hpp> -Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp -=================================================================== ---- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp -+++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.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> @@ -101,10 +25,8 @@ /********************************************************************************/ namespace gatb { -Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp -=================================================================== ---- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp -+++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp +--- 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> @@ -114,10 +36,8 @@ #include <typeinfo> /********************************************************************************/ -Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt128.hpp -=================================================================== ---- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt128.hpp -+++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt128.hpp +--- 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 @@ /********************************************************************************/ @@ -127,10 +47,8 @@ #include <gatb/system/api/types.hpp> #include <gatb/tools/misc/api/Abundance.hpp> -Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt16.hpp -=================================================================== ---- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt16.hpp -+++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt16.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> @@ -140,10 +58,8 @@ /********************************************************************************/ namespace gatb { -Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt64.hpp -=================================================================== ---- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt64.hpp -+++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt64.hpp +--- 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> @@ -153,10 +69,8 @@ extern const unsigned char revcomp_4NT[]; extern const unsigned char comp_NT []; -Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt8.hpp -=================================================================== ---- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt8.hpp -+++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt8.hpp +--- 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> @@ -166,10 +80,8 @@ /********************************************************************************/ namespace gatb { -Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp -=================================================================== ---- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp -+++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp +--- 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_ @@ -179,10 +91,8 @@ /********************************************************************************/ namespace gatb { -Index: mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Abundance.hpp -=================================================================== ---- mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Abundance.hpp -+++ mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Abundance.hpp +--- 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 @@ /********************************************************************************/ @@ -192,3 +102,72 @@ /********************************************************************************/ 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 @@ + # 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 +@@ -197,7 +197,7 @@ + # 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) Modified: trunk/packages/mapsembler2/trunk/debian/rules =================================================================== --- trunk/packages/mapsembler2/trunk/debian/rules 2014-09-18 20:13:02 UTC (rev 18072) +++ trunk/packages/mapsembler2/trunk/debian/rules 2014-09-19 11:56:20 UTC (rev 18073) @@ -3,6 +3,8 @@ # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 +DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH) + SRC_VERSION =$(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p') ifneq ($(wildcard /usr/include/hdf5/serial),) @@ -23,7 +25,7 @@ override_dh_auto_build: mkdir mapsembler2_extremities/build - cd mapsembler2_extremities/build && cmake .. && make + cd mapsembler2_extremities/build && cmake .. && make VERBOSE=1 cd mapsembler2_extend && make k=29 cd kissreads_graph && make k=29 cd kissreads && make k=29 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
