[med-svn] r18073 - in trunk/packages/mapsembler2/trunk/debian: . patches
Olivier Sallou
osallou at moszumanska.debian.org
Fri Sep 19 11:56:20 UTC 2014
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 <osallou at debian.org> Fri, 19 Sep 2014 13:41:47 +0200
+
mapsembler2 (2.2.1+dfsg-3) unstable; urgency=medium
[Gilles Filippini <pini at debian.org> ]
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 <osallou at debian.org>
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 #@!§
--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 <osallou at debian.org>
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
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