compiles on google native client.

CMakeLists.txt

@@ -44,6 +44,7 @@ IF(WIN32)
 
 ELSE(WIN32)
 
+  include_directories( ${BOOST_ROOT} )
   if( USE_CPP11 )
     SET(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -std=c++11 -pedantic -Wall -march=native")
   else()
@@ -65,11 +66,14 @@ add_executable(papara papara2_main.cpp  ${ALL_HEADERS})
 add_executable(fasta_random_sample2 fasta_random_sample2.cpp  ${ALL_HEADERS})
 add_executable(fasta_to_phy fasta_to_phy.cpp  ${ALL_HEADERS})
 add_executable(phy_to_fasta phy_to_fasta.cpp  ${ALL_HEADERS})
-add_executable(phy_cut_partition phy_cut_partition.cpp ${ALL_HEADERS})
+
 
 target_link_libraries(papara papara_core ivymike ublas_jama ${SYSDEP_LIBS} )
 target_link_libraries(phy_to_fasta ivymike ${SYSDEP_LIBS} )
-target_link_libraries(phy_cut_partition papara_core ublas_jama ivymike ${SYSDEP_LIBS} )
+
+
+#add_executable(phy_cut_partition phy_cut_partition.cpp ${ALL_HEADERS})
+#target_link_libraries(phy_cut_partition papara_core ublas_jama ivymike ${SYSDEP_LIBS} )
 
 
 if( USE_CPP11 ) 

nacl_32.cmake

@@ -0,0 +1,17 @@
+set( NACL ON )
+
+set( PLATFORM_TRIPLET           "i686-nacl" )
+set( PLATFORM_PREFIX            "/space/src/nacl_sdk/pepper_23/toolchain/linux_x86_newlib" )
+
+set( CMAKE_SYSTEM_NAME          "Linux" )
+set( CMAKE_SYSTEM_PROCESSOR     "i686" )
+set( CMAKE_FIND_ROOT_PATH       "${PLATFORM_PREFIX}/${PLATFORM_TRIPLET}" )
+set( CMAKE_C_COMPILER           "${PLATFORM_PREFIX}/bin/${PLATFORM_TRIPLET}-gcc" )
+set( CMAKE_CXX_COMPILER         "${PLATFORM_PREFIX}/bin/${PLATFORM_TRIPLET}-g++" )
+set( CMAKE_STRIP                "${PLATFORM_PREFIX}/bin/${PLATFORM_TRIPLET}-strip" )
+
+set( LUA_MATH_LIBRARY           "${PLATFORM_PREFIX}/x86_64-nacl/lib32/libm.a" CACHE PATH "" )
+set( PEPPER_LIBRARY             "${PLATFORM_PREFIX}/x86_64-nacl/lib32/libppapi.a" CACHE PATH "" )
+set( PEPPER_CXX_LIBRARY         "${PLATFORM_PREFIX}/x86_64-nacl/lib32/libppapi_cpp.a" CACHE PATH "" )
+set( PEPPER_GLES2_LIBRARY       "${PLATFORM_PREFIX}/x86_64-nacl/lib32/libppapi_gles2.a" CACHE PATH "" )
+

papara.cpp

@@ -17,7 +17,7 @@
  *  along with papara.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-
+#include <stdint.h>
 #include <iomanip>
 #include <boost/bind.hpp>
 #include <boost/dynamic_bitset.hpp>

papara.h

@@ -66,7 +66,7 @@ using namespace ivy_mike;
 
 namespace im_tree_parser = ivy_mike::tree_parser_ms;
 
-using namespace boost::numeric;
+//using namespace boost::numeric;
 
 using sequence_model::tag_aa;
 using sequence_model::tag_dna;

ublasJama-1.0.2.3/CMakeLists.txt

@@ -7,6 +7,7 @@ include_directories( ${BOOST_ROOT} )
 
 set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -D_SCL_SECURE_NO_WARNINGS") # as long as there is no support for std::array, these warnings are plain stupid!
 ELSE()
+include_directories( ${BOOST_ROOT} )
 SET(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -Wall -march=native")
 
 ENDIF()