add quiet build flag, fix warnings ing BooPHF.hpp

Author: Rob Patro

CMakeLists.txt

@@ -4,15 +4,15 @@ enable_testing()
 
 project (RapMap)
 
-set(CPACK_PACKAGE_VERSION "0.3.0")
+set(CPACK_PACKAGE_VERSION "0.4.0")
 SET(CPACK_PACKAGE_VERSION_MAJOR "0")
-set(CPACK_PACKAGE_VERSION_MINOR "3")
+set(CPACK_PACKAGE_VERSION_MINOR "4")
 set(CPACK_PACKAGE_VERSION_PATCH "0")
 set(PROJECT_VERSION ${CPACK_PACKAGE_VERSION})
 set(CPACK_GENERATOR "TGZ")
 set(CPACK_SOURCE_GENERATOR "TGZ")
 set(CPACK_PACKAGE_VENDOR "Stony Brook University")
-set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "RapMap - Wicked-fast quasi/pseudo/lightweight alignment")
+set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "RapMap - Wicked-fast qasi-mapping")
 set(CPACK_PACKAGE_NAME
   "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")
 set(CPACK_SOURCE_PACKAGE_FILE_NAME
@@ -26,8 +26,12 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
 #    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -msse4.2 -DEMPHF_USE_POPCOUNT")
 #endif(SSE4_2_FOUND)
 
-set (WARNING_IGNORE_FLAGS "-Wno-deprecated-register -Wno-c++11-narrowing -Wno-unknown-pragmas")
-set (BOOST_CXX_FLAGS "-Wno-deprecated-register -std=c++11")
+if (APPLE)
+set (WARNING_IGNORE_FLAGS "-Wno-deprecated-register -Wno-unknon-pragmas -Wreturn-type -Werror=return-type")
+else()
+set (WARNING_IGNORE_FLAGS "-Wno-unknown-pragmas -Wreturn-type -Werror=return-type")
+endif()
+
 ## Prefer static to dynamic libraries
 SET(CMAKE_FIND_LIBRARY_SUFFIXES .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
 
@@ -38,7 +42,14 @@ else()
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
 endif()
 
-set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -std=c++11 -Wno-unknown-pragmas -Wreturn-type -Werror=return-type")
+
+if (QUIET_BUILD)
+  set(WALL "")
+else()
+  set(WALL "-Wall")
+endif()
+
+set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM ${WALL} -std=c++11")
 
 ##
 # OSX is strange (some might say, stupid in this regard).  Deal with it's quirkines here.
@@ -98,10 +109,6 @@ if ("${CMAKE_CXX_COMPILER_ID}" MATCHES "GNU")
     endif()
 
     set (WARNING_IGNORE_FLAGS "${WARNING_IGNORE_FLAGS} -Wno-unused-local-typedefs")
-    set (BOOST_TOOLSET "gcc")
-    set (BOOST_CONFIGURE_TOOLSET "--with-toolset=gcc")
-	set (BCXX_FLAGS "-std=c++11")
-    set (BOOST_EXTRA_FLAGS toolset=gcc cxxflags=${BCXX_FLAGS})
 # Tentatively, we support clang now
 elseif ("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
     set(CLANG TRUE)
@@ -111,10 +118,6 @@ elseif ("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
     if (HAVE_LIBCPP)
         message ("It appears that you're compiling with clang and that libc++ is available, so I'll use that")
         set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
-	    set (BOOST_TOOLSET "clang")
-        set (BOOST_CONFIGURE_TOOLSET "--with-toolset=clang")
-	    set (BCXX_FLAGS "-stdlib=libc++ -DBOOST_HAS_INT128")
-	    set (BOOST_EXTRA_FLAGS toolset=clang cxxflags=${BCXX_FLAGS} linkflags="-stdlib=libc++")
         set (JELLYFISH_CXX_FLAGS "-stdlib=libc++")
     # Otherwise, use libstdc++ (and make it static)
     else()

include/BooPHF.hpp

@@ -533,11 +533,11 @@ we need this 2-functors scheme because HashFunctors won't work with unordered_ma
 		//for debug purposes
 		void print() const
 		{
-			printf("bit array of size %lli: \n",_size);
+			printf("bit array of size %lu: \n",_size);
 			for(uint64_t ii = 0; ii< _size; ii++)
 			{
 				if(ii%10==0)
-					printf(" (%llu) ",ii);
+					printf(" (%lu) ",ii);
 				int val = (_bitArray[ii >> 6] >> (ii & 63 ) ) & 1;
 				printf("%i",val);
 			}
@@ -546,7 +546,7 @@ we need this 2-functors scheme because HashFunctors won't work with unordered_ma
 			printf("rank array : size %lu \n",_ranks.size());
 			for (uint64_t ii = 0; ii< _ranks.size(); ii++)
 			{
-				printf("%llu :  %lli,  ",ii,_ranks[ii]);
+				printf("%lu :  %lu,  ",ii,_ranks[ii]);
 			}
 			printf("\n");
 		}