Author: Andreas Tille Aaron M. Ucko Last-Update: 2023-01-15 20:56:15 Description: use Debian packaged re2 --- a/tools/loaders/sharq/CMakeLists.txt +++ b/tools/loaders/sharq/CMakeLists.txt @@ -48,18 +48,8 @@ if( SINGLE_CONFIG ) find_package(BZip2) find_package (Threads) - # check whether RE2 is accessible - set(RE2_URL https://github.com/google/re2) - execute_process(COMMAND curl -Is ${RE2_URL} - COMMAND head -n 1 - COMMAND grep -q 200 - RESULT_VARIABLE RE2_RC) - if ("${RE2_RC}" EQUAL 0) - set( RE2_FOUND TRUE CACHE INTERNAL "" ) - else() - message(RE2_RC = "${RE2_RC}" ) - set( RE2_FOUND FALSE CACHE INTERNAL "" ) - endif() + # Debian ensures RE2 via Build-Depends + set( RE2_FOUND TRUE CACHE INTERNAL "" ) message(RE2_FOUND = ${RE2_FOUND} ) # RE2_FOUND will be used by sharQ tests @@ -81,28 +71,28 @@ if( SINGLE_CONFIG ) set(RE2_TAG 2021-09-01) #set(RE2_TAG 2023-03-01) - include (ExternalProject) - ExternalProject_Add(RE2 - PREFIX ${LOCAL_BUILD_DIR} - GIT_REPOSITORY ${RE2_URL} - GIT_TAG ${RE2_TAG} - BUILD_IN_SOURCE 1 - UPDATE_COMMAND "" # No update as we use specific tag - INSTALL_DIR ${LOCAL_LIBDIR} - INSTALL_COMMMAND "" - CMAKE_ARGS - -DCMAKE_BUILD_TYPE:STRING=Release - -DRE2_BUILD_TESTING:BOOL=OFF - -DCMAKE_INSTALL_PREFIX:PATH=${LOCAL_BUILD_DIR} - -DCMAKE_INSTALL_LIBDIR:PATH=lib - -DCMAKE_VERBOSE_MAKEFILE:BOOL=OFF - -DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON - -DCMAKE_INSTALL_MESSAGE:STRING=LAZY - -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} - -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} - -DCMAKE_OSX_DEPLOYMENT_TARGET=${CMAKE_OSX_DEPLOYMENT_TARGET} - ) - set(RE2_STATIC_LIBRARIES -L${LOCAL_LIBDIR} -lre2 ) + # include (ExternalProject) + # ExternalProject_Add(RE2 + # PREFIX ${LOCAL_BUILD_DIR} + # GIT_REPOSITORY ${RE2_URL} + # GIT_TAG ${RE2_TAG} + # BUILD_IN_SOURCE 1 + # UPDATE_COMMAND "" # No update as we use specific tag + # INSTALL_DIR ${LOCAL_LIBDIR} + # INSTALL_COMMMAND "" + # CMAKE_ARGS + # -DCMAKE_BUILD_TYPE:STRING=Release + # -DRE2_BUILD_TESTING:BOOL=OFF + # -DCMAKE_INSTALL_PREFIX:PATH=${LOCAL_BUILD_DIR} + # -DCMAKE_INSTALL_LIBDIR:PATH=lib + # -DCMAKE_VERBOSE_MAKEFILE:BOOL=OFF + # -DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON + # -DCMAKE_INSTALL_MESSAGE:STRING=LAZY + # -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} + # -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} + # -DCMAKE_OSX_DEPLOYMENT_TARGET=${CMAKE_OSX_DEPLOYMENT_TARGET} + # ) + set(RE2_STATIC_LIBRARIES -lre2 ) add_custom_target( sharq.py @@ -112,7 +102,7 @@ if( SINGLE_CONFIG ) ${BINDIR}/sharq.py) add_executable(sharq fastq_parse.cpp) - add_dependencies(sharq RE2 sharq.py) + add_dependencies(sharq sharq.py) target_include_directories(sharq PUBLIC ${LOCAL_INCDIR} ${CMAKE_SOURCE_DIR}/libs/inc ./ ../../../) if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU" OR CMAKE_CXX_COMPILER_ID STREQUAL "Clang") set(CXX_FILESYSTEM_LIBRARIES "stdc++fs") --- a/test/loaders/sharq/CMakeLists.txt +++ b/test/loaders/sharq/CMakeLists.txt @@ -50,7 +50,7 @@ message(RE2_FOUND=${RE2_FOUND}) set(LOCAL_BUILD_DIR ${CMAKE_ARCHIVE_OUTPUT_DIRECTORY}) set(LOCAL_INCDIR ${LOCAL_BUILD_DIR}/include) set(LOCAL_LIBDIR ${LOCAL_BUILD_DIR}/lib) - set(RE2_STATIC_LIBRARIES -L${LOCAL_LIBDIR} -lre2 ) + set(RE2_STATIC_LIBRARIES -lre2 ) if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU" OR CMAKE_CXX_COMPILER_ID STREQUAL "Clang") set(CXX_FILESYSTEM_LIBRARIES "stdc++fs") @@ -58,28 +58,28 @@ message(RE2_FOUND=${RE2_FOUND}) # test-regexpr add_executable(test-regexpr test-regexpr.cpp ) - add_dependencies(test-regexpr RE2) + # add_dependencies(test-regexpr RE2) target_include_directories(test-regexpr PUBLIC ${LOCAL_INCDIR}) target_link_libraries(test-regexpr ${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_READ} ${RE2_STATIC_LIBRARIES}) add_test( NAME Test_regexpr COMMAND test-regexpr WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) # test-sharq-reader add_executable(test-sharq-reader test-sharq-reader.cpp ) - add_dependencies(test-sharq-reader RE2 sharq) + add_dependencies(test-sharq-reader sharq) target_include_directories(test-sharq-reader PUBLIC ${LOCAL_INCDIR} ../../../tools/loaders/sharq) target_link_libraries(test-sharq-reader ${CXX_FILESYSTEM_LIBRARIES} ZLIB::ZLIB ${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_READ} ${BZIP2_LIBRARIES} ${RE2_STATIC_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT}) add_test( NAME Test_sharq_reader COMMAND test-sharq-reader WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) # test-sharq-parser add_executable(test-sharq-parser test-sharq-parser.cpp ) - add_dependencies(test-sharq-parser RE2 sharq) + add_dependencies(test-sharq-parser sharq) target_include_directories(test-sharq-parser PUBLIC ${LOCAL_INCDIR} ../../../tools/loaders/sharq) target_link_libraries(test-sharq-parser ${CXX_FILESYSTEM_LIBRARIES} ZLIB::ZLIB ${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_READ} ${BZIP2_LIBRARIES} ${RE2_STATIC_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT}) add_test( NAME Test_sharq_parser COMMAND test-sharq-parser WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) # test-sharq-writer add_executable(test-sharq-writer test-sharq-writer.cpp ) - add_dependencies(test-sharq-writer RE2 sharq general-loader ) # general-loader for the metadata command line tests + add_dependencies(test-sharq-writer sharq general-loader ) # general-loader for the metadata command line tests target_include_directories(test-sharq-writer PUBLIC ${LOCAL_INCDIR} ../../../tools/loaders/sharq) target_link_libraries(test-sharq-writer ${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_READ}) add_test( NAME Test_sharq_writer COMMAND test-sharq-writer WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} ) @@ -93,7 +93,7 @@ message(RE2_FOUND=${RE2_FOUND}) set( asan_defs "-fsanitize=address" ) add_executable(test-sharq-parser-asan test-sharq-parser.cpp ) - add_dependencies(test-sharq-parser-asan RE2 sharq-asan) + add_dependencies(test-sharq-parser-asan sharq-asan) target_include_directories(test-sharq-parser-asan PUBLIC ${LOCAL_INCDIR} ../../../tools/loaders/sharq) target_compile_options( test-sharq-parser-asan PRIVATE ${asan_defs} ) target_link_libraries(test-sharq-parser-asan ${CXX_FILESYSTEM_LIBRARIES} ZLIB::ZLIB ${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_READ} ${BZIP2_LIBRARIES} ${RE2_STATIC_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT}) @@ -111,7 +111,7 @@ message(RE2_FOUND=${RE2_FOUND}) set( tsan_defs "-fsanitize=thread" ) add_executable(test-sharq-parser-tsan test-sharq-parser.cpp ) - add_dependencies(test-sharq-parser-tsan RE2 sharq-tsan) + add_dependencies(test-sharq-parser-tsan sharq-tsan) target_include_directories(test-sharq-parser-tsan PUBLIC ${LOCAL_INCDIR} ../../../tools/loaders/sharq) target_compile_options( test-sharq-parser-tsan PRIVATE ${tsan_defs} ) target_link_libraries(test-sharq-parser-tsan ${CXX_FILESYSTEM_LIBRARIES} ZLIB::ZLIB ${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_READ} ${BZIP2_LIBRARIES} ${RE2_STATIC_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT})