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Author: Andreas Tille <tille@debian.org>
Aaron M. Ucko <ucko@debian.org>
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})
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