diff options
| -rw-r--r-- | biology/seqwish/Makefile | 11 | ||||
| -rw-r--r-- | biology/seqwish/files/patch-CMakeLists.txt | 52 | ||||
| -rw-r--r-- | biology/seqwish/files/patch-deps_atomic__queue_include_atomic__queue_atomic__queue.h | 36 | ||||
| -rw-r--r-- | biology/seqwish/files/patch-deps_paryfor_paryfor.hpp | 37 |
4 files changed, 125 insertions, 11 deletions
diff --git a/biology/seqwish/Makefile b/biology/seqwish/Makefile index 947bb959a891..f2391fbff1f3 100644 --- a/biology/seqwish/Makefile +++ b/biology/seqwish/Makefile @@ -1,7 +1,7 @@ PORTNAME= seqwish DISTVERSIONPREFIX= v DISTVERSION= 0.7.11 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MASTER_SITES= https://github.com/ekg/seqwish/releases/download/v${DISTVERSION}/ @@ -12,11 +12,9 @@ WWW= https://github.com/ekg/seqwish LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE -BROKEN_FreeBSD_13= compilation fails: undefined symbol: __sync_val_compare_and_swap_16 ... referenced by transclosure.cpp -BROKEN_FreeBSD_15= compilation fails with clang-19, see https://github.com/ekg/seqwish/issues/126 -BROKEN_i386= compilation fails: error: use of undeclared identifier '_pdep_u64' +LIB_DEPENDS= libsdsl.so:devel/sdsl-lite -USES= cmake:noninja compiler:c++14-lang +USES= cmake:noninja compiler:c++14-lang pkgconfig CMAKE_ARGS= -DEXTRA_FLAGS="" # disable -march=native @@ -33,4 +31,7 @@ OPENMP_CMAKE_BOOL= USE_OPENMP OPENMP_CXXFLAGS= -fopenmp OPENMP_BROKEN_OFF= https://github.com/ekg/seqwish/issues/114 +post-extract: + @${RM} -r ${WRKSRC}/deps/sdsl-lite + .include <bsd.port.mk> diff --git a/biology/seqwish/files/patch-CMakeLists.txt b/biology/seqwish/files/patch-CMakeLists.txt index 3c6ca1d2757f..1c3e0fd7147d 100644 --- a/biology/seqwish/files/patch-CMakeLists.txt +++ b/biology/seqwish/files/patch-CMakeLists.txt @@ -1,14 +1,56 @@ +# unbundle sdsl-lite + --- CMakeLists.txt.orig 2023-04-19 15:25:32 UTC +++ CMakeLists.txt -@@ -256,9 +256,9 @@ target_link_libraries(seqwish - "${sdsl-lite_LIB}/libsdsl.a" - "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a" - "${sdsl-lite-divsufsort_LIB}/libdivsufsort64.a" +@@ -79,18 +79,15 @@ include_directories("${PROJECT_SOURCE_DIR}") + # Add external projects + include(${CMAKE_ROOT}/Modules/ExternalProject.cmake) + +-# sdsl-lite (full build using its cmake config) +-ExternalProject_Add(sdsl-lite +- SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/sdsl-lite" +- CMAKE_ARGS "${CMAKE_ARGS};-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>" +- UPDATE_COMMAND "" +- INSTALL_COMMAND "") +-ExternalProject_Get_property(sdsl-lite INSTALL_DIR) +-set(sdsl-lite_INCLUDE "${INSTALL_DIR}/src/sdsl-lite-build/include") +-set(sdsl-lite-divsufsort_INCLUDE "${INSTALL_DIR}/src/sdsl-lite-build/external/libdivsufsort/include") +-set(sdsl-lite_LIB "${INSTALL_DIR}/src/sdsl-lite-build/lib") +-set(sdsl-lite-divsufsort_LIB "${INSTALL_DIR}/src/sdsl-lite-build/external/libdivsufsort/lib") ++# sdsl-lite - use system library ++find_package(PkgConfig REQUIRED) ++pkg_check_modules(SDSL REQUIRED sdsl-lite) ++pkg_check_modules(DIVSUFSORT REQUIRED libdivsufsort) ++pkg_check_modules(DIVSUFSORT64 REQUIRED libdivsufsort64) ++set(sdsl-lite_INCLUDE "${SDSL_INCLUDE_DIRS}") ++set(sdsl-lite-divsufsort_INCLUDE "${DIVSUFSORT_INCLUDE_DIRS}") ++link_directories(${SDSL_LIBRARY_DIRS} ${DIVSUFSORT_LIBRARY_DIRS} ${DIVSUFSORT64_LIBRARY_DIRS}) + + # taywee's C++ args library, header only + ExternalProject_Add(tayweeargs + SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/args" +@@ -227,7 +224,6 @@ add_executable(seqwish + ${CMAKE_SOURCE_DIR}/src/version.cpp + ) + add_dependencies(seqwish tayweeargs) +-add_dependencies(seqwish sdsl-lite) + add_dependencies(seqwish gzipreader) + add_dependencies(seqwish mmmulti) + add_dependencies(seqwish iitii) +@@ -253,11 +249,11 @@ target_include_directories(seqwish PUBLIC + "${paryfor_INCLUDE}" + "${mio_INCLUDE}") + target_link_libraries(seqwish +- "${sdsl-lite_LIB}/libsdsl.a" +- "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a" +- "${sdsl-lite-divsufsort_LIB}/libdivsufsort64.a" - "-latomic" ++ ${SDSL_LIBRARIES} ++ ${DIVSUFSORT_LIBRARIES} ++ ${DIVSUFSORT64_LIBRARIES} + #"-latomic" Threads::Threads - jemalloc + #jemalloc z) if (BUILD_STATIC) - #set(CMAKE_EXE_LINKER_FLAGS "-static") diff --git a/biology/seqwish/files/patch-deps_atomic__queue_include_atomic__queue_atomic__queue.h b/biology/seqwish/files/patch-deps_atomic__queue_include_atomic__queue_atomic__queue.h new file mode 100644 index 000000000000..caeb5f19c418 --- /dev/null +++ b/biology/seqwish/files/patch-deps_atomic__queue_include_atomic__queue_atomic__queue.h @@ -0,0 +1,36 @@ +- fix compilation error with clang-19 + +--- deps/atomic_queue/include/atomic_queue/atomic_queue.h.orig 2025-10-10 06:48:58.627210000 -0700 ++++ deps/atomic_queue/include/atomic_queue/atomic_queue.h 2025-10-10 06:49:07.323108000 -0700 +@@ -393,13 +393,13 @@ + + T do_pop(unsigned tail) noexcept { + unsigned index = details::remap_index<SHUFFLE_BITS>(tail % size_); +- return Base::template do_pop_any(states_[index], elements_[index]); ++ return Base::template do_pop_any<>(states_[index], elements_[index]); + } + + template<class U> + void do_push(U&& element, unsigned head) noexcept { + unsigned index = details::remap_index<SHUFFLE_BITS>(head % size_); +- Base::template do_push_any(std::forward<U>(element), states_[index], elements_[index]); ++ Base::template do_push_any<>(std::forward<U>(element), states_[index], elements_[index]); + } + + public: +@@ -521,13 +521,13 @@ + + T do_pop(unsigned tail) noexcept { + unsigned index = details::remap_index<SHUFFLE_BITS>(tail & (size_ - 1)); +- return Base::template do_pop_any(states_[index], elements_[index]); ++ return Base::template do_pop_any<>(states_[index], elements_[index]); + } + + template<class U> + void do_push(U&& element, unsigned head) noexcept { + unsigned index = details::remap_index<SHUFFLE_BITS>(head & (size_ - 1)); +- Base::template do_push_any(std::forward<U>(element), states_[index], elements_[index]); ++ Base::template do_push_any<>(std::forward<U>(element), states_[index], elements_[index]); + } + + public: diff --git a/biology/seqwish/files/patch-deps_paryfor_paryfor.hpp b/biology/seqwish/files/patch-deps_paryfor_paryfor.hpp index c8a0fc7b928d..4f4e2b9eb9a9 100644 --- a/biology/seqwish/files/patch-deps_paryfor_paryfor.hpp +++ b/biology/seqwish/files/patch-deps_paryfor_paryfor.hpp @@ -1,4 +1,7 @@ ---- deps/paryfor/paryfor.hpp.orig 2024-10-15 18:25:21 UTC +- fix for PPC +- fix build with clang19 + +--- deps/paryfor/paryfor.hpp.orig 2024-10-15 18:25:21 UTC +++ deps/paryfor/paryfor.hpp @@ -51,7 +51,22 @@ static inline void spin_loop_pause() noexcept { } @@ -23,3 +26,35 @@ #error "Unknown CPU architecture." #endif +@@ -453,13 +468,13 @@ class AtomicQueue2 : public AtomicQueueCommon<AtomicQ + + T do_pop(unsigned tail) noexcept { + unsigned index = details::remap_index<SHUFFLE_BITS>(tail % size_); +- return Base::template do_pop_any(states_[index], elements_[index]); ++ return Base::template do_pop_any<>(states_[index], elements_[index]); + } + + template<class U> + void do_push(U&& element, unsigned head) noexcept { + unsigned index = details::remap_index<SHUFFLE_BITS>(head % size_); +- Base::template do_push_any(std::forward<U>(element), states_[index], elements_[index]); ++ Base::template do_push_any<>(std::forward<U>(element), states_[index], elements_[index]); + } + + public: +@@ -581,13 +596,13 @@ class AtomicQueue2B : public AtomicQueueCommon<Atomic + + T do_pop(unsigned tail) noexcept { + unsigned index = details::remap_index<SHUFFLE_BITS>(tail & (size_ - 1)); +- return Base::template do_pop_any(states_[index], elements_[index]); ++ return Base::template do_pop_any<>(states_[index], elements_[index]); + } + + template<class U> + void do_push(U&& element, unsigned head) noexcept { + unsigned index = details::remap_index<SHUFFLE_BITS>(head & (size_ - 1)); +- Base::template do_push_any(std::forward<U>(element), states_[index], elements_[index]); ++ Base::template do_push_any<>(std::forward<U>(element), states_[index], elements_[index]); + } + + public: |