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biology/seqwish: Unbundle sdsl-lite and fix some clang19 compilation errors

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This commit is contained in:
Yuri Victorovich
2025-10-10 20:48:01 -07:00
parent a5bf8bdbd9
commit 67ad101165
4 changed files with 125 additions and 11 deletions
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biology/seqwish/Makefile
+6 -5
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@@ -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 ${WRKSRC}/deps/sdsl-lite
.include <bsd.port.mk>
biology/seqwish/files/patch-CMakeLists.txt
+47 -5
View File
@@ -1,14 +1,56 @@
# unbundle sdsl-lite
--- CMakeLists.txt.orig 2023-04-19 15:25:32 UTC
+++ CMakeLists.txt
@@ -256,9 +256,9 @@ target_link_libraries(seqwish
"${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")
biology/seqwish/files/patch-deps_atomic__queue_include_atomic__queue_atomic__queue.h
+36
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@@ -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:
biology/seqwish/files/patch-deps_paryfor_paryfor.hpp
+36 -1
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@@ -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: