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-rw-r--r--biology/btllib/Makefile1
-rw-r--r--biology/coverm/Makefile2
-rw-r--r--biology/kmcp/Makefile2
-rw-r--r--biology/ncbi-entrez-direct/Makefile2
-rw-r--r--biology/seqkit/Makefile2
-rw-r--r--biology/seqwish/Makefile11
-rw-r--r--biology/seqwish/files/patch-CMakeLists.txt52
-rw-r--r--biology/seqwish/files/patch-deps_atomic__queue_include_atomic__queue_atomic__queue.h36
-rw-r--r--biology/seqwish/files/patch-deps_paryfor_paryfor.hpp37
-rw-r--r--biology/taxonkit/Makefile2
-rw-r--r--biology/unikmer/Makefile2
-rw-r--r--biology/viennarna/Makefile12
-rw-r--r--biology/viennarna/files/patch-m4_ac__rna__build__requirements.m443
-rw-r--r--biology/viennarna/files/patch-src_ViennaRNA_Makefile.am22
-rw-r--r--biology/vsearch/Makefile2
-rw-r--r--biology/vsearch/distinfo6
-rw-r--r--biology/vsearch/files/patch-src_searchcore.cc22
-rw-r--r--biology/vsearch/files/patch-src_sintax.cc12
18 files changed, 225 insertions, 43 deletions
diff --git a/biology/btllib/Makefile b/biology/btllib/Makefile
index dd5daa7c9272..750b970ec0be 100644
--- a/biology/btllib/Makefile
+++ b/biology/btllib/Makefile
@@ -1,6 +1,7 @@
PORTNAME= btllib
DISTVERSIONPREFIX= v
DISTVERSION= 1.7.5
+PORTREVISION= 1
CATEGORIES= biology devel
MAINTAINER= yuri@FreeBSD.org
diff --git a/biology/coverm/Makefile b/biology/coverm/Makefile
index 9256b1dfe0c8..213b27d8d186 100644
--- a/biology/coverm/Makefile
+++ b/biology/coverm/Makefile
@@ -1,7 +1,7 @@
PORTNAME= coverm
DISTVERSIONPREFIX= v
DISTVERSION= 0.7.0
-PORTREVISION= 8
+PORTREVISION= 9
CATEGORIES= biology
MAINTAINER= yuri@FreeBSD.org
diff --git a/biology/kmcp/Makefile b/biology/kmcp/Makefile
index a8ce982e074e..3e4e393d6d7d 100644
--- a/biology/kmcp/Makefile
+++ b/biology/kmcp/Makefile
@@ -1,7 +1,7 @@
PORTNAME= kmcp
DISTVERSIONPREFIX= v
DISTVERSION= 0.9.4
-PORTREVISION= 15
+PORTREVISION= 16
CATEGORIES= biology
MAINTAINER= yuri@FreeBSD.org
diff --git a/biology/ncbi-entrez-direct/Makefile b/biology/ncbi-entrez-direct/Makefile
index eec6fb0553ef..29b571ea86c4 100644
--- a/biology/ncbi-entrez-direct/Makefile
+++ b/biology/ncbi-entrez-direct/Makefile
@@ -1,6 +1,6 @@
PORTNAME= ncbi-entrez-direct
DISTVERSION= 14.9.20210423
-PORTREVISION= 31
+PORTREVISION= 32
CATEGORIES= biology perl5
MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/${PORTVERSION}/
DISTFILES= edirect.tar.gz
diff --git a/biology/seqkit/Makefile b/biology/seqkit/Makefile
index 8296fb570d6a..a79a93af0685 100644
--- a/biology/seqkit/Makefile
+++ b/biology/seqkit/Makefile
@@ -1,7 +1,7 @@
PORTNAME= seqkit
DISTVERSIONPREFIX= v
DISTVERSION= 2.10.0
-PORTREVISION= 6
+PORTREVISION= 7
CATEGORIES= biology
MAINTAINER= yuri@FreeBSD.org
diff --git a/biology/seqwish/Makefile b/biology/seqwish/Makefile
index 947bb959a891..f2391fbff1f3 100644
--- a/biology/seqwish/Makefile
+++ b/biology/seqwish/Makefile
@@ -1,7 +1,7 @@
PORTNAME= seqwish
DISTVERSIONPREFIX= v
DISTVERSION= 0.7.11
-PORTREVISION= 1
+PORTREVISION= 2
CATEGORIES= biology
MASTER_SITES= https://github.com/ekg/seqwish/releases/download/v${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:
diff --git a/biology/taxonkit/Makefile b/biology/taxonkit/Makefile
index d84c2b6ea635..55e6a8c10b05 100644
--- a/biology/taxonkit/Makefile
+++ b/biology/taxonkit/Makefile
@@ -1,7 +1,7 @@
PORTNAME= taxonkit
DISTVERSIONPREFIX= v
DISTVERSION= 0.19.0
-PORTREVISION= 6
+PORTREVISION= 7
CATEGORIES= biology
MAINTAINER= yuri@FreeBSD.org
diff --git a/biology/unikmer/Makefile b/biology/unikmer/Makefile
index f8635b6340bc..bc494df6d906 100644
--- a/biology/unikmer/Makefile
+++ b/biology/unikmer/Makefile
@@ -1,7 +1,7 @@
PORTNAME= unikmer
DISTVERSIONPREFIX= v
DISTVERSION= 0.20.0
-PORTREVISION= 10
+PORTREVISION= 11
CATEGORIES= biology
MAINTAINER= yuri@FreeBSD.org
diff --git a/biology/viennarna/Makefile b/biology/viennarna/Makefile
index aa45c46534f4..7088761b767b 100644
--- a/biology/viennarna/Makefile
+++ b/biology/viennarna/Makefile
@@ -1,6 +1,6 @@
PORTNAME= viennarna
DISTVERSION= 2.7.0
-PORTREVISION= 1
+PORTREVISION= 2
CATEGORIES= biology
MASTER_SITES= https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_7_x/
DISTNAME= ViennaRNA-${DISTVERSION}
@@ -15,15 +15,13 @@ LICENSE_NAME= Vienna RNA License
LICENSE_FILE= ${WRKSRC}/COPYING
LICENSE_PERMS= auto-accept dist-mirror pkg-mirror
-BROKEN_FreeBSD_13= compilation fails with clang-19: see https://github.com/ViennaRNA/ViennaRNA/issues/253
-BROKEN_FreeBSD_15= compilation fails with clang-19: see https://github.com/ViennaRNA/ViennaRNA/issues/253
-
BUILD_DEPENDS= bash:shells/bash \
lapacke>0:math/lapacke \
libgd>0:graphics/gd # for the static lib
BUILD_DEPENDS+= swig:devel/swig \
xxd:sysutils/xxd
-LIB_DEPENDS= libgmp.so:math/gmp \
+LIB_DEPENDS= libdlib.so:science/dlib-cpp \
+ libgmp.so:math/gmp \
libgsl.so:math/gsl \
liblapack.so:math/lapack \
libmpfr.so:math/mpfr
@@ -57,6 +55,10 @@ PORTEXAMPLES= *
post-configure: # remove -lstdc++ from .pc file
@${REINPLACE_CMD} -e 's| -lstdc++||' ${WRKSRC}/RNAlib2.pc
+post-extract:
+ # remove bundled dlib to ensure we use system version
+ @${RM} -rf ${WRKSRC}/src/dlib-19.24
+
post-install:
# remove stray files
@${RM} ${STAGEDIR}/RNA/RNAconsensus.py
diff --git a/biology/viennarna/files/patch-m4_ac__rna__build__requirements.m4 b/biology/viennarna/files/patch-m4_ac__rna__build__requirements.m4
new file mode 100644
index 000000000000..67d75c4a94c0
--- /dev/null
+++ b/biology/viennarna/files/patch-m4_ac__rna__build__requirements.m4
@@ -0,0 +1,43 @@
+# Use system dlib instead of bundled version
+# - Replace bundled dlib detection with pkg-config
+# - Use system dlib from science/dlib-cpp port
+# - Remove hardcoded paths to bundled dlib-19.24
+--- m4/ac_rna_build_requirements.m4.orig 2024-06-01 20:46:46 UTC
++++ m4/ac_rna_build_requirements.m4
+@@ -253,28 +253,18 @@ AC_DEFUN([RNA_CHECK_DLIB], [
+
+ AC_DEFUN([RNA_CHECK_DLIB], [
+ AX_CXX_COMPILE_STDCXX(17, noext, mandatory)
+- DLIB_VERSION=19.24
+- DLIB_DIR="dlib-${DLIB_VERSION}"
+- DLIB_PATH="${srcdir}/src/${DLIB_DIR}"
+- DLIB_SRC_FILE="${DLIB_PATH}/dlib/all/source.cpp"
+
+- AC_RNA_TEST_FILE($DLIB_SRC_FILE,[],[
++ dnl Check for system dlib using pkg-config
++ PKG_CHECK_MODULES([DLIB], [dlib-1 >= 19.0], [
++ AC_DEFINE([HAVE_DLIB], [1], [Define if you have dlib])
++ ], [
+ AC_MSG_ERROR([
+-=================================================
+-Can't find dlib's source.cpp
+-
+-Make sure you've unpacked 'src/dlib-${DLIB_VERSION}.tar.bz2'!
+-
+-Usually, you only need to execute the following command:
+-
+-tar -xjf src/dlib-${DLIB_VERSION}.tar.bz2 -C src/
+-=================================================
+-])
++dlib development library not found. Please install dlib-cpp port.
++ ])
+ ])
+
+- AC_SUBST(DLIB_CPPFLAGS, "-I\$(top_srcdir)/src/${DLIB_DIR} -DDLIB_NO_GUI_SUPPORT")
+- AC_SUBST(DLIB_DIR)
+- AC_SUBST(DLIB_VERSION)
++ AC_SUBST(DLIB_CPPFLAGS, "${DLIB_CFLAGS} -DDLIB_NO_GUI_SUPPORT")
++ AC_SUBST(DLIB_LIBS, "${DLIB_LIBS}")
+
+ ])
+
diff --git a/biology/viennarna/files/patch-src_ViennaRNA_Makefile.am b/biology/viennarna/files/patch-src_ViennaRNA_Makefile.am
new file mode 100644
index 000000000000..b50bbe1659c0
--- /dev/null
+++ b/biology/viennarna/files/patch-src_ViennaRNA_Makefile.am
@@ -0,0 +1,22 @@
+# Use system dlib instead of bundled version
+# - Remove bundled dlib source compilation
+# - Link concentrations library with system dlib
+# - Avoid compiling ../@DLIB_DIR@/dlib/all/source.cpp
+--- src/ViennaRNA/Makefile.am.orig 2024-10-19 20:19:42 UTC
++++ src/ViennaRNA/Makefile.am
+@@ -76,6 +76,7 @@ libRNA_concentrations_la_CPPFLAGS = $(AM_CPPFLAGS) $(D
+ libRNA_la_LDFLAGS = -avoid-version -static $(LTO_LDFLAGS) $(PTHREAD_LIBS)
+
+ libRNA_concentrations_la_CPPFLAGS = $(AM_CPPFLAGS) $(DLIB_CPPFLAGS)
++libRNA_concentrations_la_LIBADD = $(DLIB_LIBS)
+
+ libRNA_conv_la_LIBADD = \
+ libRNA_backtrack.la \
+@@ -493,7 +494,6 @@ libRNA_concentrations_la_SOURCES = \
+
+ libRNA_concentrations_la_SOURCES = \
+ concentrations.c \
+- ../@DLIB_DIR@/dlib/all/source.cpp \
+ wrap_dlib.cpp
+
+
diff --git a/biology/vsearch/Makefile b/biology/vsearch/Makefile
index d96e1c272462..897c01f7477d 100644
--- a/biology/vsearch/Makefile
+++ b/biology/vsearch/Makefile
@@ -1,6 +1,6 @@
PORTNAME= vsearch
DISTVERSIONPREFIX= v
-DISTVERSION= 2.30.0
+DISTVERSION= 2.30.1
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
diff --git a/biology/vsearch/distinfo b/biology/vsearch/distinfo
index 2e0dbf172a12..c124a6bce96e 100644
--- a/biology/vsearch/distinfo
+++ b/biology/vsearch/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1740867400
-SHA256 (torognes-vsearch-v2.30.0_GH0.tar.gz) = 6d11ce960206ab64cf6d7907e539348d192a5b3f32f82d37c9bfbc4d789b576c
-SIZE (torognes-vsearch-v2.30.0_GH0.tar.gz) = 285775
+TIMESTAMP = 1759667807
+SHA256 (torognes-vsearch-v2.30.1_GH0.tar.gz) = f65f03538a77cd1212bd04a52bb722114765329e64bd35e10ee2aefcd81137fe
+SIZE (torognes-vsearch-v2.30.1_GH0.tar.gz) = 334663
diff --git a/biology/vsearch/files/patch-src_searchcore.cc b/biology/vsearch/files/patch-src_searchcore.cc
index 84870932c9fd..85894cf869e5 100644
--- a/biology/vsearch/files/patch-src_searchcore.cc
+++ b/biology/vsearch/files/patch-src_searchcore.cc
@@ -1,18 +1,18 @@
---- src/searchcore.cc.orig 2024-09-26 10:48:55 UTC
+--- src/searchcore.cc.orig 2025-10-05 12:35:57 UTC
+++ src/searchcore.cc
-@@ -239,9 +239,14 @@ auto search_topscores(struct searchinfo_s * si) -> voi
- if (bitmap)
+@@ -285,9 +285,14 @@ auto search_topscores(struct searchinfo_s * searchinfo
+ if (bitmap != nullptr)
{
#ifdef __x86_64__
-+ // Not sure how to enable ssse3 without enabling other
-+ // non-portable features.
-+ // This code is only used rarely, so disable ssse3 for now.
-+ // It won't affect performance much on the whole.
-+ // https://github.com/torognes/vsearch/pull/497
- if (ssse3_present)
++ // Not sure how to enable ssse3 without enabling other
++ // non-portable features.
++ // This code is only used rarely, so disable ssse3 for now.
++ // It won't affect performance much on the whole.
++ // https://github.com/torognes/vsearch/pull/497
+ if (ssse3_present != 0)
{
-- increment_counters_from_bitmap_ssse3(si->kmers,
-+ increment_counters_from_bitmap_sse2(si->kmers,
+- increment_counters_from_bitmap_ssse3(searchinfo->kmers,
++ increment_counters_from_bitmap_sse2(searchinfo->kmers,
bitmap, indexed_count);
}
else
diff --git a/biology/vsearch/files/patch-src_sintax.cc b/biology/vsearch/files/patch-src_sintax.cc
index c6cd9ec46abb..b5af8da42d6e 100644
--- a/biology/vsearch/files/patch-src_sintax.cc
+++ b/biology/vsearch/files/patch-src_sintax.cc
@@ -1,7 +1,7 @@
---- src/sintax.cc.orig 2024-09-26 10:48:55 UTC
+--- src/sintax.cc.orig 2025-10-05 12:34:38 UTC
+++ src/sintax.cc
-@@ -289,9 +289,14 @@ auto sintax_search_topscores(struct searchinfo_s * si)
- if (bitmap)
+@@ -295,9 +295,14 @@ auto sintax_search_topscores(struct searchinfo_s * sea
+ if (bitmap != nullptr)
{
#ifdef __x86_64__
+ // Not sure how to enable ssse3 without enabling other
@@ -9,10 +9,10 @@
+ // This code is only used rarely, so disable ssse3 for now.
+ // It won't affect performance much on the whole.
+ // https://github.com/torognes/vsearch/pull/497
- if (ssse3_present)
+ if (ssse3_present != 0)
{
-- increment_counters_from_bitmap_ssse3(si->kmers,
-+ increment_counters_from_bitmap_sse2(si->kmers,
+- increment_counters_from_bitmap_ssse3(searchinfo->kmers,
++ increment_counters_from_bitmap_sse2(searchinfo->kmers,
bitmap, indexed_count);
}
else
generated by cgit v1.2.3 (git 2.25.1) at 2025-10-12 10:39:05 +0000