diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/bifrost/Makefile | 13 | ||||
| -rw-r--r-- | biology/bifrost/files/patch-CMakeLists.txt | 4 | ||||
| -rw-r--r-- | biology/kallisto/Makefile | 12 | ||||
| -rw-r--r-- | biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt | 13 | ||||
| -rw-r--r-- | biology/ncbi-blast+/Makefile | 2 | ||||
| -rw-r--r-- | biology/vcftools/Makefile | 8 | ||||
| -rw-r--r-- | biology/vcftools/distinfo | 6 |
7 files changed, 39 insertions, 19 deletions
diff --git a/biology/bifrost/Makefile b/biology/bifrost/Makefile index 8820ddfa0631..082d27df32e6 100644 --- a/biology/bifrost/Makefile +++ b/biology/bifrost/Makefile @@ -18,6 +18,17 @@ USE_GITHUB= yes CMAKE_ARGS= -DCOMPILATION_ARCH=${CPUTYPE:UOFF} +CXXFLAGS+= -Wno-unqualified-std-cast-call + GH_ACCOUNT= pmelsted -.include <bsd.port.mk> +.include <bsd.port.pre.mk> + +# Build fails with clang19, but succeeds with gcc13 +# Have not figured out where this sz_link member is even supposed to come from +# DataStorage.tcc:81:69: error: no member named 'sz_link' in 'DataStorage<Unitig_data_t>' +.if ${OSVERSION} > 1500000 +USE_GCC= yes +.endif + +.include <bsd.port.post.mk> diff --git a/biology/bifrost/files/patch-CMakeLists.txt b/biology/bifrost/files/patch-CMakeLists.txt index 27893b9ec44d..4d49c5a270cc 100644 --- a/biology/bifrost/files/patch-CMakeLists.txt +++ b/biology/bifrost/files/patch-CMakeLists.txt @@ -1,6 +1,6 @@ ---- CMakeLists.txt.orig 2023-08-12 14:26:29 UTC +--- CMakeLists.txt.orig 2024-03-15 15:20:17 UTC +++ CMakeLists.txt -@@ -46,7 +46,6 @@ else(CMAKE_BUILD_TYPE MATCHES Debug) +@@ -56,7 +56,6 @@ else(CMAKE_BUILD_TYPE MATCHES Debug) set(CMAKE_EXE_LINKER_FLAGS "-pg") else(CMAKE_BUILD_TYPE MATCHES Profile) message("Build type: Release") diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile index 91193aa7facc..c2d33ef3ce82 100644 --- a/biology/kallisto/Makefile +++ b/biology/kallisto/Makefile @@ -37,12 +37,22 @@ CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON -DUSE_BAM:BOOL=ON # WIP: Remove before committing CMAKE_ARGS+= -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON MAKE_JOBS_UNSAFE= yes +CXXFLAGS+= -Wno-unqualified-std-cast-call LDFLAGS+= -lhts -lz OPTIONS_DEFINE= EXAMPLES +.include <bsd.port.pre.mk> + +# Build fails with clang19, but succeeds with gcc13 +# Have not figured out where this sz_link member is even supposed to come from +# DataStorage.tcc:81:69: error: no member named 'sz_link' in 'DataStorage<Unitig_data_t>' +.if ${OSVERSION} > 1500000 +USE_GCC= yes +.endif + post-install-EXAMPLES-on: ${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} -.include <bsd.port.mk> +.include <bsd.port.post.mk> diff --git a/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt b/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt index d25cf028cfdd..c662b37881c9 100644 --- a/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt +++ b/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt @@ -1,8 +1,8 @@ ---- ext/bifrost/CMakeLists.txt.orig 2023-06-27 10:45:00 UTC +--- ext/bifrost/CMakeLists.txt.orig 2024-09-17 05:40:08 UTC +++ ext/bifrost/CMakeLists.txt -@@ -7,18 +7,12 @@ find_package(Threads REQUIRED) +@@ -6,18 +6,12 @@ SET(MAX_GMER_SIZE "${MAX_KMER_SIZE}" CACHE STRING "MAX + # To enable a larger default k-mer size, replace MAX_KMER_SIZE with a larger multiple of 32: actual maximum k-mer size will be MAX_KMER_SIZE-1. - SET(MAX_KMER_SIZE "32" CACHE STRING "MAX_KMER_SIZE") SET(MAX_GMER_SIZE "${MAX_KMER_SIZE}" CACHE STRING "MAX_GMER_SIZE") -# Enable architecture optimizations -SET(COMPILATION_ARCH "native" CACHE STRING "COMPILATION_ARCH") @@ -12,7 +12,8 @@ # Set some default compile flags set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c11") - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") +-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") ++set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wno-unqualified-std-cast-call") -set_property(SOURCE BlockedBloomFilter.cpp APPEND_STRING PROPERTY COMPILE_FLAGS " -funroll-loops") - @@ -20,7 +21,7 @@ #check if we are on arm64 and apple, if so, disable AVX2 if(APPLE AND CMAKE_SYSTEM_PROCESSOR MATCHES "arm") message("Disabling AVX2 instructions on arm64") -@@ -30,8 +24,6 @@ if(COMPILATION_ARCH MATCHES "OFF") +@@ -29,8 +23,6 @@ else(COMPILATION_ARCH MATCHES "OFF") message("Disabling native architecture compilation (including AVX2)") else(COMPILATION_ARCH MATCHES "OFF") message("Compilation architecture: ${COMPILATION_ARCH}") @@ -29,7 +30,7 @@ endif(COMPILATION_ARCH MATCHES "OFF") if(ENABLE_AVX2 MATCHES "OFF") -@@ -56,7 +48,7 @@ else(CMAKE_BUILD_TYPE MATCHES Debug) +@@ -55,7 +47,7 @@ else(CMAKE_BUILD_TYPE MATCHES Debug) set(CMAKE_EXE_LINKER_FLAGS "-pg") else(CMAKE_BUILD_TYPE MATCHES Profile) message("Build type: Release") diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile index b87a9c2d6b60..31f6fb7db166 100644 --- a/biology/ncbi-blast+/Makefile +++ b/biology/ncbi-blast+/Makefile @@ -1,6 +1,6 @@ PORTNAME= ncbi-blast+ DISTVERSION= 2.16.0 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= biology perl5 python MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \ https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/ diff --git a/biology/vcftools/Makefile b/biology/vcftools/Makefile index e7d8ab338312..5c3b2d72c47b 100644 --- a/biology/vcftools/Makefile +++ b/biology/vcftools/Makefile @@ -1,7 +1,6 @@ PORTNAME= vcftools -PORTVERSION= 0.1.16 +PORTVERSION= 0.1.17 DISTVERSIONPREFIX= v -PORTREVISION= 2 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -11,11 +10,10 @@ WWW= https://github.com/vcftools/vcftools LICENSE= LGPL3 USES= autoreconf cpe gmake perl5 pkgconfig - -GNU_CONFIGURE= yes -GNU_CONFIGURE_MANPREFIX= ${PREFIX}/share USE_GITHUB= yes +GNU_CONFIGURE= yes +GNU_CONFIGURE_MANPREFIX= ${PREFIX}/share CXXFLAGS+= -std=c++14 CPE_VENDOR= vcftools_project diff --git a/biology/vcftools/distinfo b/biology/vcftools/distinfo index 14a425bfc4c0..5a5c2ff84384 100644 --- a/biology/vcftools/distinfo +++ b/biology/vcftools/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1533330712 -SHA256 (vcftools-vcftools-v0.1.16_GH0.tar.gz) = 575c13073efe65cbff6e2ab99eef12fe04536f5dc1f98de6674c848ca83cf302 -SIZE (vcftools-vcftools-v0.1.16_GH0.tar.gz) = 246933 +TIMESTAMP = 1747310968 +SHA256 (vcftools-vcftools-v0.1.17_GH0.tar.gz) = 00b54fc7349179c2efbdab0e4dcb65a69e7b0ab0d0d29b59cc823140d0b40bff +SIZE (vcftools-vcftools-v0.1.17_GH0.tar.gz) = 247685 |