diff --git a/biology/vcflib/Makefile b/biology/vcflib/Makefile index 665663e16c96..17002a8ccdbc 100644 --- a/biology/vcflib/Makefile +++ b/biology/vcflib/Makefile @@ -1,43 +1,43 @@ PORTNAME= vcflib DISTVERSIONPREFIX= v DISTVERSION= 1.0.5 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= C++ library and CLI tools for parsing and manipulating VCF files WWW= https://github.com/vcflib/vcflib LICENSE= MIT BUILD_DEPENDS= zig>0:lang/zig \ pybind11>=0:devel/pybind11 LIB_DEPENDS= libhts.so:biology/htslib \ libcurl.so:ftp/curl USES= cmake:noninja gmake localbase:ldflags pkgconfig python shebangfix USE_GITHUB= yes GH_ACCOUNT= ekg GH_TUPLE= ekg:fastahack:bb33265:fastahack/contrib/fastahack \ ekg:filevercmp:1a9b779:filevercmp/contrib/filevercmp \ ekg:fsom:a6ef318:fsom/contrib/fsom \ google:googletest:d225acc:googletest/contrib/googletest \ ekg:intervaltree:aa59377:intervaltree/contrib/intervaltree \ edawson:libVCFH:44b6580:libVCFH/contrib/libVCFH \ ekg:multichoose:68733cd:multichoose/contrib/multichoose \ ekg:smithwaterman:2610e25:smithwaterman/contrib/smithwaterman \ simd-everywhere:simde-no-tests:9af03cd:simd/src/simde \ vcflib:tabixpp:v1.1.2:tabixpp/contrib/tabixpp \ smarco:WFA2-lib:v2.3:wfa2/contrib/WFA2-lib SHEBANG_FILES= scripts/* # Clang and GCC disable sse2 by default on i386, but it's required for vcflib CFLAGS_i386= -msse2 CONFLICTS_INSTALL= filevercmp libdisorder # include/disorder.h include/filevercmp.h include/pdflib.hpp post-stage: ${MV} ${STAGEDIR}/usr/lib/libzig.a ${STAGEDIR}${PREFIX}/lib .include diff --git a/biology/vcflib/files/patch-contrib_WFA2-lib_system_profiler__timer.h b/biology/vcflib/files/patch-contrib_WFA2-lib_system_profiler__timer.h new file mode 100644 index 000000000000..c954e2132183 --- /dev/null +++ b/biology/vcflib/files/patch-contrib_WFA2-lib_system_profiler__timer.h @@ -0,0 +1,10 @@ +--- contrib/WFA2-lib/system/profiler_timer.h.orig 2023-01-26 13:43:09 UTC ++++ contrib/WFA2-lib/system/profiler_timer.h +@@ -33,6 +33,7 @@ + #ifndef PROFILER_TIMER_H + #define PROFILER_TIMER_H + ++#include + #include "profiler_counter.h" + + /*