diff options
| -rw-r--r-- | biology/vcflib/Makefile | 18 | ||||
| -rw-r--r-- | biology/vcflib/distinfo | 22 | ||||
| -rw-r--r-- | biology/vcflib/files/patch-CMakeLists.txt | 23 | ||||
| -rw-r--r-- | biology/vcflib/files/patch-contrib_WFA2-lib_system_profiler__timer.h | 10 |
4 files changed, 28 insertions, 45 deletions
diff --git a/biology/vcflib/Makefile b/biology/vcflib/Makefile index 17002a8ccdbc..311b78bac7ce 100644 --- a/biology/vcflib/Makefile +++ b/biology/vcflib/Makefile @@ -1,7 +1,6 @@ PORTNAME= vcflib DISTVERSIONPREFIX= v -DISTVERSION= 1.0.5 -PORTREVISION= 2 +DISTVERSION= 1.0.6 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -13,25 +12,26 @@ LICENSE= MIT BUILD_DEPENDS= zig>0:lang/zig \ pybind11>=0:devel/pybind11 LIB_DEPENDS= libhts.so:biology/htslib \ - libcurl.so:ftp/curl + libcurl.so:ftp/curl \ + libwfa2.so:biology/wfa2-lib 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:filevercmp:df20dcc:filevercmp/contrib/filevercmp \ + ekg:fsom:56695e1:fsom/contrib/fsom \ ekg:intervaltree:aa59377:intervaltree/contrib/intervaltree \ edawson:libVCFH:44b6580:libVCFH/contrib/libVCFH \ - ekg:multichoose:68733cd:multichoose/contrib/multichoose \ + ekg:multichoose:e1f94ae: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 + vcflib:tabixpp:v1.1.2:tabixpp/contrib/tabixpp SHEBANG_FILES= scripts/* +CMAKE_ARGS+= -DWFA_GITMODULE=OFF -DWFALIB=${LOCALBASE}/lib/libwfa2.so + # Clang and GCC disable sse2 by default on i386, but it's required for vcflib CFLAGS_i386= -msse2 diff --git a/biology/vcflib/distinfo b/biology/vcflib/distinfo index b009e8c070e7..b31324e88085 100644 --- a/biology/vcflib/distinfo +++ b/biology/vcflib/distinfo @@ -1,25 +1,21 @@ -TIMESTAMP = 1674400989 -SHA256 (ekg-vcflib-v1.0.5_GH0.tar.gz) = f24b8553fcb37dfe35e704a415ff4be8fd657a5d94f0101723552805946fb7a3 -SIZE (ekg-vcflib-v1.0.5_GH0.tar.gz) = 23545058 +TIMESTAMP = 1675089755 +SHA256 (ekg-vcflib-v1.0.6_GH0.tar.gz) = 3598d1a9f6c936c58be6a567f249c1df879a49b57dc5a967b83a7856a16ceeb6 +SIZE (ekg-vcflib-v1.0.6_GH0.tar.gz) = 23545077 SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760 -SHA256 (ekg-filevercmp-1a9b779_GH0.tar.gz) = 34c21d1b58295bca72b92c1cd832a4171b07ec97c19ffc0d4d8ec67e266c6070 -SIZE (ekg-filevercmp-1a9b779_GH0.tar.gz) = 3053 -SHA256 (ekg-fsom-a6ef318_GH0.tar.gz) = 68351c16d5c4b96142409e38c6828b6199eae44eaa7579bde165734d4832565b -SIZE (ekg-fsom-a6ef318_GH0.tar.gz) = 9686 -SHA256 (google-googletest-d225acc_GH0.tar.gz) = 6880e0d51fa80a508ad5674ce483c1c468315faddac10d580b5505e8e7ef6bfa -SIZE (google-googletest-d225acc_GH0.tar.gz) = 1279815 +SHA256 (ekg-filevercmp-df20dcc_GH0.tar.gz) = d34bec614be638e05eb6fa419c936b9e7de58d50b1a096a5ca02aadb7db6b059 +SIZE (ekg-filevercmp-df20dcc_GH0.tar.gz) = 3113 +SHA256 (ekg-fsom-56695e1_GH0.tar.gz) = d1cc62bf72a75b74149336799fcbe237eaa662161fb0cfdac5ba6d5825248180 +SIZE (ekg-fsom-56695e1_GH0.tar.gz) = 9767 SHA256 (ekg-intervaltree-aa59377_GH0.tar.gz) = 8d42eee645bcb196da03077c6f567f61529add3a581bb98d85f5c9cfe4b50774 SIZE (ekg-intervaltree-aa59377_GH0.tar.gz) = 72545 SHA256 (edawson-libVCFH-44b6580_GH0.tar.gz) = 3c90a6c5f1fbe88bedb4a0dcdc1e55dfa51c58f2acd9b31bceead226ab84785c SIZE (edawson-libVCFH-44b6580_GH0.tar.gz) = 2956 -SHA256 (ekg-multichoose-68733cd_GH0.tar.gz) = 909baf2e462e43e71ba0d015fbe759c0ab95331c36d6c4ec65e4a92a7b9d3297 -SIZE (ekg-multichoose-68733cd_GH0.tar.gz) = 6558 +SHA256 (ekg-multichoose-e1f94ae_GH0.tar.gz) = 78ffaa36b6f82685230a3d263c9b556ab55a97196036764473f2b1ee66997ca8 +SIZE (ekg-multichoose-e1f94ae_GH0.tar.gz) = 6585 SHA256 (ekg-smithwaterman-2610e25_GH0.tar.gz) = f907becb50945d0858d3bf7a64959905712244cbe8455b35ef1102ff893173ce SIZE (ekg-smithwaterman-2610e25_GH0.tar.gz) = 39160 SHA256 (simd-everywhere-simde-no-tests-9af03cd_GH0.tar.gz) = 99dcb7d6a2e1dc3f51401ff16eaa5dde93c793e13b514ea9cae4d9819144b8fe SIZE (simd-everywhere-simde-no-tests-9af03cd_GH0.tar.gz) = 572867 SHA256 (vcflib-tabixpp-v1.1.2_GH0.tar.gz) = c850299c3c495221818a85c9205c60185c8ed9468d5ec2ed034470bb852229dc SIZE (vcflib-tabixpp-v1.1.2_GH0.tar.gz) = 6962 -SHA256 (smarco-WFA2-lib-v2.3_GH0.tar.gz) = 64a113895c74dd746ec52d768a2d56465fb4a86c40c13fe985af549f1ca86343 -SIZE (smarco-WFA2-lib-v2.3_GH0.tar.gz) = 4149234 diff --git a/biology/vcflib/files/patch-CMakeLists.txt b/biology/vcflib/files/patch-CMakeLists.txt index 6de651bd1d98..5a7824a2dfa0 100644 --- a/biology/vcflib/files/patch-CMakeLists.txt +++ b/biology/vcflib/files/patch-CMakeLists.txt @@ -1,6 +1,6 @@ ---- CMakeLists.txt.orig 2023-01-16 08:55:05 UTC +--- CMakeLists.txt.orig 2023-01-29 04:57:02 UTC +++ CMakeLists.txt -@@ -1,7 +1,7 @@ +@@ -9,7 +9,7 @@ cmake_minimum_required(VERSION 3.16) project(vcflib) @@ -9,15 +9,12 @@ include(ExternalProject) include(FeatureSummary) -@@ -358,9 +358,9 @@ endif(HTSLIB_LOCAL) +@@ -38,7 +38,7 @@ option(PROFILING "Enable profiling" OFF) + option(GPROF "Enable gprof profiling" OFF) + option(ASAN "Use address sanitiser" OFF) + option(ZIG "Set to OFF to disable the zig code" ON) +-option(WFA_GITMODULE "Force local git submodule for WFA2LIB" ON) # disable in distros, you may need to add path to WFA_INCLUDE_DIRS ++option(WFA_GITMODULE "Force local git submodule for WFA2LIB" OFF) # disable in distros, you may need to add path to WFA_INCLUDE_DIRS - # FIXME: hard-coded compile switches need to be fixed upstream - if (ASAN) -- set(wfa_MAKE_ARGS BUILD_WFA_PARALLEL=1 BUILD_TOOLS=0 BUILD_EXAMPLES=0 CC=gcc CC_FLAGS=-fPIC setup asan lib_wfa) -+ set(wfa_MAKE_ARGS BUILD_WFA_PARALLEL=1 BUILD_TOOLS=0 BUILD_EXAMPLES=0 CC_FLAGS=-fPIC setup asan lib_wfa) - else() -- set(wfa_MAKE_ARGS BUILD_WFA_PARALLEL=1 BUILD_TOOLS=0 BUILD_EXAMPLES=0 CC=gcc CC_FLAGS=-fPIC setup lib_wfa) -+ set(wfa_MAKE_ARGS BUILD_WFA_PARALLEL=1 BUILD_TOOLS=0 BUILD_EXAMPLES=0 CC_FLAGS=-fPIC setup lib_wfa) - endif() - - # if ((${CMAKE_BUILD_TYPE} MATCHES Release) OR (${CMAKE_BUILD_TYPE} MATCHES RelWithDebInfo)) + include(CheckIPOSupported) # adds lto + check_ipo_supported(RESULT ipo_supported OUTPUT output) 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 deleted file mode 100644 index c954e2132183..000000000000 --- a/biology/vcflib/files/patch-contrib_WFA2-lib_system_profiler__timer.h +++ /dev/null @@ -1,10 +0,0 @@ ---- 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 <time.h> - #include "profiler_counter.h" - - /* |