Update to 0.8.5

PR:		209611
Submitted by:	jrm@ftfl.ca (maintainer)

biology/diamond/Makefile

@@ -2,9 +2,8 @@
 # $FreeBSD$
 
 PORTNAME=		diamond
-PORTVERSION=		0.7.12
+PORTVERSION=		0.8.5
 DISTVERSIONPREFIX=	v
-PORTREVISION=		1
 CATEGORIES=		biology
 
 MAINTAINER=		jrm@ftfl.ca
@@ -12,11 +11,9 @@ COMMENT=		BLAST-compatible local sequence aligner
 
 LICENSE=		BSD2CLAUSE
 
-LIB_DEPENDS=		libboost_system.so:devel/boost-libs
-
 ONLY_FOR_ARCHS=		amd64
 
-USES=			cmake:outsource
+USES=			cmake:outsource compiler:c++11-lang
 
 CFLAGS+=		-DNDEBUG
 
@@ -25,4 +22,8 @@ GH_ACCOUNT=		bbuchfink
 
 PLIST_FILES=		bin/diamond
 
+.if ! defined(PACKAGE_BUILDING)
+CXXFLAGS+=-march=native
+.endif
+
 .include <bsd.port.mk>

biology/diamond/distinfo

@@ -1,2 +1,3 @@
-SHA256 (bbuchfink-diamond-v0.7.12_GH0.tar.gz) = 16f8f618e4e5e81071ef8b66dc39685a1e969434ddeff3d88fa01091971b662f
-SIZE (bbuchfink-diamond-v0.7.12_GH0.tar.gz) = 1826614
+TIMESTAMP = 1464949238
+SHA256 (bbuchfink-diamond-v0.8.5_GH0.tar.gz) = 8ba092647af7c980ddd83acc6686acd2ba18744774c669027859dbaec644fda3
+SIZE (bbuchfink-diamond-v0.8.5_GH0.tar.gz) = 203133

biology/diamond/files/patch-CMakeLists.txt

@@ -1,33 +1,15 @@
---- CMakeLists.txt.orig	2016-03-29 09:23:52 UTC
+--- CMakeLists.txt.orig	2016-05-29 16:12:02 UTC
 +++ CMakeLists.txt
-@@ -9,6 +9,7 @@ if(BUILD_STATIC)
+@@ -9,12 +9,6 @@ if(BUILD_STATIC)
      set(CMAKE_EXE_LINKER_FLAGS "-static")
  endif()
  
-+FIND_PACKAGE(Threads REQUIRED)
- find_package(Boost
-   1.53.0 REQUIRED
-   COMPONENTS program_options timer iostreams thread
-@@ -16,9 +17,6 @@ find_package(Boost
- 
- find_package(ZLIB REQUIRED)
- 
--set(CMAKE_BUILD_TYPE Release)
--set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-uninitialized")
+-include(CheckCXXCompilerFlag)
+-CHECK_CXX_COMPILER_FLAG("-march=native" COMPILER_SUPPORTS_MARCHNATIVE)
+-if(COMPILER_SUPPORTS_MARCHNATIVE)
+-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
+-endif()
 -
- add_subdirectory("src/algo/blast/core")
- include_directories(
-   "${CMAKE_SOURCE_DIR}/src"
-@@ -29,6 +27,11 @@ add_executable(diamond src/main.cpp
-   src/basic/options.cpp
-   src/util/tinythread.cpp)
+ find_package(ZLIB REQUIRED)
+ find_package(Threads REQUIRED)
  
--target_link_libraries(diamond blast_core ${Boost_LIBRARIES} ${ZLIB_LIBRARY})
-+target_link_libraries(diamond blast_core ${Boost_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${ZLIB_LIBRARY})
- 
- install(TARGETS diamond DESTINATION bin)
-+
-+get_cmake_property(_variableNames VARIABLES)
-+foreach (_variableName ${_variableNames})
-+    message(STATUS "${_variableName}=${${_variableName}}")
-+endforeach()