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biology/mothur: Update to 1.45.2
Numerous bug fixes and enhancements since 1.43.0 Approved by: yuri
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@ -1,6 +1,6 @@
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PORTNAME= mothur
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PORTNAME= mothur
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DISTVERSIONPREFIX= v
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DISTVERSIONPREFIX= v
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DISTVERSION= 1.43.0
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DISTVERSION= 1.45.2
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CATEGORIES= biology
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CATEGORIES= biology
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MAINTAINER= yuri@FreeBSD.org
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MAINTAINER= yuri@FreeBSD.org
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@ -11,8 +11,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE.md
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BUILD_DEPENDS= bash:shells/bash
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BUILD_DEPENDS= bash:shells/bash
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USES= compiler:c++11-lang gmake localbase readline shebangfix
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USES= compiler:c++11-lang gmake localbase readline
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SHEBANG_FILES= source/uchime_src/mk
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USE_GITHUB= yes
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USE_GITHUB= yes
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ALL_TARGET= ${PORTNAME}
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ALL_TARGET= ${PORTNAME}
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@ -1,3 +1,3 @@
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TIMESTAMP = 1570294640
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TIMESTAMP = 1618235513
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SHA256 (mothur-mothur-v1.43.0_GH0.tar.gz) = 12ccd95a85bec3bb1564b8feabd244ea85413973740754803d01fc71ecb0a2c1
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SHA256 (mothur-mothur-v1.45.2_GH0.tar.gz) = 73fddddfeea140537b8b037da971964091b2149177e376d98d19ba8a2183e471
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SIZE (mothur-mothur-v1.43.0_GH0.tar.gz) = 1665073
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SIZE (mothur-mothur-v1.45.2_GH0.tar.gz) = 1614451
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@ -1,6 +1,16 @@
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--- Makefile.orig 2019-09-30 19:02:13 UTC
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--- Makefile.orig 2021-04-09 18:28:13 UTC
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+++ Makefile
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+++ Makefile
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@@ -100,7 +100,7 @@ endif
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@@ -53,6 +53,9 @@ endif
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CXXFLAGS += -std=c++11 -pthread -DVERSION=${VERSION} -DRELEASE_DATE=${RELEASE_DATE}
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LDFLAGS += -std=c++11 -pthread
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+# uchime requires gmake
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+MAKE ?= gmake
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+
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ifeq ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
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else
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CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
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@@ -109,7 +112,7 @@ endif
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subdirs := $(sort $(dir $(filter-out $(skipUchime), $(wildcard source/*/))))
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subdirs := $(sort $(dir $(filter-out $(skipUchime), $(wildcard source/*/))))
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subDirIncludes = $(patsubst %, -I %, $(subdirs))
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subDirIncludes = $(patsubst %, -I %, $(subdirs))
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subDirLinking = $(patsubst %, -L%, $(subdirs))
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subDirLinking = $(patsubst %, -L%, $(subdirs))
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@ -9,7 +19,7 @@
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LDFLAGS += $(subDirLinking)
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LDFLAGS += $(subDirLinking)
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@@ -109,8 +109,8 @@ endif
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@@ -118,14 +121,14 @@ endif
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#
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#
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OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs))))
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OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs))))
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OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs))))
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OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs))))
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@ -20,3 +30,10 @@
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mothur : $(OBJECTS) uchime
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mothur : $(OBJECTS) uchime
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$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
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$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
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uchime :
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- cd source/uchime_src && export CXX=$(CXX) && make clean && make && mv uchime ../../ && cd ..
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+ cd source/uchime_src && export CXX=$(CXX) && ${MAKE} clean && ${MAKE} && mv uchime ../../ && cd ..
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install : mothur
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@ -1,19 +0,0 @@
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--- source/endiannessmacros.h.orig 2020-10-19 10:22:23 UTC
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+++ source/endiannessmacros.h
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@@ -53,16 +53,6 @@
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# define SP_BIG_ENDIAN
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#endif
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-/*
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- * PowerPC
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- */
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-#if defined(__ppc__) || defined(__ppc)
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-# if defined(SP_LITTLE_ENDIAN)
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-# undef SP_LITTLE_ENDIAN
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-# endif
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-# define SP_BIG_ENDIAN
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-#endif
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-
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/* Some catch-alls */
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#if defined(__LITTLE_ENDIAN__) || defined(__LITTLEENDIAN__)
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# define SP_LITTLE_ENDIAN
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