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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2021-04-13 00:27:03 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2021-04-13 00:29:17 +0000 |
| commit | fd20bf82b699c91e1ddc0b92ddc98b038483c706 (patch) | |
| tree | e2358b41ba98a8be76f8d364fac114fe8ec8c2af | |
| parent | fdbd0bce7c7691e74abc96410a73283ed6804b70 (diff) | |
| download | ports-fd20bf82b699c91e1ddc0b92ddc98b038483c706.tar.gz ports-fd20bf82b699c91e1ddc0b92ddc98b038483c706.zip | |
biology/mothur: Update to 1.45.2
Numerous bug fixes and enhancements since 1.43.0
Approved by: yuri
| -rw-r--r-- | biology/mothur/Makefile | 5 | ||||
| -rw-r--r-- | biology/mothur/distinfo | 6 | ||||
| -rw-r--r-- | biology/mothur/files/patch-Makefile | 23 | ||||
| -rw-r--r-- | biology/mothur/files/patch-source_endiannessmacros.h | 19 |
4 files changed, 25 insertions, 28 deletions
diff --git a/biology/mothur/Makefile b/biology/mothur/Makefile index cd379b8b9e23..052c7316a429 100644 --- a/biology/mothur/Makefile +++ b/biology/mothur/Makefile @@ -1,6 +1,6 @@ PORTNAME= mothur DISTVERSIONPREFIX= v -DISTVERSION= 1.43.0 +DISTVERSION= 1.45.2 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org @@ -11,8 +11,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE.md BUILD_DEPENDS= bash:shells/bash -USES= compiler:c++11-lang gmake localbase readline shebangfix -SHEBANG_FILES= source/uchime_src/mk +USES= compiler:c++11-lang gmake localbase readline USE_GITHUB= yes ALL_TARGET= ${PORTNAME} diff --git a/biology/mothur/distinfo b/biology/mothur/distinfo index a1cbdc3202d9..aa53703b0440 100644 --- a/biology/mothur/distinfo +++ b/biology/mothur/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1570294640 -SHA256 (mothur-mothur-v1.43.0_GH0.tar.gz) = 12ccd95a85bec3bb1564b8feabd244ea85413973740754803d01fc71ecb0a2c1 -SIZE (mothur-mothur-v1.43.0_GH0.tar.gz) = 1665073 +TIMESTAMP = 1618235513 +SHA256 (mothur-mothur-v1.45.2_GH0.tar.gz) = 73fddddfeea140537b8b037da971964091b2149177e376d98d19ba8a2183e471 +SIZE (mothur-mothur-v1.45.2_GH0.tar.gz) = 1614451 diff --git a/biology/mothur/files/patch-Makefile b/biology/mothur/files/patch-Makefile index 9d0709f1ea26..106b43e4e311 100644 --- a/biology/mothur/files/patch-Makefile +++ b/biology/mothur/files/patch-Makefile @@ -1,6 +1,16 @@ ---- Makefile.orig 2019-09-30 19:02:13 UTC +--- Makefile.orig 2021-04-09 18:28:13 UTC +++ Makefile -@@ -100,7 +100,7 @@ endif +@@ -53,6 +53,9 @@ endif + CXXFLAGS += -std=c++11 -pthread -DVERSION=${VERSION} -DRELEASE_DATE=${RELEASE_DATE} + LDFLAGS += -std=c++11 -pthread + ++# uchime requires gmake ++MAKE ?= gmake ++ + ifeq ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"") + else + CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES} +@@ -109,7 +112,7 @@ endif subdirs := $(sort $(dir $(filter-out $(skipUchime), $(wildcard source/*/)))) subDirIncludes = $(patsubst %, -I %, $(subdirs)) subDirLinking = $(patsubst %, -L%, $(subdirs)) @@ -9,7 +19,7 @@ LDFLAGS += $(subDirLinking) -@@ -109,8 +109,8 @@ endif +@@ -118,14 +121,14 @@ endif # OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs)))) OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs)))) @@ -20,3 +30,10 @@ mothur : $(OBJECTS) uchime $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS) + + uchime : +- cd source/uchime_src && export CXX=$(CXX) && make clean && make && mv uchime ../../ && cd .. ++ cd source/uchime_src && export CXX=$(CXX) && ${MAKE} clean && ${MAKE} && mv uchime ../../ && cd .. + + install : mothur + diff --git a/biology/mothur/files/patch-source_endiannessmacros.h b/biology/mothur/files/patch-source_endiannessmacros.h deleted file mode 100644 index 923cfbd9e621..000000000000 --- a/biology/mothur/files/patch-source_endiannessmacros.h +++ /dev/null @@ -1,19 +0,0 @@ ---- source/endiannessmacros.h.orig 2020-10-19 10:22:23 UTC -+++ source/endiannessmacros.h -@@ -53,16 +53,6 @@ - # define SP_BIG_ENDIAN - #endif - --/* -- * PowerPC -- */ --#if defined(__ppc__) || defined(__ppc) --# if defined(SP_LITTLE_ENDIAN) --# undef SP_LITTLE_ENDIAN --# endif --# define SP_BIG_ENDIAN --#endif -- - /* Some catch-alls */ - #if defined(__LITTLE_ENDIAN__) || defined(__LITTLEENDIAN__) - # define SP_LITTLE_ENDIAN |