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biology/mothur: Update to 1.45.2

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Numerous bug fixes and enhancements since 1.43.0

Approved by:    yuri
This commit is contained in:
Jason W. Bacon 2021-04-12 19:27:03 -05:00
parent fdbd0bce7c
commit fd20bf82b6
4 changed files with 25 additions and 28 deletions
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5
biology/mothur/Makefile
View File

@ -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}

6
biology/mothur/distinfo
View File

@ -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

23
biology/mothur/files/patch-Makefile
View File

@ -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

19
biology/mothur/files/patch-source_endiannessmacros.h
View File

@ -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