git: fd20bf82b699 - main - biology/mothur: Update to 1.45.2

[Jason W. Bacon]

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=fd20bf82b699c91e1ddc0b92ddc98b038483c706

commit fd20bf82b699c91e1ddc0b92ddc98b038483c706
Author:     Jason W. Bacon <jwb at FreeBSD.org>
AuthorDate: 2021-04-13 00:27:03 +0000
Commit:     Jason W. Bacon <jwb at FreeBSD.org>
CommitDate: 2021-04-13 00:29:17 +0000

    biology/mothur: Update to 1.45.2
    
    Numerous bug fixes and enhancements since 1.43.0
    
    Approved by:    yuri
---
 biology/mothur/Makefile                            |  5 ++---
 biology/mothur/distinfo                            |  6 +++---
 biology/mothur/files/patch-Makefile                | 23 +++++++++++++++++++---
 .../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 at 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