bedtools2: cleanup

[Winston Weinert <winston%ml1.net@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Winston Weinert <winston%ml1.net@localhost>
Pushed By:	winston
Date:		Thu Apr 26 06:22:47 2018 -0500
Changeset:	35539f1aa74f93ae18cf0abc04b87fdc1319b0b3

Modified Files:
	bedtools2/Makefile
	bedtools2/distinfo
	bedtools2/patches/patch-Makefile

Log Message:
bedtools2: cleanup

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=35539f1aa74f93ae18cf0abc04b87fdc1319b0b3

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 bedtools2/Makefile               | 17 +++++++++--------
 bedtools2/distinfo               |  2 +-
 bedtools2/patches/patch-Makefile | 23 +++++++++++++++++++----
 3 files changed, 29 insertions(+), 13 deletions(-)

diffs:
diff --git a/bedtools2/Makefile b/bedtools2/Makefile
index 9375a173dc..4d926bdc93 100644
--- a/bedtools2/Makefile
+++ b/bedtools2/Makefile
@@ -1,8 +1,6 @@
 # $NetBSD$
-#
-###########################################################
-#               Generated by fbsd2pkg                     #
-###########################################################
+
+# N.B. Not sure if we need to override "python" in the Makefiles.
 
 DISTNAME=	bedtools2-${PORTVERSION}
 CATEGORIES=	biology
@@ -19,10 +17,6 @@ USE_TOOLS+=	gmake
 REPLACE_BASH=	scripts/*.sh
 REPLACE_PYTHON=	scripts/*.py
 
-# WRKSRC=		${WRKDIR}/bedtools2-${PORTVERSION}
-
-# MAKE_ENV=	PYTHONBIN=${PYTHONBIN}
-
 PORTVERSION=	2.27.1
 
 .include "../../mk/bsd.prefs.mk"
@@ -31,6 +25,13 @@ PORTVERSION=	2.27.1
 MAKE_ENV+=	POPCNT_CAPABILITY=0
 .endif
 
+pre-configure:
+	${SED} -i -e 's|@\$$(CXX)|$(CXX)|g' \
+	        ${WRKSRC}/*/Makefile \
+	        ${WRKSRC}/*/*/Makefile \
+	        ${WRKSRC}/*/*/*/Makefile \
+	        ${WRKSRC}/*/*/*/*/Makefile
+
 post-install:
 	${STRIP_CMD} ${DESTDIR}${PREFIX}/bin/bedtools
 
diff --git a/bedtools2/distinfo b/bedtools2/distinfo
index b106a62860..cf1824ff60 100644
--- a/bedtools2/distinfo
+++ b/bedtools2/distinfo
@@ -4,4 +4,4 @@ SHA1 (bedtools2-2.27.1.tar.gz) = 0f45ade764913f88b332c3126f152fd55da9a101
 RMD160 (bedtools2-2.27.1.tar.gz) = 957b40f240fd6b22374165f25b96fc4aa3fb8f5a
 SHA512 (bedtools2-2.27.1.tar.gz) = 65d58b5d9e00581ed73f2d5a58be56c888adbc4045396e62fe39abc27a2abcd974721c7fe25533d76613788e43529b5df427ad19acce7ff6e7133018cdd35f40
 Size (bedtools2-2.27.1.tar.gz) = 20003119 bytes
-SHA1 (patch-Makefile) = 4058adb49f01b5e643349f06f53fc247a2014b42
+SHA1 (patch-Makefile) = be89e0e963ca559480fa7f98ec8bd70582b6d7e2
diff --git a/bedtools2/patches/patch-Makefile b/bedtools2/patches/patch-Makefile
index c6d3004772..a80527d735 100644
--- a/bedtools2/patches/patch-Makefile
+++ b/bedtools2/patches/patch-Makefile
@@ -1,8 +1,7 @@
 $NetBSD$
 
 # Use portable shell path, respect env
-
---- Makefile.orig	2018-03-22 23:06:52.521063536 +0000
+--- Makefile.orig	2017-12-14 17:15:02.000000000 +0000
 +++ Makefile
 @@ -4,7 +4,7 @@
  # (c) 2009 Aaron Quinlan
@@ -21,7 +20,7 @@ $NetBSD$
 +export CXX		?= g++
  ifeq ($(DEBUG),1)
 -export CXXFLAGS = -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
-+#export CXXFLAGS = -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
++export CXXFLAGS += -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
  else
 -export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
 +export CXXFLAGS += -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
@@ -37,7 +36,14 @@ $NetBSD$
  
  SUBDIRS = $(SRC_DIR)/annotateBed \
  		  $(SRC_DIR)/bamToBed \
-@@ -148,7 +148,7 @@ all: print_banner $(OBJ_DIR) $(BIN_DIR)
+@@ -143,12 +143,12 @@ INCLUDES =	-I$(SRC_DIR)/utils/bedFile \
+ 
+ all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
+ 	@echo "- Building main bedtools binary."
+-	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
+-	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
  	@echo "done."
  
  	@echo "- Creating executables for old CLI."
@@ -58,3 +64,12 @@ $NetBSD$
  	done
  
  print_banner:
+@@ -193,7 +193,7 @@ clean:
+ .PHONY: clean
+ 
+ test: all
+-	@cd test; bash test.sh
++	@cd test; $(SHELL) test.sh
+ 
+ .PHONY: test
+