Package: bedtools / 2.27.1+dfsg-4

flag_no_overwrite Patch series | download
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From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: Don't overwrite CXXFLAGS & include missing CPPFLAGS as needed
--- bedtools.orig/Makefile
+++ bedtools/Makefile
@@ -18,9 +18,9 @@
 export UTIL_DIR	= src/utils
 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)
 else
-export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
+export CXXFLAGS += -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
 endif
 
 # If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
--- bedtools.orig/src/complementFile/Makefile
+++ bedtools/src/complementFile/Makefile
@@ -42,7 +42,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/coverageFile/Makefile
+++ bedtools/src/coverageFile/Makefile
@@ -38,7 +38,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/subtractFile/Makefile
+++ bedtools/src/subtractFile/Makefile
@@ -40,7 +40,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/utils/ToolBase/Makefile
+++ bedtools/src/utils/ToolBase/Makefile
@@ -30,7 +30,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(INCLUDES)
--- bedtools.orig/src/utils/driver/Makefile
+++ bedtools/src/utils/driver/Makefile
@@ -85,7 +85,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."