Description: enable hardening
Author: Sascha Steinbiss <sascha@steinbiss.name>
--- a/src/Makefile
+++ b/src/Makefile
@@ -7,7 +7,7 @@
 # Notes: - "-Wno-sign-compare" eliminates a high number of warnings (see footnote below). Please adopt
 #          a strict signed-only usage strategy to avoid mistakes since we are not warned about this.
 #        - The order of object files in $(OBJS) IS IMPORTANT (see lldouble.hh)
-CFLAGS := -Wall -Wno-sign-compare -ansi -pedantic -O3 ${CFLAGS} # -DDEBUG -g -ggdb -pg -DDEBUG_STATES -DDEBUG 
+CFLAGS := -Wall -Wno-sign-compare -ansi -pedantic -O3 ${CFLAGS} # -DDEBUG -g -ggdb -pg -DDEBUG_STATES -DDEBUG
 ifdef SQLITE
 	COMPGENEPRED = true
 endif
@@ -43,8 +43,8 @@
 
 ifdef MYSQL
 # replace RUNTIME_LIBPATH with your own run-time libpath if mysql++ is not installed system-wide, e.g.
-# RUNTIME_LIBPATH = -Wl,-rpath=/home/mario/augustus/trunks/mysql++/mysql++-3.1.0/lib 
-RUNTIME_LIBPATH = 
+# RUNTIME_LIBPATH = -Wl,-rpath=/home/mario/augustus/trunks/mysql++/mysql++-3.1.0/lib
+RUNTIME_LIBPATH =
 INCLS	+= -I/usr/include/mysql -I/usr/include/mysql++ # the path to mysql++ may have to be adjusted
 LIBS 	+=  -lmysqlclient -lmysqlpp ${RUNTIME_LIBPATH} # -L/usr/local/lib/libmysqlpp.so.3.1.0
 CFLAGS  += -DAMYSQL
@@ -64,46 +64,46 @@
 .SUFFIXES: .cc .o .so
 
 .cc.o:
-	$(CC) -c $(CFLAGS) -o $@ $< $(INCLS)
+	$(CC) -c $(CFLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(INCLS)
 
 augustus: augustus.cc $(OBJS) $(DUMOBJS)
-	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 	cp augustus ../bin/
 
 etraining: etraining.cc $(TOBJS) $(OBJS)
-	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 	cp etraining ../bin/
 
 evaluate: evaluate.cc $(OBJS) $(DUMOBJS)
-	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 
 consensusFinder: consensusFinder.cc consensus.o
-	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 	cp consensusFinder ../bin/
 
 curve2hints: curve2hints.cc exon_seg.o
-	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 	cp curve2hints ../bin/
 
 fastBlockSearch: fastBlockSearch.cc pp_fastBlockSearcher.o \
 	types.o properties.o geneticcode.o pp_profile.o lldouble.o
-	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 	cp fastBlockSearch ../bin/
 
 prepareAlign: pp_prepare_align.cc
-	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $^
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $^
 	cp prepareAlign ../bin/
 
 load2db: load2db.cc fasta.o hints.o types.o properties.o lldouble.o
-	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 	cp load2db ../bin/
 
 load2sqlitedb: load2sqlitedb.cc fasta.o hints.o types.o properties.o lldouble.o sqliteDB.o
-	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 	cp load2sqlitedb ../bin/
 
 getSeq: getSeq.cc $(OBJS) $(DUMOBJS)
-	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
 	cp getSeq ../bin/
 
 info:
