Author: Andreas Tille <tille@debian.org>
Description: Propagate hardening options
 The package is orphaned upstream, hence the patch is not forwarded.
Forwarded: no
Last-Update: 2024-08-07
Reviewed-By: Étienne Mollier <emollier@debian.org>

--- ampliconnoise.orig/FCluster/makefile
+++ ampliconnoise/FCluster/makefile
@@ -1,6 +1,6 @@
 CC     = cc
-CFLAGS = -O3
-EFLAGS =  
+CFLAGS += -O3
+EFLAGS = $(LDFLAGS)
 EFILE  = FCluster
 LIBS   = -lm 
 OBJS   = FCluster.o 
@@ -10,7 +10,7 @@
 	$(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
 
 $(OBJS) : FCluster.c FCluster.h
-	$(CC) $(CFLAGS) -c $*.c 
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
 
 clean: 
 	rm -rf *o FCluster
--- ampliconnoise.orig/FastaUnique/makefile
+++ ampliconnoise/FastaUnique/makefile
@@ -1,6 +1,6 @@
 CC     = cc
-CFLAGS = -O3 
-EFLAGS =  
+CFLAGS += -O3
+EFLAGS = $(LDFLAGS)
 EFILE  = FastaUnique
 LIBS   = -lm 
 OBJS   = FastaUnique.o 
@@ -10,7 +10,7 @@
 	$(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
 
 $(OBJS) : FastaUnique.c FastaUnique.h
-	$(CC) $(CFLAGS) -c $*.c 
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
 
 clean:
 	rm -rf *.o FastaUnique
--- ampliconnoise.orig/NDist/makefile
+++ ampliconnoise/NDist/makefile
@@ -1,6 +1,6 @@
 CC     = mpicc
-CFLAGS = -O3
-EFLAGS =  
+CFLAGS += -O3
+EFLAGS = $(LDFLAGS)
 EFILE  = NDist
 LIBS   = -lm  
 OBJS   = NDist.o 
@@ -10,7 +10,7 @@
 	$(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
 
 $(OBJS) : NDist.h
-	$(CC) $(CFLAGS) -c $*.c 
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c 
 
 clean:
 	rm -rf *.o NDist
--- ampliconnoise.orig/Perseus/makefile
+++ ampliconnoise/Perseus/makefile
@@ -1,6 +1,6 @@
 CC     = cc
-CFLAGS = -O3 
-EFLAGS =  
+CFLAGS += -O3
+EFLAGS = $(LDFLAGS)
 EFILE  = Perseus
 LIBS   = -lm -lgsl -lgslcblas
 OBJS   = Perseus.o 
@@ -10,7 +10,7 @@
 	$(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
 
 $(OBJS) : Perseus.c Perseus.h
-	$(CC) $(CFLAGS) -c $*.c 
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
 
 clean:
 	rm -rf *.o Perseus
--- ampliconnoise.orig/PerseusD/makefile
+++ ampliconnoise/PerseusD/makefile
@@ -1,6 +1,6 @@
 CC     = cc
-CFLAGS = -O3 
-EFLAGS =  
+CFLAGS += -O3
+EFLAGS = $(LDFLAGS)
 EFILE  = PerseusD
 LIBS   = -lm -lgsl -lgslcblas
 OBJS   = PerseusD.o 
@@ -10,7 +10,7 @@
 	$(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
 
 $(OBJS) : PerseusD.c PerseusD.h
-	$(CC) $(CFLAGS) -c $*.c 
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
 
 clean:
 	rm -rf *.o PerseusD
--- ampliconnoise.orig/PyroDist/makefile
+++ ampliconnoise/PyroDist/makefile
@@ -1,6 +1,6 @@
 CC     = mpicc
-CFLAGS = -O3
-EFLAGS =  
+CFLAGS += -O3
+EFLAGS = $(LDFLAGS)
 EFILE  = PyroDist
 LIBS   = -lm 
 OBJS   = PyroDist.o
@@ -10,7 +10,7 @@
 	$(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
 
 $(OBJS) : PyroDist.c PyroDist.h
-	$(CC) $(CFLAGS) -c $*.c 
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
 
 clean:
 	rm -rf *.o PyroDist
--- ampliconnoise.orig/PyroNoise/makefile
+++ ampliconnoise/PyroNoise/makefile
@@ -1,6 +1,6 @@
 CC     = mpicc
-CFLAGS = -O3
-EFLAGS = 
+CFLAGS += -O3
+EFLAGS = $(LDFLAGS)
 EFILE  = PyroNoise
 LIBS   =  -lm
 OBJS   = PyroNoise.o 
@@ -10,7 +10,7 @@
 	$(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
 
 $(OBJS) : PyroNoise.c PyroNoise.h
-	$(CC) $(CFLAGS) -c $*.c 
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
 
 clean:
 	rm -rf *.o PyroNoise
--- ampliconnoise.orig/PyroNoiseM/makefile
+++ ampliconnoise/PyroNoiseM/makefile
@@ -1,6 +1,6 @@
 CC     = mpicc
-CFLAGS = -O3
-EFLAGS = 
+CFLAGS += -O3
+EFLAGS = $(LDFLAGS)
 EFILE  = PyroNoiseM
 LIBS   =  -lm
 OBJS   = PyroNoiseM.o 
@@ -10,7 +10,7 @@
 	$(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
 
 $(OBJS) : PyroNoiseM.c PyroNoiseM.h
-	$(CC) $(CFLAGS) -c $*.c 
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
 
 clean:
 	rm -rf *.o PyroNoiseM
--- ampliconnoise.orig/SeqDist/makefile
+++ ampliconnoise/SeqDist/makefile
@@ -1,6 +1,6 @@
 CC     = mpicc
-CFLAGS = -O3
-EFLAGS =  
+CFLAGS += -O3
+EFLAGS = $(LDFLAGS)
 EFILE  = SeqDist
 LIBS   = -lm 
 OBJS   = SeqDist.o
@@ -10,7 +10,7 @@
 	$(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
 
 $(OBJS) : SeqDist.c SeqDist.h
-	$(CC) $(CFLAGS) -c $*.c 
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
 
 clean:
 	rm -rf *.o SeqDist
--- ampliconnoise.orig/SeqNoise/makefile
+++ ampliconnoise/SeqNoise/makefile
@@ -1,6 +1,6 @@
 CC     = mpicc
-CFLAGS = -O3
-EFLAGS =  
+CFLAGS += -O3
+EFLAGS = $(LDFLAGS)
 EFILE  = SeqNoise
 LIBS   = -lm 
 OBJS   = SeqNoise.o
@@ -10,7 +10,7 @@
 	$(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
 
 $(OBJS) : SeqNoise.c SeqNoise.h
-	$(CC) $(CFLAGS) -c $*.c 
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
 
 clean:
 	rm -rf *.o SeqNoise
--- ampliconnoise.orig/SplitClusterClust/makefile
+++ ampliconnoise/SplitClusterClust/makefile
@@ -1,6 +1,6 @@
 CC     = gcc
-CFLAGS = -O3
-EFLAGS =  
+CFLAGS += -O3
+EFLAGS = $(LDFLAGS)
 EFILE  = SplitClusterClust
 LIBS   = -lm 
 OBJS   = SplitClusterClust.o
@@ -10,7 +10,7 @@
 	$(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
 
 $(OBJS) : SplitClusterClust.c SplitClusterClust.h
-	$(CC) $(CFLAGS) -c $*.c 
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
 
 clean:
 	rm -rf *.o SplitClusterClust
--- ampliconnoise.orig/SplitClusterEven/makefile
+++ ampliconnoise/SplitClusterEven/makefile
@@ -1,6 +1,6 @@
 CC     = cc
-CFLAGS = -O3
-EFLAGS =  
+CFLAGS += -O3
+EFLAGS = $(LDFLAGS)
 EFILE  = SplitClusterEven
 LIBS   = -lm 
 OBJS   = SplitClusterEven.o
@@ -10,7 +10,7 @@
 	$(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
 
 $(OBJS) : SplitClusterEven.c SplitClusterEven.h
-	$(CC) $(CFLAGS) -c $*.c 
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
 
 clean:
 	rm -rf *.o SplitClusterEven
--- ampliconnoise.orig/makefile
+++ ampliconnoise/makefile
@@ -1,17 +1,17 @@
 all:
-	(cd FCluster && make)
-	(cd FastaUnique && make)
-	(cd NDist && make)
-	(cd PyroDist && make)
-	(cd PyroNoise && make)
-	(cd SeqDist && make)
-	(cd PyroNoiseM && make)
-	(cd PyroNoiseA && make)
-	(cd SeqNoise && make)
-	(cd SplitClusterEven && make)
-	(cd SplitClusterClust && make)  		
-	(cd Perseus && make) 		
-	(cd PerseusD && make) 		
+	(cd FCluster && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
+	(cd FastaUnique && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
+	(cd NDist && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
+	(cd PyroDist && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
+	(cd PyroNoise && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
+	(cd SeqDist && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
+	(cd PyroNoiseM && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
+	(cd PyroNoiseA && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
+	(cd SeqNoise && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
+	(cd SplitClusterEven && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
+	(cd SplitClusterClust && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
+	(cd Perseus && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
+	(cd PerseusD && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
 clean:
 	(cd FCluster && make clean)
 	(cd FastaUnique && make clean)
--- ampliconnoise.orig/PyroNoiseA/makefile
+++ ampliconnoise/PyroNoiseA/makefile
@@ -1,5 +1,5 @@
 CC     = mpicc
-CFLAGS = -O3
+CFLAGS += -O3
 EFLAGS = 
 EFILE  = PyroNoiseA
 LIBS   =  -lm
@@ -7,10 +7,10 @@
 
 $(EFILE) : $(OBJS)
 	@echo "linking..."
-	$(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS)
+	$(CC) $(EFLAGS) -o $(EFILE) $(OBJS) $(LIBS) $(LDFLAGS)
 
 $(OBJS) : PyroNoiseA.c PyroNoiseA.h
-	$(CC) $(CFLAGS) -c $*.c 
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c $*.c
 
 clean:
 	rm -rf *.o PyroNoiseA