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|
Author: Andreas Tille <tille@debian.org>
LastChanges: Wed, 13 Nov 2013 14:29:31 +0100
Description: Propagate hardening options
--- a/src/Makefile
+++ b/src/Makefile
@@ -7,11 +7,11 @@
CC = gcc
CXX = g++
DEFINES =
-CFLAGS = -m64 -pipe -O3 $(DEFINES)
-CXXFLAGS = -m64 -pipe -O3 $(DEFINES)
+CFLAGS += -pipe -O3 $(DEFINES)
+CXXFLAGS += -pipe -O3 $(DEFINES)
INCPATH = -I. -I/usr/include
LINK = g++
-LFLAGS = -m64
+#LFLAGS = -m64
LIBS = $(SUBLIBS)
AR = ar cqs
RANLIB =
@@ -116,19 +116,19 @@
.SUFFIXES: .o .c .cpp .cc .cxx .C
.cpp.o:
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
.cc.o:
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
.cxx.o:
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
.C.o:
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
.c.o:
- $(CC) -c $(CFLAGS) $(INCPATH) -o "$@" "$<"
+ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(INCPATH) -o "$@" "$<"
####### Build rules
@@ -136,7 +136,7 @@
all: Makefile $(TARGET) $(MANPAGES)
$(TARGET): $(OBJECTS)
- $(LINK) $(LFLAGS) -o $(TARGET) $(OBJECTS) $(OBJCOMP) $(LIBS)
+ $(LINK) $(LFLAGS) -o $(TARGET) $(OBJECTS) $(OBJCOMP) $(LIBS) $(LDFLAGS)
clean:compiler_clean
@@ -167,7 +167,7 @@
dbmatrix.h \
boolmatrix.h \
ancestralsequence.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o writefile.o writefile.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o writefile.o writefile.cpp
treenode.o: treenode.cpp config.h \
hmmodel.h \
@@ -187,7 +187,7 @@
fullprobability.h \
postprobability.h \
characterprobability.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o treenode.o treenode.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o treenode.o treenode.cpp
translatesequences.o: translatesequences.cpp translatesequences.h \
config.h \
@@ -201,7 +201,7 @@
site.h \
boolmatrix.h \
ancestralsequence.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o translatesequences.o translatesequences.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o translatesequences.o translatesequences.cpp
terminalsequence.o: terminalsequence.cpp terminalsequence.h \
sequence.h \
@@ -215,7 +215,7 @@
ancestralnode.h \
treenode.h \
ancestralsequence.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o terminalsequence.o terminalsequence.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o terminalsequence.o terminalsequence.cpp
terminalnode.o: terminalnode.cpp terminalnode.h \
treenode.h \
@@ -230,7 +230,7 @@
hmmodel.h \
ancestralnode.h \
ancestralsequence.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o terminalnode.o terminalnode.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o terminalnode.o terminalnode.cpp
site.o: site.cpp site.h \
intmatrix.h \
@@ -242,7 +242,7 @@
treenode.h \
sequence.h \
ancestralsequence.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o site.o site.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o site.o site.cpp
sequence.o: sequence.cpp sequence.h \
site.h \
@@ -250,7 +250,7 @@
flmatrix.h \
dbmatrix.h \
boolmatrix.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o sequence.o sequence.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o sequence.o sequence.cpp
readnewick.o: readnewick.cpp readnewick.h \
treenode.h \
@@ -263,10 +263,10 @@
ancestralnode.h \
ancestralsequence.h \
node.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o readnewick.o readnewick.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o readnewick.o readnewick.cpp
readfile.o: readfile.cpp readfile.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o readfile.o readfile.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o readfile.o readfile.cpp
readalignment.o: readalignment.cpp readalignment.h \
sequence.h \
@@ -282,12 +282,12 @@
config.h \
hmmodel.h \
ancestralnode.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o readalignment.o readalignment.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o readalignment.o readalignment.cpp
pwsite.o: pwsite.cpp pwsite.h \
flmatrix.h \
intmatrix.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o pwsite.o pwsite.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o pwsite.o pwsite.cpp
pwhirschberg.o: pwhirschberg.cpp config.h \
hmmodel.h \
@@ -303,7 +303,7 @@
pwhirschberg.h \
pwsite.h \
exonerate_reads.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o pwhirschberg.o pwhirschberg.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o pwhirschberg.o pwhirschberg.cpp
progressivealignment.o: progressivealignment.cpp readnewick.h \
treenode.h \
@@ -330,7 +330,7 @@
readalignment.h \
exonerate_reads.h \
bppancestors.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o progressivealignment.o progressivealignment.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o progressivealignment.o progressivealignment.cpp
prank.o: prank.cpp progressivealignment.h \
config.h \
@@ -353,7 +353,7 @@
mafft_alignment.h \
check_version.h \
prank.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o prank.o prank.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o prank.o prank.cpp
postprobability.o: postprobability.cpp config.h \
hmmodel.h \
@@ -369,7 +369,7 @@
postprobability.h \
phylomatchscore.h \
terminalsequence.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o postprobability.o postprobability.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o postprobability.o postprobability.cpp
phylomatchscore.o: phylomatchscore.cpp config.h \
hmmodel.h \
@@ -384,13 +384,13 @@
ancestralsequence.h \
phylomatchscore.h \
terminalsequence.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o phylomatchscore.o phylomatchscore.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o phylomatchscore.o phylomatchscore.cpp
node.o: node.cpp node.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o node.o node.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o node.o node.cpp
intmatrix.o: intmatrix.cpp intmatrix.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o intmatrix.o intmatrix.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o intmatrix.o intmatrix.cpp
hmmodel.o: hmmodel.cpp hmmodel.h \
dbmatrix.h \
@@ -403,7 +403,7 @@
boolmatrix.h \
ancestralsequence.h \
eigen.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o hmmodel.o hmmodel.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o hmmodel.o hmmodel.cpp
hirschberg.o: hirschberg.cpp config.h \
hmmodel.h \
@@ -420,7 +420,7 @@
hirschberg.h \
phylomatchscore.h \
terminalsequence.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o hirschberg.o hirschberg.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o hirschberg.o hirschberg.cpp
guidetree.o: guidetree.cpp guidetree.h \
flmatrix.h \
@@ -437,7 +437,7 @@
boolmatrix.h \
ancestralsequence.h \
translatesequences.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o guidetree.o guidetree.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o guidetree.o guidetree.cpp
fullprobability.o: fullprobability.cpp config.h \
hmmodel.h \
@@ -453,16 +453,16 @@
fullprobability.h \
phylomatchscore.h \
terminalsequence.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o fullprobability.o fullprobability.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o fullprobability.o fullprobability.cpp
flmatrix.o: flmatrix.cpp flmatrix.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o flmatrix.o flmatrix.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o flmatrix.o flmatrix.cpp
eigen.o: eigen.cpp eigen.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o eigen.o eigen.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o eigen.o eigen.cpp
dbmatrix.o: dbmatrix.cpp dbmatrix.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o dbmatrix.o dbmatrix.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o dbmatrix.o dbmatrix.cpp
characterprobability.o: characterprobability.cpp config.h \
hmmodel.h \
@@ -477,10 +477,10 @@
ancestralsequence.h \
characterprobability.h \
terminalsequence.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o characterprobability.o characterprobability.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o characterprobability.o characterprobability.cpp
boolmatrix.o: boolmatrix.cpp boolmatrix.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o boolmatrix.o boolmatrix.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o boolmatrix.o boolmatrix.cpp
ancestralsequence.o: ancestralsequence.cpp ancestralsequence.h \
sequence.h \
@@ -493,7 +493,7 @@
hmmodel.h \
ancestralnode.h \
treenode.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o ancestralsequence.o ancestralsequence.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o ancestralsequence.o ancestralsequence.cpp
ancestralnode.o: ancestralnode.cpp config.h \
hmmodel.h \
@@ -515,10 +515,10 @@
characterprobability.h \
terminalnode.h \
readalignment.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o ancestralnode.o ancestralnode.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o ancestralnode.o ancestralnode.cpp
check_version.o: check_version.cpp check_version.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o check_version.o check_version.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o check_version.o check_version.cpp
exonerate_reads.o: exonerate_reads.cpp exonerate_reads.h \
config.h \
@@ -533,7 +533,7 @@
boolmatrix.h \
ancestralsequence.h \
translatesequences.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o exonerate_reads.o exonerate_reads.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o exonerate_reads.o exonerate_reads.cpp
mafft_alignment.o: mafft_alignment.cpp mafft_alignment.h \
config.h \
@@ -547,7 +547,7 @@
site.h \
boolmatrix.h \
ancestralsequence.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o mafft_alignment.o mafft_alignment.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o mafft_alignment.o mafft_alignment.cpp
bppancestors.o: bppancestors.cpp bppancestors.h \
ancestralnode.h \
@@ -563,7 +563,7 @@
hmmodel.h \
readfile.h \
readnewick.h
- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o bppancestors.o bppancestors.cpp
+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o bppancestors.o bppancestors.cpp
####### Manpages
|
