Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Descriptions: Don't stomp on Debian's CFLAGS
--- hmmer.orig/configure.ac
+++ hmmer/configure.ac
@@ -78,12 +78,6 @@
 AC_INIT(HMMER, 3.3, sean@eddylab.org, hmmer)
 AC_MSG_NOTICE([Configuring HMMER3 for your system.])
 
-# remember if the user is overriding CFLAGS
-esl_cflags_env_set=no
-if test x"$CFLAGS" != x; then 
-  esl_cflags_env_set=yes
-fi
-
 ################################################################
 # 3. Info on the package
 ################################################################
@@ -234,21 +228,15 @@
 #  --enable-gcov, --enable-gprof, and --enable-debugging are mutually exclusive.
 #
 if test "$enable_gcov" = "yes"; then
-   if test "$esl_cflags_env_set" = "yes"; then 
-     AC_MSG_ERROR([--enable-gcov overrides CFLAGS, so don't set CFLAGS])
-   fi
-   CFLAGS="-g -Wall -fprofile-arcs -ftest-coverage"
+   CFLAGS="${CLFAGS} -g -Wall -fprofile-arcs -ftest-coverage"
 elif test "$enable_gprof" = "yes"; then
-   if test "$esl_cflags_env_set" = "yes"; then 
-     AC_MSG_ERROR([--enable-gprof overrides CFLAGS, so don't set CFLAGS])
-   fi
-   CFLAGS="-O -g -pg"
+   CFLAGS="${CFLAGS} -O -g -pg"
 elif test "$enable_debugging" != "no"; then
    if test "$GCC" = "yes"; then
-      CFLAGS="-g -Wall"
+      CFLAGS="${CFLAGS} -g -Wall"
    fi
-elif test "$esl_cflags_env_set" != "yes"; then
-   CFLAGS="-O3"
+else
+   CFLAGS="${CFLAGS} -O3"
 fi
 
 
--- hmmer.orig/easel/Makefile.in
+++ hmmer/easel/Makefile.in
@@ -549,7 +549,7 @@
 	@${RANLIB} libeasel.a
 
 ${ALL_OBJS}: %.o : %.c ${HDRS} esl_config.h
-	${QUIET_CC}${CC} -I. -I${srcdir} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} -c $<
+	${QUIET_CC}${CC} -I. -I${srcdir} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${CPPFLAGS} ${DEFS} -c $<
 
 
 # Driver compilation:
@@ -573,10 +573,10 @@
 	   else DFILE=${srcdir}/esl_$${BASENAME}.c ;\
         fi;\
 	if test ${V} ;\
-	   then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${UTEST_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
+	   then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
 	   else echo '    ' GEN $@ ;\
 	fi ;\
-	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
+	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
 
 ${ALL_BENCHMARKS}: libeasel.a
 	@BASENAME=`echo $@ | sed -e 's/_benchmark//'| sed -e 's/^esl_//'` ;\
@@ -587,10 +587,10 @@
 	   else DFILE=${srcdir}/esl_$${BASENAME}.c ;\
         fi;\
 	if test ${V} ;\
-	   then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
+	   then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
 	   else echo '    ' GEN $@ ;\
 	fi ;\
-	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
+	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
 
 ${ALL_EXPERIMENTS}: libeasel.a
 	@BASENAME=`echo $@ | sed -e 's/_experiment//'| sed -e 's/^esl_//'` ;\
@@ -601,10 +601,10 @@
 	   else DFILE=${srcdir}/esl_$${BASENAME}.c ;\
         fi;\
 	if test ${V} ;\
-	   then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
+	   then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
 	   else echo '    ' GEN $@ ;\
 	fi ;\
-	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
+	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
 
 ${ALL_EXAMPLES}: libeasel.a
 	@BASENAME=`echo $@ | sed -e 's/_example[0-9]*//'| sed -e 's/^esl_//'` ;\
@@ -614,10 +614,10 @@
            else DFILE=${srcdir}/esl_$${BASENAME}.c ;\
         fi ;\
 	if test ${V}; \
-	   then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
+	   then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
 	   else echo '    ' GEN $@ ;\
 	fi ;\
-	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
+	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
 
 
 
--- hmmer.orig/easel/miniapps/Makefile.in
+++ hmmer/easel/miniapps/Makefile.in
@@ -94,13 +94,13 @@
 check:  ${PROGS} easel
 
 easel:  % : %.c ../libeasel.a ${SUBCMDOBJS}
-	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${SUBCMDOBJS} ${LIBS}
+	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${SUBCMDOBJS} ${LIBS}
 
 ${PROGS}: % : %.c ../libeasel.a 
-	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${LIBS}
+	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${LIBS}
 
 ${SUBCMDOBJS}: %.o : %.c ../libeasel.a
-	${QUIET_CC}${CC} -I. -I.. -I${srcdir} -I${srcdir}/.. ${CFLAGS} ${PTHREAD_CFLAGS} ${SIMD_CFLAGS} ${DEFS} -c $<
+	${QUIET_CC}${CC} -I. -I.. -I${srcdir} -I${srcdir}/.. ${CFLAGS} ${PTHREAD_CFLAGS} ${SIMD_CFLAGS} ${CPPFLAGS} ${DEFS} -c $<
 
 install: ${PROGS} 
 	${INSTALL} -m 0755 easel ${DESTDIR}${bindir}/
--- hmmer.orig/profmark/Makefile.in
+++ hmmer/profmark/Makefile.in
@@ -43,12 +43,12 @@
 dev:    ${PROGS}
 
 ${PROGS}: % : %.o ../${ESLDIR}/libeasel.a ../src/libhmmer.a 
-	${QUIET_GEN}${CC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L../${ESLDIR} -L../src -o $@ $@.o ${LIBS}
+	${QUIET_GEN}${CC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -L../${ESLDIR} -L../src -o $@ $@.o ${LIBS}
 
 ${PROGOBJS}: ../src/hmmer.h ../src/p7_config.h
 
 .c.o: 
-	${QUIET_CC}${CC} ${ESLINC} ${SRCINC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} -o $@ -c $<		
+	${QUIET_CC}${CC} ${ESLINC} ${SRCINC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${CPPFLAGS} ${DEFS} -o $@ -c $<		
 
 clean:
 	-rm -f *.o *~ ${PROGS} 
--- hmmer.orig/src/Makefile.in
+++ hmmer/src/Makefile.in
@@ -270,13 +270,13 @@
 ${AUXPROGOBJS}: ${HDRS} p7_config.h
 
 ${PROGS} ${AUXPROGS}: % : %.o  libhmmer.a ../${ESLDIR}/libeasel.a 
-	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${MPILIBS} ${LIBS}
+	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${MPILIBS} ${LIBS}
 
 .c.o:
 	${QUIET_CC}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${CPPFLAGS} ${MYINCDIRS} -o $@ -c $<
 
 ${ITESTS}: % : %.o libhmmer.a ${HDRS} p7_config.h
-	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${MPILIBS} ${LIBS}
+	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${MPILIBS} ${LIBS}
 
 ${UTESTS}: libhmmer.a  ${HDRS} p7_config.h
 	@BASENAME=`echo $@ | sed -e 's/_utest//' | sed -e 's/^p7_//'` ;\
