diff --git a/squid/Makefile b/squid/Makefile index fafab4c..8c329b3 100644 --- a/squid/Makefile +++ b/squid/Makefile @@ -19,7 +19,6 @@ MANDIR = $(HOME)/man # On an Alliant, use fxc. # #CC = cc -CC = gcc #CC = fxc ## Any special compiler flags you want. @@ -37,7 +36,6 @@ CC = gcc # for instance. If the code builds cleanly but seg faults, try # rebuilding without optimization. # -CFLAGS = -O -m32 #CFLAGS = -g #CFLAGS = -TARG:exc_max -64 -Ofast=ip27 #specific SGI Origin200 compiler# @@ -47,8 +45,6 @@ CFLAGS = -O -m32 # Don't worry. The Makefile tests for ranlib existence and will work # fine on SGIs even if RANLIB is set. # -AR = ar rcv -RANLIB = ranlib ## Machine specific definitions # @@ -108,41 +104,41 @@ DIST = $(SRC) $(HDRS) $(READMES) Makefile all: $(LIBTARGET) alistat: $(OBJ) alistat_main.o - $(CC) $(CFLAGS) $(MDEFS) -o alistat $(OBJ) alistat_main.o $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o alistat $(OBJ) alistat_main.o $(LIBS) compalign: $(OBJ) compalign_main.o - $(CC) $(CFLAGS) $(MDEFS) -o compalign $(OBJ) compalign_main.o $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o compalign $(OBJ) compalign_main.o $(LIBS) compstruct: $(OBJ) compstruct_main.o - $(CC) $(CFLAGS) $(MDEFS) -o compstruct $(OBJ) compstruct_main.o $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o compstruct $(OBJ) compstruct_main.o $(LIBS) getseq: $(OBJ) getseq_main.o - $(CC) $(CFLAGS) $(MDEFS) -o getseq $(OBJ) getseq_main.o $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o getseq $(OBJ) getseq_main.o $(LIBS) reformat: $(OBJ) reformat_main.o - $(CC) $(CFLAGS) $(MDEFS) -o reformat $(OBJ) reformat_main.o $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o reformat $(OBJ) reformat_main.o $(LIBS) revcomp: $(OBJ) revcomp_main.o - $(CC) $(CFLAGS) $(MDEFS) -o revcomp $(OBJ) revcomp_main.o $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o revcomp $(OBJ) revcomp_main.o $(LIBS) seqstat: $(OBJ) seqstat_main.o - $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(OBJ) seqstat_main.o $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o seqstat $(OBJ) seqstat_main.o $(LIBS) seqsplit: $(OBJ) seqsplit_main.o - $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(OBJ) seqsplit_main.o $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o seqstat $(OBJ) seqsplit_main.o $(LIBS) shuffle: $(OBJ) shuffle_main.o - $(CC) $(CFLAGS) $(MDEFS) -o shuffle $(OBJ) shuffle_main.o $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o shuffle $(OBJ) shuffle_main.o $(LIBS) translate: $(OBJ) translate_main.o - $(CC) $(CFLAGS) $(MDEFS) -o translate $(OBJ) translate_main.o $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o translate $(OBJ) translate_main.o $(LIBS) weight: $(OBJ) weight_main.o - $(CC) $(CFLAGS) $(MDEFS) -o weight $(OBJ) weight_main.o $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o weight $(OBJ) weight_main.o $(LIBS) $(LIBTARGET): $(OBJ) - $(AR) $(LIBTARGET) $(OBJ) + $(AR) rcv $(LIBTARGET) $(OBJ) -if test -x /bin/ranlib; then /bin/ranlib $(LIBTARGET); else exit 0; fi -if test -x /usr/bin/ranlib; then /usr/bin/ranlib $(LIBTARGET); else exit 0; fi -if test -x $(RANLIB); then $(RANLIB) $(LIBTARGET); else exit 0; fi @@ -182,4 +178,4 @@ tags: etags -t $(SRC) $(HDRS) .c.o: - $(CC) $(CFLAGS) $(MDEFS) -c $< + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -c $< diff --git a/squid02/Makefile b/squid02/Makefile index d32240f..757e0dd 100644 --- a/squid02/Makefile +++ b/squid02/Makefile @@ -27,8 +27,6 @@ SCRIPTDIR = ${exec_prefix}/bin ## your compiler and compiler flags # -CC = gcc -CFLAGS = -g -O2 -m32 ## other defined flags for machine-specific stuff # @@ -37,8 +35,6 @@ LIBS = -lm ## Archiver command # -AR = ar rcv -RANLIB = ranlib ## instructions for installing man pages # @@ -158,10 +154,10 @@ OBJS = a2m.o\ all: version.h $(PROGS) libsquid.a $(PROGS): %: %_main.o version.h $(OBJS) - $(CC) $(CFLAGS) $(MDEFS) $(PVMLIBDIR) -o $@ $@_main.o $(OBJS) $(PVMLIBS) $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) $(PVMLIBDIR) -o $@ $@_main.o $(OBJS) $(PVMLIBS) $(LIBS) .c.o: - $(CC) $(CFLAGS) $(PVMFLAG) $(PVMINCDIR) $(MDEFS) -c $< + $(CC) $(CFLAGS) $(CPPFLAGS) $(PVMFLAG) $(PVMINCDIR) $(MDEFS) -c $< ################################################################ @@ -172,7 +168,7 @@ $(PROGS): %: %_main.o version.h $(OBJS) module: libsquid.a libsquid.a: version.h $(OBJS) - $(AR) libsquid.a $(OBJS) + $(AR) rcv libsquid.a $(OBJS) $(RANLIB) libsquid.a chmod 644 libsquid.a ################################################################# diff --git a/src/Makefile b/src/Makefile index d93182b..35c8b3d 100644 --- a/src/Makefile +++ b/src/Makefile @@ -21,7 +21,6 @@ SQUIDDIR02 = ../squid02 SQUIDSRCDIR02 = ../squid02 ## your compiler -CC = gcc #CC = cc ## any special compiler flags you want @@ -30,7 +29,6 @@ CC = gcc #CFLAGS = -g -Wall -pedantic #CFLAGS = -TARG:exc_max #CFLAGS = -g -fullwarn -wlint,-fviah -CFLAGS = -O -m32 #CFLAGS = -p # profiling # #CFLAGS = -64 -Ofast=ip27 #specific warhorse compiler# @@ -131,145 +129,145 @@ DEMOS = all: $(PROGS) main: $(OBJ) main.o - $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) cfgbuild: $(OBJ) cfgbuild.o - $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) eqrna: $(OBJ) eqrna.o - $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) eqrna_sample: $(OBJ) eqrna_sample.o - $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) shuffle: $(OBJ) shuffle.o - $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) rnamat_main: $(OBJ2) rnamat_main.o - $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS) main.o: ../src/main.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? cfgbuild.o: ../src/cfgbuild.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? eqrna.o: ../src/eqrna.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? eqrna_sample.o: ../src/eqrna_sample.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? shuffle.o: ../src/shuffle.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? rnamat_main.o: ../src/rnamat_main.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? cfgio.o: ../src/cfgio.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? cfgmodel.o: ../src/cfgmodel.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? cfgparse.o: ../src/cfgparse.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? codcreatealign.o: ../src/codcreatealign.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? coddp.o: ../src/coddp.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? coddpscanfast.o: ../src/coddpscanfast.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? codmodel.o: ../src/codmodel.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? codon.o: ../src/codon.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? codscorealign.o: ../src/codscorealign.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? er_math.o: ../src/er_math.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? er_vectop.o: ../src/er_vectop.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? evd.o: ../src/evd.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? evolcodmodel.o: ../src/evolcodmodel.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? evolemissions.o: ../src/evolemissions.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? evolmisc.o: ../src/evolmisc.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? evolnullmodel.o: ../src/evolnullmodel.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? evolothmodel.o: ../src/evolothmodel.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? evolqrnaversion.o: ../src/evolqrnaversion.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? evolscorewithmodels.o: ../src/evolscorewithmodels.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? evolscorewithmodelscanfast.o: ../src/evolscorewithmodelscanfast.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? evolriboprob.o: ../src/evolriboprob.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? evolrnadp.o: ../src/evolrnadp.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? evolrnadpscanfast.o: ../src/evolrnadpscanfast.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? evolrnamodel.o: ../src/evolrnamodel.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? evolrnascorealign.o: ../src/evolrnascorealign.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? evolve.o: ../src/evolve.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? globals.o: ../src/globals.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? hexamer.o: ../src/hexamer.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? matrix.o: ../src/matrix.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? misc.o: ../src/misc.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? nrnscfg.o: ../src/nrnscfg.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? nstack.o: ../src/nstack.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? nullmodel.o: ../src/nullmodel.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? othcreatealign.o: ../src/othcreatealign.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? othdp.o: ../src/othdp.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? othdpscanfast.o: ../src/othdpscanfast.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? othmodel.o: ../src/othmodel.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? othscorealign.o: ../src/othscorealign.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? posterior.o: ../src/posterior.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? qrnaversion.o: ../src/qrnaversion.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? riboprob.o: ../src/riboprob.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? rnacreatealign.o: ../src/rnacreatealign.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? rnadp.o: ../src/rnadp.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? rnadpscanfast.o: ../src/rnadpscanfast.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? rnaio.o: ../src/rnaio.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? rnamat.o: ../src/rnamat.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? rnamodel.o: ../src/rnamodel.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? rnaoutput.o: ../src/rnaoutput.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? rnascorealign.o: ../src/rnascorealign.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? rnascfg.o: ../src/rnascfg.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? rnascfgscanfast.o: ../src/rnascfgscanfast.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? scorewithmodels.o: ../src/scorewithmodels.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? scorewithmodelscanfast.o: ../src/scorewithmodelscanfast.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? seqio.o: ../src/seqio.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? trace.o: ../src/trace.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? traceSCFG.o: ../src/traceSCFG.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? tying.o: ../src/tying.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? install: $(PROGS) @@ -313,10 +311,10 @@ lint: /usr/lib/lint/llib-lm.ln .c.o: - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< .m.o: - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< + $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $<