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gentoo-ebuilds/sci-biology/qrna/files/qrna-2.0.4-ldflags.patch
Eli Schwartz c19c464def
sci-biology/qrna: add 2.0.4 
This is the 2006 edition of the software. It has a bunch of useful
fixes:
- it fixes Modern C porting issues
- it fixes LTO errors
- it incorporates the glibc-2.10 patch

just by upgrading! It's about time we upgrade, since it is 18 years
later.

Along the way we fix up the ebuild a bit:
- bump to EAPI 8
- acquire an actual SRC_URI, not just the gentoo mirror
- update the homepage along with the SRC_URI. The original homepage is
  dead, and the domain redirects to a new domain (whence comes the new
  distfile).

It has some shortcomings too:
- the distfile comes with free .svn directories, which have to be
  pruned.
- the distfile comes without the 80mb demos

To solve this, we use the old distfile (which I think only exists on
Gentoo's mirror network) and gate it behind a USE=examples flag, in case
anyone needs them.

Closes: https://bugs.gentoo.org/862285
Closes: https://bugs.gentoo.org/884283
Signed-off-by: Eli Schwartz <eschwartz93@gmail.com>
Signed-off-by: Sam James <sam@gentoo.org>
2024-03-21 05:57:37 +00:00

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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 $<
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