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authorDavid Seifert <soap@gentoo.org>2020-02-23 12:51:59 +0100
committerDavid Seifert <soap@gentoo.org>2020-02-23 12:51:59 +0100
commitb24fab79ca7863993080b5fafd4ce414ff132c73 (patch)
tree5d33ed177382a54c8eb7d2b71e4daffd924efb04 /sci-biology
parentmedia-gfx/krita: Drop 4.2.7.1-r1 (diff)
downloadgentoo-b24fab79ca7863993080b5fafd4ce414ff132c73.tar.gz
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sci-biology/qrna: Port to EAPI 7
Closes: https://bugs.gentoo.org/710554 Package-Manager: Portage-2.3.89, Repoman-2.3.20 Signed-off-by: David Seifert <soap@gentoo.org>
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch357
-rw-r--r--sci-biology/qrna/qrna-2.0.3c-r3.ebuild15
2 files changed, 358 insertions, 14 deletions
diff --git a/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch
index d03f650dd39..17ca27e6da5 100644
--- a/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch
+++ b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch
@@ -1,13 +1,156 @@
-diff --git a/src/Makefile b/src/Makefile
-index 1d1631b..4fa3af9 100644
+--- a/squid/Makefile
++++ b/squid/Makefile
+@@ -19,7 +19,6 @@
+ # On an Alliant, use fxc.
+ #
+ #CC = cc
+-CC = gcc
+ #CC = fxc
+
+ ## Any special compiler flags you want.
+@@ -37,7 +36,6 @@
+ # for instance. If the code builds cleanly but seg faults, try
+ # rebuilding without optimization.
+ #
+-CFLAGS = -O
+ #CFLAGS = -g
+ #CFLAGS = -TARG:exc_max -64 -Ofast=ip27 #specific SGI Origin200 compiler#
+
+@@ -47,8 +45,6 @@
+ # 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 @@
+ 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 @@
+ etags -t $(SRC) $(HDRS)
+
+ .c.o:
+- $(CC) $(CFLAGS) $(MDEFS) -c $<
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -c $<
+--- a/squid02/Makefile
++++ b/squid02/Makefile
+@@ -27,8 +27,6 @@
+
+ ## your compiler and compiler flags
+ #
+-CC = gcc
+-CFLAGS = -g -O2
+
+ ## other defined flags for machine-specific stuff
+ #
+@@ -37,8 +35,6 @@
+
+ ## Archiver command
+ #
+-AR = ar rcv
+-RANLIB = ranlib
+
+ ## instructions for installing man pages
+ #
+@@ -158,10 +154,10 @@
+ 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 @@
+ module: libsquid.a
+
+ libsquid.a: version.h $(OBJS)
+- $(AR) libsquid.a $(OBJS)
++ $(AR) rcv libsquid.a $(OBJS)
+ $(RANLIB) libsquid.a
+ chmod 644 libsquid.a
+ #################################################################
--- a/src/Makefile
+++ b/src/Makefile
-@@ -131,17 +131,17 @@ DEMOS =
+@@ -21,7 +21,6 @@
+ SQUIDSRCDIR02 = ../squid02
+
+ ## your compiler
+-CC = gcc
+ #CC = cc
+
+ ## any special compiler flags you want
+@@ -30,7 +29,6 @@
+ #CFLAGS = -g -Wall -pedantic
+ #CFLAGS = -TARG:exc_max
+ #CFLAGS = -g -fullwarn -wlint,-fviah
+-CFLAGS = -O
+ #CFLAGS = -p # profiling #
+ #CFLAGS = -64 -Ofast=ip27 #specific warhorse compiler#
+
+@@ -131,145 +129,145 @@
all: $(PROGS)
main: $(OBJ) main.o
- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) -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)
@@ -25,4 +168,208 @@ index 1d1631b..4fa3af9 100644
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS)
main.o: ../src/main.c
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -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 @@
+ /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 $<
+
+
+
diff --git a/sci-biology/qrna/qrna-2.0.3c-r3.ebuild b/sci-biology/qrna/qrna-2.0.3c-r3.ebuild
index 5c580a24d2a..34b59e9fb0a 100644
--- a/sci-biology/qrna/qrna-2.0.3c-r3.ebuild
+++ b/sci-biology/qrna/qrna-2.0.3c-r3.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
inherit toolchain-funcs
@@ -12,7 +12,6 @@ SRC_URI="mirror://gentoo/${P}.tar.bz2"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE=""
RDEPEND="
dev-lang/perl
@@ -26,15 +25,13 @@ PATCHES=(
src_prepare() {
default
- sed \
- -e "s:^CC.*:CC = $(tc-getCC):" \
- -e "/^AR/s:ar:$(tc-getAR):g" \
- -e "/^RANLIB/s:ranlib:$(tc-getRANLIB):g" \
- -e "/CFLAGS/s:=.*$:= ${CFLAGS}:" \
- -i {src,squid,squid02}/Makefile || die
rm -v squid*/*.a || die
}
+src_configure() {
+ tc-export AR CC RANLIB
+}
+
src_compile() {
local d
for d in squid squid02 src; do