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>

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 d03f650dd39e7929b999a42dab14981cff5ca0ec..17ca27e6da5a690cf8cd43d40174e6f5754abc01 100644 (file)
--- 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 5c580a24d2a30b8f170f88702b8cf795ce44db3b..34b59e9fb0a3fd31b01873314d44337b8312bb78 100644 (file)
--- 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