Version BUmp, keyworded for prefix, repecting multilib and LDFLAGS

(Portage version: 2.2_rc67/cvs/Linux x86_64)

1 files changed, 192 insertions, 0 deletions

diff --git a/sci-biology/mafft/files/6.811-respect.patch b/sci-biology/mafft/files/6.811-respect.patch
new file mode 100644
index 000000000000..ebfb2c7be7b8
--- /dev/null
+++ b/sci-biology/mafft/files/6.811-respect.patch
@@ -0,0 +1,192 @@
+diff --git a/core/Makefile b/core/Makefile
+index 8bb8baf..cf28559 100644
+--- a/core/Makefile
++++ b/core/Makefile
+@@ -1,5 +1,5 @@
+ PREFIX = /usr/local
+-LIBDIR = $(PREFIX)/lib/mafft
++LIBDIR = $(PREFIX)/GENTOOLIBDIR/mafft
+ BINDIR = $(PREFIX)/bin
+ MANDIR = $(PREFIX)/man/man1
+ 
+@@ -127,136 +127,136 @@ mltaln.h : functions.h
+ 	touch mltaln.h
+ 
+ ord : $(OBJORD)
+-	$(CC) -o $@ $(OBJORD) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJORD) $(CFLAGS) $(LIBS)
+ 
+ tbfast : $(OBJTBFAST)
+-	$(CC) -o $@ $(OBJTBFAST) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTBFAST) $(CFLAGS) $(LIBS)
+ 
+ tbfast2 : $(OBJTBFAST2)
+-	$(CC) -o $@ $(OBJTBFAST2) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTBFAST2) $(CFLAGS) $(LIBS)
+ 
+ disttbfast : $(OBJDISTTBFAST)
+-	$(CC) -o $@ $(OBJDISTTBFAST) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDISTTBFAST) $(CFLAGS) $(LIBS)
+ 
+ splittbfast : $(OBJSPLITTBFAST)
+-	$(CC) -o $@ $(OBJSPLITTBFAST) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST) $(CFLAGS) $(LIBS)
+ 
+ splitfromaln : $(OBJSPLITFROMALN)
+-	$(CC) -o $@ $(OBJSPLITFROMALN) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSPLITFROMALN) $(CFLAGS) $(LIBS)
+ 
+ splittbfast2 : $(OBJSPLITTBFAST2)
+-	$(CC) -o $@ $(OBJSPLITTBFAST2) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST2) $(CFLAGS) $(LIBS)
+ 
+ dummy : $(OBJDUMMY)
+-	$(CC) -o $@ $(OBJDUMMY) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDUMMY) $(CFLAGS) $(LIBS)
+ 
+ setcore : $(OBJSETCORE)
+-	$(CC) -o $@ $(OBJSETCORE) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSETCORE) $(CFLAGS) $(LIBS)
+ 
+ countlen : $(OBJCOUNTLEN)
+-	$(CC) -o $@ $(OBJCOUNTLEN) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJCOUNTLEN) $(CFLAGS) $(LIBS)
+ 
+ seq2regtable : $(OBJSEQ2REGTABLE)
+-	$(CC) -o $@ $(OBJSEQ2REGTABLE) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSEQ2REGTABLE) $(CFLAGS) $(LIBS)
+ 
+ regtable2seq : $(OBJREGTABLE2SEQ)
+-	$(CC) -o $@ $(OBJREGTABLE2SEQ) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJREGTABLE2SEQ) $(CFLAGS) $(LIBS)
+ 
+ f2cl : $(OBJF2CL)
+-	$(CC) -o $@ $(OBJF2CL) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJF2CL) $(CFLAGS) $(LIBS)
+ 
+ mccaskillwrap : $(OBJMCCASKILLWRAP)
+-	$(CC) -o $@ $(OBJMCCASKILLWRAP) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJMCCASKILLWRAP) $(CFLAGS) $(LIBS)
+ 
+ contrafoldwrap : $(OBJCONTRAFOLDWRAP)
+-	$(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJCONTRAFOLDWRAP) $(CFLAGS) $(LIBS)
+ 
+ pairlocalalign : $(OBJPAIRLOCALALIGN)
+-	$(CC) -o $@ $(OBJPAIRLOCALALIGN) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJPAIRLOCALALIGN) $(CFLAGS) $(LIBS)
+ 
+ pairash : $(OBJPAIRASH)
+-	$(CC) -o $@ $(OBJPAIRASH) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJPAIRASH) $(CFLAGS) $(LIBS)
+ 
+ rnatest : $(OBJRNATEST)
+-	$(CC) -o $@ $(OBJRNATEST) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJRNATEST) $(CFLAGS) $(LIBS)
+ 
+ pair2hat3s : $(OBJPAIR2HAT3S)
+-	$(CC) -o $@ $(OBJPAIR2HAT3S) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJPAIR2HAT3S) $(CFLAGS) $(LIBS)
+ 
+ multi2hat3s : $(OBJMULTI2HAT3S)
+-	$(CC) -o $@ $(OBJMULTI2HAT3S) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJMULTI2HAT3S) $(CFLAGS) $(LIBS)
+ 
+ getlag : $(OBJGETLAG)
+-	$(CC) -o $@ $(OBJGETLAG) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJGETLAG) $(CFLAGS) $(LIBS)
+ 
+ tditr : $(OBJTDITR)
+-	$(CC) -o $@ $(OBJTDITR) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTDITR) $(CFLAGS) $(LIBS)
+ 
+ dvtditr : $(OBJDVTDITR)
+-	$(CC) -o $@ $(OBJDVTDITR) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDVTDITR) $(CFLAGS) $(LIBS)
+ 
+ mafft-profile : $(OBJGALN)
+-	$(CC) -o $@ $(OBJGALN) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJGALN) $(CFLAGS) $(LIBS)
+ 
+ gapfill : $(OBJGAPFILL)
+-	$(CC) -o $@ $(OBJGAPFILL) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJGAPFILL) $(CFLAGS) $(LIBS)
+ 
+ dndfast4 : $(OBJDNDFAST4)
+-	$(CC) -o $@ $(OBJDNDFAST4) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST4) $(CFLAGS) $(LIBS)
+ 
+ dndfast5 : $(OBJDNDFAST5)
+-	$(CC) -o $@ $(OBJDNDFAST5) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST5) $(CFLAGS) $(LIBS)
+ 
+ dndfast6 : $(OBJDNDFAST6)
+-	$(CC) -o $@ $(OBJDNDFAST6) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST6) $(CFLAGS) $(LIBS)
+ 
+ dndfast7 : $(OBJDNDFAST7)
+-	$(CC) -o $@ $(OBJDNDFAST7) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST7) $(CFLAGS) $(LIBS)
+ 
+ dndblast : $(OBJDNDBLAST)
+-	$(CC) -o $@ $(OBJDNDBLAST) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDBLAST) $(CFLAGS) $(LIBS)
+ 
+ dndfast3 : $(OBJDNDFAST3)
+-	$(CC) -o $@ $(OBJDNDFAST3) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST3) $(CFLAGS) $(LIBS)
+ 
+ triplet : $(OBJTRIPLET)
+-	$(CC) -o $@ $(OBJTRIPLET) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET) $(CFLAGS) $(LIBS)
+ 
+ triplet3 : $(OBJTRIPLET3)
+-	$(CC) -o $@ $(OBJTRIPLET3) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET3) $(CFLAGS) $(LIBS)
+ 
+ sextet3 : $(OBJSEXTET3)
+-	$(CC) -o $@ $(OBJSEXTET3) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSEXTET3) $(CFLAGS) $(LIBS)
+ 
+ sextet4 : $(OBJSEXTET4)
+-	$(CC) -o $@ $(OBJSEXTET4) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSEXTET4) $(CFLAGS) $(LIBS)
+ 
+ sextet5 : $(OBJSEXTET5)
+-	$(CC) -o $@ $(OBJSEXTET5) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSEXTET5) $(CFLAGS) $(LIBS)
+ 
+ mafft-distance : $(OBJDISTANCE)
+-	$(CC) -o $@ $(OBJDISTANCE) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDISTANCE) $(CFLAGS) $(LIBS)
+ 
+ triplet5 : $(OBJTRIPLET5)
+-	$(CC) -o $@ $(OBJTRIPLET5) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET5) $(CFLAGS) $(LIBS)
+ 
+ triplet6 : $(OBJTRIPLET6)
+-	$(CC) -o $@ $(OBJTRIPLET6) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET6) $(CFLAGS) $(LIBS)
+ 
+ octet4 : $(OBJOCTET4)
+-	$(CC) -o $@ $(OBJOCTET4) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJOCTET4) $(CFLAGS) $(LIBS)
+ 
+ dndpre : $(OBJDNDPRE)
+-	$(CC) -o $@ $(OBJDNDPRE) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDPRE) $(CFLAGS) $(LIBS)
+ 
+ dndpre2 : $(OBJDNDPRESCORE)
+-	$(CC) -o $@ $(OBJDNDPRESCORE) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDPRESCORE) $(CFLAGS) $(LIBS)
+ 
+ score : $(OBJSCORE)
+-	$(CC) -o $@ $(OBJSCORE) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSCORE) $(CFLAGS) $(LIBS)
+ 
+ genMtx : $(OBJGENMTX)
+-	$(CC) -o $@ $(OBJGENMTX) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJGENMTX) $(CFLAGS) $(LIBS)
+ 
+ gapfill.o : gapfill.c $(HEADER)
+ 	$(CC) $(CFLAGS) -c gapfill.c