sci-biology/mafft/files/6.811-respect.patch

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