diff options
Diffstat (limited to 'sci-biology/mafft/files/mafft-7.037-respect.patch')
| -rw-r--r-- | sci-biology/mafft/files/mafft-7.037-respect.patch | 217 |
1 files changed, 217 insertions, 0 deletions
diff --git a/sci-biology/mafft/files/mafft-7.037-respect.patch b/sci-biology/mafft/files/mafft-7.037-respect.patch new file mode 100644 index 000000000000..6fba7153622d --- /dev/null +++ b/sci-biology/mafft/files/mafft-7.037-respect.patch @@ -0,0 +1,217 @@ + core/Makefile | 100 +++++++++++++++++++++++++++++----------------------------- + 1 file changed, 50 insertions(+), 50 deletions(-) + +diff --git a/core/Makefile b/core/Makefile +index 9acebb3..3838a45 100644 +--- a/core/Makefile ++++ b/core/Makefile +@@ -145,151 +145,151 @@ mltaln.h : functions.h + touch mltaln.h + + version : version.c mltaln.h +- $(CC) -o $@ version.c $(MYCFLAGS) ++ $(CC) $(LDFLAGS) -o $@ version.c $(MYCFLAGS) + + tbfast : $(OBJTBFAST) +- $(CC) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS) + + addsingle : $(OBJADDSINGLE) +- $(CC) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS) + + tbfast2 : $(OBJTBFAST2) +- $(CC) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS) + + disttbfast : $(OBJDISTTBFAST) +- $(CC) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS) + + makedirectionlist : $(OBJMAKEDIRECTIONLIST) +- $(CC) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS) + + splittbfast : $(OBJSPLITTBFAST) +- $(CC) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS) + + splitfromaln : $(OBJSPLITFROMALN) +- $(CC) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS) + + splittbfast2 : $(OBJSPLITTBFAST2) +- $(CC) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS) + + dummy : $(OBJDUMMY) +- $(CC) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS) + + setcore : $(OBJSETCORE) +- $(CC) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS) + + countlen : $(OBJCOUNTLEN) +- $(CC) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS) + + seq2regtable : $(OBJSEQ2REGTABLE) +- $(CC) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS) + + regtable2seq : $(OBJREGTABLE2SEQ) +- $(CC) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS) + + setdirection : $(OBJSETDIRECTION) +- $(CC) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS) + + replaceu : $(OBJREPLACEU) +- $(CC) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS) + + restoreu : $(OBJRESTOREU) +- $(CC) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS) + + f2cl : $(OBJF2CL) +- $(CC) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS) + + mccaskillwrap : $(OBJMCCASKILLWRAP) +- $(CC) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS) + + contrafoldwrap : $(OBJCONTRAFOLDWRAP) +- $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS) + + pairlocalalign : $(OBJPAIRLOCALALIGN) +- $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS) + + pairash : $(OBJPAIRASH) +- $(CC) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS) + + rnatest : $(OBJRNATEST) +- $(CC) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS) + + pair2hat3s : $(OBJPAIR2HAT3S) +- $(CC) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS) + + multi2hat3s : $(OBJMULTI2HAT3S) +- $(CC) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS) + + getlag : $(OBJGETLAG) +- $(CC) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS) + + tditr : $(OBJTDITR) +- $(CC) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS) + + dvtditr : $(OBJDVTDITR) +- $(CC) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS) + + mafft-profile : $(OBJGALN) +- $(CC) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS) + + gapfill : $(OBJGAPFILL) +- $(CC) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS) + + dndfast4 : $(OBJDNDFAST4) +- $(CC) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS) + + dndfast5 : $(OBJDNDFAST5) +- $(CC) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS) + + dndfast6 : $(OBJDNDFAST6) +- $(CC) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS) + + dndfast7 : $(OBJDNDFAST7) +- $(CC) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS) + + dndblast : $(OBJDNDBLAST) +- $(CC) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS) + + dndfast3 : $(OBJDNDFAST3) +- $(CC) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS) + + triplet : $(OBJTRIPLET) +- $(CC) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS) + + triplet3 : $(OBJTRIPLET3) +- $(CC) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS) + + sextet3 : $(OBJSEXTET3) +- $(CC) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS) + + sextet4 : $(OBJSEXTET4) +- $(CC) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS) + + sextet5 : $(OBJSEXTET5) +- $(CC) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS) + + mafft-distance : $(OBJDISTANCE) +- $(CC) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS) + + triplet5 : $(OBJTRIPLET5) +- $(CC) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS) + + triplet6 : $(OBJTRIPLET6) +- $(CC) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS) + + octet4 : $(OBJOCTET4) +- $(CC) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS) + + dndpre : $(OBJDNDPRE) +- $(CC) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS) + + dndpre2 : $(OBJDNDPRESCORE) +- $(CC) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS) + + score : $(OBJSCORE) +- $(CC) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS) + + genMtx : $(OBJGENMTX) +- $(CC) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS) + + gapfill.o : gapfill.c $(HEADER) + $(CC) $(MYCFLAGS) -c gapfill.c +@@ -525,7 +525,7 @@ install : all + chmod 755 $(SCRIPTS) + $(INSTALL) $(SCRIPTS) $(BINDIR) + chmod 755 $(PROGS) +- $(INSTALL) -s $(PROGS) $(LIBDIR) ++ $(INSTALL) $(PROGS) $(LIBDIR) + $(INSTALL) -m 644 $(MANPAGES) $(LIBDIR) + + ( cd $(BINDIR); \ |