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jlec 13/04/29 10:05:59 |
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Added: mafft-7.037-respect.patch |
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Log: |
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sci-biology/mafft: Version Bump |
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(Portage version: 2.2.0_alpha173/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916) |
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|
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Revision Changes Path |
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1.1 sci-biology/mafft/files/mafft-7.037-respect.patch |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mafft/files/mafft-7.037-respect.patch?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mafft/files/mafft-7.037-respect.patch?rev=1.1&content-type=text/plain |
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Index: mafft-7.037-respect.patch |
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=================================================================== |
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core/Makefile | 100 +++++++++++++++++++++++++++++----------------------------- |
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1 file changed, 50 insertions(+), 50 deletions(-) |
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|
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diff --git a/core/Makefile b/core/Makefile |
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index 9acebb3..3838a45 100644 |
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--- a/core/Makefile |
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+++ b/core/Makefile |
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@@ -145,151 +145,151 @@ mltaln.h : functions.h |
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touch mltaln.h |
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|
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version : version.c mltaln.h |
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- $(CC) -o $@ version.c $(MYCFLAGS) |
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+ $(CC) $(LDFLAGS) -o $@ version.c $(MYCFLAGS) |
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|
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tbfast : $(OBJTBFAST) |
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- $(CC) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS) |
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|
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addsingle : $(OBJADDSINGLE) |
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- $(CC) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS) |
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|
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tbfast2 : $(OBJTBFAST2) |
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- $(CC) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS) |
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|
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disttbfast : $(OBJDISTTBFAST) |
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- $(CC) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS) |
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|
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makedirectionlist : $(OBJMAKEDIRECTIONLIST) |
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- $(CC) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS) |
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|
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splittbfast : $(OBJSPLITTBFAST) |
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- $(CC) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS) |
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|
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splitfromaln : $(OBJSPLITFROMALN) |
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- $(CC) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS) |
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|
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splittbfast2 : $(OBJSPLITTBFAST2) |
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- $(CC) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS) |
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|
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dummy : $(OBJDUMMY) |
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- $(CC) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS) |
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|
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setcore : $(OBJSETCORE) |
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- $(CC) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS) |
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|
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countlen : $(OBJCOUNTLEN) |
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- $(CC) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS) |
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|
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seq2regtable : $(OBJSEQ2REGTABLE) |
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- $(CC) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS) |
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|
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regtable2seq : $(OBJREGTABLE2SEQ) |
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- $(CC) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS) |
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|
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setdirection : $(OBJSETDIRECTION) |
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- $(CC) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS) |
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|
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replaceu : $(OBJREPLACEU) |
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- $(CC) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS) |
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|
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restoreu : $(OBJRESTOREU) |
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- $(CC) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS) |
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|
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f2cl : $(OBJF2CL) |
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- $(CC) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS) |
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|
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mccaskillwrap : $(OBJMCCASKILLWRAP) |
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- $(CC) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS) |
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|
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contrafoldwrap : $(OBJCONTRAFOLDWRAP) |
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- $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS) |
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|
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pairlocalalign : $(OBJPAIRLOCALALIGN) |
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- $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS) |
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|
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pairash : $(OBJPAIRASH) |
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- $(CC) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS) |
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|
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rnatest : $(OBJRNATEST) |
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- $(CC) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS) |
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|
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pair2hat3s : $(OBJPAIR2HAT3S) |
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- $(CC) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS) |
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|
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multi2hat3s : $(OBJMULTI2HAT3S) |
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- $(CC) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS) |
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|
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getlag : $(OBJGETLAG) |
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- $(CC) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS) |
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|
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tditr : $(OBJTDITR) |
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- $(CC) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS) |
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|
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dvtditr : $(OBJDVTDITR) |
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- $(CC) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS) |
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|
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mafft-profile : $(OBJGALN) |
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- $(CC) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS) |
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|
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gapfill : $(OBJGAPFILL) |
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- $(CC) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS) |
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|
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dndfast4 : $(OBJDNDFAST4) |
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- $(CC) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS) |
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|
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dndfast5 : $(OBJDNDFAST5) |
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- $(CC) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS) |
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|
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dndfast6 : $(OBJDNDFAST6) |
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- $(CC) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS) |
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|
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dndfast7 : $(OBJDNDFAST7) |
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- $(CC) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS) |
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|
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dndblast : $(OBJDNDBLAST) |
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- $(CC) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS) |
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|
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dndfast3 : $(OBJDNDFAST3) |
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- $(CC) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS) |
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|
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triplet : $(OBJTRIPLET) |
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- $(CC) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS) |
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|
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triplet3 : $(OBJTRIPLET3) |
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- $(CC) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS) |
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|
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sextet3 : $(OBJSEXTET3) |
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- $(CC) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS) |
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|
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sextet4 : $(OBJSEXTET4) |
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- $(CC) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS) |
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|
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sextet5 : $(OBJSEXTET5) |
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- $(CC) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS) |
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|
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mafft-distance : $(OBJDISTANCE) |
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- $(CC) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS) |
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|
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triplet5 : $(OBJTRIPLET5) |
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- $(CC) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS) |
| 197 |
+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS) |
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|
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triplet6 : $(OBJTRIPLET6) |
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- $(CC) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS) |
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+ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS) |
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|
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octet4 : $(OBJOCTET4) |
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- $(CC) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS) |
| 205 |
+ $(CC) $(LDFLAGS) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS) |
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|
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dndpre : $(OBJDNDPRE) |
| 208 |
- $(CC) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS) |
| 209 |
+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS) |
| 210 |
|
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dndpre2 : $(OBJDNDPRESCORE) |
| 212 |
- $(CC) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS) |
| 213 |
+ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS) |
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|
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score : $(OBJSCORE) |
| 216 |
- $(CC) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS) |
| 217 |
+ $(CC) $(LDFLAGS) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS) |
| 218 |
|
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genMtx : $(OBJGENMTX) |
| 220 |
- $(CC) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS) |
| 221 |
+ $(CC) $(LDFLAGS) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS) |
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|
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gapfill.o : gapfill.c $(HEADER) |
| 224 |
$(CC) $(MYCFLAGS) -c gapfill.c |
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@@ -525,7 +525,7 @@ install : all |
| 226 |
chmod 755 $(SCRIPTS) |
| 227 |
$(INSTALL) $(SCRIPTS) $(BINDIR) |
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chmod 755 $(PROGS) |
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- $(INSTALL) -s $(PROGS) $(LIBDIR) |
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+ $(INSTALL) $(PROGS) $(LIBDIR) |
| 231 |
$(INSTALL) -m 644 $(MANPAGES) $(LIBDIR) |
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|
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( cd $(BINDIR); \ |
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