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, 0 insertions, 217 deletions
diff --git a/sci-biology/mafft/files/mafft-7.037-respect.patch b/sci-biology/mafft/files/mafft-7.037-respect.patch deleted file mode 100644 index 6fba7153622d..000000000000 --- a/sci-biology/mafft/files/mafft-7.037-respect.patch +++ /dev/null @@ -1,217 +0,0 @@ - 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); \ |