From d934827bf44b7cfcf6711964418148fa60877668 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Wed, 25 Nov 2020 22:39:15 +0000 Subject: gentoo resync : 25.11.2020 --- .../phylip/files/phylip-3.698-fno-common.patch | 70 ++++++ .../phylip/files/phylip-3.698-makefile.patch | 266 +++++++++++++++++++++ 2 files changed, 336 insertions(+) create mode 100644 sci-biology/phylip/files/phylip-3.698-fno-common.patch create mode 100644 sci-biology/phylip/files/phylip-3.698-makefile.patch (limited to 'sci-biology/phylip/files') diff --git a/sci-biology/phylip/files/phylip-3.698-fno-common.patch b/sci-biology/phylip/files/phylip-3.698-fno-common.patch new file mode 100644 index 000000000000..986b1d9650ab --- /dev/null +++ b/sci-biology/phylip/files/phylip-3.698-fno-common.patch @@ -0,0 +1,70 @@ +--- a/src/draw.c ++++ b/src/draw.c +@@ -34,6 +34,11 @@ + + char fontname[LARGE_BUF_LENGTH]; + ++long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar, ++ vrmlgroundcolornear, vrmlgroundcolorfar, vrmlplotcolor; ++ ++char afmfile[FNMLNGTH]; ++ + /* format of matrix: capheight, length[32],length[33],..length[256]*/ + + byte *full_pic ; +--- a/src/draw.h ++++ b/src/draw.h +@@ -52,10 +52,10 @@ + double intensity, x, y, z; + } vrmllighttype; + +-long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar, ++extern long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar, + vrmlgroundcolornear, vrmlgroundcolorfar, vrmlplotcolor; + +-char afmfile[FNMLNGTH]; ++extern char afmfile[FNMLNGTH]; + + double lengthtext(char *, long, char *, fonttype); + double heighttext(fonttype, char *); +--- a/src/drawtree.c ++++ b/src/drawtree.c +@@ -69,7 +69,7 @@ + uselengths, regular, rotate, empty, rescaled, + notfirst, improve, nbody, firstscreens, labelavoid; + boolean pictbold,pictitalic,pictshadow,pictoutline; +-boolean javarun; ++extern boolean javarun; + + striptype stripe; + plottertype plotter, oldplotter; +--- a/src/phylip.c ++++ b/src/phylip.c +@@ -34,6 +34,8 @@ + + #include "phylip.h" + ++boolean javarun; ++ + #ifdef WIN32 + #include + /* for console code (clear screen, text color settings) */ +--- a/src/phylip.h ++++ b/src/phylip.h +@@ -331,7 +331,7 @@ + /* Lower-triangular format. */ + #define MAT_LOWERTRI (MAT_LOWER | MAT_MACHINE) + +-boolean javarun; ++extern boolean javarun; + + typedef long *steptr; + typedef long longer[6]; +@@ -351,7 +351,6 @@ + extern long spp, words, bits; + extern boolean ibmpc, ansi, tranvsp; + extern naym *nayme; /* names of species */ +-boolean firstplotblock; // for debugging BMP output + + #define ebcdic EBCDIC + diff --git a/sci-biology/phylip/files/phylip-3.698-makefile.patch b/sci-biology/phylip/files/phylip-3.698-makefile.patch new file mode 100644 index 000000000000..f55ab98dd9cb --- /dev/null +++ b/sci-biology/phylip/files/phylip-3.698-makefile.patch @@ -0,0 +1,266 @@ +--- a/src/Makefile.unx ++++ b/src/Makefile.unx +@@ -81,7 +81,6 @@ + #CC = cc + # + # To use GCC instead: +-CC = gcc + # + # ---------------------------------------------------------------------------- + # +@@ -91,7 +90,6 @@ + # + # + #A minimal one +-CFLAGS = + # + # A basic one for debugging + #CFLAGS = -g +@@ -220,7 +218,7 @@ + @echo "Done." + @echo "" + +-put: ++put: all + @echo "Installing PHYLIP v3.6 binaries in $(EXEDIR)" + @mkdir -p $(EXEDIR) + @cp $(PROGS) $(EXEDIR) +@@ -270,195 +268,195 @@ + clique.o: clique.c disc.h phylip.h + + clique: clique.o disc.o phylip.o +- $(CC) $(CFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique ++ $(CC) $(LDFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique + + cons.o: cons.c cons.h phylip.h + + consense.o: consense.c cons.h phylip.h + + consense: consense.o phylip.o cons.o +- $(CC) $(CFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense ++ $(CC) $(LDFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense + + contml.o: contml.c cont.h phylip.h + + contml: contml.o cont.o phylip.o +- $(CC) $(CFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml ++ $(CC) $(LDFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml + + contrast.o: contrast.c cont.h phylip.h + + contrast: contrast.o cont.o phylip.o +- $(CC) $(CFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast ++ $(CC) $(LDFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast + + dnacomp.o: dnacomp.c seq.h phylip.h + + dnacomp: dnacomp.o seq.o phylip.o +- $(CC) $(CFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp ++ $(CC) $(LDFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp + + dnadist.o: dnadist.c seq.h phylip.h + + dnadist: dnadist.o seq.o phylip.o +- $(CC) $(CFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist ++ $(CC) $(LDFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist + + dnainvar.o: dnainvar.c seq.h phylip.h + + dnainvar: dnainvar.o seq.o phylip.o +- $(CC) $(CFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar ++ $(CC) $(LDFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar + + dnaml.o: dnaml.c seq.h phylip.h + + dnaml: dnaml.o seq.o phylip.o +- $(CC) $(CFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml ++ $(CC) $(LDFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml + + dnamlk.o: dnamlk.c seq.h phylip.h mlclock.h printree.h + + dnamlk: dnamlk.o seq.o phylip.o mlclock.o printree.o +- $(CC) $(CFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk ++ $(CC) $(LDFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk + + dnamove.o: dnamove.c seq.h moves.h phylip.h + + dnamove: dnamove.o seq.o moves.o phylip.o +- $(CC) $(CFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove ++ $(CC) $(LDFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove + + dnapenny.o: dnapenny.c seq.h phylip.h + + dnapenny: dnapenny.o seq.o phylip.o +- $(CC) $(CFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny ++ $(CC) $(LDFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny + + dnapars.o: dnapars.c seq.h phylip.h + + dnapars: dnapars.o seq.o phylip.o +- $(CC) $(CFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars ++ $(CC) $(LDFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars + + dolmove.o: dolmove.c disc.h moves.h dollo.h phylip.h + + dolmove: dolmove.o disc.o moves.o dollo.o phylip.o +- $(CC) $(CFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove ++ $(CC) $(LDFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove + + dollop.o: dollop.c disc.h dollo.h phylip.h + + dollop: dollop.o disc.o dollo.o phylip.o +- $(CC) $(CFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop ++ $(CC) $(LDFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop + + dolpenny.o: dolpenny.c disc.h dollo.h phylip.h + + dolpenny: dolpenny.o disc.o dollo.o phylip.o +- $(CC) $(CFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny ++ $(CC) $(LDFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny + + draw.o: draw.c draw.h phylip.h +- $(CC) $(DFLAGS) -c draw.c ++ $(CC) $(DFLAGS) $(CPPFLAGS) -c draw.c + + draw2.o: draw2.c draw.h phylip.h +- $(CC) $(DFLAGS) -c draw2.c ++ $(CC) $(DFLAGS) $(CPPFLAGS) -c draw2.c + + drawgram.o: drawgram.c draw.h phylip.h +- $(CC) $(DFLAGS) -c drawgram.c ++ $(CC) $(DFLAGS) $(CPPFLAGS) -c drawgram.c + + drawgram: drawgram.o draw.o draw2.o phylip.o +- $(CC) $(DFLAGS) draw.o draw2.o drawgram.o phylip.o $(DLIBS) -o drawgram ++ $(CC) $(LDFLAGS) draw.o draw2.o drawgram.o phylip.o $(DLIBS) -o drawgram + + # needed by java +-libdrawgram.so: drawgram.o draw.o draw2.o phylip.o +- $(CC) $(CFLAGS) -o libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS) ++libdrawgram.so: ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o libdrawgram.so -Wl,-soname,libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS) + + drawtree.o: drawtree.c draw.h phylip.h +- $(CC) $(DFLAGS) -shared -fPIC -c drawtree.c ++ $(CC) $(DFLAGS) $(CPPFLAGS) -c drawtree.c + + drawtree: drawtree.o draw.o draw2.o phylip.o +- $(CC) $(DFLAGS) draw.o draw2.o drawtree.o phylip.o $(DLIBS) -o drawtree ++ $(CC) $(LDFLAGS) draw.o draw2.o drawtree.o phylip.o $(DLIBS) -o drawtree + + # needed by java +-libdrawtree.so: drawtree.o draw.o draw2.o phylip.o +- $(CC) $(CFLAGS) -o libdrawtree.so -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS) ++libdrawtree.so: ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o libdrawtree.so -Wl,-soname,libdrawtree.so -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS) + + factor.o: factor.c phylip.h + + factor: factor.o phylip.o +- $(CC) $(CFLAGS) factor.o phylip.o $(LIBS) -o factor ++ $(CC) $(LDFLAGS) factor.o phylip.o $(LIBS) -o factor + + fitch.o: fitch.c dist.h phylip.h + + fitch: fitch.o dist.o phylip.o +- $(CC) $(CFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch ++ $(CC) $(LDFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch + + gendist.o: gendist.c phylip.h + + gendist: gendist.o phylip.o +- $(CC) $(CFLAGS) gendist.o phylip.o $(LIBS) -o gendist ++ $(CC) $(LDFLAGS) gendist.o phylip.o $(LIBS) -o gendist + + kitsch.o: kitsch.c dist.h phylip.h + + kitsch: kitsch.o dist.o phylip.o +- $(CC) $(CFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch ++ $(CC) $(LDFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch + + mix.o: mix.c disc.h wagner.h phylip.h + + mix: mix.o disc.o wagner.o phylip.o +- $(CC) $(CFLAGS) mix.o disc.o wagner.o phylip.o $(LIBS) -o mix ++ $(CC) $(LDFLAGS) mix.o disc.o wagner.o phylip.o $(LIBS) -o mix + + move.o: move.c disc.h moves.h wagner.h phylip.h + + move: move.o disc.o moves.o wagner.o phylip.o +- $(CC) $(CFLAGS) move.o disc.o moves.o wagner.o phylip.o $(LIBS) -o move ++ $(CC) $(LDFLAGS) move.o disc.o moves.o wagner.o phylip.o $(LIBS) -o move + + neighbor.o: neighbor.c dist.h phylip.h + + neighbor: neighbor.o dist.o phylip.o +- $(CC) $(CFLAGS) neighbor.o dist.o phylip.o $(LIBS) -o neighbor ++ $(CC) $(LDFLAGS) neighbor.o dist.o phylip.o $(LIBS) -o neighbor + + pars.o: pars.c discrete.h phylip.h + + pars: pars.o discrete.o phylip.o +- $(CC) $(CFLAGS) pars.o discrete.o phylip.o $(LIBS) -o pars ++ $(CC) $(LDFLAGS) pars.o discrete.o phylip.o $(LIBS) -o pars + + penny.o: penny.c disc.h wagner.h phylip.h + + penny: penny.o disc.o wagner.o phylip.o +- $(CC) $(CFLAGS) penny.o disc.o wagner.o phylip.o $(LIBS) -o penny ++ $(CC) $(LDFLAGS) penny.o disc.o wagner.o phylip.o $(LIBS) -o penny + + proml.o: proml.c seq.h phylip.h + + proml: proml.o seq.o phylip.o +- $(CC) $(CFLAGS) proml.o seq.o phylip.o $(LIBS) -o proml ++ $(CC) $(LDFLAGS) proml.o seq.o phylip.o $(LIBS) -o proml + + promlk.o: promlk.c seq.h phylip.h mlclock.h printree.h + + promlk: promlk.o seq.o phylip.o mlclock.o printree.o +- $(CC) $(CFLAGS) promlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o promlk ++ $(CC) $(LDFLAGS) promlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o promlk + + protdist.o: protdist.c seq.h phylip.h + + protdist: protdist.o seq.o phylip.o +- $(CC) $(CFLAGS) protdist.o seq.o phylip.o $(LIBS) -o protdist ++ $(CC) $(LDFLAGS) protdist.o seq.o phylip.o $(LIBS) -o protdist + + protpars.o: protpars.c seq.h phylip.h + + protpars: protpars.o seq.o phylip.o +- $(CC) $(CFLAGS) protpars.o seq.o phylip.o $(LIBS) -o protpars ++ $(CC) $(LDFLAGS) protpars.o seq.o phylip.o $(LIBS) -o protpars + + restdist.o: restdist.c seq.h phylip.h + + restdist: restdist.o seq.o phylip.o +- $(CC) $(CFLAGS) restdist.o seq.o phylip.o $(LIBS) -o restdist ++ $(CC) $(LDFLAGS) restdist.o seq.o phylip.o $(LIBS) -o restdist + + restml.o: restml.c seq.h phylip.h + + restml: restml.o seq.o phylip.o +- $(CC) $(CFLAGS) restml.o seq.o phylip.o $(LIBS) -o restml ++ $(CC) $(LDFLAGS) restml.o seq.o phylip.o $(LIBS) -o restml + + retree.o: retree.c moves.h phylip.h + + retree: retree.o moves.o phylip.o +- $(CC) $(CFLAGS) retree.o moves.o phylip.o $(LIBS) -o retree ++ $(CC) $(LDFLAGS) retree.o moves.o phylip.o $(LIBS) -o retree + + seqboot.o: seqboot.c phylip.h + + seqboot: seqboot.o seq.o phylip.o +- $(CC) $(CFLAGS) seqboot.o seq.o phylip.o $(LIBS) -o seqboot ++ $(CC) $(LDFLAGS) seqboot.o seq.o phylip.o $(LIBS) -o seqboot + + treedist.o: treedist.c cons.h phylip.h + + treedist: treedist.o phylip.o cons.o +- $(CC) $(CFLAGS) treedist.o cons.o phylip.o $(LIBS) -o treedist ++ $(CC) $(LDFLAGS) treedist.o cons.o phylip.o $(LIBS) -o treedist + + + # 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