diff options
author | David Seifert <soap@gentoo.org> | 2020-11-01 19:36:05 +0100 |
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committer | David Seifert <soap@gentoo.org> | 2020-11-01 19:36:05 +0100 |
commit | 083397d51c3f9bcbaf890477633ee33660e9155f (patch) | |
tree | d88d2cba27f2db74ab4c94135f4ce1ae4989d418 /sci-biology | |
parent | sci-biology/gmap: Remove old 2015.12.31.5 (diff) | |
download | gentoo-083397d51c3f9bcbaf890477633ee33660e9155f.tar.gz gentoo-083397d51c3f9bcbaf890477633ee33660e9155f.tar.bz2 gentoo-083397d51c3f9bcbaf890477633ee33660e9155f.zip |
sci-biology/embassy-phylipnew: Fix -fno-common
Closes: https://bugs.gentoo.org/706414
Package-Manager: Portage-3.0.8, Repoman-3.0.2
Signed-off-by: David Seifert <soap@gentoo.org>
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild | 7 | ||||
-rw-r--r-- | sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650-fno-common.patch | 627 |
2 files changed, 632 insertions, 2 deletions
diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild index 3ac088ed6ef9..c5ba6a540bfc 100644 --- a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild +++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -14,4 +14,7 @@ LICENSE+=" free-noncomm" KEYWORDS="~amd64 ~x86 ~x86-linux" S="${WORKDIR}/PHYLIPNEW-3.69.650" -PATCHES=( "${FILESDIR}"/${PN}-3.69.650_fix-build-system.patch ) +PATCHES=( + "${FILESDIR}"/${PN}-3.69.650_fix-build-system.patch + "${FILESDIR}"/${PN}-3.69.650-fno-common.patch +) diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650-fno-common.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650-fno-common.patch new file mode 100644 index 000000000000..448000547471 --- /dev/null +++ b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650-fno-common.patch @@ -0,0 +1,627 @@ +--- a/include/draw.h ++++ b/include/draw.h +@@ -116,19 +116,19 @@ + + + #ifndef X_DISPLAY_MISSING +-Display *display; /* the X display */ ++extern Display *display; /* the X display */ + extern Window mainwin; /* the main display window */ +-int x, y; /* the corner of the window */ +-unsigned int width, height; /* the width and height of the window */ ++extern int x, y; /* the corner of the window */ ++extern unsigned int width, height; /* the width and height of the window */ + #define FONT "-*-new century schoolbook-medium-r-*-*-14-*" +-char *fontrsc; /* the font resource */ +-XFontStruct *fontst; /* the font strcture for the font */ +-XGCValues gcv; /* graphics context values */ +-GC gc1; /* a graphics context */ +-XtAppContext appcontext; +-Widget toplevel; +-int nargc; +-char** nargv; ++extern char *fontrsc; /* the font resource */ ++extern XFontStruct *fontst; /* the font strcture for the font */ ++extern XGCValues gcv; /* graphics context values */ ++extern GC gc1; /* a graphics context */ ++extern XtAppContext appcontext; ++extern Widget toplevel; ++extern int nargc; ++extern char** nargv; + extern String res[16]; + + #define DEFGEOMETRY "600x400+20+50" +--- a/include/phylip.h ++++ b/include/phylip.h +@@ -349,7 +349,8 @@ + extern AjPFile embossancfile; + extern AjPFile embossmixfile; + extern AjPFile embossfactfile; +-extern long spp, words, bits; ++extern AjPPhyloState* phylostates; ++extern long spp, words, bits, outgrno; + extern boolean ibmpc, ansi, tranvsp; + extern naym *nayme; /* names of species */ + +--- a/src/clique.c ++++ b/src/clique.c +@@ -9,7 +9,6 @@ + + #define FormWide 80 /* width of outfile page */ + +-AjPPhyloState* phylostates; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phylofact = NULL; + AjPPhyloProp phyloweights = NULL; +@@ -72,10 +71,8 @@ + Char infilename[FNMLNGTH], ancfilename[FNMLNGTH], factfilename[FNMLNGTH], weightfilename[FNMLNGTH]; + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + +-long ActualChars, Cliqmin, outgrno, ++long ActualChars, Cliqmin, + col, ith, msets, setsz; + boolean ancvar, Clmin, Factors, outgropt, trout, weights, noroot, justwts, + printcomp, progress, treeprint, mulsets, firstset; +--- a/src/cons.c ++++ b/src/cons.c +@@ -6,7 +6,7 @@ + Char intreename[FNMLNGTH], intree2name[FNMLNGTH]; + node *root; + +-long numopts, outgrno, col, setsz; ++long numopts, col, setsz; + long maxgrp; /* max. no. of groups in all trees found */ + + boolean trout, firsttree, noroot, outgropt, didreroot, prntsets, +--- a/src/consense.c ++++ b/src/consense.c +@@ -19,8 +19,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + long trees_in; + +--- a/src/contml.c ++++ b/src/contml.c +@@ -69,10 +69,8 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + +-long nonodes2, loci, totalleles, df, outgrno, col, ++long nonodes2, loci, totalleles, df, col, + datasets, ith, njumble, jumb=0; + long inseed, inseed0; + long *alleles, *locus, *weight; +--- a/src/contrast.c ++++ b/src/contrast.c +@@ -40,7 +40,6 @@ + + + const char* outfilename; +-AjPFile embossoutfile; + + + +--- a/src/discboot.c ++++ b/src/discboot.c +@@ -56,7 +56,6 @@ + + + const char* outfilename; +-AjPFile embossoutfile; + + const char* outweightfilename; + AjPFile embossoutweightfile; +--- a/src/disc.c ++++ b/src/disc.c +@@ -1,7 +1,6 @@ + #include "phylip.h" + #include "disc.h" + +-AjPPhyloState* phylostates; + + /* version 3.6. (c) Copyright 1993-2002 by the University of Washington. + Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe. +--- a/src/discrete.c ++++ b/src/discrete.c +@@ -6,7 +6,7 @@ + Permission is granted to copy and use this program provided no fee is + charged for it and provided that this copyright notice is not removed. */ + +-long nonodes, endsite, outgrno, nextree, which; ++long nonodes, endsite, nextree, which; + boolean interleaved, printdata, outgropt, treeprint, dotdiff; + steptr weight, category, alias, location, ally; + sequence y, convtab; +--- a/src/dnacomp.c ++++ b/src/dnacomp.c +@@ -53,8 +53,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + node *root, *p; + long chars, col, ith, njumble, jumb, msets, numtrees; +--- a/src/dnadist.c ++++ b/src/dnadist.c +@@ -27,7 +27,6 @@ + + Char infilename[FNMLNGTH], catfilename[FNMLNGTH], weightfilename[FNMLNGTH]; + const char* outfilename; +-AjPFile embossoutfile; + + long sites, categs, weightsum, datasets, ith, rcategs; + boolean freqsfrom, jukes, kimura, logdet, gama, invar, similarity, lower, f84, +--- a/src/dnainvar.c ++++ b/src/dnainvar.c +@@ -51,7 +51,6 @@ + Char infilename[FNMLNGTH], weightfilename[FNMLNGTH]; + + const char* outfilename; +-AjPFile embossoutfile; + + long sites, msets, ith; + boolean weights, progress, prntpat, printinv, mulsets, firstset, justwts; +--- a/src/dnaml.c ++++ b/src/dnaml.c +@@ -93,12 +93,10 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + double *rate, *rrate, *probcat; + long nonodes2, sites, weightsum, categs, datasets, ith, njumble, jumb; +-long parens, outgrno; ++long parens; + boolean freqsfrom, global, jumble, weights, trout, usertree, + ctgry, rctgry, auto_, hypstate, ttr, progress, mulsets, justwts, + firstset, improve, smoothit, polishing, lngths, gama, invar,inserting=false; +--- a/src/dnamlk.c ++++ b/src/dnamlk.c +@@ -119,8 +119,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + double *rrate; + long sites, weightsum, categs, datasets, ith, njumble, jumb, numtrees, shimotrees; + /* sites = number of sites in actual sequences +--- a/src/dnamove.c ++++ b/src/dnamove.c +@@ -127,7 +127,6 @@ + node *root; + + const char* outtreename; +-AjPFile embossouttree; + + long chars, screenlines, col, treelines, leftedge, topedge, vmargin, + hscroll, vscroll, scrollinc, screenwidth, farthest, whichtree, othertree; +--- a/src/dnapenny.c ++++ b/src/dnapenny.c +@@ -47,8 +47,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + node *root, *p; + long *zeros=NULL; + long chars, howmany, howoften, col, msets, ith; +--- a/src/dollop.c ++++ b/src/dollop.c +@@ -10,7 +10,6 @@ + + #define maxtrees 100 /* maximum number of tied trees stored */ + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phyloweights = NULL; + AjPPhyloTree* phylotrees = NULL; +@@ -47,8 +46,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + + node *root; +--- a/src/dolmove.c ++++ b/src/dolmove.c +@@ -11,7 +11,6 @@ + #define overr 4 + #define which 1 + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phylofact = NULL; + AjPPhyloProp phyloweights = NULL; +@@ -73,10 +72,9 @@ + Char infilename[FNMLNGTH],intreename[FNMLNGTH], ancfilename[FNMLNGTH], factfilename[FNMLNGTH], weightfilename[FNMLNGTH]; + + const char* outtreename; +-AjPFile embossouttree; + + node *root; +-long outgrno, col, screenlines, screenwidth, scrollinc,treelines, ++long col, screenlines, screenwidth, scrollinc,treelines, + leftedge,topedge,vmargin,hscroll,vscroll,farthest; + /* outgrno indicates outgroup */ + boolean weights, thresh, ancvar, questions, dollo, factors, +--- a/src/dolpenny.c ++++ b/src/dolpenny.c +@@ -15,7 +15,6 @@ + typedef double *valptr; + typedef long *placeptr; + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phyloweights = NULL; + +@@ -40,8 +39,6 @@ + Char infilename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH]; + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + node *root; + long howmany, howoften, col, msets, ith; +--- a/src/draw.c ++++ b/src/draw.c +@@ -10,6 +10,20 @@ + #include "phylip.h" + #include "draw.h" + ++#ifndef X_DISPLAY_MISSING ++Display *display; ++int x, y; ++unsigned int width, height; ++char *fontrsc; ++XFontStruct *fontst; ++XGCValues gcv; ++GC gc1; ++XtAppContext appcontext; ++Widget toplevel; ++int nargc; ++char** nargv; ++#endif ++ + #ifdef QUICKC + struct videoconfig myscreen; + void setupgraphics(); +--- a/src/factor.c ++++ b/src/factor.c +@@ -54,7 +54,6 @@ + const char* outfactname; + const char* outancname; + AjPFile inputfile; +-AjPFile embossoutfile; + AjPFile embossoutfact; + AjPFile embossoutanc; + +--- a/src/fitch.c ++++ b/src/fitch.c +@@ -60,11 +60,9 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + Char infilename[FNMLNGTH], intreename[FNMLNGTH]; +-long nonodes2, outgrno, nums, col, datasets, ith, njumble, jumb=0, numtrees; ++long nonodes2, nums, col, datasets, ith, njumble, jumb=0, numtrees; + long inseed; + vector *x; + intvector *reps; +--- a/src/freqboot.c ++++ b/src/freqboot.c +@@ -52,7 +52,6 @@ + + + const char* outfilename; +-AjPFile embossoutfile; + + const char* outweightfilename; + AjPFile embossoutweightfile; +--- a/src/gendist.c ++++ b/src/gendist.c +@@ -24,7 +24,6 @@ + #endif + + const char* outfilename; +-AjPFile embossoutfile; + + long loci, totalleles, df, datasets, ith; + long nonodes; +--- a/src/kitsch.c ++++ b/src/kitsch.c +@@ -51,8 +51,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + + Char infilename[FNMLNGTH], intreename[FNMLNGTH]; +--- a/src/mix.c ++++ b/src/mix.c +@@ -13,7 +13,6 @@ + + typedef long *placeptr; + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloweights = NULL; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phylomix = NULL; +@@ -52,11 +51,9 @@ + Char infilename[FNMLNGTH], intreename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH], mixfilename[FNMLNGTH]; + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + node2 *root; +-long outgrno, msets, ith, njumble, jumb, numtrees; ++long msets, ith, njumble, jumb, numtrees; + /* outgrno indicates outgroup */ + long inseed, inseed0; + boolean jumble, usertree, weights, ancvar, questions, allsokal, +--- a/src/move.c ++++ b/src/move.c +@@ -13,7 +13,6 @@ + #define which 1 + + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloweights = NULL; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phylomix = NULL; +@@ -77,10 +76,9 @@ + + char infilename[FNMLNGTH],intreename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH], mixfilename[FNMLNGTH], factfilename[FNMLNGTH]; + const char* outtreename; +-AjPFile embossouttree; + + node *root; +-long outgrno, screenlines, col, treelines, leftedge, topedge, ++long screenlines, col, treelines, leftedge, topedge, + vmargin, hscroll, vscroll, scrollinc, screenwidth, farthest; + /* outgrno indicates outgroup */ + boolean weights, outgropt, ancvar, questions, allsokal, +--- a/src/neighbor.c ++++ b/src/neighbor.c +@@ -32,11 +32,9 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + Char infilename[FNMLNGTH]; +-long nonodes2, outgrno, col, datasets, ith; ++long nonodes2, col, datasets, ith; + long inseed; + vector *x; + intvector *reps; +--- a/src/pars.c ++++ b/src/pars.c +@@ -9,7 +9,6 @@ + + #define MAXNUMTREES 1000000 /* bigger than number of user trees can be */ + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloweights = NULL; + AjPPhyloTree* phylotrees = NULL; + +--- a/src/penny.c ++++ b/src/penny.c +@@ -12,7 +12,6 @@ + #define often 100 /* how often to notify how many trees examined */ + #define many 1000 /* how many multiples of howoften before stop */ + +-AjPPhyloState* phylostates = NULL; + AjPPhyloProp phyloweights = NULL; + AjPPhyloProp phyloanc = NULL; + AjPPhyloProp phylomix = NULL; +@@ -44,11 +43,9 @@ + Char infilename[FNMLNGTH], weightfilename[FNMLNGTH], ancfilename[FNMLNGTH], mixfilename[FNMLNGTH]; + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + node2 *root; +-long outgrno, rno, howmany, howoften, col, msets, ith; ++long rno, howmany, howoften, col, msets, ith; + /* outgrno indicates outgroup */ + + boolean weights, ancvar, questions, allsokal, allwagner, +--- a/src/phylip.c ++++ b/src/phylip.c +@@ -46,7 +46,8 @@ + AjPFile embossancfile; + AjPFile embossmixfile; + AjPFile embossfactfile; +-long spp, words, bits; ++AjPPhyloState* phylostates = NULL; ++long spp, words, bits, outgrno; + boolean ibmpc, ansi, tranvsp; + naym *nayme; /* names of species */ + +--- a/src/proml.c ++++ b/src/proml.c +@@ -89,8 +89,6 @@ + Char infilename[100], intreename[100], catfilename[100], weightfilename[100]; + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + double *rate, *rrate, *probcat; + long nonodes2, sites, weightsum, categs, +--- a/src/promlk.c ++++ b/src/promlk.c +@@ -88,8 +88,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + Char infilename[FNMLNGTH], intreename[FNMLNGTH], + catfilename[FNMLNGTH], weightfilename[FNMLNGTH]; +--- a/src/protdist.c ++++ b/src/protdist.c +@@ -79,7 +79,6 @@ + char infilename[100], catfilename[100], weightfilename[100]; + + const char* outfilename; +-AjPFile embossoutfile; + + + /* Local variables for makedists, propagated globally for c version: */ +--- a/src/protpars.c ++++ b/src/protpars.c +@@ -76,8 +76,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + node *root; + long chars, col, msets, ith, njumble, jumb, numtrees; +--- a/src/restboot.c ++++ b/src/restboot.c +@@ -54,7 +54,6 @@ + + + const char* outfilename; +-AjPFile embossoutfile; + + const char* outweightfilename; + AjPFile embossoutweightfile; +--- a/src/restdist.c ++++ b/src/restdist.c +@@ -13,7 +13,6 @@ + + extern sequence y; + +-AjPPhyloState* phylostates = NULL; + + + #ifndef OLDC +@@ -40,7 +39,6 @@ + Char infilename[FNMLNGTH]; + + const char* outfilename; +-AjPFile embossoutfile; + + long sites, weightsum, datasets, ith; + boolean restsites, neili, gama, weights, lower, +--- a/src/restml.c ++++ b/src/restml.c +@@ -17,7 +17,6 @@ + + AjPPhyloProp phyloweights = NULL; + AjPPhyloTree* phylotrees; +-AjPPhyloState* phylostates = NULL; + + #ifndef OLDC + /* function prototypes */ +@@ -101,8 +100,6 @@ + + const char* outfilename; + const char* outtreename; +-AjPFile embossoutfile; +-AjPFile embossouttree; + + + ajint numwts; +--- a/src/retree.c ++++ b/src/retree.c +@@ -123,7 +123,7 @@ + + node *root, *garbage; + +-long nonodes, outgrno, screenwidth, vscreenwidth, ++long nonodes, screenwidth, vscreenwidth, + screenlines, col, treenumber, leftedge, topedge, treelines, + hscroll, vscroll, scrollinc, whichtree, othertree, + numtrees, treesread; +@@ -145,7 +145,6 @@ + char intreename[FNMLNGTH]; + + const char* outtreename; +-AjPFile embossouttree; + + boolean subtree, written, readnext; + node *nuroot; +--- a/src/seqbootall.c ++++ b/src/seqbootall.c +@@ -109,7 +109,6 @@ + + + const char* outfilename; +-AjPFile embossoutfile; + + const char* outweightfilename; + AjPFile embossoutweightfile; +--- a/src/seqboot.c ++++ b/src/seqboot.c +@@ -92,7 +92,6 @@ + + + const char* outfilename; +-AjPFile embossoutfile; + + const char* outweightfilename; + AjPFile embossoutweightfile; +--- a/src/seq.c ++++ b/src/seq.c +@@ -7,7 +7,7 @@ + Permission is granted to copy and use this program provided no fee is + charged for it and provided that this copyright notice is not removed. */ + +-long nonodes, endsite, outgrno, nextree, which; ++long nonodes, endsite, nextree, which; + boolean interleaved, printdata, outgropt, treeprint, dotdiff, transvp; + steptr weight, category, alias, location, ally; + sequence y; +--- a/src/treedist.c ++++ b/src/treedist.c +@@ -16,7 +16,6 @@ + extern node *root; + + const char* outfilename; +-AjPFile embossoutfile; + + long trees_in_1, trees_in_2; + +--- a/src/treedistpair.c ++++ b/src/treedistpair.c +@@ -16,7 +16,6 @@ + extern node *root; + + const char* outfilename; +-AjPFile embossoutfile; + + long trees_in_1, trees_in_2; + |