ALT Linux Sisyphus

diff -drup seaview.0/csrc/dnapars.c seaview.1/csrc/dnapars.c

--- seaview.0/csrc/dnapars.c	2019-12-05 14:33:14.000000000 +0100
+++ seaview.1/csrc/dnapars.c	2020-02-22 00:13:57.435533320 +0100
@@ -77,41 +77,41 @@ void   load_tree(long treei);
 /* function prototypes */
 
 
-Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename,
+static Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename,
      weightfilename[FNMLNGTH];
 char basechar[32]="ACMGRSVTWYHKDBNO???????????????";
-node *root;
-long chars, col, msets, ith, njumble, jumb, maxtrees;
+static node *root;
+static long chars, col, msets, ith, njumble, jumb, maxtrees;
 /*   chars = number of sites in actual sequences */
-long inseed, inseed0;
-double threshold;
-boolean jumble, usertree, thresh, weights, thorough, rearrfirst,
+//long inseed, inseed0;
+static double threshold;
+static boolean jumble, usertree, thresh, weights, thorough, rearrfirst,
           trout, progress, stepbox, ancseq, mulsets, justwts, firstset, mulf,
           multf;
-steptr oldweight;
-longer seed;
-pointarray treenode;            /* pointers to all nodes in tree */
-long *enterorder;
-long *zeros;
+static steptr oldweight;
+static longer seed;
+static pointarray treenode;            /* pointers to all nodes in tree */
+static long *enterorder;
+static long *zeros;
 
 /* local variables for Pascal maketree, propagated globally for C version: */
 
-long minwhich;
+static long minwhich;
 static double like, minsteps, bestyet, bestlike, bstlike2;
-boolean lastrearr, recompute;
-double nsteps[maxuser];
-long **fsteps;
-node *there, *oldnufork;
-long *place;
-bestelm *bestrees;
-long *threshwt;
-baseptr nothing;
-gbases *garbage;
-node *temp, *temp1, *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1,
+static boolean lastrearr, recompute;
+static double nsteps[maxuser];
+static long **fsteps;
+static node *there, *oldnufork;
+static long *place;
+static bestelm *bestrees;
+static long *threshwt;
+static baseptr nothing;
+static gbases *garbage;
+static node *temp, *temp1, *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1,
        *tmp2, *tmp3, *tmprm, *tmpadd;
-boolean *names;
-node *grbg;
-char *progname;
+static boolean *names;
+static node *grbg;
+static char *progname;
 
 
 static void getoptions(int arg_maxtrees, dnapars_S_option s_option)
diff -drup seaview.0/csrc/phylip.c seaview.1/csrc/phylip.c
--- seaview.0/csrc/phylip.c	2019-12-05 14:33:14.000000000 +0100
+++ seaview.1/csrc/phylip.c	2020-02-21 23:56:39.801177617 +0100
@@ -143,7 +143,7 @@ void init(int argc, char** argv)
   /* Set default terminal characteristics */
   ibmpc = IBMCRT;
   ansi = ANSICRT;
-  javarun = false;
+  //javarun = false;
 
   /* Clear the screen */
   cleerhome();
diff -drup seaview.0/csrc/phylip.h seaview.1/csrc/phylip.h
--- seaview.0/csrc/phylip.h	2019-12-05 14:33:14.000000000 +0100
+++ seaview.1/csrc/phylip.h	2020-02-21 23:57:42.782897666 +0100
@@ -342,7 +342,7 @@ MALLOCRETURN    *mymalloc(long);
 /* Lower-triangular format. */
 #define MAT_LOWERTRI    (MAT_LOWER | MAT_MACHINE)
 
-boolean javarun;
+//boolean javarun;
 
 typedef long *steptr;
 typedef long longer[6];
@@ -363,7 +363,7 @@ extern long spp, words, bits;
 extern boolean ibmpc, ansi, tranvsp;
 //extern naym *nayme;                     /* names of species */
 extern char* *nayme;                     /* names of species */
-boolean firstplotblock; // for debugging BMP output
+//boolean firstplotblock; // for debugging BMP output
 
 #define ebcdic          EBCDIC
 
diff -drup seaview.0/csrc/protpars.c seaview.1/csrc/protpars.c
--- seaview.0/csrc/protpars.c	2019-12-05 14:33:14.000000000 +0100
+++ seaview.1/csrc/protpars.c	2020-02-22 00:13:49.931328198 +0100
@@ -104,30 +104,30 @@ extern void awake_from_C(void);
 
 
 
-Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename, weightfilename[FNMLNGTH];
-node *root;
-long chars, col, msets, ith, njumble, jumb;
+static Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename, weightfilename[FNMLNGTH];
+static node *root;
+static long chars, col, msets, ith, njumble, jumb;
 /*   chars = number of sites in actual sequences */
-long inseed, inseed0;
-boolean jumble, usertree, weights, thresh, trout, progress, stepbox,
+static long inseed, inseed0;
+static boolean jumble, usertree, weights, thresh, trout, progress, stepbox,
     justwts, ancseq, mulsets, firstset;
-codetype whichcode;
-long fullset, fulldel;
-pointarray treenode;   /* pointers to all nodes in tree */
-double threshold;
-steptr threshwt;
-longer seed;
-long *enterorder;
+static codetype whichcode;
+static long fullset, fulldel;
+static pointarray treenode;   /* pointers to all nodes in tree */
+static double threshold;
+static steptr threshwt;
+static longer seed;
+static long *enterorder;
 sitearray translate[(long)quest - (long)ala + 1];
 aas trans[4][4][4];
-long **fsteps;
-bestelm *bestrees;
-boolean dummy;
-gseq *garbage;
-node *temp, *temp1;
-Char ch;
-aas tmpa;
-char *progname;
+static long **fsteps;
+static bestelm *bestrees;
+static boolean dummy;
+static gseq *garbage;
+static node *temp, *temp1;
+static Char ch;
+static aas tmpa;
+static char *progname;
 
 /* Local variables for maketree, propagated globally for c version: */
 long minwhich;
diff -drup seaview.0/Makefile seaview.1/Makefile
--- seaview.0/Makefile	2019-12-28 18:12:13.000000000 +0100
+++ seaview.1/Makefile	2020-02-21 23:42:03.294287605 +0100
@@ -1,6 +1,6 @@
 #For Debian compilation, uncomment the 2 lines below 
-#HELPFILE= -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\"
-#PHYMLNAME= -DPHYMLNAME=\"phyml\"
+HELPFILE= -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\"
+PHYMLNAME= -DPHYMLNAME=\"phyml\"
 
 
 #to compile with PDF (through PDFlib Lite) rather than PostScript output, 
@@ -30,7 +30,7 @@ CSRC = csrc
 #DEBUG = -g
 #OPT = -O0
 
-OPT ?= -O3
+OPT ?= $(RPM_OPT_FLAGS)
 
 SVFLAGS = $(CPPFLAGS) $(CFLAGS) -Dunix $(OPT) -I. $(IFLTK) -I$(CSRC) $(DEBUG) $(HELPFILE) $(PHYMLNAME) $(PDF_PS_FLAGS)
 