path: root/sci-biology/unafold/files/unafold-3.8-clang16.patch

--- a/src/ct-energy.c
+++ b/src/ct-energy.c
@@ -24,8 +24,8 @@
 double auPenalty(int, int);
 double chooseDangle(int, int);
 double tstackOrDangle(int, int, int);
-int isHomodimer();
-int isCircular();
+int isHomodimer(void);
+int isCircular(void);
 
 int readStructure(FILE* file);
 
@@ -87,7 +87,7 @@
   {NULL, 0, NULL, 0}
 };
 
-void usage()
+void usage(void)
 {
   puts("Usage: ct-energy [OPTION] [FILE]...");
   puts("");
@@ -1247,7 +1247,7 @@
   return 1;
 }
 
-int isHomodimer()
+int isHomodimer(void)
 {
   int i;
 
@@ -1272,7 +1272,7 @@
   return 1;
 }
 
-int isCircular()
+int isCircular(void)
 {
   return g_prev[0] == g_len && g_next[g_len - 1] % g_len == 1;
 }
--- a/src/energy.c
+++ b/src/energy.c
@@ -15,6 +15,7 @@
 #endif
 
 #include "energy.h"
+#include "util.h"
 #include "xmalloc.h"
 
 #ifndef isinf
--- a/src/hybrid.c
+++ b/src/hybrid.c
@@ -39,10 +39,10 @@
 #endif
 
 void initializeMatrix(double**, int, double);
-void limitBasePairs();
-void prohibit();
-void force();
-void prefilter();
+void limitBasePairs(void);
+void prohibit(void);
+void force(void);
+void prefilter(void);
 void fillMatrix(double**, int, double);
 void fillMatrix_noI(double**, int, double);
 void calculateProb(double**, double*, double*, double**, double**, double, double, int, double);
@@ -706,7 +706,7 @@
       matrix[i - 1][n - 1] = (reverse ? R0(n, i) : L0(i, n));
 }
 
-void limitBasePairs()
+void limitBasePairs(void)
 {
   if (g_bpFile)
     {
@@ -740,7 +740,7 @@
     }
 }
 
-void prohibit()
+void prohibit(void)
 {
   int i, j, k;
   struct constraintListNode *top, *newTop;
@@ -788,7 +788,7 @@
 }
 
 #if ENABLE_FORCE
-void force()
+void force(void)
 {
   int i, j, k;
   struct constraintListNode *top, *newTop;
@@ -880,7 +880,7 @@
 	}
 } */
 
-void prefilter()
+void prefilter(void)
 {
   char** in;
   int i, j, k, count;
--- a/src/hybrid-min.c
+++ b/src/hybrid-min.c
@@ -53,10 +53,10 @@
 } *pairList;
 
 void initializeMatrices(double);
-void limitBasePairs();
-void prohibit();
-void force();
-void prefilter();
+void limitBasePairs(void);
+void prohibit(void);
+void force(void);
+void prefilter(void);
 void fillMatrixL(double);
 void fillMatrixR(double);
 void fillMatrixL_noI(double);
@@ -88,7 +88,7 @@
 #define min2(a, b) ((a) < (b) ? (a) : (b))
 ENERGY min4(ENERGY, ENERGY, ENERGY, ENERGY);
 void pushPairList(int, int, int, ENERGY);
-void sortPairList();
+void sortPairList(void);
 
 ENERGY *lprime, *rprime;
 
@@ -885,7 +885,7 @@
 	}
 }
 
-void limitBasePairs()
+void limitBasePairs(void)
 {
   if (g_bpFile)
     {
@@ -919,7 +919,7 @@
     }
 }
 
-void prohibit()
+void prohibit(void)
 {
   int i, j, k;
   struct constraintListNode* top;
@@ -965,7 +965,7 @@
 }
 
 #if ENABLE_FORCE
-void force()
+void force(void)
 {
   int i, j, k;
   struct constraintListNode* top;
@@ -1041,7 +1041,7 @@
   return length;
 }
 
-void prefilter()
+void prefilter(void)
 {
   int i, j;
 
@@ -1055,7 +1055,7 @@
 	}
 } */
 
-void prefilter()
+void prefilter(void)
 {
   char** in;
   int i, j, k, count;
@@ -2235,7 +2235,7 @@
   pairList = node;
 }
 
-void sortPairList()
+void sortPairList(void)
 {
   struct pairListNode *a, *b;
 
--- a/src/hybrid-plot.c
+++ b/src/hybrid-plot.c
@@ -70,13 +70,13 @@
 void displayCallbackInput(void);
 void keyboardCallbackInput(unsigned char, int, int);
 
-void fixLength();
-void fixGrid();
-void fixLabels();
-void fixZoomGrid();
-void fixZoomLabels();
+void fixLength(void);
+void fixGrid(void);
+void fixLabels(void);
+void fixZoomGrid(void);
+void fixZoomLabels(void);
 void readFiles(char*);
-void sortTemps();
+void sortTemps(void);
 double* inputRecords(FILE*);
 int filter(int, int);
 
@@ -1157,7 +1157,7 @@
     }
 }
 
-void fixLength()
+void fixLength(void)
 {
   int m, n;
 
@@ -1177,7 +1177,7 @@
     }
 }
 
-void fixGrid()
+void fixGrid(void)
 {
   int m;
 
@@ -1193,7 +1193,7 @@
     g_grid = pow(10, m + 1);
 }
 
-void fixLabels()
+void fixLabels(void)
 {
   int longestNum;
 
@@ -1202,7 +1202,7 @@
     g_labels += g_grid;
 }
 
-void fixZoomGrid()
+void fixZoomGrid(void)
 {
   int m;
 
@@ -1221,7 +1221,7 @@
     g_zoomGrid = pow(10, m + 1);
 }
 
-void fixZoomLabels()
+void fixZoomLabels(void)
 {
   int longestNum;
 
@@ -1310,7 +1310,7 @@
   return scores;
 }
 
-void sortTemps()
+void sortTemps(void)
 {
   int i, j;
   char* tempC;
--- a/src/hybrid-plot-ng.c
+++ b/src/hybrid-plot-ng.c
@@ -24,28 +24,28 @@
  */
 
 #if HAVE_GD
-void initPNG();
+void initPNG(void);
 void titlePNG(char*);
-void borderPNG();
-void gridPNG();
+void borderPNG(void);
+void gridPNG(void);
 void plotDotPNG(int, int, double);
 void vertCenterPNG(char*, int);
 void horzCenterPNG(char*, int);
 void selectionPNG(char*, int);
 #endif
 
-void initPS();
+void initPS(void);
 void titlePS(char*);
-void borderPS();
-void gridPS();
+void borderPS(void);
+void gridPS(void);
 void plotDotPS(int, int, double);
 void vertCenterPS(char*, int);
 void horzCenterPS(char*, int);
 void selectionPS(char*, int);
 
-void fixSize();
-void fixGrid();
-void fixLabels();
+void fixSize(void);
+void fixGrid(void);
+void fixLabels(void);
 double* inputRecords(FILE*);
 int filter(int, int);
 int (*getColor)(double);
@@ -114,10 +114,10 @@
   char* plotFile;
 
   /* functions to call - either PS or PNG */
-  void (*init)();
+  void (*init)(void);
   void (*title)(char*);
-  void (*border)();
-  void (*grid)();
+  void (*border)(void);
+  void (*grid)(void);
   void (*plotDot)(int, int, double);
   void (*vertCenter)(char*, int);
   void (*horzCenter)(char*, int);
@@ -474,7 +474,7 @@
   return 0;
 }
 
-void initPS()
+void initPS(void)
 {
   int i;
 
@@ -517,7 +517,7 @@
   fprintf(g_file, "(%s) showCenter\n", wordString);
 }
 
-void borderPS()
+void borderPS(void)
 {
   fputs("92 126 moveto\n", g_file);
   fputs("576 126 lineto\n", g_file);
@@ -527,7 +527,7 @@
   fputs("stroke\n", g_file);
 }
 
-void gridPS()
+void gridPS(void)
 {
   double x1, y1;
   int i, j;
@@ -639,7 +639,7 @@
 
 #if HAVE_GD
 
-void initPNG()
+void initPNG(void)
 {
   int i;
 
@@ -671,12 +671,12 @@
   gdImageString(g_image, gdFontMediumBold, 306 - 7 * strlen(wordString) / 2, 51, (unsigned char*) wordString, g_black);
 }
 
-void borderPNG()
+void borderPNG(void)
 {
   gdImageRectangle(g_image, 92, 92, 576, 576, g_black);
 }
 
-void gridPNG()
+void gridPNG(void)
 {
   int i, j;
   char buffer[8];
@@ -776,7 +776,7 @@
 
 #endif
 
-void fixSize()
+void fixSize(void)
 {
   int m, n;
 
@@ -796,7 +796,7 @@
     }
 }
 
-void fixGrid()
+void fixGrid(void)
 {
   int m;
 
@@ -812,7 +812,7 @@
     g_grid = pow(10, m + 1);
 }
 
-void fixLabels()
+void fixLabels(void)
 {
   int longestNum;
 
--- a/src/hybrid-ss.c
+++ b/src/hybrid-ss.c
@@ -47,10 +47,10 @@
 #define ssOK(i, j) 1
 #endif
 
-void initializeMatrices();
-void fillMatrices1();
+void initializeMatrices(void);
+void fillMatrices1(void);
 void fillMatrices2(double*, double*);
-void fillMatrices1_noI();
+void fillMatrices1_noI(void);
 void fillMatrices2_noI(double*, double*);
 void calculateProb(double*, double*, double*, double*, double*, double);
 void calculateProb_noI(double*, double*, double*, double*, double*);
@@ -713,7 +713,7 @@
 
 #include "hybrid-ss_init.h"
 
-void fillMatrices1()
+void fillMatrices1(void)
 {
   int i, j, k;
   FILE* file;
@@ -783,7 +783,7 @@
     }
 }
 
-void fillMatrices1_noI()
+void fillMatrices1_noI(void)
 {
   int i, j, k;
   FILE* file;
--- a/src/hybrid-ss_init.h
+++ b/src/hybrid-ss_init.h
@@ -14,7 +14,7 @@
   return length;
 } */
 
-void prefilter()
+void prefilter(void)
 {
   char** in;
   int i, j, k, count;
@@ -45,7 +45,7 @@
   free(in);
 }
 
-void initializeMatrices()
+void initializeMatrices(void)
 {
   int i, j, k;
   struct constraintListNode *top, *newTop;
--- a/src/hybrid-ss-min.c
+++ b/src/hybrid-ss-min.c
@@ -57,10 +57,10 @@
   struct pairListNode* next;
 } *pairList;
 
-void initializeMatrices();
-void fillMatrices1();
-void fillMatrices2();
-void computeQ53();
+void initializeMatrices(void);
+void fillMatrices1(void);
+void fillMatrices2(void);
+void computeQ53(void);
 void traceback(int, int, int, int*, int*, int*);
 void traceback_noI(int, int, int, int*, int*, int*);
 void setStack(int, int, int*, int*);
@@ -108,7 +108,7 @@
 int equal(ENERGY, ENERGY);
 void push(struct stackNode**, int, int, int);
 void pushPairList(int, int, int, ENERGY);
-void sortPairList();
+void sortPairList(void);
 
 int g_len;
 ENERGY *q, *qprime, *qm, *q5, *q3;
@@ -887,7 +887,7 @@
   return length;
 }
 
-void prefilter()
+void prefilter(void)
 {
   char** in;
   int i, j, k, count;
@@ -918,7 +918,7 @@
   free(in);
 }
 
-void initializeMatrices()
+void initializeMatrices(void)
 {
   int i, j, k;
   struct constraintListNode* top;
@@ -1072,7 +1072,7 @@
     }
 }
 
-void fillMatrices1()
+void fillMatrices1(void)
 {
   int i, j, k;
   FILE* file;
@@ -1181,7 +1181,7 @@
     }
 }
 
-void fillMatrices2()
+void fillMatrices2(void)
 {
   int i, j, k;
   FILE* file;
@@ -1283,7 +1283,7 @@
     }
 }
 
-void computeQ53()
+void computeQ53(void)
 {
   int i, j;
 
@@ -3137,7 +3137,7 @@
   pairList = node;
 }
 
-void sortPairList()
+void sortPairList(void)
 {
   struct pairListNode *a, *b;
 
--- a/src/hybrid-ss-noml.c
+++ b/src/hybrid-ss-noml.c
@@ -45,11 +45,11 @@
 #define ssOK(i, j) 1
 #endif
 
-void initializeMatrices();
-void fillMatrices1();
-void fillMatrices2();
-void fillMatrices1_noI();
-void fillMatrices2_noI();
+void initializeMatrices(void);
+void fillMatrices1(void);
+void fillMatrices2(void);
+void fillMatrices1_noI(void);
+void fillMatrices2_noI(void);
 void calculateProb(double*, double*, double*, double);
 void calculateProb_noI(double*, double*, double*, double);
 void traceback(int*, int*, int*);
@@ -652,7 +652,7 @@
   return length;
 } */
 
-void prefilter()
+void prefilter(void)
 {
   char** in;
   int i, j, k, count;
@@ -683,7 +683,7 @@
   free(in);
 }
 
-void initializeMatrices()
+void initializeMatrices(void)
 {
   int i, j, k;
   struct constraintListNode *top, *newTop;
@@ -826,7 +826,7 @@
 	}
 }
 
-void fillMatrices1()
+void fillMatrices1(void)
 {
   int i, j, k;
   FILE* file;
@@ -885,7 +885,7 @@
     }
 }
 
-void fillMatrices1_noI()
+void fillMatrices1_noI(void)
 {
   int i, j, k;
   FILE* file;
@@ -944,7 +944,7 @@
     }
 }
 
-void fillMatrices2()
+void fillMatrices2(void)
 {
   int i, j;
   FILE* file;
@@ -986,7 +986,7 @@
     }
 }
 
-void fillMatrices2_noI()
+void fillMatrices2_noI(void)
 {
   int i, j;
   FILE* file;
--- a/src/hybrid-ss-simple.c
+++ b/src/hybrid-ss-simple.c
@@ -47,11 +47,11 @@
 #define ssOK(i, j) 1
 #endif
 
-void initializeMatrices();
-void fillMatrices1();
-void fillMatrices2();
-void fillMatrices1_noI();
-void fillMatrices2_noI();
+void initializeMatrices(void);
+void fillMatrices1(void);
+void fillMatrices2(void);
+void fillMatrices1_noI(void);
+void fillMatrices2_noI(void);
 void calculateProb(double*, double*, double*, double);
 void calculateProb_noI(double*, double*, double*);
 void traceback(int*, int*, int*);
@@ -598,7 +598,7 @@
 
 #include "hybrid-ss_init.h"
 
-void fillMatrices1()
+void fillMatrices1(void)
 {
   int i, j, k;
   FILE* file;
@@ -658,7 +658,7 @@
     }
 }
 
-void fillMatrices1_noI()
+void fillMatrices1_noI(void)
 {
   int i, j, k;
   FILE* file;
@@ -718,7 +718,7 @@
     }
 }
 
-void fillMatrices2()
+void fillMatrices2(void)
 {
   int i, j, k;
   FILE* file;
@@ -789,7 +789,7 @@
     }
 }
 
-void fillMatrices2_noI()
+void fillMatrices2_noI(void)
 {
   int i, j, k;
   FILE* file;
--- a/src/util.h
+++ b/src/util.h
@@ -24,18 +24,18 @@
 
 /* #define NO_GU_BASEPAIRS */
 
-int roundInt(double d)
+static int roundInt(double d)
 {
   return (int) (d + .5);
 }
 
-void strcatc(char* str, char c)
+static void strcatc(char* str, char c)
 {
   str[strlen(str) + 1] = 0;
   str[strlen(str)] = c;
 }
 
-char* filename(char* file)
+static char* filename(char* file)
 {
   char* name;
 
@@ -46,7 +46,7 @@
   return name;
 }
 
-void checkArray(char** array, unsigned int* available, unsigned int used, unsigned int increment)
+static void checkArray(char** array, unsigned int* available, unsigned int used, unsigned int increment)
 {
   if (used == *available)
     {
@@ -55,7 +55,7 @@
     }
 }
 
-int input(FILE* file, char** name, char** sequence)
+static int input(FILE* file, char** name, char** sequence)
 {
   /* read string from file */
   int current, last, state;
@@ -120,7 +120,7 @@
   return 1;
 }
 
-unsigned char toNum(char c)
+static unsigned char toNum(char c)
 {
   c = toupper(c);
   switch (c)
@@ -137,7 +137,7 @@
   return 4;
 }
 
-int seqcmp(unsigned char* seq1, unsigned char* seq2, int length)
+static int seqcmp(unsigned char* seq1, unsigned char* seq2, int length)
 {
   int i;
 
@@ -149,7 +149,7 @@
   return 0;
 }
 
-void readSequence(char* file, char** name, char** string, unsigned char** seq, int* len)
+static void readSequence(char* file, char** name, char** string, unsigned char** seq, int* len)
 {
   int i;
   FILE* f;
@@ -171,14 +171,14 @@
 }
 
 #ifdef NO_GU_BASEPAIRS
-const int BPI[6][6] = {{6, 6, 6, 0, 6, 6},
+static const int BPI[6][6] = {{6, 6, 6, 0, 6, 6},
 		       {6, 6, 1, 6, 6, 6},
 		       {6, 2, 6, 6, 6, 6},
 		       {3, 6, 6, 6, 6, 6},
 		       {6, 6, 6, 6, 6, 6},
 		       {6, 6, 6, 6, 6, 6}};
 #else
-const int BPI[6][6] = {{6, 6, 6, 0, 6, 6},
+static const int BPI[6][6] = {{6, 6, 6, 0, 6, 6},
 		       {6, 6, 1, 6, 6, 6},
 		       {6, 2, 6, 4, 6, 6},
 		       {3, 6, 5, 6, 6, 6},
@@ -187,7 +187,7 @@
 #endif
 #define basePairIndex(a, b) BPI[a][b]
 
-int min3(int a, int b, int c)
+static int min3(int a, int b, int c)
 {
   if (a <= b && a <= c)
     return a;
@@ -196,7 +196,7 @@
   return c;
 }
 
-int same(unsigned char* a, unsigned char* b, int len)
+static int same(unsigned char* a, unsigned char* b, int len)
 {
   int i;
 
@@ -206,7 +206,7 @@
   return 1;
 }
 
-void version(const char* prog)
+static void version(const char* prog)
 {
   printf("%s (%s) %s\n", prog, PACKAGE_NAME, PACKAGE_VERSION);
   puts("By Nicholas R. Markham and Michael Zuker");
@@ -216,7 +216,7 @@
   exit(EXIT_SUCCESS);
 }
 
-void readOrDie(unsigned int num, const char* name, FILE* file, const char* format, ...)
+static void readOrDie(unsigned int num, const char* name, FILE* file, const char* format, ...)
 {
   va_list arg;
   va_start(arg, format);