Bug 77594

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User-Agent: Mozilla/4.0 (compatible; MSIE 6.0; Windows 98)

Description of problem:
The bug is very similar to a bug for Red Hat 7.2 gcc compiler 
bugzilla #67013. When I try to compile my C++ code it has an unrecoverable 
error. This compiler error is on a different line of the function.c file than 
the earlier bug report (and in the brand new version of Red Hat Linux 8.0).

The problem:
top.cc: In constructor `TreeTopology::TreeTopology(char*, char*)':
top.cc:151:Internal compiler error in find_function_data, at function.c: 329

Any help you can give me on this problem would be very much appreciated. I very 
much need to get my code compiled and working for a thesis project.

Version-Release number of selected component (if applicable):


How reproducible:
Always

Steps to Reproduce:
1.c++ -c -O3 -ffast-math -Wno-deprecated top.cc
2.
3.
	

Actual Results:  c++ -c -O3 -ffast-math -Wno-deprecated top.cc
top.cc: In constructor `TreeTopology::TreeTopology(char*, char*)':
top.cc:151: Internal compiler error in find_function_data, at function.c:329
Please submit a full bug report,
with preprocessed source if appropriate.
See <URL:http://bugzilla.redhat.com/bugzilla/> for instructions.
make: *** [top.o] Error 1


Expected Results:  No error

Additional info:

/* file: top.cc*/
#ifndef TOP_H
#include "top.h"
#endif 

static ifstream File;
struct Tree_Struct {
      int No;
      double Time;
      int P; };     
static struct Tree_Struct Nodes[MAX_DEPTH][MAX_NODES];      
static int Node[MAX_DEPTH];
static int Parent[MAX_DEPTH];
static int I;
static char S[MAX_SYMBOLS];

static int CheckChar(char c)
    { if (c=='A' || c=='C' || c=='G'  || c=='T' || c=='-' || c=='U') return 1;
      else return 0; }
      
static void Read (int Depth)
     { char c;
       int j;       
       if (File.eof()) return;
       while (!File.eof())
             { File>>c;                     
               if (c=='(') { I=0;
                             Read(Depth+1); }                         
               else if (c==')') { S[I]='\0';
                                  j=0;
                                  if (S[0]!=':') { Nodes[Depth][Node
[Depth]].No=abs(atoi(S));
                                                   for (j=0;j<MAX_SYMBOLS;j++)
                                                       if (S[j]==':') break; }
                                  Nodes[Depth][Node[Depth]].Time=fabs((double) 
atoi(S+j+1));
                                  for (j=0;j<MAX_SYMBOLS;j++)
                                      if (S[j]=='.') break;
                                  Nodes[Depth][Node[Depth]].Time+=(double) atoi
(S+j+1)/100000;                           
                                  Nodes[Depth][Node[Depth]].P=Parent
[Depth];                                  
                                  Parent[Depth+1]++;
                                  Node[Depth]++;
                                  I=0;                                  
                                  break; }
                    else if (c==',') { S[I]='\0';
                                       j=0;
                                       if (S[0]!=':') { Nodes[Depth][Node
[Depth]].No=abs(atoi(S));
                                                        for 
(j=0;j<MAX_SYMBOLS;j++)
                                                            if (S[j]==':') 
break; }                                               
                                       Nodes[Depth][Node[Depth]].Time=fabs
((double) atoi(S+j+1));                                       
                                       for (j=0;j<MAX_SYMBOLS;j++)
                                           if (S[j]=='.') 
break;                                     
                                       Nodes[Depth][Node[Depth]].Time+=(double) 
atoi(S+j+1)/100000;                                                             
                                       Nodes[Depth][Node[Depth]].P=Parent
[Depth];
                                       Node[Depth]++;
                                       Parent[Depth+1]++; 
                                       I=0;}
                         else { S[I]=c; 
                                I++; }}            
       }



TreeTopology::TreeTopology (char *treefile, char *seqfile)
              { register int i,j;
                int flag,Temp;             
                double Freq[4];
                int CurrentNumber;
                ifstream fs;
                ofstream f;      
                int N[MAX_DEPTH];
                
                Gaps=85;
                Conservatism=95;
  
                for (i=0;i<MAX_DEPTH;i++)
                    { Node[i]=0;
                      Parent[i]=0;               
                      for (j=0;j<MAX_NODES;j++)
                          { Nodes[i][j].No=0;
                            Nodes[i][j].Time=0;
                            Nodes[i][j].P=-1; }}
                Nodes[0][0].P=0;            
                File.open(treefile,ios::in);
                if (File.fail()) 
                   { cerr << "Unable to open the tree file\n";
                     return ; }
                Read(0);           
                File.close();      

                MaxNodes=0;                       
                Depth=0;
                
                for (i=1;i<MAX_DEPTH;i++)
                    { Temp=0;
                      flag=0;
                      for (j=0;j<MAX_NODES;j++)
                      if (Nodes[i][j].P!=-1)
                         { Temp++;
                           flag=1; }                   
                      N[i]=Temp;           
                      if (flag) Depth++;}               
                  
                fs.open(seqfile,ios::in);
                if (fs.fail()) 
                   { cerr << "Unable to open the sequence file\n";
      return; }
      
                char c;
                c=fs.get();
                while(!CheckChar(c))
                     c=fs.get();
                     
                Length=0;
                while(CheckChar(c))
                     { Length++;
                       c=fs.get(); }   
                                             
                N[0]=1;            
                
                Tree=new struct Leaves
[Depth+1];                                                
                for (i=0;i<=Depth;i++)
                    { register int Nodes=N[i];
                      Tree[i].Nodes=Nodes;
                      if (MaxNodes<Nodes) MaxNodes=Nodes;
                      Tree[i].Times=new double[Nodes];
                      Tree[i].Parent=new int [Nodes];
                      Tree[i].Number=new int [Nodes];
                      Tree[i].Strands=new Strand[Nodes](Length); }
                      
                for (i=0;i<=Depth;i++)
                    for (j=0;j<Tree[i].Nodes;j++)
                        { Tree[i].Times[j]=Nodes[i][j].Time;
                          Tree[i].Parent[j]=Nodes[i][j].P;
                          Tree[i].Number[j]=Nodes[i][j].No; }      
                                 
                NumberOfSequences=0; 
                SiteIndex=new int [Length];      
                while(!fs.eof())
                     { if (c=='\n') NumberOfSequences++;
                       c=fs.get(); }       
                fs.close();  
                
                char S[NumberOfSequences][Length];     
                fs.open(seqfile,ios::in);                       
                c=fs.get();
                for (i=0;i<NumberOfSequences;i++)
                    { while(!CheckChar(c))
                           c=fs.get();
                      for (j=0;j<Length;j++)
                          { if (!CheckChar(c)) 
                               { cerr<<"Bad character in the sequences file !
\n";
                                 return; }
                      if (c=='U') {S[i][j]='T';}           
                      else {S[i][j]=c;}
                      c=fs.get(); }}                       
                fs.close();                     
                      
                for (i=0;i<Length;i++)
                    { CurrentNumber=NumberOfSequences;
                      for (j=0;j<4;j++)
                          Freq[j]=0;
                      for (j=0;j<NumberOfSequences;j++)
                          switch (S[j][i])
                          { case 'A' : Freq[0]++;
                                       break;
                            case 'C' : Freq[1]++;
                                       break;           
                            case 'G' : Freq[2]++;
                                       break;
                            case 'T' : Freq[3]++; 
                                       break;
                            default : CurrentNumber--
; }                                              
                      SiteIndex[i]=0;                     
                      if ((Freq[0]+Freq[1]+Freq[2]+Freq[3])/NumberOfSequences>
(double)Gaps/100) SiteIndex[i]=1;
                      for (j=0;j<4;j++)
                          if (Freq[j]/CurrentNumber>(double)Conservatism/100) 
SiteIndex [i]=0; }
                f.open("sequences.txt",ios::out); 
                for (i=0;i<=Depth;i++)
                    for (j=0;j<Tree[i].Nodes;j++)
                        { Temp=Nodes[i][j].No;            
                          if (Temp==0) f<<'X';
                          else for (int k=0;k<Length;k++)
                                   if (S[Temp-1][k]=='-') f<<'N';
                                   else f<<S[Temp-1][k]; 
                          
f<<'\n'; }                                                  
                 }
                 
TreeTopology::~TreeTopology()
              { register int i;
                delete SiteIndex;
                for (i=0;i<=Depth;i++)
                    { delete Tree[i].Times;
                      delete Tree[i].Parent;
                      delete Tree[i].Number;
                      delete [] Tree[i].Strands; }                
                delete [] Tree;   }