Program: 179548
Project: 179548
Buggy source:
@SuppressWarnings({"String_Node_Str","String_Node_Str"}) @Override public void run(){
  if (!connected) {
    connectToServer();
  }
  if (connected) {
    isRunning=true;
    while (!stopOperation) {
      try {
        NetworkMessage msg=new NetworkMessage();
        Schema<NetworkMessage> schema=RuntimeSchema.getSchema(NetworkMessage.class);
        byte[] bytes=new byte[32];
        int bytesRead=0;
        do {
          if (bytesRead == bytes.length) {
            byte[] newBytes=copyOf(bytes,2 * bytes.length);
            bytes=newBytes;
          }
          bytesRead+=in.read(bytes,bytesRead,bytes.length - bytesRead);
        }
 while (bytesRead == bytes.length);
        if (bytesRead != -1) {
          Log.i(NetworkVariables.TAG,"String_Node_Str" + bytesRead);
          ProtostuffIOUtil.mergeFrom(copyOf(bytes,bytesRead),msg,schema);
          processNetworkMessage(msg);
        }
 else {
          System.err.println("String_Node_Str");
          fireEvent(new NetworkEvent(this,"String_Node_Str"),ConnectionLostListener.class);
          shutdownThread();
        }
      }
 catch (      InterruptedIOException e) {
      }
catch (      IOException e) {
        System.err.println("String_Node_Str" + e);
        fireEvent(new NetworkEvent(this,"String_Node_Str" + e),ConnectionLostListener.class);
        this.shutdownThread();
        break;
      }
catch (      NullPointerException e) {
        Log.e(NetworkVariables.TAG,"String_Node_Str",e);
      }
 finally {
        buffer.clear();
      }
    }
  }
 else {
    shutdownThread();
  }
}

Fixed version (ground truth):
@SuppressWarnings({"String_Node_Str","String_Node_Str"}) @Override public void run(){
  if (!connected) {
    connectToServer();
  }
  if (connected) {
    isRunning=true;
    while (!stopOperation) {
      try {
        NetworkMessage msg=new NetworkMessage();
        Schema<NetworkMessage> schema=RuntimeSchema.getSchema(NetworkMessage.class);
        byte[] messageSizeBytes=new byte[6];
        int success=in.read(messageSizeBytes);
        if (success == 6) {
          String mSizeString=new String(messageSizeBytes);
          int mSize=Integer.parseInt(mSizeString);
          byte[] object=new byte[mSize];
          int bytesRead=0;
          while (bytesRead != mSize) {
            bytesRead+=in.read(object,bytesRead,object.length - bytesRead);
          }
          System.out.println("String_Node_Str" + bytesRead);
          ProtostuffIOUtil.mergeFrom(object,msg,schema);
          processNetworkMessage(msg);
        }
 else {
          if (success == -1) {
            System.err.println("String_Node_Str");
            shutdownThread();
          }
        }
      }
 catch (      InterruptedIOException e) {
      }
catch (      IOException e) {
        System.err.println("String_Node_Str" + e);
        fireEvent(new NetworkEvent(this,"String_Node_Str" + e),ConnectionLostListener.class);
        this.shutdownThread();
        break;
      }
catch (      NullPointerException e) {
        Log.e(NetworkVariables.TAG,"String_Node_Str",e);
      }
catch (      RuntimeException e) {
        System.err.println("String_Node_Str");
      }
 finally {
        buffer.clear();
      }
    }
  }
 else {
    shutdownThread();
  }
}