Darn... try this:

for i in `find / -name "*.h" 2>/dev/null`; do if grep -
E '^extern int ftime' "$i">/dev/null; then echo "ok: 
$i"; fi; done

If this still doesn't work, you'll have to patch the 
source :)
In htslib.c, patch both mtime_local and filetime:

// number of millisec since 1970
HTS_INLINE double mtime_local() {
  // struct timeb B;
  // ftime( &B );
  return (double) ( ((double) time_local() * (double) 
1000.0)
        + ((double) 0) );
}


/* sets file time. -1 if error */
int set_filetime(char* file,struct tm* tm_time) {
  struct utimbuf tim;
  // struct timeb B;
  // B.timezone=0;
  // ftime( &B ); 
  // tim.actime=tim.modtime=mktime(tm_time) - 
B.timezone*60; 
  tim.actime=tim.modtime=mktime(tm_time); 
  return utime(file,&tim);
}

But this is a hack.. please tell me if the ftime() 
could be found or not!