Flawfinder version 2.0.10, (C) 2001-2019 David A. Wheeler.
Number of rules (primarily dangerous function names) in C/C++ ruleset: 223
Examining data/fsm-lite-1.0/configuration.cpp
Examining data/fsm-lite-1.0/configuration.h
Examining data/fsm-lite-1.0/default.h
Examining data/fsm-lite-1.0/fsm-lite.cpp
Examining data/fsm-lite-1.0/input_reader.cpp
Examining data/fsm-lite-1.0/input_reader.h

FINAL RESULTS:

data/fsm-lite-1.0/configuration.cpp:83:17:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
    while ((c = getopt_long(argc, argv, "l:t:m:M:f:s:S:vDh",
data/fsm-lite-1.0/configuration.cpp:11:36:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
    : prog(argv[0]), listfile(""), tmpfile(""), inputformat(input_reader::input_fasta),
data/fsm-lite-1.0/configuration.h:17:17:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
    std::string tmpfile;
data/fsm-lite-1.0/input_reader.cpp:200:18:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
    ofstream ofs(tmpfile.c_str());

ANALYSIS SUMMARY:

Hits = 4
Lines analyzed = 683 in approximately 0.04 seconds (16446 lines/second)
Physical Source Lines of Code (SLOC) = 563
Hits@level = [0]   0 [1]   0 [2]   3 [3]   1 [4]   0 [5]   0
Hits@level+ = [0+]   4 [1+]   4 [2+]   4 [3+]   1 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 7.1048 [1+] 7.1048 [2+] 7.1048 [3+] 1.7762 [4+]   0 [5+]   0
Dot directories skipped = 1 (--followdotdir overrides)
Minimum risk level = 1
Not every hit is necessarily a security vulnerability.
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://dwheeler.com/secure-programs) for more information.