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/deepnano-0.0+git20170813.e8a621e/align_2d.cc
Examining data/deepnano-0.0+git20170813.e8a621e/r9/training/realign.cc
Examining data/deepnano-0.0+git20170813.e8a621e/training/realign.cc

FINAL RESULTS:

data/deepnano-0.0+git20170813.e8a621e/r9/training/realign.cc:58:3:  [4] (buffer) scanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
  scanf("%s\n", ss);
data/deepnano-0.0+git20170813.e8a621e/training/realign.cc:58:3:  [4] (buffer) scanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
  scanf("%s\n", ss);
data/deepnano-0.0+git20170813.e8a621e/r9/training/realign.cc:53:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char x_[3];
data/deepnano-0.0+git20170813.e8a621e/r9/training/realign.cc:57:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char ss[100000];
data/deepnano-0.0+git20170813.e8a621e/training/realign.cc:53:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char x_[3];
data/deepnano-0.0+git20170813.e8a621e/training/realign.cc:57:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char ss[100000];

ANALYSIS SUMMARY:

Hits = 6
Lines analyzed = 512 in approximately 0.09 seconds (5610 lines/second)
Physical Source Lines of Code (SLOC) = 424
Hits@level = [0]  16 [1]   0 [2]   4 [3]   0 [4]   2 [5]   0
Hits@level+ = [0+]  22 [1+]   6 [2+]   6 [3+]   2 [4+]   2 [5+]   0
Hits/KSLOC@level+ = [0+] 51.8868 [1+] 14.1509 [2+] 14.1509 [3+] 4.71698 [4+] 4.71698 [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.