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/probcons-1.12/Defaults.h
Examining data/probcons-1.12/EvolutionaryTree.h
Examining data/probcons-1.12/FileBuffer.h
Examining data/probcons-1.12/MakeGnuPlot.cc
Examining data/probcons-1.12/MultiSequence.h
Examining data/probcons-1.12/ScoreType.h
Examining data/probcons-1.12/Sequence.h
Examining data/probcons-1.12/SparseMatrix.h
Examining data/probcons-1.12/debian/Defaults-RNA.h
Examining data/probcons-1.12/ProbabilisticModel.h
Examining data/probcons-1.12/ProjectPairwise.cc
Examining data/probcons-1.12/CompareToRef.cc
Examining data/probcons-1.12/FixRef.cc
Examining data/probcons-1.12/SafeVector.h
Examining data/probcons-1.12/Main.cc

FINAL RESULTS:

data/probcons-1.12/MakeGnuPlot.cc:53:7:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
  if (system ("gnuplot temporary_gnuplot_script") == -1){
data/probcons-1.12/Sequence.h:154:5:  [4] (buffer) sscanf:
  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.
    sscanf (header.c_str(), "%s", name);
data/probcons-1.12/FixRef.cc:953:9:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    if (random() % 2)
data/probcons-1.12/CompareToRef.cc:98:7:  [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 buffer[10000];
data/probcons-1.12/FileBuffer.h:27:3:  [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 buffer[BufferSize];
data/probcons-1.12/FixRef.cc:259:18:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE *file = fopen (filename, "w");
data/probcons-1.12/FixRef.cc:659:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    data.open (parametersInputFilename.c_str());
data/probcons-1.12/FixRef.cc:688:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    data.open (matrixFilename.c_str());
data/probcons-1.12/Main.cc:275:18:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE *file = fopen (filename, "w");
data/probcons-1.12/Main.cc:932:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    data.open (parametersInputFilename.c_str());
data/probcons-1.12/Sequence.h:153:5:  [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 name[1024];
data/probcons-1.12/FileBuffer.h:58:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      file.read (buffer, BufferSize);

ANALYSIS SUMMARY:

Hits = 12
Lines analyzed = 6196 in approximately 0.18 seconds (35134 lines/second)
Physical Source Lines of Code (SLOC) = 3696
Hits@level = [0]  19 [1]   1 [2]   8 [3]   1 [4]   2 [5]   0
Hits@level+ = [0+]  31 [1+]  12 [2+]  11 [3+]   3 [4+]   2 [5+]   0
Hits/KSLOC@level+ = [0+] 8.38745 [1+] 3.24675 [2+] 2.97619 [3+] 0.811688 [4+] 0.541126 [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.