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/beast-mcmc-1.10.4+dfsg/native/AminoAcidLikelihoodCore.c
Examining data/beast-mcmc-1.10.4+dfsg/native/AminoAcidLikelihoodCore.h
Examining data/beast-mcmc-1.10.4+dfsg/native/GeneralLikelihoodCore.c
Examining data/beast-mcmc-1.10.4+dfsg/native/GeneralLikelihoodCore.h
Examining data/beast-mcmc-1.10.4+dfsg/native/NativeMemoryLikelihoodCore.c
Examining data/beast-mcmc-1.10.4+dfsg/native/NativeMemoryLikelihoodCore.h
Examining data/beast-mcmc-1.10.4+dfsg/native/NativeSubstitutionModel.c
Examining data/beast-mcmc-1.10.4+dfsg/native/NativeSubstitutionModel.h
Examining data/beast-mcmc-1.10.4+dfsg/native/NucleotideLikelihoodCore.c
Examining data/beast-mcmc-1.10.4+dfsg/native/NucleotideLikelihoodCore.h
Examining data/beast-mcmc-1.10.4+dfsg/native/deprecated/NewNativeLikelihoodCore.c
Examining data/beast-mcmc-1.10.4+dfsg/native/deprecated/NewNativeLikelihoodCore.h
Examining data/beast-mcmc-1.10.4+dfsg/native/deprecated/expokit/SparseMatrixExponential.cpp
Examining data/beast-mcmc-1.10.4+dfsg/native/deprecated/expokit/SparseMatrixExponential.h

FINAL RESULTS:

data/beast-mcmc-1.10.4+dfsg/native/NativeSubstitutionModel.c:38:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(to,from,length*SIZE_REAL);
data/beast-mcmc-1.10.4+dfsg/native/deprecated/NewNativeLikelihoodCore.c:140:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(partials[0][tipIndex] + k, tipPartials, sizeof(double) * patternCount * STATE_COUNT);
data/beast-mcmc-1.10.4+dfsg/native/deprecated/NewNativeLikelihoodCore.c:665:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(storedCMatrix, cMatrix, sizeof(double) * STATE_COUNT * STATE_COUNT * STATE_COUNT);
data/beast-mcmc-1.10.4+dfsg/native/deprecated/NewNativeLikelihoodCore.c:666:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(storedEigenValues, eigenValues, sizeof(double) * STATE_COUNT);
data/beast-mcmc-1.10.4+dfsg/native/deprecated/NewNativeLikelihoodCore.c:668:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(storedFrequencies, frequencies, sizeof(double) * STATE_COUNT);
data/beast-mcmc-1.10.4+dfsg/native/deprecated/NewNativeLikelihoodCore.c:669:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(storedCategoryRates, categoryRates, sizeof(double) * matrixCount);
data/beast-mcmc-1.10.4+dfsg/native/deprecated/NewNativeLikelihoodCore.c:670:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(storedCategoryProportions, categoryProportions, sizeof(double) * matrixCount);
data/beast-mcmc-1.10.4+dfsg/native/deprecated/NewNativeLikelihoodCore.c:672:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(storedMatricesIndices, currentMatricesIndices, sizeof(int) * nodeCount);
data/beast-mcmc-1.10.4+dfsg/native/deprecated/NewNativeLikelihoodCore.c:673:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(storedPartialsIndices, currentPartialsIndices, sizeof(int) * nodeCount);

ANALYSIS SUMMARY:

Hits = 9
Lines analyzed = 4903 in approximately 0.64 seconds (7640 lines/second)
Physical Source Lines of Code (SLOC) = 3504
Hits@level = [0]  39 [1]   0 [2]   9 [3]   0 [4]   0 [5]   0
Hits@level+ = [0+]  48 [1+]   9 [2+]   9 [3+]   0 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 13.6986 [1+] 2.56849 [2+] 2.56849 [3+]   0 [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.