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.