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/fastml-3.11/libs/phylogeny/bestHKYparam.h Examining data/fastml-3.11/libs/phylogeny/hky.h Examining data/fastml-3.11/libs/phylogeny/computePosteriorExpectationOfSubstitutions.h Examining data/fastml-3.11/libs/phylogeny/computePosteriorExpectationOfSubstitutions_nonReversibleSp.h Examining data/fastml-3.11/libs/phylogeny/betaDistributionFixedCategoriesWithOmegaUniform.cpp Examining data/fastml-3.11/libs/phylogeny/nj.cpp Examining data/fastml-3.11/libs/phylogeny/bestAlpha.h Examining data/fastml-3.11/libs/phylogeny/splitTreeUtil.cpp Examining data/fastml-3.11/libs/phylogeny/fromInstructionFile.h Examining data/fastml-3.11/libs/phylogeny/fastaFormat.h Examining data/fastml-3.11/libs/phylogeny/simulateRateShiftJumps.cpp Examining data/fastml-3.11/libs/phylogeny/phylipSequentialFormat.h Examining data/fastml-3.11/libs/phylogeny/gammaDistributionLaguerre.h Examining data/fastml-3.11/libs/phylogeny/codonJC.cpp Examining data/fastml-3.11/libs/phylogeny/likeDistPropEB.cpp Examining data/fastml-3.11/libs/phylogeny/computeMarginalAlg.h Examining data/fastml-3.11/libs/phylogeny/countTableComponent.cpp Examining data/fastml-3.11/libs/phylogeny/fromCountTableComponentToDistanceProp.cpp Examining data/fastml-3.11/libs/phylogeny/simulateJumpsAbstract.cpp Examining data/fastml-3.11/libs/phylogeny/betaOmegaDistribution.h Examining data/fastml-3.11/libs/phylogeny/AddLog.cpp Examining data/fastml-3.11/libs/phylogeny/checkcovFanctors.h Examining data/fastml-3.11/libs/phylogeny/hky.cpp Examining data/fastml-3.11/libs/phylogeny/treeIt.cpp Examining data/fastml-3.11/libs/phylogeny/integerAlphabet.cpp Examining data/fastml-3.11/libs/phylogeny/aaJC.cpp Examining data/fastml-3.11/libs/phylogeny/datMatrixHolder.h Examining data/fastml-3.11/libs/phylogeny/betaDistributionFixedCategories.cpp Examining data/fastml-3.11/libs/phylogeny/posteriorDistance.cpp Examining data/fastml-3.11/libs/phylogeny/pairwiseGammaDistance.cpp Examining data/fastml-3.11/libs/phylogeny/bestAlpha.cpp Examining data/fastml-3.11/libs/phylogeny/bestGtrModelParams.h Examining data/fastml-3.11/libs/phylogeny/bblEMProportionalEB.h Examining data/fastml-3.11/libs/phylogeny/bestTamura92param.h Examining data/fastml-3.11/libs/phylogeny/simulateTree.h Examining data/fastml-3.11/libs/phylogeny/optGammaMixtureEM.h Examining data/fastml-3.11/libs/phylogeny/computeMarginalAlg.cpp Examining data/fastml-3.11/libs/phylogeny/multipleStochasticProcess.cpp Examining data/fastml-3.11/libs/phylogeny/indelModel.h Examining data/fastml-3.11/libs/phylogeny/bootstrap.h Examining data/fastml-3.11/libs/phylogeny/optGammaMixtureLS.cpp Examining data/fastml-3.11/libs/phylogeny/bestParamUSSRV.h Examining data/fastml-3.11/libs/phylogeny/talRandom.h Examining data/fastml-3.11/libs/phylogeny/GamMixtureOptimizer.h Examining data/fastml-3.11/libs/phylogeny/simulateWithDependence.cpp Examining data/fastml-3.11/libs/phylogeny/bblEM2codon.h Examining data/fastml-3.11/libs/phylogeny/datMatrixHolder.cpp Examining data/fastml-3.11/libs/phylogeny/bblEMfixRoot.cpp Examining data/fastml-3.11/libs/phylogeny/AddLog.h Examining data/fastml-3.11/libs/phylogeny/errorMsg.cpp Examining data/fastml-3.11/libs/phylogeny/NNiSep.h Examining data/fastml-3.11/libs/phylogeny/someUtil.cpp