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/rate4site-3.0.0/src/phylogeny/getopt.h Examining data/rate4site-3.0.0/src/phylogeny/errorMsg.h Examining data/rate4site-3.0.0/src/phylogeny/definitions.h Examining data/rate4site-3.0.0/src/phylogeny/doubleRep.h Examining data/rate4site-3.0.0/src/phylogeny/ConversionUtils.h Examining data/rate4site-3.0.0/src/phylogeny/sequenceContainer.h Examining data/rate4site-3.0.0/src/phylogeny/sequence.h Examining data/rate4site-3.0.0/src/phylogeny/alphabet.h Examining data/rate4site-3.0.0/src/phylogeny/mulAlphabet.h Examining data/rate4site-3.0.0/src/phylogeny/someUtil.h Examining data/rate4site-3.0.0/src/phylogeny/logFile.h Examining data/rate4site-3.0.0/src/phylogeny/gainLossAlphabet.h Examining data/rate4site-3.0.0/src/phylogeny/pijAccelerator.h Examining data/rate4site-3.0.0/src/phylogeny/replacementModel.h Examining data/rate4site-3.0.0/src/phylogeny/distribution.h Examining data/rate4site-3.0.0/src/phylogeny/readTree.h Examining data/rate4site-3.0.0/src/phylogeny/nucleotide.h Examining data/rate4site-3.0.0/src/phylogeny/amino.h Examining data/rate4site-3.0.0/src/phylogeny/geneticCodeHolder.h Examining data/rate4site-3.0.0/src/phylogeny/codon.h Examining data/rate4site-3.0.0/src/phylogeny/evaluateCharacterFreq.h Examining data/rate4site-3.0.0/src/phylogeny/uniDistribution.h Examining data/rate4site-3.0.0/src/phylogeny/generalGammaDistribution.h Examining data/rate4site-3.0.0/src/phylogeny/readDatMatrix.h Examining data/rate4site-3.0.0/src/phylogeny/datMatrixHolder.h Examining data/rate4site-3.0.0/src/phylogeny/chebyshevAccelerator.h Examining data/rate4site-3.0.0/src/phylogeny/nucJC.h Examining data/rate4site-3.0.0/src/phylogeny/aaJC.h Examining data/rate4site-3.0.0/src/phylogeny/gtrModel.h Examining data/rate4site-3.0.0/src/phylogeny/fromQtoPt.h Examining data/rate4site-3.0.0/src/phylogeny/trivialAccelerator.h Examining data/rate4site-3.0.0/src/phylogeny/distanceMethod.h Examining data/rate4site-3.0.0/src/phylogeny/distanceTable.h Examining data/rate4site-3.0.0/src/phylogeny/nj.h Examining data/rate4site-3.0.0/src/phylogeny/njConstrain.h Examining data/rate4site-3.0.0/src/phylogeny/distances2Tree.h Examining data/rate4site-3.0.0/src/phylogeny/numRec.h Examining data/rate4site-3.0.0/src/phylogeny/uniformDistribution.h Examining data/rate4site-3.0.0/src/phylogeny/checkcovFanctors.h Examining data/rate4site-3.0.0/src/phylogeny/likelihoodComputation.h Examining data/rate4site-3.0.0/src/phylogeny/computePijComponent.h Examining data/rate4site-3.0.0/src/phylogeny/stochasticProcess.h Examining data/rate4site-3.0.0/src/phylogeny/suffStatComponent.h Examining data/rate4site-3.0.0/src/phylogeny/unObservableData.h Examining data/rate4site-3.0.0/src/phylogeny/likeDist.h Examining data/rate4site-3.0.0/src/phylogeny/countTableComponent.h Examining data/rate4site-3.0.0/src/phylogeny/jcDistance.h Examining data/rate4site-3.0.0/src/phylogeny/fastStartTree.h Examining data/rate4site-3.0.0/src/phylogeny/checkcovFanctorsWithFactors.h Examining data/rate4site-3.0.0/src/phylogeny/likelihoodComputationFactors.h Examining data/rate4site-3.0.0/src/phylogeny/bestAlpha.h Examining data/rate4site-3.0.0/src/phylogeny/gammaDistribution.h Examining data/rate4site-3.0.0/src/phylogeny/siteSpecificRate.h Examining data/rate4site-3.0.0/src/phylogeny/recognizeFormat.h Examining data/rate4site-3.0.0/src/phylogeny/bblEM.h Examining data/rate4site-3.0.0/src/phylogeny/bestGtrModelParams.h Examining data/rate4site-3.0.0/src/phylogeny/tamura92.h Examining data/rate4site-3.0.0/src/phylogeny/bestHKYparam.h Examining data/rate4site-3.0.0/src/phylogeny/hky.h Examining data/rate4site-3.0.0/src/phylogeny/bestTamura92param.h Examining data/rate4site-3.0.0/src/phylogeny/talRandom.h Examining data/rate4site-3.0.0/src/phylogeny/computeSubstitutionCounts.h Examining data/rate4site-3.0.0/src/phylogeny/fromCountTableComponentToDistance.h Examining data/rate4site-3.0.0/src/phylogeny/computeCounts.h Examining data/rate4site-3.0.0/src/phylogeny/computeDownAlg.h Examining data/rate4site-3.0.0/src/phylogeny/computeUpAlg.h Examining data/rate4site-3.0.0/src/phylogeny/gammaUtilities.h Examining data/rate4site-3.0.0/src/phylogeny/seqContainerTreeMap.h Examining data/rate4site-3.0.0/src/phylogeny/treeUtil.h Examining data/rate4site-3.0.0/src/phylogeny/matrixUtils.h Examining data/rate4site-3.0.0/src/phylogeny/computePosteriorExpectationOfSubstitutions.h Examining data/rate4site-3.0.0/src/phylogeny/computePosteriorExpectationOfSubstitutions_nonReversibleSp.h Examining data/rate4site-3.0.0/src/phylogeny/multipleStochasticProcess.h Examining data/rate4site-3.0.0/src/phylogeny/simulateJumps.h Examining data/rate4site-3.0.0/src/phylogeny/simulateJumpsAbstract.h Examining data/rate4site-3.0.0/src/phylogeny/simulateCodonsJumps.h Examining data/rate4site-3.0.0/src/phylogeny/treeIt.h Examining data/rate4site-3.0.0/src/phylogeny/likelihoodComputationGL.h Examining data/rate4site-3.0.0/src/phylogeny/tree.h Examining data/rate4site-3.0.0/src/phylogeny/bblEMProportionalEB.h Examining data/rate4site-3.0.0/src/phylogeny/fromCountTableComponentToDistancePropEB.h Examining data/rate4site-3.0.0/src/phylogeny/likeDistPropEB.h Examining data/rate4site-3.0.0/src/phylogeny/bblLSProportionalEB.h Examining data/rate4site-3.0.0/src/phylogeny/phylipFormat.h Examining data/rate4site-3.0.0/src/phylogeny/maseFormat.h Examining data/rate4site-3.0.0/src/phylogeny/clustalFormat.h Examining data/rate4site-3.0.0/src/phylogeny/fastaFormat.h Examining data/rate4site-3.0.0/src/phylogeny/phylipSequentialFormat.h Examining data/rate4site-3.0.0/src/phylogeny/molphyFormat.h Examining data/rate4site-3.0.0/src/phylogeny/getRandomWeights.h Examining data/rate4site-3.0.0/src/phylogeny/nexusFormat.h Examining data/rate4site-3.0.0/src/phylogeny/alphabet.cpp Examining data/rate4site-3.0.0/src/phylogeny/sequenceContainer.cpp Examining data/rate4site-3.0.0/src/phylogeny/sequence.cpp Examining data/rate4site-3.0.0/src/phylogeny/mulAlphabet.cpp Examining data/rate4site-3.0.0/src/phylogeny/someUtil.cpp