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/libbpp-phyl-2.4.1/src/Bpp/Phyl/AncestralStateReconstruction.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionList.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionList.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionTools.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionTools.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/BioNJ.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/BioNJ.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/DistanceEstimation.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/DistanceEstimation.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/DistanceMethod.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/HierarchicalClustering.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/NeighborJoining.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/NeighborJoining.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/PGMA.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/PGMA.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/CladogramPlot.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/CladogramPlot.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/PhylogramPlot.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/TreeDrawing.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/TreeDrawingListener.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTransitionModelFormat.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTreeReaderFormat.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTreeWriterFormat.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoDistanceMatrix.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoFrequenciesSet.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoSubstitutionModel.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoTree.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoTreeFactory.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoTreeFactory.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Newick.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Newick.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/NexusIoTree.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/NexusIoTree.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Nhx.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Nhx.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RASTools.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RASTools.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp Examining data/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h