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