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/avogadrolibs-1.93.0+git20200509.e169315/avogadro/command/avobabel.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/command/cjsontocml.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/command/qube.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/array.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/atom.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/atomtyper-inline.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/atomtyper.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/avogadrocore.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/avospglib.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/basisset.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/bond.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/color3f.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/coordinateblockgenerator.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/coordinateblockgenerator.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/coordinateset.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/crystaltools.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/crystaltools.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/cube.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/cube.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/elementdata.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/elements.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/elements.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/gaussianset.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/gaussianset.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/gaussiansettools.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/gaussiansettools.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/graph.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/graph.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/matrix.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/mdlvalence_p.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/mesh.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/mesh.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/molecule.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/molecule.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/mutex.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/mutex.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/nameatomtyper.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/nameatomtyper.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/residue.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/residue.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/residuedata.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/ringperceiver.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/ringperceiver.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/sharedmutex.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/sharedmutex.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/slaterset.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/slaterset.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/slatersettools.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/slatersettools.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/spacegroupdata.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/spacegroups.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/spacegroups.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/symbolatomtyper.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/symbolatomtyper.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/types.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/unitcell.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/unitcell.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/utilities.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/variant-inline.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/variant.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/variantmap.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/variantmap.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/vector.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/version.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/avospglib.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/cjsonformat.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/cjsonformat.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/cmlformat.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/cmlformat.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/fileformat.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/fileformat.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/fileformatmanager.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/fileformatmanager.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/gromacsformat.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/gromacsformat.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/hdf5dataformat.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/hdf5dataformat.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/lammpsformat.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/lammpsformat.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/mdlformat.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/mdlformat.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/mmtfformat.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/mmtfformat.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/pdbformat.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/pdbformat.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/vaspformat.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/vaspformat.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/xyzformat.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/xyzformat.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/batchjob.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/batchjob.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/inputgenerator.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/inputgenerator.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/inputgeneratordialog.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/inputgeneratordialog.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/inputgeneratorwidget.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/inputgeneratorwidget.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/molequeuedialog.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/molequeuedialog.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/molequeuemanager.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/molequeuemanager.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/molequeuequeuelistmodel.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/molequeuequeuelistmodel.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/molequeuewidget.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/molequeuewidget.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/protocall/matrixserialization.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/protocall/matrixserialization.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/protocall/moleculedeserializer.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/protocall/moleculedeserializer.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/protocall/moleculeserializer.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/protocall/moleculeserializer.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/protocall/utils.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/backgroundfileformat.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/backgroundfileformat.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/containerwidget.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/containerwidget.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/customelementdialog.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/customelementdialog.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/elementdetail_p.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/elementdetail_p.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/elementitem_p.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/elementitem_p.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/elementtranslator.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/elementtranslator.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/extensionplugin.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/extensionplugin.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/filebrowsewidget.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/filebrowsewidget.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/fileformatdialog.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/fileformatdialog.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/generichighlighter.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/generichighlighter.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/hydrogentools.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/hydrogentools.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/interfacescript.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/interfacescript.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/interfacewidget.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/interfacewidget.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/meshgenerator.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/meshgenerator.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/molecule.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/molecule.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/moleculemodel.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/moleculemodel.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/multiviewwidget.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/multiviewwidget.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/periodictablescene_p.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/periodictablescene_p.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/periodictableview.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/periodictableview.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/persistentatom.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/persistentbond.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/pythonscript.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/pythonscript.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/rwmolecule.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/rwmolecule.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/sceneplugin.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/sceneplugin.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/scenepluginmodel.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/scenepluginmodel.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/scriptloader.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/scriptloader.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/toolplugin.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/toolplugin.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/utilities.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/utilities.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/viewfactory.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/viewfactory.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtopengl/activeobjects.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtopengl/activeobjects.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtopengl/glwidget.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtopengl/glwidget.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtopengl/qttextrenderstrategy.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtopengl/qttextrenderstrategy.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/3dmol/3dmol.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/3dmol/3dmol.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/3dmol/3dmoldialog.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/3dmol/3dmoldialog.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/apbs/apbs.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/apbs/apbs.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/apbs/apbsdialog.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/apbs/apbsdialog.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/apbs/apbsoutputdialog.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/apbs/apbsoutputdialog.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/apbs/opendxreader.cpp
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Examining data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/molequeuequeuelistmodeltest.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/rwmoleculetest.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtopengl/glwidgettest.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtopengl/qttextlabeltest.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtopengl/qttextrenderstrategytest.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/tests/rendering/absoluteoverlayquadstrategytest.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/tests/rendering/absolutequadstrategytest.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/tests/rendering/billboardquadstrategytest.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/tests/rendering/cameratest.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/tests/rendering/nodetest.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/tests/rendering/overlayquadstrategytest.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/tests/rendering/spheregeometrytest.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/gif-h/gif.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/libgwavi/avi-utils.c
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/libgwavi/avi-utils.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/libgwavi/fileio.c
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/libgwavi/fileio.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/libgwavi/gwavi.c
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/libgwavi/gwavi.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/libgwavi/gwavi_private.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/adl_serializer.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/conversions/from_json.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/conversions/to_chars.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/conversions/to_json.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/exceptions.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/input/binary_reader.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/input/input_adapters.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/input/json_sax.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/input/lexer.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/input/parser.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/iterators/internal_iterator.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/iterators/iter_impl.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/iterators/iteration_proxy.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/iterators/json_reverse_iterator.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/iterators/primitive_iterator.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/json_pointer.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/json_ref.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/macro_scope.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/macro_unscope.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/meta/cpp_future.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/meta/detected.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/meta/is_sax.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/meta/type_traits.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/meta/void_t.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/output/binary_writer.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/output/output_adapters.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/output/serializer.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/value_t.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/json.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/json_fwd.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugiconfig.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.hpp
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/struct/struct.c
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/struct/struct.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/struct/struct_endian.c
Examining data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/struct/struct_endian.h
Examining data/avogadrolibs-1.93.0+git20200509.e169315/utilities/bodr/bodrparse.cxx
Examining data/avogadrolibs-1.93.0+git20200509.e169315/utilities/encodefile/encodefile.cxx
Examining data/avogadrolibs-1.93.0+git20200509.e169315/utilities/resdata/resdataparse.cxx
Examining data/avogadrolibs-1.93.0+git20200509.e169315/utilities/vtktesting/imageregressiontest.h

FINAL RESULTS:

data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/pythonscript.cpp:78:28:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
  realArgs.append(QLocale::system().name());
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/plugindownloader/zipextracter.cpp:57:3:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
  strcpy(result, str.c_str());
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/command/qube.cpp:74:23:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
      orbitalNumber = atoi(argv[++i]);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:86:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buff[BUFSIZ];
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:87:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char fmt[BUFSIZ];
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:91:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char raw[84];
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/fileformat.cpp:40:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
bool FileFormat::open(const std::string& fileName_, Operation mode_)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/fileformat.cpp:103:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  bool result = open(fileName_, Read);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/fileformat.cpp:115:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  bool result = open(fileName_, Write);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/fileformat.h:83:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  bool open(const std::string& fileName, Operation mode);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/hdf5dataformat.cpp:167:26:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      if (FILE* handle = fopen(filename_.c_str(), "r")) {
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/lammpsformat.cpp:495:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char atomline[200];
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/lammpsformat.cpp:496:7:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
      sprintf(atomline, "%-*d %d %10f %10f %10f\n",
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/lammpsformat.cpp:512:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char bondline[200];
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/lammpsformat.cpp:517:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        sprintf(bondline, "%-*d %7d %7d %7d\n",
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/lammpsformat.cpp:527:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        sprintf(bondline, "%-*d %7d %7d %7d\n",
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/lammpsformat.cpp:538:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        sprintf(bondline, "%-*d %7d %7d %7d\n",
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/lammpsformat.cpp:550:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char simBoxBlock[200];
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/lammpsformat.cpp:553:5:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
    sprintf(simBoxBlock,
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/lammpsformat.cpp:560:5:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
    sprintf(simBoxBlock,
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/inputgenerator.cpp:207:49:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                if (refFile.exists() && refFile.open(QFile::ReadOnly)) {
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/inputgeneratorwidget.cpp:472:24:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if (!QFile(fileName).open(QFile::WriteOnly)) {
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/inputgeneratorwidget.cpp:486:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if (file.open(QFile::WriteOnly | QFile::Text)) {
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/inputgeneratorwidget.cpp:544:43:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      if (!QFile(info.absoluteFilePath()).open(QFile::WriteOnly)) {
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/molequeue/inputgeneratorwidget.cpp:597:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if (file.open(QFile::WriteOnly | QFile::Text)) {
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/interfacescript.cpp:309:49:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                if (refFile.exists() && refFile.open(QFile::ReadOnly)) {
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/scriptloader.cpp:87:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            jsonFile.open(QIODevice::ReadOnly | QIODevice::Text);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/apbs/apbsdialog.cpp:200:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  file.open(QFile::WriteOnly);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/apbs/opendxreader.cpp:41:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if (!file.open(QFile::ReadOnly)) {
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/clientserver/avogadroserver.cpp:157:12:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    port = atoi(argv[1]);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/clientserver/avoremotemoleculeservice.cpp:32:32:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
void AvoRemoteMoleculeService::open(const OpenRequest* input,
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/clientserver/avoremotemoleculeservice.h:33:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  void open(const OpenRequest* input, OpenResponse* output,
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/clientserver/clientserver.cpp:191:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  proxy.open(&request, response, callback);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/cp2kinput/cp2kinputdialog.cpp:970:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if (file.open(QFile::WriteOnly | QFile::Text)) {
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/gamessinput/gamessinputdialog.cpp:679:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if (file.open(QFile::WriteOnly | QFile::Text)) {
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/lammpsinput/lammpsinputdialog.cpp:289:48:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if (!QFile(jobFileInfo.absoluteFilePath()).open(QFile::WriteOnly)) {
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/lammpsinput/lammpsinputdialog.cpp:304:48:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if (!QFile(molFileInfo.absoluteFilePath()).open(QFile::WriteOnly)) {
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/lammpsinput/lammpsinputdialog.cpp:357:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if (jobFile.open(QFile::WriteOnly | QFile::Text)) {
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/lammpsinput/lammpsinputdialog.cpp:371:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if (molFile.open(QFile::WriteOnly | QFile::Text)) {
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/openmminput/openmminputdialog.cpp:387:48:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if (!QFile(jobFileInfo.absoluteFilePath()).open(QFile::WriteOnly)) {
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/openmminput/openmminputdialog.cpp:402:48:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if (!QFile(molFileInfo.absoluteFilePath()).open(QFile::WriteOnly)) {
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/openmminput/openmminputdialog.cpp:455:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if (jobFile.open(QFile::WriteOnly | QFile::Text)) {
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/openmminput/openmminputdialog.cpp:469:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if (molFile.open(QFile::WriteOnly | QFile::Text)) {
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/playertool/playertool.cpp:328:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      buffer.open(QIODevice::WriteOnly);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/plugindownloader/downloaderwidget.cpp:278:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    out.open(QIODevice::WriteOnly);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/povray/povray.cpp:85:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if (!file.open(QIODevice::WriteOnly))
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimcriticalpointlocator.cpp:116:29:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  nuclearCriticalPointsFile.open(QIODevice::ReadOnly);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimcriticalpointlocator.cpp:514:29:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  nuclearCriticalPointsFile.open(QIODevice::WriteOnly);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimcriticalpointlocator.cpp:932:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  temporaryFile.open();
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimcubature.cpp:419:5:  [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(pts, p, sizeof(double) * dim);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimcubature.cpp:442:7:  [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(pts, p, sizeof(double) * dim);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimcubature.cpp:445:7:  [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(pts, p, sizeof(double) * dim);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimcubature.cpp:448:7:  [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(pts, p, sizeof(double) * dim);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimcubature.cpp:451:7:  [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(pts, p, sizeof(double) * dim);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimcubature.cpp:465:3:  [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(pts, p, sizeof(double) * dim);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimcubature.cpp:470:5:  [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(pts, p, sizeof(double) * dim);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimcubature.cpp:474:5:  [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(pts, p, sizeof(double) * dim);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimcubature.cpp:478:5:  [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(pts, p, sizeof(double) * dim);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimcubature.cpp:482:5:  [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(pts, p, sizeof(double) * dim);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimcubature.cpp:2377:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  temporaryFile.open();
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.cpp:86:10:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  double atol[4], rtol[4], t, tout, y[4];
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.cpp:112:5:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    atol[0] = 0.0;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.cpp:116:5:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    atol[1] = 5.0E-5;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.cpp:117:5:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    atol[2] = 5.0E-5;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.cpp:118:5:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    atol[3] = 5.0E-5;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.cpp:147:41:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    lsoda(neq, y, &t, tout, itol, rtol, atol, itask, &istate, iopt, jt, iwork1,
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.cpp:829:66:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                                 int itol, double* rtol, double* atol,
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.cpp:1116:13:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    atoli = atol[1];
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.cpp:1121:17:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        atoli = atol[i];
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.cpp:1194:23:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    ewset(itol, rtol, atol, y);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.cpp:1240:17:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        atoli = atol[1];
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.cpp:1243:21:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
            atoli = atol[i];
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.cpp:1387:25:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
      ewset(itol, rtol, atol, yh[1]);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.cpp:1914:66:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
void QTAIMLSODAIntegrator::ewset(int itol, double* rtol, double* atol,
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.cpp:1922:44:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        ewt[i] = rtol[1] * fabs(ycur[i]) + atol[1];
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.cpp:1926:44:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        ewt[i] = rtol[1] * fabs(ycur[i]) + atol[i];
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.cpp:1930:44:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        ewt[i] = rtol[i] * fabs(ycur[i]) + atol[1];
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.cpp:1934:44:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        ewt[i] = rtol[i] * fabs(ycur[i]) + atol[i];
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.h:94:22:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
             double* atol, int itask, int* istate, int iopt, int jt, int iwork1,
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimlsodaintegrator.h:99:46:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  void ewset(int itol, double* rtol, double* atol, double* ycur);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimwavefunction.cpp:50:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  success = file.open(QIODevice::ReadOnly | QIODevice::Text);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimwavefunction.h:48:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    file.open(QIODevice::WriteOnly);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/qtaim/qtaimwavefunction.h:76:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    file.open(QIODevice::ReadOnly);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/surfaces/surfaces.cpp:473:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    buffer.open(QIODevice::WriteOnly);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/symmetry/symmetry.cpp:199:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char point_group[6];
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/vrml/vrml.cpp:85:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if (!file.open(QIODevice::WriteOnly))
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/quantumio/gamessukout.cpp:196:7:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  ifs.open(filename.c_str());
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/quantumio/gamessukout.cpp:288:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char coordEnd[86] = "         "
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/quantumio/gamessukout.h:118:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[BUFF_SIZE];
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/rendering/meshgeometry.h:41:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    unsigned char padding[4]; //  4 bytes
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/rendering/scene.h:85:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char padding[4];  //  4 bytes
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/rendering/textproperties.h:157:36:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  void setColorRgba(const unsigned char rgba[4]);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/rendering/textproperties.h:159:27:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  void colorRgba(unsigned char rgba[4]) const;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/rendering/textproperties.h:162:35:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  void setColorRgb(const unsigned char rgb[3]);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/rendering/textproperties.h:164:26:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  void colorRgb(unsigned char rgb[3]) const;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/rendering/textproperties.h:183:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char m_rgba[4];
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/rendering/textproperties.h:241:57:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
inline void TextProperties::setColorRgba(const unsigned char rgba[4])
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/rendering/textproperties.h:254:48:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
inline void TextProperties::colorRgba(unsigned char rgba[4]) const
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/rendering/textproperties.h:275:56:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
inline void TextProperties::setColorRgb(const unsigned char rgb[3])
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/rendering/textproperties.h:287:47:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
inline void TextProperties::colorRgb(unsigned char rgb[3]) const
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/hdf5test.cpp:31:18:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  FILE* handle = fopen(filename, "r");
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/lammpstest.cpp:42:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  multi.open(AVOGADRO_DATA "/data/silicon_bulk.dump",
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/lammpstest.cpp:106:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  format.open(AVOGADRO_DATA "/data/silicon_bulk.dump", FileFormat::Read);
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/lammpstest.cpp:112:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  format.open(AVOGADRO_DATA "/data/silicon_bulk.dump",
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/mdltest.cpp:125:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  multi.open(AVOGADRO_DATA "/data/multi.sdf",
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/mdltest.cpp:162:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  multi.open(AVOGADRO_DATA "/data/multi.sdf",
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/mdltest.cpp:174:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  multi.open("multitmp.sdf", FileFormat::Write | FileFormat::MultiMolecule);
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/mdltest.cpp:180:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  multi.open("multitmp.sdf", FileFormat::Read | FileFormat::MultiMolecule);
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/mdltest.cpp:195:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  multi.open(AVOGADRO_DATA "/data/pubchem3.sdf",
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/vasptest.cpp:131:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  format.open(AVOGADRO_DATA "/data/rutile.POSCAR", FileFormat::Read);
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/vasptest.cpp:140:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  multi.open(AVOGADRO_DATA "/data/ti_bulk.OUTCAR",
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/vasptest.cpp:195:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  format.open(AVOGADRO_DATA "/data/ti_bulk.OUTCAR", FileFormat::Read);
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/vasptest.cpp:201:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  format.open(AVOGADRO_DATA "/data/ti_bulk.OUTCAR",
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/xyztest.cpp:142:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  format.open(AVOGADRO_DATA "/data/multi.xyz", FileFormat::Read);
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/xyztest.cpp:148:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  format.open(AVOGADRO_DATA "/data/multi.xyz",
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/xyztest.cpp:158:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  multi.open(AVOGADRO_DATA "/data/multi.xyz",
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/xyztest.cpp:197:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  multi.open(AVOGADRO_DATA "/data/multi.xyz",
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/xyztest.cpp:209:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  multi.open("multitmp.xyz", FileFormat::Write | FileFormat::MultiMolecule);
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/xyztest.cpp:215:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  multi.open("multitmp.xyz", FileFormat::Read | FileFormat::MultiMolecule);
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/inputgeneratortest.cpp:107:24:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  EXPECT_TRUE(testFile.open(QFile::ReadOnly));
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/inputgeneratorwidgettest.cpp:98:24:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  EXPECT_TRUE(testFile.open(QFile::ReadOnly | QFile::Text));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/gif-h/gif.h:373:3:  [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(destroyableImage, nextFrame, imageSize);
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/gif-h/gif.h:743:15:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  writer->f = fopen(filename, "wb");
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/libgwavi/gwavi.c:84:14:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if ((out = fopen(filename, "wb+")) == NULL) {
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/libgwavi/gwavi.c:115:9:  [2] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant string.
  (void)strcpy(gwavi->stream_header_v.data_type, "vids");
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/libgwavi/gwavi.c:116:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  (void)memcpy(gwavi->stream_header_v.codec, fourcc, 4);
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/libgwavi/gwavi.c:140:5:  [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(gwavi->stream_header_a.data_type, "auds", 4);
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/libgwavi/gwavi.c:462:3:  [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(gwavi->stream_header_v.codec, fourcc, 4);
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/libgwavi/gwavi_private.h:37:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char data_type[5];  /* fccType */
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/libgwavi/gwavi_private.h:38:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char codec[5];      /* fccHandler */
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/conversions/to_chars.hpp:42:10:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    std::memcpy(&target, &source, sizeof(Source));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/input/binary_reader.hpp:898:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        std::memcpy(&result, vec.data(), sizeof(NumberType));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/input/binary_reader.hpp:1675:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char cr[3];
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/input/lexer.hpp:1179:17:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
                char cs[9];
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/output/binary_writer.hpp:695:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        std::memcpy(vec.data(), &n, sizeof(NumberType));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:85:50:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
#define PUGI__STATIC_ASSERT(cond) { static const char condition_failed[(cond) ? 1 : -1] = {0}; (void)condition_failed[0]; }
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:96:12:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
using std::memcpy;
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:281:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char data[1];
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:1030:24:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	static const unsigned char chartype_table[256] =
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:1060:24:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	static const unsigned char chartypex_table[256] =
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:1168:4:  [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(buffer, contents, size);
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:1408:3:  [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(out_buffer, data, prefix_length);
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:1546:4:  [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(dest, source, (source_length + 1) * sizeof(char_t));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:1559:4:  [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(buf, source, (source_length + 1) * sizeof(char_t));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:2890:4:  [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(buffer + bufsize, data, length * sizeof(char_t));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:3361:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char buf[128];
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:3362:3:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
		sprintf(buf, "%d", value);
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:3369:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char buf[128];
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:3370:3:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
		sprintf(buf, "%u", value);
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:3377:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char buf[128];
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:3378:3:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
		sprintf(buf, "%g", value);
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:3536:4:  [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(write, chunk->data, chunk->size);
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:3627:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char mode_ascii[4] = {0};
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:3631:18:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		FILE* result = fopen(path_utf8, mode_ascii);
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:5213:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		FILE* file = fopen(path_, "rb");
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:5317:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		FILE* file = fopen(path_, (flags & format_save_file_text) ? "w" : "wb");
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:5656:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char data[
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:5752:5:  [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(result, ptr, old_size);
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:5873:4:  [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(result, string, length * sizeof(char_t));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:5933:22:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
				if (!_uses_heap) memcpy(result, _buffer, target_length * sizeof(char_t));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:5936:5:  [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(result + target_length, o._buffer, source_length * sizeof(char_t));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:6304:3:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
		sprintf(buffer, "%.*e", DBL_DIG, value);
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:6312:18:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		int exponent = atoi(exponent_string + 1);
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:6339:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char mantissa_buffer[64];
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:6453:3:  [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(scratch, begin, length * sizeof(char_t));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:6677:3:  [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(result->name, name, (length + 1) * sizeof(char_t));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:6749:3:  [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(scratch, begin, length * sizeof(char_t));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:6878:4:  [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(_end, begin_, count * sizeof(xpath_node));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:8771:5:  [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(c, value.begin, length * sizeof(char_t));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:9738:4:  [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(storage, begin_, size_ * sizeof(xpath_node));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:9913:3:  [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(copy, value, size);
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:10111:4:  [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(buffer, r.c_str(), (size - 1) * sizeof(char_t));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.hpp:854:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char _memory[192];
data/avogadrolibs-1.93.0+git20200509.e169315/utilities/bodr/bodrparse.cxx:43:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char c[3];
data/avogadrolibs-1.93.0+git20200509.e169315/utilities/bodr/bodrparse.cxx:137:44:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                static_cast<unsigned char>(atoi(scalarNode.child_value()));
data/avogadrolibs-1.93.0+git20200509.e169315/utilities/encodefile/encodefile.cxx:36:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buffer[256];
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/core/array.h:373:15:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
         std::equal(lhs.begin(), lhs.end(), rhs.begin());
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/cjsonformat.cpp:83:19:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool CjsonFormat::read(std::istream& file, Molecule& molecule)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/cjsonformat.h:50:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& in, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/cmlformat.cpp:276:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      if (attribute && strlen(attribute.value()) == 1) {
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/cmlformat.cpp:416:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool CmlFormat::read(std::istream& file, Core::Molecule& mol)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/cmlformat.h:58:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& in, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:81:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool DcdFormat::read(std::istream& inStream, Core::Molecule& mol)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:109:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:122:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:156:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:160:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:166:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:171:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:175:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:184:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:192:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:196:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:213:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:223:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:227:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:240:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:248:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:264:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      inStream.read(buff, leadingNum);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:266:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, sizeof(int));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:277:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:283:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:289:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:295:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:300:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:306:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:311:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:337:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:341:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, sizeToRead);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:343:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, sizeof(int));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:368:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:374:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:379:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:385:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:390:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:396:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:401:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:414:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:418:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      inStream.read(buff, sizeToRead);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.cpp:420:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      inStream.read(buff, sizeof(int));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/dcdformat.h:55:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& inStream, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/fileformat.cpp:90:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  return read(*m_in, molecule);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/fileformat.cpp:130:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  return read(stream, molecule);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/fileformat.h:126:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  virtual bool read(std::istream& in, Core::Molecule& molecule) = 0;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/gromacsformat.cpp:65:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool GromacsFormat::read(std::istream& in, Molecule& molecule)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/gromacsformat.h:59:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& in, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/lammpsformat.cpp:61:30:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool LammpsTrajectoryFormat::read(std::istream& inStream, Core::Molecule& mol)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/lammpsformat.cpp:421:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool LammpsDataFormat::read(std::istream& inStream, Core::Molecule& mol)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/lammpsformat.h:64:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& inStream, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/lammpsformat.h:95:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& inStream, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/mdlformat.cpp:55:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool MdlFormat::read(std::istream& in, Core::Molecule& mol)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/mdlformat.h:61:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& in, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/mmtfformat.cpp:56:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool MMTFFormat::read(std::istream& file, Molecule& molecule)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/mmtfformat.h:64:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& in, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/pdbformat.cpp:34:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool PdbFormat::read(std::istream& in, Core::Molecule& mol)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/pdbformat.h:60:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& in, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:104:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool TrrFormat::read(std::istream& inStream, Core::Molecule& mol)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:120:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:133:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:138:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:150:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:163:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:170:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:182:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:198:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:230:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
          inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:235:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
          inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:282:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:295:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:300:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:312:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:326:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:333:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:346:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
          inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:362:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
          inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:393:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.cpp:398:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            inStream.read(buff, struct_calcsize(fmt));
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/trrformat.h:58:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& inStream, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/vaspformat.cpp:51:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool PoscarFormat::read(std::istream& inStream, Core::Molecule& mol)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/vaspformat.cpp:342:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool OutcarFormat::read(std::istream& inStream, Core::Molecule& mol)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/vaspformat.h:58:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& inStream, Core::Molecule& mol) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/vaspformat.h:90:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& inStream, Core::Molecule& mol);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/xyzformat.cpp:63:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool XyzFormat::read(std::istream& inStream, Core::Molecule& mol)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/io/xyzformat.h:58:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& inStream, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/backgroundfileformat.cpp:35:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void BackgroundFileFormat::read()
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtgui/backgroundfileformat.h:94:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void read();
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/openbabel/obfileformat.cpp:95:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool OBFileFormat::read(std::istream& in, Core::Molecule& molecule)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/openbabel/obfileformat.cpp:144:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read(input.data(), length);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/openbabel/obfileformat.h:45:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& in, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/scriptfileformats/fileformatscript.cpp:58:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool FileFormatScript::read(std::istream& in, Core::Molecule& molecule)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/scriptfileformats/fileformatscript.cpp:78:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  in.read(buffer.data(), size);
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/qtplugins/scriptfileformats/fileformatscript.h:146:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& in, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/quantumio/gamessus.cpp:63:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool GAMESSUSOutput::read(std::istream& in, Core::Molecule& molecule)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/quantumio/gamessus.h:54:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& in, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/quantumio/gaussiancube.cpp:48:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool GaussianCube::read(std::istream& in, Core::Molecule& molecule)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/quantumio/gaussiancube.h:55:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& in, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/quantumio/gaussianfchk.cpp:62:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool GaussianFchk::read(std::istream& in, Core::Molecule& molecule)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/quantumio/gaussianfchk.h:57:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& in, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/quantumio/molden.cpp:65:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool MoldenFile::read(std::istream& in, Core::Molecule& molecule)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/quantumio/molden.h:54:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& in, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/quantumio/mopacaux.cpp:58:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool MopacAux::read(std::istream& in, Core::Molecule& molecule)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/quantumio/mopacaux.h:55:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& in, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/quantumio/nwchemjson.cpp:55:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool NWChemJson::read(std::istream& file, Molecule& molecule)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/quantumio/nwchemjson.h:56:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& in, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/quantumio/nwchemlog.cpp:59:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool NWChemLog::read(std::istream& in, Core::Molecule& molecule)
data/avogadrolibs-1.93.0+git20200509.e169315/avogadro/quantumio/nwchemlog.h:52:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream& in, Core::Molecule& molecule) override;
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/fileformatmanagertest.cpp:176:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool read(std::istream&, Molecule&) override { return false; }
data/avogadrolibs-1.93.0+git20200509.e169315/tests/io/lammpstest.cpp:39:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
TEST(LammpsTest, read)
data/avogadrolibs-1.93.0+git20200509.e169315/tests/protocall/moleculeserialization.cpp:48:8:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  bool equal(const Avogadro::MatrixX& mat1, const Avogadro::MatrixX& mat2)
data/avogadrolibs-1.93.0+git20200509.e169315/tests/protocall/moleculeserialization.cpp:92:23:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    EXPECT_TRUE(this->equal(expected2d[i], actual2d[i]));
data/avogadrolibs-1.93.0+git20200509.e169315/tests/protocall/moleculeserialization.cpp:100:23:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    EXPECT_TRUE(this->equal(expected3d[i], actual3d[i]));
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/rwmoleculetest.cpp:329:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  ASSERT_TRUE(std::equal(mol.atomicNumbers().begin(), mol.atomicNumbers().end(),
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/rwmoleculetest.cpp:333:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(mol.atomicNumbers().begin(), mol.atomicNumbers().end(),
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/rwmoleculetest.cpp:393:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(mol.atomPositions3d().begin(),
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/rwmoleculetest.cpp:396:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(mol.atomPositions3d().begin(),
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/rwmoleculetest.cpp:399:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(mol.atomPositions3d().begin(),
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/rwmoleculetest.cpp:415:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(mol.atomPositions3d().begin(),
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/rwmoleculetest.cpp:419:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(mol.atomPositions3d().begin(),
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/rwmoleculetest.cpp:422:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(mol.atomPositions3d().begin(),
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/rwmoleculetest.cpp:482:10:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    std::equal(pos.begin(), pos.end(), mol.atomPositions3d().begin()));
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/rwmoleculetest.cpp:584:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(pairs.begin(), pairs.end(), mol.bondPairs().begin()));
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/rwmoleculetest.cpp:585:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(ords.begin(), ords.end(), mol.bondOrders().begin()));
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/rwmoleculetest.cpp:613:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(rep.begin(), rep.end(), mol.bondOrders().begin()));
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/rwmoleculetest.cpp:615:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(old.begin(), old.end(), mol.bondOrders().begin()));
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/rwmoleculetest.cpp:617:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(rep.begin(), rep.end(), mol.bondOrders().begin()));
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/rwmoleculetest.cpp:708:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(rep.begin(), rep.end(), mol.bondPairs().begin()));
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/rwmoleculetest.cpp:710:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(old.begin(), old.end(), mol.bondPairs().begin()));
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtgui/rwmoleculetest.cpp:712:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(rep.begin(), rep.end(), mol.bondPairs().begin()));
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtopengl/qttextrenderstrategytest.cpp:75:13:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  if (!std::equal(bbox, bbox + 4, refbbox_1) &&
data/avogadrolibs-1.93.0+git20200509.e169315/tests/qtopengl/qttextrenderstrategytest.cpp:76:13:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      !std::equal(bbox, bbox + 4, refbbox_2)) {
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/nlohmann/detail/input/input_adapters.hpp:322:30:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                        std::strlen(reinterpret_cast<const char*>(b))) {}
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:171:10:  [1] (buffer) wcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		return wcslen(s);
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:173:10:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		return strlen(s);
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:3516:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			stream.read(chunk->data, static_cast<std::streamsize>(sizeof(chunk->data) / sizeof(T)));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:3568:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		stream.read(static_cast<T*>(buffer.data), static_cast<std::streamsize>(read_length));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:3607:19:  [1] (buffer) wcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		size_t length = wcslen(str);
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:5341:34:  [1] (buffer) wcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		return impl::as_utf8_impl(str, wcslen(str));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:5353:34:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		return impl::as_wide_impl(str, strlen(str));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:6294:35:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		truncate_zeros(buffer, buffer + strlen(buffer));
data/avogadrolibs-1.93.0+git20200509.e169315/thirdparty/pugixml/pugixml.cpp:6305:10:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		assert(strlen(buffer) < buffer_size);

ANALYSIS SUMMARY:

Hits = 320
Lines analyzed = 151949 in approximately 3.72 seconds (40804 lines/second)
Physical Source Lines of Code (SLOC) = 100252
Hits@level = [0] 118 [1] 144 [2] 174 [3]   0 [4]   2 [5]   0
Hits@level+ = [0+] 438 [1+] 320 [2+] 176 [3+]   2 [4+]   2 [5+]   0
Hits/KSLOC@level+ = [0+] 4.36899 [1+] 3.19196 [2+] 1.75558 [3+] 0.0199497 [4+] 0.0199497 [5+]   0
Dot directories skipped = 3 (--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.