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/libpappsomspp-0.8.8/src/pappsomspp/amino_acid/aa.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/amino_acid/aa.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/amino_acid/aabase.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/amino_acid/aabase.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/amino_acid/aamodification.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/amino_acid/aamodification.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/amino_acid/atomnumberinterface.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/exception/exceptionnotfound.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/exception/exceptionnotimplemented.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/exception/exceptionnotpossible.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/exception/exceptionoutofrange.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/exportinmportconfig.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/fasta/fastafileindexer.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/fasta/fastafileindexer.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/fasta/fastahandlerinterface.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/fasta/fastaoutputstream.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/fasta/fastaoutputstream.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/fasta/fastareader.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/fasta/fastareader.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/fasta/fastawriterinterface.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grpexperiment.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grpexperiment.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grpgroup.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grpgroup.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grpgroupingmonitor.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grpgroupingmonitor.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grpmappeptidetogroup.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grpmappeptidetogroup.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grpmappeptidetosubgroupset.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grpmappeptidetosubgroupset.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grppeptide.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grppeptide.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grppeptideset.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grppeptideset.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grpprotein.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grpprotein.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grpsubgroup.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grpsubgroup.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grpsubgroupset.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/grouping/grpsubgroupset.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/massspectrum/massspectrum.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/massspectrum/massspectrum.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/massspectrum/massspectrumid.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/massspectrum/massspectrumid.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/massspectrum/qualifiedmassspectrum.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/massspectrum/qualifiedmassspectrum.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/msfile/msfileaccessor.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/msfile/msfileaccessor.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/msfile/msfilereader.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/msfile/msfilereader.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/msfile/pwizmsfilereader.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/msfile/pwizmsfilereader.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/msfile/timsmsfilereader.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/msfile/timsmsfilereader.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/msfile/xymsfilereader.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/msfile/xymsfilereader.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/alignment/msrunalignment.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/alignment/msrunalignment.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/alignment/msrunretentiontime.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/alignment/msrunretentiontime.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/alignment/template.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/msrundatasettree.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/msrundatasettree.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/msrundatasettreenode.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/msrundatasettreenode.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/msrundatasettreevisitor.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/msrunid.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/msrunid.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/msrunreader.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/msrunreader.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/output/mgfoutput.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/output/mgfoutput.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/output/mzxmloutput.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/output/mzxmloutput.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/private/pwizmsrunreader.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/private/pwizmsrunreader.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/private/timsmsrunreader.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/private/timsmsrunreader.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/private/timsmsrunreaderms2.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/private/timsmsrunreaderms2.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/private/timsmsrunreaderms2selected.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/private/timsmsrunreaderms2selected.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/xymsrunreader.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/msrun/xymsrunreader.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/mzrange.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/mzrange.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/obo/filterobopsimodsink.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/obo/filterobopsimodsink.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/obo/filterobopsimodtermaccession.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/obo/filterobopsimodtermaccession.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/obo/filterobopsimodtermdiffmono.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/obo/filterobopsimodtermdiffmono.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/obo/filterobopsimodtermlabel.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/obo/filterobopsimodtermlabel.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/obo/filterobopsimodtermname.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/obo/filterobopsimodtermname.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/obo/obopsimod.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/obo/obopsimod.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/pappsoexception.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/ion.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/ion.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptide.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptide.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptidefragment.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptidefragment.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptidefragmention.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptidefragmention.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptidefragmentionlistbase.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptidefragmentionlistbase.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptideinterface.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptideinterface.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptidenaturalisotope.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptidenaturalisotope.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptidenaturalisotopeaverage.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptidenaturalisotopeaverage.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptidenaturalisotopelist.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptidenaturalisotopelist.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptiderawfragmentmasses.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptiderawfragmentmasses.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptidestrparser.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/peptide/peptidestrparser.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/precision.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/precision.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/combiners/massdatacombinerinterface.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/combiners/massdatacombinerinterface.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/combiners/massspectrumcombiner.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/combiners/massspectrumcombiner.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/combiners/massspectrumcombinerfactory.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/combiners/massspectrumcombinerfactory.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/combiners/massspectrumminuscombiner.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/combiners/massspectrumminuscombiner.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/combiners/massspectrumpluscombiner.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/combiners/massspectrumpluscombiner.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/combiners/tracecombiner.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/combiners/tracecombiner.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/combiners/traceminuscombiner.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/combiners/traceminuscombiner.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/combiners/tracepluscombiner.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/combiners/tracepluscombiner.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/detection/tracedetectioninterface.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/detection/tracedetectionmoulon.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/detection/tracedetectionmoulon.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/detection/tracedetectionzivy.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/detection/tracedetectionzivy.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/detection/tracepeak.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/detection/tracepeak.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filterchargedeconvolution.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filterchargedeconvolution.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filtercomplementionenhancer.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filtercomplementionenhancer.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filterinterface.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filterlocalmaximum.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filterlocalmaximum.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filtermorpho.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filtermorpho.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filterpass.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filterpass.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filterpseudocentroid.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filterpseudocentroid.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filterremovec13.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filterremovec13.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filterresample.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filterresample.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filtersuite.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filtersuite.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filtertandemremovec13.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filtertandemremovec13.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filtertriangle.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/filtertriangle.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/pwiz/ms/peakpickerqtof.hpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/pwiz/ms/simplepicker.hpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/pwiz/resample/convert2dense.hpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/savgolfilter.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/savgolfilter.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/tandemwrapper/xtandeminputsaxhandler.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/tandemwrapper/xtandeminputsaxhandler.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/tandemwrapper/xtandemoutputsaxhandler.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/tandemwrapper/xtandemoutputsaxhandler.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/processing/tandemwrapper/xtandempresetsaxhandler.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/enzyme.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/enzyme.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/enzymeproductinterface.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidebuilder.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidebuilder.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidefixedmodificationbuilder.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidefixedmodificationbuilder.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidemethioninremove.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidemethioninremove.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidemodificatorbase.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidemodificatorbase.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidemodificatorpipeline.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidemodificatorpipeline.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidemodificatortee.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidemodificatortee.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidesemienzyme.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidesemienzyme.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidesizefilter.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidesizefilter.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidevariablemodificationbuilder.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidevariablemodificationbuilder.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidevariablemodificationreplacement.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/peptidevariablemodificationreplacement.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/protein.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/protein.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/proteinpeptidelist.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/protein/proteinpeptidelist.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/psm/experimental/ionisotoperatioscore.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/psm/experimental/ionisotoperatioscore.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/psm/morpheus/morpheusscore.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/psm/morpheus/morpheusscore.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/psm/peakionisotopematch.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/psm/peakionisotopematch.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/psm/peakionmatch.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/psm/peakionmatch.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/psm/peptideisotopespectrummatch.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/psm/peptideisotopespectrummatch.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/psm/peptidespectrummatch.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/psm/peptidespectrummatch.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/psm/xtandem/xtandemhyperscore.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/psm/xtandem/xtandemhyperscore.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/psm/xtandem/xtandemhyperscorebis.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/psm/xtandem/xtandemhyperscorebis.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/psm/xtandem/xtandemspectrumprocess.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/psm/xtandem/xtandemspectrumprocess.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/trace/datapoint.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/trace/datapoint.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/trace/linearregression.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/trace/linearregression.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/trace/maptrace.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/trace/maptrace.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/trace/trace.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/trace/trace.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/types.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/utils.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/utils.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/timsbindec.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/timsbindec.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/timsdata.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/timsdata.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/timsframe.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/timsframe.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/timsframebase.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/timsframebase.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/timsms2centroidfilter.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/timsms2centroidfilter.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/xicextractor/timsdirectxicextractor.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/xicextractor/timsdirectxicextractor.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/xicextractor/timsxic.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/xicextractor/timsxic.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/xicextractor/timsxicextractorinterface.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/xicextractor/timsxicextractorinterface.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/graphicdevicewidget.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/graphicdevicewidget.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/massspectrumwidget/massspectrumwidget.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/massspectrumwidget/qcpspectrum.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/basecolormapplotwidget.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/basecolormapplotwidget.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/baseplotwidget.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/baseplotwidget.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/basetraceplotwidget.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/basetraceplotwidget.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/colormapplotconfig.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/colormapplotconfig.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/driftspecmassspeccolormapplotwidget.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/driftspecmassspeccolormapplotwidget.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/driftspectraceplotwidget.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/driftspectraceplotwidget.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/massspectraceplotwidget.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/massspectraceplotwidget.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/ticxicchromdriftspeccolormapplotwidget.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/ticxicchromdriftspeccolormapplotwidget.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/ticxicchrommassspeccolormapplotwidget.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/ticxicchrommassspeccolormapplotwidget.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/ticxicchromtraceplotwidget.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/plotwidget/ticxicchromtraceplotwidget.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/precisionwidget/precisionwidget.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/precisionwidget/precisionwidget.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/xicwidget/qcpxic.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/xicwidget/qcpxic.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/xicwidget/xicwidget.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/widget/xicwidget/xicwidget.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/xic/qualifiedxic.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/xic/qualifiedxic.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/xic/xic.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/xic/xic.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/xic/xicpeptidefragmention.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/xic/xicpeptidefragmention.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/xic/xicpeptidefragmentionnaturalisotope.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/xic/xicpeptidefragmentionnaturalisotope.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/xic/xicpeptideinterface.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/xic/xicpeptideinterface.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/xicextractor/msrunxicextractorfactory.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/xicextractor/msrunxicextractorfactory.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/xicextractor/msrunxicextractorinterface.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/xicextractor/msrunxicextractorinterface.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/xicextractor/private/msrunslice.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/xicextractor/private/msrunslice.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/xicextractor/private/msrunxicextractor.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/xicextractor/private/msrunxicextractor.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/xicextractor/private/msrunxicextractordisk.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/xicextractor/private/msrunxicextractordisk.h Examining data/libpappsomspp-0.8.8/src/pappsomspp/xicextractor/private/msrunxicextractordiskbuffer.cpp Examining data/libpappsomspp-0.8.8/src/pappsomspp/xicextractor/private/msrunxicextractordiskbuffer.h Examining data/libpappsomspp-0.8.8/src/testwin64/test.cpp Examining data/libpappsomspp-0.8.8/test/common.h Examining data/libpappsomspp-0.8.8/test/saxparsers/xtandemresultshandler.cpp Examining data/libpappsomspp-0.8.8/test/saxparsers/xtandemresultshandler.h Examining data/libpappsomspp-0.8.8/test/test_aa.cpp Examining data/libpappsomspp-0.8.8/test/test_big_hyperscore.cpp Examining data/libpappsomspp-0.8.8/test/test_fasta_reader.cpp Examining data/libpappsomspp-0.8.8/test/test_fragmentationcid.cpp Examining data/libpappsomspp-0.8.8/test/test_hyperscore.cpp Examining data/libpappsomspp-0.8.8/test/test_isotope_with_spectrum.cpp Examining data/libpappsomspp-0.8.8/test/test_massrange.cpp Examining data/libpappsomspp-0.8.8/test/test_msrunalignment.cpp Examining data/libpappsomspp-0.8.8/test/test_msrunoutput.cpp Examining data/libpappsomspp-0.8.8/test/test_natural_isotope_average.cpp Examining data/libpappsomspp-0.8.8/test/test_peptide.cpp Examining data/libpappsomspp-0.8.8/test/test_peptidefragment.cpp Examining data/libpappsomspp-0.8.8/test/test_peptidenaturalisotopelist.cpp Examining data/libpappsomspp-0.8.8/test/test_protein.cpp Examining data/libpappsomspp-0.8.8/test/test_psm.cpp Examining data/libpappsomspp-0.8.8/test/test_rawmasslist.cpp Examining data/libpappsomspp-0.8.8/test/test_scan_15968.cpp Examining data/libpappsomspp-0.8.8/test/test_timsframe.cpp Examining data/libpappsomspp-0.8.8/test/test_trace_filters.cpp Examining data/libpappsomspp-0.8.8/test/test_xic.cpp Examining data/libpappsomspp-0.8.8/test/test_xicextractor.cpp Examining data/libpappsomspp-0.8.8/test/test_xtandem_spectrum.cpp FINAL RESULTS: data/libpappsomspp-0.8.8/src/pappsomspp/fasta/fastafileindexer.cpp:47:19: [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(m_fasta_file.open(QIODevice::ReadOnly)) data/libpappsomspp-0.8.8/src/pappsomspp/fasta/fastafileindexer.cpp:122:19: [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). FastaFileIndexer::open() data/libpappsomspp-0.8.8/src/pappsomspp/fasta/fastafileindexer.cpp:126:19: [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(m_fasta_file.open(QIODevice::ReadOnly)) data/libpappsomspp-0.8.8/src/pappsomspp/fasta/fastafileindexer.cpp:152:3: [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). open(); data/libpappsomspp-0.8.8/src/pappsomspp/fasta/fastafileindexer.h:41:16: [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). virtual void open() = 0; data/libpappsomspp-0.8.8/src/pappsomspp/fasta/fastafileindexer.h:61:8: [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() override; data/libpappsomspp-0.8.8/src/pappsomspp/fasta/fastareader.cpp:45:16: [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(fastaFile.open(QIODevice::ReadOnly)) data/libpappsomspp-0.8.8/src/pappsomspp/msfile/xymsfilereader.cpp:50:12: [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::ReadOnly | QFile::Text)) data/libpappsomspp-0.8.8/src/pappsomspp/msrun/xymsrunreader.cpp:62:12: [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::ReadOnly | QFile::Text)) data/libpappsomspp-0.8.8/src/pappsomspp/msrun/xymsrunreader.cpp:145:12: [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::ReadOnly | QFile::Text)) data/libpappsomspp-0.8.8/src/pappsomspp/obo/obopsimod.cpp:153:11: [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). obofile.open(QIODevice::ReadOnly); data/libpappsomspp-0.8.8/src/pappsomspp/processing/filters/savgolfilter.cpp:241:9: [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. free((char *)(m[nrl] + ncl - 1)); data/libpappsomspp-0.8.8/src/pappsomspp/processing/tandemwrapper/tandemwrapperrun.cpp:389:18: [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). if(output_file.open(QIODevice::WriteOnly)) data/libpappsomspp-0.8.8/src/pappsomspp/processing/tandemwrapper/xtandeminputsaxhandler.cpp:51:36: [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(!m_destinationTandemInputFile.open(QIODevice::WriteOnly)) data/libpappsomspp-0.8.8/src/pappsomspp/processing/tandemwrapper/xtandemoutputsaxhandler.cpp:42:37: [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(!m_destinationTandemOutputFile.open(QIODevice::WriteOnly)) data/libpappsomspp-0.8.8/src/pappsomspp/utils.cpp:149:11: [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::Truncate)) data/libpappsomspp-0.8.8/src/pappsomspp/utils.cpp:172:11: [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::Append)) data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/timsbindec.cpp:51:12: [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(QIODevice::ReadOnly)) data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/timsbindec.cpp:150:12: [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(QIODevice::ReadOnly)) data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/timsdata.cpp:169:11: [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(!qdb.open()) data/libpappsomspp-0.8.8/src/pappsomspp/xicextractor/private/msrunxicextractordisk.cpp:256:18: [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). if(!slice_file.open(QIODevice::WriteOnly | QIODevice::Append)) data/libpappsomspp-0.8.8/src/pappsomspp/xicextractor/private/msrunxicextractordisk.cpp:294:22: [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). if(!slice_file.open(QIODevice::ReadOnly)) data/libpappsomspp-0.8.8/src/pappsomspp/xicextractor/private/msrunxicextractordiskbuffer.cpp:149:34: [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(!slice_file.open(QIODevice::WriteOnly)) data/libpappsomspp-0.8.8/src/pappsomspp/xicextractor/private/msrunxicextractordiskbuffer.cpp:158:34: [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(!slice_file.open(QIODevice::WriteOnly | QIODevice::Append)) data/libpappsomspp-0.8.8/test/test_trace_filters.cpp:243:11: [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 | QIODevice::Text)) data/libpappsomspp-0.8.8/test/test_trace_filters.cpp:279:12: [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(file2.open(QIODevice::WriteOnly | QIODevice::Text)) data/libpappsomspp-0.8.8/test/test_trace_filters.cpp:325:12: [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(file3.open(QIODevice::WriteOnly | QIODevice::Text)) data/libpappsomspp-0.8.8/test/test_trace_filters.cpp:357:12: [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(file4.open(QIODevice::WriteOnly | QIODevice::Text)) data/libpappsomspp-0.8.8/test/test_trace_filters.cpp:379:12: [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(file5.open(QIODevice::WriteOnly | QIODevice::Text)) data/libpappsomspp-0.8.8/src/pappsomspp/msfile/pwizmsfilereader.cpp:118:25: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). defaultReaderList.read(Utils::toUtf8StandardString(m_fileName), data/libpappsomspp-0.8.8/src/pappsomspp/msrun/private/pwizmsrunreader.cpp:86:25: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). defaultReaderList.read(file_name_std, msDataPtrVector); data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/timsbindec.cpp:169:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). file.read((char *)&frame_length, 4); data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/timsbindec.cpp:176:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). file.read((char *)&scan_number, 4); data/libpappsomspp-0.8.8/src/pappsomspp/vendors/tims/timsbindec.cpp:190:38: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). QByteArray frame_byte_array = file.read((qint64)frame_length + 2); ANALYSIS SUMMARY: Hits = 34 Lines analyzed = 58672 in approximately 1.46 seconds (40050 lines/second) Physical Source Lines of Code (SLOC) = 35795 Hits@level = [0] 0 [1] 5 [2] 29 [3] 0 [4] 0 [5] 0 Hits@level+ = [0+] 34 [1+] 34 [2+] 29 [3+] 0 [4+] 0 [5+] 0 Hits/KSLOC@level+ = [0+] 0.949853 [1+] 0.949853 [2+] 0.810169 [3+] 0 [4+] 0 [5+] 0 Dot directories skipped = 1 (--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.