2026-05-03 02:17
ftp://ftp.de.debian.org/debian/pool/main/libb/libbpp-popgen/libbpp-popgen_2.4.1.orig.tar.gz
cppcheck-options: --library=posix --library=gnu --library=bsd  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j1
platform: Linux-6.8.0-111-generic-x86_64-with-glibc2.39
python: 3.12.3
client-version: 1.3.70
compiler: g++ (Ubuntu 14.2.0-4ubuntu2~24.04.1) 14.2.0
cppcheck: head 2.20.0
head-info: e5c4a73 (2026-05-01 11:10:43 +0200)
count: 347 352
elapsed-time: 3.9 3.5
head-timing-info:

old-timing-info:

head results:
bpp-popgen-2.4.1/src/Bpp/PopGen/BasicAlleleInfo.h:104:3: warning: The class 'BasicAlleleInfo' defines member function with name 'clone' also defined in its parent class 'AlleleInfo'. [duplInheritedMember]
bpp-popgen-2.4.1/src/Bpp/PopGen/AlleleInfo.h:87:3: note: Parent function 'AlleleInfo::clone'
bpp-popgen-2.4.1/src/Bpp/PopGen/BasicAlleleInfo.h:104:3: note: Derived function 'BasicAlleleInfo::clone'
bpp-popgen-2.4.1/src/Bpp/PopGen/BasicAlleleInfo.h:69:3: style: Class 'BasicAlleleInfo' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:134:29: style: The function 'getIdentifier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:91:29: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:134:29: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:174:29: style: The function 'getIdentifier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:91:29: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:174:29: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:214:29: style: The function 'getIdentifier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:91:29: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:214:29: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:254:29: style: The function 'getIdentifier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:91:29: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:254:29: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:294:29: style: The function 'getIdentifier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:91:29: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:294:29: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/BasicAlleleInfo.h:76:12: style: The destructor '~BasicAlleleInfo' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/AlleleInfo.h:63:12: note: Virtual destructor in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/BasicAlleleInfo.h:76:12: note: Destructor in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/BasicAlleleInfo.h:110:8: style: The function 'setId' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/AlleleInfo.h:70:16: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/BasicAlleleInfo.h:110:8: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/BasicAlleleInfo.h:111:22: style: The function 'getId' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/AlleleInfo.h:75:30: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/BasicAlleleInfo.h:111:22: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/BiAlleleMonolocusGenotype.h:75:3: style: Class 'BiAlleleMonolocusGenotype' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bpp-popgen-2.4.1/src/Bpp/PopGen/BiAlleleMonolocusGenotype.h:85:4: style: The destructor '~BiAlleleMonolocusGenotype' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/MonolocusGenotype.h:67:12: note: Virtual destructor in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/BiAlleleMonolocusGenotype.h:85:4: note: Destructor in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/BiAlleleMonolocusGenotype.h:119:23: style: The function 'getAlleleIndex' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/MonolocusGenotype.h:81:31: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/BiAlleleMonolocusGenotype.h:119:23: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/BiAlleleMonolocusGenotype.cpp:55:74: performance: Function parameter 'allele_index' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/LocusInfo.h:84:3: style: Class 'LocusInfo' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/AnalyzedLoci.h:74:3: style: Class 'AnalyzedLoci' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/AnalyzedLoci.cpp:95:0: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/AnalyzedLoci.cpp:108:0: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/AnalyzedLoci.cpp:194:0: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/AnalyzedLoci.cpp:135:76: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/AnalyzedSequences.h:82:3: style: Class 'AnalyzedSequences' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/AnalyzedSequences.cpp:97:13: style: Variable 'alpha' can be declared as pointer to const [constVariablePointer]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:78:19: warning: 'operator=' should check for assignment to self to avoid problems with dynamic memory. [operatorEqToSelf]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Date.h:75:3: style: Class 'Date' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bpp-popgen-2.4.1/src/Bpp/PopGen/MonoAlleleMonolocusGenotype.h:66:3: style: Class 'MonoAlleleMonolocusGenotype' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bpp-popgen-2.4.1/src/Bpp/PopGen/MonoAlleleMonolocusGenotype.h:71:3: style: Class 'MonoAlleleMonolocusGenotype' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotype.h:77:3: style: Class 'MultilocusGenotype' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Individual.h:96:3: style: Class 'Individual' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Group.h:82:3: style: Class 'Group' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainer.h:115:3: style: Class 'PolymorphismSequenceContainer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainer.h:132:3: style: Class 'PolymorphismSequenceContainer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainer.h:150:3: style: Class 'PolymorphismSequenceContainer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Locality.h:73:3: style: Class 'Locality < double >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bpp-popgen-2.4.1/src/Bpp/PopGen/MonoAlleleMonolocusGenotype.h:81:4: style: The destructor '~MonoAlleleMonolocusGenotype' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/MonolocusGenotype.h:67:12: note: Virtual destructor in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/MonoAlleleMonolocusGenotype.h:81:4: note: Destructor in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/MonoAlleleMonolocusGenotype.h:100:23: style: The function 'getAlleleIndex' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/MonolocusGenotype.h:81:31: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/MonoAlleleMonolocusGenotype.h:100:23: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:1280:7: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:1293:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:1320:7: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:1332:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:405:43: style:inconclusive: Function 'addIndividualToGroup' argument 1 names different: declaration 'group_position' definition 'group'. [funcArgNamesDifferent]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.h:255:36: note: Function 'addIndividualToGroup' argument 1 names different: declaration 'group_position' definition 'group'.
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:405:43: note: Function 'addIndividualToGroup' argument 1 names different: declaration 'group_position' definition 'group'.
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:423:48: style:inconclusive: Function 'addEmptyIndividualToGroup' argument 1 names different: declaration 'group_position' definition 'group'. [funcArgNamesDifferent]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.h:263:41: note: Function 'addEmptyIndividualToGroup' argument 1 names different: declaration 'group_position' definition 'group'.
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:423:48: note: Function 'addEmptyIndividualToGroup' argument 1 names different: declaration 'group_position' definition 'group'.
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:1251:12: performance:inconclusive: Use const reference for 'name' to avoid unnecessary data copying. [redundantCopyLocalConst]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:1282:12: performance:inconclusive: Use const reference for 'name' to avoid unnecessary data copying. [redundantCopyLocalConst]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:945:164: performance: Function parameter 'allele_keys' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:973:168: performance: Function parameter 'allele_id' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Locality.h:73:33: performance: Function parameter 'name' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Locality.h:83:33: performance: Function parameter 'name' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:119:45: style: Parameter 'locality' can be declared as reference to const [constParameterReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:1278:36: style: Variable 'gnfe' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:1291:41: style: Variable 'ioobe' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:1317:36: style: Variable 'gnfe' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:1329:41: style: Variable 'ioobe' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:123:0: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:135:0: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:209:0: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:221:0: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:233:0: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:259:5: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:273:0: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:390:0: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:1271:100: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.cpp:1310:100: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSetTools.cpp:58:7: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSetTools.cpp:84:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSetTools.cpp:56:23: style: Variable 'e' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSetTools.cpp:82:25: style: Variable 'e' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSetTools.cpp:68:73: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Group.cpp:78:15: warning:inconclusive: Member variable 'Group::name_' is not assigned a value in 'Group::operator='. [operatorEqVarError]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Group.cpp:105:34: style: Variable 'bie' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Group.cpp:114:0: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Group.cpp:124:0: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Group.cpp:191:0: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Group.cpp:602:7: style: Consider using std::count_if algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Individual.cpp:587:38: style:inconclusive: Technically the member function 'bpp::Individual::getMonolocusGenotype' can be const. [functionConst]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Individual.h:445:28: note: Technically the member function 'bpp::Individual::getMonolocusGenotype' can be const.
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Individual.cpp:587:38: note: Technically the member function 'bpp::Individual::getMonolocusGenotype' can be const.
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Individual.cpp:547:99: performance: Function parameter 'allele_keys' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Individual.cpp:567:103: performance: Function parameter 'allele_id' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Individual.cpp:440:0: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.cpp:54:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/IODataSet.h:67:21: style: Either there is a missing 'override', or the member function 'bpp::IODataSet::getDataType' can be static. [functionStatic]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:60:12: style: The destructor '~AbstractIDataSet' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/IDataSet.h:59:12: note: Virtual destructor in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:60:12: note: Destructor in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:67:16: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/IDataSet.h:65:16: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:67:16: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:69:16: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/IDataSet.h:70:16: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:69:16: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:71:20: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/IDataSet.h:75:20: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:71:20: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:73:20: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/IDataSet.h:80:20: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:73:20: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:60:12: style: The destructor '~AbstractIDataSet' overrides a destructor in a base class but is identical to the overridden function [uselessOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/IDataSet.h:59:12: note: Virtual destructor in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:60:12: note: Destructor in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractODataSet.cpp:54:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractODataSet.h:57:12: style: The destructor '~AbstractODataSet' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/ODataSet.h:59:12: note: Virtual destructor in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractODataSet.h:57:12: note: Destructor in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractODataSet.h:64:16: style: The function 'write' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/ODataSet.h:65:16: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractODataSet.h:64:16: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractODataSet.h:65:16: style: The function 'write' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/ODataSet.h:70:16: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractODataSet.h:65:16: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractODataSet.h:57:12: style: The destructor '~AbstractODataSet' overrides a destructor in a base class but is identical to the overridden function [uselessOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/ODataSet.h:59:12: note: Virtual destructor in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractODataSet.h:57:12: note: Destructor in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Darwin/DarwinDon.h:81:21: style: Either there is a missing 'override', or the member function 'bpp::DarwinDon::getFormatName' can be static. [functionStatic]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Darwin/DarwinDon.h:85:21: style: Either there is a missing 'override', or the member function 'bpp::DarwinDon::getFormatDescription' can be static. [functionStatic]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Darwin/DarwinDon.h:64:4: style: The destructor '~DarwinDon' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractODataSet.h:57:12: note: Virtual destructor in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Darwin/DarwinDon.h:64:4: note: Destructor in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Darwin/DarwinDon.h:71:8: style: The function 'write' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractODataSet.h:64:16: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Darwin/DarwinDon.h:71:8: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Darwin/DarwinDon.h:72:8: style: The function 'write' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractODataSet.h:65:16: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Darwin/DarwinDon.h:72:8: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Darwin/DarwinVarSingle.h:66:3: style: Class 'DarwinVarSingle' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Darwin/DarwinVarSingle.h:67:4: style: The destructor '~DarwinVarSingle' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractODataSet.h:57:12: note: Virtual destructor in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Darwin/DarwinVarSingle.h:67:4: note: Destructor in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Darwin/DarwinVarSingle.h:74:8: style: The function 'write' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractODataSet.h:64:16: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Darwin/DarwinVarSingle.h:74:8: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Darwin/DarwinVarSingle.h:75:8: style: The function 'write' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractODataSet.h:65:16: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Darwin/DarwinVarSingle.h:75:8: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/MultiAlleleMonolocusGenotype.h:73:3: style: Class 'MultiAlleleMonolocusGenotype' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.h:179:5: style: Class 'Record' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultiAlleleMonolocusGenotype.h:83:4: style: The destructor '~MultiAlleleMonolocusGenotype' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/MonolocusGenotype.h:67:12: note: Virtual destructor in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/MultiAlleleMonolocusGenotype.h:83:4: note: Destructor in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/MultiAlleleMonolocusGenotype.h:107:23: style: The function 'getAlleleIndex' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/MonolocusGenotype.h:81:31: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/MultiAlleleMonolocusGenotype.h:107:23: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.h:85:4: style: The destructor '~GeneMapperCsvExport' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:60:12: note: Virtual destructor in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.h:85:4: note: Destructor in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.h:99:8: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:67:16: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.h:99:8: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.h:100:8: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:69:16: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.h:100:8: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.h:101:12: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:71:20: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.h:101:12: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.h:102:12: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:73:20: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.h:102:12: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.cpp:84:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.cpp:82:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.cpp:151:30: style: Variable 's' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.cpp:99:33: style: Variable 'ind_count' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.cpp:133:27: style: Unused variable: alleles_pos [unusedVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.cpp:149:124: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.cpp:152:77: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genepop/Genepop.cpp:69:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genepop/Genepop.h:84:21: style: Either there is a missing 'override', or the member function 'bpp::Genepop::getFormatName' can be static. [functionStatic]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genepop/Genepop.h:89:21: style: Either there is a missing 'override', or the member function 'bpp::Genepop::getFormatDescription' can be static. [functionStatic]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genepop/Genepop.h:65:4: style: The destructor '~Genepop' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:60:12: note: Virtual destructor in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genepop/Genepop.h:65:4: note: Destructor in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genepop/Genepop.h:72:8: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:67:16: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genepop/Genepop.h:72:8: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genepop/Genepop.h:73:8: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:69:16: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genepop/Genepop.h:73:8: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genepop/Genepop.h:74:12: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:71:20: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genepop/Genepop.h:74:12: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genepop/Genepop.h:75:12: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:73:20: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genepop/Genepop.h:75:12: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genepop/Genepop.cpp:69:29: style: Condition '!eof_ok' is always true [knownConditionTrueFalse]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genepop/Genepop.cpp:67:10: note: Assuming that condition '!eof_ok' is not redundant
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genepop/Genepop.cpp:69:29: note: Condition '!eof_ok' is always true
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genepop/Genepop.cpp:65:14: style: Variable 'temp' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genepop/Genepop.cpp:132:79: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genetix/Genetix.h:85:21: style: Either there is a missing 'override', or the member function 'bpp::Genetix::getFormatName' can be static. [functionStatic]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genetix/Genetix.h:89:21: style: Either there is a missing 'override', or the member function 'bpp::Genetix::getFormatDescription' can be static. [functionStatic]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genetix/Genetix.h:66:4: style: The destructor '~Genetix' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:60:12: note: Virtual destructor in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genetix/Genetix.h:66:4: note: Destructor in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genetix/Genetix.h:73:8: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:67:16: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genetix/Genetix.h:73:8: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genetix/Genetix.h:74:8: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:69:16: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genetix/Genetix.h:74:8: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genetix/Genetix.h:75:12: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:71:20: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genetix/Genetix.h:75:12: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genetix/Genetix.h:76:12: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:73:20: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/Genetix/Genetix.h:76:12: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp:159:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp:300:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp:320:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp:349:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp:359:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp:403:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp:549:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp:698:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp:343:19: style:inconclusive: Either there is a missing 'override', or the member function 'bpp::PopgenlibIO::parseSequence_' can be const. [functionConst]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.h:86:8: note: Either there is a missing 'override', or the member function 'bpp::PopgenlibIO::parseSequence_' can be const.
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp:343:19: note: Either there is a missing 'override', or the member function 'bpp::PopgenlibIO::parseSequence_' can be const.
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.h:174:21: style: Either there is a missing 'override', or the member function 'bpp::PopgenlibIO::getFormatName' can be static. [functionStatic]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.h:178:21: style: Either there is a missing 'override', or the member function 'bpp::PopgenlibIO::getFormatDescription' can be static. [functionStatic]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.h:94:4: style: The destructor '~PopgenlibIO' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:60:12: note: Virtual destructor in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.h:94:4: note: Destructor in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.h:151:8: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:67:16: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.h:151:8: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.h:152:8: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:69:16: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.h:152:8: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.h:153:12: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:71:20: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.h:153:12: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.h:154:12: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h:73:20: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.h:154:12: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.h:163:8: style: The function 'write' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractODataSet.h:64:16: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.h:163:8: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.h:165:8: style: The function 'write' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/AbstractODataSet.h:65:16: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.h:165:8: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp:70:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp:138:10: style: The scope of the variable 'temp' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp:302:10: style: The scope of the variable 'temp' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp:323:10: style: The scope of the variable 'temp' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp:363:10: style: The scope of the variable 'temp' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp:68:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp:138:15: style: Variable 'temp' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Io/PopgenlibIO.cpp:140:16: style: Unused variable: tmp_ss [unusedVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/MultiSeqIndividual.h:98:3: style: Class 'MultiSeqIndividual' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/MultiSeqIndividual.h:148:15: performance: Function 'getId()' should return member 'id_' by const reference. [returnByReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/MultiSeqIndividual.cpp:477:3: warning: Possible leak in public function. The pointer 'genotype_' is not deallocated before it is allocated. [publicAllocationError]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/MultiSeqIndividual.cpp:173:50: performance: Function parameter 'id' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/MultiSeqIndividual.cpp:398:37: style: Variable 'snfe' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/MultiSeqIndividual.cpp:421:37: style: Variable 'ioobe' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/MultiSeqIndividual.cpp:433:57: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:134:29: style: The function 'getIdentifier' overrides a function in a base class but just delegates back to the base class. [uselessOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:91:29: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:134:29: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:174:29: style: The function 'getIdentifier' overrides a function in a base class but just delegates back to the base class. [uselessOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:91:29: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:174:29: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:214:29: style: The function 'getIdentifier' overrides a function in a base class but just delegates back to the base class. [uselessOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:91:29: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:214:29: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:254:29: style: The function 'getIdentifier' overrides a function in a base class but just delegates back to the base class. [uselessOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:91:29: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:254:29: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:294:29: style: The function 'getIdentifier' overrides a function in a base class but just delegates back to the base class. [uselessOverride]
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:91:29: note: Virtual function in base class
bpp-popgen-2.4.1/src/Bpp/PopGen/GeneralExceptions.h:294:29: note: Function in derived class
bpp-popgen-2.4.1/src/Bpp/PopGen/LocusInfo.cpp:88:0: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/LocusInfo.cpp:98:0: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/LocusInfo.cpp:115:0: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/MonoAlleleMonolocusGenotype.cpp:49:78: performance: Function parameter 'allele_index' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/MonolocusGenotypeTools.cpp:50:120: performance: Function parameter 'allele_keys' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultiAlleleMonolocusGenotype.cpp:47:80: performance: Function parameter 'allele_index' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotype.cpp:167:7: style: Consider using std::count_if algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:426:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:783:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:344:7: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:392:7: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:430:30: style: Variable 'f_stats[it->first].Fit' is reassigned a value before the old one has been used. [redundantAssignment]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:426:30: note: f_stats[it->first].Fit is assigned
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:430:30: note: f_stats[it->first].Fit is overwritten
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:699:10: style: The scope of the variable 'Au' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:699:14: style: The scope of the variable 'Bu' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:699:18: style: The scope of the variable 'Cu' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:701:7: style: The scope of the variable 'nb_alleles' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:735:188: style:inconclusive: Function 'getDistanceMatrix' argument 4 names different: declaration 'distance_method' definition 'distance_methode'. [funcArgNamesDifferent]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.h:289:182: note: Function 'getDistanceMatrix' argument 4 names different: declaration 'distance_method' definition 'distance_methode'.
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:735:188: note: Function 'getDistanceMatrix' argument 4 names different: declaration 'distance_method' definition 'distance_methode'.
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:317:104: performance: Function parameter 'locus_positions' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:362:104: performance: Function parameter 'locus_positions' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:576:113: performance: Function parameter 'locus_positions' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:607:113: performance: Function parameter 'locus_positions' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:637:155: performance: Function parameter 'locus_positions' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:637:184: performance: Function parameter 'groups' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:667:155: performance: Function parameter 'locus_positions' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:667:184: performance: Function parameter 'groups' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:697:113: performance: Function parameter 'locus_positions' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:735:137: performance: Function parameter 'locus_positions' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:735:188: performance: Function parameter 'distance_methode' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:342:23: style: Variable 'e' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:390:23: style: Variable 'e' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:85:19: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:131:19: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:269:9: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:292:12: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:586:10: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:617:10: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:701:18: style: Variable 'nb_alleles' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:135:89: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:244:73: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:267:99: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:290:87: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:419:102: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:445:110: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:461:110: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:475:110: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:502:79: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:514:73: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:518:73: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:530:75: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:534:75: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:539:79: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:550:73: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:556:71: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:567:110: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:584:81: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:594:114: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:615:81: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:625:114: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:715:114: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp:739:69: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainer.cpp:264:77: performance: Function parameter 'name' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainer.cpp:276:77: performance: Function parameter 'name' should be passed by const reference. [passedByValue]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainer.cpp:223:0: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainer.cpp:244:7: style: Consider using std::count_if algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainer.cpp:61:73: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainer.cpp:87:73: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainer.cpp:205:63: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp:238:88: portability: Expression 'alleles[j][k[j]++],alleles[j][k[j]++]' depends on order of evaluation of side effects. Behavior is Unspecified according to c++17 [unknownEvaluationOrder]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp:325:88: portability: Expression 'alleles[j][k[j]++],alleles[j][k[j]++]' depends on order of evaluation of side effects. Behavior is Unspecified according to c++17 [unknownEvaluationOrder]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp:115:73: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp:134:75: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp:185:73: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp:251:73: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp:270:75: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp:336:73: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp:351:75: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismMultiGContainerTools.cpp:369:73: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainer.cpp:259:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainer.cpp:276:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainer.cpp:460:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainer.cpp:512:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainer.cpp:257:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainer.cpp:274:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainer.cpp:458:31: style: Variable 'bie' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainer.cpp:510:31: style: Variable 'bie' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainer.cpp:362:3: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp:65:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp:84:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp:95:11: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp:250:7: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp:280:7: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp:450:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp:55:10: style: The scope of the variable 'key' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp:238:34: style: The scope of the variable 'npsc' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp:268:34: style: The scope of the variable 'npsc' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp:572:10: style: The scope of the variable 'key' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp:61:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp:81:27: style: Variable 'ioe' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp:92:43: style: Variable 'snfe' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp:246:23: style: Variable 'e' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp:276:23: style: Variable 'e' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp:402:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp:448:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp:71:83: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/PolymorphismSequenceContainerTools.cpp:578:83: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:1505:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:954:28: style: The member function 'bpp::SequenceStatistics::fstHudson92' can be static. [functionStatic]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.h:737:10: note: The member function 'bpp::SequenceStatistics::fstHudson92' can be static.
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:954:28: note: The member function 'bpp::SequenceStatistics::fstHudson92' can be static.
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:75:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:96:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:122:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:142:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:159:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:179:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:195:15: style: The scope of the variable 'site_in' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:196:15: style: The scope of the variable 'site_out' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:217:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:234:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:263:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:315:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:490:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:520:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:552:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:601:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:624:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:638:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:672:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:686:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:700:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:715:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:730:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:744:15: style: The scope of the variable 'site' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:758:15: style: The scope of the variable 'siteIn' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:759:15: style: The scope of the variable 'siteOut' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:760:15: style: The scope of the variable 'siteCons' can be reduced. [variableScope]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:346:15: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:394:15: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:424:7: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:466:7: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:480:7: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:1522:7: style: Consider using std::count_if algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:1537:7: style: Consider using std::count_if algorithm instead of a raw loop. [useStlAlgorithm]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:75:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:96:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:122:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:142:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:159:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:179:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:195:23: style: Variable 'site_in' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:196:24: style: Variable 'site_out' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:217:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:234:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:263:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:315:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:490:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:520:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:552:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:601:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:672:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:686:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:700:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:715:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:730:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:744:20: style: Variable 'site' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:758:22: style: Variable 'siteIn' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:759:23: style: Variable 'siteOut' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:760:24: style: Variable 'siteCons' is assigned a value that is never used. [unreadVariable]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:334:78: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:344:78: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:378:78: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:392:78: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:421:82: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:562:76: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:1031:76: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:1519:88: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:1534:88: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bpp-popgen-2.4.1/src/Bpp/PopGen/SequenceStatistics.cpp:1552:90: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
diff:
2.20.0 bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.h:506:157: performance: Function parameter 'allele_keys' should be passed by const reference. [passedByValue]
2.20.0 bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/DataSet.h:517:161: performance: Function parameter 'allele_id' should be passed by const reference. [passedByValue]
2.20.0 bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Individual.h:425:31: performance: Function parameter 'allele_keys' should be passed by const reference. [passedByValue]
2.20.0 bpp-popgen-2.4.1/src/Bpp/PopGen/DataSet/Individual.h:436:36: performance: Function parameter 'allele_id' should be passed by const reference. [passedByValue]
2.20.0 bpp-popgen-2.4.1/src/Bpp/PopGen/MonolocusGenotypeTools.h:75:105: performance: Function parameter 'allele_keys' should be passed by const reference. [passedByValue]


DONE