2024-03-25 12:29 ftp://ftp.de.debian.org/debian/pool/main/r/r-cran-rncl/r-cran-rncl_0.8.7.orig.tar.gz cppcheck-options: --library=posix --library=gnu --showtime=top5 --check-library --inconclusive --enable=style,information --inline-suppr --disable=missingInclude --suppress=unmatchedSuppression --template=daca2 --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=valueFlowBailoutIncompleteVar -D__GNUC__ --platform=unix64 -j4 platform: Linux-6.1.0-0.deb11.6-amd64-x86_64-with-glibc2.31 python: 3.9.2 client-version: 1.3.45 compiler: g++ (Debian 10.2.1-6) 10.2.1 20210110 cppcheck: head 2.13.0 head-info: fd7bd50 (2024-03-25 07:57:46 +0100) count: 418 411 elapsed-time: 5.0 7.3 head-timing-info: Tokenizer::simplifyTokens1::ValueFlow: 4.62576s (avg. 4.62576s - 1 result(s)) valueFlowAfterAssign(tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 1.65539s (avg. 0.413846s - 4 result(s)) valueFlowCondition(SimpleConditionHandler{}, tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 1.10494s (avg. 0.276234s - 4 result(s)) valueFlowLifetime(tokenlist, errorLogger, settings): 0.595043s (avg. 0.119009s - 5 result(s)) valueFlowCondition(SymbolicConditionHandler{}, tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 0.570311s (avg. 0.142578s - 4 result(s)) Overall time: 4.97823s old-timing-info: Tokenizer::simplifyTokens1::ValueFlow: 6.90924s (avg. 6.90924s - 1 result(s)) valueFlowAfterAssign(tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 2.81952s (avg. 0.70488s - 4 result(s)) valueFlowCondition(SimpleConditionHandler{}, tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 2.15023s (avg. 0.537558s - 4 result(s)) valueFlowLifetime(tokenlist, errorLogger, settings): 0.66891s (avg. 0.133782s - 5 result(s)) valueFlowCondition(SymbolicConditionHandler{}, tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 0.48027s (avg. 0.120067s - 4 result(s)) Overall time: 7.21479s head results: rncl/src/RcppExports.cpp:23:1: error: There is an unknown macro here somewhere. Configuration is required. If END_RCPP is a macro then please configure it. [unknownMacro] rncl/src/collapse_singles.cpp:33:5: style: Variable 'y' is reassigned a value before the old one has been used. [redundantAssignment] rncl/src/collapse_singles.cpp:32:0: note: y is assigned rncl/src/collapse_singles.cpp:33:5: note: y is overwritten rncl/src/collapse_singles.cpp:39:7: style: Variable 'y' is reassigned a value before the old one has been used. [redundantAssignment] rncl/src/collapse_singles.cpp:38:0: note: y is assigned rncl/src/collapse_singles.cpp:39:7: note: y is overwritten rncl/src/ncl/nxsblock.h:132:11: style:inconclusive: Technically the member function 'NxsBlock::IsEmpty' can be const. [functionConst] rncl/src/nxsblock.cpp:454:16: note: Technically the member function 'NxsBlock::IsEmpty' can be const. rncl/src/ncl/nxsblock.h:132:11: note: Technically the member function 'NxsBlock::IsEmpty' can be const. rncl/src/ncl/nxsblock.h:136:11: style:inconclusive: Technically the member function 'NxsBlock::IsEnabled' can be const. [functionConst] rncl/src/nxsblock.cpp:433:16: note: Technically the member function 'NxsBlock::IsEnabled' can be const. rncl/src/ncl/nxsblock.h:136:11: note: Technically the member function 'NxsBlock::IsEnabled' can be const. rncl/src/ncl/nxsblock.h:137:11: style:inconclusive: Technically the member function 'NxsBlock::IsUserSupplied' can be const. [functionConst] rncl/src/nxsblock.cpp:444:16: note: Technically the member function 'NxsBlock::IsUserSupplied' can be const. rncl/src/ncl/nxsblock.h:137:11: note: Technically the member function 'NxsBlock::IsUserSupplied' can be const. rncl/src/ncl/nxsreader.h:440:3: style: Class 'ExceptionRaisingNxsReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] rncl/src/ncl/nxsreader.h:445:8: style: The function 'NexusError' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] rncl/src/ncl/nxsreader.h:227:16: note: Virtual function in base class rncl/src/ncl/nxsreader.h:445:8: note: Function in derived class rncl/src/ncl/nxsreader.h:449:16: style: The function 'NexusWarn' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] rncl/src/ncl/nxsreader.h:207:16: note: Virtual function in base class rncl/src/ncl/nxsreader.h:449:16: note: Function in derived class rncl/src/ncl/nxsreader.h:451:8: style: The function 'SkippingBlock' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] rncl/src/ncl/nxsreader.h:197:16: note: Virtual function in base class rncl/src/ncl/nxsreader.h:451:8: note: Function in derived class rncl/src/ncl/nxsreader.h:452:8: style: The function 'SkippingDisabledBlock' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] rncl/src/ncl/nxsreader.h:196:16: note: Virtual function in base class rncl/src/ncl/nxsreader.h:452:8: note: Function in derived class rncl/src/ncl/nxsreader.h:463:16: style: The function 'ClearContent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] rncl/src/ncl/nxsreader.h:268:16: note: Virtual function in base class rncl/src/ncl/nxsreader.h:463:16: note: Function in derived class rncl/src/ncl/nxsreader.h:492:12: style: The destructor '~DefaultErrorReportNxsReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] rncl/src/ncl/nxsreader.h:167:14: note: Virtual destructor in base class rncl/src/ncl/nxsreader.h:492:12: note: Destructor in derived class rncl/src/ncl/nxsreader.h:495:16: style: The function 'EnteringBlock' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] rncl/src/ncl/nxsreader.h:193:16: note: Virtual function in base class rncl/src/ncl/nxsreader.h:495:16: note: Function in derived class rncl/src/ncl/nxsreader.h:501:8: style: The function 'SkippingBlock' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] rncl/src/ncl/nxsreader.h:197:16: note: Virtual function in base class rncl/src/ncl/nxsreader.h:501:8: note: Function in derived class rncl/src/ncl/nxsreader.h:511:8: style: The function 'SkippingDisabledBlock' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] rncl/src/ncl/nxsreader.h:196:16: note: Virtual function in base class rncl/src/ncl/nxsreader.h:511:8: note: Function in derived class rncl/src/ncl/nxsreader.h:524:8: style: The function 'NexusWarn' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] rncl/src/ncl/nxsreader.h:207:16: note: Virtual function in base class rncl/src/ncl/nxsreader.h:524:8: note: Function in derived class rncl/src/ncl/nxsreader.h:553:8: style: The function 'NexusError' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] rncl/src/ncl/nxsreader.h:227:16: note: Virtual function in base class rncl/src/ncl/nxsreader.h:553:8: note: Function in derived class rncl/src/ncl/nxsreader.h:463:16: style: The function 'ClearContent' overrides a function in a base class but just delegates back to the base class. [uselessOverride] rncl/src/ncl/nxsreader.h:268:16: note: Virtual function in base class rncl/src/ncl/nxsreader.h:463:16: note: Function in derived class rncl/src/nxsblock.cpp:117:75: style:inconclusive: Function 'WarnDangerousContent' argument 2 names different: declaration 't' definition 'token'. [funcArgNamesDifferent] rncl/src/ncl/nxsblock.h:237:71: note: Function 'WarnDangerousContent' argument 2 names different: declaration 't' definition 'token'. rncl/src/nxsblock.cpp:117:75: note: Function 'WarnDangerousContent' argument 2 names different: declaration 't' definition 'token'. rncl/src/nxsblock.cpp:125:84: style:inconclusive: Function 'WarnDangerousContent' argument 2 names different: declaration 't' definition 'token'. [funcArgNamesDifferent] rncl/src/ncl/nxsblock.h:238:80: note: Function 'WarnDangerousContent' argument 2 names different: declaration 't' definition 'token'. rncl/src/nxsblock.cpp:125:84: note: Function 'WarnDangerousContent' argument 2 names different: declaration 't' definition 'token'. rncl/src/nxsblock.cpp:596:45: style: Parameter 'b' can be declared as reference to const [constParameterReference] rncl/src/ncl/nxsmultiformat.h:111:3: style: Class 'MultiFormatReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] rncl/src/GetNCL.cpp:235:14: style: C-style pointer casting [cstyleCast] rncl/src/GetNCL.cpp:271:14: style: C-style pointer casting [cstyleCast] rncl/src/GetNCL.cpp:368:15: style: Local variable 'eachChar' shadows outer variable [shadowVariable] rncl/src/GetNCL.cpp:340:16: note: Shadowed declaration rncl/src/GetNCL.cpp:368:15: note: Shadow variable rncl/src/GetNCL.cpp:234:24: style: Variable 'par' can be declared as pointer to const [constVariablePointer] rncl/src/nxsdatablock.cpp:55:76: style:inconclusive: Function 'GetBlockReaderForID' argument 1 names different: declaration 'NCL_BLOCKTYPE_ATTR_NAME' definition 'idneeded'. [funcArgNamesDifferent] rncl/src/ncl/nxsdatablock.h:66:67: note: Function 'GetBlockReaderForID' argument 1 names different: declaration 'NCL_BLOCKTYPE_ATTR_NAME' definition 'idneeded'. rncl/src/nxsdatablock.cpp:55:76: note: Function 'GetBlockReaderForID' argument 1 names different: declaration 'NCL_BLOCKTYPE_ATTR_NAME' definition 'idneeded'. rncl/src/ncl/nxscxxdiscretematrix.h:44:3: style: Class 'NxsCXXDiscreteMatrix' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] rncl/src/ncl/nxsutilcopy.h:79:2: style: Struct 'CompileTimeChecker' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] rncl/src/nxscxxdiscretematrix.cpp:381:41: style: Condition 'hadGaps' is always true [knownConditionTrueFalse] rncl/src/nxscxxdiscretematrix.cpp:378:6: note: Assuming that condition 'hadGaps' is not redundant rncl/src/nxscxxdiscretematrix.cpp:381:41: note: Condition 'hadGaps' is always true rncl/src/nxscxxdiscretematrix.cpp:458:50: style: Condition '(unsigned int)(rawC+negSCLOffset)=recodeVecLen' is not redundant rncl/src/nxscxxdiscretematrix.cpp:458:50: note: Condition '(unsigned int)(rawC+negSCLOffset)0' is always true [knownConditionTrueFalse] rncl/src/nxscharactersblock.cpp:2413:14: note: Assuming that condition 'nStates==0' is not redundant rncl/src/nxscharactersblock.cpp:2429:14: note: Assuming condition is false rncl/src/nxscharactersblock.cpp:2469:21: note: Condition 'nStates>0' is always true rncl/src/nxscharactersblock.cpp:4267:39: style: Condition 'currChar!=lastChar' is always true [knownConditionTrueFalse] rncl/src/nxscharactersblock.cpp:4233:40: note: Assuming that condition 'currChar=0' is not redundant rncl/src/nxscharactersblock.cpp:5202:27: note: Condition 'currStateCode<0' is always false rncl/src/nxscharactersblock.cpp:3243:2: style:inconclusive: Statements following 'throw' will never be executed. [unreachableCode] rncl/src/nxscharactersblock.cpp:3013:11: style: The scope of the variable 'curr_ind_mapped' can be reduced. [variableScope] rncl/src/nxscharactersblock.cpp:3864:7: style: The scope of the variable 'save' can be reduced. [variableScope] rncl/src/nxscharactersblock.cpp:4935:36: style: The scope of the variable 'mapper' can be reduced. [variableScope] rncl/src/nxscharactersblock.cpp:1207:30: style:inconclusive: Function 'NewCodonsCharactersBlock' argument 1 names different: declaration 'charBlock' definition 'dnaBlock'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:966:31: note: Function 'NewCodonsCharactersBlock' argument 1 names different: declaration 'charBlock' definition 'dnaBlock'. rncl/src/nxscharactersblock.cpp:1207:30: note: Function 'NewCodonsCharactersBlock' argument 1 names different: declaration 'charBlock' definition 'dnaBlock'. rncl/src/nxscharactersblock.cpp:1400:84: style:inconclusive: Function 'GetDoubleWeights' argument 1 names different: declaration 'wtsetname' definition 'set_name'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:185:59: note: Function 'GetDoubleWeights' argument 1 names different: declaration 'wtsetname' definition 'set_name'. rncl/src/nxscharactersblock.cpp:1400:84: note: Function 'GetDoubleWeights' argument 1 names different: declaration 'wtsetname' definition 'set_name'. rncl/src/nxscharactersblock.cpp:1472:36: style:inconclusive: Function 'NxsDiscreteDatatypeMapper' argument 1 names different: declaration 'datatype' definition 'datatypeE'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1150:63: note: Function 'NxsDiscreteDatatypeMapper' argument 1 names different: declaration 'datatype' definition 'datatypeE'. rncl/src/nxscharactersblock.cpp:1472:36: note: Function 'NxsDiscreteDatatypeMapper' argument 1 names different: declaration 'datatype' definition 'datatypeE'. rncl/src/nxscharactersblock.cpp:1473:22: style:inconclusive: Function 'NxsDiscreteDatatypeMapper' argument 2 names different: declaration 'symbols' definition 'symbolsStr'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1150:93: note: Function 'NxsDiscreteDatatypeMapper' argument 2 names different: declaration 'symbols' definition 'symbolsStr'. rncl/src/nxscharactersblock.cpp:1473:22: note: Function 'NxsDiscreteDatatypeMapper' argument 2 names different: declaration 'symbols' definition 'symbolsStr'. rncl/src/nxscharactersblock.cpp:1475:7: style:inconclusive: Function 'NxsDiscreteDatatypeMapper' argument 4 names different: declaration 'gapChar' definition 'gap'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1151:32: note: Function 'NxsDiscreteDatatypeMapper' argument 4 names different: declaration 'gapChar' definition 'gap'. rncl/src/nxscharactersblock.cpp:1475:7: note: Function 'NxsDiscreteDatatypeMapper' argument 4 names different: declaration 'gapChar' definition 'gap'. rncl/src/nxscharactersblock.cpp:1476:7: style:inconclusive: Function 'NxsDiscreteDatatypeMapper' argument 5 names different: declaration 'matchChar' definition 'matchingChar'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1151:46: note: Function 'NxsDiscreteDatatypeMapper' argument 5 names different: declaration 'matchChar' definition 'matchingChar'. rncl/src/nxscharactersblock.cpp:1476:7: note: Function 'NxsDiscreteDatatypeMapper' argument 5 names different: declaration 'matchChar' definition 'matchingChar'. rncl/src/nxscharactersblock.cpp:1477:7: style:inconclusive: Function 'NxsDiscreteDatatypeMapper' argument 6 names different: declaration 'respectCase' definition 'respectingCase'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1152:14: note: Function 'NxsDiscreteDatatypeMapper' argument 6 names different: declaration 'respectCase' definition 'respectingCase'. rncl/src/nxscharactersblock.cpp:1477:7: note: Function 'NxsDiscreteDatatypeMapper' argument 6 names different: declaration 'respectCase' definition 'respectingCase'. rncl/src/nxscharactersblock.cpp:1478:36: style:inconclusive: Function 'NxsDiscreteDatatypeMapper' argument 7 names different: declaration 'extraEquates' definition 'moreEquates'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1152:61: note: Function 'NxsDiscreteDatatypeMapper' argument 7 names different: declaration 'extraEquates' definition 'moreEquates'. rncl/src/nxscharactersblock.cpp:1478:36: note: Function 'NxsDiscreteDatatypeMapper' argument 7 names different: declaration 'extraEquates' definition 'moreEquates'. rncl/src/nxscharactersblock.cpp:2355:7: style:inconclusive: Function 'NxsDiscreteDatatypeMapper' argument 2 names different: declaration 'hasGaps' definition 'usegaps'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1149:79: note: Function 'NxsDiscreteDatatypeMapper' argument 2 names different: declaration 'hasGaps' definition 'usegaps'. rncl/src/nxscharactersblock.cpp:2355:7: note: Function 'NxsDiscreteDatatypeMapper' argument 2 names different: declaration 'hasGaps' definition 'usegaps'. rncl/src/nxscharactersblock.cpp:2637:158: style:inconclusive: Function 'StateCodeForStateSet' argument 4 names different: declaration 'symbol' definition 'nexusSymbol'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1257:45: note: Function 'StateCodeForStateSet' argument 4 names different: declaration 'symbol' definition 'nexusSymbol'. rncl/src/nxscharactersblock.cpp:2637:158: note: Function 'StateCodeForStateSet' argument 4 names different: declaration 'symbol' definition 'nexusSymbol'. rncl/src/nxscharactersblock.cpp:2710:73: style:inconclusive: Function 'ValidateStateIndex' argument 1 names different: declaration 'state' definition 'c'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1305:48: note: Function 'ValidateStateIndex' argument 1 names different: declaration 'state' definition 'c'. rncl/src/nxscharactersblock.cpp:2710:73: note: Function 'ValidateStateIndex' argument 1 names different: declaration 'state' definition 'c'. rncl/src/nxscharactersblock.cpp:2731:72: style:inconclusive: Function 'ValidateStateCode' argument 1 names different: declaration 'state' definition 'c'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1306:47: note: Function 'ValidateStateCode' argument 1 names different: declaration 'state' definition 'c'. rncl/src/nxscharactersblock.cpp:2731:72: note: Function 'ValidateStateCode' argument 1 names different: declaration 'state' definition 'c'. rncl/src/nxscharactersblock.cpp:2777:68: style:inconclusive: Function 'IsPolymorphic' argument 1 names different: declaration 'stateCode' definition 'c'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1182:43: note: Function 'IsPolymorphic' argument 1 names different: declaration 'stateCode' definition 'c'. rncl/src/nxscharactersblock.cpp:2777:68: note: Function 'IsPolymorphic' argument 1 names different: declaration 'stateCode' definition 'c'. rncl/src/nxscharactersblock.cpp:2791:72: style:inconclusive: Function 'PositionInSymbols' argument 1 names different: declaration 'currChar' definition 'c'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1183:53: note: Function 'PositionInSymbols' argument 1 names different: declaration 'currChar' definition 'c'. rncl/src/nxscharactersblock.cpp:2791:72: note: Function 'PositionInSymbols' argument 1 names different: declaration 'currChar' definition 'c'. rncl/src/nxscharactersblock.cpp:2852:82: style:inconclusive: Function 'GetNumStatesInStateCode' argument 1 names different: declaration 'stateCode' definition 'scode'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1233:57: note: Function 'GetNumStatesInStateCode' argument 1 names different: declaration 'stateCode' definition 'scode'. rncl/src/nxscharactersblock.cpp:2852:82: note: Function 'GetNumStatesInStateCode' argument 1 names different: declaration 'stateCode' definition 'scode'. rncl/src/nxscharactersblock.cpp:3041:12: style:inconclusive: Function 'StateCodeForNexusChar' argument 3 names different: declaration 'taxInd' definition 'taxNum'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1245:20: note: Function 'StateCodeForNexusChar' argument 3 names different: declaration 'taxInd' definition 'taxNum'. rncl/src/nxscharactersblock.cpp:3041:12: note: Function 'StateCodeForNexusChar' argument 3 names different: declaration 'taxInd' definition 'taxNum'. rncl/src/nxscharactersblock.cpp:3042:12: style:inconclusive: Function 'StateCodeForNexusChar' argument 4 names different: declaration 'charInd' definition 'charNum'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1245:37: note: Function 'StateCodeForNexusChar' argument 4 names different: declaration 'charInd' definition 'charNum'. rncl/src/nxscharactersblock.cpp:3042:12: note: Function 'StateCodeForNexusChar' argument 4 names different: declaration 'charInd' definition 'charNum'. rncl/src/nxscharactersblock.cpp:3101:18: style:inconclusive: Function 'StateCodeForNexusPossibleMultiStateSet' argument 4 names different: declaration 'taxInd' definition 'taxNum'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1301:20: note: Function 'StateCodeForNexusPossibleMultiStateSet' argument 4 names different: declaration 'taxInd' definition 'taxNum'. rncl/src/nxscharactersblock.cpp:3101:18: note: Function 'StateCodeForNexusPossibleMultiStateSet' argument 4 names different: declaration 'taxInd' definition 'taxNum'. rncl/src/nxscharactersblock.cpp:3102:18: style:inconclusive: Function 'StateCodeForNexusPossibleMultiStateSet' argument 5 names different: declaration 'charInd' definition 'charNum'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1301:37: note: Function 'StateCodeForNexusPossibleMultiStateSet' argument 5 names different: declaration 'charInd' definition 'charNum'. rncl/src/nxscharactersblock.cpp:3102:18: note: Function 'StateCodeForNexusPossibleMultiStateSet' argument 5 names different: declaration 'charInd' definition 'charNum'. rncl/src/nxscharactersblock.cpp:3125:18: style:inconclusive: Function 'StateCodeForNexusMultiStateSet' argument 4 names different: declaration 'taxInd' definition 'taxNum'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1298:20: note: Function 'StateCodeForNexusMultiStateSet' argument 4 names different: declaration 'taxInd' definition 'taxNum'. rncl/src/nxscharactersblock.cpp:3125:18: note: Function 'StateCodeForNexusMultiStateSet' argument 4 names different: declaration 'taxInd' definition 'taxNum'. rncl/src/nxscharactersblock.cpp:3126:18: style:inconclusive: Function 'StateCodeForNexusMultiStateSet' argument 5 names different: declaration 'charInd' definition 'charNum'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1298:37: note: Function 'StateCodeForNexusMultiStateSet' argument 5 names different: declaration 'charInd' definition 'charNum'. rncl/src/nxscharactersblock.cpp:3126:18: note: Function 'StateCodeForNexusMultiStateSet' argument 5 names different: declaration 'charInd' definition 'charNum'. rncl/src/nxscharactersblock.cpp:3478:108: style:inconclusive: Function 'AddNewCodonPosPartition' argument 3 names different: declaration 'isDefault' definition 'isDef'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:857:98: note: Function 'AddNewCodonPosPartition' argument 3 names different: declaration 'isDefault' definition 'isDef'. rncl/src/nxscharactersblock.cpp:3478:108: note: Function 'AddNewCodonPosPartition' argument 3 names different: declaration 'isDefault' definition 'isDef'. rncl/src/nxscharactersblock.cpp:3544:22: style:inconclusive: Function 'CharLabelToNumber' argument 1 names different: declaration 's' definition 'inp'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:818:58: note: Function 'CharLabelToNumber' argument 1 names different: declaration 's' definition 'inp'. rncl/src/nxscharactersblock.cpp:3544:22: note: Function 'CharLabelToNumber' argument 1 names different: declaration 's' definition 'inp'. rncl/src/nxscharactersblock.cpp:3616:12: style:inconclusive: Function 'WriteStatesForTaxonAsNexus' argument 3 names different: declaration 'begChar' definition 'beginCharInd'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:888:80: note: Function 'WriteStatesForTaxonAsNexus' argument 3 names different: declaration 'begChar' definition 'beginCharInd'. rncl/src/nxscharactersblock.cpp:3616:12: note: Function 'WriteStatesForTaxonAsNexus' argument 3 names different: declaration 'begChar' definition 'beginCharInd'. rncl/src/nxscharactersblock.cpp:3617:12: style:inconclusive: Function 'WriteStatesForTaxonAsNexus' argument 4 names different: declaration 'endChar' definition 'endCharInd'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:888:98: note: Function 'WriteStatesForTaxonAsNexus' argument 4 names different: declaration 'endChar' definition 'endCharInd'. rncl/src/nxscharactersblock.cpp:3617:12: note: Function 'WriteStatesForTaxonAsNexus' argument 4 names different: declaration 'endChar' definition 'endCharInd'. rncl/src/nxscharactersblock.cpp:4856:12: style:inconclusive: Function 'WriteStatesForMatrixRow' argument 2 names different: declaration 'taxon' definition 'currTaxonIndex'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1009:19: note: Function 'WriteStatesForMatrixRow' argument 2 names different: declaration 'taxon' definition 'currTaxonIndex'. rncl/src/nxscharactersblock.cpp:4856:12: note: Function 'WriteStatesForMatrixRow' argument 2 names different: declaration 'taxon' definition 'currTaxonIndex'. rncl/src/nxscharactersblock.cpp:4858:12: style:inconclusive: Function 'WriteStatesForMatrixRow' argument 4 names different: declaration 'begChar' definition 'beginChar'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1011:19: note: Function 'WriteStatesForMatrixRow' argument 4 names different: declaration 'begChar' definition 'beginChar'. rncl/src/nxscharactersblock.cpp:4858:12: note: Function 'WriteStatesForMatrixRow' argument 4 names different: declaration 'begChar' definition 'beginChar'. rncl/src/nxscharactersblock.cpp:5146:12: style:inconclusive: Function 'ShowStateLabels' argument 2 names different: declaration 'i' definition 'taxInd'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:884:52: note: Function 'ShowStateLabels' argument 2 names different: declaration 'i' definition 'taxInd'. rncl/src/nxscharactersblock.cpp:5146:12: note: Function 'ShowStateLabels' argument 2 names different: declaration 'i' definition 'taxInd'. rncl/src/nxscharactersblock.cpp:5147:12: style:inconclusive: Function 'ShowStateLabels' argument 3 names different: declaration 'c' definition 'charInd'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:884:64: note: Function 'ShowStateLabels' argument 3 names different: declaration 'c' definition 'charInd'. rncl/src/nxscharactersblock.cpp:5147:12: note: Function 'ShowStateLabels' argument 3 names different: declaration 'c' definition 'charInd'. rncl/src/nxscharactersblock.cpp:5247:12: style:inconclusive: Function 'GetNumStates' argument 1 names different: declaration 'i' definition 'taxInd'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:658:34: note: Function 'GetNumStates' argument 1 names different: declaration 'i' definition 'taxInd'. rncl/src/nxscharactersblock.cpp:5247:12: note: Function 'GetNumStates' argument 1 names different: declaration 'i' definition 'taxInd'. rncl/src/nxscharactersblock.cpp:5248:12: style:inconclusive: Function 'GetNumStates' argument 2 names different: declaration 'j' definition 'charInd'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:658:46: note: Function 'GetNumStates' argument 2 names different: declaration 'j' definition 'charInd'. rncl/src/nxscharactersblock.cpp:5248:12: note: Function 'GetNumStates' argument 2 names different: declaration 'j' definition 'charInd'. rncl/src/nxscharactersblock.cpp:5294:12: style:inconclusive: Function 'IsMissingState' argument 1 names different: declaration 'i' definition 'taxInd'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:668:32: note: Function 'IsMissingState' argument 1 names different: declaration 'i' definition 'taxInd'. rncl/src/nxscharactersblock.cpp:5294:12: note: Function 'IsMissingState' argument 1 names different: declaration 'i' definition 'taxInd'. rncl/src/nxscharactersblock.cpp:5295:12: style:inconclusive: Function 'IsMissingState' argument 2 names different: declaration 'j' definition 'charInd'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:668:44: note: Function 'IsMissingState' argument 2 names different: declaration 'j' definition 'charInd'. rncl/src/nxscharactersblock.cpp:5295:12: note: Function 'IsMissingState' argument 2 names different: declaration 'j' definition 'charInd'. rncl/src/nxscharactersblock.cpp:5416:12: style:inconclusive: Function 'IsPolymorphic' argument 1 names different: declaration 'i' definition 'taxInd'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:670:31: note: Function 'IsPolymorphic' argument 1 names different: declaration 'i' definition 'taxInd'. rncl/src/nxscharactersblock.cpp:5416:12: note: Function 'IsPolymorphic' argument 1 names different: declaration 'i' definition 'taxInd'. rncl/src/nxscharactersblock.cpp:5417:12: style:inconclusive: Function 'IsPolymorphic' argument 2 names different: declaration 'j' definition 'charInd'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:670:43: note: Function 'IsPolymorphic' argument 2 names different: declaration 'j' definition 'charInd'. rncl/src/nxscharactersblock.cpp:5417:12: note: Function 'IsPolymorphic' argument 2 names different: declaration 'j' definition 'charInd'. rncl/src/nxscharactersblock.cpp:5437:12: style:inconclusive: Function 'ShowStates' argument 2 names different: declaration 'i' definition 'taxInd'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1031:47: note: Function 'ShowStates' argument 2 names different: declaration 'i' definition 'taxInd'. rncl/src/nxscharactersblock.cpp:5437:12: note: Function 'ShowStates' argument 2 names different: declaration 'i' definition 'taxInd'. rncl/src/nxscharactersblock.cpp:5438:12: style:inconclusive: Function 'ShowStates' argument 3 names different: declaration 'j' definition 'charInd'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1031:59: note: Function 'ShowStates' argument 3 names different: declaration 'j' definition 'charInd'. rncl/src/nxscharactersblock.cpp:5438:12: note: Function 'ShowStates' argument 3 names different: declaration 'j' definition 'charInd'. rncl/src/nxscharactersblock.cpp:5491:88: style:inconclusive: Function 'GetBlockReaderForID' argument 1 names different: declaration 'NCL_BLOCKTYPE_ATTR_NAME' definition 'idneeded'. [funcArgNamesDifferent] rncl/src/ncl/nxscharactersblock.h:1113:72: note: Function 'GetBlockReaderForID' argument 1 names different: declaration 'NCL_BLOCKTYPE_ATTR_NAME' definition 'idneeded'. rncl/src/nxscharactersblock.cpp:5491:88: note: Function 'GetBlockReaderForID' argument 1 names different: declaration 'NCL_BLOCKTYPE_ATTR_NAME' definition 'idneeded'. rncl/src/nxscharactersblock.cpp:492:25: style: Variable 'row' can be declared as reference to const [constVariableReference] rncl/src/nxscharactersblock.cpp:2652:29: style: Variable 'stateSetInfo' can be declared as reference to const [constVariableReference] rncl/src/nxscharactersblock.cpp:3891:44: style: Variable 'x' can be declared as reference to const [constVariableReference] rncl/src/nxscharactersblock.cpp:4560:44: style: Variable 'x' can be declared as reference to const [constVariableReference] rncl/src/nxscharactersblock.cpp:5228:21: style: Parameter 'd' can be declared as reference to const [constParameterReference] rncl/src/nxscharactersblock.cpp:4106:23: style: Variable 'ftDiscRowPtr' can be declared as pointer to const [constVariablePointer] rncl/src/nxscharactersblock.cpp:5404:19: performance: Searching before insertion is not necessary. [stlFindInsert] rncl/src/nxscharactersblock.cpp:5030:13: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] rncl/src/nxscharactersblock.cpp:3864:12: style: Variable 'save' is assigned a value that is never used. [unreadVariable] rncl/src/nxscharactersblock.cpp:5338:31: style: Unused variable: iv [unusedVariable] rncl/src/nxscharactersblock.cpp:4748:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] diff: 2.13.0 rncl/src/ncl/nxscharactersblock.h:1277:37: warning: Either the condition 'stateIntersectionMatrix.empty()' is redundant or expression 'stateIntersectionMatrix.at(sc)' cause access out of bounds. [containerOutOfBounds] rncl/src/ncl/nxscharactersblock.h:1273:37: note: Assuming that condition 'stateIntersectionMatrix.empty()' is not redundant rncl/src/ncl/nxscharactersblock.h:1277:37: note: Access out of bounds head rncl/src/ncl/nxscharactersblock.h:1277:37: warning: Either the condition 'stateIntersectionMatrix.empty()' is redundant or expression 'stateIntersectionMatrix.at(sc)' causes access out of bounds. [containerOutOfBounds] rncl/src/ncl/nxscharactersblock.h:1273:37: note: Assuming that condition 'stateIntersectionMatrix.empty()' is not redundant rncl/src/ncl/nxscharactersblock.h:1277:37: note: Access out of bounds 2.13.0 rncl/src/ncl/nxscharactersblock.h:1734:16: warning: Either the condition 'p<(int)symbols.length()' is redundant or '(int)p' can have the value greater or equal to symbols.size(). Expression 'symbols[(int)p]' cause access out of bounds. [containerOutOfBounds] rncl/src/ncl/nxscharactersblock.h:1733:2: note: Assuming that condition 'p<(int)symbols.length()' is not redundant rncl/src/ncl/nxscharactersblock.h:1734:16: note: Access out of bounds head rncl/src/ncl/nxscharactersblock.h:1734:16: warning: Either the condition 'p<(int)symbols.length()' is redundant or '(int)p' can have the value greater or equal to symbols.size(). Expression 'symbols[(int)p]' causes access out of bounds. [containerOutOfBounds] rncl/src/ncl/nxscharactersblock.h:1733:2: note: Assuming that condition 'p<(int)symbols.length()' is not redundant rncl/src/ncl/nxscharactersblock.h:1734:16: note: Access out of bounds head rncl/src/ncl/nxscharactersblock.h:510:12: style: The destructor '~NxsCharactersBlock' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] rncl/src/ncl/nxstaxablock.h:315:12: note: Virtual destructor in base class rncl/src/ncl/nxscharactersblock.h:510:12: note: Destructor in derived class head rncl/src/ncl/nxspublicblocks.h:316:12: style: The destructor '~PublicNexusReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] rncl/src/ncl/nxsreader.h:167:14: note: Virtual destructor in base class rncl/src/ncl/nxspublicblocks.h:316:12: note: Destructor in derived class head rncl/src/ncl/nxsreader.h:492:12: style: The destructor '~DefaultErrorReportNxsReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] rncl/src/ncl/nxsreader.h:167:14: note: Virtual destructor in base class rncl/src/ncl/nxsreader.h:492:12: note: Destructor in derived class head rncl/src/ncl/nxstreesblock.h:631:15: style: The destructor '~NxsTreesBlock' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] rncl/src/ncl/nxstaxablock.h:315:12: note: Virtual destructor in base class rncl/src/ncl/nxstreesblock.h:631:15: note: Destructor in derived class head rncl/src/nxsassumptionsblock.cpp:1732:12: style: The destructor '~WtSetVectorItemValidator' overrides a destructor in a base class but is identical to the overridden function [uselessOverride] rncl/src/nxsassumptionsblock.cpp:1725:12: note: Virtual destructor in base class rncl/src/nxsassumptionsblock.cpp:1732:12: note: Destructor in derived class head rncl/src/nxsassumptionsblock.cpp:1732:12: style: The destructor '~WtSetVectorItemValidator' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] rncl/src/nxsassumptionsblock.cpp:1725:12: note: Virtual destructor in base class rncl/src/nxsassumptionsblock.cpp:1732:12: note: Destructor in derived class head rncl/src/nxsmultiformat.cpp:1494:6: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm] DONE