2024-03-26 17:55 ftp://ftp.de.debian.org/debian/pool/main/c/comet-ms/comet-ms_2019015+cleaned1.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: 61552d0 (2024-03-26 14:25:53 +0100) count: 373 366 elapsed-time: 21.6 271.7 head-timing-info: Tokenizer::simplifyTokens1::ValueFlow: 20.9534s (avg. 20.9534s - 1 result(s)) valueFlowCondition(SimpleConditionHandler{}, tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 8.3471s (avg. 2.78237s - 3 result(s)) valueFlowCondition(SymbolicConditionHandler{}, tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 7.01157s (avg. 2.33719s - 3 result(s)) valueFlowAfterAssign(tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 2.58086s (avg. 0.860285s - 3 result(s)) valueFlowForLoop(tokenlist, symboldatabase, errorLogger, settings): 1.31229s (avg. 0.437429s - 3 result(s)) Overall time: 21.3742s old-timing-info: Tokenizer::simplifyTokens1::ValueFlow: 271.102s (avg. 271.102s - 1 result(s)) valueFlowCondition(SimpleConditionHandler{}, tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 224.781s (avg. 74.927s - 3 result(s)) valueFlowCondition(SymbolicConditionHandler{}, tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 34.3245s (avg. 11.4415s - 3 result(s)) valueFlowAfterAssign(tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 5.16105s (avg. 1.72035s - 3 result(s)) valueFlowSymbolic(tokenlist, symboldatabase, settings): 2.61281s (avg. 2.61281s - 1 result(s)) Overall time: 271.515s head results: comet-2019015+cleaned/CometSearch/CometData.h:295:4: warning: Member variable 'EnzymeInfo::iOneMinusOffset' is not initialized in the copy constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometData.h:295:4: warning: Member variable 'EnzymeInfo::iTwoMinusOffset' is not initialized in the copy constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometData.h:295:4: warning: Member variable 'EnzymeInfo::iOneMinusOffset2' is not initialized in the copy constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometData.h:295:4: warning: Member variable 'EnzymeInfo::iTwoMinusOffset2' is not initialized in the copy constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometData.h:324:16: warning: Member variable 'EnzymeInfo::iOneMinusOffset' is not assigned a value in 'EnzymeInfo::operator='. [operatorEqVarError] comet-2019015+cleaned/CometSearch/CometData.h:324:16: warning: Member variable 'EnzymeInfo::iTwoMinusOffset' is not assigned a value in 'EnzymeInfo::operator='. [operatorEqVarError] comet-2019015+cleaned/CometSearch/CometData.h:324:16: warning: Member variable 'EnzymeInfo::iOneMinusOffset2' is not assigned a value in 'EnzymeInfo::operator='. [operatorEqVarError] comet-2019015+cleaned/CometSearch/CometData.h:324:16: warning: Member variable 'EnzymeInfo::iTwoMinusOffset2' is not assigned a value in 'EnzymeInfo::operator='. [operatorEqVarError] comet-2019015+cleaned/CometSearch/CometDataInternal.h:446:18: warning:inconclusive: Member variable 'VarModParams::bBinaryModSearch' is not assigned a value in 'VarModParams::operator='. [operatorEqVarError] comet-2019015+cleaned/CometSearch/CometDataInternal.h:446:18: warning:inconclusive: Member variable 'VarModParams::bRequireVarMod' is not assigned a value in 'VarModParams::operator='. [operatorEqVarError] comet-2019015+cleaned/CometSearch/CometDataInternal.h:597:4: warning: Member variable 'StaticParams::szHostName' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometDataInternal.h:597:4: warning: Member variable 'StaticParams::szOutFileTimeString' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometDataInternal.h:597:4: warning: Member variable 'StaticParams::szIonSeries' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometDataInternal.h:597:4: warning: Member variable 'StaticParams::szDisplayLine' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometDataInternal.h:597:4: warning: Member variable 'StaticParams::iElapseTime' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometDataInternal.h:597:4: warning: Member variable 'StaticParams::szDate' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometDataInternal.h:597:4: warning: Member variable 'StaticParams::bPrintDuplReferences' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometDataInternal.h:597:4: warning: Member variable 'StaticParams::precalcMasses' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometDataInternal.h:597:4: warning: Member variable 'StaticParams::dInverseBinWidth' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometDataInternal.h:597:4: warning: Member variable 'StaticParams::dOneMinusBinOffset' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometDataInternal.h:597:4: warning: Member variable 'StaticParams::peaksInformation' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometDataInternal.h:602:18: warning: Member variable 'StaticParams::peffInfo' is not assigned a value in 'StaticParams::operator='. [operatorEqVarError] comet-2019015+cleaned/CometSearch/CometDataInternal.h:602:18: warning: Member variable 'StaticParams::bIndexDb' is not assigned a value in 'StaticParams::operator='. [operatorEqVarError] comet-2019015+cleaned/CometSearch/CometDataInternal.h:602:18: warning: Member variable 'StaticParams::szDIAWindowsFile' is not assigned a value in 'StaticParams::operator='. [operatorEqVarError] comet-2019015+cleaned/CometSearch/CometDataInternal.h:602:18: warning:inconclusive: Member variable 'StaticParams::bSkipToStartScan' is not assigned a value in 'StaticParams::operator='. [operatorEqVarError] comet-2019015+cleaned/CometSearch/CometDataInternal.h:602:18: warning:inconclusive: Member variable 'StaticParams::tRealTimeStart' is not assigned a value in 'StaticParams::operator='. [operatorEqVarError] comet-2019015+cleaned/CometSearch/CometDataInternal.h:852:4: warning: Member variable 'Query::iSpScoreData' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometDataInternal.h:852:4: warning: Member variable 'Query::iFastXcorrData' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometDataInternal.h:852:4: warning: Member variable 'Query::iFastXcorrDataNL' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometData.h:185:12: style:inconclusive: Technically the member function 'Fragment::ToMz' can be const. [functionConst] comet-2019015+cleaned/CometSearch/CometData.h:413:4: style: Struct 'InputFileInfo' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] comet-2019015+cleaned/CometSearch/CometSearchManager.h:30:5: style: The destructor '~CometSearchManager' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:30:16: note: Virtual destructor in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:30:5: note: Destructor in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:35:17: style: The function 'CreateIndex' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:31:18: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:35:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:36:17: style: The function 'DoSearch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:32:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:36:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:37:17: style: The function 'InitializeSingleSpectrumSearch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:33:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:37:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:38:17: style: The function 'FinalizeSingleSpectrumSearch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:34:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:38:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:39:17: style: The function 'DoSingleSpectrumSearch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:35:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:39:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:48:17: style: The function 'AddInputFiles' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:44:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:48:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:49:17: style: The function 'SetOutputFileBaseName' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:45:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:49:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:50:17: style: The function 'SetParam' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:46:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:50:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:51:17: style: The function 'GetParamValue' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:47:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:51:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:54:17: style: The function 'SetParam' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:48:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:54:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:55:17: style: The function 'GetParamValue' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:49:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:55:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:56:17: style: The function 'SetParam' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:50:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:56:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:57:17: style: The function 'GetParamValue' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:51:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:57:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:58:17: style: The function 'SetParam' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:52:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:58:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:59:17: style: The function 'GetParamValue' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:53:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:59:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:60:17: style: The function 'SetParam' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:54:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:60:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:61:17: style: The function 'GetParamValue' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:55:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:61:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:62:17: style: The function 'SetParam' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:56:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:62:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:63:17: style: The function 'GetParamValue' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:57:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:63:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:64:17: style: The function 'SetParam' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:58:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:64:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:65:17: style: The function 'GetParamValue' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:59:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:65:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:66:17: style: The function 'SetParam' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:60:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:66:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:67:17: style: The function 'GetParamValue' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:61:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:67:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:68:17: style: The function 'SetParam' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:62:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:68:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:69:17: style: The function 'GetParamValue' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:63:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:69:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:70:17: style: The function 'IsValidCometVersion' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:64:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:70:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:71:17: style: The function 'IsSearchError' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:65:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:71:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:72:17: style: The function 'GetStatusMessage' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:66:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:72:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:73:17: style: The function 'CancelSearch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:67:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:73:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:74:17: style: The function 'IsCancelSearch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:68:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:74:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometSearchManager.h:75:17: style: The function 'ResetSearchStatus' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:69:20: note: Virtual function in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:75:17: note: Function in derived class comet-2019015+cleaned/CometSearch/CometDataInternal.h:665:16: style: Local variable 'i' shadows outer variable [shadowVariable] comet-2019015+cleaned/CometSearch/CometDataInternal.h:636:11: note: Shadowed declaration comet-2019015+cleaned/CometSearch/CometDataInternal.h:665:16: note: Shadow variable comet-2019015+cleaned/CometSearch/CometData.h:61:40: style: Parameter 'a' can be declared as reference to const [constParameterReference] comet-2019015+cleaned/CometSearch/CometData.h:92:34: style: Parameter 'a' can be declared as reference to const [constParameterReference] comet-2019015+cleaned/CometSearch/CometData.h:132:31: style: Parameter 'a' can be declared as reference to const [constParameterReference] comet-2019015+cleaned/CometSearch/CometData.h:175:35: style: Parameter 'a' can be declared as reference to const [constParameterReference] comet-2019015+cleaned/CometSearch/CometData.h:226:32: style: Parameter 'a' can be declared as reference to const [constParameterReference] comet-2019015+cleaned/CometSearch/CometData.h:324:38: style: Parameter 'a' can be declared as reference to const [constParameterReference] comet-2019015+cleaned/CometSearch/CometData.h:426:46: style: Parameter 'inputObj' can be declared as reference to const [constParameterReference] comet-2019015+cleaned/CometSearch/CometDataInternal.h:125:32: style: Parameter 'a' can be declared as reference to const [constParameterReference] comet-2019015+cleaned/CometSearch/CometDataInternal.h:330:30: style: Parameter 'a' can be declared as reference to const [constParameterReference] comet-2019015+cleaned/CometSearch/CometDataInternal.h:399:36: style: Parameter 'a' can be declared as reference to const [constParameterReference] comet-2019015+cleaned/CometSearch/CometDataInternal.h:423:44: style: Parameter 'a' can be declared as reference to const [constParameterReference] comet-2019015+cleaned/CometSearch/CometDataInternal.h:446:42: style: Parameter 'a' can be declared as reference to const [constParameterReference] comet-2019015+cleaned/CometSearch/CometDataInternal.h:477:34: style: Parameter 'a' can be declared as reference to const [constParameterReference] comet-2019015+cleaned/CometSearch/CometDataInternal.h:509:48: style: Parameter 'a' can be declared as reference to const [constParameterReference] comet-2019015+cleaned/CometSearch/CometDataInternal.h:528:36: style: Parameter 'a' can be declared as reference to const [constParameterReference] comet-2019015+cleaned/CometSearch/CometDataInternal.h:545:32: style: Parameter 'a' can be declared as reference to const [constParameterReference] comet-2019015+cleaned/CometSearch/CometDataInternal.h:602:42: style: Parameter 'a' can be declared as reference to const [constParameterReference] comet-2019015+cleaned/CometSearch/CometMassSpecUtils.cpp:31:55: style: Parameter 'pdAAforward' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometMassSpecUtils.cpp:32:55: style: Parameter 'pdAAreverse' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometCheckForUpdates.cpp:177:13: style: Obsolescent function 'gethostbyname' called. It is recommended to use 'getaddrinfo' instead. [prohibitedgethostbynameCalled] comet-2019015+cleaned/CometSearch/CometCheckForUpdates.cpp:179:7: error: Resource leak: sockfd [resourceLeak] comet-2019015+cleaned/CometSearch/CometCheckForUpdates.cpp:188:24: style: C-style pointer casting [cstyleCast] comet-2019015+cleaned/CometSearch/CometCheckForUpdates.cpp:53:16: style: The scope of the variable 'page' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometCheckForUpdates.cpp:91:13: style: The scope of the variable 'pStr' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometCheckForUpdates.cpp:150:16: style: The scope of the variable 'bytes' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometCheckForUpdates.cpp:91:13: style: Variable 'pStr' can be declared as pointer to const [constVariablePointer] comet-2019015+cleaned/CometSearch/CometCheckForUpdates.cpp:146:10: style: Variable 'host' can be declared as pointer to const [constVariablePointer] comet-2019015+cleaned/CometSearch/CometCheckForUpdates.cpp:148:20: style: Variable 'server' can be declared as pointer to const [constVariablePointer] comet-2019015+cleaned/Comet.cpp:394:22: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled] comet-2019015+cleaned/Comet.cpp:400:25: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled] comet-2019015+cleaned/Comet.cpp:432:22: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled] comet-2019015+cleaned/Comet.cpp:438:25: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled] comet-2019015+cleaned/Comet.cpp:1276:11: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled] comet-2019015+cleaned/Comet.cpp:1308:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled] comet-2019015+cleaned/Comet.cpp:1311:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled] comet-2019015+cleaned/Comet.cpp:1318:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled] comet-2019015+cleaned/Comet.cpp:1321:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled] comet-2019015+cleaned/Comet.cpp:1389:20: style: Condition 'arg!=NULL' is always true [knownConditionTrueFalse] comet-2019015+cleaned/Comet.cpp:1202:12: style: Local variable 'szErrorMsg' shadows outer variable [shadowVariable] comet-2019015+cleaned/Comet.cpp:213:10: note: Shadowed declaration comet-2019015+cleaned/Comet.cpp:1202:12: note: Shadow variable comet-2019015+cleaned/Comet.cpp:1211:12: style: Local variable 'szErrorMsg' shadows outer variable [shadowVariable] comet-2019015+cleaned/Comet.cpp:213:10: note: Shadowed declaration comet-2019015+cleaned/Comet.cpp:1211:12: note: Shadow variable comet-2019015+cleaned/Comet.cpp:1220:12: style: Local variable 'szErrorMsg' shadows outer variable [shadowVariable] comet-2019015+cleaned/Comet.cpp:213:10: note: Shadowed declaration comet-2019015+cleaned/Comet.cpp:1220:12: note: Shadow variable comet-2019015+cleaned/Comet.cpp:1229:12: style: Local variable 'szErrorMsg' shadows outer variable [shadowVariable] comet-2019015+cleaned/Comet.cpp:213:10: note: Shadowed declaration comet-2019015+cleaned/Comet.cpp:1229:12: note: Shadow variable comet-2019015+cleaned/Comet.cpp:68:18: style: Parameter 'pszCmd' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/Comet.cpp:104:23: style: Parameter 'arg' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/Comet.cpp:195:27: style: Parameter 'pszParamsFile' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/Comet.cpp:388:22: style: Variable 'tok' can be declared as pointer to const [constVariablePointer] comet-2019015+cleaned/Comet.cpp:389:21: style: Variable 'delims' can be declared as const array [constVariable] comet-2019015+cleaned/Comet.cpp:426:22: style: Variable 'tok' can be declared as pointer to const [constVariablePointer] comet-2019015+cleaned/Comet.cpp:427:21: style: Variable 'delims' can be declared as const array [constVariable] comet-2019015+cleaned/Comet.cpp:1245:10: style: Variable 'tok' can be declared as pointer to const [constVariablePointer] comet-2019015+cleaned/Comet.cpp:1612:30: style: Parameter 'pszInputFileName' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:1612:68: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled] comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2181:77: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled] comet-2019015+cleaned/CometSearch/CometSearch.h:29:4: warning:inconclusive: Member variable 'SearchThreadData::dbEntry' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometSearch.h:29:4: warning:inconclusive: Member variable 'SearchThreadData::pbSearchMemoryPool' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometSearch.h:33:4: warning: Member variable 'SearchThreadData::pbSearchMemoryPool' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometPreprocess.h:30:4: warning:inconclusive: Member variable 'PreprocessThreadData::iAnalysisType' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometPreprocess.h:30:4: warning:inconclusive: Member variable 'PreprocessThreadData::iFileLastScan' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometPreprocess.h:30:4: warning:inconclusive: Member variable 'PreprocessThreadData::pbMemoryPool' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometPreprocess.h:34:4: warning: Member variable 'PreprocessThreadData::pbMemoryPool' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometStatus.h:36:7: performance: Variable '_strStatusMessage' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] comet-2019015+cleaned/CometSearch/CometPreprocess.h:38:7: performance: Variable 'mstSpectrum' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] comet-2019015+cleaned/CometSearch/ThreadPool.h:209:9: style:inconclusive: Technically the member function 'ThreadPool::ShouldCheckQueuedParams' can be const. [functionConst] comet-2019015+cleaned/CometSearch/ThreadPool.h:270:6: style:inconclusive: Technically the member function 'ThreadManager::GetParam' can be const. [functionConst] comet-2019015+cleaned/CometSearch/CometSearch.h:33:4: style: Struct 'SearchThreadData' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] comet-2019015+cleaned/CometSearch/CometPostAnalysis.h:30:4: style: Struct 'PostAnalysisThreadData' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] comet-2019015+cleaned/CometSearch/ThreadPool.h:246:4: style: Class 'ThreadManager' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:277:4: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg] comet-2019015+cleaned/CometSearch/ThreadPool.h:209:9: style:inconclusive: Technically the member function 'ThreadPool < PreprocessThreadData * >::ShouldCheckQueuedParams' can be const. [functionConst] comet-2019015+cleaned/CometSearch/ThreadPool.h:268:9: performance:inconclusive: Technically the member function 'ThreadManager < PreprocessThreadData * >::SetParam' can be static (but you may consider moving to unnamed namespace). [functionStatic] comet-2019015+cleaned/CometSearch/ThreadPool.h:246:4: style: Class 'ThreadManager < PreprocessThreadData * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1936:31: warning: Identical inner 'if' condition is always true. [identicalInnerCondition] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1934:34: note: outer condition: dIntensity>pdTmpRawData[iBinIon] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1936:31: note: identical inner condition: dIntensity>pdTmpRawData[iBinIon] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:339:8: style: Condition '!LoadIons(pScoring,pdTmpRawData,mstSpectrum,&pPre)' is always false [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:339:17: note: Calling function 'LoadIons' returns 1 comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:339:8: note: Condition '!LoadIons(pScoring,pdTmpRawData,mstSpectrum,&pPre)' is always false comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:571:11: style: Condition '!Smooth(pdTmpRawData,pScoring->_spectrumInfoInternal.iArraySize,pdTmpSmoothedSpectrum)' is always false [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:571:18: note: Calling function 'Smooth' returns 1 comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:571:11: note: Condition '!Smooth(pdTmpRawData,pScoring->_spectrumInfoInternal.iArraySize,pdTmpSmoothedSpectrum)' is always false comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:574:11: style: Condition '!PeakExtract(pdTmpRawData,pScoring->_spectrumInfoInternal.iArraySize,pdTmpPeakExtracted)' is always false [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:574:23: note: Calling function 'PeakExtract' returns 1 comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:574:11: note: Condition '!PeakExtract(pdTmpRawData,pScoring->_spectrumInfoInternal.iArraySize,pdTmpPeakExtracted)' is always false comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:2123:11: style: Condition '!Smooth(pdTmpRawData,pScoring->_spectrumInfoInternal.iArraySize,pdTmpSmoothedSpectrum)' is always false [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:2123:18: note: Calling function 'Smooth' returns 1 comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:2123:11: note: Condition '!Smooth(pdTmpRawData,pScoring->_spectrumInfoInternal.iArraySize,pdTmpSmoothedSpectrum)' is always false comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:2126:11: style: Condition '!PeakExtract(pdTmpRawData,pScoring->_spectrumInfoInternal.iArraySize,pdTmpPeakExtracted)' is always false [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:2126:23: note: Calling function 'PeakExtract' returns 1 comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:2126:11: note: Condition '!PeakExtract(pdTmpRawData,pScoring->_spectrumInfoInternal.iArraySize,pdTmpPeakExtracted)' is always false comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:482:7: error: Resource leak: fpcheck [resourceLeak] comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2787:7: error: Resource leak: fptr [resourceLeak] comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2797:7: error: Resource leak: fptr [resourceLeak] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:56:8: style: The scope of the variable 'iScanNumber' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1214:14: style: The scope of the variable 'dStartWindowMZ' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1216:14: style: The scope of the variable 'dEndWindowMZ' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1265:11: style: The scope of the variable 'dIon' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1266:11: style: The scope of the variable 'dIntensity' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1406:11: style: The scope of the variable 'dMaxWindowInten' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1606:9: style: The scope of the variable 'ii' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1608:11: style: The scope of the variable 'dMaxInten' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1609:11: style: The scope of the variable 'dGap' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1908:11: style: The scope of the variable 'dIon' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1909:11: style: The scope of the variable 'dIntensity' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:292:42: style:inconclusive: Function 'Preprocess' argument 6 names different: declaration 'pdSmoothedSpectrum' definition 'pdTmpSmoothedSpectrum'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometPreprocess.h:115:35: note: Function 'Preprocess' argument 6 names different: declaration 'pdSmoothedSpectrum' definition 'pdTmpSmoothedSpectrum'. comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:292:42: note: Function 'Preprocess' argument 6 names different: declaration 'pdSmoothedSpectrum' definition 'pdTmpSmoothedSpectrum'. comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1448:38: style:inconclusive: Function 'Smooth' argument 3 names different: declaration 'pdSmoothedSpectrum' definition 'pdTmpSmoothedSpectrum'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometPreprocess.h:127:31: note: Function 'Smooth' argument 3 names different: declaration 'pdSmoothedSpectrum' definition 'pdTmpSmoothedSpectrum'. comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1448:38: note: Function 'Smooth' argument 3 names different: declaration 'pdSmoothedSpectrum' definition 'pdTmpSmoothedSpectrum'. comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:413:14: style: Local variable 'dTmp' shadows outer variable [shadowVariable] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:396:11: note: Shadowed declaration comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:413:14: note: Shadow variable comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:420:14: style: Local variable 'iTmp' shadows outer variable [shadowVariable] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:331:11: note: Shadowed declaration comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:420:14: note: Shadow variable comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:436:14: style: Local variable 'iTmp' shadows outer variable [shadowVariable] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:331:11: note: Shadowed declaration comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:436:14: note: Shadow variable comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1994:14: style: Local variable 'dTmp' shadows outer variable [shadowVariable] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1977:11: note: Shadowed declaration comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1994:14: note: Shadow variable comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:2001:14: style: Local variable 'iTmp' shadows outer variable [shadowVariable] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1893:11: note: Shadowed declaration comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:2001:14: note: Shadow variable comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:2017:14: style: Local variable 'iTmp' shadows outer variable [shadowVariable] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1893:11: note: Shadowed declaration comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:2017:14: note: Shadow variable comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1229:10: warning:inconclusive: Found suspicious operator '*', result is not used. [constStatement] comet-2019015+cleaned/CometSearch/CometPreprocess.h:34:35: style: Parameter 'spec_in' can be declared as reference to const [constParameterReference] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1396:44: style: Parameter 'pdTmpRawData' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1398:50: style: Parameter 'pScoring' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1399:61: style: Parameter 'pPre' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1550:42: style: Parameter 'pdTmpRawData' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1822:56: style: Parameter 'pdMass' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1823:56: style: Parameter 'pdInten' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1229:13: warning: In expression like '*A++' the result of '*' is unused. Did you intend to write '(*A)++;'? [clarifyStatement] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1226:99: warning: Missing bounds check for extra iterator increment in loop. [StlMissingComparison] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1229:11: note: Missing bounds check for extra iterator increment in loop. comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1226:99: note: Missing bounds check for extra iterator increment in loop. comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2341:57: style:inconclusive: Function 'DoSingleSpectrumSearch' argument 3 names different: declaration 'dMass' definition 'pdMass'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometSearchManager.h:41:48: note: Function 'DoSingleSpectrumSearch' argument 3 names different: declaration 'dMass' definition 'pdMass'. comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2341:57: note: Function 'DoSingleSpectrumSearch' argument 3 names different: declaration 'dMass' definition 'pdMass'. comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2342:57: style:inconclusive: Function 'DoSingleSpectrumSearch' argument 4 names different: declaration 'dInten' definition 'pdInten'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometSearchManager.h:42:48: note: Function 'DoSingleSpectrumSearch' argument 4 names different: declaration 'dInten' definition 'pdInten'. comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2342:57: note: Function 'DoSingleSpectrumSearch' argument 4 names different: declaration 'dInten' definition 'pdInten'. comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2347:58: style:inconclusive: Function 'DoSingleSpectrumSearch' argument 9 names different: declaration 'pScores' definition 'score'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometSearchManager.h:47:49: note: Function 'DoSingleSpectrumSearch' argument 9 names different: declaration 'pScores' definition 'score'. comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2347:58: note: Function 'DoSingleSpectrumSearch' argument 9 names different: declaration 'pScores' definition 'score'. comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:1974:21: style: Local variable 'szOut' shadows outer variable [shadowVariable] comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:1522:9: note: Shadowed declaration comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:1974:21: note: Shadow variable comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2175:21: style: Local variable 'szOut' shadows outer variable [shadowVariable] comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:1522:9: note: Shadowed declaration comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2175:21: note: Shadow variable comet-2019015+cleaned/CometSearch/CometSearch.h:33:31: style: Parameter 'dbEntry_in' can be declared as reference to const [constParameterReference] comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:103:44: style: Parameter 'pFileInfo' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:56:20: style: Variable 'iScanNumber' is assigned a value that is never used. [unreadVariable] comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2009:22: error:inconclusive: Using iterator to local container 'g_pvQuery' that may be invalid. [invalidContainer] comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2007:66: note: Iterator to container is created here. comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2009:25: note: Assuming condition is true. comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2012:25: note: Assuming condition is true. comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2012:25: note: Assuming condition is true. comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2009:25: note: Assuming condition is true. comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2014:32: note: After calling 'erase', iterators or references to the container's data may be invalid . comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:37:31: note: Variable created here. comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2009:22: note: Using iterator to local container 'g_pvQuery' that may be invalid. comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2254:20: error: Uninitialized variable: szOutputDecoySQT [legacyUninitvar] comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2222:20: error: Uninitialized variable: szOutputPepXML [legacyUninitvar] comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2230:20: error: Uninitialized variable: szOutputDecoyPepXML [legacyUninitvar] comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2238:20: error: Uninitialized variable: szOutputPercolator [legacyUninitvar] comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2262:20: error: Uninitialized variable: szOutputTxt [legacyUninitvar] comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2270:20: error: Uninitialized variable: szOutputDecoyTxt [legacyUninitvar] comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2939:29: style: Variable 'lNumMatchedProteins' is assigned a value that is never used. [unreadVariable] comet-2019015+cleaned/CometSearch/CometWriteOut.cpp:263:23: error: Uninitialized variable: szProteinName [legacyUninitvar] comet-2019015+cleaned/CometSearch/CometWriteOut.cpp:554:28: style: Variable 'dFragmentIonMass' is assigned a value that is never used. [unreadVariable] comet-2019015+cleaned/CometSearch/CometWritePercolator.cpp:49:17: style: Condition '!PrintResults(i,fpout,fpdb,0)' is always false [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometWritePercolator.cpp:49:30: note: Calling function 'PrintResults' returns 1 comet-2019015+cleaned/CometSearch/CometWritePercolator.cpp:49:17: note: Condition '!PrintResults(i,fpout,fpdb,0)' is always false comet-2019015+cleaned/CometSearch/CometWritePercolator.cpp:57:17: style: Condition '!PrintResults(i,fpout,fpdb,1)' is always false [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometWritePercolator.cpp:57:30: note: Calling function 'PrintResults' returns 1 comet-2019015+cleaned/CometSearch/CometWritePercolator.cpp:57:17: note: Condition '!PrintResults(i,fpout,fpdb,1)' is always false comet-2019015+cleaned/CometSearch/CometWritePercolator.cpp:302:4: portability: %f in format string (no. 1) requires 'double' but the argument type is 'int {aka signed int}'. [invalidPrintfArgType_float] comet-2019015+cleaned/CometSearch/CometWritePercolator.cpp:104:47: style:inconclusive: Function 'PrintResults' argument 2 names different: declaration 'fpOut' definition 'fpout'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometWritePercolator.h:33:35: note: Function 'PrintResults' argument 2 names different: declaration 'fpOut' definition 'fpout'. comet-2019015+cleaned/CometSearch/CometWritePercolator.cpp:104:47: note: Function 'PrintResults' argument 2 names different: declaration 'fpOut' definition 'fpout'. comet-2019015+cleaned/CometSearch/CometWritePercolator.cpp:251:59: style:inconclusive: Function 'PrintPercolatorSearchHit' argument 5 names different: declaration 'fpOut' definition 'fpout'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometWritePercolator.h:40:43: note: Function 'PrintPercolatorSearchHit' argument 5 names different: declaration 'fpOut' definition 'fpout'. comet-2019015+cleaned/CometSearch/CometWritePercolator.cpp:251:59: note: Function 'PrintPercolatorSearchHit' argument 5 names different: declaration 'fpOut' definition 'fpout'. comet-2019015+cleaned/CometSearch/CometWritePercolator.cpp:404:43: style:inconclusive: Function 'CalcNTTNMC' argument 2 names different: declaration 'iWhichQuery' definition 'iWhichResult'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometWritePercolator.h:45:31: note: Function 'CalcNTTNMC' argument 2 names different: declaration 'iWhichQuery' definition 'iWhichResult'. comet-2019015+cleaned/CometSearch/CometWritePercolator.cpp:404:43: note: Function 'CalcNTTNMC' argument 2 names different: declaration 'iWhichQuery' definition 'iWhichResult'. comet-2019015+cleaned/CometSearch/CometWritePercolator.cpp:403:48: style: Parameter 'pOutput' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometWriteSqt.cpp:67:53: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled] comet-2019015+cleaned/CometSearch/CometWriteSqt.cpp:168:40: style:inconclusive: Function 'PrintResults' argument 3 names different: declaration 'fpOut' definition 'fpout'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometWriteSqt.h:37:35: note: Function 'PrintResults' argument 3 names different: declaration 'fpOut' definition 'fpout'. comet-2019015+cleaned/CometSearch/CometWriteSqt.cpp:168:40: note: Function 'PrintResults' argument 3 names different: declaration 'fpOut' definition 'fpout'. comet-2019015+cleaned/CometSearch/CometWriteSqt.cpp:247:40: style:inconclusive: Function 'PrintSqtLine' argument 4 names different: declaration 'fpOut' definition 'fpout'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometWriteSqt.h:42:35: note: Function 'PrintSqtLine' argument 4 names different: declaration 'fpOut' definition 'fpout'. comet-2019015+cleaned/CometSearch/CometWriteSqt.cpp:247:40: note: Function 'PrintSqtLine' argument 4 names different: declaration 'fpOut' definition 'fpout'. comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:99:4: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg] comet-2019015+cleaned/CometSearch/ThreadPool.h:209:9: style:inconclusive: Technically the member function 'ThreadPool < PostAnalysisThreadData * >::ShouldCheckQueuedParams' can be const. [functionConst] comet-2019015+cleaned/CometSearch/ThreadPool.h:268:9: performance:inconclusive: Technically the member function 'ThreadManager < PostAnalysisThreadData * >::SetParam' can be static (but you may consider moving to unnamed namespace). [functionStatic] comet-2019015+cleaned/CometSearch/ThreadPool.h:246:4: style: Class 'ThreadManager < PostAnalysisThreadData * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:501:11: style: The scope of the variable 'Sx' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:501:15: style: The scope of the variable 'Sxy' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:504:11: style: The scope of the variable 'SumX' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:504:17: style: The scope of the variable 'SumY' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:512:8: style: The scope of the variable 'iNumPoints' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:641:11: style: The scope of the variable 'dFastXcorr' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:494:47: style:inconclusive: Function 'LinearRegression' argument 1 names different: declaration 'pHistogram' definition 'piHistogram'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometPostAnalysis.h:57:38: note: Function 'LinearRegression' argument 1 names different: declaration 'pHistogram' definition 'piHistogram'. comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:494:47: note: Function 'LinearRegression' argument 1 names different: declaration 'pHistogram' definition 'piHistogram'. comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:495:50: style:inconclusive: Function 'LinearRegression' argument 2 names different: declaration 'dSlope' definition 'slope'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometPostAnalysis.h:58:41: note: Function 'LinearRegression' argument 2 names different: declaration 'dSlope' definition 'slope'. comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:495:50: note: Function 'LinearRegression' argument 2 names different: declaration 'dSlope' definition 'slope'. comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:496:50: style:inconclusive: Function 'LinearRegression' argument 3 names different: declaration 'dIntercept' definition 'intercept'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometPostAnalysis.h:59:41: note: Function 'LinearRegression' argument 3 names different: declaration 'dIntercept' definition 'intercept'. comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:496:50: note: Function 'LinearRegression' argument 3 names different: declaration 'dIntercept' definition 'intercept'. comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:497:47: style:inconclusive: Function 'LinearRegression' argument 4 names different: declaration 'iMaxCorr' definition 'iMaxXcorr'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometPostAnalysis.h:60:38: note: Function 'LinearRegression' argument 4 names different: declaration 'iMaxCorr' definition 'iMaxXcorr'. comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:497:47: note: Function 'LinearRegression' argument 4 names different: declaration 'iMaxCorr' definition 'iMaxXcorr'. comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:498:47: style:inconclusive: Function 'LinearRegression' argument 5 names different: declaration 'iStartCorr' definition 'iStartXcorr'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometPostAnalysis.h:61:38: note: Function 'LinearRegression' argument 5 names different: declaration 'iStartCorr' definition 'iStartXcorr'. comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:498:47: note: Function 'LinearRegression' argument 5 names different: declaration 'iStartCorr' definition 'iStartXcorr'. comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:499:47: style:inconclusive: Function 'LinearRegression' argument 6 names different: declaration 'iNextCorr' definition 'iNextXcorr'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometPostAnalysis.h:62:38: note: Function 'LinearRegression' argument 6 names different: declaration 'iNextCorr' definition 'iNextXcorr'. comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:499:47: note: Function 'LinearRegression' argument 6 names different: declaration 'iNextCorr' definition 'iNextXcorr'. comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:259:34: style: Variable 'dFragmentIonMass' is assigned a value that is never used. [unreadVariable] comet-2019015+cleaned/CometSearch/CometPostAnalysis.cpp:668:5: style: Variable 'j' is assigned a value that is never used. [unreadVariable] comet-2019015+cleaned/CometSearch/CometWriteTxt.cpp:635:50: style: Condition 'g_staticParams.variableModParameters.bVarModSearch' is always true [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometWriteTxt.cpp:628:47: note: Assuming that condition 'g_staticParams.variableModParameters.bVarModSearch' is not redundant comet-2019015+cleaned/CometSearch/CometWriteTxt.cpp:635:50: note: Condition 'g_staticParams.variableModParameters.bVarModSearch' is always true comet-2019015+cleaned/CometSearch/Threading.cpp:71:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] comet-2019015+cleaned/CometSearch/Threading.cpp:66:18: style: C-style pointer casting [cstyleCast] comet-2019015+cleaned/CometSearch/CometWriteTxt.cpp:290:40: style:inconclusive: Function 'PrintResults' argument 3 names different: declaration 'fpOut' definition 'fpout'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometWriteTxt.h:38:35: note: Function 'PrintResults' argument 3 names different: declaration 'fpOut' definition 'fpout'. comet-2019015+cleaned/CometSearch/CometWriteTxt.cpp:290:40: note: Function 'PrintResults' argument 3 names different: declaration 'fpOut' definition 'fpout'. comet-2019015+cleaned/CometSearch/CometWriteTxt.cpp:561:49: style: Parameter 'pOutput' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometWriteTxt.cpp:694:16: style: Variable 'bFirst' is assigned a value that is never used. [unreadVariable] comet-2019015+cleaned/CometSearch/CometWritePepXML.cpp:72:46: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled] comet-2019015+cleaned/CometSearch/CometWritePepXML.cpp:525:14: style: The scope of the variable 'dDeltaCnStar' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometWritePepXML.cpp:392:46: style:inconclusive: Function 'WriteStaticMod' argument 3 names different: declaration 'varModName' definition 'paramName'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometWritePepXML.h:72:38: note: Function 'WriteStaticMod' argument 3 names different: declaration 'varModName' definition 'paramName'. comet-2019015+cleaned/CometSearch/CometWritePepXML.cpp:392:46: note: Function 'WriteStaticMod' argument 3 names different: declaration 'varModName' definition 'paramName'. comet-2019015+cleaned/CometSearch/CometWritePepXML.cpp:414:43: style:inconclusive: Function 'PrintResults' argument 3 names different: declaration 'fpOut' definition 'fpout'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometWritePepXML.h:40:35: note: Function 'PrintResults' argument 3 names different: declaration 'fpOut' definition 'fpout'. comet-2019015+cleaned/CometSearch/CometWritePepXML.cpp:414:43: note: Function 'PrintResults' argument 3 names different: declaration 'fpOut' definition 'fpout'. comet-2019015+cleaned/CometSearch/CometWritePepXML.cpp:607:51: style:inconclusive: Function 'PrintPepXMLSearchHit' argument 6 names different: declaration 'fpOut' definition 'fpout'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometWritePepXML.h:48:43: note: Function 'PrintPepXMLSearchHit' argument 6 names different: declaration 'fpOut' definition 'fpout'. comet-2019015+cleaned/CometSearch/CometWritePepXML.cpp:607:51: note: Function 'PrintPepXMLSearchHit' argument 6 names different: declaration 'fpOut' definition 'fpout'. comet-2019015+cleaned/CometSearch/CometWritePepXML.cpp:955:39: style:inconclusive: Function 'CalcNTTNMC' argument 2 names different: declaration 'iWhichQuery' definition 'iWhichResult'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometWritePepXML.h:61:31: note: Function 'CalcNTTNMC' argument 2 names different: declaration 'iWhichQuery' definition 'iWhichResult'. comet-2019015+cleaned/CometSearch/CometWritePepXML.cpp:955:39: note: Function 'CalcNTTNMC' argument 2 names different: declaration 'iWhichQuery' definition 'iWhichResult'. comet-2019015+cleaned/CometSearch/CometWritePepXML.cpp:272:48: performance: Function parameter 'varModName' should be passed by const reference. [passedByValue] comet-2019015+cleaned/CometSearch/CometWritePepXML.cpp:392:46: performance: Function parameter 'paramName' should be passed by const reference. [passedByValue] comet-2019015+cleaned/CometSearch/CometWritePepXML.cpp:617:11: style: Variable 'pQuery' can be declared as pointer to const [constVariablePointer] comet-2019015+cleaned/CometSearch/CometWritePepXML.cpp:925:37: style: Parameter 'szAttribute' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometWritePepXML.cpp:954:44: style: Parameter 'pOutput' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometWritePepXML.cpp:525:27: style: Variable 'dDeltaCnStar' is assigned a value that is never used. [unreadVariable] comet-2019015+cleaned/CometSearch/CometSearch.cpp:867:4: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1213:21: style: Array index 'iStart10' is used before limits check. [arrayIndexThenCheck] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1074:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1079:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1112:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1115:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1124:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled] comet-2019015+cleaned/CometSearch/CometSearch.cpp:30:14: warning: Member variable 'CometSearch::_pdAAforward' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometSearch.cpp:30:14: warning: Member variable 'CometSearch::_pdAAreverse' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometSearch.cpp:30:14: warning: Member variable 'CometSearch::_pdAAforwardDecoy' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometSearch.cpp:30:14: warning: Member variable 'CometSearch::_pdAAreverseDecoy' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometSearch.cpp:30:14: warning: Member variable 'CometSearch::_varModInfo' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometSearch.cpp:30:14: warning: Member variable 'CometSearch::_proteinInfo' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometSearch.cpp:30:14: warning: Member variable 'CometSearch::_uiBinnedIonMasses' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometSearch.cpp:30:14: warning: Member variable 'CometSearch::_uiBinnedIonMassesDecoy' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometSearch.cpp:30:14: warning: Member variable 'CometSearch::_uiBinnedPrecursorNL' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometSearch.cpp:30:14: warning: Member variable 'CometSearch::_uiBinnedPrecursorNLDecoy' is not initialized in the constructor. [uninitMemberVar] comet-2019015+cleaned/CometSearch/CometSearch.h:80:9: performance:inconclusive: Technically the member function 'CometSearch::ReadOBO' can be static (but you may consider moving to unnamed namespace). [functionStatic] comet-2019015+cleaned/CometSearch/CometSearch.cpp:715:19: note: Technically the member function 'CometSearch::ReadOBO' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/CometSearch.h:80:9: note: Technically the member function 'CometSearch::ReadOBO' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/CometSearch.h:85:8: performance:inconclusive: Technically the member function 'CometSearch::BinarySearchPeffStrMod' can be static (but you may consider moving to unnamed namespace). [functionStatic] comet-2019015+cleaned/CometSearch/CometSearch.cpp:2524:18: note: Technically the member function 'CometSearch::BinarySearchPeffStrMod' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/CometSearch.h:85:8: note: Technically the member function 'CometSearch::BinarySearchPeffStrMod' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/CometSearch.h:89:8: performance:inconclusive: Technically the member function 'CometSearch::BinarySearchMass' can be static (but you may consider moving to unnamed namespace). [functionStatic] comet-2019015+cleaned/CometSearch/CometSearch.cpp:2547:18: note: Technically the member function 'CometSearch::BinarySearchMass' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/CometSearch.h:89:8: note: Technically the member function 'CometSearch::BinarySearchMass' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/CometSearch.h:92:9: style:inconclusive: Technically the member function 'CometSearch::SubtractVarMods' can be const. [functionConst] comet-2019015+cleaned/CometSearch/CometSearch.cpp:3896:19: note: Technically the member function 'CometSearch::SubtractVarMods' can be const. comet-2019015+cleaned/CometSearch/CometSearch.h:92:9: note: Technically the member function 'CometSearch::SubtractVarMods' can be const. comet-2019015+cleaned/CometSearch/CometSearch.h:95:9: style:inconclusive: Technically the member function 'CometSearch::CountVarMods' can be const. [functionConst] comet-2019015+cleaned/CometSearch/CometSearch.cpp:3933:19: note: Technically the member function 'CometSearch::CountVarMods' can be const. comet-2019015+cleaned/CometSearch/CometSearch.h:95:9: note: Technically the member function 'CometSearch::CountVarMods' can be const. comet-2019015+cleaned/CometSearch/CometSearch.h:122:9: style:inconclusive: Technically the member function 'CometSearch::CheckEnzymeTermini' can be const. [functionConst] comet-2019015+cleaned/CometSearch/CometSearch.cpp:2377:19: note: Technically the member function 'CometSearch::CheckEnzymeTermini' can be const. comet-2019015+cleaned/CometSearch/CometSearch.h:122:9: note: Technically the member function 'CometSearch::CheckEnzymeTermini' can be const. comet-2019015+cleaned/CometSearch/CometSearch.h:125:9: performance:inconclusive: Technically the member function 'CometSearch::CheckEnzymeStartTermini' can be static (but you may consider moving to unnamed namespace). [functionStatic] comet-2019015+cleaned/CometSearch/CometSearch.cpp:2469:19: note: Technically the member function 'CometSearch::CheckEnzymeStartTermini' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/CometSearch.h:125:9: note: Technically the member function 'CometSearch::CheckEnzymeStartTermini' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/CometSearch.h:127:9: style:inconclusive: Technically the member function 'CometSearch::CheckEnzymeEndTermini' can be const. [functionConst] comet-2019015+cleaned/CometSearch/CometSearch.cpp:2497:19: note: Technically the member function 'CometSearch::CheckEnzymeEndTermini' can be const. comet-2019015+cleaned/CometSearch/CometSearch.h:127:9: note: Technically the member function 'CometSearch::CheckEnzymeEndTermini' can be const. comet-2019015+cleaned/CometSearch/CometSearch.h:129:9: performance:inconclusive: Technically the member function 'CometSearch::CheckMassMatch' can be static (but you may consider moving to unnamed namespace). [functionStatic] comet-2019015+cleaned/CometSearch/CometSearch.cpp:2584:19: note: Technically the member function 'CometSearch::CheckMassMatch' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/CometSearch.h:129:9: note: Technically the member function 'CometSearch::CheckMassMatch' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/CometSearch.h:131:11: style:inconclusive: Technically the member function 'CometSearch::GetFragmentIonMass' can be const. [functionConst] comet-2019015+cleaned/CometSearch/CometSearch.cpp:3298:21: note: Technically the member function 'CometSearch::GetFragmentIonMass' can be const. comet-2019015+cleaned/CometSearch/CometSearch.h:131:11: note: Technically the member function 'CometSearch::GetFragmentIonMass' can be const. comet-2019015+cleaned/CometSearch/CometSearch.h:136:8: performance:inconclusive: Technically the member function 'CometSearch::CheckDuplicate' can be static (but you may consider moving to unnamed namespace). [functionStatic] comet-2019015+cleaned/CometSearch/CometSearch.cpp:3630:18: note: Technically the member function 'CometSearch::CheckDuplicate' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/CometSearch.h:136:8: note: Technically the member function 'CometSearch::CheckDuplicate' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/CometSearch.h:164:11: performance:inconclusive: Technically the member function 'CometSearch::TotalVarModMass' can be static (but you may consider moving to unnamed namespace). [functionStatic] comet-2019015+cleaned/CometSearch/CometSearch.cpp:4788:21: note: Technically the member function 'CometSearch::TotalVarModMass' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/CometSearch.h:164:11: note: Technically the member function 'CometSearch::TotalVarModMass' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/CometSearch.h:173:9: performance:inconclusive: Technically the member function 'CometSearch::twiddle' can be static (but you may consider moving to unnamed namespace). [functionStatic] comet-2019015+cleaned/CometSearch/CometSearch.cpp:4971:18: note: Technically the member function 'CometSearch::twiddle' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/CometSearch.h:173:9: note: Technically the member function 'CometSearch::twiddle' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/CometSearch.h:174:9: performance:inconclusive: Technically the member function 'CometSearch::inittwiddle' can be static (but you may consider moving to unnamed namespace). [functionStatic] comet-2019015+cleaned/CometSearch/CometSearch.cpp:5029:19: note: Technically the member function 'CometSearch::inittwiddle' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/CometSearch.h:174:9: note: Technically the member function 'CometSearch::inittwiddle' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/CometSearch.h:206:9: performance:inconclusive: Technically the member function 'CometSearch::GetAA' can be static (but you may consider moving to unnamed namespace). [functionStatic] comet-2019015+cleaned/CometSearch/CometSearch.cpp:2985:19: note: Technically the member function 'CometSearch::GetAA' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/CometSearch.h:206:9: note: Technically the member function 'CometSearch::GetAA' can be static (but you may consider moving to unnamed namespace). comet-2019015+cleaned/CometSearch/ThreadPool.h:209:9: style:inconclusive: Technically the member function 'ThreadPool < SearchThreadData * >::ShouldCheckQueuedParams' can be const. [functionConst] comet-2019015+cleaned/CometSearch/ThreadPool.h:268:9: performance:inconclusive: Technically the member function 'ThreadManager < SearchThreadData * >::SetParam' can be static (but you may consider moving to unnamed namespace). [functionStatic] comet-2019015+cleaned/CometSearch/ThreadPool.h:246:4: style: Class 'ThreadManager < SearchThreadData * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1717:26: style: The statement 'if (bFirstTimeThroughLoopForPeptide) bFirstTimeThroughLoopForPeptide=false' is logically equivalent to 'bFirstTimeThroughLoopForPeptide=false'. [duplicateConditionalAssign] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1718:58: note: Assignment 'bFirstTimeThroughLoopForPeptide=false' comet-2019015+cleaned/CometSearch/CometSearch.cpp:1717:26: note: Condition 'bFirstTimeThroughLoopForPeptide' is redundant comet-2019015+cleaned/CometSearch/CometSearch.cpp:882:11: style: Condition '!SearchForPeptides(dbe,(char*)dbe.strSeq.c_str(),false,pbDuplFragment)' is always false [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometSearch.cpp:882:29: note: Calling function 'SearchForPeptides' returns 1 comet-2019015+cleaned/CometSearch/CometSearch.cpp:882:11: note: Condition '!SearchForPeptides(dbe,(char*)dbe.strSeq.c_str(),false,pbDuplFragment)' is always false comet-2019015+cleaned/CometSearch/CometSearch.cpp:889:14: style: Condition '!SearchForPeptides(dbe,(char*)dbe.strSeq.c_str()+1,true,pbDuplFragment)' is always false [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometSearch.cpp:889:32: note: Calling function 'SearchForPeptides' returns 1 comet-2019015+cleaned/CometSearch/CometSearch.cpp:889:14: note: Condition '!SearchForPeptides(dbe,(char*)dbe.strSeq.c_str()+1,true,pbDuplFragment)' is always false comet-2019015+cleaned/CometSearch/CometSearch.cpp:925:14: style: Condition '!SearchForPeptides(dbe,_proteinInfo.pszProteinSeq,false,pbDuplFragment)' is always false [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometSearch.cpp:925:32: note: Calling function 'SearchForPeptides' returns 1 comet-2019015+cleaned/CometSearch/CometSearch.cpp:925:14: note: Condition '!SearchForPeptides(dbe,_proteinInfo.pszProteinSeq,false,pbDuplFragment)' is always false comet-2019015+cleaned/CometSearch/CometSearch.cpp:937:17: style: Condition '!SearchForPeptides(dbe,_proteinInfo.pszProteinSeq,false,pbDuplFragment)' is always false [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometSearch.cpp:937:35: note: Calling function 'SearchForPeptides' returns 1 comet-2019015+cleaned/CometSearch/CometSearch.cpp:937:17: note: Condition '!SearchForPeptides(dbe,_proteinInfo.pszProteinSeq,false,pbDuplFragment)' is always false comet-2019015+cleaned/CometSearch/CometSearch.cpp:1001:20: style: Condition '!SearchForPeptides(dbe,_proteinInfo.pszProteinSeq,false,pbDuplFragment)' is always false [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1001:38: note: Calling function 'SearchForPeptides' returns 1 comet-2019015+cleaned/CometSearch/CometSearch.cpp:1001:20: note: Condition '!SearchForPeptides(dbe,_proteinInfo.pszProteinSeq,false,pbDuplFragment)' is always false comet-2019015+cleaned/CometSearch/CometSearch.cpp:1018:17: style: Condition '!SearchForPeptides(dbe,_proteinInfo.pszProteinSeq,false,pbDuplFragment)' is always false [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1018:35: note: Calling function 'SearchForPeptides' returns 1 comet-2019015+cleaned/CometSearch/CometSearch.cpp:1018:17: note: Condition '!SearchForPeptides(dbe,_proteinInfo.pszProteinSeq,false,pbDuplFragment)' is always false comet-2019015+cleaned/CometSearch/CometSearch.cpp:1948:56: style: Condition 'g_staticParams.variableModParameters.bVarModSearch' is always true [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1944:53: note: Assuming that condition 'g_staticParams.variableModParameters.bVarModSearch' is not redundant comet-2019015+cleaned/CometSearch/CometSearch.cpp:1948:56: note: Condition 'g_staticParams.variableModParameters.bVarModSearch' is always true comet-2019015+cleaned/CometSearch/CometSearch.cpp:4121:84: style: Condition '(int)dbe->vectorPeffMod.size()>0' is always true [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometSearch.cpp:4118:39: note: Assuming that condition '(int)dbe->vectorPeffMod.size()>0' is not redundant comet-2019015+cleaned/CometSearch/CometSearch.cpp:4121:84: note: Condition '(int)dbe->vectorPeffMod.size()>0' is always true comet-2019015+cleaned/CometSearch/CometSearch.cpp:4880:14: style: Condition '!MergeVarMods(szProteinSeq,iWhichQuery,pbDuplFragment,bDoPeffAnalysis,vPeffArray,dbe,lNumIterations)' is always false [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometSearch.cpp:4880:27: note: Calling function 'MergeVarMods' returns 1 comet-2019015+cleaned/CometSearch/CometSearch.cpp:4880:14: note: Condition '!MergeVarMods(szProteinSeq,iWhichQuery,pbDuplFragment,bDoPeffAnalysis,vPeffArray,dbe,lNumIterations)' is always false comet-2019015+cleaned/CometSearch/CometSearch.cpp:4899:17: style: Condition '!MergeVarMods(szProteinSeq,iWhichQuery,pbDuplFragment,bDoPeffAnalysis,vPeffArray,dbe,lNumIterations)' is always false [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometSearch.cpp:4899:30: note: Calling function 'MergeVarMods' returns 1 comet-2019015+cleaned/CometSearch/CometSearch.cpp:4899:17: note: Condition '!MergeVarMods(szProteinSeq,iWhichQuery,pbDuplFragment,bDoPeffAnalysis,vPeffArray,dbe,lNumIterations)' is always false comet-2019015+cleaned/CometSearch/CometSearch.cpp:4913:14: style: Condition '!MergeVarMods(szProteinSeq,iWhichQuery,pbDuplFragment,bDoPeffAnalysis,vPeffArray,dbe,lNumIterations)' is always false [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometSearch.cpp:4913:27: note: Calling function 'MergeVarMods' returns 1 comet-2019015+cleaned/CometSearch/CometSearch.cpp:4913:14: note: Condition '!MergeVarMods(szProteinSeq,iWhichQuery,pbDuplFragment,bDoPeffAnalysis,vPeffArray,dbe,lNumIterations)' is always false comet-2019015+cleaned/CometSearch/CometSearch.cpp:5323:24: style: Condition 'bValidPeffPosition' is always true [knownConditionTrueFalse] comet-2019015+cleaned/CometSearch/CometSearch.cpp:5307:45: note: Assignment 'bValidPeffPosition=true', assigned value is 1 comet-2019015+cleaned/CometSearch/CometSearch.cpp:5323:24: note: Condition 'bValidPeffPosition' is always true comet-2019015+cleaned/CometSearch/CometSearch.cpp:762:19: error: Width 16 given in format string (no. 1) is larger than destination buffer 'szTmp[16]', use %15s to prevent overflowing it. [invalidScanfFormatWidth] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1174:7: warning: %zu in format string (no. 3) requires 'size_t' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint] comet-2019015+cleaned/CometSearch/CometSearch.cpp:172:13: error: Resource leak: fp [resourceLeak] comet-2019015+cleaned/CometSearch/CometSearch.cpp:185:13: error: Resource leak: fp [resourceLeak] comet-2019015+cleaned/CometSearch/CometSearch.cpp:185:13: error: Memory leak: szPeffLine [memleak] comet-2019015+cleaned/CometSearch/CometSearch.cpp:164:23: style: C-style pointer casting [cstyleCast] comet-2019015+cleaned/CometSearch/CometSearch.cpp:177:19: style: C-style pointer casting [cstyleCast] comet-2019015+cleaned/CometSearch/CometSearch.cpp:317:32: style: C-style pointer casting [cstyleCast] comet-2019015+cleaned/CometSearch/CometSearch.cpp:362:33: style: C-style pointer casting [cstyleCast] comet-2019015+cleaned/CometSearch/CometSearch.cpp:508:33: style: C-style pointer casting [cstyleCast] comet-2019015+cleaned/CometSearch/CometSearch.cpp:882:35: style: C-style pointer casting [cstyleCast] comet-2019015+cleaned/CometSearch/CometSearch.cpp:889:38: style: C-style pointer casting [cstyleCast] comet-2019015+cleaned/CometSearch/CometSearch.cpp:898:33: style: C-style pointer casting [cstyleCast] comet-2019015+cleaned/CometSearch/CometSearch.cpp:922:37: style: C-style pointer casting [cstyleCast] comet-2019015+cleaned/CometSearch/CometSearch.cpp:934:40: style: C-style pointer casting [cstyleCast] comet-2019015+cleaned/CometSearch/CometSearch.cpp:969:26: style: C-style pointer casting [cstyleCast] comet-2019015+cleaned/CometSearch/CometSearch.cpp:2916:18: style: C-style pointer casting [cstyleCast] comet-2019015+cleaned/CometSearch/CometSearch.cpp:2951:18: style: C-style pointer casting [cstyleCast] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1764:31: style: Redundant initialization for 'dBion'. The initialized value is overwritten before it is read. [redundantInitialization] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1731:38: note: dBion is initialized comet-2019015+cleaned/CometSearch/CometSearch.cpp:1764:31: note: dBion is overwritten comet-2019015+cleaned/CometSearch/CometSearch.cpp:1765:31: style: Redundant initialization for 'dYion'. The initialized value is overwritten before it is read. [redundantInitialization] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1732:38: note: dYion is initialized comet-2019015+cleaned/CometSearch/CometSearch.cpp:1765:31: note: dYion is overwritten comet-2019015+cleaned/CometSearch/CometSearch.cpp:399:29: style: The scope of the variable 'iPos' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometSearch.cpp:751:21: style: The scope of the variable 'szTmp' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1352:8: style: The scope of the variable 'iLenPeptide' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1612:27: style: The scope of the variable 'szDecoyPeptide' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1626:29: style: The scope of the variable 'iPosForward' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1627:29: style: The scope of the variable 'iPosReverse' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1774:29: style: The scope of the variable 'iPosForward' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1775:29: style: The scope of the variable 'iPosReverse' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometSearch.cpp:2385:12: style: The scope of the variable 'bBreakPoint' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometSearch.cpp:3439:17: style: The scope of the variable 'iVal' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometSearch.cpp:3586:17: style: The scope of the variable 'iVal' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometSearch.cpp:3685:23: style: The scope of the variable 'iVal' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometSearch.cpp:3803:23: style: The scope of the variable 'iVal' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometSearch.cpp:4089:8: style: The scope of the variable 'ii' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometSearch.cpp:4645:50: style: The scope of the variable 'iSumTmpVarModCounts' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometSearch.cpp:5767:20: style: The scope of the variable 'iPosForward' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometSearch.cpp:5768:20: style: The scope of the variable 'iPosReverse' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometSearch.cpp:5769:20: style: The scope of the variable 'iPosReverseModSite' can be reduced. [variableScope] comet-2019015+cleaned/CometSearch/CometSearch.cpp:608:38: style: Checking if unsigned expression 'dbe.strName.length()' is less than zero. [unsignedLessThanZero] comet-2019015+cleaned/CometSearch/CometSearch.cpp:716:46: style:inconclusive: Function 'ReadOBO' argument 2 names different: declaration 'vectorUniModOBO' definition 'vectorPeffOBO'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometSearch.h:81:36: note: Function 'ReadOBO' argument 2 names different: declaration 'vectorUniModOBO' definition 'vectorPeffOBO'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:716:46: note: Function 'ReadOBO' argument 2 names different: declaration 'vectorUniModOBO' definition 'vectorPeffOBO'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:1960:43: style:inconclusive: Function 'AnalyzeIndexPep' argument 2 names different: declaration 'sTmp' definition 'sDBI'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometSearch.h:202:33: note: Function 'AnalyzeIndexPep' argument 2 names different: declaration 'sTmp' definition 'sDBI'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:1960:43: note: Function 'AnalyzeIndexPep' argument 2 names different: declaration 'sTmp' definition 'sDBI'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:2498:45: style:inconclusive: Function 'CheckEnzymeEndTermini' argument 2 names different: declaration 'iStartPos' definition 'iEndPos'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometSearch.h:128:35: note: Function 'CheckEnzymeEndTermini' argument 2 names different: declaration 'iStartPos' definition 'iEndPos'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:2498:45: note: Function 'CheckEnzymeEndTermini' argument 2 names different: declaration 'iStartPos' definition 'iEndPos'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:2902:40: style:inconclusive: Function 'TranslateNA2AA' argument 3 names different: declaration 'sDNASequence' definition 'szDNASequence'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometSearch.h:200:30: note: Function 'TranslateNA2AA' argument 3 names different: declaration 'sDNASequence' definition 'szDNASequence'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:2902:40: note: Function 'TranslateNA2AA' argument 3 names different: declaration 'sDNASequence' definition 'szDNASequence'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:2987:31: style:inconclusive: Function 'GetAA' argument 3 names different: declaration 'sDNASequence' definition 'szDNASequence'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometSearch.h:208:21: note: Function 'GetAA' argument 3 names different: declaration 'sDNASequence' definition 'szDNASequence'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:2987:31: note: Function 'GetAA' argument 3 names different: declaration 'sDNASequence' definition 'szDNASequence'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:3301:48: style:inconclusive: Function 'GetFragmentIonMass' argument 4 names different: declaration 'pdAAforward' definition '_pdAAforward'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometSearch.h:134:38: note: Function 'GetFragmentIonMass' argument 4 names different: declaration 'pdAAforward' definition '_pdAAforward'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:3301:48: note: Function 'GetFragmentIonMass' argument 4 names different: declaration 'pdAAforward' definition '_pdAAforward'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:3302:48: style:inconclusive: Function 'GetFragmentIonMass' argument 5 names different: declaration 'pdAAreverse' definition '_pdAAreverse'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometSearch.h:135:38: note: Function 'GetFragmentIonMass' argument 5 names different: declaration 'pdAAreverse' definition '_pdAAreverse'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:3302:48: note: Function 'GetFragmentIonMass' argument 5 names different: declaration 'pdAAreverse' definition '_pdAAreverse'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:3339:39: style:inconclusive: Function 'StorePeptide' argument 8 names different: declaration 'dScoreSp' definition 'dXcorr'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometSearch.h:154:29: note: Function 'StorePeptide' argument 8 names different: declaration 'dScoreSp' definition 'dXcorr'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:3339:39: note: Function 'StorePeptide' argument 8 names different: declaration 'dScoreSp' definition 'dXcorr'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:3340:37: style:inconclusive: Function 'StorePeptide' argument 9 names different: declaration 'bStoreSeparateDecoy' definition 'bDecoyPep'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometSearch.h:155:27: note: Function 'StorePeptide' argument 9 names different: declaration 'bStoreSeparateDecoy' definition 'bDecoyPep'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:3340:37: note: Function 'StorePeptide' argument 9 names different: declaration 'bStoreSeparateDecoy' definition 'bDecoyPep'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:3638:38: style:inconclusive: Function 'CheckDuplicate' argument 9 names different: declaration 'bDecoyResults' definition 'bDecoyPep'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometSearch.h:144:28: note: Function 'CheckDuplicate' argument 9 names different: declaration 'bDecoyResults' definition 'bDecoyPep'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:3638:38: note: Function 'CheckDuplicate' argument 9 names different: declaration 'bDecoyResults' definition 'bDecoyPep'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:4082:41: style:inconclusive: Function 'VariableModSearch' argument 2 names different: declaration 'varModCounts' definition 'piVarModCounts'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometSearch.h:159:31: note: Function 'VariableModSearch' argument 2 names different: declaration 'varModCounts' definition 'piVarModCounts'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:4082:41: note: Function 'VariableModSearch' argument 2 names different: declaration 'varModCounts' definition 'piVarModCounts'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:4804:37: style:inconclusive: Function 'PermuteMods' argument 4 names different: declaration 'pbDuplFragments' definition 'pbDuplFragment'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometSearch.h:168:27: note: Function 'PermuteMods' argument 4 names different: declaration 'pbDuplFragments' definition 'pbDuplFragment'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:4804:37: note: Function 'PermuteMods' argument 4 names different: declaration 'pbDuplFragments' definition 'pbDuplFragment'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:5055:38: style:inconclusive: Function 'MergeVarMods' argument 3 names different: declaration 'pbDuplFragments' definition 'pbDuplFragment'. [funcArgNamesDifferent] comet-2019015+cleaned/CometSearch/CometSearch.h:177:28: note: Function 'MergeVarMods' argument 3 names different: declaration 'pbDuplFragments' definition 'pbDuplFragment'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:5055:38: note: Function 'MergeVarMods' argument 3 names different: declaration 'pbDuplFragments' definition 'pbDuplFragment'. comet-2019015+cleaned/CometSearch/CometSearch.cpp:429:38: style: Local variable 'strModID' shadows outer variable [shadowVariable] comet-2019015+cleaned/CometSearch/CometSearch.cpp:400:32: note: Shadowed declaration comet-2019015+cleaned/CometSearch/CometSearch.cpp:429:38: note: Shadow variable comet-2019015+cleaned/CometSearch/CometSearch.cpp:4426:53: style: Local variable 'ii' shadows outer variable [shadowVariable] comet-2019015+cleaned/CometSearch/CometSearch.cpp:4089:8: note: Shadowed declaration comet-2019015+cleaned/CometSearch/CometSearch.cpp:4426:53: note: Shadow variable comet-2019015+cleaned/CometSearch/CometSearch.cpp:4633:47: style: Local variable 'ii' shadows outer variable [shadowVariable] comet-2019015+cleaned/CometSearch/CometSearch.cpp:4089:8: note: Shadowed declaration comet-2019015+cleaned/CometSearch/CometSearch.cpp:4633:47: note: Shadow variable comet-2019015+cleaned/CometSearch/CometSearch.cpp:794:33: performance: Function parameter 'strMod' should be passed by const reference. [passedByValue] comet-2019015+cleaned/CometSearch/CometSearch.cpp:2526:48: performance: Function parameter 'strMod' should be passed by const reference. [passedByValue] comet-2019015+cleaned/CometSearch/CometSearch.cpp:715:33: style: Parameter 'szOBO' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1064:16: style: Variable 'tok' can be declared as pointer to const [constVariablePointer] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1065:15: style: Variable 'delims' can be declared as const array [constVariable] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1106:16: style: Variable 'tok' can be declared as pointer to const [constVariablePointer] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1107:15: style: Variable 'delims' can be declared as const array [constVariable] comet-2019015+cleaned/CometSearch/CometSearch.cpp:2377:44: style: Parameter 'szProteinSeq' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometSearch.cpp:2469:49: style: Parameter 'szProteinSeq' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometSearch.cpp:2497:47: style: Parameter 'szProteinSeq' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometSearch.cpp:2900:39: style: Parameter 'frame' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometSearch.cpp:2987:31: style: Parameter 'szDNASequence' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometSearch.cpp:3301:48: style: Parameter '_pdAAforward' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometSearch.cpp:3302:48: style: Parameter '_pdAAreverse' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometSearch.cpp:3337:38: style: Parameter 'szProteinSeq' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometSearch.cpp:3341:37: style: Parameter 'piVarModSites' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometSearch.cpp:3637:39: style: Parameter 'szProteinSeq' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometSearch.cpp:3639:38: style: Parameter 'piVarModSites' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometSearch.cpp:4082:41: style: Parameter 'piVarModCounts' can be declared as const array [constParameter] comet-2019015+cleaned/CometSearch/CometSearch.cpp:4788:42: style: Parameter 'pVarModCounts' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometSearch.cpp:5056:38: style: Parameter 'bDoPeffAnalysis' can be declared as pointer to const [constParameterPointer] comet-2019015+cleaned/CometSearch/CometSearch.cpp:625:71: error: Uninitialized variable: sEntry.iWhichProtein [uninitvar] comet-2019015+cleaned/CometSearch/CometSearch.cpp:121:23: style: Variable 'bTrimDescr' is assigned a value that is never used. [unreadVariable] comet-2019015+cleaned/CometSearch/CometSearch.cpp:127:31: style: Variable 'iLen' is assigned a value that is never used. [unreadVariable] comet-2019015+cleaned/CometSearch/CometSearch.cpp:158:16: style: Variable 'lCurrPos' is assigned a value that is never used. [unreadVariable] comet-2019015+cleaned/CometSearch/CometSearch.cpp:787:25: style: Variable 'strErrorMsg' is assigned a value that is never used. [unreadVariable] comet-2019015+cleaned/CometSearch/CometSearch.cpp:826:28: style: Variable 'strErrorMsg' is assigned a value that is never used. [unreadVariable] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1198:14: style: Variable 'iStart' is assigned a value that is never used. [unreadVariable] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1200:12: style: Variable 'iEnd' is assigned a value that is never used. [unreadVariable] comet-2019015+cleaned/CometSearch/CometSearch.cpp:1352:20: style: Variable 'iLenPeptide' is assigned a value that is never used. [unreadVariable] comet-2019015+cleaned/CometSearch/CometSearch.cpp:5319:41: style: Variable 'bValidPeffPosition' is assigned a value that is never used. [unreadVariable] diff: head comet-2019015+cleaned/CometSearch/CometPreprocess.cpp:1550:42: style: Parameter 'pdTmpRawData' can be declared as pointer to const [constParameterPointer] head comet-2019015+cleaned/CometSearch/CometSearch.cpp:172:13: error: Resource leak: fp [resourceLeak] head comet-2019015+cleaned/CometSearch/CometSearch.cpp:185:13: error: Memory leak: szPeffLine [memleak] head comet-2019015+cleaned/CometSearch/CometSearch.cpp:185:13: error: Resource leak: fp [resourceLeak] 2.13.0 comet-2019015+cleaned/CometSearch/CometSearch.cpp:1960:43: performance: Function parameter 'sDBI' should be passed by const reference. [passedByValue] 2.13.0 comet-2019015+cleaned/CometSearch/CometSearch.cpp:4973:23: style: The scope of the variable 'k' can be reduced. [variableScope] head comet-2019015+cleaned/CometSearch/CometSearch.cpp:751:21: style: The scope of the variable 'szTmp' can be reduced. [variableScope] head comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2787:7: error: Resource leak: fptr [resourceLeak] head comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:2797:7: error: Resource leak: fptr [resourceLeak] head comet-2019015+cleaned/CometSearch/CometSearchManager.cpp:482:7: error: Resource leak: fpcheck [resourceLeak] head comet-2019015+cleaned/CometSearch/CometSearchManager.h:30:5: style: The destructor '~CometSearchManager' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] comet-2019015+cleaned/CometSearch/CometInterfaces.h:30:16: note: Virtual destructor in base class comet-2019015+cleaned/CometSearch/CometSearchManager.h:30:5: note: Destructor in derived class DONE