2024-03-25 11:49 ftp://ftp.de.debian.org/debian/pool/main/r/r-bioc-bitseq/r-bioc-bitseq_1.34.0+dfsg.orig.tar.xz cppcheck-options: --library=posix --library=gnu --library=bsd --library=openmp --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning -D__GNUC__ --platform=unix64 -j1 platform: Linux-6.5.0-25-generic-x86_64-with-glibc2.35 python: 3.10.12 client-version: 1.3.55 compiler: g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 cppcheck: head 2.13.0 head-info: fd7bd50 (2024-03-25 07:57:46 +0100) count: 340 269 elapsed-time: 8.0 54.0 head-timing-info: old-timing-info: head results: BitSeq/src/ArgumentParser.cpp:37:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] BitSeq/src/ArgumentParser.cpp:43:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] BitSeq/src/ArgumentParser.cpp:49:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] BitSeq/src/ArgumentParser.cpp:55:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] BitSeq/src/ArgumentParser.cpp:64:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] BitSeq/src/ArgumentParser.cpp:69:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/ArgumentParser.cpp:93:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] BitSeq/src/ArgumentParser.cpp:169:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/ArgumentParser.cpp:188:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/ArgumentParser.cpp:207:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/ArgumentParser.cpp:225:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/ArgumentParser.cpp:284:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable type [valueFlowBailoutIncompleteVar] BitSeq/src/ArgumentParser.cpp:306:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/ArgumentParser.h:32:12: performance:inconclusive: Technically the member function 'ArgumentParser::appendDescription < long >' can be static (but you may consider moving to unnamed namespace). [functionStatic] BitSeq/src/ArgumentParser.cpp:243:22: note: Technically the member function 'ArgumentParser::appendDescription < long >' can be static (but you may consider moving to unnamed namespace). BitSeq/src/ArgumentParser.h:32:12: note: Technically the member function 'ArgumentParser::appendDescription < long >' can be static (but you may consider moving to unnamed namespace). BitSeq/src/ArgumentParser.h:32:12: performance:inconclusive: Technically the member function 'ArgumentParser::appendDescription < double >' can be static (but you may consider moving to unnamed namespace). [functionStatic] BitSeq/src/ArgumentParser.cpp:243:22: note: Technically the member function 'ArgumentParser::appendDescription < double >' can be static (but you may consider moving to unnamed namespace). BitSeq/src/ArgumentParser.h:32:12: note: Technically the member function 'ArgumentParser::appendDescription < double >' can be static (but you may consider moving to unnamed namespace). BitSeq/src/ArgumentParser.h:32:12: performance:inconclusive: Technically the member function 'ArgumentParser::appendDescription < std :: string >' can be static (but you may consider moving to unnamed namespace). [functionStatic] BitSeq/src/ArgumentParser.cpp:243:22: note: Technically the member function 'ArgumentParser::appendDescription < std :: string >' can be static (but you may consider moving to unnamed namespace). BitSeq/src/ArgumentParser.h:32:12: note: Technically the member function 'ArgumentParser::appendDescription < std :: string >' can be static (but you may consider moving to unnamed namespace). BitSeq/src/PosteriorSamples.h:37:9: style:inconclusive: Technically the member function 'PosteriorSamples::logged' can be const. [functionConst] BitSeq/src/ArgumentParser.h:39:7: style: Class 'ArgumentParser' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] BitSeq/src/TranscriptInfo.h:47:7: style: Class 'TranscriptInfo' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] BitSeq/src/ArgumentParser.cpp:73:32: style:inconclusive: Function 'parse' argument 1 names different: declaration 'n' definition 'argc'. [funcArgNamesDifferent] BitSeq/src/ArgumentParser.h:52:22: note: Function 'parse' argument 1 names different: declaration 'n' definition 'argc'. BitSeq/src/ArgumentParser.cpp:73:32: note: Function 'parse' argument 1 names different: declaration 'n' definition 'argc'. BitSeq/src/ArgumentParser.cpp:243:63: performance: Function parameter 'defValue' should be passed by const reference. [passedByValue] BitSeq/src/ArgumentParser.cpp:73:44: style: Parameter 'argv' can be declared as const array [constParameter] BitSeq/src/ArgumentParser.cpp:153:68: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] BitSeq/src/ArgumentParser.cpp:156:66: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] BitSeq/src/ArgumentParser.cpp:159:68: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] BitSeq/src/ArgumentParser.cpp:162:66: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] BitSeq/src/ArgumentParser.cpp:254:53: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] BitSeq/src/ArgumentParser.cpp:264:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] BitSeq/src/Sampler.h:90:26: style:inconclusive: Technically the member function 'Sampler::getThetaActLog' can be const. [functionConst] BitSeq/src/GibbsParameters.h:25:7: style: Class 'gibbsParameters' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] BitSeq/src/TagAlignments.h:22:7: style: Class 'TagAlignments' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] BitSeq/src/CollapsedSampler.h:13:17: style: The function 'update' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] BitSeq/src/Sampler.h:95:17: note: Virtual function in base class BitSeq/src/CollapsedSampler.h:13:17: note: Function in derived class BitSeq/src/CollapsedSampler.h:14:17: style: The function 'sample' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] BitSeq/src/Sampler.h:93:17: note: Virtual function in base class BitSeq/src/CollapsedSampler.h:14:17: note: Function in derived class BitSeq/src/CollapsedSampler.cpp:31:11: style: The scope of the variable 'probNorm' can be reduced. [variableScope] BitSeq/src/CollapsedSampler.cpp:31:20: style: The scope of the variable 'r' can be reduced. [variableScope] BitSeq/src/CollapsedSampler.cpp:32:18: style: The scope of the variable 'readsAlignmentsN' can be reduced. [variableScope] BitSeq/src/FileHeader.cpp:20:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/FileHeader.cpp:87:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LOG_FORMAT [valueFlowBailoutIncompleteVar] BitSeq/src/FileHeader.h:28:4: style: Class 'FileHeader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] BitSeq/src/FileHeader.cpp:24:19: style: The scope of the variable 'words' can be reduced. [variableScope] BitSeq/src/FileHeader.cpp:41:32: performance: Searching before insertion is not necessary. Instead of 'values[words[i]]=no_value' consider using 'values.try_emplace(words[i], no_value);'. [stlFindInsert] BitSeq/src/GibbsParameters.cpp:107:4: performance: Variable 'gs_samplesFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] BitSeq/src/GibbsParameters.cpp:108:4: performance: Variable 'gs_meansFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] BitSeq/src/GibbsParameters.h:21:12: style:inconclusive: Technically the member function 'gibbsParameters::parameter' can be const. [functionConst] BitSeq/src/GibbsParameters.cpp:86:23: note: Technically the member function 'gibbsParameters::parameter' can be const. BitSeq/src/GibbsParameters.h:21:12: note: Technically the member function 'gibbsParameters::parameter' can be const. BitSeq/src/GibbsParameters.h:22:12: style:inconclusive: Technically the member function 'gibbsParameters::parameter' can be const. [functionConst] BitSeq/src/GibbsParameters.cpp:78:23: note: Technically the member function 'gibbsParameters::parameter' can be const. BitSeq/src/GibbsParameters.h:22:12: note: Technically the member function 'gibbsParameters::parameter' can be const. BitSeq/src/GibbsParameters.h:23:12: style:inconclusive: Technically the member function 'gibbsParameters::parameter' can be const. [functionConst] BitSeq/src/GibbsParameters.cpp:70:23: note: Technically the member function 'gibbsParameters::parameter' can be const. BitSeq/src/GibbsParameters.h:23:12: note: Technically the member function 'gibbsParameters::parameter' can be const. BitSeq/src/GibbsParameters.cpp:24:44: performance: Function parameter 'paramFileName' should be passed by const reference. [passedByValue] BitSeq/src/GibbsParameters.cpp:70:40: performance: Function parameter 'name' should be passed by const reference. [passedByValue] BitSeq/src/GibbsParameters.cpp:78:40: performance: Function parameter 'name' should be passed by const reference. [passedByValue] BitSeq/src/GibbsParameters.cpp:86:40: performance: Function parameter 'name' should be passed by const reference. [passedByValue] BitSeq/src/GibbsParameters.cpp:28:53: style: Parameter 'args' can be declared as reference to const [constParameterReference] BitSeq/src/GibbsSampler.h:15:17: style: The function 'update' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] BitSeq/src/Sampler.h:95:17: note: Virtual function in base class BitSeq/src/GibbsSampler.h:15:17: note: Function in derived class BitSeq/src/GibbsSampler.h:16:17: style: The function 'sample' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] BitSeq/src/Sampler.h:93:17: note: Virtual function in base class BitSeq/src/GibbsSampler.h:16:17: note: Function in derived class BitSeq/src/GibbsSampler.cpp:23:11: style: The scope of the variable 'probNorm' can be reduced. [variableScope] BitSeq/src/GibbsSampler.cpp:23:20: style: The scope of the variable 'r' can be reduced. [variableScope] BitSeq/src/GibbsSampler.cpp:24:18: style: The scope of the variable 'readsAlignmentsN' can be reduced. [variableScope] BitSeq/src/MyTimer.cpp:12:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] BitSeq/src/MyTimer.h:14:9: performance:inconclusive: Technically the member function 'MyTimer::adjust' can be static (but you may consider moving to unnamed namespace). [functionStatic] BitSeq/src/MyTimer.cpp:7:15: note: Technically the member function 'MyTimer::adjust' can be static (but you may consider moving to unnamed namespace). BitSeq/src/MyTimer.h:14:9: note: Technically the member function 'MyTimer::adjust' can be static (but you may consider moving to unnamed namespace). BitSeq/src/MyTimer.h:16:9: style:inconclusive: Technically the member function 'MyTimer::write' can be const. [functionConst] BitSeq/src/MyTimer.cpp:11:15: note: Technically the member function 'MyTimer::write' can be const. BitSeq/src/MyTimer.h:16:9: note: Technically the member function 'MyTimer::write' can be const. BitSeq/src/PosteriorSamples.cpp:33:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/PosteriorSamples.cpp:45:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/PosteriorSamples.cpp:60:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/PosteriorSamples.cpp:100:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cur [valueFlowBailoutIncompleteVar] BitSeq/src/PosteriorSamples.cpp:138:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] BitSeq/src/PosteriorSamples.cpp:151:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] BitSeq/src/PosteriorSamples.cpp:228:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/PosteriorSamples.cpp:237:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] BitSeq/src/PosteriorSamples.cpp:247:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/PosteriorSamples.cpp:268:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/PosteriorSamples.h:27:4: warning:inconclusive: Member variable 'PosteriorSamples::samplesF' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy] BitSeq/src/PosteriorSamples.h:27:4: warning:inconclusive: Member variable 'PosteriorSamples::lines' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy] BitSeq/src/PosteriorSamples.h:27:4: warning:inconclusive: Member variable 'PosteriorSamples::samples' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy] BitSeq/src/PosteriorSamples.h:28:22: warning:inconclusive: Member variable 'PosteriorSamples::lines' is not assigned a value in 'PosteriorSamples::operator='. [operatorEqVarError] BitSeq/src/PosteriorSamples.h:28:22: warning:inconclusive: Member variable 'PosteriorSamples::samples' is not assigned a value in 'PosteriorSamples::operator='. [operatorEqVarError] BitSeq/src/PosteriorSamples.cpp:128:13: warning: Member variable 'Conditions::M' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/PosteriorSamples.cpp:128:13: warning: Member variable 'Conditions::N' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/PosteriorSamples.cpp:128:13: warning: Member variable 'Conditions::areLogged' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/PosteriorSamples.h:50:12: performance:inconclusive: Technically the member function 'Conditions::getIndex' can be static (but you may consider moving to unnamed namespace). [functionStatic] BitSeq/src/PosteriorSamples.cpp:133:18: note: Technically the member function 'Conditions::getIndex' can be static (but you may consider moving to unnamed namespace). BitSeq/src/PosteriorSamples.h:50:12: note: Technically the member function 'Conditions::getIndex' can be static (but you may consider moving to unnamed namespace). BitSeq/src/PosteriorSamples.cpp:77:11: style: The scope of the variable 'str' can be reduced. [variableScope] BitSeq/src/PosteriorSamples.cpp:145:11: style: The scope of the variable 'j' can be reduced. [variableScope] BitSeq/src/PosteriorSamples.cpp:145:13: style: The scope of the variable 'x' can be reduced. [variableScope] BitSeq/src/PosteriorSamples.cpp:29:36: performance: Function parameter 'fileName' should be passed by const reference. [passedByValue] BitSeq/src/PosteriorSamples.cpp:39:56: performance: Function parameter 'fileName' should be passed by const reference. [passedByValue] BitSeq/src/PosteriorSamples.cpp:140:30: performance: Function parameter 'trFileName' should be passed by const reference. [passedByValue] BitSeq/src/PosteriorSamples.cpp:140:57: performance: Function parameter 'filesGot' should be passed by const reference. [passedByValue] BitSeq/src/PosteriorSamples.cpp:144:30: performance: Function parameter 'trFileName' should be passed by const reference. [passedByValue] BitSeq/src/PosteriorSamples.cpp:226:41: performance: Function parameter 'norms' should be passed by const reference. [passedByValue] BitSeq/src/ReadDistribution.cpp:67:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar] BitSeq/src/ReadDistribution.cpp:80:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar] BitSeq/src/ReadDistribution.cpp:113:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/ReadDistribution.cpp:143:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/ReadDistribution.cpp:178:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/ReadDistribution.cpp:206:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/ReadDistribution.cpp:315:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/ReadDistribution.cpp:428:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scientific [valueFlowBailoutIncompleteVar] BitSeq/src/ReadDistribution.cpp:485:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FREVERSE [valueFlowBailoutIncompleteVar] BitSeq/src/ReadDistribution.cpp:533:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FREVERSE [valueFlowBailoutIncompleteVar] BitSeq/src/ReadDistribution.cpp:615:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/ReadDistribution.cpp:715:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable readM_3 [valueFlowBailoutIncompleteVar] BitSeq/src/ReadDistribution.cpp:735:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable readM_5 [valueFlowBailoutIncompleteVar] BitSeq/src/ReadDistribution.cpp:759:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable trNumberOfBins [valueFlowBailoutIncompleteVar] BitSeq/src/ReadDistribution.cpp:772:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FullPair [valueFlowBailoutIncompleteVar] BitSeq/src/ReadDistribution.cpp:808:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FullPair [valueFlowBailoutIncompleteVar] BitSeq/src/ReadDistribution.cpp:964:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mate_5 [valueFlowBailoutIncompleteVar] BitSeq/src/ReadDistribution.cpp:1018:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/ReadDistribution.cpp:128:16: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg] BitSeq/src/ReadDistribution.cpp:658:13: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall] BitSeq/src/ReadDistribution.cpp:88:19: warning: Member variable 'ReadDistribution::fragSeen' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/ReadDistribution.cpp:88:19: warning: Member variable 'ReadDistribution::logLengthSum' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/ReadDistribution.cpp:88:19: warning: Member variable 'ReadDistribution::logLengthSqSum' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/ReadDistribution.cpp:88:19: warning: Member variable 'ReadDistribution::unstranded' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/ReadDistribution.cpp:88:19: warning: Member variable 'ReadDistribution::trInf' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/ReadDistribution.cpp:88:19: warning: Member variable 'ReadDistribution::trSeq' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/ReadDistribution.cpp:88:19: warning: Member variable 'ReadDistribution::trExp' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/TranscriptExpression.h:31:12: style:inconclusive: Technically the member function 'TranscriptExpression::getM' can be const. [functionConst] BitSeq/src/TranscriptExpression.h:32:12: style:inconclusive: Technically the member function 'TranscriptExpression::isLogged' can be const. [functionConst] BitSeq/src/TranscriptExpression.h:33:14: style:inconclusive: Technically the member function 'TranscriptExpression::exp' can be const. [functionConst] BitSeq/src/TranscriptExpression.h:34:14: style:inconclusive: Technically the member function 'TranscriptExpression::var' can be const. [functionConst] BitSeq/src/TranscriptExpression.h:35:12: style:inconclusive: Technically the member function 'TranscriptExpression::id' can be const. [functionConst] BitSeq/src/ReadDistribution.h:111:19: performance:inconclusive: Technically the member function 'ReadDistribution::getBase' can be static (but you may consider moving to unnamed namespace). [functionStatic] BitSeq/src/ReadDistribution.cpp:798:31: note: Technically the member function 'ReadDistribution::getBase' can be static (but you may consider moving to unnamed namespace). BitSeq/src/ReadDistribution.h:111:19: note: Technically the member function 'ReadDistribution::getBase' can be static (but you may consider moving to unnamed namespace). BitSeq/src/TranscriptExpression.h:28:7: style: Class 'TranscriptExpression' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] BitSeq/src/TranscriptSequence.h:60:7: style: Class 'TranscriptSequence' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] BitSeq/src/ReadDistribution.h:59:7: style: Class 'VlmmNode' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] BitSeq/src/ReadDistribution.cpp:265:35: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition] BitSeq/src/ReadDistribution.cpp:687:40: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition] BitSeq/src/ReadDistribution.cpp:228:15: style: The scope of the variable 'logLen' can be reduced. [variableScope] BitSeq/src/ReadDistribution.cpp:325:11: style: The scope of the variable 'lFreqSum' can be reduced. [variableScope] BitSeq/src/ReadDistribution.cpp:397:11: style: The scope of the variable 'IexpSum5' can be reduced. [variableScope] BitSeq/src/ReadDistribution.cpp:397:20: style: The scope of the variable 'IexpSum3' can be reduced. [variableScope] BitSeq/src/ReadDistribution.cpp:433:13: style: The scope of the variable 'g' can be reduced. [variableScope] BitSeq/src/ReadDistribution.cpp:837:23: style: The scope of the variable 'w' can be reduced. [variableScope] BitSeq/src/ReadDistribution.cpp:915:15: style: The scope of the variable 'trLen' can be reduced. [variableScope] BitSeq/src/ReadDistribution.cpp:934:12: style: The scope of the variable 'threadID' can be reduced. [variableScope] BitSeq/src/ReadDistribution.cpp:1042:12: style: The scope of the variable 'i' can be reduced. [variableScope] BitSeq/src/ReadDistribution.cpp:1067:13: style: The scope of the variable 'k' can be reduced. [variableScope] BitSeq/src/ReadDistribution.cpp:1107:12: style: The scope of the variable 'i' can be reduced. [variableScope] BitSeq/src/ReadDistribution.cpp:420:16: style: Local variable 'j' shadows outer variable [shadowVariable] BitSeq/src/ReadDistribution.cpp:334:11: note: Shadowed declaration BitSeq/src/ReadDistribution.cpp:420:16: note: Shadow variable BitSeq/src/ReadDistribution.cpp:424:43: performance: Function parameter 'logFileName' should be passed by const reference. [passedByValue] BitSeq/src/ReadDistribution.cpp:526:13: style: Variable 'qualP' can be declared as pointer to const [constVariablePointer] BitSeq/src/ReadDistribution.cpp:405:18: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] BitSeq/src/ReadDistribution.cpp:128:21: style: Variable 'procN' is assigned a value that is never used. [unreadVariable] BitSeq/src/ReadDistribution.cpp:917:11: style: Unused variable: trRS [unusedVariable] BitSeq/src/ReadDistribution.cpp:1042:13: style: Variable 'i' is assigned a value that is never used. [unreadVariable] BitSeq/src/ReadDistribution.cpp:1042:17: style: Variable 'j' is assigned a value that is never used. [unreadVariable] BitSeq/src/ReadDistribution.cpp:1042:21: style: Variable 'k' is assigned a value that is never used. [unreadVariable] BitSeq/src/ReadDistribution.cpp:1066:14: style: Variable 'sum' is assigned a value that is never used. [unreadVariable] BitSeq/src/ReadDistribution.cpp:1107:13: style: Variable 'i' is assigned a value that is never used. [unreadVariable] BitSeq/src/ReadDistribution.cpp:1107:17: style: Variable 'j' is assigned a value that is never used. [unreadVariable] BitSeq/src/ReadDistribution.cpp:1107:21: style: Variable 'k' is assigned a value that is never used. [unreadVariable] BitSeq/src/ReadDistribution.cpp:348:69: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] BitSeq/src/ReadDistribution.cpp:364:69: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] BitSeq/src/ReadDistribution.cpp:404:65: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] BitSeq/src/ReadDistribution.cpp:411:115: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] BitSeq/src/ReadDistribution.cpp:412:126: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] BitSeq/src/ReadDistribution.cpp:466:81: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] BitSeq/src/ReadDistribution.cpp:469:81: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] BitSeq/src/Sampler.cpp:64:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] BitSeq/src/Sampler.cpp:71:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] BitSeq/src/Sampler.cpp:80:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] BitSeq/src/Sampler.cpp:97:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] BitSeq/src/Sampler.cpp:105:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/Sampler.cpp:125:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scientific [valueFlowBailoutIncompleteVar] BitSeq/src/Sampler.cpp:154:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] BitSeq/src/Sampler.cpp:200:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/Sampler.cpp:8:10: warning: Member variable 'Sampler::beta' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/Sampler.cpp:8:10: warning: Member variable 'Sampler::dir' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/Sampler.cpp:8:10: warning: Member variable 'Sampler::alignments' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/Sampler.cpp:8:10: warning: Member variable 'Sampler::doLog' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/Sampler.cpp:8:10: warning: Member variable 'Sampler::save' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/Sampler.cpp:8:10: warning: Member variable 'Sampler::outFile' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/Sampler.cpp:8:10: warning: Member variable 'Sampler::saveNorm' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/Sampler.cpp:8:10: warning: Member variable 'Sampler::logRate' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/Sampler.cpp:8:10: warning: Member variable 'Sampler::sumC0' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/Sampler.h:53:9: style:inconclusive: Technically the member function 'Sampler::getTau' can be const. [functionConst] BitSeq/src/Sampler.cpp:101:15: note: Technically the member function 'Sampler::getTau' can be const. BitSeq/src/Sampler.h:53:9: note: Technically the member function 'Sampler::getTau' can be const. BitSeq/src/Sampler.h:72:9: style:inconclusive: Technically the member function 'Sampler::getAverageC0' can be const. [functionConst] BitSeq/src/Sampler.cpp:55:15: note: Technically the member function 'Sampler::getAverageC0' can be const. BitSeq/src/Sampler.h:72:9: note: Technically the member function 'Sampler::getAverageC0' can be const. BitSeq/src/Sampler.h:81:9: style:inconclusive: Technically the member function 'Sampler::getThetaSums' can be const. [functionConst] BitSeq/src/Sampler.cpp:92:15: note: Technically the member function 'Sampler::getThetaSums' can be const. BitSeq/src/Sampler.h:81:9: note: Technically the member function 'Sampler::getThetaSums' can be const. BitSeq/src/Sampler.cpp:152:11: style: The scope of the variable 's' can be reduced. [variableScope] BitSeq/src/SimpleSparse.cpp:18:20: warning: Invalid log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg] BitSeq/src/SimpleSparse.cpp:14:18: note: Assignment 'sumE=0', assigned value is 0 BitSeq/src/SimpleSparse.cpp:16:18: note: Assuming condition is false BitSeq/src/SimpleSparse.cpp:18:20: note: Invalid argument BitSeq/src/SimpleSparse.cpp:66:15: warning: Member variable 'SimpleSparse::colStart' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/SimpleSparse.cpp:76:15: warning: Member variable 'SimpleSparse::colStart' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/SimpleSparse.cpp:73:4: warning: Class 'SimpleSparse' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] BitSeq/src/SimpleSparse.cpp:73:4: warning: Class 'SimpleSparse' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] BitSeq/src/SimpleSparse.h:17:4: style: Class 'SimpleSparse' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] BitSeq/src/SimpleSparse.cpp:43:11: style: The scope of the variable 'logRowSum' can be reduced. [variableScope] BitSeq/src/SimpleSparse.cpp:55:11: style: The scope of the variable 'logRowSum' can be reduced. [variableScope] BitSeq/src/SimpleSparse.cpp:43:21: style: Variable 'logRowSum' is assigned a value that is never used. [unreadVariable] BitSeq/src/SimpleSparse.cpp:55:21: style: Variable 'logRowSum' is assigned a value that is never used. [unreadVariable] BitSeq/src/TagAlignments.cpp:11:16: warning: Member variable 'TagAlignments::M' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/TagAlignments.cpp:11:16: warning: Member variable 'TagAlignments::currentRead' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/TagAlignments.cpp:11:16: warning: Member variable 'TagAlignments::reservedN' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/TranscriptExpression.cpp:32:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/TranscriptExpression.h:24:19: performance:inconclusive: Technically the member function 'TranscriptExpression::guessFileType' can be static (but you may consider moving to unnamed namespace). [functionStatic] BitSeq/src/TranscriptExpression.cpp:7:35: note: Technically the member function 'TranscriptExpression::guessFileType' can be static (but you may consider moving to unnamed namespace). BitSeq/src/TranscriptExpression.h:24:19: note: Technically the member function 'TranscriptExpression::guessFileType' can be static (but you may consider moving to unnamed namespace). BitSeq/src/TranscriptExpression.cpp:23:4: style: Instance of 'TranscriptExpression' object is destroyed immediately. [unusedScopedObject] BitSeq/src/TranscriptInfo.cpp:19:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar] BitSeq/src/TranscriptInfo.cpp:29:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar] BitSeq/src/TranscriptInfo.cpp:126:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/TranscriptInfo.cpp:192:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/TranscriptInfo.cpp:228:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/TranscriptInfo.cpp:241:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/TranscriptInfo.cpp:118:4: performance: Variable 'noName' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] BitSeq/src/TranscriptInfo.cpp:228:7: portability: %ld in format string (no. 1) requires 'long' but the argument type is 'std::size_t {aka unsigned long}'. [invalidPrintfArgType_sint] BitSeq/src/TranscriptInfo.cpp:241:7: portability: %ld in format string (no. 1) requires 'long' but the argument type is 'std::size_t {aka unsigned long}'. [invalidPrintfArgType_sint] BitSeq/src/TranscriptInfo.cpp:33:11: style: The scope of the variable 'length' can be reduced. [variableScope] BitSeq/src/TranscriptInfo.cpp:8:39: performance: Function parameter 'fileName' should be passed by const reference. [passedByValue] BitSeq/src/TranscriptInfo.cpp:27:43: performance: Function parameter 'fileName' should be passed by const reference. [passedByValue] BitSeq/src/TranscriptInfo.cpp:42:45: performance: Function parameter 'gNames' should be passed by const reference. [passedByValue] BitSeq/src/TranscriptInfo.cpp:42:67: performance: Function parameter 'tNames' should be passed by const reference. [passedByValue] BitSeq/src/TranscriptInfo.cpp:42:88: performance: Function parameter 'lengths' should be passed by const reference. [passedByValue] BitSeq/src/TranscriptInfo.cpp:117:39: performance: Function parameter 'fileName' should be passed by const reference. [passedByValue] BitSeq/src/TranscriptInfo.cpp:122:38: performance: Function parameter 'fileName' should be passed by const reference. [passedByValue] BitSeq/src/TranscriptInfo.cpp:190:56: performance: Function parameter 'effL' should be passed by const reference. [passedByValue] BitSeq/src/TranscriptInfo.cpp:196:16: style: Variable 'sumL' is assigned a value that is never used. [unreadVariable] BitSeq/src/TranscriptInfo.cpp:196:25: style: Variable 'sumN' is assigned a value that is never used. [unreadVariable] BitSeq/src/TranscriptInfo.cpp:198:11: style: Variable 'sumN' is assigned a value that is never used. [unreadVariable] BitSeq/src/TranscriptInfo.cpp:199:11: style: Variable 'sumL' is assigned a value that is never used. [unreadVariable] BitSeq/src/TranscriptSequence.cpp:29:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/TranscriptSequence.cpp:101:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/TranscriptSequence.cpp:15:21: warning: Member variable 'TranscriptSequence::gotTrNames' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/TranscriptSequence.cpp:22:21: warning: Member variable 'TranscriptSequence::cM' is not initialized in the constructor. [uninitMemberVar] BitSeq/src/TranscriptSequence.cpp:22:47: performance: Function parameter 'fileName' should be passed by const reference. [passedByValue] BitSeq/src/TranscriptSequence.cpp:26:46: performance: Function parameter 'fileName' should be passed by const reference. [passedByValue] BitSeq/src/TranscriptSequence.cpp:23:4: style: Instance of 'TranscriptSequence' object is destroyed immediately. [unusedScopedObject] BitSeq/src/VariationalBayes.cpp:101:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/VariationalBayes.cpp:253:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] BitSeq/src/VariationalBayes.cpp:356:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scientific [valueFlowBailoutIncompleteVar] BitSeq/src/VariationalBayes.cpp:72:27: warning: Invalid std::lgamma() argument nr 1. The value is 0 but the valid values are '!0.0:'. [invalidFunctionArg] BitSeq/src/VariationalBayes.cpp:67:18: note: Assignment 'alphaS=0', assigned value is 0 BitSeq/src/VariationalBayes.cpp:68:13: note: Assuming condition is false BitSeq/src/VariationalBayes.cpp:72:27: note: Invalid argument BitSeq/src/VariationalBayes.cpp:32:4: performance: Variable 'logFileName' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] BitSeq/src/VariationalBayes.cpp:49:7: warning: Class 'VariationalBayes' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] BitSeq/src/VariationalBayes.cpp:49:7: warning: Class 'VariationalBayes' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] BitSeq/src/VariationalBayes.h:31:7: style: Class 'VariationalBayes' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] BitSeq/src/asa103/asa103.hpp:47:10: style: The scope of the variable 'd1' can be reduced. [variableScope] BitSeq/src/VariationalBayes.cpp:129:63: style: The scope of the variable 'valBetaDiv' can be reduced. [variableScope] BitSeq/src/VariationalBayes.cpp:348:11: style: The scope of the variable 'gammaSum' can be reduced. [variableScope] BitSeq/src/VariationalBayes.cpp:348:21: style: The scope of the variable 'norm' can be reduced. [variableScope] BitSeq/src/VariationalBayes.cpp:21:38: performance: Function parameter 'logFileName' should be passed by const reference. [passedByValue] BitSeq/src/VariationalBayes.cpp:81:38: style: Parameter 'vals' can be declared as const array [constParameter] BitSeq/src/VariationalBayes.cpp:81:52: style: Parameter 'adds' can be declared as const array [constParameter] BitSeq/src/common.cpp:8:36: performance: Function parameter 'compileDate' should be passed by const reference. [passedByValue] BitSeq/src/common.cpp:8:56: performance: Function parameter 'compileTime' should be passed by const reference. [passedByValue] BitSeq/src/common.cpp:8:22: style: Parameter 'argv0' can be declared as pointer to const [constParameterPointer] BitSeq/src/estimateDE.cpp:173:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] BitSeq/src/estimateDE.cpp:217:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/estimateDE.cpp:312:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/estimateDE.cpp:209:14: style: The scope of the variable 'fileName' can be reduced. [variableScope] BitSeq/src/estimateDE.cpp:293:21: style: The scope of the variable 'divC' can be reduced. [variableScope] BitSeq/src/estimateDE.cpp:293:27: style: The scope of the variable 'mu_0' can be reduced. [variableScope] BitSeq/src/estimateDE.cpp:294:15: style: The scope of the variable 'RC' can be reduced. [variableScope] BitSeq/src/estimateDE.cpp:41:32: style: Parameter 'argc' can be declared as pointer to const [constParameterPointer] BitSeq/src/estimateExpression.cpp:55:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/estimateExpression.cpp:282:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] BitSeq/src/estimateExpression.cpp:557:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/estimateExpression.cpp:575:11: style: The if condition is the same as the previous if condition [duplicateCondition] BitSeq/src/estimateExpression.cpp:574:11: note: First condition BitSeq/src/estimateExpression.cpp:575:11: note: Second condition BitSeq/src/estimateExpression.cpp:438:18: style: Variable 'samplesHave' is reassigned a value before the old one has been used. [redundantAssignment] BitSeq/src/estimateExpression.cpp:277:19: note: samplesHave is assigned BitSeq/src/estimateExpression.cpp:438:18: note: samplesHave is overwritten BitSeq/src/estimateExpression.cpp:453:14: style: The scope of the variable 'sumSaved' can be reduced. [variableScope] BitSeq/src/estimateExpression.cpp:453:24: style: The scope of the variable 'thetaSqSum' can be reduced. [variableScope] BitSeq/src/estimateExpression.cpp:453:36: style: The scope of the variable 'thetaSum' can be reduced. [variableScope] BitSeq/src/estimateExpression.cpp:453:46: style: The scope of the variable 'sumNorm' can be reduced. [variableScope] BitSeq/src/estimateExpression.cpp:453:68: style: The scope of the variable 'thetaVar' can be reduced. [variableScope] BitSeq/src/estimateExpression.cpp:146:75: style: Parameter 'args' can be declared as reference to const [constParameterReference] BitSeq/src/estimateExpression.cpp:146:26: style: Parameter 'alignments' can be declared as pointer to const [constParameterPointer] BitSeq/src/estimateExpression.cpp:506:40: style: Parameter 'argc' can be declared as pointer to const [constParameterPointer] BitSeq/src/estimateExpression.cpp:149:24: style: Variable 'samplesHave' is assigned a value that is never used. [unreadVariable] BitSeq/src/estimateExpression.cpp:156:43: style: Variable 's2j' is assigned a value that is never used. [unreadVariable] BitSeq/src/estimateExpression.cpp:438:18: style: Variable 'samplesHave' is assigned a value that is never used. [unreadVariable] BitSeq/src/estimateExpression.cpp:156:61: style: Unused variable: av [unusedVariable] BitSeq/src/estimateExpression.cpp:156:64: style: Unused variable: var [unusedVariable] BitSeq/src/estimateHyperPar.cpp:76:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/estimateHyperPar.cpp:67:17: style: The scope of the variable 'RTN' can be reduced. [variableScope] BitSeq/src/estimateHyperPar.cpp:68:9: style: The scope of the variable 'storeAll' can be reduced. [variableScope] BitSeq/src/estimateHyperPar.cpp:120:62: style: The scope of the variable 'mean' can be reduced. [variableScope] BitSeq/src/estimateHyperPar.cpp:121:26: style: The scope of the variable 'samplesREDO' can be reduced. [variableScope] BitSeq/src/estimateHyperPar.cpp:121:50: style: The scope of the variable 'm' can be reduced. [variableScope] BitSeq/src/estimateHyperPar.cpp:121:60: style: The scope of the variable 'subM' can be reduced. [variableScope] BitSeq/src/estimateHyperPar.cpp:38:38: style: Parameter 'argc' can be declared as pointer to const [constParameterPointer] BitSeq/src/estimateHyperPar.cpp:122:19: style: Variable 'breaked' is assigned a value that is never used. [unreadVariable] BitSeq/src/estimateHyperPar.cpp:127:15: style: Variable 'old_mult' is assigned a value that is never used. [unreadVariable] BitSeq/src/estimateHyperPar.cpp:129:12: style: Variable 'prob' is assigned a value that is never used. [unreadVariable] BitSeq/src/estimateHyperPar.cpp:235:26: style: Variable 'prob' is assigned a value that is never used. [unreadVariable] BitSeq/src/estimateVBExpression.cpp:32:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/estimateVBExpression.cpp:138:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/estimateVBExpression.cpp:171:11: style: The if condition is the same as the previous if condition [duplicateCondition] BitSeq/src/estimateVBExpression.cpp:169:11: note: First condition BitSeq/src/estimateVBExpression.cpp:171:11: note: Second condition BitSeq/src/estimateVBExpression.cpp:176:11: style: The if condition is the same as the previous if condition [duplicateCondition] BitSeq/src/estimateVBExpression.cpp:175:11: note: First condition BitSeq/src/estimateVBExpression.cpp:176:11: note: Second condition BitSeq/src/estimateVBExpression.cpp:108:42: style: Parameter 'argc' can be declared as pointer to const [constParameterPointer] BitSeq/src/estimateVBExpression.cpp:22:18: style: Unused variable: strand [unusedVariable] BitSeq/src/estimateVBExpression.cpp:22:25: style: Unused variable: blank [unusedVariable] BitSeq/src/getGeneExpression.cpp:43:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] BitSeq/src/getGeneExpression.cpp:75:15: style: The scope of the variable 'gM' can be reduced. [variableScope] BitSeq/src/getGeneExpression.cpp:17:39: style: Parameter 'argc' can be declared as pointer to const [constParameterPointer] BitSeq/src/getVariance.cpp:36:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/getVariance.cpp:75:13: style: The scope of the variable 'mSq' can be reduced. [variableScope] BitSeq/src/getVariance.cpp:75:17: style: The scope of the variable 'count' can be reduced. [variableScope] BitSeq/src/getVariance.cpp:75:23: style: The scope of the variable 'sqDif' can be reduced. [variableScope] BitSeq/src/getVariance.cpp:76:9: style: The scope of the variable 'good' can be reduced. [variableScope] BitSeq/src/getVariance.cpp:17:33: style: Parameter 'argc' can be declared as pointer to const [constParameterPointer] BitSeq/src/getWithinGeneExpression.cpp:58:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/getWithinGeneExpression.cpp:244:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] BitSeq/src/getWithinGeneExpression.cpp:183:19: style: The scope of the variable 'var' can be reduced. [variableScope] BitSeq/src/getWithinGeneExpression.cpp:183:23: style: The scope of the variable 'var2' can be reduced. [variableScope] BitSeq/src/getWithinGeneExpression.cpp:216:9: style: The scope of the variable 'N' can be reduced. [variableScope] BitSeq/src/getWithinGeneExpression.cpp:217:11: style: The scope of the variable 'l' can be reduced. [variableScope] BitSeq/src/getWithinGeneExpression.cpp:36:45: style: Parameter 'argc' can be declared as pointer to const [constParameterPointer] BitSeq/src/lowess.cpp:68:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/lowess.cpp:33:9: style: The scope of the variable 'nleft' can be reduced. [variableScope] BitSeq/src/lowess.cpp:33:15: style: The scope of the variable 'nright' can be reduced. [variableScope] BitSeq/src/lowess.cpp:33:23: style: The scope of the variable 'i' can be reduced. [variableScope] BitSeq/src/lowess.cpp:33:35: style: The scope of the variable 'last' can be reduced. [variableScope] BitSeq/src/lowess.cpp:33:41: style: The scope of the variable 'm1' can be reduced. [variableScope] BitSeq/src/lowess.cpp:33:45: style: The scope of the variable 'm2' can be reduced. [variableScope] BitSeq/src/lowess.cpp:34:16: style: The scope of the variable 'cmad' can be reduced. [variableScope] BitSeq/src/lowess.cpp:34:33: style: The scope of the variable 'c1' can be reduced. [variableScope] BitSeq/src/lowess.cpp:34:37: style: The scope of the variable 'c9' can be reduced. [variableScope] BitSeq/src/lowess.cpp:111:14: style: The scope of the variable 'b' can be reduced. [variableScope] BitSeq/src/lowess.cpp:111:17: style: The scope of the variable 'c' can be reduced. [variableScope] BitSeq/src/lowess.cpp:111:23: style: The scope of the variable 'r' can be reduced. [variableScope] BitSeq/src/lowess.cpp:108:159: style: Parameter 'rw' can be declared as reference to const [constParameterReference] BitSeq/src/lowess.cpp:70:28: warning: Either the condition 'last<0' is redundant, otherwise there is negative array index -1. [negativeContainerIndex] BitSeq/src/lowess.cpp:67:20: note: Assuming that condition 'last<0' is not redundant BitSeq/src/lowess.cpp:70:28: note: Negative array index BitSeq/src/lowess.cpp:72:30: warning: Either the condition 'last<0' is redundant, otherwise there is negative array index -1. [negativeContainerIndex] BitSeq/src/lowess.cpp:67:20: note: Assuming that condition 'last<0' is not redundant BitSeq/src/lowess.cpp:72:30: note: Negative array index BitSeq/src/lowess.cpp:73:52: warning: Either the condition 'last<0' is redundant, otherwise there is negative array index -1. [negativeContainerIndex] BitSeq/src/lowess.cpp:67:20: note: Assuming that condition 'last<0' is not redundant BitSeq/src/lowess.cpp:73:52: note: Negative array index BitSeq/src/misc.cpp:36:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/misc.cpp:53:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/misc.cpp:61:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/misc.cpp:69:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/misc.cpp:132:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/misc.cpp:146:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/misc.cpp:201:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/misc.cpp:218:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/misc.cpp:26:20: warning: Invalid std::log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg] BitSeq/src/misc.cpp:23:18: note: Assignment 'sumE=0', assigned value is 0 BitSeq/src/misc.cpp:24:23: note: Assuming condition is false BitSeq/src/misc.cpp:26:20: note: Invalid argument BitSeq/src/parseAlignment.cpp:120:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/parseAlignment.cpp:531:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FPROPER_PAIR [valueFlowBailoutIncompleteVar] BitSeq/src/parseAlignment.cpp:553:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/parseAlignment.cpp:572:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/parseAlignment.cpp:581:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/parseAlignment.cpp:28:7: style: Class 'TagAlignment' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] BitSeq/src/parseAlignment.cpp:282:16: style: The if condition is the same as the previous if condition [duplicateCondition] BitSeq/src/parseAlignment.cpp:280:16: note: First condition BitSeq/src/parseAlignment.cpp:282:16: note: Second condition BitSeq/src/parseAlignment.cpp:59:36: style: Parameter 'argc' can be declared as pointer to const [constParameterPointer] BitSeq/src/parseAlignment.cpp:445:88: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] BitSeq/src/transposeFiles.cpp:21:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] BitSeq/src/transposeFiles.cpp:113:12: style: The scope of the variable 'done' can be reduced. [variableScope] BitSeq/src/transposeFiles.cpp:13:56: performance: Function parameter 'outFileName' should be passed by const reference. [passedByValue] BitSeq/src/transposeFiles.cpp:13:90: performance: Function parameter 'message' should be passed by const reference. [passedByValue] diff: head BitSeq/src/ArgumentParser.cpp:169:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/ArgumentParser.cpp:188:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/ArgumentParser.cpp:207:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/ArgumentParser.cpp:225:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/ArgumentParser.cpp:284:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable type [valueFlowBailoutIncompleteVar] head BitSeq/src/ArgumentParser.cpp:306:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/ArgumentParser.cpp:43:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head BitSeq/src/ArgumentParser.cpp:49:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head BitSeq/src/ArgumentParser.cpp:55:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head BitSeq/src/ArgumentParser.cpp:64:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head BitSeq/src/ArgumentParser.cpp:69:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/ArgumentParser.cpp:73:44: style: Parameter 'argv' can be declared as const array [constParameter] head BitSeq/src/ArgumentParser.cpp:93:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head BitSeq/src/FileHeader.cpp:87:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LOG_FORMAT [valueFlowBailoutIncompleteVar] head BitSeq/src/PosteriorSamples.cpp:100:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cur [valueFlowBailoutIncompleteVar] head BitSeq/src/PosteriorSamples.cpp:138:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head BitSeq/src/PosteriorSamples.cpp:151:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head BitSeq/src/PosteriorSamples.cpp:228:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/PosteriorSamples.cpp:237:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head BitSeq/src/PosteriorSamples.cpp:247:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/PosteriorSamples.cpp:268:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/PosteriorSamples.cpp:45:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/PosteriorSamples.cpp:60:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/ReadDistribution.cpp:1018:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/ReadDistribution.cpp:113:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/ReadDistribution.cpp:143:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/ReadDistribution.cpp:178:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/ReadDistribution.cpp:206:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.13.0 BitSeq/src/ReadDistribution.cpp:265:35: style:inconclusive: Boolean expression '!frag->second->core.flag' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean] head BitSeq/src/ReadDistribution.cpp:315:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/ReadDistribution.cpp:428:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scientific [valueFlowBailoutIncompleteVar] head BitSeq/src/ReadDistribution.cpp:485:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FREVERSE [valueFlowBailoutIncompleteVar] head BitSeq/src/ReadDistribution.cpp:533:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FREVERSE [valueFlowBailoutIncompleteVar] head BitSeq/src/ReadDistribution.cpp:615:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.13.0 BitSeq/src/ReadDistribution.cpp:687:40: style:inconclusive: Boolean expression '!frag->second->core.flag' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean] head BitSeq/src/ReadDistribution.cpp:715:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable readM_3 [valueFlowBailoutIncompleteVar] head BitSeq/src/ReadDistribution.cpp:735:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable readM_5 [valueFlowBailoutIncompleteVar] head BitSeq/src/ReadDistribution.cpp:759:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable trNumberOfBins [valueFlowBailoutIncompleteVar] head BitSeq/src/ReadDistribution.cpp:772:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FullPair [valueFlowBailoutIncompleteVar] head BitSeq/src/ReadDistribution.cpp:808:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FullPair [valueFlowBailoutIncompleteVar] head BitSeq/src/ReadDistribution.cpp:80:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar] head BitSeq/src/ReadDistribution.cpp:964:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mate_5 [valueFlowBailoutIncompleteVar] head BitSeq/src/Sampler.cpp:105:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/Sampler.cpp:125:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scientific [valueFlowBailoutIncompleteVar] head BitSeq/src/Sampler.cpp:154:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head BitSeq/src/Sampler.cpp:200:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/Sampler.cpp:71:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head BitSeq/src/Sampler.cpp:80:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head BitSeq/src/Sampler.cpp:97:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head BitSeq/src/TranscriptInfo.cpp:126:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/TranscriptInfo.cpp:192:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/TranscriptInfo.cpp:228:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/TranscriptInfo.cpp:241:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/TranscriptInfo.cpp:29:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar] head BitSeq/src/TranscriptSequence.cpp:101:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/VariationalBayes.cpp:253:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] head BitSeq/src/VariationalBayes.cpp:356:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scientific [valueFlowBailoutIncompleteVar] head BitSeq/src/VariationalBayes.cpp:72:27: warning: Invalid std::lgamma() argument nr 1. The value is 0 but the valid values are '!0.0:'. [invalidFunctionArg] BitSeq/src/VariationalBayes.cpp:67:18: note: Assignment 'alphaS=0', assigned value is 0 BitSeq/src/VariationalBayes.cpp:68:13: note: Assuming condition is false BitSeq/src/VariationalBayes.cpp:72:27: note: Invalid argument head BitSeq/src/estimateDE.cpp:217:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/estimateDE.cpp:312:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/estimateExpression.cpp:282:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head BitSeq/src/estimateExpression.cpp:557:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/estimateVBExpression.cpp:138:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/getWithinGeneExpression.cpp:244:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] head BitSeq/src/misc.cpp:132:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/misc.cpp:146:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/misc.cpp:201:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/misc.cpp:218:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/misc.cpp:53:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/misc.cpp:61:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/misc.cpp:69:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/parseAlignment.cpp:531:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FPROPER_PAIR [valueFlowBailoutIncompleteVar] head BitSeq/src/parseAlignment.cpp:553:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/parseAlignment.cpp:572:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head BitSeq/src/parseAlignment.cpp:581:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] DONE