2026-05-03 17:36 ftp://ftp.de.debian.org/debian/pool/main/m/murasaki/murasaki_1.68.6.orig.tar.gz cppcheck-options: --library=posix --library=gnu --library=bsd --library=boost --library=bsd --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j1 platform: Linux-6.8.0-1047-aws-aarch64-with-glibc2.35 python: 3.10.12 client-version: 1.4.0 compiler: g++ (Ubuntu 11.4.0-1ubuntu1~22.04.3) 11.4.0 cppcheck: head 2.20.0 head-info: e5c4a73 (2026-05-01 11:10:43 +0200) count: 873 838 elapsed-time: 14.2 12.5 head-timing-info: old-timing-info: head results: murasaki/src/dinkymath.h:139:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar] murasaki/src/dinkymath.h:161:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] murasaki/src/align-and.cc:55:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/itree.h:790:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __throw_exception_again [valueFlowBailoutIncompleteVar] murasaki/src/itree.h:1104:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/itree.h:64:2: style: Non-boolean value returned from function returning bool [returnNonBoolInBooleanFunction] murasaki/src/alignments.h:93:10: warning: Member variable 'Anchor::backref' is not initialized in the constructor. [uninitMemberVar] murasaki/src/itree.h:44:5: warning:inconclusive: Member variable 'Interval < long >::start' is not initialized in the constructor. [uninitMemberVar] murasaki/src/itree.h:44:5: warning:inconclusive: Member variable 'Interval < long >::stop' is not initialized in the constructor. [uninitMemberVar] murasaki/src/itree.h:407:15: style: The member function 'Itree::itree < long , Anchor * , std :: allocator < itree_node < long , Anchor * > > >::itree_reset_max' can be static. [functionStatic] murasaki/src/itree.h:415:15: style: The member function 'Itree::itree < long , Anchor * , std :: allocator < itree_node < long , Anchor * > > >::itree_reset_max' can be static. [functionStatic] murasaki/src/itree.h:742:3: style: The member function 'Itree::itree < long , Anchor * , std :: allocator < itree_node < long , Anchor * > > >::itree_black_count' can be static. [functionStatic] murasaki/src/itree.h:871:10: style: The member function 'Itree::itree < long , Anchor * , std :: allocator < itree_node < long , Anchor * > > >::_M_key_compare' can be static. [functionStatic] murasaki/src/itree.h:875:10: style: The member function 'Itree::itree < long , Anchor * , std :: allocator < itree_node < long , Anchor * > > >::_M_stop_start_compare' can be static. [functionStatic] murasaki/src/itree.h:879:10: style: The member function 'Itree::itree < long , Anchor * , std :: allocator < itree_node < long , Anchor * > > >::_M_max_compare' can be static. [functionStatic] murasaki/src/itree.h:883:10: style: The member function 'Itree::itree < long , Anchor * , std :: allocator < itree_node < long , Anchor * > > >::_M_edge_max_compare' can be static. [functionStatic] murasaki/src/itree.h:1074:19: style: The member function 'Itree::itree < long , Anchor * , std :: allocator < itree_node < long , Anchor * > > >::drawSubTree' can be static. [functionStatic] murasaki/src/itree.h:1145:5: style: The member function 'Itree::itree < long , Anchor * , std :: allocator < itree_node < long , Anchor * > > >::_itree_black_count' can be static. [functionStatic] murasaki/src/itree.h:407:15: style: The member function 'Itree::itree < long , long , std :: allocator < itree_node < long , long > > >::itree_reset_max' can be static. [functionStatic] murasaki/src/itree.h:415:15: style: The member function 'Itree::itree < long , long , std :: allocator < itree_node < long , long > > >::itree_reset_max' can be static. [functionStatic] murasaki/src/itree.h:742:3: style: The member function 'Itree::itree < long , long , std :: allocator < itree_node < long , long > > >::itree_black_count' can be static. [functionStatic] murasaki/src/itree.h:871:10: style: The member function 'Itree::itree < long , long , std :: allocator < itree_node < long , long > > >::_M_key_compare' can be static. [functionStatic] murasaki/src/itree.h:875:10: style: The member function 'Itree::itree < long , long , std :: allocator < itree_node < long , long > > >::_M_stop_start_compare' can be static. [functionStatic] murasaki/src/itree.h:879:10: style: The member function 'Itree::itree < long , long , std :: allocator < itree_node < long , long > > >::_M_max_compare' can be static. [functionStatic] murasaki/src/itree.h:883:10: style: The member function 'Itree::itree < long , long , std :: allocator < itree_node < long , long > > >::_M_edge_max_compare' can be static. [functionStatic] murasaki/src/itree.h:1074:19: style: The member function 'Itree::itree < long , long , std :: allocator < itree_node < long , long > > >::drawSubTree' can be static. [functionStatic] murasaki/src/itree.h:1145:5: style: The member function 'Itree::itree < long , long , std :: allocator < itree_node < long , long > > >::_itree_black_count' can be static. [functionStatic] murasaki/src/itree.h:57:10: style:inconclusive: Technically the member function 'Itree::Interval < long >::cmp' can be const. [functionConst] murasaki/src/itree.h:66:10: style:inconclusive: Technically the member function 'Itree::Interval < long >::treeOrder' can be const. [functionConst] murasaki/src/timing.h:47:3: style: Class 'Timer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/dinkymath.h:103:3: style: Class 'ProgressTicker' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/dinkymath.h:118:3: style: Class 'EtaBar' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/alignments.h:75:3: style: Class 'RegionSet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/itree.h:223:5: style: Struct 'itree_iterator < long , Anchor * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/itree.h:223:5: style: Struct 'itree_iterator < long , long >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/itree.h:107:5: style: Class 'itree_node < long , Anchor * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/itree.h:107:5: style: Class 'itree_node < long , long >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/align-and.cc:176:29: warning: Possible null pointer dereference: result [nullPointer] murasaki/src/align-and.cc:122:21: note: Assignment 'result=0', assigned value is 0 murasaki/src/align-and.cc:123:17: note: Assuming condition is false murasaki/src/align-and.cc:176:29: note: Null pointer dereference murasaki/src/align-and.cc:177:11: warning: Possible null pointer dereference: result [nullPointer] murasaki/src/align-and.cc:122:21: note: Assignment 'result=0', assigned value is 0 murasaki/src/align-and.cc:123:17: note: Assuming condition is false murasaki/src/align-and.cc:177:11: note: Null pointer dereference murasaki/src/itree.h:572:18: style: The scope of the variable '__leftmost' can be reduced. [variableScope] murasaki/src/itree.h:573:18: style: The scope of the variable '__rightmost' can be reduced. [variableScope] murasaki/src/dinkymath.h:144:38: performance: Function parameter 'd' should be passed by const reference. [passedByValue] murasaki/src/dinkymath.h:157:24: performance: Function parameter 'm' should be passed by const reference. [passedByValue] murasaki/src/dinkymath.h:157:33: performance: Function parameter 'filename' should be passed by const reference. [passedByValue] murasaki/src/dinkymath.h:157:49: performance: Function parameter 'description' should be passed by const reference. [passedByValue] murasaki/src/align-and.cc:64:26: style: Variable 'long_options' can be declared as const array [constVariable] murasaki/src/itree.h:415:57: style: Parameter '__z' can be declared as pointer to const [constParameterPointer] murasaki/src/itree.h:879:56: style: Parameter '__x' can be declared as pointer to const [constParameterPointer] murasaki/src/itree.h:883:61: style: Parameter '__x' can be declared as pointer to const [constParameterPointer] murasaki/src/itree.h:888:26: style: Parameter '__x' can be declared as pointer to const [constParameterPointer] murasaki/src/itree.h:913:18: style: Variable 'prev' can be declared as pointer to const [constVariablePointer] murasaki/src/itree.h:1098:15: style: Variable '__L' can be declared as pointer to const [constVariablePointer] murasaki/src/itree.h:1099:15: style: Variable '__R' can be declared as pointer to const [constVariablePointer] murasaki/src/dinkymath.h:134:8: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] murasaki/src/itree.h:913:22: style: Variable 'prev' is assigned a value that is never used. [unreadVariable] murasaki/src/align-best.cc:56:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/align-best.cc:168:20: style: Local variable 'overlaps' shadows outer variable [shadowVariable] murasaki/src/align-best.cc:155:18: note: Shadowed declaration murasaki/src/align-best.cc:168:20: note: Shadow variable murasaki/src/align-best.cc:67:26: style: Variable 'long_options' can be declared as const array [constVariable] murasaki/src/align-best.cc:155:18: style: Unused variable: overlaps [unusedVariable] murasaki/src/align-compare.cc:79:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/align-compare.cc:175:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/align-compare.cc:61:7: style: The scope of the variable 'optc' can be reduced. [variableScope] murasaki/src/align-compare.cc:173:44: style: Parameter 'results' can be declared as reference to const [constParameterReference] murasaki/src/align-compare.cc:195:36: style: Parameter 'ref' can be declared as reference to const [constParameterReference] murasaki/src/align-compare.cc:65:26: style: Variable 'long_options' can be declared as const array [constVariable] murasaki/src/align-coverage.cc:59:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/align-coverage.cc:197:152: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] murasaki/src/align-coverage.cc:201:112: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] murasaki/src/seqread.h:84:17: style:inconclusive: Technically the member function 'SequenceByteReader::size' can be const. [functionConst] murasaki/src/seqread.h:88:22: style:inconclusive: Technically the member function 'SequenceByteReader::format' can be const. [functionConst] murasaki/src/seqread.h:89:15: style:inconclusive: Technically the member function 'SequenceByteReader::getSubSeqId' can be const. [functionConst] murasaki/src/seqread.h:90:17: style:inconclusive: Technically the member function 'SequenceByteReader::getSubSeqName' can be const. [functionConst] murasaki/src/seqread.h:126:24: style:inconclusive: Technically the member function 'SequenceFileReader::get_filename' can be const. [functionConst] murasaki/src/seqread.h:45:3: style: Class 'SeqReadException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/seqread.h:82:3: style: Class 'SequenceByteReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/seqread.h:119:3: style: Class 'SequenceFileReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/seqread.h:120:3: style: Class 'SequenceFileReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/seqread.h:47:12: performance: Function 'reason()' should return member 'reason_' by const reference. [returnByReference] murasaki/src/seqread.h:90:17: performance: Function 'getSubSeqName()' should return member 'subSeqName' by const reference. [returnByReference] murasaki/src/align-coverage.cc:182:6: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/align-coverage.cc:57:7: style: The scope of the variable 'optc' can be reduced. [variableScope] murasaki/src/align-coverage.cc:60:10: style: The scope of the variable 'outfile' can be reduced. [variableScope] murasaki/src/align-coverage.cc:147:10: style: The scope of the variable 'detLength' can be reduced. [variableScope] murasaki/src/align-coverage.cc:147:22: style: The scope of the variable 'seqLength' can be reduced. [variableScope] murasaki/src/align-coverage.cc:147:34: style: The scope of the variable 'coverLength' can be reduced. [variableScope] murasaki/src/align-coverage.cc:148:10: style: The scope of the variable 'seqStats' can be reduced. [variableScope] murasaki/src/align-coverage.cc:196:38: performance: Function parameter 'filename' should be passed by const reference. [passedByValue] murasaki/src/align-coverage.cc:69:26: style: Variable 'long_options' can be declared as const array [constVariable] murasaki/src/align-coverage.cc:184:15: style: Variable 'seqStats' is assigned a value that is never used. [unreadVariable] murasaki/src/align-or.cc:53:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/align-or.cc:132:29: warning: Possible null pointer dereference: result [nullPointer] murasaki/src/align-or.cc:111:21: note: Assignment 'result=0', assigned value is 0 murasaki/src/align-or.cc:112:17: note: Assuming condition is false murasaki/src/align-or.cc:132:29: note: Null pointer dereference murasaki/src/align-or.cc:133:11: warning: Possible null pointer dereference: result [nullPointer] murasaki/src/align-or.cc:111:21: note: Assignment 'result=0', assigned value is 0 murasaki/src/align-or.cc:112:17: note: Assuming condition is false murasaki/src/align-or.cc:133:11: note: Null pointer dereference murasaki/src/align-or.cc:51:7: style: The scope of the variable 'optc' can be reduced. [variableScope] murasaki/src/align-or.cc:62:26: style: Variable 'long_options' can be declared as const array [constVariable] murasaki/src/alignments.cc:99:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/alignments.cc:127:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/alignments.cc:176:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar] murasaki/src/alignments.cc:352:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable space_p [valueFlowBailoutIncompleteVar] murasaki/src/alignments.cc:387:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar] murasaki/src/alignments.cc:328:19: warning: Member variable 'AnchorFileReader::linenum' is not initialized in the constructor. [uninitMemberVar] murasaki/src/alignments.cc:247:14: style:inconclusive: Technically the member function 'Anchor::operator==' can be const. [functionConst] murasaki/src/alignments.h:97:8: note: Technically the member function 'Anchor::operator==' can be const. murasaki/src/alignments.cc:247:14: note: Technically the member function 'Anchor::operator==' can be const. murasaki/src/alignments.cc:73:50: style:inconclusive: Function 'loadAnchors' argument 2 names different: declaration 'tree' definition 'alignment'. [funcArgNamesDifferent] murasaki/src/alignments.h:274:50: note: Function 'loadAnchors' argument 2 names different: declaration 'tree' definition 'alignment'. murasaki/src/alignments.cc:73:50: note: Function 'loadAnchors' argument 2 names different: declaration 'tree' definition 'alignment'. murasaki/src/alignments.cc:86:28: style:inconclusive: Function 'writeSeqs' argument 1 names different: declaration '' definition 'alignfile'. [funcArgNamesDifferentUnnamed] murasaki/src/alignments.cc:121:28: style:inconclusive: Function 'checkSeqs' argument 1 names different: declaration '' definition 'alignfile'. [funcArgNamesDifferentUnnamed] murasaki/src/alignments.cc:272:40: style:inconclusive: Function 'mergeAdd' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/alignments.cc:303:32: style:inconclusive: Function 'remove' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/alignments.cc:335:49: style:inconclusive: Function 'readline' argument 1 names different: declaration 'out' definition 'parts'. [funcArgNamesDifferent] murasaki/src/alignments.h:266:33: note: Function 'readline' argument 1 names different: declaration 'out' definition 'parts'. murasaki/src/alignments.cc:335:49: note: Function 'readline' argument 1 names different: declaration 'out' definition 'parts'. murasaki/src/alignments.cc:380:63: style:inconclusive: Function 'merge' argument 1 names different: declaration 'r' definition 'in'. [funcArgNamesDifferent] murasaki/src/alignments.h:248:35: note: Function 'merge' argument 1 names different: declaration 'r' definition 'in'. murasaki/src/alignments.cc:380:63: note: Function 'merge' argument 1 names different: declaration 'r' definition 'in'. murasaki/src/alignments.cc:403:36: style:inconclusive: Function 'RegionSet' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/alignments.cc:92:12: style: Local variable 'prefix' shadows outer variable [shadowVariable] murasaki/src/alignments.cc:87:22: note: Shadowed declaration murasaki/src/alignments.cc:92:12: note: Shadow variable murasaki/src/alignments.cc:217:51: performance: Function parameter 'parts' should be passed by const reference. [passedByValue] murasaki/src/alignments.cc:317:14: warning: Either the condition 'si::start' is not initialized in the constructor. [uninitMemberVar] murasaki/src/itree.h:44:5: warning:inconclusive: Member variable 'Interval < int >::stop' is not initialized in the constructor. [uninitMemberVar] murasaki/src/exceptions.h:29:7: style:inconclusive: Either there is a missing 'override', or the member function 'MurasakiAbortException::status' can be const. [functionConst] murasaki/src/binseq.hh:100:17: style:inconclusive: Technically the member function 'SequenceBinary::getBinaryFilename' can be const. [functionConst] murasaki/src/binseq.hh:101:17: style:inconclusive: Technically the member function 'SequenceBinary::getBaseFilename' can be const. [functionConst] murasaki/src/sequence.h:205:17: style:inconclusive: Technically the member function 'BitSequence::readBitCount' can be const. [functionConst] murasaki/src/sequence.h:206:14: style:inconclusive: Technically the member function 'BitSequence::hashLength' can be const. [functionConst] murasaki/src/sequence.h:307:27: style:inconclusive: Technically the member function 'HashMethod::inputlist' can be const. [functionConst] murasaki/src/sequence.h:346:15: style:inconclusive: Technically the member function 'Window::firstWord' can be const. [functionConst] murasaki/src/sequence.h:358:14: style:inconclusive: Technically the member function 'Sequence::getId' can be const. [functionConst] murasaki/src/sequence.h:393:17: style:inconclusive: Technically the member function 'Location::bitSeqPos' can be const. [functionConst] murasaki/src/sequence.h:537:15: style:inconclusive: Technically the member function 'RepeatMap::size' can be const. [functionConst] murasaki/src/arrayhash.cc:70:17: style: The member function 'ArrayHash::pickup' can be static. [functionStatic] murasaki/src/arrayhash.h:62:8: note: The member function 'ArrayHash::pickup' can be static. murasaki/src/arrayhash.cc:70:17: note: The member function 'ArrayHash::pickup' can be static. murasaki/src/shmvector.hh:60:8: style:inconclusive: Technically the member function 'ShmVector < pair < int , int > >::hasShm' can be const. [functionConst] murasaki/src/shmvector.hh:271:10: style:inconclusive: Technically the member function 'ShmVector < pair < int , int > >::capacity' can be const. [functionConst] murasaki/src/shmvector.hh:302:10: style:inconclusive: Technically the member function 'ShmVector < pair < int , int > >::size' can be const. [functionConst] murasaki/src/shmvector.hh:305:8: style:inconclusive: Technically the member function 'ShmVector < pair < int , int > >::empty' can be const. [functionConst] murasaki/src/shmvector.hh:123:10: style:inconclusive: Technically the member function 'ShmVector < pair < int , int > >::ShmVectorIterator::operator<' can be const. [functionConst] murasaki/src/shmvector.hh:126:21: style:inconclusive: Technically the member function 'ShmVector < pair < int , int > >::ShmVectorIterator::operator-' can be const. [functionConst] murasaki/src/itree.h:407:15: style: The member function 'Itree::itree < int , AnchorSet * , std :: allocator < itree_node < int , AnchorSet * > > >::itree_reset_max' can be static. [functionStatic] murasaki/src/itree.h:415:15: style: The member function 'Itree::itree < int , AnchorSet * , std :: allocator < itree_node < int , AnchorSet * > > >::itree_reset_max' can be static. [functionStatic] murasaki/src/itree.h:742:3: style: The member function 'Itree::itree < int , AnchorSet * , std :: allocator < itree_node < int , AnchorSet * > > >::itree_black_count' can be static. [functionStatic] murasaki/src/itree.h:871:10: style: The member function 'Itree::itree < int , AnchorSet * , std :: allocator < itree_node < int , AnchorSet * > > >::_M_key_compare' can be static. [functionStatic] murasaki/src/itree.h:875:10: style: The member function 'Itree::itree < int , AnchorSet * , std :: allocator < itree_node < int , AnchorSet * > > >::_M_stop_start_compare' can be static. [functionStatic] murasaki/src/itree.h:879:10: style: The member function 'Itree::itree < int , AnchorSet * , std :: allocator < itree_node < int , AnchorSet * > > >::_M_max_compare' can be static. [functionStatic] murasaki/src/itree.h:883:10: style: The member function 'Itree::itree < int , AnchorSet * , std :: allocator < itree_node < int , AnchorSet * > > >::_M_edge_max_compare' can be static. [functionStatic] murasaki/src/itree.h:1074:19: style: The member function 'Itree::itree < int , AnchorSet * , std :: allocator < itree_node < int , AnchorSet * > > >::drawSubTree' can be static. [functionStatic] murasaki/src/itree.h:1145:5: style: The member function 'Itree::itree < int , AnchorSet * , std :: allocator < itree_node < int , AnchorSet * > > >::_itree_black_count' can be static. [functionStatic] murasaki/src/itree.h:57:10: style:inconclusive: Technically the member function 'Itree::Interval < int >::cmp' can be const. [functionConst] murasaki/src/itree.h:66:10: style:inconclusive: Technically the member function 'Itree::Interval < int >::treeOrder' can be const. [functionConst] murasaki/src/cmultiset.h:58:7: style:inconclusive: Technically the member function 'cmultiset < Location >::size' can be const. [functionConst] murasaki/src/cmultiset.h:59:8: style:inconclusive: Technically the member function 'cmultiset < Location >::empty' can be const. [functionConst] murasaki/src/cmultiset.h:80:7: style:inconclusive: Technically the member function 'cmultiset < Location >::cap' can be const. [functionConst] murasaki/src/cmultiset.h:81:8: style:inconclusive: Technically the member function 'cmultiset < Location >::order' can be const. [functionConst] murasaki/src/cmultiset.h:446:41: style:inconclusive: Technically the member function 'cmultiset < Location >::sanityCheck' can be const. [functionConst] murasaki/src/cmultiset.h:84:7: note: Technically the member function 'cmultiset < Location >::sanityCheck' can be const. murasaki/src/cmultiset.h:446:41: note: Technically the member function 'cmultiset < Location >::sanityCheck' can be const. murasaki/src/cmultiset.h:279:41: style:inconclusive: Technically the member function 'cmultiset < Location >::nextMatch' can be const. [functionConst] murasaki/src/cmultiset.h:104:7: note: Technically the member function 'cmultiset < Location >::nextMatch' can be const. murasaki/src/cmultiset.h:279:41: note: Technically the member function 'cmultiset < Location >::nextMatch' can be const. murasaki/src/cmultiset.h:295:41: style:inconclusive: Technically the member function 'cmultiset < Location >::prevMatch' can be const. [functionConst] murasaki/src/cmultiset.h:105:7: note: Technically the member function 'cmultiset < Location >::prevMatch' can be const. murasaki/src/cmultiset.h:295:41: note: Technically the member function 'cmultiset < Location >::prevMatch' can be const. murasaki/src/arrayhash.cc:56:3: warning: Class 'ArrayHash' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] murasaki/src/arrayhash.cc:56:3: warning: Class 'ArrayHash' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] murasaki/src/cmultiset.h:136:8: warning: Class 'cmultiset < Location >' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] murasaki/src/cmultiset.h:136:8: warning: Class 'cmultiset < Location >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] murasaki/src/arrayhash.h:51:21: warning: The class 'ArrayHash' defines member function with name 'linear_cost' also defined in its parent class 'Hash'. [duplInheritedMember] murasaki/src/sequence.h:421:21: note: Parent function 'Hash::linear_cost' murasaki/src/arrayhash.h:51:21: note: Derived function 'ArrayHash::linear_cost' murasaki/src/arrayhash.h:54:21: warning: The class 'ArrayHash' defines member function with name 'bucket_prep_cost' also defined in its parent class 'Hash'. [duplInheritedMember] murasaki/src/sequence.h:422:21: note: Parent function 'Hash::bucket_prep_cost' murasaki/src/arrayhash.h:54:21: note: Derived function 'ArrayHash::bucket_prep_cost' murasaki/src/exceptions.h:8:2: style: Class 'MurasakiException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/exceptions.h:20:2: style: Class 'MurasakiDebugException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/binseq.hh:62:3: style: Class 'SeqBinException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/binseq.hh:113:3: style: Class 'SequenceBinary' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/binseq.hh:114:3: style: Class 'SequenceBinary' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/binseq.hh:123:3: style: Class 'DeSerial' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/sequence.h:227:3: style: Class 'BitSequence' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/sequence.h:228:3: style: Class 'BitSequence' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/sequence.h:293:3: style: Class 'HashMethod' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/sequence.h:352:3: style: Class 'Sequence' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/sequence.h:453:3: style: Class 'IntervalSet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/sequence.h:539:3: style: Class 'RepeatMap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/arrayhash.h:46:3: style: Class 'ArrayHash' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/shmvector.hh:251:3: style: Class 'ShmVector < pair < int , int > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/itree.h:223:5: style: Struct 'itree_iterator < int , AnchorSet * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/itree.h:107:5: style: Class 'itree_node < int , AnchorSet * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/arrayhash.h:38:8: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:409:16: note: Virtual function in base class murasaki/src/arrayhash.h:38:8: note: Function in derived class murasaki/src/arrayhash.h:39:8: style: The function 'add' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:410:16: note: Virtual function in base class murasaki/src/arrayhash.h:39:8: note: Function in derived class murasaki/src/arrayhash.h:40:8: style: The function 'getMatchingSets' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:412:16: note: Virtual function in base class murasaki/src/arrayhash.h:40:8: note: Function in derived class murasaki/src/arrayhash.h:41:8: style: The function 'lookup' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:411:16: note: Virtual function in base class murasaki/src/arrayhash.h:41:8: note: Function in derived class murasaki/src/arrayhash.h:42:8: style: The function 'emptyAt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:413:16: note: Virtual function in base class murasaki/src/arrayhash.h:42:8: note: Function in derived class murasaki/src/arrayhash.h:43:8: style: The function 'sizeAt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:414:16: note: Virtual function in base class murasaki/src/arrayhash.h:43:8: note: Function in derived class murasaki/src/arrayhash.h:44:8: style: The function 'sizeAt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:415:16: note: Virtual function in base class murasaki/src/arrayhash.h:44:8: note: Function in derived class murasaki/src/arrayhash.h:48:8: style: The function 'dump' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:425:16: note: Virtual function in base class murasaki/src/arrayhash.h:48:8: note: Function in derived class murasaki/src/arrayhash.h:49:8: style: The function 'load' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:426:16: note: Virtual function in base class murasaki/src/arrayhash.h:49:8: note: Function in derived class murasaki/src/binseq.hh:64:10: performance: Function 'reason()' should return member 'reason_' by const reference. [returnByReference] murasaki/src/binseq.hh:100:17: performance: Function 'getBinaryFilename()' should return member 'binaryFilename' by const reference. [returnByReference] murasaki/src/binseq.hh:101:17: performance: Function 'getBaseFilename()' should return member 'baseFilename' by const reference. [returnByReference] murasaki/src/shmvector.hh:268:5: error: Unhandled exception thrown in function declared not to throw exceptions. [throwInNoexceptFunction] murasaki/src/shmvector.hh:225:20: warning: Either the condition 'old_data' is redundant or there is possible null pointer dereference: old_data. [nullPointerRedundantCheck] murasaki/src/shmvector.hh:228:10: note: Assuming that condition 'old_data' is not redundant murasaki/src/shmvector.hh:225:20: note: Null pointer dereference murasaki/src/binseq.hh:127:13: style: C-style pointer casting [cstyleCast] murasaki/src/binseq.hh:136:12: style: C-style pointer casting [cstyleCast] murasaki/src/arrayhash.cc:130:9: style: C-style pointer casting [cstyleCast] murasaki/src/arrayhash.cc:143:13: style: C-style pointer casting [cstyleCast] murasaki/src/cmultiset.h:128:11: style: C-style pointer casting [cstyleCast] murasaki/src/cmultiset.h:193:22: style: C-style pointer casting [cstyleCast] murasaki/src/cmultiset.h:193:42: style: C-style pointer casting [cstyleCast] murasaki/src/cmultiset.h:195:22: style: C-style pointer casting [cstyleCast] murasaki/src/cmultiset.h:195:44: style: C-style pointer casting [cstyleCast] murasaki/src/cmultiset.h:197:23: style: C-style pointer casting [cstyleCast] murasaki/src/cmultiset.h:197:45: style: C-style pointer casting [cstyleCast] murasaki/src/cmultiset.h:197:85: style: C-style pointer casting [cstyleCast] murasaki/src/cmultiset.h:197:105: style: C-style pointer casting [cstyleCast] murasaki/src/cmultiset.h:210:13: style: C-style pointer casting [cstyleCast] murasaki/src/cmultiset.h:242:11: style: C-style pointer casting [cstyleCast] murasaki/src/cmultiset.h:259:11: style: C-style pointer casting [cstyleCast] murasaki/src/cmultiset.h:112:18: style: C-style pointer casting [cstyleCast] murasaki/src/cmultiset.h:113:18: style: C-style pointer casting [cstyleCast] murasaki/src/binseq.hh:127:9: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/binseq.hh:136:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/arrayhash.cc:109:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/arrayhash.cc:110:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/arrayhash.cc:114:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/arrayhash.cc:119:13: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/arrayhash.cc:120:13: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/arrayhash.cc:133:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/arrayhash.cc:134:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/arrayhash.cc:145:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/cmultiset.h:320:10: style: The scope of the variable 'r' can be reduced. [variableScope] murasaki/src/cmultiset.h:350:7: style: The scope of the variable 'c' can be reduced. [variableScope] murasaki/src/cmultiset.h:350:10: style: The scope of the variable 'r' can be reduced. [variableScope] murasaki/src/shmvector.hh:90:14: style: Redundant pointer operation on '_p' - it's already a pointer. [redundantPointerOp] murasaki/src/arrayhash.cc:48:55: style:inconclusive: Function 'add' argument 2 names different: declaration 'val' definition 'a'. [funcArgNamesDifferent] murasaki/src/arrayhash.h:39:45: note: Function 'add' argument 2 names different: declaration 'val' definition 'a'. murasaki/src/arrayhash.cc:48:55: note: Function 'add' argument 2 names different: declaration 'val' definition 'a'. murasaki/src/arrayhash.cc:70:64: style:inconclusive: Function 'pickup' argument 2 names different: declaration '' definition 'range'. [funcArgNamesDifferentUnnamed] murasaki/src/shmvector.hh:80:7: warning:inconclusive: Found suspicious operator '*', result is not used. [constStatement] murasaki/src/shmvector.hh:156:34: style: Parameter 'parent' can be declared as pointer to const [constParameterPointer] murasaki/src/arrayhash.cc:71:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/arrayhash.cc:156:66: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/arrayhash.cc:174:64: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/binseq.cc:47:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar] murasaki/src/binseq.cc:107:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar] murasaki/src/binseq.cc:187:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/binseq.cc:313:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/binseq.cc:348:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] murasaki/src/binseq.cc:179:17: warning: Member variable 'SequenceBinary::fdmem_len' is not initialized in the constructor. [uninitMemberVar] murasaki/src/binseq.cc:321:22: style: The member function 'SequenceBinary::bitToBase' can be static. [functionStatic] murasaki/src/binseq.hh:91:8: note: The member function 'SequenceBinary::bitToBase' can be static. murasaki/src/binseq.cc:321:22: note: The member function 'SequenceBinary::bitToBase' can be static. murasaki/src/binseq.cc:80:24: style:inconclusive: Technically the member function 'SequenceBinary::deriveLocalBinaryFilename' can be const. [functionConst] murasaki/src/binseq.hh:107:10: note: Technically the member function 'SequenceBinary::deriveLocalBinaryFilename' can be const. murasaki/src/binseq.cc:80:24: note: Technically the member function 'SequenceBinary::deriveLocalBinaryFilename' can be const. murasaki/src/binseq.cc:117:7: warning: Class 'SequenceBinary' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] murasaki/src/binseq.cc:117:7: warning: Class 'SequenceBinary' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] murasaki/src/binseq.cc:70:4: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/binseq.cc:95:4: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/binseq.cc:52:15: style: C-style pointer casting [cstyleCast] murasaki/src/binseq.cc:53:15: style: C-style pointer casting [cstyleCast] murasaki/src/binseq.cc:54:15: style: C-style pointer casting [cstyleCast] murasaki/src/binseq.cc:120:14: style: C-style pointer casting [cstyleCast] murasaki/src/binseq.cc:55:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/binseq.cc:56:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/binseq.cc:57:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/binseq.cc:59:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/binseq.cc:61:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/binseq.cc:66:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/binseq.cc:194:23: style: The scope of the variable 'unmasked' can be reduced. [variableScope] murasaki/src/binseq.cc:345:8: style: The scope of the variable 'wrapCount' can be reduced. [variableScope] murasaki/src/binseq.cc:100:53: style:inconclusive: Function 'SequenceBinary' argument 2 names different: declaration 'complete' definition 'completeLoad'. [funcArgNamesDifferent] murasaki/src/binseq.hh:113:39: note: Function 'SequenceBinary' argument 2 names different: declaration 'complete' definition 'completeLoad'. murasaki/src/binseq.cc:100:53: note: Function 'SequenceBinary' argument 2 names different: declaration 'complete' definition 'completeLoad'. murasaki/src/binseq.cc:44:34: performance: Function parameter 'filename' should be passed by const reference. [passedByValue] murasaki/src/binseq.cc:91:36: performance: Function parameter 'filename' should be passed by const reference. [passedByValue] murasaki/src/binseq.cc:194:31: style: Variable 'unmasked' is assigned a value that is never used. [unreadVariable] murasaki/src/binseq.cc:345:17: style: Variable 'wrapCount' is assigned a value that is never used. [unreadVariable] murasaki/src/cgr-compare.cc:72:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] murasaki/src/cgr.h:46:3: style: Class 'Cgr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/cgr.h:49:3: style: Class 'Cgr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/cgr.h:96:3: style: Class 'PGMException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/cgr.h:106:3: style: Class 'PGMFileException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/cgr.h:98:12: performance: Function 'reason()' should return member 'reason_' by const reference. [returnByReference] murasaki/src/cgr.h:111:12: performance: Function 'reason()' should return member 'reason_' by const reference. [returnByReference] murasaki/src/cgr-compare.cc:95:7: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/cgr-compare.cc:75:34: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak] murasaki/src/cgr-compare.cc:54:7: style: The scope of the variable 'optc' can be reduced. [variableScope] murasaki/src/cgr-compare.cc:58:26: style: Variable 'long_options' can be declared as const array [constVariable] murasaki/src/cgr-compare.cc:115:59: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/cgr-compare.cc:125:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/cgr-compare.cc:126:24: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/cgr-compare.cc:140:65: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/cgr-compare.cc:144:7: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/cgr-compare.cc:161:16: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/cgr-image.cc:69:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] murasaki/src/cgr-image.cc:125:6: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/cgr-image.cc:163:5: warning: Either the condition 'cgr' is redundant or there is possible null pointer dereference: cgr. [nullPointerRedundantCheck] murasaki/src/cgr-image.cc:165:8: note: Assuming that condition 'cgr' is not redundant murasaki/src/cgr-image.cc:163:5: note: Null pointer dereference murasaki/src/cgr-image.cc:46:7: style: The scope of the variable 'optc' can be reduced. [variableScope] murasaki/src/cgr-image.cc:129:20: style: Checking if unsigned expression 'fwd.length()' is less than zero. [unsignedLessThanZero] murasaki/src/cgr-image.cc:114:20: style: Local variable 'argv' shadows outer argument [shadowArgument] murasaki/src/cgr-image.cc:45:26: note: Shadowed declaration murasaki/src/cgr-image.cc:114:20: note: Shadow variable murasaki/src/cgr-image.cc:50:26: style: Variable 'long_options' can be declared as const array [constVariable] murasaki/src/cgr-random.cc:72:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/cgr-random.cc:148:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/cgr-random.cc:168:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/cgr-random.cc:94:5: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/cgr-random.cc:57:7: style: The scope of the variable 'optc' can be reduced. [variableScope] murasaki/src/cgr-random.cc:124:22: style: Local variable 'argv' shadows outer argument [shadowArgument] murasaki/src/cgr-random.cc:56:26: note: Shadowed declaration murasaki/src/cgr-random.cc:124:22: note: Shadow variable murasaki/src/cgr-random.cc:153:16: style: Local variable 'i' shadows outer variable [shadowVariable] murasaki/src/cgr-random.cc:141:7: note: Shadowed declaration murasaki/src/cgr-random.cc:153:16: note: Shadow variable murasaki/src/cgr-random.cc:61:26: style: Variable 'long_options' can be declared as const array [constVariable] murasaki/src/cgr-random.cc:144:8: style: Variable 'prev' can be declared as pointer to const [constVariablePointer] murasaki/src/cgr-sample.cc:78:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] murasaki/src/cgr-sample.cc:45:8: style:inconclusive: Technically the member function 'lidx::operator()' can be const. [functionConst] murasaki/src/cgr-sample.cc:134:7: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/cgr-sample.cc:147:6: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/cgr-sample.cc:81:34: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak] murasaki/src/cgr-sample.cc:89:34: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak] murasaki/src/cgr-sample.cc:97:34: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak] murasaki/src/cgr-sample.cc:105:34: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak] murasaki/src/cgr-sample.cc:113:34: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak] murasaki/src/cgr-sample.cc:51:7: style: The scope of the variable 'optc' can be reduced. [variableScope] murasaki/src/cgr-sample.cc:54:8: style: The scope of the variable 'repeatmask' can be reduced. [variableScope] murasaki/src/cgr-sample.cc:152:20: style: Checking if unsigned expression 'fwd.length()' is less than zero. [unsignedLessThanZero] murasaki/src/cgr-sample.cc:58:26: style: Variable 'long_options' can be declared as const array [constVariable] murasaki/src/cgr.cc:79:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/cgr.cc:90:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/cgr.cc:101:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/cgr.cc:112:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/cgr.cc:125:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/cgr.cc:142:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/cgr.cc:237:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar] murasaki/src/cgr.cc:275:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar] murasaki/src/cgr.cc:287:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/cgr.cc:297:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/cgr.cc:315:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/cgr.cc:332:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/cgr.cc:347:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/cgr.cc:359:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar] murasaki/src/cgr.cc:378:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/cgr.cc:456:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable int_p [valueFlowBailoutIncompleteVar] murasaki/src/cgr.cc:503:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar] murasaki/src/cgr.cc:571:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/cgr.cc:399:12: warning: Member variable 'PgmBuffer::maxval' is not initialized in the constructor. [uninitMemberVar] murasaki/src/cgr.cc:370:10: style:inconclusive: Technically the member function 'Cgr::get' can be const. [functionConst] murasaki/src/cgr.h:60:7: note: Technically the member function 'Cgr::get' can be const. murasaki/src/cgr.cc:370:10: note: Technically the member function 'Cgr::get' can be const. murasaki/src/cgr.cc:652:17: style:inconclusive: Technically the member function 'PgmBuffer::allSameRez' can be const. [functionConst] murasaki/src/cgr.h:86:8: note: Technically the member function 'PgmBuffer::allSameRez' can be const. murasaki/src/cgr.cc:652:17: note: Technically the member function 'PgmBuffer::allSameRez' can be const. murasaki/src/cgr.cc:122:50: warning: Class 'Cgr' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] murasaki/src/cgr.cc:339:10: error: Mismatching allocation and deallocation: alt [mismatchAllocDealloc] murasaki/src/cgr.cc:330:12: note: Mismatching allocation and deallocation: alt murasaki/src/cgr.cc:339:10: note: Mismatching allocation and deallocation: alt murasaki/src/cgr.cc:78:10: warning: Either the condition '!data' is redundant or there is possible null pointer dereference: data. [nullPointerRedundantCheck] murasaki/src/cgr.cc:80:6: note: Assuming that condition '!data' is not redundant murasaki/src/cgr.cc:78:10: note: Null pointer dereference murasaki/src/cgr.cc:89:10: warning: Either the condition '!data' is redundant or there is possible null pointer dereference: data. [nullPointerRedundantCheck] murasaki/src/cgr.cc:91:6: note: Assuming that condition '!data' is not redundant murasaki/src/cgr.cc:89:10: note: Null pointer dereference murasaki/src/cgr.cc:261:11: style: C-style pointer casting [cstyleCast] murasaki/src/cgr.cc:595:11: style: C-style pointer casting [cstyleCast] murasaki/src/cgr.cc:253:11: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/cgr.cc:546:18: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/cgr.cc:588:11: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/cgr.cc:141:9: style: Redundant initialization for 'redist'. The initialized value is overwritten before it is read. [redundantInitialization] murasaki/src/cgr.cc:140:13: note: redist is initialized murasaki/src/cgr.cc:141:9: note: redist is overwritten murasaki/src/cgr.cc:292:6: style: Variable 'res' is reassigned a value before the old one has been used. [redundantAssignment] murasaki/src/cgr.cc:289:6: note: res is assigned murasaki/src/cgr.cc:292:6: note: res is overwritten murasaki/src/cgr.cc:435:7: style: The scope of the variable 'wordwidth' can be reduced. [variableScope] murasaki/src/cgr.cc:592:15: style: The scope of the variable 'buf' can be reduced. [variableScope] murasaki/src/cgr.cc:632:10: style: The scope of the variable 'avg' can be reduced. [variableScope] murasaki/src/cgr.cc:634:10: style: The scope of the variable 'variance' can be reduced. [variableScope] murasaki/src/cgr.cc:86:14: style:inconclusive: Function 'Cgr' argument 1 names different: declaration 'res' definition 'iter'. [funcArgNamesDifferent] murasaki/src/cgr.h:46:11: note: Function 'Cgr' argument 1 names different: declaration 'res' definition 'iter'. murasaki/src/cgr.cc:86:14: note: Function 'Cgr' argument 1 names different: declaration 'res' definition 'iter'. murasaki/src/cgr.cc:97:21: style:inconclusive: Function 'Cgr' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/cgr.cc:108:21: style:inconclusive: Function 'Cgr' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/cgr.cc:108:28: style:inconclusive: Function 'Cgr' argument 2 names different: declaration '' definition 'dohalve'. [funcArgNamesDifferentUnnamed] murasaki/src/cgr.cc:121:27: style:inconclusive: Function 'Cgr' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/cgr.cc:139:22: style:inconclusive: Function 'merge' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/cgr.cc:168:28: style:inconclusive: Function 'halve' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/cgr.cc:179:26: style:inconclusive: Function 'operator[]' argument 1 names different: declaration '' definition 'row'. [funcArgNamesDifferentUnnamed] murasaki/src/cgr.cc:225:34: style:inconclusive: Function 'operator[]' argument 1 names different: declaration '' definition 'str'. [funcArgNamesDifferentUnnamed] murasaki/src/cgr.cc:229:36: style:inconclusive: Function 'operator[]' argument 1 names different: declaration '' definition 'str'. [funcArgNamesDifferentUnnamed] murasaki/src/cgr.cc:343:38: style:inconclusive: Function 'sampleHighLow' argument 1 names different: declaration 'low' definition 'lown'. [funcArgNamesDifferent] murasaki/src/cgr.h:54:35: note: Function 'sampleHighLow' argument 1 names different: declaration 'low' definition 'lown'. murasaki/src/cgr.cc:343:38: note: Function 'sampleHighLow' argument 1 names different: declaration 'low' definition 'lown'. murasaki/src/cgr.cc:343:47: style:inconclusive: Function 'sampleHighLow' argument 2 names different: declaration 'high' definition 'highn'. [funcArgNamesDifferent] murasaki/src/cgr.h:54:43: note: Function 'sampleHighLow' argument 2 names different: declaration 'high' definition 'highn'. murasaki/src/cgr.cc:343:47: note: Function 'sampleHighLow' argument 2 names different: declaration 'high' definition 'highn'. murasaki/src/cgr.cc:370:23: style:inconclusive: Function 'get' argument 1 names different: declaration 'i' definition 'idx'. [funcArgNamesDifferent] murasaki/src/cgr.h:60:20: note: Function 'get' argument 1 names different: declaration 'i' definition 'idx'. murasaki/src/cgr.cc:370:23: note: Function 'get' argument 1 names different: declaration 'i' definition 'idx'. murasaki/src/cgr.cc:405:29: style:inconclusive: Function 'loadCgr' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/cgr.cc:494:8: style: Local variable 'maxval' shadows outer variable [shadowVariable] murasaki/src/cgr.h:91:8: note: Shadowed declaration murasaki/src/cgr.cc:494:8: note: Shadow variable murasaki/src/cgr.cc:624:10: style: Local variable 'sum' shadows outer function [shadowFunction] murasaki/src/dinkymath.h:131:3: note: Shadowed declaration murasaki/src/cgr.cc:624:10: note: Shadow variable murasaki/src/cgr.cc:633:10: style: Local variable 'sum' shadows outer function [shadowFunction] murasaki/src/dinkymath.h:131:3: note: Shadowed declaration murasaki/src/cgr.cc:633:10: note: Shadow variable murasaki/src/cgr.cc:282:26: performance: Function parameter 'file' should be passed by const reference. [passedByValue] murasaki/src/cgr.cc:424:31: performance: Function parameter 'file' should be passed by const reference. [passedByValue] murasaki/src/cgr.cc:491:37: performance: Function parameter 'file' should be passed by const reference. [passedByValue] murasaki/src/cgr.cc:631:49: performance: Function parameter 'others' should be passed by const reference. [passedByValue] murasaki/src/cgr.cc:652:47: performance: Function parameter 'others' should be passed by const reference. [passedByValue] murasaki/src/cgr.cc:405:29: style: Parameter 'a' can be declared as reference to const [constParameterReference] murasaki/src/cgr.cc:149:14: style: Variable 'rowend' can be declared as pointer to const [constVariablePointer] murasaki/src/cgr.cc:157:14: style: Variable 'rowend' can be declared as pointer to const [constVariablePointer] murasaki/src/cgr.cc:250:12: style: Variable 'end' can be declared as pointer to const [constVariablePointer] murasaki/src/cgr.cc:251:16: style: Variable 'i' can be declared as pointer to const [constVariablePointer] murasaki/src/cgr.cc:258:12: style: Variable 'end' can be declared as pointer to const [constVariablePointer] murasaki/src/cgr.cc:259:16: style: Variable 'i' can be declared as pointer to const [constVariablePointer] murasaki/src/cgr.cc:275:14: style: Variable 'i' can be declared as pointer to const [constVariablePointer] murasaki/src/cgr.cc:418:12: style: Variable 'i' can be declared as pointer to const [constVariablePointer] murasaki/src/cgr.cc:626:8: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] murasaki/src/cgr.cc:641:10: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] murasaki/src/cgr.cc:646:15: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] murasaki/src/cgr.cc:654:0: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm] murasaki/src/cgr.cc:141:9: style: Variable 'redist' is assigned a value that is never used. [unreadVariable] murasaki/src/cgr.cc:292:6: style: Variable 'res' is assigned a value that is never used. [unreadVariable] murasaki/src/cgr.cc:632:13: style: Variable 'avg' is assigned a value that is never used. [unreadVariable] murasaki/src/cgr.cc:634:18: style: Variable 'variance' is assigned a value that is never used. [unreadVariable] murasaki/src/cgr.cc:564:59: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/cgr.cc:587:63: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/cgr.cc:593:63: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/cgr.cc:625:59: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/cgr.cc:640:75: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/cgr.cc:645:75: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/cgr.cc:653:69: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/cmultiset.h:128:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar] murasaki/src/cmultiset.h:210:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar] murasaki/src/cmultiset.h:242:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar] murasaki/src/cmultiset.h:250:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar] murasaki/src/cmultiset.h:259:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar] murasaki/src/dinkymath.cc:73:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] murasaki/src/dinkymath.cc:197:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/dinkymath.cc:222:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/dinkymath.cc:234:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/dinkymath.cc:279:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar] murasaki/src/dinkymath.cc:323:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/dinkymath.cc:274:21: style:inconclusive: Technically the member function 'RandomTraverse::remaining' can be const. [functionConst] murasaki/src/dinkymath.h:94:7: note: Technically the member function 'RandomTraverse::remaining' can be const. murasaki/src/dinkymath.cc:274:21: note: Technically the member function 'RandomTraverse::remaining' can be const. murasaki/src/dinkymath.cc:221:22: style: The member function 'ProgressTicker::done' can be static. [functionStatic] murasaki/src/dinkymath.h:107:8: note: The member function 'ProgressTicker::done' can be static. murasaki/src/dinkymath.cc:221:22: note: The member function 'ProgressTicker::done' can be static. murasaki/src/cmultiset.h:58:7: style:inconclusive: Technically the member function 'cmultiset::size' can be const. [functionConst] murasaki/src/cmultiset.h:59:8: style:inconclusive: Technically the member function 'cmultiset::empty' can be const. [functionConst] murasaki/src/cmultiset.h:80:7: style:inconclusive: Technically the member function 'cmultiset::cap' can be const. [functionConst] murasaki/src/cmultiset.h:81:8: style:inconclusive: Technically the member function 'cmultiset::order' can be const. [functionConst] murasaki/src/cmultiset.h:446:41: style:inconclusive: Technically the member function 'cmultiset::sanityCheck' can be const. [functionConst] murasaki/src/cmultiset.h:84:7: note: Technically the member function 'cmultiset::sanityCheck' can be const. murasaki/src/cmultiset.h:446:41: note: Technically the member function 'cmultiset::sanityCheck' can be const. murasaki/src/cmultiset.h:279:41: style:inconclusive: Technically the member function 'cmultiset::nextMatch' can be const. [functionConst] murasaki/src/cmultiset.h:104:7: note: Technically the member function 'cmultiset::nextMatch' can be const. murasaki/src/cmultiset.h:279:41: note: Technically the member function 'cmultiset::nextMatch' can be const. murasaki/src/cmultiset.h:295:41: style:inconclusive: Technically the member function 'cmultiset::prevMatch' can be const. [functionConst] murasaki/src/cmultiset.h:105:7: note: Technically the member function 'cmultiset::prevMatch' can be const. murasaki/src/cmultiset.h:295:41: note: Technically the member function 'cmultiset::prevMatch' can be const. murasaki/src/cmultiset.h:136:8: warning: Class 'cmultiset' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] murasaki/src/cmultiset.h:136:8: warning: Class 'cmultiset' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] murasaki/src/dinkymath.cc:40:7: style: The scope of the variable 'last' can be reduced. [variableScope] murasaki/src/dinkymath.cc:53:7: style: The scope of the variable 'last' can be reduced. [variableScope] murasaki/src/dinkymath.cc:226:14: style: The scope of the variable 'lineDelay' can be reduced. [variableScope] murasaki/src/dinkymath.cc:286:12: style: The scope of the variable 't' can be reduced. [variableScope] murasaki/src/dinkymath.cc:68:72: style:inconclusive: Function 'writeOutVector' argument 4 names different: declaration '' definition 'from'. [funcArgNamesDifferentUnnamed] murasaki/src/dinkymath.cc:68:81: style:inconclusive: Function 'writeOutVector' argument 5 names different: declaration '' definition 'to'. [funcArgNamesDifferentUnnamed] murasaki/src/dinkymath.cc:78:20: style:inconclusive: Function 'dstring' argument 1 names different: declaration '' definition 'i'. [funcArgNamesDifferentUnnamed] murasaki/src/dinkymath.cc:84:21: style:inconclusive: Function 'dstring' argument 1 names different: declaration '' definition 'i'. [funcArgNamesDifferentUnnamed] murasaki/src/dinkymath.cc:90:22: style:inconclusive: Function 'fstring' argument 1 names different: declaration '' definition 'f'. [funcArgNamesDifferentUnnamed] murasaki/src/dinkymath.cc:113:34: style:inconclusive: Function 'humanMemory' argument 1 names different: declaration 'bytes' definition 'b'. [funcArgNamesDifferent] murasaki/src/dinkymath.h:81:34: note: Function 'humanMemory' argument 1 names different: declaration 'bytes' definition 'b'. murasaki/src/dinkymath.cc:113:34: note: Function 'humanMemory' argument 1 names different: declaration 'bytes' definition 'b'. murasaki/src/dinkymath.cc:131:27: style:inconclusive: Function 'humanMemory' argument 1 names different: declaration 'bytes' definition 'f'. [funcArgNamesDifferent] murasaki/src/dinkymath.h:84:27: note: Function 'humanMemory' argument 1 names different: declaration 'bytes' definition 'f'. murasaki/src/dinkymath.cc:131:27: note: Function 'humanMemory' argument 1 names different: declaration 'bytes' definition 'f'. murasaki/src/dinkymath.cc:184:36: style:inconclusive: Function 'tick' argument 1 names different: declaration 'i' definition 'ini'. [funcArgNamesDifferent] murasaki/src/dinkymath.h:104:22: note: Function 'tick' argument 1 names different: declaration 'i' definition 'ini'. murasaki/src/dinkymath.cc:184:36: note: Function 'tick' argument 1 names different: declaration 'i' definition 'ini'. murasaki/src/dinkymath.cc:247:36: style:inconclusive: Function 'RandomTraverse' argument 1 names different: declaration 'min' definition '_min'. [funcArgNamesDifferent] murasaki/src/dinkymath.h:95:22: note: Function 'RandomTraverse' argument 1 names different: declaration 'min' definition '_min'. murasaki/src/dinkymath.cc:247:36: note: Function 'RandomTraverse' argument 1 names different: declaration 'min' definition '_min'. murasaki/src/dinkymath.cc:247:45: style:inconclusive: Function 'RandomTraverse' argument 2 names different: declaration 'max' definition '_max'. [funcArgNamesDifferent] murasaki/src/dinkymath.h:95:30: note: Function 'RandomTraverse' argument 2 names different: declaration 'max' definition '_max'. murasaki/src/dinkymath.cc:247:45: note: Function 'RandomTraverse' argument 2 names different: declaration 'max' definition '_max'. murasaki/src/dinkymath.cc:299:23: style:inconclusive: Function 'percent' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/dinkymath.cc:299:32: style:inconclusive: Function 'percent' argument 2 names different: declaration '' definition 'b'. [funcArgNamesDifferentUnnamed] murasaki/src/dinkymath.cc:316:22: style:inconclusive: Function 'tick' argument 1 names different: declaration 'to' definition 'at'. [funcArgNamesDifferent] murasaki/src/dinkymath.h:120:23: note: Function 'tick' argument 1 names different: declaration 'to' definition 'at'. murasaki/src/dinkymath.cc:316:22: note: Function 'tick' argument 1 names different: declaration 'to' definition 'at'. murasaki/src/dinkymath.cc:187:9: style: Local variable 'percent' shadows outer function [shadowFunction] murasaki/src/dinkymath.h:87:8: note: Shadowed declaration murasaki/src/dinkymath.cc:187:9: note: Shadow variable murasaki/src/dinkymath.cc:228:7: style: Local variable 'percent' shadows outer function [shadowFunction] murasaki/src/dinkymath.h:87:8: note: Shadowed declaration murasaki/src/dinkymath.cc:228:7: note: Shadow variable murasaki/src/dinkymath.cc:266:24: style: Local variable 'next' shadows outer function [shadowFunction] murasaki/src/dinkymath.h:93:7: note: Shadowed declaration murasaki/src/dinkymath.cc:266:24: note: Shadow variable murasaki/src/dinkymath.cc:317:7: style: Local variable 'diff' shadows outer function [shadowFunction] murasaki/src/timing.h:64:8: note: Shadowed declaration murasaki/src/dinkymath.cc:317:7: note: Shadow variable murasaki/src/dinkymath.cc:68:27: performance: Function parameter 'filename' should be passed by const reference. [passedByValue] murasaki/src/dinkymath.cc:68:62: performance: Function parameter 'delim' should be passed by const reference. [passedByValue] murasaki/src/dinkymath.cc:278:22: performance: Function parameter 'filename' should be passed by const reference. [passedByValue] murasaki/src/dinkymath.cc:278:38: performance: Function parameter 'content' should be passed by const reference. [passedByValue] murasaki/src/cmultiset.h:108:32: style: Parameter 'i' can be declared as pointer to const [constParameterPointer] murasaki/src/cmultiset.h:205:58: style: Parameter 'tokens' can be declared as pointer to const [constParameterPointer] murasaki/src/dinkymath.cc:40:11: style: Variable 'last' is assigned a value that is never used. [unreadVariable] murasaki/src/dinkymath.cc:44:11: style: Variable 'last' is assigned a value that is never used. [unreadVariable] murasaki/src/dinkymath.cc:53:11: style: Variable 'last' is assigned a value that is never used. [unreadVariable] murasaki/src/dinkymath.cc:57:11: style: Variable 'last' is assigned a value that is never used. [unreadVariable] murasaki/src/dinkymath.cc:187:16: style: Variable 'percent' is assigned a value that is never used. [unreadVariable] murasaki/src/ecolist.h:56:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable minChunks [valueFlowBailoutIncompleteVar] murasaki/src/ecolist.h:75:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable minChunks [valueFlowBailoutIncompleteVar] murasaki/src/bitmap.h:20:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/bitmap.h:29:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/bitmap.h:35:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/bitmap.h:41:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/bitmap.h:46:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/ecolist.h:106:17: style:inconclusive: Technically the member function 'Ecolist::getSize' can be const. [functionConst] murasaki/src/bitmap.h:9:3: warning: Class 'bitmap' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] murasaki/src/bitmap.h:9:3: warning: Class 'bitmap' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] murasaki/src/ecohash.cc:37:3: warning: Class 'EcoHash' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] murasaki/src/ecohash.cc:37:3: warning: Class 'EcoHash' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] murasaki/src/ecohash.h:49:21: warning: The class 'EcoHash' defines member function with name 'linear_cost' also defined in its parent class 'Hash'. [duplInheritedMember] murasaki/src/sequence.h:421:21: note: Parent function 'Hash::linear_cost' murasaki/src/ecohash.h:49:21: note: Derived function 'EcoHash::linear_cost' murasaki/src/ecohash.h:52:21: warning: The class 'EcoHash' defines member function with name 'bucket_prep_cost' also defined in its parent class 'Hash'. [duplInheritedMember] murasaki/src/sequence.h:422:21: note: Parent function 'Hash::bucket_prep_cost' murasaki/src/ecohash.h:52:21: note: Derived function 'EcoHash::bucket_prep_cost' murasaki/src/ecolist.h:66:5: style: Class 'EcolistIterator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/bitmap.h:8:10: style: Class 'bitmap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/ecohash.h:62:3: style: Class 'EcoHash' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/ecohash.h:40:8: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:409:16: note: Virtual function in base class murasaki/src/ecohash.h:40:8: note: Function in derived class murasaki/src/ecohash.h:41:8: style: The function 'add' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:410:16: note: Virtual function in base class murasaki/src/ecohash.h:41:8: note: Function in derived class murasaki/src/ecohash.h:42:8: style: The function 'getMatchingSets' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:412:16: note: Virtual function in base class murasaki/src/ecohash.h:42:8: note: Function in derived class murasaki/src/ecohash.h:43:8: style: The function 'lookup' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:411:16: note: Virtual function in base class murasaki/src/ecohash.h:43:8: note: Function in derived class murasaki/src/ecohash.h:44:8: style: The function 'emptyAt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:413:16: note: Virtual function in base class murasaki/src/ecohash.h:44:8: note: Function in derived class murasaki/src/ecohash.h:45:8: style: The function 'sizeAt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:414:16: note: Virtual function in base class murasaki/src/ecohash.h:45:8: note: Function in derived class murasaki/src/ecohash.h:46:8: style: The function 'sizeAt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:415:16: note: Virtual function in base class murasaki/src/ecohash.h:46:8: note: Function in derived class murasaki/src/ecohash.h:63:4: style: The destructor '~EcoHash' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:437:12: note: Virtual destructor in base class murasaki/src/ecohash.h:63:4: note: Destructor in derived class murasaki/src/ecolist.cc:166:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/ecolist.cc:209:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/ecolist.cc:230:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/ecolist.cc:307:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable initBlocks [valueFlowBailoutIncompleteVar] murasaki/src/ecolist.cc:319:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable initBlocks [valueFlowBailoutIncompleteVar] murasaki/src/ecolist.cc:365:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable initBlocks [valueFlowBailoutIncompleteVar] murasaki/src/ecolist.cc:378:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable initBlocks [valueFlowBailoutIncompleteVar] murasaki/src/ecolist.cc:82:28: style:inconclusive: Technically the member function 'Ecolist::end' can be const. [functionConst] murasaki/src/ecolist.h:102:12: note: Technically the member function 'Ecolist::end' can be const. murasaki/src/ecolist.cc:82:28: note: Technically the member function 'Ecolist::end' can be const. murasaki/src/ecolist.cc:121:31: style:inconclusive: Technically the member function 'Ecolist::bi_end' can be const. [functionConst] murasaki/src/ecolist.h:104:15: note: Technically the member function 'Ecolist::bi_end' can be const. murasaki/src/ecolist.cc:121:31: note: Technically the member function 'Ecolist::bi_end' can be const. murasaki/src/ecolist.cc:70:17: style:inconclusive: Technically the member function 'Ecolist::capacity' can be const. [functionConst] murasaki/src/ecolist.h:105:10: note: Technically the member function 'Ecolist::capacity' can be const. murasaki/src/ecolist.cc:70:17: note: Technically the member function 'Ecolist::capacity' can be const. murasaki/src/ecolist.cc:461:15: style: The member function 'Ecolist::swap' can be static. [functionStatic] murasaki/src/ecolist.h:124:8: note: The member function 'Ecolist::swap' can be static. murasaki/src/ecolist.cc:461:15: note: The member function 'Ecolist::swap' can be static. murasaki/src/ecolist.cc:54:38: style:inconclusive: Function 'push' argument 2 names different: declaration 'pos' definition 'idx'. [funcArgNamesDifferent] murasaki/src/ecolist.h:123:31: note: Function 'push' argument 2 names different: declaration 'pos' definition 'idx'. murasaki/src/ecolist.cc:54:38: note: Function 'push' argument 2 names different: declaration 'pos' definition 'idx'. murasaki/src/ecolist.cc:62:51: style:inconclusive: Function 'getValAt' argument 1 names different: declaration 'idx' definition 'loc'. [funcArgNamesDifferent] murasaki/src/ecolist.h:100:39: note: Function 'getValAt' argument 1 names different: declaration 'idx' definition 'loc'. murasaki/src/ecolist.cc:62:51: note: Function 'getValAt' argument 1 names different: declaration 'idx' definition 'loc'. murasaki/src/ecolist.cc:98:38: style:inconclusive: Function 'at' argument 1 names different: declaration 'pos' definition 'remain'. [funcArgNamesDifferent] murasaki/src/ecolist.h:107:22: note: Function 'at' argument 1 names different: declaration 'pos' definition 'remain'. murasaki/src/ecolist.cc:98:38: note: Function 'at' argument 1 names different: declaration 'pos' definition 'remain'. murasaki/src/ecolist.cc:138:44: style:inconclusive: Function 'bi_at' argument 1 names different: declaration 'pos' definition 'remain'. [funcArgNamesDifferent] murasaki/src/ecolist.h:108:28: note: Function 'bi_at' argument 1 names different: declaration 'pos' definition 'remain'. murasaki/src/ecolist.cc:138:44: note: Function 'bi_at' argument 1 names different: declaration 'pos' definition 'remain'. murasaki/src/ecolist.cc:159:120: style:inconclusive: Function 'init' argument 6 names different: declaration '' definition 'frugal'. [funcArgNamesDifferentUnnamed] murasaki/src/ecolist.cc:285:50: style:inconclusive: Function 'EcolistIterator' argument 1 names different: declaration 'start' definition '_start'. [funcArgNamesDifferent] murasaki/src/ecolist.h:65:28: note: Function 'EcolistIterator' argument 1 names different: declaration 'start' definition '_start'. murasaki/src/ecolist.cc:285:50: note: Function 'EcolistIterator' argument 1 names different: declaration 'start' definition '_start'. murasaki/src/ecolist.cc:285:64: style:inconclusive: Function 'EcolistIterator' argument 2 names different: declaration 'p' definition '_p'. [funcArgNamesDifferent] murasaki/src/ecolist.h:65:41: note: Function 'EcolistIterator' argument 2 names different: declaration 'p' definition '_p'. murasaki/src/ecolist.cc:285:64: note: Function 'EcolistIterator' argument 2 names different: declaration 'p' definition '_p'. murasaki/src/ecolist.cc:285:74: style:inconclusive: Function 'EcolistIterator' argument 3 names different: declaration 'ite' definition '_ite'. [funcArgNamesDifferent] murasaki/src/ecolist.h:65:50: note: Function 'EcolistIterator' argument 3 names different: declaration 'ite' definition '_ite'. murasaki/src/ecolist.cc:285:74: note: Function 'EcolistIterator' argument 3 names different: declaration 'ite' definition '_ite'. murasaki/src/ecolist.cc:289:71: style:inconclusive: Function 'EcolistIterator' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/ecolist.cc:316:74: style:inconclusive: Function 'operator++' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/ecolist.cc:328:56: style:inconclusive: Function 'operator!=' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/ecolist.cc:332:56: style:inconclusive: Function 'operator==' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/ecolist.cc:347:76: style:inconclusive: Function 'BidirectionalEcolistIterator' argument 1 names different: declaration 'start' definition '_start'. [funcArgNamesDifferent] murasaki/src/ecolist.h:45:41: note: Function 'BidirectionalEcolistIterator' argument 1 names different: declaration 'start' definition '_start'. murasaki/src/ecolist.cc:347:76: note: Function 'BidirectionalEcolistIterator' argument 1 names different: declaration 'start' definition '_start'. murasaki/src/ecolist.cc:347:96: style:inconclusive: Function 'BidirectionalEcolistIterator' argument 2 names different: declaration 'prev' definition '_prev'. [funcArgNamesDifferent] murasaki/src/ecolist.h:45:60: note: Function 'BidirectionalEcolistIterator' argument 2 names different: declaration 'prev' definition '_prev'. murasaki/src/ecolist.cc:347:96: note: Function 'BidirectionalEcolistIterator' argument 2 names different: declaration 'prev' definition '_prev'. murasaki/src/ecolist.cc:347:109: style:inconclusive: Function 'BidirectionalEcolistIterator' argument 3 names different: declaration 'p' definition '_p'. [funcArgNamesDifferent] murasaki/src/ecolist.h:45:72: note: Function 'BidirectionalEcolistIterator' argument 3 names different: declaration 'p' definition '_p'. murasaki/src/ecolist.cc:347:109: note: Function 'BidirectionalEcolistIterator' argument 3 names different: declaration 'p' definition '_p'. murasaki/src/ecolist.cc:347:119: style:inconclusive: Function 'BidirectionalEcolistIterator' argument 4 names different: declaration 'ite' definition '_ite'. [funcArgNamesDifferent] murasaki/src/ecolist.h:45:81: note: Function 'BidirectionalEcolistIterator' argument 4 names different: declaration 'ite' definition '_ite'. murasaki/src/ecolist.cc:347:119: note: Function 'BidirectionalEcolistIterator' argument 4 names different: declaration 'ite' definition '_ite'. murasaki/src/ecolist.cc:375:100: style:inconclusive: Function 'operator++' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/ecolist.cc:399:100: style:inconclusive: Function 'operator--' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/ecolist.cc:411:69: style:inconclusive: Function 'operator!=' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/ecolist.cc:415:69: style:inconclusive: Function 'operator==' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/ecolist.cc:461:30: style: Parameter 'a' can be declared as reference to const [constParameterReference] murasaki/src/ecolist.cc:461:42: style: Parameter 'b' can be declared as reference to const [constParameterReference] murasaki/src/ecolist.cc:73:14: style: Variable 'root' can be declared as pointer to const [constVariablePointer] murasaki/src/ecolist.cc:489:9: style: Variable 'high' is assigned a value that is never used. [unreadVariable] murasaki/src/ecolist.cc:507:9: style: Variable 'high' is assigned a value that is never used. [unreadVariable] murasaki/src/ecolist.cc:479:29: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/geneparse.cc:55:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/geneparse.cc:121:6: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/geneparse.cc:135:3: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/geneparse.cc:161:8: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/geneparse.cc:62:26: style: Variable 'long_options' can be declared as const array [constVariable] murasaki/src/geneparse.cc:77:12: style: Unused variable: prefreq [unusedVariable] murasaki/src/genopts.cc:63:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] murasaki/src/getsegments.cc:53:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/getsegments.cc:186:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] murasaki/src/getsegments.cc:90:6: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/getsegments.cc:112:8: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/getsegments.cc:153:6: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/getsegments.cc:118:3: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/getsegments.cc:56:7: style: The scope of the variable 'optc' can be reduced. [variableScope] murasaki/src/getsegments.cc:95:20: style: The scope of the variable 'segments' can be reduced. [variableScope] murasaki/src/getsegments.cc:96:14: style: The scope of the variable 'size' can be reduced. [variableScope] murasaki/src/getsegments.cc:128:74: performance: Function parameter 'filename' should be passed by const reference. [passedByValue] murasaki/src/getsegments.cc:60:26: style: Variable 'long_options' can be declared as const array [constVariable] murasaki/src/getsegments.cc:54:10: style: Unused variable: customOutput [unusedVariable] murasaki/src/getsegments.cc:68:12: style: Unused variable: prefreq [unusedVariable] murasaki/src/mbfa.cc:68:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/mbfa.cc:90:8: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/mbfa.cc:107:8: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/mbfa.cc:145:4: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/mbfa.cc:49:7: style: The scope of the variable 'optc' can be reduced. [variableScope] murasaki/src/mbfa.cc:119:18: style: Local variable 'i' shadows outer variable [shadowVariable] murasaki/src/mbfa.cc:84:11: note: Shadowed declaration murasaki/src/mbfa.cc:119:18: note: Shadow variable murasaki/src/mbfa.cc:151:25: performance: Function parameter 'a' should be passed by const reference. [passedByValue] murasaki/src/mbfa.cc:151:34: performance: Function parameter 'b' should be passed by const reference. [passedByValue] murasaki/src/mbfa.cc:53:26: style: Variable 'long_options' can be declared as const array [constVariable] murasaki/src/mbfa.cc:64:12: style: Unused variable: prefreq [unusedVariable] murasaki/src/msethash.cc:36:3: warning: Class 'MSetHash' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] murasaki/src/msethash.cc:36:3: warning: Class 'MSetHash' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] murasaki/src/msethash.h:40:21: warning: The class 'MSetHash' defines member function with name 'linear_cost' also defined in its parent class 'Hash'. [duplInheritedMember] murasaki/src/sequence.h:421:21: note: Parent function 'Hash::linear_cost' murasaki/src/msethash.h:40:21: note: Derived function 'MSetHash::linear_cost' murasaki/src/msethash.h:43:21: warning: The class 'MSetHash' defines member function with name 'bucket_prep_cost' also defined in its parent class 'Hash'. [duplInheritedMember] murasaki/src/sequence.h:422:21: note: Parent function 'Hash::bucket_prep_cost' murasaki/src/msethash.h:43:21: note: Derived function 'MSetHash::bucket_prep_cost' murasaki/src/msethash.h:38:3: style: Class 'MSetHash' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/msethash.h:29:8: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:409:16: note: Virtual function in base class murasaki/src/msethash.h:29:8: note: Function in derived class murasaki/src/msethash.h:30:8: style: The function 'add' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:410:16: note: Virtual function in base class murasaki/src/msethash.h:30:8: note: Function in derived class murasaki/src/msethash.h:31:8: style: The function 'getMatchingSets' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:412:16: note: Virtual function in base class murasaki/src/msethash.h:31:8: note: Function in derived class murasaki/src/msethash.h:32:8: style: The function 'lookup' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:411:16: note: Virtual function in base class murasaki/src/msethash.h:32:8: note: Function in derived class murasaki/src/msethash.h:34:8: style: The function 'emptyAt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:413:16: note: Virtual function in base class murasaki/src/msethash.h:34:8: note: Function in derived class murasaki/src/msethash.h:35:8: style: The function 'sizeAt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:414:16: note: Virtual function in base class murasaki/src/msethash.h:35:8: note: Function in derived class murasaki/src/msethash.h:36:8: style: The function 'sizeAt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:415:16: note: Virtual function in base class murasaki/src/msethash.h:36:8: note: Function in derived class murasaki/src/murasaki.cc:114:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/murasaki.cc:132:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/murasaki.cc:201:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar] murasaki/src/murasaki.cc:249:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] murasaki/src/murasaki.cc:574:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar] murasaki/src/murasaki.cc:832:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/murasaki.cc:856:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/murasaki.cc:906:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/murasaki.cc:1074:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/murasaki.cc:1232:95: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] murasaki/src/murasaki.cc:1249:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] murasaki/src/murasaki.cc:1316:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/murasaki.cc:119:18: warning: Member variable 'MurasakiRuntime::mpi_tag' is not initialized in the constructor. [uninitMemberVar] murasaki/src/murasaki.cc:119:18: warning: Member variable 'MurasakiRuntime::stdoe' is not initialized in the constructor. [uninitMemberVar] murasaki/src/murasaki.cc:119:18: warning: Member variable 'MurasakiRuntime::stdoename' is not initialized in the constructor. [uninitMemberVar] murasaki/src/murasaki.cc:1296:23: style: The member function 'MurasakiRuntime::success' can be static. [functionStatic] murasaki/src/murasaki.h:90:8: note: The member function 'MurasakiRuntime::success' can be static. murasaki/src/murasaki.cc:1296:23: note: The member function 'MurasakiRuntime::success' can be static. murasaki/src/openhash.h:50:21: warning: The class 'OpenHash' defines member function with name 'linear_cost' also defined in its parent class 'Hash'. [duplInheritedMember] murasaki/src/sequence.h:421:21: note: Parent function 'Hash::linear_cost' murasaki/src/openhash.h:50:21: note: Derived function 'OpenHash::linear_cost' murasaki/src/openhash.h:53:21: warning: The class 'OpenHash' defines member function with name 'bucket_prep_cost' also defined in its parent class 'Hash'. [duplInheritedMember] murasaki/src/sequence.h:422:21: note: Parent function 'Hash::bucket_prep_cost' murasaki/src/openhash.h:53:21: note: Derived function 'OpenHash::bucket_prep_cost' murasaki/src/openhash.h:66:3: style: Class 'OpenHash' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/openhash.h:41:8: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:409:16: note: Virtual function in base class murasaki/src/openhash.h:41:8: note: Function in derived class murasaki/src/openhash.h:42:8: style: The function 'add' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:410:16: note: Virtual function in base class murasaki/src/openhash.h:42:8: note: Function in derived class murasaki/src/openhash.h:43:8: style: The function 'getMatchingSets' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:412:16: note: Virtual function in base class murasaki/src/openhash.h:43:8: note: Function in derived class murasaki/src/openhash.h:44:8: style: The function 'lookup' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:411:16: note: Virtual function in base class murasaki/src/openhash.h:44:8: note: Function in derived class murasaki/src/openhash.h:45:8: style: The function 'emptyAt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:413:16: note: Virtual function in base class murasaki/src/openhash.h:45:8: note: Function in derived class murasaki/src/openhash.h:46:8: style: The function 'sizeAt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:414:16: note: Virtual function in base class murasaki/src/openhash.h:46:8: note: Function in derived class murasaki/src/openhash.h:47:8: style: The function 'sizeAt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:415:16: note: Virtual function in base class murasaki/src/openhash.h:47:8: note: Function in derived class murasaki/src/openhash.h:59:8: style: The function 'writePerformanceData' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:418:16: note: Virtual function in base class murasaki/src/openhash.h:59:8: note: Function in derived class murasaki/src/openhash.h:67:4: style: The destructor '~OpenHash' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] murasaki/src/sequence.h:437:12: note: Virtual destructor in base class murasaki/src/openhash.h:67:4: note: Destructor in derived class murasaki/src/murasaki.cc:1107:6: style: Condition '!features.empty()' is always true [knownConditionTrueFalse] murasaki/src/murasaki.cc:1317:8: style: Condition 'anchorProgress_fh' is always true [knownConditionTrueFalse] murasaki/src/murasaki.cc:113:22: error: Unhandled exception thrown in function that is an entry point. [throwInEntryPoint] murasaki/src/murasaki.cc:1232:64: style: The comparison 'a == seqs[i]->fwd' is always true because 'a' and 'seqs[i]->fwd' represent the same value. [knownConditionTrueFalse] murasaki/src/murasaki.cc:1231:27: note: 'a' is assigned value 'seqs[i]->fwd' here. murasaki/src/murasaki.cc:1232:64: note: The comparison 'a == seqs[i]->fwd' is always true because 'a' and 'seqs[i]->fwd' represent the same value. murasaki/src/murasaki.cc:850:48: style:inconclusive: Function 'writeHisto' argument 2 names different: declaration 'detailed' definition 'details'. [funcArgNamesDifferent] murasaki/src/murasaki.h:60:48: note: Function 'writeHisto' argument 2 names different: declaration 'detailed' definition 'details'. murasaki/src/murasaki.cc:850:48: note: Function 'writeHisto' argument 2 names different: declaration 'detailed' definition 'details'. murasaki/src/murasaki.cc:136:24: style: Local variable 'e' shadows outer variable [shadowVariable] murasaki/src/murasaki.cc:131:20: note: Shadowed declaration murasaki/src/murasaki.cc:136:24: note: Shadow variable murasaki/src/murasaki.cc:609:15: style: Local variable 'i' shadows outer variable [shadowVariable] murasaki/src/murasaki.cc:568:18: note: Shadowed declaration murasaki/src/murasaki.cc:609:15: note: Shadow variable murasaki/src/murasaki.cc:836:14: style: Local variable 'of' shadows outer variable [shadowVariable] murasaki/src/murasaki.cc:823:12: note: Shadowed declaration murasaki/src/murasaki.cc:836:14: note: Shadow variable murasaki/src/murasaki.cc:840:14: style: Local variable 'of' shadows outer variable [shadowVariable] murasaki/src/murasaki.cc:823:12: note: Shadowed declaration murasaki/src/murasaki.cc:840:14: note: Shadow variable murasaki/src/murasaki.cc:857:14: style: Local variable 'histo' shadows outer variable [shadowVariable] murasaki/src/murasaki.cc:851:12: note: Shadowed declaration murasaki/src/murasaki.cc:857:14: note: Shadow variable murasaki/src/murasaki.cc:845:26: performance: Function parameter 'record' should be passed by const reference. [passedByValue] murasaki/src/murasaki.cc:850:24: performance: Function parameter 'hashHisto_record' should be passed by const reference. [passedByValue] murasaki/src/murasaki.cc:850:48: performance: Function parameter 'details' should be passed by const reference. [passedByValue] murasaki/src/murasaki.cc:962:28: style: Parameter 'l' can be declared as reference to const [constParameterReference] murasaki/src/murasaki.cc:1061:8: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] murasaki/src/murasaki.cc:866:42: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/murasaki.cc:990:4: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/murasaki.cc:1030:9: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/murasaki.cc:1030:31: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/murasaki.cc:1323:66: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/openhash.cc:121:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/openhash.cc:46:3: warning: Class 'OpenHash' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] murasaki/src/openhash.cc:46:3: warning: Class 'OpenHash' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] murasaki/src/options.cc:242:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable opterr [valueFlowBailoutIncompleteVar] murasaki/src/options.cc:598:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] murasaki/src/options.cc:629:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/options.cc:711:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] murasaki/src/options.cc:95:10: warning: Member variable 'Options::seqreadOptions' is not initialized in the constructor. [uninitMemberVar] murasaki/src/options.cc:150:15: style: The member function 'Options::preInit' can be static. [functionStatic] murasaki/src/options.h:122:8: note: The member function 'Options::preInit' can be static. murasaki/src/options.cc:150:15: note: The member function 'Options::preInit' can be static. murasaki/src/options.cc:71:15: style: The member function 'Options::staticInit' can be static. [functionStatic] murasaki/src/options.h:132:8: note: The member function 'Options::staticInit' can be static. murasaki/src/options.cc:71:15: note: The member function 'Options::staticInit' can be static. murasaki/src/options.cc:759:42: style: Condition 'largeSeqs' is always false [knownConditionTrueFalse] murasaki/src/options.cc:757:18: note: Assignment 'largeSeqs=false', assigned value is 0 murasaki/src/options.cc:759:42: note: Condition 'largeSeqs' is always false murasaki/src/options.cc:395:11: portability: %lu in format string (no. 1) requires 'unsigned long *' but the argument type is 'Score * {aka signed long *}'. [invalidScanfArgType_int] murasaki/src/options.cc:240:7: style: The scope of the variable 'optc' can be reduced. [variableScope] murasaki/src/options.cc:391:20: style: Checking if unsigned expression 'seedfilter' is less than zero. [unsignedLessThanZero] murasaki/src/options.cc:403:20: style: Checking if unsigned expression 'hashfilter' is less than zero. [unsignedLessThanZero] murasaki/src/options.cc:409:21: style: Checking if unsigned expression 'mergeFilter' is less than zero. [unsignedLessThanZero] murasaki/src/options.cc:797:33: style:inconclusive: Function 'loadConfig' argument 1 names different: declaration 'config' definition 'file'. [funcArgNamesDifferent] murasaki/src/options.h:123:26: note: Function 'loadConfig' argument 1 names different: declaration 'config' definition 'file'. murasaki/src/options.cc:797:33: note: Function 'loadConfig' argument 1 names different: declaration 'config' definition 'file'. murasaki/src/options.cc:90:34: performance: Function parameter 'name' should be passed by const reference. [passedByValue] murasaki/src/options.cc:797:33: performance: Function parameter 'file' should be passed by const reference. [passedByValue] murasaki/src/options.cc:141:21: style: Variable 'e' can be declared as reference to const [constVariableReference] murasaki/src/options.cc:147:21: style: Variable 'e' can be declared as reference to const [constVariableReference] murasaki/src/options.cc:79:29: style: Variable 'oi' can be declared as pointer to const [constVariablePointer] murasaki/src/options.cc:68:40: error: va_list 'argp' was opened but not closed by va_end(). [va_end_missing] murasaki/src/revcomptable.cxx:1:9: error: syntax error: keyword 'return' is not allowed in global scope [syntaxError] murasaki/src/scoring.cc:85:54: style:inconclusive: Function 'minimumPairScore' argument 1 names different: declaration 'output' definition 'pairs'. [funcArgNamesDifferent] murasaki/src/scoring.h:37:54: note: Function 'minimumPairScore' argument 1 names different: declaration 'output' definition 'pairs'. murasaki/src/scoring.cc:85:54: note: Function 'minimumPairScore' argument 1 names different: declaration 'output' definition 'pairs'. murasaki/src/seqread.cc:98:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/seqread.cc:145:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stop [valueFlowBailoutIncompleteVar] murasaki/src/seqread.cc:266:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/seqread.cc:319:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/seqread.cc:330:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/seqread.cc:353:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/seqread.cc:452:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/seqread.cc:475:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/seqread.cc:194:3: style: Obsolescent function 'bzero' called. It is recommended to use 'memset' instead. [prohibitedbzeroCalled] murasaki/src/seqread.cc:343:26: style:inconclusive: Technically the member function 'SequenceByteReader::eof' can be const. [functionConst] murasaki/src/seqread.h:85:8: note: Technically the member function 'SequenceByteReader::eof' can be const. murasaki/src/seqread.cc:343:26: note: Technically the member function 'SequenceByteReader::eof' can be const. murasaki/src/seqread.cc:494:28: style:inconclusive: Technically the member function 'SequenceFileReader::size' can be const. [functionConst] murasaki/src/seqread.h:124:10: note: Technically the member function 'SequenceFileReader::size' can be const. murasaki/src/seqread.cc:494:28: note: Technically the member function 'SequenceFileReader::size' can be const. murasaki/src/seqread.cc:393:3: warning: Class 'SequenceFileReader' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] murasaki/src/seqread.cc:393:3: warning: Class 'SequenceFileReader' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] murasaki/src/seqread.cc:450:17: style: Condition 'boost::filesystem::exists(filename)' is always true [knownConditionTrueFalse] murasaki/src/seqread.cc:446:6: note: Assuming that condition '!boost::filesystem::exists(filename)' is not redundant murasaki/src/seqread.cc:450:17: note: Condition 'boost::filesystem::exists(filename)' is always true murasaki/src/seqread.cc:273:6: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/seqread.cc:422:15: style: C-style pointer casting [cstyleCast] murasaki/src/seqread.cc:381:53: style:inconclusive: Function 'SequenceFileReader' argument 1 names different: declaration 'filename' definition '_filename'. [funcArgNamesDifferent] murasaki/src/seqread.h:120:35: note: Function 'SequenceFileReader' argument 1 names different: declaration 'filename' definition '_filename'. murasaki/src/seqread.cc:381:53: note: Function 'SequenceFileReader' argument 1 names different: declaration 'filename' definition '_filename'. murasaki/src/seqread.cc:381:67: style:inconclusive: Function 'SequenceFileReader' argument 2 names different: declaration 'options' definition '_options'. [funcArgNamesDifferent] murasaki/src/seqread.h:120:48: note: Function 'SequenceFileReader' argument 2 names different: declaration 'options' definition '_options'. murasaki/src/seqread.cc:381:67: note: Function 'SequenceFileReader' argument 2 names different: declaration 'options' definition '_options'. murasaki/src/seqread.cc:461:12: style: Local variable 'size' shadows outer function [shadowFunction] murasaki/src/seqread.h:124:10: note: Shadowed declaration murasaki/src/seqread.cc:461:12: note: Shadow variable murasaki/src/seqread.cc:71:73: performance: Function parameter 'filename' should be passed by const reference. [passedByValue] murasaki/src/seqread.cc:381:53: performance: Function parameter '_filename' should be passed by const reference. [passedByValue] murasaki/src/sequence.cc:127:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:138:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:197:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:223:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:230:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:245:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:261:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:273:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:345:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:366:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:370:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:388:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:391:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:396:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:402:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:424:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:574:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:625:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:660:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:690:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:731:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:772:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:820:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:910:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:916:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:1015:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:1059:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:1097:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:1135:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:1249:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:1315:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:1366:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:1398:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:1443:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:1624:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:1660:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable b [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:1745:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:1792:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:1858:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:1914:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:1967:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:2003:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:2048:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:2078:84: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:2507:98: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:2557:102: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:2682:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:2844:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:2936:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:2952:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:2965:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:2982:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:2994:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:3029:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:3041:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:3055:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:3066:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:3162:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:3175:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:3212:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:3252:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:3341:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:3382:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WORDSIZE [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:3421:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hex [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:3447:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] murasaki/src/hashing.h:53:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/sequence.cc:1964:12: style: Array index 'baseSeq' is used before limits check. [arrayIndexThenCheck] murasaki/src/sequence.cc:3259:5: style: Obsolescent function 'bzero' called. It is recommended to use 'memset' instead. [prohibitedbzeroCalled] murasaki/src/sequence.cc:1369:14: warning: Member variable 'BitSequence::shmUsed' is not initialized in the constructor. [uninitMemberVar] murasaki/src/sequence.cc:1369:14: warning: Member variable 'BitSequence::hasher' is not initialized in the constructor. [uninitMemberVar] murasaki/src/sequence.cc:1869:13: warning:inconclusive: Member variable 'HashMethod::entropy' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy] murasaki/src/sequence.cc:1869:13: warning:inconclusive: Member variable 'HashMethod::used' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy] murasaki/src/sequence.cc:1869:13: warning: Member variable 'HashMethod::entropyHi' is not initialized in the copy constructor. [uninitMemberVar] murasaki/src/sequence.cc:1869:13: warning: Member variable 'HashMethod::entropyLo' is not initialized in the copy constructor. [uninitMemberVar] murasaki/src/sequence.cc:1869:13: warning: Member variable 'HashMethod::entropyTotal' is not initialized in the copy constructor. [uninitMemberVar] murasaki/src/sequence.cc:1869:13: warning: Member variable 'HashMethod::entropyMean' is not initialized in the copy constructor. [uninitMemberVar] murasaki/src/sequence.cc:1869:13: warning: Member variable 'HashMethod::entropyStd' is not initialized in the copy constructor. [uninitMemberVar] murasaki/src/sequence.cc:1869:13: warning: Member variable 'HashMethod::totalCorrelationPenalty' is not initialized in the copy constructor. [uninitMemberVar] murasaki/src/sequence.cc:1910:13: warning: Member variable 'HashMethod::sources' is not initialized in the constructor. [uninitMemberVar] murasaki/src/sequence.cc:1910:13: warning: Member variable 'HashMethod::empties' is not initialized in the constructor. [uninitMemberVar] murasaki/src/sequence.cc:1910:13: warning: Member variable 'HashMethod::fitness' is not initialized in the constructor. [uninitMemberVar] murasaki/src/sequence.cc:1910:13: warning: Member variable 'HashMethod::entropyHi' is not initialized in the constructor. [uninitMemberVar] murasaki/src/sequence.cc:1910:13: warning: Member variable 'HashMethod::entropyLo' is not initialized in the constructor. [uninitMemberVar] murasaki/src/sequence.cc:1910:13: warning: Member variable 'HashMethod::entropyTotal' is not initialized in the constructor. [uninitMemberVar] murasaki/src/sequence.cc:1910:13: warning: Member variable 'HashMethod::entropyMean' is not initialized in the constructor. [uninitMemberVar] murasaki/src/sequence.cc:1910:13: warning: Member variable 'HashMethod::entropyStd' is not initialized in the constructor. [uninitMemberVar] murasaki/src/sequence.cc:1910:13: warning: Member variable 'HashMethod::totalCorrelationPenalty' is not initialized in the constructor. [uninitMemberVar] murasaki/src/sequence.cc:357:11: warning:inconclusive: Member variable 'Sequence::baseFilename' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy] murasaki/src/sequence.cc:388:18: style: The member function 'BitSequence::wordsize' can be static. [functionStatic] murasaki/src/sequence.h:197:7: note: The member function 'BitSequence::wordsize' can be static. murasaki/src/sequence.cc:388:18: note: The member function 'BitSequence::wordsize' can be static. murasaki/src/sequence.cc:769:19: style:inconclusive: Technically the member function 'BitSequence::equal' can be const. [functionConst] murasaki/src/sequence.h:221:8: note: Technically the member function 'BitSequence::equal' can be const. murasaki/src/sequence.cc:769:19: note: Technically the member function 'BitSequence::equal' can be const. murasaki/src/sequence.cc:509:19: style: The member function 'BitSequence::mpi_distribute' can be static. [functionStatic] murasaki/src/sequence.h:248:8: note: The member function 'BitSequence::mpi_distribute' can be static. murasaki/src/sequence.cc:509:19: note: The member function 'BitSequence::mpi_distribute' can be static. murasaki/src/sequence.cc:436:19: style: The member function 'BitSequence::shm_distribute' can be static. [functionStatic] murasaki/src/sequence.h:253:8: note: The member function 'BitSequence::shm_distribute' can be static. murasaki/src/sequence.cc:436:19: note: The member function 'BitSequence::shm_distribute' can be static. murasaki/src/sequence.cc:1298:19: style: The member function 'BitSequence::mmap_msync' can be static. [functionStatic] murasaki/src/sequence.h:254:8: note: The member function 'BitSequence::mmap_msync' can be static. murasaki/src/sequence.cc:1298:19: note: The member function 'BitSequence::mmap_msync' can be static. murasaki/src/sequence.cc:1419:20: style: The member function 'HashMethod::srcSetToString' can be static. [functionStatic] murasaki/src/sequence.h:289:10: note: The member function 'HashMethod::srcSetToString' can be static. murasaki/src/sequence.cc:1419:20: note: The member function 'HashMethod::srcSetToString' can be static. murasaki/src/sequence.cc:1705:20: style:inconclusive: Technically the member function 'HashMethod::prettyPrint' can be const. [functionConst] murasaki/src/sequence.h:296:10: note: Technically the member function 'HashMethod::prettyPrint' can be const. murasaki/src/sequence.cc:1705:20: note: Technically the member function 'HashMethod::prettyPrint' can be const. murasaki/src/sequence.cc:810:37: style:inconclusive: Technically the member function 'Location::localRegionIte' can be const. [functionConst] murasaki/src/sequence.h:395:29: note: Technically the member function 'Location::localRegionIte' can be const. murasaki/src/sequence.cc:810:37: note: Technically the member function 'Location::localRegionIte' can be const. murasaki/src/sequence.cc:2830:20: style:inconclusive: Technically the member function 'IntervalSet::score' can be const. [functionConst] murasaki/src/sequence.h:472:9: note: Technically the member function 'IntervalSet::score' can be const. murasaki/src/sequence.cc:2830:20: note: Technically the member function 'IntervalSet::score' can be const. murasaki/src/hashing.h:66:8: style:inconclusive: Technically the member function 'SBox < unsigned short >::confuse' can be const. [functionConst] murasaki/src/sequence.cc:344:5: warning: Class 'Sequence' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] murasaki/src/hashing.h:45:5: warning: Class 'SBox < unsigned short >' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] murasaki/src/hashing.h:45:5: warning: Class 'SBox < unsigned short >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] murasaki/src/hashing.h:43:3: style: Class 'SBox < unsigned short >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] murasaki/src/sequence.cc:2458:8: style: The if condition is the same as the previous if condition [duplicateCondition] murasaki/src/sequence.cc:2456:8: note: First condition murasaki/src/sequence.cc:2458:8: note: Second condition murasaki/src/sequence.cc:1853:16: style: Condition 'fate<5' is always false [knownConditionTrueFalse] murasaki/src/sequence.cc:1851:10: note: Assuming that condition 'fate<50' is not redundant murasaki/src/sequence.cc:1853:16: note: Condition 'fate<5' is always false murasaki/src/sequence.cc:1062:8: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/sequence.cc:1072:3: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/sequence.cc:1081:4: style: Exception should be caught by reference. [catchExceptionByValue] murasaki/src/sequence.cc:126:15: style: C-style pointer casting [cstyleCast] murasaki/src/sequence.cc:2023:11: style: C-style pointer casting [cstyleCast] murasaki/src/sequence.cc:1993:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/sequence.cc:1994:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/sequence.cc:1999:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/sequence.cc:2008:13: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/sequence.cc:2009:13: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/sequence.cc:2019:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/sequence.cc:2020:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/sequence.cc:2024:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] murasaki/src/sequence.cc:440:3: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak] murasaki/src/sequence.cc:1644:10: style: The scope of the variable 'improved' can be reduced. [variableScope] murasaki/src/sequence.cc:2016:13: style: The scope of the variable 'buf' can be reduced. [variableScope] murasaki/src/sequence.cc:3241:10: style: The scope of the variable 'size' can be reduced. [variableScope] murasaki/src/sequence.cc:3242:9: style: The scope of the variable 'df' can be reduced. [variableScope] murasaki/src/sequence.cc:3330:10: style: The scope of the variable 'shortest' can be reduced. [variableScope] murasaki/src/sequence.cc:271:19: style:inconclusive: Function 'popCount' argument 1 names different: declaration 'w' definition 't'. [funcArgNamesDifferent] murasaki/src/sequence.h:118:19: note: Function 'popCount' argument 1 names different: declaration 'w' definition 't'. murasaki/src/sequence.cc:271:19: note: Function 'popCount' argument 1 names different: declaration 'w' definition 't'. murasaki/src/sequence.cc:298:27: style:inconclusive: Function 'Sequence' argument 1 names different: declaration '' definition '_filename'. [funcArgNamesDifferentUnnamed] murasaki/src/sequence.cc:357:36: style:inconclusive: Function 'Sequence' argument 1 names different: declaration 'obj' definition 'a'. [funcArgNamesDifferent] murasaki/src/sequence.h:353:28: note: Function 'Sequence' argument 1 names different: declaration 'obj' definition 'a'. murasaki/src/sequence.cc:357:36: note: Function 'Sequence' argument 1 names different: declaration 'obj' definition 'a'. murasaki/src/sequence.cc:685:37: style:inconclusive: Function 'cmpRight' argument 1 names different: declaration 'pos' definition 'base_pos'. [funcArgNamesDifferent] murasaki/src/sequence.h:214:26: note: Function 'cmpRight' argument 1 names different: declaration 'pos' definition 'base_pos'. murasaki/src/sequence.cc:685:37: note: Function 'cmpRight' argument 1 names different: declaration 'pos' definition 'base_pos'. murasaki/src/sequence.cc:685:73: style:inconclusive: Function 'cmpRight' argument 3 names different: declaration 'targetPos' definition 'base_targetPos'. [funcArgNamesDifferent] murasaki/src/sequence.h:214:57: note: Function 'cmpRight' argument 3 names different: declaration 'targetPos' definition 'base_targetPos'. murasaki/src/sequence.cc:685:73: note: Function 'cmpRight' argument 3 names different: declaration 'targetPos' definition 'base_targetPos'. murasaki/src/sequence.cc:727:36: style:inconclusive: Function 'cmpLeft' argument 1 names different: declaration 'pos' definition 'base_pos'. [funcArgNamesDifferent] murasaki/src/sequence.h:215:25: note: Function 'cmpLeft' argument 1 names different: declaration 'pos' definition 'base_pos'. murasaki/src/sequence.cc:727:36: note: Function 'cmpLeft' argument 1 names different: declaration 'pos' definition 'base_pos'. murasaki/src/sequence.cc:727:72: style:inconclusive: Function 'cmpLeft' argument 3 names different: declaration 'targetPos' definition 'base_targetPos'. [funcArgNamesDifferent] murasaki/src/sequence.h:215:56: note: Function 'cmpLeft' argument 3 names different: declaration 'targetPos' definition 'base_targetPos'. murasaki/src/sequence.cc:727:72: note: Function 'cmpLeft' argument 3 names different: declaration 'targetPos' definition 'base_targetPos'. murasaki/src/sequence.cc:1093:52: style:inconclusive: Function 'loadBinary' argument 1 names different: declaration 'reader' definition 'binseq'. [funcArgNamesDifferent] murasaki/src/sequence.h:260:41: note: Function 'loadBinary' argument 1 names different: declaration 'reader' definition 'binseq'. murasaki/src/sequence.cc:1093:52: note: Function 'loadBinary' argument 1 names different: declaration 'reader' definition 'binseq'. murasaki/src/sequence.cc:1938:30: style:inconclusive: Function 'Location' argument 1 names different: declaration '' definition 's'. [funcArgNamesDifferentUnnamed] murasaki/src/sequence.cc:1938:39: style:inconclusive: Function 'Location' argument 2 names different: declaration '' definition 'p'. [funcArgNamesDifferentUnnamed] murasaki/src/sequence.cc:1941:27: style:inconclusive: Function 'Location' argument 1 names different: declaration '' definition 's'. [funcArgNamesDifferentUnnamed] murasaki/src/sequence.cc:1941:36: style:inconclusive: Function 'Location' argument 2 names different: declaration '' definition 'p'. [funcArgNamesDifferentUnnamed] murasaki/src/sequence.cc:1953:52: style:inconclusive: Function 'sizeAt' argument 2 names different: declaration 'val' definition 'a'. [funcArgNamesDifferent] murasaki/src/sequence.h:415:56: note: Function 'sizeAt' argument 2 names different: declaration 'val' definition 'a'. murasaki/src/sequence.cc:1953:52: note: Function 'sizeAt' argument 2 names different: declaration 'val' definition 'a'. murasaki/src/sequence.cc:2532:63: style:inconclusive: Function 'colinear' argument 2 names different: declaration 'MaxDist' definition 'maxDist'. [funcArgNamesDifferent] murasaki/src/sequence.h:468:52: note: Function 'colinear' argument 2 names different: declaration 'MaxDist' definition 'maxDist'. murasaki/src/sequence.cc:2532:63: note: Function 'colinear' argument 2 names different: declaration 'MaxDist' definition 'maxDist'. murasaki/src/sequence.cc:2586:45: style:inconclusive: Function 'coalesce' argument 1 names different: declaration 'neighbor' definition 'a'. [funcArgNamesDifferent] murasaki/src/sequence.h:462:34: note: Function 'coalesce' argument 1 names different: declaration 'neighbor' definition 'a'. murasaki/src/sequence.cc:2586:45: note: Function 'coalesce' argument 1 names different: declaration 'neighbor' definition 'a'. murasaki/src/sequence.cc:2656:53: style:inconclusive: Function 'AnchorSet' argument 2 names different: declaration 'used' definition 'usedMap'. [funcArgNamesDifferent] murasaki/src/sequence.h:487:43: note: Function 'AnchorSet' argument 2 names different: declaration 'used' definition 'usedMap'. murasaki/src/sequence.cc:2656:53: note: Function 'AnchorSet' argument 2 names different: declaration 'used' definition 'usedMap'. murasaki/src/sequence.cc:2664:32: style:inconclusive: Function 'add' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/sequence.cc:2903:39: style:inconclusive: Function 'wordToMaskedString' argument 2 names different: declaration 'pat' definition 'p'. [funcArgNamesDifferent] murasaki/src/sequence.h:122:39: note: Function 'wordToMaskedString' argument 2 names different: declaration 'pat' definition 'p'. murasaki/src/sequence.cc:2903:39: note: Function 'wordToMaskedString' argument 2 names different: declaration 'pat' definition 'p'. murasaki/src/sequence.cc:3024:31: style:inconclusive: Function 'Window' argument 1 names different: declaration 'i' definition 'a'. [funcArgNamesDifferent] murasaki/src/sequence.h:335:25: note: Function 'Window' argument 1 names different: declaration 'i' definition 'a'. murasaki/src/sequence.cc:3024:31: note: Function 'Window' argument 1 names different: declaration 'i' definition 'a'. murasaki/src/sequence.cc:3037:29: style:inconclusive: Function 'Window' argument 1 names different: declaration 's' definition '_seq'. [funcArgNamesDifferent] murasaki/src/sequence.h:333:23: note: Function 'Window' argument 1 names different: declaration 's' definition '_seq'. murasaki/src/sequence.cc:3037:29: note: Function 'Window' argument 1 names different: declaration 's' definition '_seq'. murasaki/src/sequence.cc:3037:41: style:inconclusive: Function 'Window' argument 2 names different: declaration 'pos' definition '_pos'. [funcArgNamesDifferent] murasaki/src/sequence.h:333:32: note: Function 'Window' argument 2 names different: declaration 'pos' definition '_pos'. murasaki/src/sequence.cc:3037:41: note: Function 'Window' argument 2 names different: declaration 'pos' definition '_pos'. murasaki/src/sequence.cc:3037:59: style:inconclusive: Function 'Window' argument 3 names different: declaration 'p' definition '_pat'. [funcArgNamesDifferent] murasaki/src/sequence.h:333:49: note: Function 'Window' argument 3 names different: declaration 'p' definition '_pat'. murasaki/src/sequence.cc:3037:59: note: Function 'Window' argument 3 names different: declaration 'p' definition '_pat'. murasaki/src/sequence.cc:3532:48: style:inconclusive: Function 'BaseIterator' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] murasaki/src/sequence.cc:1072:26: style: Local variable 'e' shadows outer variable [shadowVariable] murasaki/src/sequence.cc:1062:31: note: Shadowed declaration murasaki/src/sequence.cc:1072:26: note: Shadow variable murasaki/src/sequence.cc:1148:35: style: Local variable 'subSeqBounds' shadows outer function [shadowFunction] murasaki/src/sequence.h:245:11: note: Shadowed declaration murasaki/src/sequence.cc:1148:35: note: Shadow variable murasaki/src/sequence.cc:1973:12: style: Local variable 'sum' shadows outer function [shadowFunction] murasaki/src/dinkymath.h:131:3: note: Shadowed declaration murasaki/src/sequence.cc:1973:12: note: Shadow variable murasaki/src/sequence.cc:2234:32: style: Local variable 'i' shadows outer variable [shadowVariable] murasaki/src/sequence.cc:2200:7: note: Shadowed declaration murasaki/src/sequence.cc:2234:32: note: Shadow variable murasaki/src/sequence.cc:2274:33: style: Local variable 'i' shadows outer variable [shadowVariable] murasaki/src/sequence.cc:2247:7: note: Shadowed declaration murasaki/src/sequence.cc:2274:33: note: Shadow variable murasaki/src/sequence.cc:2497:10: style: Local variable 'offset' shadows outer function [shadowFunction] murasaki/src/sequence.h:466:10: note: Shadowed declaration murasaki/src/sequence.cc:2497:10: note: Shadow variable murasaki/src/sequence.cc:3066:32: style: Local variable 'frame' shadows outer variable [shadowVariable] murasaki/src/sequence.h:325:14: note: Shadowed declaration murasaki/src/sequence.cc:3066:32: note: Shadow variable murasaki/src/sequence.cc:3207:26: style: Local variable 'i' shadows outer variable [shadowVariable] murasaki/src/sequence.cc:3185:27: note: Shadowed declaration murasaki/src/sequence.cc:3207:26: note: Shadow variable murasaki/src/sequence.cc:3266:26: style: Local variable 'i' shadows outer variable [shadowVariable] murasaki/src/sequence.cc:3262:31: note: Shadowed declaration murasaki/src/sequence.cc:3266:26: note: Shadow variable murasaki/src/sequence.cc:3296:10: style: Local variable 'sum' shadows outer function [shadowFunction] murasaki/src/dinkymath.h:131:3: note: Shadowed declaration murasaki/src/sequence.cc:3296:10: note: Shadow variable murasaki/src/sequence.cc:3339:19: style: Local variable 'offset' shadows outer function [shadowFunction] murasaki/src/sequence.h:466:10: note: Shadowed declaration murasaki/src/sequence.cc:3339:19: note: Shadow variable murasaki/src/sequence.cc:1858:45: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation] murasaki/src/cryptohasher.h:11:41: performance: Function parameter 'words' should be passed by const reference. [passedByValue] murasaki/src/sequence.cc:123:37: performance: Function parameter 'seqs' should be passed by const reference. [passedByValue] murasaki/src/sequence.cc:596:25: performance: Function parameter 's' should be passed by const reference. [passedByValue] murasaki/src/sequence.cc:2818:37: performance: Function parameter 'delim' should be passed by const reference. [passedByValue] murasaki/src/sequence.cc:3403:29: performance: Function parameter 'name' should be passed by const reference. [passedByValue] murasaki/src/sequence.cc:769:49: style: Parameter 'target' can be declared as reference to const [constParameterReference] murasaki/src/sequence.cc:769:86: style: Parameter 'patt' can be declared as reference to const [constParameterReference] murasaki/src/sequence.cc:2664:32: style: Parameter 'a' can be declared as reference to const [constParameterReference] murasaki/src/sequence.cc:854:24: style: Variable 'region' can be declared as pointer to const [constVariablePointer] murasaki/src/sequence.cc:863:24: style: Variable 'region' can be declared as pointer to const [constVariablePointer] murasaki/src/sequence.cc:2679:16: style: Variable 'as' can be declared as pointer to const [constVariablePointer] murasaki/src/sequence.cc:2679:31: style: Variable 'bs' can be declared as pointer to const [constVariablePointer] murasaki/src/sequence.cc:2679:46: style: Variable 'pat' can be declared as pointer to const [constVariablePointer] murasaki/src/sequence.cc:3403:48: style: Parameter 'pat' can be declared as pointer to const [constParameterPointer] murasaki/src/sequence.cc:3504:49: style: Parameter 's' can be declared as pointer to const [constParameterPointer] murasaki/src/sequence.cc:1479:14: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] murasaki/src/sequence.cc:1572:7: style: Consider using std::count_if algorithm instead of a raw loop. [useStlAlgorithm] murasaki/src/sequence.cc:1600:13: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] murasaki/src/sequence.cc:1975:5: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] murasaki/src/sequence.cc:3363:8: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] murasaki/src/sequence.cc:1027:12: warning:inconclusive: Array index -1 is out of bounds. [negativeContainerIndex] murasaki/src/sequence.cc:1024:16: note: Assignment 'i=0', assigned value is 0 murasaki/src/sequence.cc:1026:25: note: Assignment 'inpi=reverse?(_length-i-1):i', assigned value is -1 murasaki/src/sequence.cc:1027:12: note: Negative array index murasaki/src/sequence.cc:853:29: style: Variable 'target' is assigned a value that is never used. [unreadVariable] murasaki/src/sequence.cc:862:29: style: Variable 'target' is assigned a value that is never used. [unreadVariable] murasaki/src/sequence.cc:1644:18: style: Variable 'improved' is assigned a value that is never used. [unreadVariable] murasaki/src/sequence.cc:2015:12: style: Unused variable: l [unusedVariable] murasaki/src/sequence.cc:3330:18: style: Variable 'shortest' is assigned a value that is never used. [unreadVariable] murasaki/src/sequence.cc:3334:15: style: Variable 'shortest' is assigned a value that is never used. [unreadVariable] murasaki/src/sequence.cc:1410:64: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:1435:60: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:1588:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:1599:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:1738:3: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:1739:78: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:1772:3: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:1773:82: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:1813:60: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:1824:24: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:1997:75: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:2073:4: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:2108:19: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:2140:24: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:2161:22: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:2229:7: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:2234:71: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:2276:7: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:2594:74: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:3096:36: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:3115:36: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:3142:24: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:3158:24: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:3171:24: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:3186:24: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:3206:2: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:3207:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:3230:24: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:3263:21: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:3266:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:3308:70: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:3318:70: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:3354:73: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:3397:73: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:3499:7: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:3499:41: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/sequence.cc:3499:48: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] murasaki/src/testeco.cc:43:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] murasaki/src/testeco.cc:72:22: style: Condition 'entry==check' is always false [knownConditionTrueFalse] murasaki/src/testeco.cc:94:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak] murasaki/src/testeco.cc:45:14: style: Local variable 'seqs' shadows outer variable [shadowVariable] murasaki/src/murasaki.h:46:26: note: Shadowed declaration murasaki/src/testeco.cc:45:14: note: Shadow variable murasaki/src/testeco.cc:52:14: style: Local variable 'repeats' shadows outer variable [shadowVariable] murasaki/src/murasaki.h:42:19: note: Shadowed declaration murasaki/src/testeco.cc:52:14: note: Shadow variable murasaki/src/testeco.cc:112:10: warning: Either the condition 'i>=0' is redundant, otherwise there is negative array index -1. [negativeContainerIndex] murasaki/src/testeco.cc:108:13: note: Assuming that condition 'i>=0' is not redundant murasaki/src/testeco.cc:112:10: note: Negative array index murasaki/src/timing.cc:118:10: style: The scope of the variable 'str' can be reduced. [variableScope] murasaki/src/timing.cc:75:40: style:inconclusive: Function 'operator-=' argument 1 names different: declaration 'b' definition 'a'. [funcArgNamesDifferent] murasaki/src/timing.h:54:35: note: Function 'operator-=' argument 1 names different: declaration 'b' definition 'a'. murasaki/src/timing.cc:75:40: note: Function 'operator-=' argument 1 names different: declaration 'b' definition 'a'. murasaki/src/timing.cc:112:22: style:inconclusive: Function 'elapsed' argument 1 names different: declaration 'a' definition 'start'. [funcArgNamesDifferent] murasaki/src/timing.h:63:22: note: Function 'elapsed' argument 1 names different: declaration 'a' definition 'start'. murasaki/src/timing.cc:112:22: note: Function 'elapsed' argument 1 names different: declaration 'a' definition 'start'. murasaki/src/timing.cc:112:34: style:inconclusive: Function 'elapsed' argument 2 names different: declaration 'b' definition 'stop'. [funcArgNamesDifferent] murasaki/src/timing.h:63:30: note: Function 'elapsed' argument 2 names different: declaration 'b' definition 'stop'. murasaki/src/timing.cc:112:34: note: Function 'elapsed' argument 2 names different: declaration 'b' definition 'stop'. murasaki/src/wordsize.cc:6:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] diff: head murasaki/src/alignments.cc:121:28: style:inconclusive: Function 'checkSeqs' argument 1 names different: declaration '' definition 'alignfile'. [funcArgNamesDifferentUnnamed] head murasaki/src/alignments.cc:272:40: style:inconclusive: Function 'mergeAdd' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] head murasaki/src/alignments.cc:303:32: style:inconclusive: Function 'remove' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] head murasaki/src/alignments.cc:403:36: style:inconclusive: Function 'RegionSet' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] head murasaki/src/alignments.cc:86:28: style:inconclusive: Function 'writeSeqs' argument 1 names different: declaration '' definition 'alignfile'. [funcArgNamesDifferentUnnamed] 2.20.0 murasaki/src/alignments.h:239:42: performance: Function parameter 'parts' should be passed by const reference. [passedByValue] head murasaki/src/arrayhash.cc:70:64: style:inconclusive: Function 'pickup' argument 2 names different: declaration '' definition 'range'. [funcArgNamesDifferentUnnamed] head murasaki/src/cgr.cc:108:21: style:inconclusive: Function 'Cgr' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] head murasaki/src/cgr.cc:108:28: style:inconclusive: Function 'Cgr' argument 2 names different: declaration '' definition 'dohalve'. [funcArgNamesDifferentUnnamed] head murasaki/src/cgr.cc:121:27: style:inconclusive: Function 'Cgr' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] head murasaki/src/cgr.cc:139:22: style:inconclusive: Function 'merge' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] head murasaki/src/cgr.cc:168:28: style:inconclusive: Function 'halve' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] head murasaki/src/cgr.cc:179:26: style:inconclusive: Function 'operator[]' argument 1 names different: declaration '' definition 'row'. [funcArgNamesDifferentUnnamed] head murasaki/src/cgr.cc:225:34: style:inconclusive: Function 'operator[]' argument 1 names different: declaration '' definition 'str'. [funcArgNamesDifferentUnnamed] head murasaki/src/cgr.cc:229:36: style:inconclusive: Function 'operator[]' argument 1 names different: declaration '' definition 'str'. [funcArgNamesDifferentUnnamed] head murasaki/src/cgr.cc:405:29: style:inconclusive: Function 'loadCgr' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] head murasaki/src/cgr.cc:97:21: style:inconclusive: Function 'Cgr' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] head murasaki/src/dinkymath.cc:278:22: performance: Function parameter 'filename' should be passed by const reference. [passedByValue] head murasaki/src/dinkymath.cc:278:38: performance: Function parameter 'content' should be passed by const reference. [passedByValue] head murasaki/src/dinkymath.cc:299:23: style:inconclusive: Function 'percent' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] head murasaki/src/dinkymath.cc:299:32: style:inconclusive: Function 'percent' argument 2 names different: declaration '' definition 'b'. [funcArgNamesDifferentUnnamed] head murasaki/src/dinkymath.cc:68:72: style:inconclusive: Function 'writeOutVector' argument 4 names different: declaration '' definition 'from'. [funcArgNamesDifferentUnnamed] head murasaki/src/dinkymath.cc:68:81: style:inconclusive: Function 'writeOutVector' argument 5 names different: declaration '' definition 'to'. [funcArgNamesDifferentUnnamed] head murasaki/src/dinkymath.cc:78:20: style:inconclusive: Function 'dstring' argument 1 names different: declaration '' definition 'i'. [funcArgNamesDifferentUnnamed] head murasaki/src/dinkymath.cc:84:21: style:inconclusive: Function 'dstring' argument 1 names different: declaration '' definition 'i'. [funcArgNamesDifferentUnnamed] head murasaki/src/dinkymath.cc:90:22: style:inconclusive: Function 'fstring' argument 1 names different: declaration '' definition 'f'. [funcArgNamesDifferentUnnamed] head murasaki/src/ecolist.cc:159:120: style:inconclusive: Function 'init' argument 6 names different: declaration '' definition 'frugal'. [funcArgNamesDifferentUnnamed] head murasaki/src/ecolist.cc:289:71: style:inconclusive: Function 'EcolistIterator' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] head murasaki/src/ecolist.cc:316:74: style:inconclusive: Function 'operator++' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] head murasaki/src/ecolist.cc:328:56: style:inconclusive: Function 'operator!=' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] head murasaki/src/ecolist.cc:332:56: style:inconclusive: Function 'operator==' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] head murasaki/src/ecolist.cc:375:100: style:inconclusive: Function 'operator++' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] head murasaki/src/ecolist.cc:399:100: style:inconclusive: Function 'operator--' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] head murasaki/src/ecolist.cc:411:69: style:inconclusive: Function 'operator!=' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] head murasaki/src/ecolist.cc:415:69: style:inconclusive: Function 'operator==' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] 2.20.0 murasaki/src/murasaki.cc:891:37: style: Condition '(progress=ticker.tick(p-1))>=0' is always true [knownConditionTrueFalse] 2.20.0 murasaki/src/seqread.h:119:47: performance: Function parameter 'filename' should be passed by const reference. [passedByValue] 2.20.0 murasaki/src/seqread.h:120:35: performance: Function parameter 'filename' should be passed by const reference. [passedByValue] 2.20.0 murasaki/src/seqread.h:68:59: performance: Function parameter 'filename' should be passed by const reference. [passedByValue] 2.20.0 murasaki/src/seqread.h:82:47: performance: Function parameter 'filename' should be passed by const reference. [passedByValue] head murasaki/src/sequence.cc:1938:30: style:inconclusive: Function 'Location' argument 1 names different: declaration '' definition 's'. [funcArgNamesDifferentUnnamed] head murasaki/src/sequence.cc:1938:39: style:inconclusive: Function 'Location' argument 2 names different: declaration '' definition 'p'. [funcArgNamesDifferentUnnamed] head murasaki/src/sequence.cc:1941:27: style:inconclusive: Function 'Location' argument 1 names different: declaration '' definition 's'. [funcArgNamesDifferentUnnamed] head murasaki/src/sequence.cc:1941:36: style:inconclusive: Function 'Location' argument 2 names different: declaration '' definition 'p'. [funcArgNamesDifferentUnnamed] head murasaki/src/sequence.cc:2664:32: style:inconclusive: Function 'add' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] head murasaki/src/sequence.cc:298:27: style:inconclusive: Function 'Sequence' argument 1 names different: declaration '' definition '_filename'. [funcArgNamesDifferentUnnamed] head murasaki/src/sequence.cc:3532:48: style:inconclusive: Function 'BaseIterator' argument 1 names different: declaration '' definition 'a'. [funcArgNamesDifferentUnnamed] DONE