2024-04-21 02:03
ftp://ftp.de.debian.org/debian/pool/main/p/phyx/phyx_1.3.1+ds.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=openmp  --showtime=top5 --check-library --inconclusive --enable=style,information --inline-suppr --disable=missingInclude --suppress=unmatchedSuppression --template=daca2 --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning -D__GNUC__ --platform=unix64 -j1
platform: Linux-6.6.15-amd64-x86_64-with-glibc2.37
python: 3.11.8
client-version: 1.3.49
compiler: g++ (Debian 13.2.0-13) 13.2.0
cppcheck: head 2.13.0
head-info: fb15ac6 (2024-04-20 19:16:41 +0200)
count: 610 386
elapsed-time: 20.4 100.9
head-timing-info:
 Tokenizer::simplifyTokens1::ValueFlow: 16.5327s (avg. 0.147614s - 112 result(s))
 valueFlowCondition(SimpleConditionHandler{}, tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 5.40615s (avg. 0.018264s - 296 result(s))
 valueFlowAfterAssign(tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 5.22276s (avg. 0.0176445s - 296 result(s))
 valueFlowCondition(SymbolicConditionHandler{}, tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 2.05208s (avg. 0.00693272s - 296 result(s))
 valueFlowContainerSize(tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 0.992165s (avg. 0.00335191s - 296 result(s))
 Overall time: 19.572s

old-timing-info:
 Tokenizer::simplifyTokens1::ValueFlow: 96.8669s (avg. 0.864883s - 112 result(s))
 valueFlowCondition(SimpleConditionHandler{}, tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 58.6705s (avg. 0.198211s - 296 result(s))
 valueFlowAfterAssign(tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 16.9432s (avg. 0.0572406s - 296 result(s))
 valueFlowLifetime(tokenlist, errorLogger, settings): 13.4166s (avg. 0.0328838s - 408 result(s))
 valueFlowSymbolic(tokenlist, symboldatabase, settings): 4.83141s (avg. 0.0431376s - 112 result(s))
 Overall time: 99.7273s

head results:
phyx-1.3.1/src/utils.h:143:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/aa2cdn.cpp:46:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/aa2cdn.cpp:122:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/aa2cdn.cpp:152:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/aa2cdn.cpp:12:10: style:inconclusive: Technically the member function 'SequenceIDListCompare::operator()' can be const. [functionConst]
phyx-1.3.1/src/superdouble.h:44:5: style: Class 'Superdouble' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
phyx-1.3.1/src/aa2cdn.h:28:27: performance: Function 'get_codon_alignment()' should return member 'codon_seqs_' by const reference. [returnByReference]
phyx-1.3.1/src/aa2cdn.cpp:87:17: style: The scope of the variable 'nucseq' can be reduced. [variableScope]
phyx-1.3.1/src/aa2cdn.cpp:101:17: style: The scope of the variable 'aaseq' can be reduced. [variableScope]
phyx-1.3.1/src/aa2cdn.cpp:102:17: style: The scope of the variable 'nucseq' can be reduced. [variableScope]
phyx-1.3.1/src/aa2cdn.cpp:103:17: style: The scope of the variable 'codonseq' can be reduced. [variableScope]
phyx-1.3.1/src/aa2cdn.cpp:48:21: style: Variable 'd' can be declared as reference to const [constVariableReference]
phyx-1.3.1/src/aa2cdn.cpp:151:17: style: Variable 'codon_seq' can be declared as reference to const [constVariableReference]
phyx-1.3.1/src/bd_fit.cpp:62:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/bd_fit.cpp:113:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_PRAXIS [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/bd_fit.cpp:189:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/bd_fit.h:41:10: style:inconclusive: Technically the member function 'BDFit::get_aic' can be const. [functionConst]
phyx-1.3.1/src/bd_fit.cpp:177:13: note: Technically the member function 'BDFit::get_aic' can be const.
phyx-1.3.1/src/bd_fit.h:41:10: note: Technically the member function 'BDFit::get_aic' can be const.
phyx-1.3.1/src/vector_node_object.h:15:5: style: Class 'VectorNodeObject < Superdouble >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
phyx-1.3.1/src/vector_node_object.h:21:14: style: The destructor '~VectorNodeObject < Superdouble >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
phyx-1.3.1/src/node_object.h:10:14: note: Virtual destructor in base class
phyx-1.3.1/src/vector_node_object.h:21:14: note: Destructor in derived class
phyx-1.3.1/src/vector_node_object.h:24:27: style: The function 'clone' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
phyx-1.3.1/src/node_object.h:13:26: note: Virtual function in base class
phyx-1.3.1/src/vector_node_object.h:24:27: note: Function in derived class
phyx-1.3.1/src/bd_fit.cpp:150:77: style: Parameter 'grad' can be declared as reference to const. However it seems that 'nlopt_bd_log_lik' is a callback function, if 'grad' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
phyx-1.3.1/src/bd_fit.cpp:117:27: note: You might need to cast the function pointer here
phyx-1.3.1/src/bd_fit.cpp:150:77: note: Parameter 'grad' can be declared as reference to const
phyx-1.3.1/src/bd_fit.cpp:155:10: style: Variable 'd' can be declared as pointer to const [constVariablePointer]
phyx-1.3.1/src/bd_fit.cpp:166:17: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/bd_sim.cpp:78:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/bd_sim.cpp:105:24: style: Variable 'totallength' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/bd_sim.cpp:114:21: style: Variable 'totallength' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/vector_node_object.h:24:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/vector_node_object.h:24:27: warning: The class 'VectorNodeObject' defines member function with name 'clone' also defined in its parent class 'NodeObject'. [duplInheritedMember]
phyx-1.3.1/src/node_object.h:13:26: note: Parent function 'NodeObject::clone'
phyx-1.3.1/src/vector_node_object.h:24:27: note: Derived function 'VectorNodeObject::clone'
phyx-1.3.1/src/vector_node_object.h:15:5: style: Class 'VectorNodeObject' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
phyx-1.3.1/src/vector_node_object.h:21:14: style: The destructor '~VectorNodeObject' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
phyx-1.3.1/src/node_object.h:10:14: note: Virtual destructor in base class
phyx-1.3.1/src/vector_node_object.h:21:14: note: Destructor in derived class
phyx-1.3.1/src/branch_segment.h:31:22: performance: Function 'getFossilAreas()' should return member 'fossilareaindices' by const reference. [returnByReference]
phyx-1.3.1/src/clean_seq.cpp:24:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/clean_seq.cpp:45:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/clean_seq.cpp:76:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/clean_seq.cpp:91:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/clean_seq.cpp:119:86: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/clean_seq.cpp:228:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/clean_seq.h:49:27: performance: Function 'get_cleaned_seqs()' should return member 'cleaned_seqs_' by const reference. [returnByReference]
phyx-1.3.1/src/clean_seq.cpp:195:17: style: The scope of the variable 'name' can be reduced. [variableScope]
phyx-1.3.1/src/comp_test.cpp:29:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/comp_test.cpp:72:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/comp_test.cpp:102:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/comp_test.cpp:129:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/comp_test.cpp:178:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/comp_test.h:45:12: performance:inconclusive: Technically the member function 'CompTest::get_cell_value' can be static (but you may consider moving to unnamed namespace). [functionStatic]
phyx-1.3.1/src/comp_test.cpp:197:18: note: Technically the member function 'CompTest::get_cell_value' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/comp_test.h:45:12: note: Technically the member function 'CompTest::get_cell_value' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/comp_test.h:48:12: performance:inconclusive: Technically the member function 'CompTest::lower_incomplete_gamma_function' can be static (but you may consider moving to unnamed namespace). [functionStatic]
phyx-1.3.1/src/comp_test.cpp:206:18: note: Technically the member function 'CompTest::lower_incomplete_gamma_function' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/comp_test.h:48:12: note: Technically the member function 'CompTest::lower_incomplete_gamma_function' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/comp_test.cpp:81:17: style: The scope of the variable 'seq' can be reduced. [variableScope]
phyx-1.3.1/src/comp_test.cpp:83:22: style: Local variable 'sum' shadows outer function [shadowFunction]
phyx-1.3.1/src/utils.h:61:8: note: Shadowed declaration
phyx-1.3.1/src/comp_test.cpp:83:22: note: Shadow variable
phyx-1.3.1/src/comp_test.cpp:214:12: style: Local variable 'sum' shadows outer function [shadowFunction]
phyx-1.3.1/src/utils.h:61:8: note: Shadowed declaration
phyx-1.3.1/src/comp_test.cpp:214:12: note: Shadow variable
phyx-1.3.1/src/comp_test.cpp:161:21: style: Variable 'observed' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/comp_test.cpp:162:21: style: Variable 'expected' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/comp_test.cpp:163:18: style: Variable 'cellv' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/concat.cpp:40:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/concat.cpp:138:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/concat.h:21:10: performance:inconclusive: Technically the member function 'SequenceConcatenater::delete_sequence' can be static (but you may consider moving to unnamed namespace). [functionStatic]
phyx-1.3.1/src/concat.cpp:100:28: note: Technically the member function 'SequenceConcatenater::delete_sequence' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/concat.h:21:10: note: Technically the member function 'SequenceConcatenater::delete_sequence' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/concat.cpp:120:22: style: Parameter 'partfile' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/cont_models.cpp:114:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/cont_models.cpp:138:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/cont_models.cpp:18:23: style:inconclusive: Function 'calc_vcv' argument 1 names different: declaration 'tr' definition 'tree'. [funcArgNamesDifferent]
phyx-1.3.1/src/cont_models.h:20:22: note: Function 'calc_vcv' argument 1 names different: declaration 'tr' definition 'tree'.
phyx-1.3.1/src/cont_models.cpp:18:23: note: Function 'calc_vcv' argument 1 names different: declaration 'tr' definition 'tree'.
phyx-1.3.1/src/cont_models.cpp:109:39: style: Parameter 'x' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/cont_models.cpp:109:50: style: Parameter 'mu' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/cont_models.cpp:131:43: style: Parameter 'x' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/cont_models.cpp:131:54: style: Parameter 'mu' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/cont_models.cpp:180:11: style: Variable 'count' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/cont_models.cpp:183:15: style: Variable 'count' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/edlib.cpp:52:5: warning: Member variable 'Block::P' is not initialized in the constructor. [uninitMemberVar]
phyx-1.3.1/src/edlib.cpp:52:5: warning: Member variable 'Block::M' is not initialized in the constructor. [uninitMemberVar]
phyx-1.3.1/src/edlib.cpp:52:5: warning: Member variable 'Block::score' is not initialized in the constructor. [uninitMemberVar]
phyx-1.3.1/src/edlib.cpp:30:9: warning: Struct 'AlignmentData' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
phyx-1.3.1/src/edlib.cpp:30:9: warning: Struct 'AlignmentData' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
phyx-1.3.1/src/edlib.cpp:111:47: style:inconclusive: Function 'edlibAlign' argument 3 names different: declaration 'target' definition 'targetOriginal'. [funcArgNamesDifferent]
phyx-1.3.1/src/edlib.h:191:45: note: Function 'edlibAlign' argument 3 names different: declaration 'target' definition 'targetOriginal'.
phyx-1.3.1/src/edlib.cpp:111:47: note: Function 'edlibAlign' argument 3 names different: declaration 'target' definition 'targetOriginal'.
phyx-1.3.1/src/edlib.cpp:391:18: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
phyx-1.3.1/src/edlib.cpp:779:18: style: Variable 'hout' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/log.cpp:8:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/log.cpp:10:16: style: Variable 's' can be declared as pointer to const [constVariableReference]
phyx-1.3.1/src/log_manip.cpp:76:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable right [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/log_manip.cpp:222:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/log_manip.cpp:324:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/log_manip.cpp:393:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/log_manip.cpp:428:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/log_manip.cpp:466:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/log_manip.cpp:536:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/log_manip.cpp:596:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/log_manip.cpp:670:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/log_manip.cpp:755:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/log_manip.h:51:10: performance:inconclusive: Technically the member function 'LogManipulator::calculate_summary_statistics' can be static (but you may consider moving to unnamed namespace). [functionStatic]
phyx-1.3.1/src/log_manip.cpp:114:22: note: Technically the member function 'LogManipulator::calculate_summary_statistics' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/log_manip.h:51:10: note: Technically the member function 'LogManipulator::calculate_summary_statistics' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/log_manip.cpp:282:30: style: Local variable 'sample' shadows outer function [shadowFunction]
phyx-1.3.1/src/log_manip.h:63:10: note: Shadowed declaration
phyx-1.3.1/src/log_manip.cpp:282:30: note: Shadow variable
phyx-1.3.1/src/log_manip.cpp:737:57: style: Parameter 'sample' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/log_manip.cpp:747:61: style: Parameter 'sample' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/log_manip.cpp:748:14: style: Parameter 'sample_num' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/log_manip.cpp:143:17: style: Variable 'del1' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/log_manip.cpp:144:17: style: Variable 'del2' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/main_aa2cdn.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_aa2cdn.cpp:84:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_bd_fit.cpp:24:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_bd_fit.cpp:84:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_bd_sim.cpp:23:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_bd_sim.cpp:97:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/string_node_object.h:19:14: style: The destructor '~StringNodeObject' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
phyx-1.3.1/src/node_object.h:10:14: note: Virtual destructor in base class
phyx-1.3.1/src/string_node_object.h:19:14: note: Destructor in derived class
phyx-1.3.1/src/string_node_object.h:22:24: style: The function 'clone' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
phyx-1.3.1/src/node_object.h:13:26: note: Virtual function in base class
phyx-1.3.1/src/string_node_object.h:22:24: note: Function in derived class
phyx-1.3.1/src/main_boot.cpp:25:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_boot.cpp:88:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_bp.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_bp.cpp:100:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_bp.cpp:324:23: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/main_bp.cpp:336:24: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/main_bp.cpp:443:27: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/main_bp.cpp:475:32: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/main_bp.cpp:478:31: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/main_bp.cpp:534:25: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/main_bp.cpp:540:31: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/main_bp.cpp:557:38: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/main_bp.cpp:566:47: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/main_bp.cpp:605:25: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/main_bp.cpp:611:31: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/main_bp.cpp:643:23: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/main_cat.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_cat.cpp:94:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_clsq.cpp:22:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_clsq.cpp:101:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_cltr.cpp:23:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_cltr.cpp:94:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_colt.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_colt.cpp:86:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_comp.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_comp.cpp:72:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_consq.cpp:20:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_consq.cpp:74:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_contrates.cpp:26:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_contrates.cpp:87:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_fqfilt.cpp:18:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_fqfilt.cpp:73:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_log.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_log.cpp:116:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_lssq.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_lssq.cpp:102:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_lstr.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_lstr.cpp:101:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_mono.cpp:23:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_mono.cpp:92:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_mrca.cpp:23:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_mrca.cpp:81:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_mrca_cut.cpp:23:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_mrca_cut.cpp:84:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_mrca_name.cpp:28:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_mrca_name.cpp:92:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_nj.cpp:28:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_nj.cpp:93:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_nni.cpp:22:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_nni.cpp:79:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_nw.cpp:27:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_nw.cpp:98:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_nw.cpp:86:9: style: The scope of the variable 'num_threads' can be reduced. [variableScope]
phyx-1.3.1/src/main_nw.cpp:155:17: style: Unused variable: retstring [unusedVariable]
phyx-1.3.1/src/main_poly.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_poly.cpp:79:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_recode.cpp:25:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_recode.cpp:92:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_revcomp.cpp:25:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_revcomp.cpp:132:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_revcomp.cpp:118:12: style: The scope of the variable 'sguess_samplenum' can be reduced. [variableScope]
phyx-1.3.1/src/main_rls.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_rls.cpp:95:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_rls.cpp:176:22: style: Variable 'success' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/main_rls.cpp:290:38: style: Variable 'terp' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/main_rls.cpp:307:38: style: Variable 'terp' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/main_rls.cpp:315:38: style: Variable 'terp' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/main_rls.cpp:322:38: style: Variable 'terp' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/main_rlt.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_rlt.cpp:95:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_rmk.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_rmk.cpp:75:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_rms.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_rms.cpp:95:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_rms.cpp:83:17: style: Unused variable: rmf [unusedVariable]
phyx-1.3.1/src/main_rmt.cpp:22:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_rmt.cpp:96:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_rmt.cpp:202:28: style: Variable 'num_names' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/main_rr.cpp:23:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_rr.cpp:96:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_rr.cpp:220:70: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/main_rr.cpp:258:70: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/main_s2fa.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_s2fa.cpp:75:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_s2nex.cpp:20:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_s2nex.cpp:75:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_s2phy.cpp:20:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_s2phy.cpp:75:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_seqgen.cpp:20:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_seqgen.cpp:155:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_ssort.cpp:22:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_ssort.cpp:103:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_ssort.cpp:61:10: style:inconclusive: Technically the member function 'SequenceIDListCompare::operator()' can be const. [functionConst]
phyx-1.3.1/src/main_ssort.cpp:67:10: style:inconclusive: Technically the member function 'SequenceRevIDListCompare::operator()' can be const. [functionConst]
phyx-1.3.1/src/main_ssort.cpp:73:10: style:inconclusive: Technically the member function 'SequenceLengthListCompare::operator()' can be const. [functionConst]
phyx-1.3.1/src/main_ssort.cpp:79:10: style:inconclusive: Technically the member function 'SequenceRevLengthListCompare::operator()' can be const. [functionConst]
phyx-1.3.1/src/main_ssplit.cpp:27:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_ssplit.cpp:33:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_ssplit.cpp:90:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_ssplit.cpp:21:40: style: Parameter 'seq' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/main_sstat.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_sstat.cpp:75:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_strec.cpp:29:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_strec.cpp:98:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_strec.cpp:148:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_strec.cpp:863:17: style: The if condition is the same as the previous if condition [duplicateCondition]
phyx-1.3.1/src/main_strec.cpp:860:17: note: First condition
phyx-1.3.1/src/main_strec.cpp:863:17: note: Second condition
phyx-1.3.1/src/main_strec.cpp:244:17: style: The scope of the variable 'outfile_stochnum_any' can be reduced. [variableScope]
phyx-1.3.1/src/main_strec.cpp:677:42: style: The scope of the variable 'lhoods' can be reduced. [variableScope]
phyx-1.3.1/src/main_strec.cpp:602:30: style: Local variable 'i' shadows outer variable [shadowVariable]
phyx-1.3.1/src/main_strec.cpp:533:27: note: Shadowed declaration
phyx-1.3.1/src/main_strec.cpp:602:30: note: Shadow variable
phyx-1.3.1/src/main_strec.cpp:84:53: performance: Function parameter 'runseqs' should be passed by const reference. [passedByValue]
phyx-1.3.1/src/main_strec.cpp:130:12: style: Variable 'outanc' can be declared as pointer to const [constVariablePointer]
phyx-1.3.1/src/main_strec.cpp:131:12: style: Variable 'outnum' can be declared as pointer to const [constVariablePointer]
phyx-1.3.1/src/main_strec.cpp:132:12: style: Variable 'outnumany' can be declared as pointer to const [constVariablePointer]
phyx-1.3.1/src/main_strec.cpp:133:12: style: Variable 'outtime' can be declared as pointer to const [constVariablePointer]
phyx-1.3.1/src/main_sw.cpp:26:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_sw.cpp:97:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_sw.cpp:85:9: style: The scope of the variable 'num_threads' can be reduced. [variableScope]
phyx-1.3.1/src/main_sw.cpp:155:17: style: Unused variable: retstring [unusedVariable]
phyx-1.3.1/src/main_t2new.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_t2new.cpp:74:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_t2nex.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_t2nex.cpp:74:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_tcol.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_tcol.cpp:86:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_tcomb.cpp:29:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_tcomb.cpp:87:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_tgen.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_tgen.cpp:90:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_tlate.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_tlate.cpp:81:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_trt.cpp:22:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_trt.cpp:90:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_tscale.cpp:20:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_tscale.cpp:82:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_upgma.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_upgma.cpp:73:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_vcf2fa.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/main_vcf2fa.cpp:76:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/nj.cpp:25:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/nj.h:27:10: performance:inconclusive: Technically the member function 'NJOI::FetchLengths' can be static (but you may consider moving to unnamed namespace). [functionStatic]
phyx-1.3.1/src/nj.cpp:87:12: note: Technically the member function 'NJOI::FetchLengths' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/nj.h:27:10: note: Technically the member function 'NJOI::FetchLengths' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/nj.h:33:10: performance:inconclusive: Technically the member function 'NJOI::Choose_Smallest' can be static (but you may consider moving to unnamed namespace). [functionStatic]
phyx-1.3.1/src/nj.cpp:159:12: note: Technically the member function 'NJOI::Choose_Smallest' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/nj.h:33:10: note: Technically the member function 'NJOI::Choose_Smallest' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/nj.h:42:17: performance: Function 'get_newick()' should return member 'newick_string_' by const reference. [returnByReference]
phyx-1.3.1/src/nj.cpp:212:17: style: The scope of the variable 'fasta' can be reduced. [variableScope]
phyx-1.3.1/src/nj.cpp:212:24: style: The scope of the variable 'SeqName' can be reduced. [variableScope]
phyx-1.3.1/src/nj.cpp:13:39: style: Parameter 'threads' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/nj.cpp:88:41: style: Parameter 'LengthMatrix' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/nj.cpp:102:89: style: Parameter 'mini1' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/nj.cpp:103:20: style: Parameter 'mini2' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/nj.cpp:103:35: style: Parameter 'brlength1' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/nj.cpp:103:54: style: Parameter 'brlength2' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/nj.cpp:180:83: style: Parameter 'NumbKeys' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/nj.cpp:208:91: style: Parameter 'sequences' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/nj.cpp:112:19: style: Variable 'ColRow' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/node.h:41:10: style:inconclusive: Technically the member function 'Node::isExternal' can be const. [functionConst]
phyx-1.3.1/src/node.cpp:52:12: note: Technically the member function 'Node::isExternal' can be const.
phyx-1.3.1/src/node.h:41:10: note: Technically the member function 'Node::isExternal' can be const.
phyx-1.3.1/src/node.h:42:10: style:inconclusive: Technically the member function 'Node::isInternal' can be const. [functionConst]
phyx-1.3.1/src/node.cpp:61:12: note: Technically the member function 'Node::isInternal' can be const.
phyx-1.3.1/src/node.h:42:10: note: Technically the member function 'Node::isInternal' can be const.
phyx-1.3.1/src/node.h:43:10: style:inconclusive: Technically the member function 'Node::isRoot' can be const. [functionConst]
phyx-1.3.1/src/node.cpp:70:12: note: Technically the member function 'Node::isRoot' can be const.
phyx-1.3.1/src/node.h:43:10: note: Technically the member function 'Node::isRoot' can be const.
phyx-1.3.1/src/node.h:45:10: style:inconclusive: Technically the member function 'Node::hasParent' can be const. [functionConst]
phyx-1.3.1/src/node.cpp:92:12: note: Technically the member function 'Node::hasParent' can be const.
phyx-1.3.1/src/node.h:45:10: note: Technically the member function 'Node::hasParent' can be const.
phyx-1.3.1/src/node.h:70:18: style:inconclusive: Technically the member function 'Node::getChildCount' can be const. [functionConst]
phyx-1.3.1/src/node.cpp:375:20: note: Technically the member function 'Node::getChildCount' can be const.
phyx-1.3.1/src/node.h:70:18: note: Technically the member function 'Node::getChildCount' can be const.
phyx-1.3.1/src/node.h:40:24: performance: Function 'getChildren()' should return member 'children_' by const reference. [returnByReference]
phyx-1.3.1/src/node.h:61:17: performance: Function 'getName()' should return member 'name_' by const reference. [returnByReference]
phyx-1.3.1/src/node.h:62:17: performance: Function 'getComment()' should return member 'comment_' by const reference. [returnByReference]
phyx-1.3.1/src/node.cpp:158:28: style: Parameter 'test' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/node.cpp:380:62: style: Parameter 'obj' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/node.cpp:388:82: style: Parameter 'obj' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/node.cpp:160:17: style: Variable 'chi' can be declared as pointer to const [constVariableReference]
phyx-1.3.1/src/node.cpp:161:27: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/optimize_cont_models_nlopt.cpp:29:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/optimize_cont_models_nlopt.cpp:108:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_SBPLX [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/optimize_cont_models_nlopt.cpp:142:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_SBPLX [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/optimize_cont_models_nlopt.cpp:173:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_SBPLX [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/optimize_cont_models_nlopt.cpp:30:26: style: C-style pointer casting [cstyleCast]
phyx-1.3.1/src/optimize_cont_models_nlopt.cpp:44:26: style: C-style pointer casting [cstyleCast]
phyx-1.3.1/src/optimize_cont_models_nlopt.cpp:61:26: style: C-style pointer casting [cstyleCast]
phyx-1.3.1/src/optimize_cont_models_nlopt.cpp:86:31: style: C-style pointer casting [cstyleCast]
phyx-1.3.1/src/optimize_cont_models_nlopt.cpp:99:60: style: Parameter '_x' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/optimize_cont_models_nlopt.cpp:99:69: style: Parameter '_vcv' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/optimize_cont_models_nlopt.cpp:134:63: style: Parameter '_x' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/optimize_cont_models_nlopt.cpp:134:72: style: Parameter '_vcv' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/optimize_state_reconstructor_nlopt.cpp:49:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_NELDERMEAD [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/optimize_state_reconstructor_periods_nlopt.cpp:23:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n_rows [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/optimize_state_reconstructor_periods_nlopt.cpp:58:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_NELDERMEAD [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/delta.cpp:164:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gsl_multimin_fminimizer_nmsimplex2rand [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/delta.h:10:12: performance:inconclusive: Technically the member function 'Delta::cdf' can be static (but you may consider moving to unnamed namespace). [functionStatic]
phyx-1.3.1/src/orphan_files/delta.cpp:101:15: note: Technically the member function 'Delta::cdf' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/orphan_files/delta.h:10:12: note: Technically the member function 'Delta::cdf' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/orphan_files/delta.h:14:12: performance:inconclusive: Technically the member function 'Delta::shift' can be static (but you may consider moving to unnamed namespace). [functionStatic]
phyx-1.3.1/src/orphan_files/delta.cpp:21:15: note: Technically the member function 'Delta::shift' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/orphan_files/delta.h:14:12: note: Technically the member function 'Delta::shift' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/orphan_files/delta.h:15:12: performance:inconclusive: Technically the member function 'Delta::bigshift' can be static (but you may consider moving to unnamed namespace). [functionStatic]
phyx-1.3.1/src/orphan_files/delta.cpp:60:15: note: Technically the member function 'Delta::bigshift' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/orphan_files/delta.h:15:12: note: Technically the member function 'Delta::bigshift' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/orphan_files/delta.h:29:5: style: Class 'OptimizeShift' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
phyx-1.3.1/src/orphan_files/delta.cpp:157:13: style: C-style pointer casting [cstyleCast]
phyx-1.3.1/src/orphan_files/delta.cpp:170:12: style: The scope of the variable 'size' can be reduced. [variableScope]
phyx-1.3.1/src/orphan_files/delta.cpp:182:14: style: Variable 'F' can be declared as pointer to const [constVariablePointer]
phyx-1.3.1/src/orphan_files/distmatrix.cpp:58:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/distmatrix.cpp:109:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/distmatrix.cpp:30:17: style: The scope of the variable 'fasta' can be reduced. [variableScope]
phyx-1.3.1/src/orphan_files/distmatrix.cpp:80:11: style: The scope of the variable 'count' can be reduced. [variableScope]
phyx-1.3.1/src/orphan_files/distmatrix.cpp:46:15: style: Local variable 'count' shadows outer variable [shadowVariable]
phyx-1.3.1/src/orphan_files/distmatrix.cpp:31:9: note: Shadowed declaration
phyx-1.3.1/src/orphan_files/distmatrix.cpp:46:15: note: Shadow variable
phyx-1.3.1/src/orphan_files/distmatrix.cpp:15:34: style: Parameter 'sequence1' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/orphan_files/distmatrix.cpp:15:58: style: Parameter 'sequence2' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/orphan_files/distmatrix.cpp:31:15: style: Variable 'count' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/orphan_files/distmatrix.cpp:46:21: style: Variable 'count' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/orphan_files/distmatrix.cpp:113:12: style: Variable 'Matrix' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/orphan_files/distmatrix.cpp:106:42: style: Unused variable: iter [unusedVariable]
phyx-1.3.1/src/orphan_files/distmatrix.cpp:35:61: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
phyx-1.3.1/src/orphan_files/distmatrix.cpp:37:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
phyx-1.3.1/src/orphan_files/distmatrix.cpp:42:61: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
phyx-1.3.1/src/orphan_files/distmatrix.cpp:48:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
phyx-1.3.1/src/orphan_files/main.cpp:23:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/main_bpseq.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/main_bpseq.cpp:69:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/main_bpseq.cpp:56:10: style: The scope of the variable 'conditional' can be reduced. [variableScope]
phyx-1.3.1/src/orphan_files/main_bpseq.cpp:331:34: style: Unused variable: matches [unusedVariable]
phyx-1.3.1/src/orphan_files/main_contbl.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/main_contbl.cpp:70:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/main_contbl.cpp:60:9: style: Variable 'analysis' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/orphan_files/main_delta.cpp:28:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/main_delta.cpp:39:20: style: Local variable 'tr' shadows outer variable [shadowVariable]
phyx-1.3.1/src/orphan_files/main_delta.cpp:25:16: note: Shadowed declaration
phyx-1.3.1/src/orphan_files/main_delta.cpp:39:20: note: Shadow variable
phyx-1.3.1/src/orphan_files/main_delta.cpp:57:27: warning: Uninitialized variable: tree [uninitvar]
phyx-1.3.1/src/orphan_files/main_delta.cpp:44:24: note: Assuming condition is false
phyx-1.3.1/src/orphan_files/main_delta.cpp:57:27: note: Uninitialized variable: tree
phyx-1.3.1/src/orphan_files/main_kaks.cpp:13:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/main_kaks.cpp:55:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/main_kaks.cpp:77:20: style: Variable 'pios' can be declared as pointer to const [constVariablePointer]
phyx-1.3.1/src/orphan_files/main_kaks.cpp:78:20: style: Variable 'poos' can be declared as pointer to const [constVariablePointer]
phyx-1.3.1/src/orphan_files/main_kaks.cpp:84:14: style: Variable 'poos' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/orphan_files/main_kaks.cpp:86:14: style: Variable 'poos' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/orphan_files/main_kaks.cpp:90:14: style: Variable 'pios' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/orphan_files/main_kaks.cpp:92:14: style: Variable 'pios' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/orphan_files/main_medusa.cpp:18:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/main_medusa.cpp:66:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/main_medusa.cpp:119:12: style: The scope of the variable 'tree' can be reduced. [variableScope]
phyx-1.3.1/src/orphan_files/main_seq_test.cpp:11:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/main_sm0.cpp:27:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/main_sm0.cpp:73:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/main_sm0.cpp:150:12: style: Condition 'ft==1' is always true [knownConditionTrueFalse]
phyx-1.3.1/src/orphan_files/main_sm0.cpp:144:12: note: Assuming that condition 'ft!=1' is not redundant
phyx-1.3.1/src/orphan_files/main_sm0.cpp:150:12: note: Condition 'ft==1' is always true
phyx-1.3.1/src/orphan_files/main_sm2a.cpp:27:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/main_sm2a.cpp:73:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/main_sm2a.cpp:148:12: style: Condition 'ft==1' is always true [knownConditionTrueFalse]
phyx-1.3.1/src/orphan_files/main_sm2a.cpp:142:12: note: Assuming that condition 'ft!=1' is not redundant
phyx-1.3.1/src/orphan_files/main_sm2a.cpp:148:12: note: Condition 'ft==1' is always true
phyx-1.3.1/src/orphan_files/main_tdist.cpp:30:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/main_tdist.cpp:83:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/main_tdist.cpp:72:17: style: The scope of the variable 'dist' can be reduced. [variableScope]
phyx-1.3.1/src/orphan_files/main_tdist.cpp:147:12: style: The scope of the variable 'tree' can be reduced. [variableScope]
phyx-1.3.1/src/orphan_files/main_test.cpp:53:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/mcmc.cpp:31:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/mcmc.cpp:85:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/mcmc.cpp:35:12: style: The scope of the variable 'newlike' can be reduced. [variableScope]
phyx-1.3.1/src/orphan_files/mcmc.cpp:89:12: style: The scope of the variable 'newlike' can be reduced. [variableScope]
phyx-1.3.1/src/orphan_files/mcmc.cpp:72:10: style: Parameter 'inq1' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/orphan_files/mcmc.cpp:35:20: style: Variable 'newlike' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/orphan_files/mcmc.cpp:89:20: style: Variable 'newlike' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/orphan_files/optimize_state_reconstructor_gsl.cpp:22:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n_rows [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/optimize_state_reconstructor_gsl.cpp:54:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gsl_multimin_fminimizer_nmsimplex2 [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/optimize_state_reconstructor_gsl.cpp:45:12: style: C-style pointer casting [cstyleCast]
phyx-1.3.1/src/orphan_files/optimize_state_reconstructor_gsl.cpp:60:12: style: The scope of the variable 'size' can be reduced. [variableScope]
phyx-1.3.1/src/orphan_files/optimize_state_reconstructor_gsl.cpp:68:23: style: Local variable 'i' shadows outer variable [shadowVariable]
phyx-1.3.1/src/orphan_files/optimize_state_reconstructor_gsl.cpp:58:22: note: Shadowed declaration
phyx-1.3.1/src/orphan_files/optimize_state_reconstructor_gsl.cpp:68:23: note: Shadow variable
phyx-1.3.1/src/orphan_files/optimize_state_reconstructor_gsl.cpp:104:23: style: Local variable 'i' shadows outer variable [shadowVariable]
phyx-1.3.1/src/orphan_files/optimize_state_reconstructor_gsl.cpp:58:22: note: Shadowed declaration
phyx-1.3.1/src/orphan_files/optimize_state_reconstructor_gsl.cpp:104:23: note: Shadow variable
phyx-1.3.1/src/orphan_files/state_reconstructor_simple.cpp:35:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/state_reconstructor_simple.cpp:61:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/orphan_files/state_reconstructor_simple.cpp:24:27: warning: Member variable 'StateReconstructorSimple::pp0' is not initialized in the constructor. [uninitMemberVar]
phyx-1.3.1/src/orphan_files/state_reconstructor_simple.cpp:24:27: warning: Member variable 'StateReconstructorSimple::pp1' is not initialized in the constructor. [uninitMemberVar]
phyx-1.3.1/src/orphan_files/state_reconstructor_simple.cpp:24:27: warning: Member variable 'StateReconstructorSimple::pp2' is not initialized in the constructor. [uninitMemberVar]
phyx-1.3.1/src/pairwise_alignment.cpp:162:16: style: Condition 'j>0' is always true [knownConditionTrueFalse]
phyx-1.3.1/src/pairwise_alignment.cpp:156:23: note: Assuming that condition 'j>0' is not redundant
phyx-1.3.1/src/pairwise_alignment.cpp:158:30: note: Assuming condition is false
phyx-1.3.1/src/pairwise_alignment.cpp:162:16: note: Condition 'j>0' is always true
phyx-1.3.1/src/pairwise_alignment.cpp:162:25: style: Condition 'i>0' is always true [knownConditionTrueFalse]
phyx-1.3.1/src/pairwise_alignment.cpp:156:14: note: Assuming that condition 'i>0' is not redundant
phyx-1.3.1/src/pairwise_alignment.cpp:158:30: note: Assuming condition is false
phyx-1.3.1/src/pairwise_alignment.cpp:162:25: note: Condition 'i>0' is always true
phyx-1.3.1/src/pairwise_alignment.cpp:166:15: style: Condition 'j>0' is always true [knownConditionTrueFalse]
phyx-1.3.1/src/pairwise_alignment.cpp:156:23: note: Assuming that condition 'j>0' is not redundant
phyx-1.3.1/src/pairwise_alignment.cpp:158:30: note: Assuming condition is false
phyx-1.3.1/src/pairwise_alignment.cpp:166:15: note: Condition 'j>0' is always true
phyx-1.3.1/src/pairwise_alignment.cpp:170:15: style: Condition 'i>0' is always true [knownConditionTrueFalse]
phyx-1.3.1/src/pairwise_alignment.cpp:156:14: note: Assuming that condition 'i>0' is not redundant
phyx-1.3.1/src/pairwise_alignment.cpp:158:30: note: Assuming condition is false
phyx-1.3.1/src/pairwise_alignment.cpp:170:15: note: Condition 'i>0' is always true
phyx-1.3.1/src/polytomy.cpp:40:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/polytomy.cpp:39:17: style: Condition 'verbose' is always false [knownConditionTrueFalse]
phyx-1.3.1/src/polytomy.cpp:23:20: note: Assignment 'verbose=false', assigned value is 0
phyx-1.3.1/src/polytomy.cpp:39:17: note: Condition 'verbose' is always false
phyx-1.3.1/src/rate_model.cpp:116:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n_rows [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/rate_model.cpp:81:62: style: Parameter 'inQ' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/rate_model.cpp:95:31: style: Parameter 'inQ' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/rate_model.cpp:115:35: style: Parameter 'inQ' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/rate_model.cpp:134:29: style: Parameter 'inQ' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/rate_model.cpp:351:72: style: Parameter 'bigpibf' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/rate_model.cpp:352:14: style: Parameter 'bigpiK' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/rate_model.cpp:352:27: style: Parameter 'bigpiw' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/rate_model.cpp:400:51: style: Parameter 'codon_index' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/rate_model.cpp:401:35: style: Parameter 'codon_list' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/recode.cpp:40:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/recode.cpp:113:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/recode.h:44:10: style:inconclusive: Technically the member function 'SequenceRecoder::check_valid_scheme' can be const. [functionConst]
phyx-1.3.1/src/recode.cpp:93:23: note: Technically the member function 'SequenceRecoder::check_valid_scheme' can be const.
phyx-1.3.1/src/recode.h:44:10: note: Technically the member function 'SequenceRecoder::check_valid_scheme' can be const.
phyx-1.3.1/src/recode.h:46:10: style:inconclusive: Technically the member function 'SequenceRecoder::recode_seq' can be const. [functionConst]
phyx-1.3.1/src/recode.cpp:133:23: note: Technically the member function 'SequenceRecoder::recode_seq' can be const.
phyx-1.3.1/src/recode.h:46:10: note: Technically the member function 'SequenceRecoder::recode_seq' can be const.
phyx-1.3.1/src/relabel.cpp:57:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/relabel.cpp:139:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/relabel.cpp:19:10: warning: Member variable 'Relabel::num_taxa_' is not initialized in the constructor. [uninitMemberVar]
phyx-1.3.1/src/relabel.cpp:20:5: performance: Variable 'regex_pattern_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
phyx-1.3.1/src/relabel.cpp:21:5: performance: Variable 'regex_replace_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
phyx-1.3.1/src/relabel.cpp:19:32: style: Parameter 'regex_pattern' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/relabel.cpp:19:60: style: Parameter 'regex_replace' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/seq_gen.cpp:408:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_gen.cpp:535:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_gen.h:87:27: performance: Function 'get_sequences()' should return member 'res' by const reference. [returnByReference]
phyx-1.3.1/src/seq_gen.cpp:265:6: style: Redundant initialization for 'B'. The initialized value is overwritten before it is read. [redundantInitialization]
phyx-1.3.1/src/seq_gen.cpp:255:11: note: B is initialized
phyx-1.3.1/src/seq_gen.cpp:265:6: note: B is overwritten
phyx-1.3.1/src/seq_gen.cpp:156:45: style:inconclusive: Function 'simulate_sequence' argument 2 names different: declaration 'Matrix' definition 'QMatrix'. [funcArgNamesDifferent]
phyx-1.3.1/src/seq_gen.h:70:96: note: Function 'simulate_sequence' argument 2 names different: declaration 'Matrix' definition 'QMatrix'.
phyx-1.3.1/src/seq_gen.cpp:156:45: note: Function 'simulate_sequence' argument 2 names different: declaration 'Matrix' definition 'QMatrix'.
phyx-1.3.1/src/seq_gen.cpp:172:18: style: Local variable 'i' shadows outer variable [shadowVariable]
phyx-1.3.1/src/seq_gen.cpp:161:23: note: Shadowed declaration
phyx-1.3.1/src/seq_gen.cpp:172:18: note: Shadow variable
phyx-1.3.1/src/seq_gen.cpp:156:45: style: Parameter 'QMatrix' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/seq_gen.cpp:338:44: warning: Either the condition 'multi_rates_.size()!=0' is redundant or expression 'multi_rates_[0]' causes access out of bounds. [containerOutOfBounds]
phyx-1.3.1/src/seq_gen.cpp:340:72: note: Assuming that condition 'multi_rates_.size()!=0' is not redundant
phyx-1.3.1/src/seq_gen.cpp:338:44: note: Access out of bounds
phyx-1.3.1/src/seq_gen.cpp:158:47: style: Variable 'PMatrix' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/seq_gen.cpp:194:41: style: Variable 't' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/seq_gen.cpp:287:15: style: Variable 'check' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/seq_gen.cpp:415:21: style: Variable 'str' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/seq_info.cpp:158:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_info.cpp:195:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable right [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_info.cpp:249:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_info.cpp:363:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_info.cpp:402:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_info.cpp:459:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_info.cpp:171:17: style: The scope of the variable 'name' can be reduced. [variableScope]
phyx-1.3.1/src/seq_info.cpp:343:21: style: The scope of the variable 'name' can be reduced. [variableScope]
phyx-1.3.1/src/seq_info.cpp:54:18: style: Local variable 'sum' shadows outer function [shadowFunction]
phyx-1.3.1/src/utils.h:61:8: note: Shadowed declaration
phyx-1.3.1/src/seq_info.cpp:54:18: note: Shadow variable
phyx-1.3.1/src/seq_info.cpp:286:21: style: Variable 'seq' can be declared as reference to const [constVariableReference]
phyx-1.3.1/src/seq_info.cpp:307:22: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/seq_info.cpp:324:23: style: Variable 'miss' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/seq_info.cpp:334:18: style: Variable 'miss' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/seq_models.cpp:53:15: performance: Range variable 'line' should be declared as const reference. [iterateByValue]
phyx-1.3.1/src/seq_models.cpp:48:63: style: Parameter 'lines' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/seq_models.cpp:21:17: warning: Either the condition 'line.empty()' is redundant or expression 'line[0]' causes access out of bounds. [containerOutOfBounds]
phyx-1.3.1/src/seq_models.cpp:21:41: note: Assuming that condition 'line.empty()' is not redundant
phyx-1.3.1/src/seq_models.cpp:21:17: note: Access out of bounds
phyx-1.3.1/src/seq_models.cpp:33:23: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/seq_models.cpp:66:23: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/seq_reader.cpp:39:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_reader.cpp:87:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_reader.cpp:271:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_reader.cpp:344:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_reader.cpp:627:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_reader.cpp:776:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_reader.cpp:1092:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_reader.cpp:1192:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_reader.cpp:947:10: style: The scope of the variable 'first' can be reduced. [variableScope]
phyx-1.3.1/src/seq_reader.cpp:432:33: style: Variable 'tk' can be declared as reference to const [constVariableReference]
phyx-1.3.1/src/seq_reader.cpp:454:33: style: Variable 'token' can be declared as reference to const [constVariableReference]
phyx-1.3.1/src/seq_reader.cpp:951:30: style: Unused variable: names [unusedVariable]
phyx-1.3.1/src/seq_sample.cpp:44:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_sample.cpp:211:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_sample.cpp:303:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_sample.cpp:325:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_sample.h:25:31: performance:inconclusive: Technically the member function 'SequenceSampler::get_bootstrap_sites' can be static (but you may consider moving to unnamed namespace). [functionStatic]
phyx-1.3.1/src/seq_sample.cpp:94:44: note: Technically the member function 'SequenceSampler::get_bootstrap_sites' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/seq_sample.h:25:31: note: Technically the member function 'SequenceSampler::get_bootstrap_sites' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/seq_sample.h:38:25: performance:inconclusive: Technically the member function 'SequenceSampler::find_duplicates_missing' can be static (but you may consider moving to unnamed namespace). [functionStatic]
phyx-1.3.1/src/seq_sample.cpp:277:38: note: Technically the member function 'SequenceSampler::find_duplicates_missing' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/seq_sample.h:38:25: note: Technically the member function 'SequenceSampler::find_duplicates_missing' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/seq_sample.h:45:17: style:inconclusive: Technically the member function 'SequenceSampler::get_resampled_seq' can be const. [functionConst]
phyx-1.3.1/src/seq_sample.cpp:68:30: note: Technically the member function 'SequenceSampler::get_resampled_seq' can be const.
phyx-1.3.1/src/seq_sample.h:45:17: note: Technically the member function 'SequenceSampler::get_resampled_seq' can be const.
phyx-1.3.1/src/seq_sample.h:43:31: performance: Function 'get_sampled_sites()' should return member 'sample_sites_' by const reference. [returnByReference]
phyx-1.3.1/src/seq_sample.cpp:268:14: style: Condition 'diff!=0' is always true [knownConditionTrueFalse]
phyx-1.3.1/src/seq_sample.cpp:266:37: note: Assignment 'diff=max-count+1', assigned value is greater than 0
phyx-1.3.1/src/seq_sample.cpp:268:14: note: Condition 'diff!=0' is always true
phyx-1.3.1/src/seq_sample.cpp:141:54: style: Parameter 'partf' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/seq_utils.cpp:160:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_utils.cpp:256:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_utils.cpp:310:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_utils.cpp:393:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_utils.cpp:413:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_utils.cpp:423:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/seq_utils.cpp:157:70: style: Parameter 'alpha' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/seq_utils.cpp:168:25: style: Variable 'seq' can be declared as reference to const [constVariableReference]
phyx-1.3.1/src/seq_utils.cpp:178:25: style: Variable 'seq' can be declared as reference to const [constVariableReference]
phyx-1.3.1/src/seq_utils.cpp:344:74: style: Parameter 'origseqs' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/seq_utils.cpp:365:83: style: Parameter 'origseqs' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/seq_utils.cpp:475:39: style: Parameter 'seq' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/sequence.cpp:83:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/sequence.h:43:12: style:inconclusive: Technically the member function 'Sequence::get_cont_char' can be const. [functionConst]
phyx-1.3.1/src/sequence.cpp:164:18: note: Technically the member function 'Sequence::get_cont_char' can be const.
phyx-1.3.1/src/sequence.h:43:12: note: Technically the member function 'Sequence::get_cont_char' can be const.
phyx-1.3.1/src/sequence.h:44:9: style:inconclusive: Technically the member function 'Sequence::get_num_cont_char' can be const. [functionConst]
phyx-1.3.1/src/sequence.cpp:169:15: note: Technically the member function 'Sequence::get_num_cont_char' can be const.
phyx-1.3.1/src/sequence.h:44:9: note: Technically the member function 'Sequence::get_num_cont_char' can be const.
phyx-1.3.1/src/sequence.h:47:9: style:inconclusive: Technically the member function 'Sequence::get_multistate_char' can be const. [functionConst]
phyx-1.3.1/src/sequence.cpp:184:15: note: Technically the member function 'Sequence::get_multistate_char' can be const.
phyx-1.3.1/src/sequence.h:47:9: note: Technically the member function 'Sequence::get_multistate_char' can be const.
phyx-1.3.1/src/sequence.h:48:9: style:inconclusive: Technically the member function 'Sequence::get_num_multistate_char' can be const. [functionConst]
phyx-1.3.1/src/sequence.cpp:189:15: note: Technically the member function 'Sequence::get_num_multistate_char' can be const.
phyx-1.3.1/src/sequence.h:48:9: note: Technically the member function 'Sequence::get_num_multistate_char' can be const.
phyx-1.3.1/src/sequence.h:55:17: style:inconclusive: Technically the member function 'Sequence::reverse_complement' can be const. [functionConst]
phyx-1.3.1/src/sequence.cpp:210:23: note: Technically the member function 'Sequence::reverse_complement' can be const.
phyx-1.3.1/src/sequence.h:55:17: note: Technically the member function 'Sequence::reverse_complement' can be const.
phyx-1.3.1/src/sequence.h:60:17: style:inconclusive: Technically the member function 'Sequence::seq_to_upper' can be const. [functionConst]
phyx-1.3.1/src/sequence.cpp:287:23: note: Technically the member function 'Sequence::seq_to_upper' can be const.
phyx-1.3.1/src/sequence.h:60:17: note: Technically the member function 'Sequence::seq_to_upper' can be const.
phyx-1.3.1/src/sequence.h:39:17: performance: Function 'get_sequence()' should return member 'seq_' by const reference. [returnByReference]
phyx-1.3.1/src/sequence.h:40:17: performance: Function 'get_id()' should return member 'id_' by const reference. [returnByReference]
phyx-1.3.1/src/sequence.h:53:25: performance: Function 'get_qualarr()' should return member 'qualarr_' by const reference. [returnByReference]
phyx-1.3.1/src/sequence.cpp:228:42: style: Parameter 'stri' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/sequence.cpp:232:18: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/sstat.cpp:18:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/sstat.cpp:108:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/state_reconstructor.cpp:48:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/state_reconstructor.cpp:133:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/state_reconstructor.cpp:184:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/state_reconstructor.cpp:519:63: style: Expression 'exp(x) - 1' can be replaced by 'expm1(x)' to avoid loss of precision. [unpreciseMathCall]
phyx-1.3.1/src/state_reconstructor.cpp:526:64: style: Expression 'exp(x) - 1' can be replaced by 'expm1(x)' to avoid loss of precision. [unpreciseMathCall]
phyx-1.3.1/src/state_reconstructor.cpp:596:63: style: Expression 'exp(x) - 1' can be replaced by 'expm1(x)' to avoid loss of precision. [unpreciseMathCall]
phyx-1.3.1/src/state_reconstructor.cpp:603:64: style: Expression 'exp(x) - 1' can be replaced by 'expm1(x)' to avoid loss of precision. [unpreciseMathCall]
phyx-1.3.1/src/vector_node_object.h:15:5: style: Class 'VectorNodeObject < double >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
phyx-1.3.1/src/vector_node_object.h:21:14: style: The destructor '~VectorNodeObject < double >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
phyx-1.3.1/src/node_object.h:10:14: note: Virtual destructor in base class
phyx-1.3.1/src/vector_node_object.h:21:14: note: Destructor in derived class
phyx-1.3.1/src/state_reconstructor.cpp:72:24: style: The scope of the variable 't' can be reduced. [variableScope]
phyx-1.3.1/src/state_reconstructor.cpp:126:71: style:inconclusive: Function 'set_tip_conditionals' argument 1 names different: declaration 'distrib_data' definition 'data'. [funcArgNamesDifferent]
phyx-1.3.1/src/state_reconstructor.h:57:55: note: Function 'set_tip_conditionals' argument 1 names different: declaration 'distrib_data' definition 'data'.
phyx-1.3.1/src/state_reconstructor.cpp:126:71: note: Function 'set_tip_conditionals' argument 1 names different: declaration 'distrib_data' definition 'data'.
phyx-1.3.1/src/state_reconstructor.cpp:173:85: style:inconclusive: Function 'set_tip_conditionals_already_given' argument 1 names different: declaration 'distrib_data' definition 'data'. [funcArgNamesDifferent]
phyx-1.3.1/src/state_reconstructor.h:58:69: note: Function 'set_tip_conditionals_already_given' argument 1 names different: declaration 'distrib_data' definition 'data'.
phyx-1.3.1/src/state_reconstructor.cpp:173:85: note: Function 'set_tip_conditionals_already_given' argument 1 names different: declaration 'distrib_data' definition 'data'.
phyx-1.3.1/src/state_reconstructor.cpp:34:60: style: Parameter 'ps' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/state_reconstructor.cpp:35:33: style: Parameter 'rms' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/state_reconstructor.cpp:126:71: style: Parameter 'data' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/state_reconstructor.cpp:173:85: style: Parameter 'data' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/state_reconstructor.cpp:236:79: style: Parameter 'node' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/state_reconstructor.cpp:375:40: style: Variable 'talph' can be declared as pointer to const [constVariablePointer]
phyx-1.3.1/src/state_reconstructor.cpp:422:22: style: Variable 'tempA[j]' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/superdouble.h:62:12: style:inconclusive: Technically the member function 'Superdouble::getMantissa' can be const. [functionConst]
phyx-1.3.1/src/superdouble.cpp:29:21: note: Technically the member function 'Superdouble::getMantissa' can be const.
phyx-1.3.1/src/superdouble.h:62:12: note: Technically the member function 'Superdouble::getMantissa' can be const.
phyx-1.3.1/src/superdouble.cpp:59:50: performance: Function parameter 'x' should be passed by const reference. [passedByValue]
phyx-1.3.1/src/superdouble.cpp:87:50: performance: Function parameter 'x' should be passed by const reference. [passedByValue]
phyx-1.3.1/src/superdouble.cpp:95:50: performance: Function parameter 'x' should be passed by const reference. [passedByValue]
phyx-1.3.1/src/superdouble.cpp:110:50: performance: Function parameter 'x' should be passed by const reference. [passedByValue]
phyx-1.3.1/src/superdouble.cpp:139:44: performance: Function parameter 'x' should be passed by const reference. [passedByValue]
phyx-1.3.1/src/superdouble.cpp:147:44: performance: Function parameter 'x' should be passed by const reference. [passedByValue]
phyx-1.3.1/src/superdouble.cpp:154:44: performance: Function parameter 'x' should be passed by const reference. [passedByValue]
phyx-1.3.1/src/superdouble.cpp:181:44: performance: Function parameter 'x' should be passed by const reference. [passedByValue]
phyx-1.3.1/src/tgen.cpp:227:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/tgen.h:25:18: style:inconclusive: Technically the member function 'TopologyGenerator::get_num_edges' can be const. [functionConst]
phyx-1.3.1/src/tgen.cpp:40:33: note: Technically the member function 'TopologyGenerator::get_num_edges' can be const.
phyx-1.3.1/src/tgen.h:25:18: note: Technically the member function 'TopologyGenerator::get_num_edges' can be const.
phyx-1.3.1/src/tgen.h:28:61: performance:inconclusive: Technically the member function 'TopologyGenerator::add_taxon_unrooted' can be static (but you may consider moving to unnamed namespace). [functionStatic]
phyx-1.3.1/src/tgen.cpp:79:76: note: Technically the member function 'TopologyGenerator::add_taxon_unrooted' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/tgen.h:28:61: note: Technically the member function 'TopologyGenerator::add_taxon_unrooted' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/tgen.h:31:61: style:inconclusive: Technically the member function 'TopologyGenerator::add_taxon_rooted' can be const. [functionConst]
phyx-1.3.1/src/tgen.cpp:109:76: note: Technically the member function 'TopologyGenerator::add_taxon_rooted' can be const.
phyx-1.3.1/src/tgen.h:31:61: note: Technically the member function 'TopologyGenerator::add_taxon_rooted' can be const.
phyx-1.3.1/src/tgen.h:34:10: style:inconclusive: Technically the member function 'TopologyGenerator::newick_from_tree_map' can be const. [functionConst]
phyx-1.3.1/src/tgen.cpp:195:25: note: Technically the member function 'TopologyGenerator::newick_from_tree_map' can be const.
phyx-1.3.1/src/tgen.h:34:10: note: Technically the member function 'TopologyGenerator::newick_from_tree_map' can be const.
phyx-1.3.1/src/tgen.cpp:223:46: style: The scope of the variable 'tree' can be reduced. [variableScope]
phyx-1.3.1/src/tgen.cpp:80:65: performance: Function parameter 'edges' should be passed by const reference. [passedByValue]
phyx-1.3.1/src/tgen.cpp:110:65: performance: Function parameter 'edges' should be passed by const reference. [passedByValue]
phyx-1.3.1/src/timer.cpp:20:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/timer.cpp:10:5: performance: Variable 'start_time_point_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
phyx-1.3.1/src/tlate.cpp:325:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/tlate.cpp:293:17: style: The scope of the variable 'codon' can be reduced. [variableScope]
phyx-1.3.1/src/tlate.cpp:308:15: style: Variable 'codon' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/tree.cpp:195:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/tree.cpp:264:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/tree.h:25:10: performance:inconclusive: Technically the member function 'Tree::exchangeInfo' can be static (but you may consider moving to unnamed namespace). [functionStatic]
phyx-1.3.1/src/tree.cpp:466:12: note: Technically the member function 'Tree::exchangeInfo' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/tree.h:25:10: note: Technically the member function 'Tree::exchangeInfo' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/tree.h:27:12: performance:inconclusive: Technically the member function 'Tree::getMRCATraverse' can be static (but you may consider moving to unnamed namespace). [functionStatic]
phyx-1.3.1/src/tree.cpp:590:14: note: Technically the member function 'Tree::getMRCATraverse' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/tree.h:27:12: note: Technically the member function 'Tree::getMRCATraverse' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/tree.h:28:10: performance:inconclusive: Technically the member function 'Tree::setHeightFromRootToNode' can be static (but you may consider moving to unnamed namespace). [functionStatic]
phyx-1.3.1/src/tree.cpp:398:12: note: Technically the member function 'Tree::setHeightFromRootToNode' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/tree.h:28:10: note: Technically the member function 'Tree::setHeightFromRootToNode' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/tree.h:60:10: style:inconclusive: Technically the member function 'Tree::duplicateRootSupport' can be const. [functionConst]
phyx-1.3.1/src/tree.cpp:237:12: note: Technically the member function 'Tree::duplicateRootSupport' can be const.
phyx-1.3.1/src/tree.h:60:10: note: Technically the member function 'Tree::duplicateRootSupport' can be const.
phyx-1.3.1/src/tree.h:61:10: style:inconclusive: Technically the member function 'Tree::tritomyRoot' can be const. [functionConst]
phyx-1.3.1/src/tree.cpp:274:12: note: Technically the member function 'Tree::tritomyRoot' can be const.
phyx-1.3.1/src/tree.h:61:10: note: Technically the member function 'Tree::tritomyRoot' can be const.
phyx-1.3.1/src/tree.h:66:10: performance:inconclusive: Technically the member function 'Tree::exchangeNodes' can be static (but you may consider moving to unnamed namespace). [functionStatic]
phyx-1.3.1/src/tree.cpp:479:12: note: Technically the member function 'Tree::exchangeNodes' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/tree.h:66:10: note: Technically the member function 'Tree::exchangeNodes' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/tree.cpp:469:13: warning: Either the condition 'node->getParent()!=nullptr' is redundant or there is possible null pointer dereference: node1. [nullPointerRedundantCheck]
phyx-1.3.1/src/tree.cpp:453:27: note: Assuming that condition 'node->getParent()!=nullptr' is not redundant
phyx-1.3.1/src/tree.cpp:457:33: note: Calling function 'exchangeInfo', 1st argument 'node->getParent()' value is 0
phyx-1.3.1/src/tree.cpp:469:13: note: Null pointer dereference
phyx-1.3.1/src/tree.cpp:470:5: warning: Either the condition 'node->getParent()!=nullptr' is redundant or there is possible null pointer dereference: node1. [nullPointerRedundantCheck]
phyx-1.3.1/src/tree.cpp:453:27: note: Assuming that condition 'node->getParent()!=nullptr' is not redundant
phyx-1.3.1/src/tree.cpp:457:33: note: Calling function 'exchangeInfo', 1st argument 'node->getParent()' value is 0
phyx-1.3.1/src/tree.cpp:470:5: note: Null pointer dereference
phyx-1.3.1/src/tree.cpp:473:13: warning: Either the condition 'node->getParent()!=nullptr' is redundant or there is possible null pointer dereference: node1. [nullPointerRedundantCheck]
phyx-1.3.1/src/tree.cpp:453:27: note: Assuming that condition 'node->getParent()!=nullptr' is not redundant
phyx-1.3.1/src/tree.cpp:457:33: note: Calling function 'exchangeInfo', 1st argument 'node->getParent()' value is 0
phyx-1.3.1/src/tree.cpp:473:13: note: Null pointer dereference
phyx-1.3.1/src/tree.cpp:474:5: warning: Either the condition 'node->getParent()!=nullptr' is redundant or there is possible null pointer dereference: node1. [nullPointerRedundantCheck]
phyx-1.3.1/src/tree.cpp:453:27: note: Assuming that condition 'node->getParent()!=nullptr' is not redundant
phyx-1.3.1/src/tree.cpp:457:33: note: Calling function 'exchangeInfo', 1st argument 'node->getParent()' value is 0
phyx-1.3.1/src/tree.cpp:474:5: note: Null pointer dereference
phyx-1.3.1/src/tree.cpp:320:48: performance: Function parameter 'innodes' should be passed by const reference. [passedByValue]
phyx-1.3.1/src/tree.cpp:67:44: style: Parameter 'name' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/tree.cpp:114:36: style: Parameter 'name' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/tree.cpp:370:57: style: Parameter 'innodes' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/tree.cpp:274:32: style: Parameter 'toberoot' can be declared as pointer to const [constParameterPointer]
phyx-1.3.1/src/tree.cpp:608:21: style: Variable 'i' can be declared as pointer to const [constVariableReference]
phyx-1.3.1/src/tree.cpp:328:18: style: Consider using std::copy algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/tree.cpp:609:30: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/tree_info.cpp:28:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boolalpha [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/tree_info.cpp:97:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boolalpha [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/tree_reader.cpp:47:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/tree_reader.cpp:259:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/tree_reader.cpp:294:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/tree_reader.cpp:385:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/tree_reader.cpp:447:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/tree_reader.h:14:12: performance:inconclusive: Technically the member function 'TreeReader::readTree' can be static (but you may consider moving to unnamed namespace). [functionStatic]
phyx-1.3.1/src/tree_reader.cpp:24:20: note: Technically the member function 'TreeReader::readTree' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/tree_reader.h:14:12: note: Technically the member function 'TreeReader::readTree' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/tree_reader.cpp:31:19: style: Variable 'in_quote' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/tree_utils.cpp:99:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/tree_utils.cpp:150:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/tree_utils.cpp:198:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/tree_utils.cpp:215:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/tree_utils.cpp:305:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/tree_utils.cpp:569:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/tree_utils.cpp:777:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/tree_utils.cpp:214:9: style: Condition 'debug' is always true [knownConditionTrueFalse]
phyx-1.3.1/src/tree_utils.cpp:210:18: note: Assignment 'debug=true', assigned value is 1
phyx-1.3.1/src/tree_utils.cpp:214:9: note: Condition 'debug' is always true
phyx-1.3.1/src/tree_utils.cpp:220:13: style: Condition 'debug' is always true [knownConditionTrueFalse]
phyx-1.3.1/src/tree_utils.cpp:210:18: note: Assignment 'debug=true', assigned value is 1
phyx-1.3.1/src/tree_utils.cpp:220:13: note: Condition 'debug' is always true
phyx-1.3.1/src/tree_utils.cpp:304:9: style: Condition 'debug' is always true [knownConditionTrueFalse]
phyx-1.3.1/src/tree_utils.cpp:302:18: note: Assignment 'debug=true', assigned value is 1
phyx-1.3.1/src/tree_utils.cpp:304:9: note: Condition 'debug' is always true
phyx-1.3.1/src/utils.h:155:7: style: Local variable 'EPSILON' shadows outer variable [shadowVariable]
phyx-1.3.1/src/constants.h:10:14: note: Shadowed declaration
phyx-1.3.1/src/utils.h:155:7: note: Shadow variable
phyx-1.3.1/src/tree_utils.cpp:563:68: performance: Function parameter 'names' should be passed by const reference. [passedByValue]
phyx-1.3.1/src/tree_utils.cpp:85:58: style: Parameter 'names' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/tree_utils.cpp:22:12: style: Variable 'mrca' can be declared as pointer to const [constVariablePointer]
phyx-1.3.1/src/tree_utils.cpp:24:12: style: Variable 'cur' can be declared as pointer to const [constVariablePointer]
phyx-1.3.1/src/tree_utils.cpp:41:35: style: Parameter 'n' can be declared as pointer to const [constParameterPointer]
phyx-1.3.1/src/tree_utils.cpp:291:25: style: Variable 't' can be declared as pointer to const [constVariableReference]
phyx-1.3.1/src/tree_utils.cpp:330:16: style: Variable 'middle' can be declared as pointer to const [constVariablePointer]
phyx-1.3.1/src/tree_utils.cpp:376:24: style: Parameter 'tr' can be declared as pointer to const [constParameterPointer]
phyx-1.3.1/src/tree_utils.cpp:417:32: style: Parameter 'tr' can be declared as pointer to const [constParameterPointer]
phyx-1.3.1/src/tree_utils.cpp:567:16: style: Variable 'nd' can be declared as pointer to const [constVariablePointer]
phyx-1.3.1/src/tree_utils.cpp:580:12: style: Variable 'nd' can be declared as pointer to const [constVariablePointer]
phyx-1.3.1/src/tree_utils.cpp:627:28: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
phyx-1.3.1/src/tree_utils.cpp:659:16: style: Variable 'nd' can be declared as pointer to const [constVariablePointer]
phyx-1.3.1/src/tree_utils.cpp:736:37: style: Parameter 'tree' can be declared as pointer to const [constParameterPointer]
phyx-1.3.1/src/tree_utils.cpp:744:36: style: Parameter 'tree' can be declared as pointer to const [constParameterPointer]
phyx-1.3.1/src/tree_utils.cpp:752:37: style: Parameter 'tree' can be declared as pointer to const [constParameterPointer]
phyx-1.3.1/src/tree_utils.cpp:761:28: style: Parameter 'tr' can be declared as pointer to const [constParameterPointer]
phyx-1.3.1/src/tree_utils.cpp:156:31: style: Consider using std::copy_if algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/upgma.cpp:26:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/upgma.cpp:20:5: performance: Variable 'seqs_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
phyx-1.3.1/src/upgma.h:26:12: performance:inconclusive: Technically the member function 'UPGMA::get_smallest_distance' can be static (but you may consider moving to unnamed namespace). [functionStatic]
phyx-1.3.1/src/upgma.cpp:77:15: note: Technically the member function 'UPGMA::get_smallest_distance' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/upgma.h:26:12: note: Technically the member function 'UPGMA::get_smallest_distance' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/upgma.h:32:40: performance: Function 'get_matrix()' should return member 'full_distmatrix_' by const reference. [returnByReference]
phyx-1.3.1/src/upgma.cpp:41:22: style: Variable 'tempScore' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/upgma.cpp:154:25: style: Variable 'tempDist' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/utils.cpp:42:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/utils.cpp:50:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/utils.cpp:63:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/utils.cpp:76:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/utils.cpp:90:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/utils.cpp:103:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/utils.cpp:134:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/utils.cpp:207:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable eofbit [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/utils.cpp:243:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/utils.cpp:339:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/utils.cpp:576:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/utils.cpp:594:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/utils.cpp:673:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/utils.cpp:691:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/utils.cpp:781:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _1 [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/utils.cpp:809:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable POLLIN [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/utils.cpp:858:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/utils.cpp:875:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/utils.cpp:510:17: style: Local variable 'sum' shadows outer function [shadowFunction]
phyx-1.3.1/src/utils.h:61:8: note: Shadowed declaration
phyx-1.3.1/src/utils.cpp:510:17: note: Shadow variable
phyx-1.3.1/src/utils.cpp:170:17: style: Variable 'label' can be declared as reference to const [constVariableReference]
phyx-1.3.1/src/utils.cpp:412:17: style: Variable 'mati' can be declared as reference to const [constVariableReference]
phyx-1.3.1/src/utils.cpp:422:17: style: Variable 'mati' can be declared as reference to const [constVariableReference]
phyx-1.3.1/src/utils.cpp:498:36: style: Parameter 'in' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/utils.cpp:509:73: style: Parameter 'in' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/utils.cpp:521:41: style: Parameter 'vec1' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/utils.cpp:551:57: style: Parameter 'sts' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/utils.cpp:560:49: style: Parameter 'sts' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/utils.cpp:631:62: style: Parameter 'tline' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/utils.cpp:839:68: style: Parameter 'a' can be declared as reference to const [constParameterReference]
phyx-1.3.1/src/utils.cpp:48:44: style: Parameter 'in' can be declared as pointer to const [constParameterPointer]
phyx-1.3.1/src/utils.cpp:48:55: style: Parameter 'out' can be declared as pointer to const [constParameterPointer]
phyx-1.3.1/src/utils.cpp:337:26: style: Parameter 'pname' can be declared as pointer to const [constParameterPointer]
phyx-1.3.1/src/utils.cpp:413:11: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/utils.cpp:424:15: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/utils.cpp:502:15: style: Consider using std::count_if algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/utils.cpp:512:13: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/utils.cpp:843:17: style: Consider using std::copy_if algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/utils.cpp:888:20: style: Consider using std::copy_if algorithm instead of a raw loop. [useStlAlgorithm]
phyx-1.3.1/src/utils.cpp:901:25: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
phyx-1.3.1/src/vcf_reader.cpp:103:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
phyx-1.3.1/src/vcf_reader.h:14:30: performance:inconclusive: Technically the member function 'VcfReader::get_alts' can be static (but you may consider moving to unnamed namespace). [functionStatic]
phyx-1.3.1/src/vcf_reader.cpp:89:37: note: Technically the member function 'VcfReader::get_alts' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/vcf_reader.h:14:30: note: Technically the member function 'VcfReader::get_alts' can be static (but you may consider moving to unnamed namespace).
phyx-1.3.1/src/vcf_reader.h:19:10: style:inconclusive: Technically the member function 'VcfReader::write_seqs' can be const. [functionConst]
phyx-1.3.1/src/vcf_reader.cpp:101:17: note: Technically the member function 'VcfReader::write_seqs' can be const.
phyx-1.3.1/src/vcf_reader.h:19:10: note: Technically the member function 'VcfReader::write_seqs' can be const.
phyx-1.3.1/src/bd_fit.cpp:19:23: error: The one definition rule is violated, different classes/structs have the same name 'analysis_data' [ctuOneDefinitionRuleViolation]
phyx-1.3.1/src/optimize_cont_models_nlopt.cpp:14:9: note: The one definition rule is violated, different classes/structs have the same name 'analysis_data'
phyx-1.3.1/src/bd_fit.cpp:19:23: note: The one definition rule is violated, different classes/structs have the same name 'analysis_data'
phyx-1.3.1/src/tree.cpp:469:13: warning: Null pointer dereference: node1 [ctunullpointer]
phyx-1.3.1/src/tree.cpp:453:27: note: Assuming that condition 'node->getParent()!=nullptr' is not redundant
phyx-1.3.1/src/tree.cpp:457:17: note: Calling function exchangeInfo, 1st argument is null
phyx-1.3.1/src/tree.cpp:469:13: note: Dereferencing argument node1 that is null
diff:
head phyx-1.3.1/src/aa2cdn.cpp:122:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/aa2cdn.cpp:152:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/aa2cdn.cpp:46:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/aa2cdn.h:28:27: performance: Function 'get_codon_alignment()' should return member 'codon_seqs_' by const reference. [returnByReference]
head phyx-1.3.1/src/bd_fit.cpp:113:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_PRAXIS [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/bd_fit.cpp:150:77: style: Parameter 'grad' can be declared as reference to const. However it seems that 'nlopt_bd_log_lik' is a callback function, if 'grad' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
     phyx-1.3.1/src/bd_fit.cpp:117:27: note: You might need to cast the function pointer here
     phyx-1.3.1/src/bd_fit.cpp:150:77: note: Parameter 'grad' can be declared as reference to const
head phyx-1.3.1/src/bd_fit.cpp:189:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/bd_sim.cpp:78:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/branch_segment.h:31:22: performance: Function 'getFossilAreas()' should return member 'fossilareaindices' by const reference. [returnByReference]
head phyx-1.3.1/src/clean_seq.cpp:119:86: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/clean_seq.cpp:228:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/clean_seq.cpp:24:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/clean_seq.cpp:45:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/clean_seq.cpp:76:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/clean_seq.cpp:91:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/clean_seq.h:49:27: performance: Function 'get_cleaned_seqs()' should return member 'cleaned_seqs_' by const reference. [returnByReference]
head phyx-1.3.1/src/comp_test.cpp:102:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/comp_test.cpp:129:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/comp_test.cpp:178:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/comp_test.cpp:29:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/comp_test.cpp:72:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/concat.cpp:138:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/concat.cpp:40:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/cont_models.cpp:138:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.13.0 phyx-1.3.1/src/edlib.cpp:570:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/log_manip.cpp:222:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/log_manip.cpp:324:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/log_manip.cpp:393:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/log_manip.cpp:428:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/log_manip.cpp:466:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/log_manip.cpp:536:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/log_manip.cpp:596:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/log_manip.cpp:670:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/log_manip.cpp:755:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/log_manip.cpp:76:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable right [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_aa2cdn.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_aa2cdn.cpp:84:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_bd_fit.cpp:24:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_bd_fit.cpp:84:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_bd_sim.cpp:23:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_bd_sim.cpp:97:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_boot.cpp:25:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_boot.cpp:88:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_bp.cpp:100:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_bp.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_cat.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_cat.cpp:94:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_clsq.cpp:101:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_clsq.cpp:22:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.13.0 phyx-1.3.1/src/main_cltr.cpp:177:29: style: Variable 'ct' is assigned a value that is never used. [unreadVariable]
2.13.0 phyx-1.3.1/src/main_cltr.cpp:190:29: style: Variable 'ct' is assigned a value that is never used. [unreadVariable]
head phyx-1.3.1/src/main_cltr.cpp:23:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_cltr.cpp:94:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_colt.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_colt.cpp:86:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_comp.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_comp.cpp:72:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_consq.cpp:20:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_consq.cpp:74:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_contrates.cpp:26:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_contrates.cpp:87:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_fqfilt.cpp:18:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_fqfilt.cpp:73:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_log.cpp:116:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_log.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_lssq.cpp:102:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_lssq.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_lstr.cpp:101:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
2.13.0 phyx-1.3.1/src/main_lstr.cpp:216:32: style: Variable 'ti' is assigned a value that is never used. [unreadVariable]
head phyx-1.3.1/src/main_lstr.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.13.0 phyx-1.3.1/src/main_lstr.cpp:237:32: style: Variable 'ti' is assigned a value that is never used. [unreadVariable]
head phyx-1.3.1/src/main_mono.cpp:23:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_mono.cpp:92:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_mrca.cpp:23:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_mrca.cpp:81:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_mrca_cut.cpp:23:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_mrca_cut.cpp:84:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_mrca_name.cpp:28:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_mrca_name.cpp:92:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_nj.cpp:28:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_nj.cpp:93:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_nni.cpp:22:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_nni.cpp:79:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_nw.cpp:27:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_nw.cpp:98:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_poly.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_poly.cpp:79:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_recode.cpp:25:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_recode.cpp:92:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_revcomp.cpp:132:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_revcomp.cpp:25:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_rls.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_rls.cpp:95:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_rlt.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_rlt.cpp:95:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_rmk.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_rmk.cpp:75:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_rms.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_rms.cpp:95:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_rmt.cpp:22:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_rmt.cpp:96:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_rr.cpp:23:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_rr.cpp:96:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_s2fa.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_s2fa.cpp:75:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_s2nex.cpp:20:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_s2nex.cpp:75:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_s2phy.cpp:20:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_s2phy.cpp:75:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_seqgen.cpp:155:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_seqgen.cpp:20:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_ssort.cpp:103:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_ssort.cpp:22:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_ssplit.cpp:27:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_ssplit.cpp:33:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_ssplit.cpp:90:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_sstat.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_sstat.cpp:75:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_strec.cpp:148:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_strec.cpp:29:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_strec.cpp:98:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_sw.cpp:26:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_sw.cpp:97:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_t2new.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_t2new.cpp:74:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_t2nex.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_t2nex.cpp:74:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_tcol.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_tcol.cpp:86:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_tcomb.cpp:29:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_tcomb.cpp:87:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_tgen.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_tgen.cpp:90:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_tlate.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_tlate.cpp:81:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_trt.cpp:22:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_trt.cpp:90:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_tscale.cpp:20:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_tscale.cpp:82:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_upgma.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_upgma.cpp:73:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_vcf2fa.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/main_vcf2fa.cpp:76:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/nj.cpp:25:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/nj.h:42:17: performance: Function 'get_newick()' should return member 'newick_string_' by const reference. [returnByReference]
head phyx-1.3.1/src/node.h:40:24: performance: Function 'getChildren()' should return member 'children_' by const reference. [returnByReference]
head phyx-1.3.1/src/node.h:61:17: performance: Function 'getName()' should return member 'name_' by const reference. [returnByReference]
head phyx-1.3.1/src/node.h:62:17: performance: Function 'getComment()' should return member 'comment_' by const reference. [returnByReference]
head phyx-1.3.1/src/optimize_cont_models_nlopt.cpp:108:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_SBPLX [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/optimize_cont_models_nlopt.cpp:142:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_SBPLX [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/optimize_cont_models_nlopt.cpp:173:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_SBPLX [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/optimize_state_reconstructor_periods_nlopt.cpp:58:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_NELDERMEAD [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/orphan_files/distmatrix.cpp:109:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/orphan_files/main_bpseq.cpp:69:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/orphan_files/main_contbl.cpp:70:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/orphan_files/main_kaks.cpp:55:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/orphan_files/main_medusa.cpp:66:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/orphan_files/main_sm0.cpp:73:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/orphan_files/main_sm2a.cpp:73:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/orphan_files/main_tdist.cpp:83:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/orphan_files/mcmc.cpp:72:10: style: Parameter 'inq1' can be declared as reference to const [constParameterReference]
head phyx-1.3.1/src/orphan_files/mcmc.cpp:85:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/orphan_files/optimize_state_reconstructor_gsl.cpp:54:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gsl_multimin_fminimizer_nmsimplex2 [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/orphan_files/state_reconstructor_simple.cpp:61:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.13.0 phyx-1.3.1/src/pairwise_alignment.cpp:173:15: style: Condition 'i>0' is always true [knownConditionTrueFalse]
     phyx-1.3.1/src/pairwise_alignment.cpp:156:14: note: Assuming that condition 'i>0' is not redundant
     phyx-1.3.1/src/pairwise_alignment.cpp:158:30: note: Assuming condition is false
     phyx-1.3.1/src/pairwise_alignment.cpp:173:15: note: Condition 'i>0' is always true
2.13.0 phyx-1.3.1/src/pairwise_alignment.cpp:173:24: style: Condition 'j>0' is always true [knownConditionTrueFalse]
     phyx-1.3.1/src/pairwise_alignment.cpp:156:23: note: Assuming that condition 'j>0' is not redundant
     phyx-1.3.1/src/pairwise_alignment.cpp:158:30: note: Assuming condition is false
     phyx-1.3.1/src/pairwise_alignment.cpp:173:24: note: Condition 'j>0' is always true
2.13.0 phyx-1.3.1/src/pairwise_alignment.cpp:178:22: style: Condition 'i>0' is always true [knownConditionTrueFalse]
     phyx-1.3.1/src/pairwise_alignment.cpp:156:14: note: Assuming that condition 'i>0' is not redundant
     phyx-1.3.1/src/pairwise_alignment.cpp:158:30: note: Assuming condition is false
     phyx-1.3.1/src/pairwise_alignment.cpp:178:22: note: Condition 'i>0' is always true
2.13.0 phyx-1.3.1/src/pairwise_alignment.cpp:182:22: style: Condition 'j>0' is always true [knownConditionTrueFalse]
     phyx-1.3.1/src/pairwise_alignment.cpp:156:23: note: Assuming that condition 'j>0' is not redundant
     phyx-1.3.1/src/pairwise_alignment.cpp:158:30: note: Assuming condition is false
     phyx-1.3.1/src/pairwise_alignment.cpp:182:22: note: Condition 'j>0' is always true
head phyx-1.3.1/src/polytomy.cpp:40:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.13.0 phyx-1.3.1/src/polytomy.cpp:51:25: style: Condition 'verbose' is always false [knownConditionTrueFalse]
     phyx-1.3.1/src/polytomy.cpp:23:20: note: Assignment 'verbose=false', assigned value is 0
     phyx-1.3.1/src/polytomy.cpp:47:35: note: Assuming container is not empty
     phyx-1.3.1/src/polytomy.cpp:51:25: note: Condition 'verbose' is always false
2.13.0 phyx-1.3.1/src/polytomy.cpp:58:25: style: Condition 'verbose' is always false [knownConditionTrueFalse]
     phyx-1.3.1/src/polytomy.cpp:23:20: note: Assignment 'verbose=false', assigned value is 0
     phyx-1.3.1/src/polytomy.cpp:47:35: note: Assuming container is not empty
     phyx-1.3.1/src/polytomy.cpp:58:25: note: Condition 'verbose' is always false
2.13.0 phyx-1.3.1/src/polytomy.cpp:64:29: style: Condition 'verbose' is always false [knownConditionTrueFalse]
     phyx-1.3.1/src/polytomy.cpp:23:20: note: Assignment 'verbose=false', assigned value is 0
     phyx-1.3.1/src/polytomy.cpp:47:35: note: Assuming container is not empty
     phyx-1.3.1/src/polytomy.cpp:62:43: note: Assuming container is not empty
     phyx-1.3.1/src/polytomy.cpp:64:29: note: Condition 'verbose' is always false
head phyx-1.3.1/src/rate_model.cpp:400:51: style: Parameter 'codon_index' can be declared as reference to const [constParameterReference]
head phyx-1.3.1/src/recode.cpp:113:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/recode.cpp:40:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/relabel.cpp:139:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/relabel.cpp:57:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.13.0 phyx-1.3.1/src/seq_gen.cpp:338:44: warning: Either the condition 'multi_rates_.size()!=0' is redundant or expression 'multi_rates_[0]' cause access out of bounds. [containerOutOfBounds]
     phyx-1.3.1/src/seq_gen.cpp:340:72: note: Assuming that condition 'multi_rates_.size()!=0' is not redundant
     phyx-1.3.1/src/seq_gen.cpp:338:44: note: Access out of bounds
head phyx-1.3.1/src/seq_gen.cpp:338:44: warning: Either the condition 'multi_rates_.size()!=0' is redundant or expression 'multi_rates_[0]' causes access out of bounds. [containerOutOfBounds]
     phyx-1.3.1/src/seq_gen.cpp:340:72: note: Assuming that condition 'multi_rates_.size()!=0' is not redundant
     phyx-1.3.1/src/seq_gen.cpp:338:44: note: Access out of bounds
head phyx-1.3.1/src/seq_gen.cpp:408:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_gen.cpp:535:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_gen.h:87:27: performance: Function 'get_sequences()' should return member 'res' by const reference. [returnByReference]
head phyx-1.3.1/src/seq_info.cpp:158:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_info.cpp:195:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable right [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_info.cpp:249:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_info.cpp:363:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_info.cpp:402:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_info.cpp:459:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.13.0 phyx-1.3.1/src/seq_models.cpp:21:17: warning: Either the condition 'line.empty()' is redundant or expression 'line[0]' cause access out of bounds. [containerOutOfBounds]
     phyx-1.3.1/src/seq_models.cpp:21:41: note: Assuming that condition 'line.empty()' is not redundant
     phyx-1.3.1/src/seq_models.cpp:21:17: note: Access out of bounds
head phyx-1.3.1/src/seq_models.cpp:21:17: warning: Either the condition 'line.empty()' is redundant or expression 'line[0]' causes access out of bounds. [containerOutOfBounds]
     phyx-1.3.1/src/seq_models.cpp:21:41: note: Assuming that condition 'line.empty()' is not redundant
     phyx-1.3.1/src/seq_models.cpp:21:17: note: Access out of bounds
head phyx-1.3.1/src/seq_reader.cpp:1092:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_reader.cpp:1192:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_reader.cpp:271:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_reader.cpp:344:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_reader.cpp:39:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_reader.cpp:627:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_reader.cpp:776:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_reader.cpp:87:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_reader.cpp:947:10: style: The scope of the variable 'first' can be reduced. [variableScope]
head phyx-1.3.1/src/seq_sample.cpp:211:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_sample.cpp:303:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_sample.cpp:325:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_sample.cpp:44:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_sample.h:43:31: performance: Function 'get_sampled_sites()' should return member 'sample_sites_' by const reference. [returnByReference]
head phyx-1.3.1/src/seq_utils.cpp:160:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_utils.cpp:256:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_utils.cpp:310:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_utils.cpp:393:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_utils.cpp:413:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/seq_utils.cpp:423:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/sequence.cpp:83:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/sequence.h:39:17: performance: Function 'get_sequence()' should return member 'seq_' by const reference. [returnByReference]
head phyx-1.3.1/src/sequence.h:40:17: performance: Function 'get_id()' should return member 'id_' by const reference. [returnByReference]
head phyx-1.3.1/src/sequence.h:53:25: performance: Function 'get_qualarr()' should return member 'qualarr_' by const reference. [returnByReference]
head phyx-1.3.1/src/sstat.cpp:108:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/sstat.cpp:18:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/state_reconstructor.cpp:133:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/state_reconstructor.cpp:184:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/state_reconstructor.cpp:48:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/string_node_object.h:19:14: style: The destructor '~StringNodeObject' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
     phyx-1.3.1/src/node_object.h:10:14: note: Virtual destructor in base class
     phyx-1.3.1/src/string_node_object.h:19:14: note: Destructor in derived class
head phyx-1.3.1/src/tgen.cpp:227:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/tlate.cpp:325:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/tree.cpp:264:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/tree_info.cpp:97:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boolalpha [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/tree_reader.cpp:259:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/tree_reader.cpp:294:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/tree_reader.cpp:385:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/tree_reader.cpp:447:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/tree_reader.cpp:47:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/tree_utils.cpp:150:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/tree_utils.cpp:198:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/tree_utils.cpp:215:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.13.0 phyx-1.3.1/src/tree_utils.cpp:224:17: style: Condition 'debug' is always true [knownConditionTrueFalse]
     phyx-1.3.1/src/tree_utils.cpp:210:18: note: Assignment 'debug=true', assigned value is 1
     phyx-1.3.1/src/tree_utils.cpp:224:17: note: Condition 'debug' is always true
2.13.0 phyx-1.3.1/src/tree_utils.cpp:232:17: style: Condition 'debug' is always true [knownConditionTrueFalse]
     phyx-1.3.1/src/tree_utils.cpp:210:18: note: Assignment 'debug=true', assigned value is 1
     phyx-1.3.1/src/tree_utils.cpp:223:41: note: Assuming condition is false
     phyx-1.3.1/src/tree_utils.cpp:232:17: note: Condition 'debug' is always true
2.13.0 phyx-1.3.1/src/tree_utils.cpp:241:25: style: Condition 'debug' is always true [knownConditionTrueFalse]
     phyx-1.3.1/src/tree_utils.cpp:210:18: note: Assignment 'debug=true', assigned value is 1
     phyx-1.3.1/src/tree_utils.cpp:223:41: note: Assuming condition is false
     phyx-1.3.1/src/tree_utils.cpp:241:25: note: Condition 'debug' is always true
2.13.0 phyx-1.3.1/src/tree_utils.cpp:250:21: style: Condition 'debug' is always true [knownConditionTrueFalse]
     phyx-1.3.1/src/tree_utils.cpp:210:18: note: Assignment 'debug=true', assigned value is 1
     phyx-1.3.1/src/tree_utils.cpp:223:41: note: Assuming condition is false
     phyx-1.3.1/src/tree_utils.cpp:250:21: note: Condition 'debug' is always true
2.13.0 phyx-1.3.1/src/tree_utils.cpp:262:13: style: Condition 'debug' is always true [knownConditionTrueFalse]
     phyx-1.3.1/src/tree_utils.cpp:210:18: note: Assignment 'debug=true', assigned value is 1
     phyx-1.3.1/src/tree_utils.cpp:223:41: note: Assuming condition is false
     phyx-1.3.1/src/tree_utils.cpp:262:13: note: Condition 'debug' is always true
2.13.0 phyx-1.3.1/src/tree_utils.cpp:269:25: style: Condition 'debug' is always true [knownConditionTrueFalse]
     phyx-1.3.1/src/tree_utils.cpp:210:18: note: Assignment 'debug=true', assigned value is 1
     phyx-1.3.1/src/tree_utils.cpp:223:41: note: Assuming condition is false
     phyx-1.3.1/src/tree_utils.cpp:269:25: note: Condition 'debug' is always true
2.13.0 phyx-1.3.1/src/tree_utils.cpp:277:17: style: Condition 'debug' is always true [knownConditionTrueFalse]
     phyx-1.3.1/src/tree_utils.cpp:210:18: note: Assignment 'debug=true', assigned value is 1
     phyx-1.3.1/src/tree_utils.cpp:223:41: note: Assuming condition is false
     phyx-1.3.1/src/tree_utils.cpp:277:17: note: Condition 'debug' is always true
2.13.0 phyx-1.3.1/src/tree_utils.cpp:285:9: style: Condition 'debug' is always true [knownConditionTrueFalse]
     phyx-1.3.1/src/tree_utils.cpp:210:18: note: Assignment 'debug=true', assigned value is 1
     phyx-1.3.1/src/tree_utils.cpp:223:41: note: Assuming condition is false
     phyx-1.3.1/src/tree_utils.cpp:285:9: note: Condition 'debug' is always true
head phyx-1.3.1/src/tree_utils.cpp:305:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/tree_utils.cpp:569:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/tree_utils.cpp:777:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/tree_utils.cpp:99:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/upgma.cpp:26:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/upgma.h:32:40: performance: Function 'get_matrix()' should return member 'full_distmatrix_' by const reference. [returnByReference]
head phyx-1.3.1/src/utils.cpp:103:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/utils.cpp:134:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/utils.cpp:207:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable eofbit [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/utils.cpp:243:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/utils.cpp:339:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/utils.cpp:42:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/utils.cpp:50:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/utils.cpp:576:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/utils.cpp:594:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/utils.cpp:63:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/utils.cpp:673:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/utils.cpp:691:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/utils.cpp:76:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/utils.cpp:781:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _1 [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/utils.cpp:809:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable POLLIN [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/utils.cpp:858:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/utils.cpp:875:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/utils.cpp:90:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/vcf_reader.cpp:103:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head phyx-1.3.1/src/vector_node_object.h:21:14: style: The destructor '~VectorNodeObject < Superdouble >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
     phyx-1.3.1/src/node_object.h:10:14: note: Virtual destructor in base class
     phyx-1.3.1/src/vector_node_object.h:21:14: note: Destructor in derived class
head phyx-1.3.1/src/vector_node_object.h:21:14: style: The destructor '~VectorNodeObject < double >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
     phyx-1.3.1/src/node_object.h:10:14: note: Virtual destructor in base class
     phyx-1.3.1/src/vector_node_object.h:21:14: note: Destructor in derived class
head phyx-1.3.1/src/vector_node_object.h:21:14: style: The destructor '~VectorNodeObject' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
     phyx-1.3.1/src/node_object.h:10:14: note: Virtual destructor in base class
     phyx-1.3.1/src/vector_node_object.h:21:14: note: Destructor in derived class


DONE