2025-11-23 17:53
ftp://ftp.de.debian.org/debian/pool/main/r/r-bioc-ebseq/r-bioc-ebseq_2.4.0.orig.tar.gz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=boost  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j4
platform: Linux-6.12.57+deb13-amd64-x86_64-with-glibc2.41
python: 3.13.5
client-version: 1.3.67
compiler: g++ (Debian 14.2.0-19) 14.2.0
cppcheck: head 2.18.0
head-info: cb76e52 (2025-11-22 14:47:37 +0100)
count: 108 108
elapsed-time: 0.4 0.4
head-timing-info:

old-timing-info:

head results:
EBSeq/src/EBSeq.hpp:69:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Rcout [valueFlowBailoutIncompleteVar]
EBSeq/src/negativeBinomial.hpp:22:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
EBSeq/src/negativeBinomial.hpp:217:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _clusinfo [valueFlowBailoutIncompleteVar]
EBSeq/src/negativeBinomial.hpp:311:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lgamma [valueFlowBailoutIncompleteVar]
EBSeq/src/negativeBinomial.hpp:922:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lgamma [valueFlowBailoutIncompleteVar]
EBSeq/src/negativeBinomial.hpp:950:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable digamma [valueFlowBailoutIncompleteVar]
EBSeq/src/negativeBinomial.hpp:20:9: warning: Member variable 'NB::_nequal' is not initialized in the constructor. [uninitMemberVar]
EBSeq/src/negativeBinomial.hpp:20:9: warning: Member variable 'NB::_alpha' is not initialized in the constructor. [uninitMemberVar]
EBSeq/src/negativeBinomial.hpp:20:9: warning: Member variable 'NB::_ng' is not initialized in the constructor. [uninitMemberVar]
EBSeq/src/negativeBinomial.hpp:20:9: warning: Member variable 'NB::_uncertainty' is not initialized in the constructor. [uninitMemberVar]
EBSeq/src/negativeBinomial.hpp:20:9: warning: Member variable 'NB::_filter' is not initialized in the constructor. [uninitMemberVar]
EBSeq/src/negativeBinomial.hpp:20:9: warning: Member variable 'NB::_threshold' is not initialized in the constructor. [uninitMemberVar]
EBSeq/src/negativeBinomial.hpp:20:9: warning: Member variable 'NB::_shrinkthre' is not initialized in the constructor. [uninitMemberVar]
EBSeq/src/negativeBinomial.hpp:214:9: warning: Member variable 'NB::_nequal' is not initialized in the constructor. [uninitMemberVar]
EBSeq/src/negativeBinomial.hpp:214:9: warning: Member variable 'NB::_alpha' is not initialized in the constructor. [uninitMemberVar]
EBSeq/src/negativeBinomial.hpp:214:9: warning: Member variable 'NB::_ng' is not initialized in the constructor. [uninitMemberVar]
EBSeq/src/negativeBinomial.hpp:214:9: warning: Member variable 'NB::_uncertainty' is not initialized in the constructor. [uninitMemberVar]
EBSeq/src/negativeBinomial.hpp:214:9: warning: Member variable 'NB::_filter' is not initialized in the constructor. [uninitMemberVar]
EBSeq/src/negativeBinomial.hpp:214:9: warning: Member variable 'NB::_threshold' is not initialized in the constructor. [uninitMemberVar]
EBSeq/src/negativeBinomial.hpp:214:9: warning: Member variable 'NB::_shrinkthre' is not initialized in the constructor. [uninitMemberVar]
EBSeq/src/negativeBinomial.hpp:214:9: warning: Member variable 'NB::_has_user_specified_parti' is not initialized in the constructor. [uninitMemberVar]
EBSeq/src/EBSeq.hpp:19:13: performance: Variable '_clusinfo' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
EBSeq/src/EBSeq.hpp:28:16: style:inconclusive: Technically the member function 'EBS::EBSeq::getSUM' can be const. [functionConst]
EBSeq/src/EBSeq.hpp:33:16: style:inconclusive: Technically the member function 'EBS::EBSeq::getMEAN' can be const. [functionConst]
EBSeq/src/negativeBinomial.hpp:304:22: performance:inconclusive: Technically the member function 'EBS::NB::lbeta' can be static (but you may consider moving to unnamed namespace). [functionStatic]
EBSeq/src/negativeBinomial.hpp:341:39: style:inconclusive: Technically the member function 'EBS::NB::getDEP' can be const. [functionConst]
EBSeq/src/negativeBinomial.hpp:346:16: style:inconclusive: Technically the member function 'EBS::NB::getR' can be const. [functionConst]
EBSeq/src/negativeBinomial.hpp:352:16: style:inconclusive: Technically the member function 'EBS::NB::getVar' can be const. [functionConst]
EBSeq/src/negativeBinomial.hpp:357:16: style:inconclusive: Technically the member function 'EBS::NB::getQ' can be const. [functionConst]
EBSeq/src/negativeBinomial.hpp:362:16: style:inconclusive: Technically the member function 'EBS::NB::getPoolVar' can be const. [functionConst]
EBSeq/src/negativeBinomial.hpp:367:29: style:inconclusive: Technically the member function 'EBS::NB::getGUC' can be const. [functionConst]
EBSeq/src/negativeBinomial.hpp:372:29: style:inconclusive: Technically the member function 'EBS::NB::getPAT' can be const. [functionConst]
EBSeq/src/negativeBinomial.hpp:378:16: style:inconclusive: Technically the member function 'EBS::NB::getKernel' can be const. [functionConst]
EBSeq/src/negativeBinomial.hpp:388:15: style:inconclusive: Technically the member function 'EBS::NB::getALP' can be const. [functionConst]
EBSeq/src/negativeBinomial.hpp:393:25: style:inconclusive: Technically the member function 'EBS::NB::getBETA' can be const. [functionConst]
EBSeq/src/negativeBinomial.hpp:420:25: style:inconclusive: Technically the member function 'EBS::NB::getP' can be const. [functionConst]
EBSeq/src/negativeBinomial.hpp:792:14: style:inconclusive: Technically the member function 'EBS::NB::equalHandle' can be const. [functionConst]
EBSeq/src/negativeBinomial.hpp:336:16: style: The function 'DEPsize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
EBSeq/src/EBSeq.hpp:123:24: note: Virtual function in base class
EBSeq/src/negativeBinomial.hpp:336:16: note: Function in derived class
EBSeq/src/negativeBinomial.hpp:398:16: style: The function 'getPOST' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
EBSeq/src/EBSeq.hpp:39:24: note: Virtual function in base class
EBSeq/src/negativeBinomial.hpp:398:16: note: Function in derived class
EBSeq/src/negativeBinomial.hpp:403:15: style: The function 'getOBJ' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
EBSeq/src/EBSeq.hpp:120:23: note: Virtual function in base class
EBSeq/src/negativeBinomial.hpp:403:15: note: Function in derived class
EBSeq/src/negativeBinomial.hpp:427:14: style: The function 'Estep' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
EBSeq/src/EBSeq.hpp:111:22: note: Virtual function in base class
EBSeq/src/negativeBinomial.hpp:427:14: note: Function in derived class
EBSeq/src/negativeBinomial.hpp:436:14: style: The function 'Mstep' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
EBSeq/src/EBSeq.hpp:114:22: note: Virtual function in base class
EBSeq/src/negativeBinomial.hpp:436:14: note: Function in derived class
EBSeq/src/negativeBinomial.hpp:579:14: style: The function 'DEpat' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
EBSeq/src/EBSeq.hpp:108:22: note: Virtual function in base class
EBSeq/src/negativeBinomial.hpp:579:14: note: Function in derived class
EBSeq/src/negativeBinomial.hpp:843:14: style: The function 'shrinkage' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
EBSeq/src/EBSeq.hpp:117:22: note: Virtual function in base class
EBSeq/src/negativeBinomial.hpp:843:14: note: Function in derived class
EBSeq/src/negativeBinomial.hpp:903:14: style: The function 'kernel' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
EBSeq/src/EBSeq.hpp:105:22: note: Virtual function in base class
EBSeq/src/negativeBinomial.hpp:903:14: note: Function in derived class
EBSeq/src/negativeBinomial.hpp:930:14: style: The function 'gradientAscent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
EBSeq/src/EBSeq.hpp:102:22: note: Virtual function in base class
EBSeq/src/negativeBinomial.hpp:930:14: note: Function in derived class
EBSeq/src/negativeBinomial.hpp:341:39: performance: Function 'getDEP()' should return member '_dep' by const reference. [returnByReference]
EBSeq/src/negativeBinomial.hpp:367:29: performance: Function 'getGUC()' should return member '_guc' by const reference. [returnByReference]
EBSeq/src/negativeBinomial.hpp:372:29: performance: Function 'getPAT()' should return member '_pat' by const reference. [returnByReference]
EBSeq/src/negativeBinomial.hpp:145:31: style: Redundant initialization for 'maxholder'. The initialized value is overwritten before it is read. [redundantInitialization]
EBSeq/src/negativeBinomial.hpp:139:36: note: maxholder is initialized
EBSeq/src/negativeBinomial.hpp:145:31: note: maxholder is overwritten
EBSeq/src/negativeBinomial.hpp:151:31: style: Variable 'maxholder' is reassigned a value before the old one has been used. [redundantAssignment]
EBSeq/src/negativeBinomial.hpp:145:31: note: maxholder is assigned
EBSeq/src/negativeBinomial.hpp:151:31: note: maxholder is overwritten
EBSeq/src/loadData.hpp:21:21: style: The scope of the variable 'element' can be reduced. [variableScope]
EBSeq/src/loadData.hpp:23:21: style: The scope of the variable 'line' can be reduced. [variableScope]
EBSeq/src/loadData.hpp:27:16: style: The scope of the variable 'i' can be reduced. [variableScope]
EBSeq/src/loadData.hpp:27:22: style: The scope of the variable 'j' can be reduced. [variableScope]
EBSeq/src/agglomerativeClustering.hpp:74:19: style: The scope of the variable 'minDist' can be reduced. [variableScope]
EBSeq/src/agglomerativeClustering.hpp:76:19: style: The scope of the variable 'minDistNode' can be reduced. [variableScope]
EBSeq/src/negativeBinomial.hpp:222:71: performance: Function parameter 'iLabel' should be passed by const reference. [passedByValue]
EBSeq/src/negativeBinomial.hpp:222:98: performance: Function parameter 'lrate' should be passed by const reference. [passedByValue]
EBSeq/src/negativeBinomial.hpp:751:26: performance: Range variable 'x' should be declared as const reference. [iterateByValue]
EBSeq/src/loadData.hpp:15:33: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
EBSeq/src/partition.hpp:70:61: style: Parameter 'part' can be declared as reference to const [constParameterReference]
EBSeq/src/partition.hpp:85:62: style: Parameter 'bits' can be declared as reference to const [constParameterReference]
EBSeq/src/partition.hpp:139:59: style: Parameter 'part' can be declared as reference to const [constParameterReference]
EBSeq/src/partition.hpp:196:51: style: Parameter 'part' can be declared as reference to const [constParameterReference]
EBSeq/src/helper.hpp:58:48: style: Parameter 'clus' can be declared as reference to const [constParameterReference]
EBSeq/src/aggregate.hpp:16:40: style: Parameter 'vec' can be declared as reference to const [constParameterReference]
EBSeq/src/aggregate.hpp:16:55: style: Parameter 'clusInfo' can be declared as reference to const [constParameterReference]
EBSeq/src/aggregate.hpp:35:49: style: Parameter 'clusInfo' can be declared as reference to const [constParameterReference]
EBSeq/src/aggregate.hpp:54:49: style: Parameter 'clusInfo' can be declared as reference to const [constParameterReference]
EBSeq/src/aggregate.hpp:54:76: style: Parameter 'sizeFactor' can be declared as reference to const [constParameterReference]
EBSeq/src/aggregate.hpp:73:51: style: Parameter 'clusInfo' can be declared as reference to const [constParameterReference]
EBSeq/src/aggregate.hpp:93:68: style: Parameter 'clusInfo' can be declared as reference to const [constParameterReference]
EBSeq/src/aggregate.hpp:114:68: style: Parameter 'clusInfo' can be declared as reference to const [constParameterReference]
EBSeq/src/aggregate.hpp:114:95: style: Parameter 'sizeFactor' can be declared as reference to const [constParameterReference]
EBSeq/src/agglomerativeClustering.hpp:181:44: style: Parameter 'cs1' can be declared as reference to const [constParameterReference]
EBSeq/src/agglomerativeClustering.hpp:181:56: style: Parameter 'cs2' can be declared as reference to const [constParameterReference]
EBSeq/src/agglomerativeClustering.hpp:181:68: style: Parameter 'rs1' can be declared as reference to const [constParameterReference]
EBSeq/src/agglomerativeClustering.hpp:181:80: style: Parameter 'rs2' can be declared as reference to const [constParameterReference]
EBSeq/src/agglomerativeClustering.hpp:181:92: style: Parameter 'alpha' can be declared as reference to const [constParameterReference]
EBSeq/src/agglomerativeClustering.hpp:181:106: style: Parameter 'beta' can be declared as reference to const [constParameterReference]
EBSeq/src/agglomerativeClustering.hpp:181:117: style: Parameter 'n1' can be declared as reference to const [constParameterReference]
EBSeq/src/agglomerativeClustering.hpp:181:126: style: Parameter 'n2' can be declared as reference to const [constParameterReference]
EBSeq/src/agglomerativeClustering.hpp:181:137: style: Parameter 'filter' can be declared as reference to const [constParameterReference]
EBSeq/src/negativeBinomial.hpp:20:128: style: Parameter 'AllParti' can be declared as reference to const [constParameterReference]
EBSeq/src/negativeBinomial.hpp:214:113: style: Parameter 'r' can be declared as reference to const [constParameterReference]
EBSeq/src/negativeBinomial.hpp:408:57: style: Parameter 'beta' can be declared as reference to const [constParameterReference]
EBSeq/src/negativeBinomial.hpp:415:36: style: Parameter 'p' can be declared as reference to const [constParameterReference]
EBSeq/src/negativeBinomial.hpp:792:45: style: Parameter 'baseBit' can be declared as reference to const [constParameterReference]
EBSeq/src/negativeBinomial.hpp:793:33: style: Parameter 'alpha' can be declared as reference to const [constParameterReference]
EBSeq/src/negativeBinomial.hpp:793:47: style: Parameter 'beta' can be declared as reference to const [constParameterReference]
EBSeq/src/negativeBinomial.hpp:793:60: style: Parameter 'th1' can be declared as reference to const [constParameterReference]
EBSeq/src/negativeBinomial.hpp:793:72: style: Parameter 'th2' can be declared as reference to const [constParameterReference]
EBSeq/src/negativeBinomial.hpp:889:34: style: Parameter 's1' can be declared as reference to const [constParameterReference]
EBSeq/src/negativeBinomial.hpp:889:45: style: Parameter 's2' can be declared as reference to const [constParameterReference]
EBSeq/src/negativeBinomial.hpp:889:56: style: Parameter 'r1' can be declared as reference to const [constParameterReference]
EBSeq/src/negativeBinomial.hpp:889:67: style: Parameter 'r2' can be declared as reference to const [constParameterReference]
EBSeq/src/negativeBinomial.hpp:890:32: style: Parameter 'n1' can be declared as reference to const [constParameterReference]
EBSeq/src/negativeBinomial.hpp:890:41: style: Parameter 'n2' can be declared as reference to const [constParameterReference]
EBSeq/src/negativeBinomial.hpp:890:52: style: Parameter 'alpha' can be declared as reference to const [constParameterReference]
EBSeq/src/negativeBinomial.hpp:890:66: style: Parameter 'beta' can be declared as reference to const [constParameterReference]
EBSeq/src/negativeBinomial.hpp:890:79: style: Parameter 'filter' can be declared as reference to const [constParameterReference]
EBSeq/src/partition.hpp:183:40: style: Parameter 'part' can be declared as reference to const [constParameterReference]
EBSeq/src/negativeBinomial.hpp:740:36: performance: Searching before insertion is not necessary. [stlFindInsert]
EBSeq/src/negativeBinomial.hpp:778:36: performance: Searching before insertion is not necessary. [stlFindInsert]
EBSeq/src/helper.hpp:50:20: style: Consider using std::copy_if algorithm instead of a raw loop. [useStlAlgorithm]
EBSeq/src/negativeBinomial.hpp:252:35: style: Consider using std::copy_if algorithm instead of a raw loop. [useStlAlgorithm]
EBSeq/src/negativeBinomial.hpp:711:25: style: Consider using std::count_if algorithm instead of a raw loop. [useStlAlgorithm]
diff:


DONE