2024-03-26 08:56 ftp://ftp.de.debian.org/debian/pool/main/a/abyss/abyss_2.3.7.orig.tar.xz cppcheck-options: --library=posix --library=gnu --showtime=top5 --check-library --inconclusive --enable=style,information --inline-suppr --disable=missingInclude --suppress=unmatchedSuppression --template=daca2 --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=valueFlowBailoutIncompleteVar -D__GNUC__ --platform=unix64 -j4 platform: Linux-6.1.0-0.deb11.6-amd64-x86_64-with-glibc2.31 python: 3.9.2 client-version: 1.3.45 compiler: g++ (Debian 10.2.1-6) 10.2.1 20210110 cppcheck: head 2.13.0 head-info: 82f05c8 (2024-03-25 22:58:58 +0100) count: 629 615 elapsed-time: 4.4 13.7 head-timing-info: Tokenizer::simplifyTokens1::ValueFlow: 3.83491s (avg. 3.83491s - 1 result(s)) valueFlowLifetime(tokenlist, errorLogger, settings): 1.05913s (avg. 0.264782s - 4 result(s)) valueFlowUninit(tokenlist, errorLogger, settings): 0.768621s (avg. 0.256207s - 3 result(s)) valueFlowAfterAssign(tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 0.633255s (avg. 0.211085s - 3 result(s)) valueFlowCondition(SymbolicConditionHandler{}, tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 0.610074s (avg. 0.203358s - 3 result(s)) Overall time: 3.9187s old-timing-info: Tokenizer::simplifyTokens1::ValueFlow: 13.2453s (avg. 13.2453s - 1 result(s)) valueFlowLifetime(tokenlist, errorLogger, settings): 8.2164s (avg. 1.64328s - 5 result(s)) valueFlowConditionExpressions(tokenlist, symboldatabase, errorLogger, *settings): 1.73592s (avg. 1.73592s - 1 result(s)) valueFlowAfterAssign(tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 1.41618s (avg. 0.354045s - 4 result(s)) valueFlowCondition(SimpleConditionHandler{}, tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 0.654347s (avg. 0.163587s - 4 result(s)) Overall time: 13.3322s head results: abyss-2.3.7/AdjList/AdjList.cpp:38:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/Align/align.cc:22:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/Align/mergepairs.cc:24:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/Align/alignGlobal.h:19:11: style:inconclusive: Technically the member function 'NWAlignment::size' can be const. [functionConst] abyss-2.3.7/Align/alignGlobal.h:20:14: style:inconclusive: Technically the member function 'NWAlignment::consensus' can be const. [functionConst] abyss-2.3.7/Align/alignGlobal.cc:144:36: style:inconclusive: Function 'alignGlobal' argument 1 names different: declaration 'a' definition 'seqA'. [funcArgNamesDifferent] abyss-2.3.7/Align/alignGlobal.h:41:22: note: Function 'alignGlobal' argument 1 names different: declaration 'a' definition 'seqA'. abyss-2.3.7/Align/alignGlobal.cc:144:36: note: Function 'alignGlobal' argument 1 names different: declaration 'a' definition 'seqA'. abyss-2.3.7/Align/alignGlobal.cc:144:56: style:inconclusive: Function 'alignGlobal' argument 2 names different: declaration 'b' definition 'seqB'. [funcArgNamesDifferent] abyss-2.3.7/Align/alignGlobal.h:41:44: note: Function 'alignGlobal' argument 2 names different: declaration 'b' definition 'seqB'. abyss-2.3.7/Align/alignGlobal.cc:144:56: note: Function 'alignGlobal' argument 2 names different: declaration 'b' definition 'seqB'. abyss-2.3.7/Align/alignGlobal.cc:86:9: style: Local variable 'a' shadows outer variable [shadowVariable] abyss-2.3.7/Align/alignGlobal.cc:65:8: note: Shadowed declaration abyss-2.3.7/Align/alignGlobal.cc:86:9: note: Shadow variable abyss-2.3.7/Align/alignGlobal.cc:78:10: style: Local variable 'a' shadows outer variable [shadowVariable] abyss-2.3.7/Align/alignGlobal.cc:65:8: note: Shadowed declaration abyss-2.3.7/Align/alignGlobal.cc:78:10: note: Shadow variable abyss-2.3.7/Align/alignGlobal.cc:102:9: style: Local variable 'b' shadows outer variable [shadowVariable] abyss-2.3.7/Align/alignGlobal.cc:65:23: note: Shadowed declaration abyss-2.3.7/Align/alignGlobal.cc:102:9: note: Shadow variable abyss-2.3.7/Align/alignGlobal.cc:94:10: style: Local variable 'b' shadows outer variable [shadowVariable] abyss-2.3.7/Align/alignGlobal.cc:65:23: note: Shadowed declaration abyss-2.3.7/Align/alignGlobal.cc:94:10: note: Shadow variable abyss-2.3.7/Assembly/Options.cc:26:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/BloomDBG/bloom-dbg.cc:37:18: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/Common/ConstString.h:106:1: error: There is an unknown macro here somewhere. Configuration is required. If NAMESPACE_STD_HASH_BEGIN is a macro then please configure it. [unknownMacro] abyss-2.3.7/Bloom/bloom.cc:50:18: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/Common/Kmer.h:155:1: error: There is an unknown macro here somewhere. Configuration is required. If NAMESPACE_STD_HASH_BEGIN is a macro then please configure it. [unknownMacro] abyss-2.3.7/Align/dialign.cpp:333:28: style: Expression is always false because 'else if' condition matches previous condition at line 328. [multiCondition] abyss-2.3.7/Align/dialign.cpp:194:22: warning: Either the condition 'scol==NULL' is redundant or there is possible null pointer dereference: scol. [nullPointerRedundantCheck] abyss-2.3.7/Align/dialign.cpp:195:9: note: Assuming that condition 'scol==NULL' is not redundant abyss-2.3.7/Align/dialign.cpp:194:22: note: Null pointer dereference abyss-2.3.7/Align/dialign.cpp:28:25: style: C-style pointer casting [cstyleCast] abyss-2.3.7/Align/dialign.cpp:30:16: style: C-style pointer casting [cstyleCast] abyss-2.3.7/Align/dialign.cpp:31:16: style: C-style pointer casting [cstyleCast] abyss-2.3.7/Align/dialign.cpp:38:12: style: C-style pointer casting [cstyleCast] abyss-2.3.7/Align/dialign.cpp:45:12: style: C-style pointer casting [cstyleCast] abyss-2.3.7/Align/dialign.cpp:56:17: style: C-style pointer casting [cstyleCast] abyss-2.3.7/Align/dialign.cpp:60:12: style: C-style pointer casting [cstyleCast] abyss-2.3.7/Align/dialign.cpp:62:16: style: C-style pointer casting [cstyleCast] abyss-2.3.7/Align/dialign.cpp:69:13: style: C-style pointer casting [cstyleCast] abyss-2.3.7/Align/dialign.cpp:71:17: style: C-style pointer casting [cstyleCast] abyss-2.3.7/Align/dialign.cpp:193:26: style: C-style pointer casting [cstyleCast] abyss-2.3.7/Align/dialign.cpp:194:36: style: C-style pointer casting [cstyleCast] abyss-2.3.7/Align/dialign.cpp:212:15: style: C-style pointer casting [cstyleCast] abyss-2.3.7/Align/dialign.cpp:312:18: style: C-style pointer casting [cstyleCast] abyss-2.3.7/Align/dialign.cpp:202:7: style: The scope of the variable 'seq' can be reduced. [variableScope] abyss-2.3.7/Align/dialign.cpp:279:6: style: The scope of the variable 'i' can be reduced. [variableScope] abyss-2.3.7/Align/dialign.cpp:194:14: style: Variable 'seqs' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/Align/dialign.cpp:235:15: style: Variable 'sq' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/Align/dialign.cpp:241:20: style: Variable 'ap1' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/Align/dialign.cpp:344:16: style: Variable 'newFound' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/Common/Timer.h:13:3: style: Class 'Timer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/Align/smith_waterman.cpp:58:2: style: Struct 'index_cmp < double * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/Align/smith_waterman.cpp:244:11: style: The scope of the variable 'num_of_match' can be reduced. [variableScope] abyss-2.3.7/Align/smith_waterman.cpp:245:9: style: The scope of the variable 'H_max' can be reduced. [variableScope] abyss-2.3.7/Align/smith_waterman.cpp:246:17: style: The scope of the variable 'j_max' can be reduced. [variableScope] abyss-2.3.7/Align/smith_waterman.cpp:35:36: performance: Function parameter 'align' should be passed by const reference. [passedByValue] abyss-2.3.7/Align/smith_waterman.cpp:35:12: style: Parameter 'alignPos' can be declared as const array [constParameter] abyss-2.3.7/Align/smith_waterman.cpp:215:11: style: Variable 'scores' can be declared as const array [constVariable] abyss-2.3.7/Align/smith_waterman.cpp:223:12: style: Variable 'pMax' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/Align/smith_waterman.cpp:244:24: style: Variable 'num_of_match' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/Align/smith_waterman.cpp:245:15: style: Variable 'H_max' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/Common/Sequence.h:51:33: style: Parameter 'seq' can be declared as reference to const [constParameterReference] abyss-2.3.7/Consensus/Consensus.cpp:22:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/DAssembler/DAssembler.cpp:22:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/DAssembler/RotatedRead.h:9:7: style: Class 'RotatedRead' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/DataBase/DB.h:120:2: warning: Member variable 'DB::db' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/DataBase/DB.h:120:2: warning: Member variable 'DB::stmt' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/DataBase/DB.h:120:2: warning: Member variable 'DB::verbose_val' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/DataBase/DB.h:49:14: performance:inconclusive: Technically the member function 'DB::getSqliteName' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/DataBase/DB.h:58:7: performance:inconclusive: Technically the member function 'DB::openDB' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/DataBase/DB.h:94:7: performance:inconclusive: Technically the member function 'DB::closeDB' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/DataBase/DB.h:181:14: performance:inconclusive: Technically the member function 'DB::activateForeignKey' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/DataBase/DB.h:187:7: performance:inconclusive: Technically the member function 'DB::query' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/DataBase/DB.h:80:17: style: C-style pointer casting [cstyleCast] abyss-2.3.7/DataBase/DB.h:140:8: style: Parameter 'd' can be declared as reference to const [constParameterReference] abyss-2.3.7/DataBase/DB.h:154:8: style: Parameter 'd' can be declared as reference to const [constParameterReference] abyss-2.3.7/DataBase/DB.h:77:10: style: Parameter 'info' can be declared as pointer to const [constParameterPointer] abyss-2.3.7/Common/Histogram.h:196:23: style: Local variable 'minimum' shadows outer function [shadowFunction] abyss-2.3.7/Common/Histogram.h:73:4: note: Shadowed declaration abyss-2.3.7/Common/Histogram.h:196:23: note: Shadow variable abyss-2.3.7/Common/Histogram.h:197:13: style: Local variable 'count' shadows outer function [shadowFunction] abyss-2.3.7/Common/Histogram.h:55:12: note: Shadowed declaration abyss-2.3.7/Common/Histogram.h:197:13: note: Shadow variable abyss-2.3.7/Common/Histogram.h:303:13: style: Local variable 'count' shadows outer function [shadowFunction] abyss-2.3.7/Common/Histogram.h:55:12: note: Shadowed declaration abyss-2.3.7/Common/Histogram.h:303:13: note: Shadow variable abyss-2.3.7/Common/Histogram.cpp:51:30: style: Local variable 'count' shadows outer function [shadowFunction] abyss-2.3.7/Common/Histogram.h:55:12: note: Shadowed declaration abyss-2.3.7/Common/Histogram.cpp:51:30: note: Shadow variable abyss-2.3.7/Common/Histogram.h:69:6: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] abyss-2.3.7/Common/Histogram.h:90:6: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] abyss-2.3.7/Common/Histogram.h:100:10: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] abyss-2.3.7/Common/Histogram.h:181:10: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] abyss-2.3.7/Common/Histogram.h:180:24: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] abyss-2.3.7/Common/Histogram.cpp:14:23: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] abyss-2.3.7/Common/Histogram.cpp:32:23: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] abyss-2.3.7/Common/Histogram.cpp:53:23: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] abyss-2.3.7/DataLayer/FastaWriter.cpp:21:18: warning: Class 'FastaWriter' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] abyss-2.3.7/DataLayer/FastaWriter.cpp:21:18: warning: Class 'FastaWriter' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] abyss-2.3.7/DataLayer/FastaWriter.h:11:3: style: Class 'FastaWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/DataLayer/abyss-tofastq.cc:22:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/DataLayer/fac.cc:21:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/DistanceEst/DistanceEst.cpp:33:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/DataBase/DB.h:49:14: style: Unused private function: 'DB::getSqliteName' [unusedPrivateFunction] abyss-2.3.7/DataBase/DB.h:58:7: style: Unused private function: 'DB::openDB' [unusedPrivateFunction] abyss-2.3.7/DataBase/DB.h:76:13: style: Unused private function: 'DB::callback' [unusedPrivateFunction] abyss-2.3.7/DataBase/DB.h:88:22: style: Unused private function: 'DB::getRand' [unusedPrivateFunction] abyss-2.3.7/DataBase/DB.h:112:14: performance:inconclusive: Technically the member function 'DB::getPath' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/DataBase/DB.cc:116:12: note: Technically the member function 'DB::getPath' can be static (but you may consider moving to unnamed namespace). abyss-2.3.7/DataBase/DB.h:112:14: note: Technically the member function 'DB::getPath' can be static (but you may consider moving to unnamed namespace). abyss-2.3.7/DataBase/DB.h:228:14: performance:inconclusive: Technically the member function 'DB::getProperTableName' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/DataBase/DB.cc:36:12: note: Technically the member function 'DB::getProperTableName' can be static (but you may consider moving to unnamed namespace). abyss-2.3.7/DataBase/DB.h:228:14: note: Technically the member function 'DB::getProperTableName' can be static (but you may consider moving to unnamed namespace). abyss-2.3.7/DataBase/DB.cc:62:11: style: Condition 'query(sst.str())' is always true [knownConditionTrueFalse] abyss-2.3.7/DataBase/DB.cc:62:11: note: Calling function 'query' returns 1 abyss-2.3.7/DataBase/DB.cc:62:11: note: Condition 'query(sst.str())' is always true abyss-2.3.7/DataBase/DB.cc:78:11: style: Condition 'query(sst.str())' is always true [knownConditionTrueFalse] abyss-2.3.7/DataBase/DB.cc:78:11: note: Calling function 'query' returns 1 abyss-2.3.7/DataBase/DB.cc:78:11: note: Condition 'query(sst.str())' is always true abyss-2.3.7/DataBase/DB.cc:99:13: style: Condition 'query(uStream.str())' is always true [knownConditionTrueFalse] abyss-2.3.7/DataBase/DB.cc:99:13: note: Calling function 'query' returns 1 abyss-2.3.7/DataBase/DB.cc:99:13: note: Condition 'query(uStream.str())' is always true abyss-2.3.7/DataBase/DB.cc:199:11: style: Condition 'query(sqlStream.str())' is always true [knownConditionTrueFalse] abyss-2.3.7/DataBase/DB.cc:199:11: note: Calling function 'query' returns 1 abyss-2.3.7/DataBase/DB.cc:199:11: note: Condition 'query(sqlStream.str())' is always true abyss-2.3.7/DataBase/DB.cc:206:11: style: Condition 'query(sqlStream.str())' is always true [knownConditionTrueFalse] abyss-2.3.7/DataBase/DB.cc:206:11: note: Calling function 'query' returns 1 abyss-2.3.7/DataBase/DB.cc:206:11: note: Condition 'query(sqlStream.str())' is always true abyss-2.3.7/DataBase/DB.cc:139:7: error: Out of bounds access in expression 'v[0]' because 'v' is empty. [containerOutOfBounds] abyss-2.3.7/DataBase/DB.cc:138:18: note: Calling function 'readSqlToVec' returns size=0 abyss-2.3.7/DataBase/DB.cc:138:18: note: Assignment 'v=readSqlToVec(select_cmd.str())', assigned value is size=0 abyss-2.3.7/DataBase/DB.cc:139:7: note: Access out of bounds abyss-2.3.7/DataBase/DB.cc:141:13: error: Out of bounds access in expression 'v[0]' because 'v' is empty. [containerOutOfBounds] abyss-2.3.7/DataBase/DB.cc:138:18: note: Calling function 'readSqlToVec' returns size=0 abyss-2.3.7/DataBase/DB.cc:138:18: note: Assignment 'v=readSqlToVec(select_cmd.str())', assigned value is size=0 abyss-2.3.7/DataBase/DB.cc:141:13: note: Access out of bounds abyss-2.3.7/DataBase/DB.cc:142:17: error: Out of bounds access in expression 'v[0]' because 'v' is empty. [containerOutOfBounds] abyss-2.3.7/DataBase/DB.cc:138:18: note: Calling function 'readSqlToVec' returns size=0 abyss-2.3.7/DataBase/DB.cc:138:18: note: Assignment 'v=readSqlToVec(select_cmd.str())', assigned value is size=0 abyss-2.3.7/DataBase/DB.cc:142:17: note: Access out of bounds abyss-2.3.7/FMIndex/abyss-dawg.cc:24:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/DistanceEst/MLE.cpp:134:32: warning: Invalid std::log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg] abyss-2.3.7/DistanceEst/MLE.cpp:127:14: note: Assignment 'c=0', assigned value is 0 abyss-2.3.7/DistanceEst/MLE.cpp:128:34: note: Assuming condition is false abyss-2.3.7/DistanceEst/MLE.cpp:134:32: note: Invalid argument abyss-2.3.7/DistanceEst/MLE.cpp:44:3: style: Class 'HannWindow' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/DistanceEst/MLE.cpp:164:40: style:inconclusive: Function 'maximumLikelihoodEstimate' argument 1 names different: declaration 'k' definition 'l'. [funcArgNamesDifferent] abyss-2.3.7/DistanceEst/MLE.h:8:40: note: Function 'maximumLikelihoodEstimate' argument 1 names different: declaration 'k' definition 'l'. abyss-2.3.7/DistanceEst/MLE.cpp:164:40: note: Function 'maximumLikelihoodEstimate' argument 1 names different: declaration 'k' definition 'l'. abyss-2.3.7/DistanceEst/MLE.cpp:66:11: style: Local variable 'sum' shadows outer variable [shadowVariable] abyss-2.3.7/DistanceEst/MLE.cpp:73:10: note: Shadowed declaration abyss-2.3.7/DistanceEst/MLE.cpp:66:11: note: Shadow variable abyss-2.3.7/FilterGraph/FilterGraph.cc:40:18: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/FMIndex/count.cc:22:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/FMIndex/bit_array.cc:151:5: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg] abyss-2.3.7/FMIndex/bit_array.h:44:3: style: Class 'BitArray' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/FMIndex/bit_array.cc:203:13: style: C-style pointer casting [cstyleCast] abyss-2.3.7/FMIndex/bit_array.cc:204:13: style: C-style pointer casting [cstyleCast] abyss-2.3.7/FMIndex/bit_array.cc:209:11: style: C-style pointer casting [cstyleCast] abyss-2.3.7/FMIndex/bit_array.cc:211:11: style: C-style pointer casting [cstyleCast] abyss-2.3.7/FMIndex/bit_array.cc:29:29: style:inconclusive: Function 'BitArray' argument 1 names different: declaration 'size' definition 'length'. [funcArgNamesDifferent] abyss-2.3.7/FMIndex/bit_array.h:44:21: note: Function 'BitArray' argument 1 names different: declaration 'size' definition 'length'. abyss-2.3.7/FMIndex/bit_array.cc:29:29: note: Function 'BitArray' argument 1 names different: declaration 'size' definition 'length'. abyss-2.3.7/FMIndex/bit_array.cc:44:30: style:inconclusive: Function 'Init' argument 1 names different: declaration 'size' definition 'length'. [funcArgNamesDifferent] abyss-2.3.7/FMIndex/bit_array.h:48:22: note: Function 'Init' argument 1 names different: declaration 'size' definition 'length'. abyss-2.3.7/FMIndex/bit_array.cc:44:30: note: Function 'Init' argument 1 names different: declaration 'size' definition 'length'. abyss-2.3.7/FMIndex/bit_array.cc:100:14: style: Local variable 'length' shadows outer function [shadowFunction] abyss-2.3.7/FMIndex/bit_array.h:45:12: note: Shadowed declaration abyss-2.3.7/FMIndex/bit_array.cc:100:14: note: Shadow variable abyss-2.3.7/FMIndex/bit_array.cc:151:10: style: Variable 'rank' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/GapFiller/gapfill.cpp:28:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/KAligner/KAligner.cpp:34:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/Graph/SAMIO.h:30:36: error: There is an unknown macro here somewhere. Configuration is required. If VERSION is a macro then please configure it. [unknownMacro] abyss-2.3.7/Layout/layout.cc:26:52: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/LogKmerCount/logcounter.cc:28:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/Konnector/konnector.cc:41:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/Map/index.cc:23:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/Map/overlap.cc:44:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/Map/map.cc:38:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/MergePaths/MergeContigs.cpp:39:18: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/MergePaths/PathConsensus.cpp:39:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/Overlap/Overlap.cpp:39:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/MergePaths/MergePaths.cpp:43:18: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/PairedDBG/KmerPair.h:220:1: error: There is an unknown macro here somewhere. Configuration is required. If NAMESPACE_STD_HASH_BEGIN is a macro then please configure it. [unknownMacro] abyss-2.3.7/Parallel/Messages.h:96:3: warning:inconclusive: Member variable 'SetFlagMessage::m_flag' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/Parallel/Messages.h:117:3: warning:inconclusive: Member variable 'RemoveExtensionMessage::m_dir' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/Parallel/Messages.h:141:3: warning:inconclusive: Member variable 'SeqDataRequest::m_group' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/Parallel/Messages.h:141:3: warning:inconclusive: Member variable 'SeqDataRequest::m_id' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/Parallel/Messages.h:164:3: warning:inconclusive: Member variable 'SeqDataResponse::m_group' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/Parallel/Messages.h:164:3: warning:inconclusive: Member variable 'SeqDataResponse::m_id' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/Parallel/Messages.h:164:3: warning:inconclusive: Member variable 'SeqDataResponse::m_multiplicity' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/Parallel/Messages.h:192:3: warning:inconclusive: Member variable 'SetBaseMessage::m_dir' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/Parallel/CommLayer.h:44:13: style:inconclusive: Technically the member function 'CommLayer::checkMessage' can be const. [functionConst] abyss-2.3.7/Parallel/CommLayer.cpp:61:22: note: Technically the member function 'CommLayer::checkMessage' can be const. abyss-2.3.7/Parallel/CommLayer.h:44:13: note: Technically the member function 'CommLayer::checkMessage' can be const. abyss-2.3.7/Parallel/CommLayer.h:47:8: style:inconclusive: Technically the member function 'CommLayer::receiveEmpty' can be const. [functionConst] abyss-2.3.7/Parallel/CommLayer.cpp:71:17: note: Technically the member function 'CommLayer::receiveEmpty' can be const. abyss-2.3.7/Parallel/CommLayer.h:47:8: note: Technically the member function 'CommLayer::receiveEmpty' can be const. abyss-2.3.7/Parallel/CommLayer.h:50:8: performance:inconclusive: Technically the member function 'CommLayer::barrier' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/Parallel/CommLayer.cpp:78:17: note: Technically the member function 'CommLayer::barrier' can be static (but you may consider moving to unnamed namespace). abyss-2.3.7/Parallel/CommLayer.h:50:8: note: Technically the member function 'CommLayer::barrier' can be static (but you may consider moving to unnamed namespace). abyss-2.3.7/Parallel/CommLayer.h:56:22: performance:inconclusive: Technically the member function 'CommLayer::reduce' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/Parallel/CommLayer.cpp:106:31: note: Technically the member function 'CommLayer::reduce' can be static (but you may consider moving to unnamed namespace). abyss-2.3.7/Parallel/CommLayer.h:56:22: note: Technically the member function 'CommLayer::reduce' can be static (but you may consider moving to unnamed namespace). abyss-2.3.7/Parallel/CommLayer.h:57:25: performance:inconclusive: Technically the member function 'CommLayer::reduce' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/Parallel/CommLayer.cpp:117:29: note: Technically the member function 'CommLayer::reduce' can be static (but you may consider moving to unnamed namespace). abyss-2.3.7/Parallel/CommLayer.h:57:25: note: Technically the member function 'CommLayer::reduce' can be static (but you may consider moving to unnamed namespace). abyss-2.3.7/Parallel/CommLayer.h:58:30: performance:inconclusive: Technically the member function 'CommLayer::reduce' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/Parallel/CommLayer.cpp:129:34: note: Technically the member function 'CommLayer::reduce' can be static (but you may consider moving to unnamed namespace). abyss-2.3.7/Parallel/CommLayer.h:58:30: note: Technically the member function 'CommLayer::reduce' can be static (but you may consider moving to unnamed namespace). abyss-2.3.7/Parallel/CommLayer.h:75:8: performance:inconclusive: Technically the member function 'CommLayer::sendBufferedMessage' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/Parallel/CommLayer.cpp:200:17: note: Technically the member function 'CommLayer::sendBufferedMessage' can be static (but you may consider moving to unnamed namespace). abyss-2.3.7/Parallel/CommLayer.h:75:8: note: Technically the member function 'CommLayer::sendBufferedMessage' can be static (but you may consider moving to unnamed namespace). abyss-2.3.7/Parallel/CommLayer.cpp:16:4: warning: Class 'CommLayer' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] abyss-2.3.7/Parallel/CommLayer.cpp:16:4: warning: Class 'CommLayer' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] abyss-2.3.7/Parallel/MessageBuffer.h:31:8: warning: The class 'MessageBuffer' defines member function with name 'sendCheckPointMessage' also defined in its parent class 'CommLayer'. [duplInheritedMember] abyss-2.3.7/Parallel/CommLayer.cpp:141:21: note: Parent function 'CommLayer::sendCheckPointMessage' abyss-2.3.7/Parallel/MessageBuffer.h:31:8: note: Derived function 'MessageBuffer::sendCheckPointMessage' abyss-2.3.7/Parallel/MessageBuffer.h:37:8: warning: The class 'MessageBuffer' defines member function with name 'sendControlMessage' also defined in its parent class 'CommLayer'. [duplInheritedMember] abyss-2.3.7/Parallel/CommLayer.cpp:156:17: note: Parent function 'CommLayer::sendControlMessage' abyss-2.3.7/Parallel/MessageBuffer.h:37:8: note: Derived function 'MessageBuffer::sendControlMessage' abyss-2.3.7/Parallel/MessageBuffer.h:43:8: warning: The class 'MessageBuffer' defines member function with name 'sendControlMessageToNode' also defined in its parent class 'CommLayer'. [duplInheritedMember] abyss-2.3.7/Parallel/CommLayer.cpp:164:21: note: Parent function 'CommLayer::sendControlMessageToNode' abyss-2.3.7/Parallel/MessageBuffer.h:43:8: note: Derived function 'MessageBuffer::sendControlMessageToNode' abyss-2.3.7/Parallel/Messages.h:71:3: style: Class 'SeqAddMessage' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/Parallel/Messages.h:84:3: style: Class 'SeqRemoveMessage' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/Parallel/Messages.h:73:8: style: The function 'handle' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:44:16: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:73:8: note: Function in derived class abyss-2.3.7/Parallel/Messages.h:74:10: style: The function 'serialize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:54:18: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:74:10: note: Function in derived class abyss-2.3.7/Parallel/Messages.h:86:8: style: The function 'handle' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:44:16: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:86:8: note: Function in derived class abyss-2.3.7/Parallel/Messages.h:87:10: style: The function 'serialize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:54:18: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:87:10: note: Function in derived class abyss-2.3.7/Parallel/Messages.h:100:10: style: The function 'getNetworkSize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:47:18: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:100:10: note: Function in derived class abyss-2.3.7/Parallel/Messages.h:105:8: style: The function 'handle' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:44:16: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:105:8: note: Function in derived class abyss-2.3.7/Parallel/Messages.h:106:10: style: The function 'serialize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:54:18: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:106:10: note: Function in derived class abyss-2.3.7/Parallel/Messages.h:107:10: style: The function 'unserialize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:55:18: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:107:10: note: Function in derived class abyss-2.3.7/Parallel/Messages.h:122:10: style: The function 'getNetworkSize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:47:18: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:122:10: note: Function in derived class abyss-2.3.7/Parallel/Messages.h:128:8: style: The function 'handle' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:44:16: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:128:8: note: Function in derived class abyss-2.3.7/Parallel/Messages.h:129:10: style: The function 'serialize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:54:18: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:129:10: note: Function in derived class abyss-2.3.7/Parallel/NetworkSequenceCollection.h:66:3: warning: Member variable 'NetworkSequenceCollection::m_numDataNodes' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/Parallel/Messages.h:130:10: style: The function 'unserialize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:55:18: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:130:10: note: Function in derived class abyss-2.3.7/Parallel/NetworkSequenceCollection.h:66:3: warning: Member variable 'NetworkSequenceCollection::m_numReachedCheckpoint' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/Parallel/Messages.h:145:10: style: The function 'getNetworkSize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:47:18: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:145:10: note: Function in derived class abyss-2.3.7/Parallel/NetworkSequenceCollection.h:66:3: warning: Member variable 'NetworkSequenceCollection::m_checkpointSum' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/Parallel/Messages.h:151:8: style: The function 'handle' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:44:16: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:151:8: note: Function in derived class abyss-2.3.7/Parallel/NetworkSequenceCollection.h:66:3: warning: Member variable 'NetworkSequenceCollection::m_numBasesAdjSet' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/Parallel/Messages.h:152:10: style: The function 'serialize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:54:18: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:152:10: note: Function in derived class abyss-2.3.7/Parallel/NetworkSequenceCollection.h:66:3: warning: Member variable 'NetworkSequenceCollection::m_lowCoverageContigs' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/Parallel/Messages.h:153:10: style: The function 'unserialize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:55:18: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:153:10: note: Function in derived class abyss-2.3.7/Parallel/NetworkSequenceCollection.h:66:3: warning: Member variable 'NetworkSequenceCollection::m_lowCoverageKmer' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/Parallel/Messages.h:170:10: style: The function 'getNetworkSize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:47:18: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:170:10: note: Function in derived class abyss-2.3.7/Parallel/Messages.h:177:8: style: The function 'handle' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:44:16: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:177:8: note: Function in derived class abyss-2.3.7/Parallel/Messages.h:178:10: style: The function 'serialize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:54:18: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:178:10: note: Function in derived class abyss-2.3.7/Parallel/Messages.h:179:10: style: The function 'unserialize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:55:18: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:179:10: note: Function in derived class abyss-2.3.7/Parallel/Messages.h:197:10: style: The function 'getNetworkSize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:47:18: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:197:10: note: Function in derived class abyss-2.3.7/Parallel/Messages.h:203:8: style: The function 'handle' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:44:16: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:203:8: note: Function in derived class abyss-2.3.7/Parallel/Messages.h:204:10: style: The function 'serialize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:54:18: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:204:10: note: Function in derived class abyss-2.3.7/Parallel/Messages.h:205:10: style: The function 'unserialize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] abyss-2.3.7/Parallel/Messages.h:55:18: note: Virtual function in base class abyss-2.3.7/Parallel/Messages.h:205:10: note: Function in derived class abyss-2.3.7/Parallel/NetworkSequenceCollection.h:152:8: performance:inconclusive: Technically the member function 'NetworkSequenceCollection::attach' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/Parallel/NetworkSequenceCollection.h:153:8: performance:inconclusive: Technically the member function 'NetworkSequenceCollection::detach' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/Parallel/MessageBuffer.h:31:8: warning: The class 'MessageBuffer' defines member function with name 'sendCheckPointMessage' also defined in its parent class 'CommLayer'. [duplInheritedMember] abyss-2.3.7/Parallel/CommLayer.h:72:12: note: Parent function 'CommLayer::sendCheckPointMessage' abyss-2.3.7/Parallel/MessageBuffer.h:31:8: note: Derived function 'MessageBuffer::sendCheckPointMessage' abyss-2.3.7/Parallel/MessageBuffer.h:37:8: warning: The class 'MessageBuffer' defines member function with name 'sendControlMessage' also defined in its parent class 'CommLayer'. [duplInheritedMember] abyss-2.3.7/Parallel/CommLayer.h:62:8: note: Parent function 'CommLayer::sendControlMessage' abyss-2.3.7/Parallel/MessageBuffer.h:37:8: note: Derived function 'MessageBuffer::sendControlMessage' abyss-2.3.7/Parallel/MessageBuffer.h:43:8: warning: The class 'MessageBuffer' defines member function with name 'sendControlMessageToNode' also defined in its parent class 'CommLayer'. [duplInheritedMember] abyss-2.3.7/Parallel/CommLayer.h:65:12: note: Parent function 'CommLayer::sendControlMessageToNode' abyss-2.3.7/Parallel/MessageBuffer.h:43:8: note: Derived function 'MessageBuffer::sendControlMessageToNode' abyss-2.3.7/Parallel/CommLayer.cpp:223:5: style: C-style pointer casting [cstyleCast] abyss-2.3.7/Parallel/CommLayer.cpp:256:5: style: C-style pointer casting [cstyleCast] abyss-2.3.7/Parallel/CommLayer.cpp:165:13: style:inconclusive: Function 'sendControlMessageToNode' argument 2 names different: declaration 'command' definition 'm'. [funcArgNamesDifferent] abyss-2.3.7/Parallel/CommLayer.h:66:15: note: Function 'sendControlMessageToNode' argument 2 names different: declaration 'command' definition 'm'. abyss-2.3.7/Parallel/CommLayer.cpp:165:13: note: Function 'sendControlMessageToNode' argument 2 names different: declaration 'command' definition 'm'. abyss-2.3.7/Parallel/Messages.cpp:21:23: style: C-style pointer casting [cstyleCast] abyss-2.3.7/ParseAligns/ParseAligns.cpp:30:18: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/ParseAligns/abyss-fixmate.cc:28:18: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/PathOverlap/PathOverlap.cpp:33:25: error: There is an unknown macro here somewhere. Configuration is required. If VERSION is a macro then please configure it. [unknownMacro] abyss-2.3.7/PopBubbles/PopBubbles.cpp:49:18: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/RResolver/Contigs.h:34:2: style: Class 'ContigSequence' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/RResolver/Contigs.cpp:181:33: style:inconclusive: Function 'numVerticesRemoved' argument 1 names different: declaration 'contigGraph' definition 'graph'. [funcArgNamesDifferent] abyss-2.3.7/RResolver/Contigs.h:88:33: note: Function 'numVerticesRemoved' argument 1 names different: declaration 'contigGraph' definition 'graph'. abyss-2.3.7/RResolver/Contigs.cpp:181:33: note: Function 'numVerticesRemoved' argument 1 names different: declaration 'contigGraph' definition 'graph'. abyss-2.3.7/RResolver/Contigs.cpp:233:14: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] abyss-2.3.7/RResolver/Contigs.cpp:221:20: style: Variable 'seen[node.id()]' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/RResolver/RAlgorithmsShort.h:154:7: style:inconclusive: Technically the member function 'Support::operator>' can be const. [functionConst] abyss-2.3.7/RResolver/RAlgorithmsShort.h:156:7: style:inconclusive: Technically the member function 'Support::operator<' can be const. [functionConst] abyss-2.3.7/RResolver/RAlgorithmsShort.h:110:2: style: Class 'Support' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/RResolver/RAlgorithmsShort.h:168:2: style: Class 'ReadSize' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/RResolver/BloomFilters.cpp:213:37: style:inconclusive: Function 'buildFilters' argument 1 names different: declaration 'read_filepaths' definition 'readFilepaths'. [funcArgNamesDifferent] abyss-2.3.7/RResolver/BloomFilters.h:30:37: note: Function 'buildFilters' argument 1 names different: declaration 'read_filepaths' definition 'readFilepaths'. abyss-2.3.7/RResolver/BloomFilters.cpp:213:37: note: Function 'buildFilters' argument 1 names different: declaration 'read_filepaths' definition 'readFilepaths'. abyss-2.3.7/RResolver/BloomFilters.cpp:215:18: style:inconclusive: Function 'buildFilters' argument 3 names different: declaration 'bloom_bytes_total' definition 'bloomBytesTotal'. [funcArgNamesDifferent] abyss-2.3.7/RResolver/BloomFilters.h:32:18: note: Function 'buildFilters' argument 3 names different: declaration 'bloom_bytes_total' definition 'bloomBytesTotal'. abyss-2.3.7/RResolver/BloomFilters.cpp:215:18: note: Function 'buildFilters' argument 3 names different: declaration 'bloom_bytes_total' definition 'bloomBytesTotal'. abyss-2.3.7/RResolver/BloomFilters.cpp:192:7: style: Local variable 'i' shadows outer variable [shadowVariable] abyss-2.3.7/RResolver/BloomFilters.cpp:144:6: note: Shadowed declaration abyss-2.3.7/RResolver/BloomFilters.cpp:192:7: note: Shadow variable abyss-2.3.7/RResolver/BloomFilters.cpp:155:15: style: Local variable 'i' shadows outer variable [shadowVariable] abyss-2.3.7/RResolver/BloomFilters.cpp:144:6: note: Shadowed declaration abyss-2.3.7/RResolver/BloomFilters.cpp:155:15: note: Shadow variable abyss-2.3.7/RResolver/BloomFilters.cpp:168:8: style: Local variable 'i' shadows outer variable [shadowVariable] abyss-2.3.7/RResolver/BloomFilters.cpp:144:6: note: Shadowed declaration abyss-2.3.7/RResolver/BloomFilters.cpp:168:8: note: Shadow variable abyss-2.3.7/RResolver/BloomFilters.cpp:203:15: style: Local variable 'i' shadows outer variable [shadowVariable] abyss-2.3.7/RResolver/BloomFilters.cpp:144:6: note: Shadowed declaration abyss-2.3.7/RResolver/BloomFilters.cpp:203:15: note: Shadow variable abyss-2.3.7/RResolver/BloomFilters.cpp:82:12: performance: Range variable 'combination' should be declared as const reference. [iterateByValue] abyss-2.3.7/RResolver/BloomFilters.cpp:60:18: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm] abyss-2.3.7/KAligner/Aligner.h:30:2: style: Struct 'Position' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/KAligner/Aligner.cpp:59:19: style:inconclusive: Function 'addReferenceSequence' argument 1 names different: declaration 'id' definition 'idString'. [funcArgNamesDifferent] abyss-2.3.7/KAligner/Aligner.h:87:44: note: Function 'addReferenceSequence' argument 1 names different: declaration 'id' definition 'idString'. abyss-2.3.7/KAligner/Aligner.cpp:59:19: note: Function 'addReferenceSequence' argument 1 names different: declaration 'id' definition 'idString'. abyss-2.3.7/KAligner/Aligner.cpp:62:6: style: Local variable 'size' shadows outer function [shadowFunction] abyss-2.3.7/KAligner/Aligner.h:93:9: note: Shadowed declaration abyss-2.3.7/KAligner/Aligner.cpp:62:6: note: Shadow variable abyss-2.3.7/RResolver/RResolverShort.cpp:22:18: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/KAligner/Aligner.cpp:216:4: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:63:16: warning: Assert statement calls a function which may have desired side effects: 'receiveEmpty'. [assertWithSideEffect] abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:242:19: warning: Assert statement calls a function which may have desired side effects: 'receiveEmpty'. [assertWithSideEffect] abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:1019:16: warning: Assert statement calls a function which may have desired side effects: 'receiveEmpty'. [assertWithSideEffect] abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:1034:17: warning: Assert statement calls a function which may have desired side effects: 'receiveEmpty'. [assertWithSideEffect] abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:1156:16: warning: Assert statement calls a function which may have desired side effects: 'receiveEmpty'. [assertWithSideEffect] abyss-2.3.7/Parallel/NetworkSequenceCollection.h:212:7: performance:inconclusive: Technically the member function 'NetworkSequenceCollection::computeNodeID' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:1500:32: note: Technically the member function 'NetworkSequenceCollection::computeNodeID' can be static (but you may consider moving to unnamed namespace). abyss-2.3.7/Parallel/NetworkSequenceCollection.h:212:7: note: Technically the member function 'NetworkSequenceCollection::computeNodeID' can be static (but you may consider moving to unnamed namespace). abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:731:49: style:inconclusive: Function 'notify' argument 1 names different: declaration 'seq' definition 'key'. [funcArgNamesDifferent] abyss-2.3.7/Parallel/NetworkSequenceCollection.h:175:24: note: Function 'notify' argument 1 names different: declaration 'seq' definition 'key'. abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:731:49: note: Function 'notify' argument 1 names different: declaration 'seq' definition 'key'. abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:776:51: style:inconclusive: Function 'handle' argument 2 names different: declaration 'm' definition 'message'. [funcArgNamesDifferent] abyss-2.3.7/Parallel/NetworkSequenceCollection.h:143:59: note: Function 'handle' argument 2 names different: declaration 'm' definition 'message'. abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:776:51: note: Function 'handle' argument 2 names different: declaration 'm' definition 'message'. abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:1174:16: style:inconclusive: Function 'assembleContig' argument 1 names different: declaration 'fileWriter' definition 'writer'. [funcArgNamesDifferent] abyss-2.3.7/Parallel/NetworkSequenceCollection.h:202:18: note: Function 'assembleContig' argument 1 names different: declaration 'fileWriter' definition 'writer'. abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:1174:16: note: Function 'assembleContig' argument 1 names different: declaration 'fileWriter' definition 'writer'. abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:1316:49: style:inconclusive: Function 'generateExtensionRequest' argument 3 names different: declaration 'seq' definition 'kmer'. [funcArgNamesDifferent] abyss-2.3.7/Parallel/NetworkSequenceCollection.h:185:51: note: Function 'generateExtensionRequest' argument 3 names different: declaration 'seq' definition 'kmer'. abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:1316:49: note: Function 'generateExtensionRequest' argument 3 names different: declaration 'seq' definition 'kmer'. abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:715:28: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:923:40: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:939:36: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:1023:29: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:1079:4: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] abyss-2.3.7/Scaffold/drawgraph.cc:35:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/Scaffold/junction.cc:31:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/Scaffold/longseqdist.cpp:25:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/Scaffold/scaffold.cc:697:1: error: There is an unknown macro here somewhere. Configuration is required. If NAMESPACE_STD_HASH_BEGIN is a macro then please configure it. [unknownMacro] abyss-2.3.7/Sealer/sealer.cc:57:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/SimpleGraph/SimpleGraph.cpp:30:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/RResolver/SequenceTree.cpp:193:73: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] abyss-2.3.7/RResolver/SequenceTree.cpp:197:83: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] abyss-2.3.7/Unittest/BloomDBG/RollingHashTest.cpp:18:15: style: class member 'RollingHashTest::m_kmerMask' is never used. [unusedStructMember] abyss-2.3.7/Unittest/Graph/AllPathsSearchTest.cpp:57:1: error: syntax error [syntaxError] abyss-2.3.7/Unittest/DBG/LoadAlgorithmTest.cpp:26:22: style: Unused variable: kmers [unusedVariable] abyss-2.3.7/Unittest/Graph/ConstrainedBFSVisitorTest.cpp:39:1: error: syntax error [syntaxError] abyss-2.3.7/Unittest/Graph/BidirectionalBFSTest.cpp:125:1: error: syntax error [syntaxError] abyss-2.3.7/Unittest/Common/StringUtilTest.cpp:27:16: style: Condition '1==myString.length()' is always true [knownConditionTrueFalse] abyss-2.3.7/Unittest/Common/StringUtilTest.cpp:30:16: style: Condition '1==anotherString.length()' is always true [knownConditionTrueFalse] abyss-2.3.7/Unittest/Common/StringUtilTest.cpp:132:13: style: Variable 'temp.myVar' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/Unittest/Graph/ConstrainedBidiBFSVisitorTest.cpp:52:1: error: syntax error [syntaxError] abyss-2.3.7/Unittest/Graph/HashGraphTest.cpp:44:1: error: syntax error [syntaxError] abyss-2.3.7/Unittest/Konnector/DBGBloomAlgorithmsTest.cpp:38:19: style: class member 'GetStartKmerPosTest::bloomFilterSize' is never used. [unusedStructMember] abyss-2.3.7/Unittest/Konnector/DBGBloomAlgorithmsTest.cpp:143:19: style: class member 'CorrectSingleBaseErrorTest::bloomFilterSize' is never used. [unusedStructMember] abyss-2.3.7/Unittest/Konnector/konnectorTest.cpp:63:22: style: Unused variable: mergedSeqs [unusedVariable] abyss-2.3.7/Unittest/PairedDBG/LoadAlgorithmTest.cpp:30:26: style: Unused variable: kmerPairs [unusedVariable] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:45:8: style: C-style reference casting [cstyleCast] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:291:9: style: The scope of the variable 'batch' can be reduced. [variableScope] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:313:23: style: The scope of the variable 'BASES' can be reduced. [variableScope] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:319:7: style: The scope of the variable 'offset' can be reduced. [variableScope] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:694:7: style: The scope of the variable 'pathsSupported' can be reduced. [variableScope] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:694:27: style: The scope of the variable 'pathsUnsupported' can be reduced. [variableScope] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:541:10: style: Local variable 'end' shadows outer variable [shadowVariable] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:522:8: note: Shadowed declaration abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:541:10: note: Shadow variable abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:175:80: performance: Function parameter 'a' should be passed by const reference. [passedByValue] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:175:92: performance: Function parameter 'b' should be passed by const reference. [passedByValue] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:214:80: performance: Function parameter 'a' should be passed by const reference. [passedByValue] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:214:92: performance: Function parameter 'b' should be passed by const reference. [passedByValue] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:231:80: performance: Function parameter 'a' should be passed by const reference. [passedByValue] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:231:92: performance: Function parameter 'b' should be passed by const reference. [passedByValue] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:878:36: performance: Function parameter 'originalIntigs' should be passed by const reference. [passedByValue] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:879:36: performance: Function parameter 'originalOutigs' should be passed by const reference. [passedByValue] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:1278:12: performance: Range variable 'batch' should be declared as const reference. [iterateByValue] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:313:23: style: Variable 'BASES' can be declared as const array [constVariable] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:988:15: style: Redundant checking of STL container element existence before removing it. [redundantIfRemove] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:141:31: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:226:21: style: Consider using std::copy_if algorithm instead of a raw loop. [useStlAlgorithm] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:426:23: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:433:28: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:508:35: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:513:35: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:902:26: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:907:26: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:1036:36: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:1157:19: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:1167:19: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm] abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:1277:41: style: Unused variable: histograms [unusedVariable] abyss-2.3.7/dialign/io.c:1093:14: error: Deallocation of a pointer pointing to a string literal ("Multiple Sequence Alignment (with translation)") results in undefined behaviour. [autovarInvalidDeallocation] abyss-2.3.7/dialign/io.c:848:12: note: Assignment 'line="Multiple Sequence Alignment (with translation)"', assigned value is "Multiple Sequence Alignment (with translation)" abyss-2.3.7/dialign/io.c:849:24: note: Calling function 'output_line', 1st argument 'line' value is "Multiple Sequence Alignment (with translation)" abyss-2.3.7/dialign/io.c:1074:10: note: Assuming condition is false abyss-2.3.7/dialign/io.c:1093:14: note: Deallocating memory that was not dynamically allocated abyss-2.3.7/dialign/io.c:1116:14: error: Deallocation of a pointer pointing to a string literal ("reading frame 1 : 123 123 123 123 ...") results in undefined behaviour. [autovarInvalidDeallocation] abyss-2.3.7/dialign/io.c:868:12: note: Assignment 'line="reading frame 1 : 123 123 123 123 ..."', assigned value is "reading frame 1 : 123 123 123 123 ..." abyss-2.3.7/dialign/io.c:869:29: note: Calling function 'output_line_left', 1st argument 'line' value is "reading frame 1 : 123 123 123 123 ..." abyss-2.3.7/dialign/io.c:1102:10: note: Assuming condition is false abyss-2.3.7/dialign/io.c:1116:14: note: Deallocating memory that was not dynamically allocated abyss-2.3.7/dialign/io.c:371:7: warning: %li in format string (no. 1) requires 'long *' but the argument type is 'unsigned long *'. [invalidScanfArgType_int] abyss-2.3.7/dialign/io.c:371:7: warning: %li in format string (no. 2) requires 'long *' but the argument type is 'unsigned long *'. [invalidScanfArgType_int] abyss-2.3.7/dialign/io.c:377:24: warning: %li in format string (no. 1) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint] abyss-2.3.7/dialign/io.c:377:24: warning: %li in format string (no. 2) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint] abyss-2.3.7/dialign/io.c:380:22: portability: %li in format string (no. 1) requires 'long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint] abyss-2.3.7/dialign/io.c:548:19: warning: %i in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] abyss-2.3.7/dialign/io.c:605:6: warning: %i in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] abyss-2.3.7/dialign/io.c:605:6: warning: %i in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] abyss-2.3.7/dialign/io.c:677:6: warning: %i in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] abyss-2.3.7/dialign/io.c:677:6: warning: %i in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] abyss-2.3.7/dialign/io.c:1148:2: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] abyss-2.3.7/dialign/io.c:282:5: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf] abyss-2.3.7/dialign/io.c:844:18: error: Common realloc mistake: 'output' nulled but not freed upon failure [memleakOnRealloc] abyss-2.3.7/dialign/io.c:906:19: error: Common realloc mistake: 'output' nulled but not freed upon failure [memleakOnRealloc] abyss-2.3.7/dialign/io.c:923:18: error: Common realloc mistake: 'output' nulled but not freed upon failure [memleakOnRealloc] abyss-2.3.7/dialign/io.c:985:19: error: Common realloc mistake: 'output' nulled but not freed upon failure [memleakOnRealloc] abyss-2.3.7/dialign/io.c:1002:17: error: Common realloc mistake: 'output' nulled but not freed upon failure [memleakOnRealloc] abyss-2.3.7/dialign/io.c:1035:16: error: Common realloc mistake: 'output' nulled but not freed upon failure [memleakOnRealloc] abyss-2.3.7/dialign/io.c:1056:15: error: Common realloc mistake: 'output' nulled but not freed upon failure [memleakOnRealloc] abyss-2.3.7/dialign/io.c:221:20: warning: Either the condition 'smatrix==NULL' is redundant or there is possible null pointer dereference: smatrix. [nullPointerRedundantCheck] abyss-2.3.7/dialign/io.c:224:13: note: Assuming that condition 'smatrix==NULL' is not redundant abyss-2.3.7/dialign/io.c:221:20: note: Null pointer dereference abyss-2.3.7/dialign/io.c:222:20: warning: Either the condition 'smatrix==NULL' is redundant or there is possible null pointer dereference: smatrix. [nullPointerRedundantCheck] abyss-2.3.7/dialign/io.c:224:13: note: Assuming that condition 'smatrix==NULL' is not redundant abyss-2.3.7/dialign/io.c:222:20: note: Null pointer dereference abyss-2.3.7/dialign/io.c:321:3: warning: Either the condition 'pdist==NULL' is redundant or there is possible null pointer dereference: pdist. [nullPointerRedundantCheck] abyss-2.3.7/dialign/io.c:323:11: note: Assuming that condition 'pdist==NULL' is not redundant abyss-2.3.7/dialign/io.c:321:3: note: Null pointer dereference abyss-2.3.7/dialign/io.c:401:23: warning: Either the condition 'scol==NULL' is redundant or there is possible null pointer dereference: scol. [nullPointerRedundantCheck] abyss-2.3.7/dialign/io.c:404:10: note: Assuming that condition 'scol==NULL' is not redundant abyss-2.3.7/dialign/io.c:401:23: note: Null pointer dereference abyss-2.3.7/dialign/io.c:730:7: style: Variable 'max' is reassigned a value before the old one has been used. [redundantAssignment] abyss-2.3.7/dialign/io.c:722:7: note: max is assigned abyss-2.3.7/dialign/io.c:730:7: note: max is overwritten abyss-2.3.7/dialign/io.c:778:7: style: Variable 'max' is reassigned a value before the old one has been used. [redundantAssignment] abyss-2.3.7/dialign/io.c:770:7: note: max is assigned abyss-2.3.7/dialign/io.c:778:7: note: max is overwritten abyss-2.3.7/dialign/io.c:500:25: error: Division by zero. [zerodiv] abyss-2.3.7/dialign/io.c:414:18: note: Assignment 'scol->length=0', assigned value is 0 abyss-2.3.7/dialign/io.c:423:61: note: Assuming condition is false abyss-2.3.7/dialign/io.c:500:25: note: Division by zero abyss-2.3.7/dialign/io.c:819:36: style:inconclusive: Function 'print_info' argument 1 names different: declaration 'align' definition 'algn'. [funcArgNamesDifferent] abyss-2.3.7/dialign/io.h:40:36: note: Function 'print_info' argument 1 names different: declaration 'align' definition 'algn'. abyss-2.3.7/dialign/io.c:819:36: note: Function 'print_info' argument 1 names different: declaration 'align' definition 'algn'. abyss-2.3.7/dialign/io.c:60:18: style: Parameter 'message' can be declared as pointer to const [constParameterPointer] abyss-2.3.7/dialign/io.c:70:19: style: Parameter 'msg1' can be declared as pointer to const [constParameterPointer] abyss-2.3.7/dialign/io.c:70:31: style: Parameter 'msg2' can be declared as pointer to const [constParameterPointer] abyss-2.3.7/dialign/io.c:95:28: style: Parameter 'dir' can be declared as pointer to const [constParameterPointer] abyss-2.3.7/dialign/io.c:95:39: style: Parameter 'file' can be declared as pointer to const [constParameterPointer] abyss-2.3.7/dialign/io.c:114:29: style: Parameter 'aSeq' can be declared as pointer to const [constParameterPointer] abyss-2.3.7/dialign/io.c:155:9: style: Variable 'data' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/io.c:187:42: style: Parameter 'aSmatrix' can be declared as pointer to const [constParameterPointer] abyss-2.3.7/dialign/io.c:401:15: style: Variable 'seqs' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/io.c:562:15: style: Variable 'sq' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/io.c:574:20: style: Variable 'ap1' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/io.c:635:8: style: Variable 'tmp' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/io.c:640:15: style: Variable 'sq' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/io.c:651:20: style: Variable 'ap1' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/io.c:718:15: style: Variable 'sq' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/io.c:723:20: style: Variable 'ap1' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/io.c:761:8: style: Variable 'tmp' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/io.c:766:15: style: Variable 'sq' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/io.c:771:20: style: Variable 'ap1' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/io.c:891:12: style: Variable 'tmp' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/io.c:970:12: style: Variable 'tmp' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/io.c:264:25: style: Variable 'avg_score' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/io.c:277:17: style: Variable 'avg_score' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/io.c:635:12: style: Variable 'tmp' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/io.c:761:12: style: Variable 'tmp' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/io.c:1107:4: style: Variable 'y' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/museq.c:186:22: warning: %i in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] abyss-2.3.7/dialign/museq.c:254:26: warning: %i in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] abyss-2.3.7/dialign/museq.c:160:19: warning: Either the condition 'anchors!=NULL' is redundant or there is possible null pointer dereference: anchors. [nullPointerRedundantCheck] abyss-2.3.7/dialign/museq.c:168:15: note: Assuming that condition 'anchors!=NULL' is not redundant abyss-2.3.7/dialign/museq.c:160:19: note: Null pointer dereference abyss-2.3.7/dialign/museq.c:161:25: warning: Either the condition 'anchors!=NULL' is redundant or there is possible null pointer dereference: anchors. [nullPointerRedundantCheck] abyss-2.3.7/dialign/museq.c:168:15: note: Assuming that condition 'anchors!=NULL' is not redundant abyss-2.3.7/dialign/museq.c:161:25: note: Null pointer dereference abyss-2.3.7/dialign/museq.c:234:7: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch] abyss-2.3.7/dialign/museq.c:236:7: note: Found duplicate branches for 'if' and 'else'. abyss-2.3.7/dialign/museq.c:234:7: note: Found duplicate branches for 'if' and 'else'. abyss-2.3.7/dialign/museq.c:239:7: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch] abyss-2.3.7/dialign/museq.c:241:7: note: Found duplicate branches for 'if' and 'else'. abyss-2.3.7/dialign/museq.c:239:7: note: Found duplicate branches for 'if' and 'else'. abyss-2.3.7/dialign/museq.c:120:18: error: Uninitialized struct member: in_seq_col.length [uninitStructMember] abyss-2.3.7/dialign/museq.c:225:17: style: Variable 'newFound' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/orf.c:28:6: warning: Either the condition '(ret_seq_col=calloc(1,sizeof(struct seq_col)))==NULL' is redundant or there is possible null pointer dereference: ret_seq_col. [nullPointerRedundantCheck] abyss-2.3.7/dialign/orf.c:24:53: note: Assuming that condition '(ret_seq_col=calloc(1,sizeof(struct seq_col)))==NULL' is not redundant abyss-2.3.7/dialign/orf.c:28:6: note: Null pointer dereference abyss-2.3.7/dialign/orf.c:53:36: style:inconclusive: Function 'orf_finder' argument 1 names different: declaration 'in_seq_col' definition 'in_seq'. [funcArgNamesDifferent] abyss-2.3.7/dialign/orf.h:37:36: note: Function 'orf_finder' argument 1 names different: declaration 'in_seq_col' definition 'in_seq'. abyss-2.3.7/dialign/orf.c:53:36: note: Function 'orf_finder' argument 1 names different: declaration 'in_seq_col' definition 'in_seq'. abyss-2.3.7/dialign/orf.c:44:3: style: Variable 'seq' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/parameters.c:114:22: style:inconclusive: Function 'check_input' argument 1 names different: declaration 'length' definition 'argc'. [funcArgNamesDifferent] abyss-2.3.7/dialign/parameters.h:156:22: note: Function 'check_input' argument 1 names different: declaration 'length' definition 'argc'. abyss-2.3.7/dialign/parameters.c:114:22: note: Function 'check_input' argument 1 names different: declaration 'length' definition 'argc'. abyss-2.3.7/dialign/parameters.c:114:35: style:inconclusive: Function 'check_input' argument 2 names different: declaration 'arguments' definition 'argv'. [funcArgNamesDifferent] abyss-2.3.7/dialign/parameters.h:156:37: note: Function 'check_input' argument 2 names different: declaration 'arguments' definition 'argv'. abyss-2.3.7/dialign/parameters.c:114:35: note: Function 'check_input' argument 2 names different: declaration 'arguments' definition 'argv'. abyss-2.3.7/dialign/alig.c:273:46: style: Condition '1||(tap->predFPos<0)' is always true [knownConditionTrueFalse] abyss-2.3.7/dialign/alig.c:283:45: style: Condition '1||(tap->succFPos<0)' is always true [knownConditionTrueFalse] abyss-2.3.7/dialign/alig.c:657:8: style: Condition '!skip' is always true [knownConditionTrueFalse] abyss-2.3.7/dialign/alig.c:605:12: note: Assignment 'skip=0', assigned value is 0 abyss-2.3.7/dialign/alig.c:657:8: note: Condition '!skip' is always true abyss-2.3.7/dialign/alig.c:1027:37: style: Condition '!(tproc[ts]==predF[ts]&&succF!=NULL&&succF[ts]==predF[ts])' is always true [knownConditionTrueFalse] abyss-2.3.7/dialign/alig.c:1027:22: note: Assuming that condition 'tproc[ts]max_dlen' is reassigned a value before the old one has been used. [redundantAssignment] abyss-2.3.7/dialign/prob.c:87:19: note: sdist->max_dlen is assigned abyss-2.3.7/dialign/prob.c:92:19: note: sdist->max_dlen is overwritten abyss-2.3.7/dialign/translate.c:471:16: style: Variable 'tmp_char' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/prob.c:40:8: style: Variable 'n2c' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/prob.c:88:8: style: Variable 'sdata' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/prob.c:89:8: style: Variable 'smdist' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/prob.c:129:9: style: Variable 'data1' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/prob.c:130:9: style: Variable 'data2' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/prob.c:131:8: style: Variable 'c2n' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/prob.c:136:22: style: Variable 'factor' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/prob.c:144:12: style: Variable 'factor' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/prob.c:162:13: style: Variable 'dg.length' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/prob.c:165:15: style: Variable 'seenmax' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/kmerprint/kmerprint.cc:20:14: error: There is an unknown macro here somewhere. Configuration is required. If PACKAGE_NAME is a macro then please configure it. [unknownMacro] abyss-2.3.7/vendor/btl_bloomfilter/Examples/RollingFilterLoad.cpp:36:9: style: Variable 'hashes' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/btl_bloomfilter/Tests/AdHoc/ParallelFilter.cpp:114:9: style: Variable 'good' is reassigned a value before the old one has been used. [redundantAssignment] abyss-2.3.7/vendor/btl_bloomfilter/Tests/AdHoc/ParallelFilter.cpp:113:9: note: good is assigned abyss-2.3.7/vendor/btl_bloomfilter/Tests/AdHoc/ParallelFilter.cpp:114:9: note: good is overwritten abyss-2.3.7/vendor/btl_bloomfilter/Tests/AdHoc/ParallelFilter.cpp:96:14: style: Variable 'kmer' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/btl_bloomfilter/Tests/Unit/BloomFilterTests.cpp:34:8: style: Variable 'tmpdir' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/vendor/btl_bloomfilter/Tests/Unit/CountingBloomFilterTests.cpp:35:8: style: Variable 'tmpdir' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/vendor/btl_bloomfilter/pythonInterface/BloomFilter_pythonwrapper.cpp:158:7: style:inconclusive: Technically the member function 'BloomFilter::insert' can be const. [functionConst] abyss-2.3.7/vendor/btl_bloomfilter/pythonInterface/BloomFilter_pythonwrapper.cpp:210:7: style:inconclusive: Technically the member function 'BloomFilter::contains' can be const. [functionConst] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:3238:8: debug: Failed to instantiate template "value_accept". The checking continues anyway. [templateInstantiation] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:3034:24: debug: Failed to instantiate template "parse_object_array". The checking continues anyway. [templateInstantiation] abyss-2.3.7/dialign/assemble.c:495:3: warning: Either the condition 'diags==NULL' is redundant or there is possible null pointer dereference: diags. [nullPointerRedundantCheck] abyss-2.3.7/dialign/assemble.c:489:13: note: Assuming that condition 'diags==NULL' is not redundant abyss-2.3.7/dialign/assemble.c:495:3: note: Null pointer dereference abyss-2.3.7/dialign/assemble.c:496:3: warning: Either the condition 'diags==NULL' is redundant or there is possible null pointer dereference: diags. [nullPointerRedundantCheck] abyss-2.3.7/dialign/assemble.c:489:13: note: Assuming that condition 'diags==NULL' is not redundant abyss-2.3.7/dialign/assemble.c:496:3: note: Null pointer dereference abyss-2.3.7/dialign/assemble.c:368:18: style: Variable 'rdg' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/assemble.c:577:54: style: Parameter 'layer' can be declared as pointer to const [constParameterPointer] abyss-2.3.7/dialign/assemble.c:599:20: style: Variable 'ap2_1' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/assemble.c:600:20: style: Variable 'ap2_2' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/assemble.c:106:11: style: Variable 'ep1' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/assemble.c:418:19: style: Variable 'oldweight' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/assemble.c:420:4: style: Variable 'i' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/assemble.c:432:13: style: Variable 'changed' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/assemble.c:448:13: style: Variable 'prevweight' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/assemble.c:544:12: style: Variable 'oldweight' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/assemble.c:609:13: style: Variable 'lpos2' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/assemble.c:628:11: style: Variable 'sl1_2' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/assemble.c:629:11: style: Variable 'sl1_1' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/assemble.c:758:13: style: Variable 'ap2_1' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/assemble.c:759:13: style: Variable 'ap2_2' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/assemble.c:910:20: style: Variable 'multi_weight_fac' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/assemble.c:1057:10: style: Variable 'diag_p' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/assemble.c:854:19: style: Unused variable: l [unusedVariable] abyss-2.3.7/dialign/assemble.c:854:22: style: Unused variable: l1 [unusedVariable] abyss-2.3.7/dialign/assemble.c:854:25: style: Unused variable: l2 [unusedVariable] abyss-2.3.7/dialign/assemble.c:866:8: style: Unused variable: changed [unusedVariable] abyss-2.3.7/dialign/assemble.c:912:7: style: Unused variable: survive [unusedVariable] abyss-2.3.7/dialign/assemble.c:1385:14: style: Variable 'avg_weight' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/assemble.c:1327:16: style: Unused variable: dg [unusedVariable] abyss-2.3.7/dialign/assemble.c:1327:21: style: Unused variable: tdg [unusedVariable] abyss-2.3.7/vendor/btl_bloomfilter/vendor/ntHashIterator.hpp:27:5: warning: Member variable 'ntHashIterator::m_h' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/vendor/btl_bloomfilter/vendor/ntHashIterator.hpp:27:5: warning: Member variable 'ntHashIterator::m_k' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/vendor/btl_bloomfilter/vendor/ntHashIterator.hpp:27:5: warning: Member variable 'ntHashIterator::m_fhVal' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/vendor/btl_bloomfilter/vendor/ntHashIterator.hpp:27:5: warning: Member variable 'ntHashIterator::m_rhVal' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/vendor/btl_bloomfilter/vendor/ntHashIterator.hpp:47:9: performance: Variable 'm_seq' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:1927:14: style:inconclusive: Technically the member function 'cpptoml::parser::throw_parse_exception' can be const. [functionConst] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:2647:14: performance:inconclusive: Technically the member function 'cpptoml::parser::hex_to_digit' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:2857:27: performance:inconclusive: Technically the member function 'cpptoml::parser::find_end_of_number' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:2875:27: performance:inconclusive: Technically the member function 'cpptoml::parser::find_end_of_date' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:2890:27: performance:inconclusive: Technically the member function 'cpptoml::parser::find_end_of_time' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:3138:10: performance:inconclusive: Technically the member function 'cpptoml::parser::consume_whitespace' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:3145:10: performance:inconclusive: Technically the member function 'cpptoml::parser::consume_backwards_whitespace' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/vendor/btl_bloomfilter/BloomFilter.hpp:168:7: style:inconclusive: Technically the member function 'BloomFilter::insert' can be const. [functionConst] abyss-2.3.7/vendor/btl_bloomfilter/BloomFilter.hpp:182:7: style:inconclusive: Technically the member function 'BloomFilter::insert' can be const. [functionConst] abyss-2.3.7/vendor/btl_bloomfilter/BloomFilter.hpp:197:7: style:inconclusive: Technically the member function 'BloomFilter::insertAndCheck' can be const. [functionConst] abyss-2.3.7/vendor/btl_bloomfilter/BloomFilter.hpp:216:7: style:inconclusive: Technically the member function 'BloomFilter::insertAndCheck' can be const. [functionConst] abyss-2.3.7/vendor/btl_bloomfilter/BloomFilter.hpp:354:11: style:inconclusive: Technically the member function 'BloomFilter::getnEntry' can be const. [functionConst] abyss-2.3.7/vendor/btl_bloomfilter/BloomFilter.hpp:356:11: style:inconclusive: Technically the member function 'BloomFilter::gettEntry' can be const. [functionConst] abyss-2.3.7/vendor/btl_bloomfilter/BloomFilter.hpp:419:9: performance:inconclusive: Technically the member function 'BloomFilter::calcFPR_hashNum' can be static (but you may consider moving to unnamed namespace). [functionStatic] abyss-2.3.7/vendor/btl_bloomfilter/KmerBloomFilter.hpp:63:7: style:inconclusive: Technically the member function 'KmerBloomFilter::insert' can be const. [functionConst] abyss-2.3.7/vendor/btl_bloomfilter/vendor/ntHashIterator.hpp:39:37: warning: Class 'ntHashIterator' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] abyss-2.3.7/vendor/btl_bloomfilter/vendor/IOUtil.h:41:2: style: Struct 'expect' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/vendor/btl_bloomfilter/vendor/IOUtil.h:75:2: style: Struct 'Ignore' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/vendor/btl_bloomfilter/vendor/IOUtil.h:88:2: style: Struct 'Skip' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:171:5: style: Class 'fill_guard' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:769:5: style: Class 'array_exception' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:1180:5: style: Class 'table_array' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:1197:9: style: Struct 'make_shared_enabler' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:1751:5: style: Class 'parse_exception' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:1881:5: style: Class 'parser' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:3307:5: style: Class 'toml_writer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/vendor/btl_bloomfilter/BloomFilter.hpp:98:2: style: Class 'BloomFilter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/vendor/btl_bloomfilter/KmerBloomFilter.hpp:37:2: style: Class 'KmerBloomFilter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:661:5: style: Class 'value < double >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:661:5: style: Class 'value < int64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:661:5: style: Class 'value < std :: string >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:661:5: style: Class 'value < bool >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:661:5: style: Class 'value < local_time >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:67:5: style: Class 'option < parse_type >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:2483:17: warning: Identical condition 'ret', second condition is always false [identicalConditionAfterEarlyExit] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:2470:13: note: If condition 'ret' is true, the function will return/exit abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:2483:17: note: Testing identical condition 'ret' abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:2484:24: warning: Identical condition and return expression 'ret', return value is always 0 [identicalConditionAfterEarlyExit] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:2470:13: note: If condition 'ret' is true, the function will return/exit abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:2484:24: note: Returning identical expression 'ret' abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:2914:13: style: The scope of the variable 'power' can be reduced. [variableScope] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:2967:13: style: The scope of the variable 'hoff' can be reduced. [variableScope] abyss-2.3.7/vendor/btl_bloomfilter/vendor/cpptoml/include/cpptoml.h:2968:13: style: The scope of the variable 'moff' can be reduced. [variableScope] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:326:22: style: The scope of the variable 'tVal' can be reduced. [variableScope] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:346:22: style: The scope of the variable 'tVal' can be reduced. [variableScope] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:358:22: style: The scope of the variable 'tVal' can be reduced. [variableScope] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:370:22: style: The scope of the variable 'tVal' can be reduced. [variableScope] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:382:22: style: The scope of the variable 'tVal' can be reduced. [variableScope] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:420:22: style: The scope of the variable 'tVal' can be reduced. [variableScope] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:469:22: style: The scope of the variable 'tVal' can be reduced. [variableScope] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:497:22: style: The scope of the variable 'tVal' can be reduced. [variableScope] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:525:22: style: The scope of the variable 'tVal' can be reduced. [variableScope] abyss-2.3.7/vendor/gtest-1.7.0/src/gtest-printers.cc:197:14: debug: Failed to instantiate template "PrintAsCharLiteralTo". The checking continues anyway. [templateInstantiation] abyss-2.3.7/vendor/btl_bloomfilter/KmerBloomFilter.hpp:56:18: style: Local variable 'bit' shadows outer variable [shadowVariable] abyss-2.3.7/vendor/btl_bloomfilter/KmerBloomFilter.hpp:51:17: note: Shadowed declaration abyss-2.3.7/vendor/btl_bloomfilter/KmerBloomFilter.hpp:56:18: note: Shadow variable abyss-2.3.7/vendor/btl_bloomfilter/KmerBloomFilter.hpp:70:11: style: Local variable 'normalizedValue' shadows outer variable [shadowVariable] abyss-2.3.7/vendor/btl_bloomfilter/KmerBloomFilter.hpp:66:10: note: Shadowed declaration abyss-2.3.7/vendor/btl_bloomfilter/KmerBloomFilter.hpp:70:11: note: Shadow variable abyss-2.3.7/vendor/btl_bloomfilter/swig/testBloom_rolling.cpp:12:20: performance: Function parameter 'file' should be passed by const reference. [passedByValue] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:537:36: style: Parameter 'fkVal' can be declared as reference to const [constParameterReference] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:537:53: style: Parameter 'rkVal' can be declared as reference to const [constParameterReference] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:326:26: style: Variable 'tVal' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:346:26: style: Variable 'tVal' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:358:26: style: Variable 'tVal' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:370:26: style: Variable 'tVal' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:382:26: style: Variable 'tVal' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:420:26: style: Variable 'tVal' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:469:26: style: Variable 'tVal' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:497:26: style: Variable 'tVal' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/btl_bloomfilter/vendor/nthash.hpp:525:26: style: Variable 'tVal' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/btl_bloomfilter/swig/testBloom_rolling.cpp:38:10: style: Unused variable: t [unusedVariable] abyss-2.3.7/vendor/gtest-1.7.0/src/gtest.cc:202:17: error: There is an unknown macro here somewhere. Configuration is required. If GTEST_NAME_ is a macro then please configure it. [unknownMacro] abyss-2.3.7/vendor/btl_bloomfilter/swig/writeBloom_rolling.cpp:12:20: performance: Function parameter 'file' should be passed by const reference. [passedByValue] abyss-2.3.7/vendor/nthash/lib/xxhash.c:324:43: style:inconclusive: Function 'XXH32' argument 2 names different: declaration 'length' definition 'len'. [funcArgNamesDifferent] abyss-2.3.7/vendor/nthash/lib/xxhash.h:119:53: note: Function 'XXH32' argument 2 names different: declaration 'length' definition 'len'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:324:43: note: Function 'XXH32' argument 2 names different: declaration 'length' definition 'len'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:464:53: style:inconclusive: Function 'XXH64' argument 2 names different: declaration 'length' definition 'len'. [funcArgNamesDifferent] abyss-2.3.7/vendor/nthash/lib/xxhash.h:120:53: note: Function 'XXH64' argument 2 names different: declaration 'length' definition 'len'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:464:53: note: Function 'XXH64' argument 2 names different: declaration 'length' definition 'len'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:547:42: style:inconclusive: Function 'XXH32_reset' argument 1 names different: declaration 'statePtr' definition 'state_in'. [funcArgNamesDifferent] abyss-2.3.7/vendor/nthash/lib/xxhash.h:165:44: note: Function 'XXH32_reset' argument 1 names different: declaration 'statePtr' definition 'state_in'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:547:42: note: Function 'XXH32_reset' argument 1 names different: declaration 'statePtr' definition 'state_in'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:560:42: style:inconclusive: Function 'XXH64_reset' argument 1 names different: declaration 'statePtr' definition 'state_in'. [funcArgNamesDifferent] abyss-2.3.7/vendor/nthash/lib/xxhash.h:169:49: note: Function 'XXH64_reset' argument 1 names different: declaration 'statePtr' definition 'state_in'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:560:42: note: Function 'XXH64_reset' argument 1 names different: declaration 'statePtr' definition 'state_in'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:663:44: style:inconclusive: Function 'XXH32_update' argument 1 names different: declaration 'statePtr' definition 'state_in'. [funcArgNamesDifferent] abyss-2.3.7/vendor/nthash/lib/xxhash.h:166:44: note: Function 'XXH32_update' argument 1 names different: declaration 'statePtr' definition 'state_in'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:663:44: note: Function 'XXH32_update' argument 1 names different: declaration 'statePtr' definition 'state_in'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:663:80: style:inconclusive: Function 'XXH32_update' argument 3 names different: declaration 'length' definition 'len'. [funcArgNamesDifferent] abyss-2.3.7/vendor/nthash/lib/xxhash.h:166:80: note: Function 'XXH32_update' argument 3 names different: declaration 'length' definition 'len'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:663:80: note: Function 'XXH32_update' argument 3 names different: declaration 'length' definition 'len'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:717:40: style:inconclusive: Function 'XXH32_digest' argument 1 names different: declaration 'statePtr' definition 'state_in'. [funcArgNamesDifferent] abyss-2.3.7/vendor/nthash/lib/xxhash.h:167:50: note: Function 'XXH32_digest' argument 1 names different: declaration 'statePtr' definition 'state_in'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:717:40: note: Function 'XXH32_digest' argument 1 names different: declaration 'statePtr' definition 'state_in'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:817:44: style:inconclusive: Function 'XXH64_update' argument 1 names different: declaration 'statePtr' definition 'state_in'. [funcArgNamesDifferent] abyss-2.3.7/vendor/nthash/lib/xxhash.h:170:49: note: Function 'XXH64_update' argument 1 names different: declaration 'statePtr' definition 'state_in'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:817:44: note: Function 'XXH64_update' argument 1 names different: declaration 'statePtr' definition 'state_in'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:817:80: style:inconclusive: Function 'XXH64_update' argument 3 names different: declaration 'length' definition 'len'. [funcArgNamesDifferent] abyss-2.3.7/vendor/nthash/lib/xxhash.h:170:85: note: Function 'XXH64_update' argument 3 names different: declaration 'length' definition 'len'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:817:80: note: Function 'XXH64_update' argument 3 names different: declaration 'length' definition 'len'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:911:55: style:inconclusive: Function 'XXH64_digest' argument 1 names different: declaration 'statePtr' definition 'state_in'. [funcArgNamesDifferent] abyss-2.3.7/vendor/nthash/lib/xxhash.h:171:55: note: Function 'XXH64_digest' argument 1 names different: declaration 'statePtr' definition 'state_in'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:911:55: note: Function 'XXH64_digest' argument 1 names different: declaration 'statePtr' definition 'state_in'. abyss-2.3.7/vendor/nthash/lib/xxhash.c:613:16: style: Variable 'p32' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/nthash/lib/xxhash.c:767:16: style: Variable 'p64' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/nthash/lib/seedgen.cpp:92:48: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck] abyss-2.3.7/vendor/nthash/lib/seedgen.cpp:146:48: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck] abyss-2.3.7/vendor/nthash/nttest.cpp:108:13: style: Variable 'good' is reassigned a value before the old one has been used. [redundantAssignment] abyss-2.3.7/vendor/nthash/nttest.cpp:107:13: note: good is assigned abyss-2.3.7/vendor/nthash/nttest.cpp:108:13: note: good is overwritten abyss-2.3.7/vendor/nthash/nttest.cpp:109:13: style: Variable 'good' is reassigned a value before the old one has been used. [redundantAssignment] abyss-2.3.7/vendor/nthash/nttest.cpp:108:13: note: good is assigned abyss-2.3.7/vendor/nthash/nttest.cpp:109:13: note: good is overwritten abyss-2.3.7/vendor/nthash/nttest.cpp:110:13: style: Variable 'good' is reassigned a value before the old one has been used. [redundantAssignment] abyss-2.3.7/vendor/nthash/nttest.cpp:109:13: note: good is assigned abyss-2.3.7/vendor/nthash/nttest.cpp:110:13: note: good is overwritten abyss-2.3.7/vendor/nthash/nthash.hpp:326:22: style: The scope of the variable 'tVal' can be reduced. [variableScope] abyss-2.3.7/vendor/nthash/nthash.hpp:346:22: style: The scope of the variable 'tVal' can be reduced. [variableScope] abyss-2.3.7/vendor/nthash/nthash.hpp:358:22: style: The scope of the variable 'tVal' can be reduced. [variableScope] abyss-2.3.7/vendor/nthash/nthash.hpp:370:22: style: The scope of the variable 'tVal' can be reduced. [variableScope] abyss-2.3.7/vendor/nthash/nthash.hpp:382:22: style: The scope of the variable 'tVal' can be reduced. [variableScope] abyss-2.3.7/vendor/nthash/nthash.hpp:420:22: style: The scope of the variable 'tVal' can be reduced. [variableScope] abyss-2.3.7/vendor/nthash/nthash.hpp:469:22: style: The scope of the variable 'tVal' can be reduced. [variableScope] abyss-2.3.7/vendor/nthash/nthash.hpp:497:22: style: The scope of the variable 'tVal' can be reduced. [variableScope] abyss-2.3.7/vendor/nthash/nthash.hpp:525:22: style: The scope of the variable 'tVal' can be reduced. [variableScope] abyss-2.3.7/vendor/nthash/nttest.cpp:401:22: style: Local variable 'i' shadows outer variable [shadowVariable] abyss-2.3.7/vendor/nthash/nttest.cpp:399:17: note: Shadowed declaration abyss-2.3.7/vendor/nthash/nttest.cpp:401:22: note: Shadow variable abyss-2.3.7/vendor/nthash/nthash.hpp:537:36: style: Parameter 'fkVal' can be declared as reference to const [constParameterReference] abyss-2.3.7/vendor/nthash/nthash.hpp:537:53: style: Parameter 'rkVal' can be declared as reference to const [constParameterReference] abyss-2.3.7/vendor/nthash/nthash.hpp:326:26: style: Variable 'tVal' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/nthash/nthash.hpp:346:26: style: Variable 'tVal' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/nthash/nthash.hpp:358:26: style: Variable 'tVal' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/nthash/nthash.hpp:370:26: style: Variable 'tVal' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/nthash/nthash.hpp:382:26: style: Variable 'tVal' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/nthash/nthash.hpp:420:26: style: Variable 'tVal' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/nthash/nthash.hpp:469:26: style: Variable 'tVal' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/nthash/nthash.hpp:497:26: style: Variable 'tVal' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/nthash/nthash.hpp:525:26: style: Variable 'tVal' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/vendor/nthash/stHashIterator.hpp:39:5: warning: Member variable 'stHashIterator::m_h' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/vendor/nthash/stHashIterator.hpp:39:5: warning: Member variable 'stHashIterator::m_h2' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/vendor/nthash/stHashIterator.hpp:39:5: warning: Member variable 'stHashIterator::m_k' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/vendor/nthash/stHashIterator.hpp:39:5: warning: Member variable 'stHashIterator::m_fhVal' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/vendor/nthash/stHashIterator.hpp:39:5: warning: Member variable 'stHashIterator::m_rhVal' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/vendor/nthash/stHashIterator.hpp:54:57: warning: Class 'stHashIterator' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] abyss-2.3.7/vendor/nthash/stHashIterator.hpp:54:57: warning: Class 'stHashIterator' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] abyss-2.3.7/vendor/nthash/sttest.cpp:34:14: style: Variable 'good' is reassigned a value before the old one has been used. [redundantAssignment] abyss-2.3.7/vendor/nthash/sttest.cpp:33:14: note: good is assigned abyss-2.3.7/vendor/nthash/sttest.cpp:34:14: note: good is overwritten abyss-2.3.7/vendor/nthash/sttest.cpp:35:14: style: Variable 'good' is reassigned a value before the old one has been used. [redundantAssignment] abyss-2.3.7/vendor/nthash/sttest.cpp:34:14: note: good is assigned abyss-2.3.7/vendor/nthash/sttest.cpp:35:14: note: good is overwritten abyss-2.3.7/vendor/nthash/sttest.cpp:36:14: style: Variable 'good' is reassigned a value before the old one has been used. [redundantAssignment] abyss-2.3.7/vendor/nthash/sttest.cpp:35:14: note: good is assigned abyss-2.3.7/vendor/nthash/sttest.cpp:36:14: note: good is overwritten abyss-2.3.7/vendor/nthash/ssHashIterator.hpp:27:5: warning: Member variable 'ssHashIterator::m_k' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/vendor/nthash/ssHashIterator.hpp:27:5: warning: Member variable 'ssHashIterator::m_hVal' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/vendor/nthash/ssHashIterator.hpp:27:5: warning: Member variable 'ssHashIterator::m_sVal' is not initialized in the constructor. [uninitMemberVar] abyss-2.3.7/vendor/nthash/sstest.cpp:18:14: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm] abyss-2.3.7/dialign/diag.c:37:5: warning: %i in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] abyss-2.3.7/dialign/diag.c:41:5: warning: %i in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] abyss-2.3.7/dialign/diag.c:1828:25: warning: %i in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] abyss-2.3.7/dialign/diag.c:1828:25: warning: %i in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] abyss-2.3.7/dialign/diag.c:1980:25: warning: %i in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] abyss-2.3.7/dialign/diag.c:1980:25: warning: %i in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] abyss-2.3.7/dialign/diag.c:844:8: error: Common realloc mistake: 'pool_diags' nulled but not freed upon failure [memleakOnRealloc] abyss-2.3.7/dialign/diag.c:949:3: error: Common realloc mistake: 'data' nulled but not freed upon failure [memleakOnRealloc] abyss-2.3.7/dialign/diag.c:1189:5: error: Common realloc mistake: 'pool_diags' nulled but not freed upon failure [memleakOnRealloc] abyss-2.3.7/dialign/diag.c:1245:3: error: Common realloc mistake: 'data' nulled but not freed upon failure [memleakOnRealloc] abyss-2.3.7/dialign/diag.c:1462:5: error: Common realloc mistake: 'pool_diags' nulled but not freed upon failure [memleakOnRealloc] abyss-2.3.7/dialign/diag.c:1520:3: error: Common realloc mistake: 'data' nulled but not freed upon failure [memleakOnRealloc] abyss-2.3.7/dialign/diag.c:407:3: warning: Either the condition 'dc==NULL' is redundant or there is possible null pointer dereference: dc. [nullPointerRedundantCheck] abyss-2.3.7/dialign/diag.c:404:8: note: Assuming that condition 'dc==NULL' is not redundant abyss-2.3.7/dialign/diag.c:407:3: note: Null pointer dereference abyss-2.3.7/dialign/diag.c:410:3: warning: Either the condition 'dc==NULL' is redundant or there is possible null pointer dereference: dc. [nullPointerRedundantCheck] abyss-2.3.7/dialign/diag.c:404:8: note: Assuming that condition 'dc==NULL' is not redundant abyss-2.3.7/dialign/diag.c:410:3: note: Null pointer dereference abyss-2.3.7/dialign/diag.c:411:6: warning: Either the condition 'dc==NULL' is redundant or there is possible null pointer dereference: dc. [nullPointerRedundantCheck] abyss-2.3.7/dialign/diag.c:404:8: note: Assuming that condition 'dc==NULL' is not redundant abyss-2.3.7/dialign/diag.c:411:6: note: Null pointer dereference abyss-2.3.7/dialign/diag.c:2079:7: warning: Either the condition 'sdcol!=NULL' is redundant or there is possible null pointer dereference: sdcol. [nullPointerRedundantCheck] abyss-2.3.7/dialign/diag.c:2081:15: note: Assuming that condition 'sdcol!=NULL' is not redundant abyss-2.3.7/dialign/diag.c:2079:7: note: Null pointer dereference abyss-2.3.7/dialign/diag.c:501:11: style: The comparison 'slen2 > maxslen' is always false because 'slen2' and 'maxslen' represent the same value. [knownConditionTrueFalse] abyss-2.3.7/dialign/diag.c:476:16: note: 'slen2' is assigned value 'slen1' here. abyss-2.3.7/dialign/diag.c:500:17: note: 'maxslen' is assigned value 'slen1' here. abyss-2.3.7/dialign/diag.c:501:11: note: The comparison 'slen2 > maxslen' is always false because 'slen2' and 'maxslen' represent the same value. abyss-2.3.7/dialign/diag.c:208:18: style: Checking if unsigned expression 'dg->length' is less than zero. [unsignedLessThanZero] abyss-2.3.7/dialign/diag.c:739:9: warning:inconclusive: Found suspicious equality comparison. Did you intend to assign a value instead? [constStatement] abyss-2.3.7/dialign/diag.c:123:22: style: Variable 'smatrix' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:151:23: style: Variable 'smatrix' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:228:11: style: Variable 'data1' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:229:11: style: Variable 'data2' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:231:10: style: Variable 'c2n' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:232:10: style: Variable 'sdata' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:331:20: style: Variable 'seq_p' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:331:28: style: Variable 'd_seq_p1' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:493:8: style: Variable 'c2n' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:494:8: style: Variable 'sdata' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:495:9: style: Variable 'data1' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:496:9: style: Variable 'data2' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:987:8: style: Variable 'c2n' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:988:8: style: Variable 'sdata' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:989:9: style: Variable 'data1' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:990:9: style: Variable 'data2' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:1292:8: style: Variable 'c2n' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:1293:8: style: Variable 'sdata' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:1294:9: style: Variable 'data1' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:1295:9: style: Variable 'data2' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:1329:25: style: Variable 'tap' can be declared as pointer to const [constVariablePointer] abyss-2.3.7/dialign/diag.c:223:17: style: Variable 'np' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/diag.c:490:11: style: Variable 'sn1' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/diag.c:491:11: style: Variable 'sn2' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/diag.c:513:15: style: Variable 'hasAli' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/diag.c:518:13: style: Variable 'score1' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/diag.c:518:23: style: Variable 'score2' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/diag.c:517:18: style: Unused variable: cons_maxd [unusedVariable] abyss-2.3.7/dialign/diag.c:535:8: style: Unused variable: mstatus [unusedVariable] abyss-2.3.7/dialign/diag.c:1010:16: style: Variable 'score1' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/diag.c:1010:26: style: Variable 'score2' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/diag.c:1110:12: style: Variable 'cons_maxd' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/diag.c:1299:13: style: Variable 'score1' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/diag.c:1299:23: style: Variable 'score2' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/diag.c:1318:14: style: Variable 'pooled' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/diag.c:1448:15: style: Variable 'kscore' is assigned a value that is never used. [unreadVariable] abyss-2.3.7/dialign/diag.c:1449:13: style: Variable 'klen' is assigned a value that is never used. [unreadVariable] diff: 2.13.0 abyss-2.3.7/Parallel/NetworkSequenceCollection.cpp:940:3: error: Iterator '*rmIter' from different container 'm_activeBranchGroups' are used together. [mismatchingContainerIterator] head abyss-2.3.7/RResolver/RAlgorithmsShort.cpp:45:8: style: C-style reference casting [cstyleCast] head abyss-2.3.7/dialign/alig.c:273:46: style: Condition '1||(tap->predFPos<0)' is always true [knownConditionTrueFalse] head abyss-2.3.7/dialign/alig.c:283:45: style: Condition '1||(tap->succFPos<0)' is always true [knownConditionTrueFalse] 2.13.0 abyss-2.3.7/dialign/assemble.c:349:21: warning: Either the condition 'diags==NULL' is redundant or there is possible null pointer dereference: diags. [nullPointerRedundantCheck] abyss-2.3.7/dialign/assemble.c:489:13: note: Assuming that condition 'diags==NULL' is not redundant abyss-2.3.7/dialign/assemble.c:500:24: note: Calling function 'heapify_diag_array', 1st argument 'diags' value is 0 abyss-2.3.7/dialign/assemble.c:349:21: note: Null pointer dereference 2.13.0 abyss-2.3.7/dialign/assemble.c:498:10: style: Condition 'dlen>=2' is always true [knownConditionTrueFalse] abyss-2.3.7/dialign/assemble.c:428:13: note: Assuming that condition 'dlen>0' is not redundant abyss-2.3.7/dialign/assemble.c:494:3: note: dlen is incremented', new value is 1 abyss-2.3.7/dialign/assemble.c:498:10: note: Condition 'dlen>=2' is always true head abyss-2.3.7/dialign/diag.c:1294:9: style: Variable 'data1' can be declared as pointer to const [constVariablePointer] head abyss-2.3.7/dialign/diag.c:1295:9: style: Variable 'data2' can be declared as pointer to const [constVariablePointer] head abyss-2.3.7/dialign/diag.c:228:11: style: Variable 'data1' can be declared as pointer to const [constVariablePointer] head abyss-2.3.7/dialign/diag.c:229:11: style: Variable 'data2' can be declared as pointer to const [constVariablePointer] head abyss-2.3.7/dialign/diag.c:232:10: style: Variable 'sdata' can be declared as pointer to const [constVariablePointer] head abyss-2.3.7/dialign/diag.c:495:9: style: Variable 'data1' can be declared as pointer to const [constVariablePointer] head abyss-2.3.7/dialign/diag.c:496:9: style: Variable 'data2' can be declared as pointer to const [constVariablePointer] head abyss-2.3.7/dialign/diag.c:989:9: style: Variable 'data1' can be declared as pointer to const [constVariablePointer] head abyss-2.3.7/dialign/diag.c:990:9: style: Variable 'data2' can be declared as pointer to const [constVariablePointer] head abyss-2.3.7/dialign/io.c:1093:14: error: Deallocation of a pointer pointing to a string literal ("Multiple Sequence Alignment (with translation)") results in undefined behaviour. [autovarInvalidDeallocation] abyss-2.3.7/dialign/io.c:848:12: note: Assignment 'line="Multiple Sequence Alignment (with translation)"', assigned value is "Multiple Sequence Alignment (with translation)" abyss-2.3.7/dialign/io.c:849:24: note: Calling function 'output_line', 1st argument 'line' value is "Multiple Sequence Alignment (with translation)" abyss-2.3.7/dialign/io.c:1074:10: note: Assuming condition is false abyss-2.3.7/dialign/io.c:1093:14: note: Deallocating memory that was not dynamically allocated head abyss-2.3.7/dialign/prob.c:129:9: style: Variable 'data1' can be declared as pointer to const [constVariablePointer] head abyss-2.3.7/dialign/prob.c:130:9: style: Variable 'data2' can be declared as pointer to const [constVariablePointer] head abyss-2.3.7/dialign/prob.c:40:8: style: Variable 'n2c' can be declared as pointer to const [constVariablePointer] head abyss-2.3.7/dialign/prob.c:88:8: style: Variable 'sdata' can be declared as pointer to const [constVariablePointer] DONE