2025-09-13 14:57 ftp://ftp.de.debian.org/debian/pool/main/k/kmer/kmer_0~20150903+r2013.orig.tar.gz cppcheck-options: --library=posix --library=gnu --library=bsd --library=bsd --library=python --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j1 platform: Linux-6.8.0-79-generic-x86_64-with-glibc2.39 python: 3.12.3 client-version: 1.3.69 compiler: g++ (Ubuntu 14.2.0-4ubuntu2~24.04) 14.2.0 cppcheck: head 2.18.0 head-info: fea194b (2025-09-13 13:40:14 +0200) count: 1591 1581 elapsed-time: 48.8 49.4 head-timing-info: old-timing-info: head results: kmer-code-2013-trunk/ESTmapper/mergeCounts.C:10:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/ESTmapper/terminate.C:34:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/ESTmapper/terminate.C:82:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint32FMT [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/ESTmapper/terminate.C:120:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/ESTmapper/terminate.C:60:12: style:inconclusive: Technically the member function 'iidReaderWriter::thisIID' can be const. [functionConst] kmer-code-2013-trunk/ESTmapper/terminate.C:32:7: warning: Class 'iidReaderWriter' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/ESTmapper/terminate.C:32:7: warning: Class 'iidReaderWriter' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/ESTmapper/terminate.C:69:5: warning: Possible leak in public function. The pointer 'iids' is not deallocated before it is allocated. [publicAllocationError] kmer-code-2013-trunk/ESTmapper/terminate.C:26:39: style: Parameter 'otfile' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-span.H:75:48: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:550:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:283:22: style: Condition 'tmp==CC[j]+RR[j]' is always false [knownConditionTrueFalse] kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:279:9: note: tmp is assigned '(CC[j]+RR[j])<=(DD[j]+SS[j]-g)?(CC[j]+RR[j]):(DD[j]+SS[j]-g)' here. kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:283:22: note: Condition 'tmp==CC[j]+RR[j]' is always false kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:291:19: style: Condition 'tmp==CC[len2]+RR[len2]' is always false [knownConditionTrueFalse] kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:287:7: note: tmp is assigned '(CC[len2]+RR[len2])<=(DD[len2]+SS[len2]-g*(midiminEndRunLen' is always true [knownConditionTrueFalse] kmer-code-2013-trunk/atac-driver/matchExtender/matchExtender-func.C:352:31: note: Assuming that condition 'good_run_len==minEndRunLen' is not redundant kmer-code-2013-trunk/atac-driver/matchExtender/matchExtender-func.C:355:31: note: Condition 'good_run_len>minEndRunLen' is always true kmer-code-2013-trunk/atac-driver/matchExtender/match.H:36:17: style: Parameter 'matchId' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/atac-driver/matchExtender/matchExtender.C:192:39: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/atac-driver/mismatchCounter/mismatchCounter.C:197:40: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/atac-driver/statsGenerator/statsGenerator.C:91:36: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:226:71: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/leaff/blocks.C:32:30: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/leaff/dups.C:26:37: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/leaff/fragmenter.C:101:36: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/leaff/gc.C:68:36: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/leaff/leaff.C:311:63: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/leaff/partition.C:55:52: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/leaff/simseq.C:110:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/leaff/simseq.C:130:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/leaff/simseq.C:46:3: warning: If memory allocation fails, then there is a possible null pointer dereference: newtp [nullPointerOutOfMemory] kmer-code-2013-trunk/leaff/simseq.C:44:47: note: Assuming allocation function fails kmer-code-2013-trunk/leaff/simseq.C:44:25: note: Assignment 'newtp=(struct EditScript_t*)malloc(sizeof(struct EditScript_t))', assigned value is 0 kmer-code-2013-trunk/leaff/simseq.C:46:3: note: Null pointer dereference kmer-code-2013-trunk/leaff/simseq.C:47:3: warning: If memory allocation fails, then there is a possible null pointer dereference: newtp [nullPointerOutOfMemory] kmer-code-2013-trunk/leaff/simseq.C:44:47: note: Assuming allocation function fails kmer-code-2013-trunk/leaff/simseq.C:44:25: note: Assignment 'newtp=(struct EditScript_t*)malloc(sizeof(struct EditScript_t))', assigned value is 0 kmer-code-2013-trunk/leaff/simseq.C:47:3: note: Null pointer dereference kmer-code-2013-trunk/leaff/simseq.C:48:3: warning: If memory allocation fails, then there is a possible null pointer dereference: newtp [nullPointerOutOfMemory] kmer-code-2013-trunk/leaff/simseq.C:44:47: note: Assuming allocation function fails kmer-code-2013-trunk/leaff/simseq.C:44:25: note: Assignment 'newtp=(struct EditScript_t*)malloc(sizeof(struct EditScript_t))', assigned value is 0 kmer-code-2013-trunk/leaff/simseq.C:48:3: note: Null pointer dereference kmer-code-2013-trunk/leaff/simseq.C:44:25: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/leaff/simseq.C:58:10: style: The scope of the variable 'num' can be reduced. [variableScope] kmer-code-2013-trunk/leaff/simseq.C:58:15: style: The scope of the variable 'optype' can be reduced. [variableScope] kmer-code-2013-trunk/leaff/simseq.C:196:17: style: The scope of the variable 'start' can be reduced. [variableScope] kmer-code-2013-trunk/leaff/simseq.C:120:31: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/leaff/simseq.C:122:9: style: Variable 's' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/leaff/simseq.C:123:9: style: Variable 'let_4' can be declared as const array [constVariable] kmer-code-2013-trunk/leaff/simseq.C:124:9: style: Variable 'let_3A' can be declared as const array [constVariable] kmer-code-2013-trunk/leaff/simseq.C:125:9: style: Variable 'let_3C' can be declared as const array [constVariable] kmer-code-2013-trunk/leaff/simseq.C:126:9: style: Variable 'let_3G' can be declared as const array [constVariable] kmer-code-2013-trunk/leaff/simseq.C:127:9: style: Variable 'let_3T' can be declared as const array [constVariable] kmer-code-2013-trunk/leaff/stats.C:110:30: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libbio/alphabet-generate.c:37:11: warning: If resource allocation fails, then there is a possible null pointer dereference: H [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assignment 'H=fopen("alphabet.h","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:37:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:38:11: warning: If resource allocation fails, then there is a possible null pointer dereference: H [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assignment 'H=fopen("alphabet.h","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:38:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:39:11: warning: If resource allocation fails, then there is a possible null pointer dereference: H [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assignment 'H=fopen("alphabet.h","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:39:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:40:11: warning: If resource allocation fails, then there is a possible null pointer dereference: H [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assignment 'H=fopen("alphabet.h","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:40:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:41:11: warning: If resource allocation fails, then there is a possible null pointer dereference: H [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assignment 'H=fopen("alphabet.h","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:41:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:42:11: warning: If resource allocation fails, then there is a possible null pointer dereference: H [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assignment 'H=fopen("alphabet.h","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:42:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:43:11: warning: If resource allocation fails, then there is a possible null pointer dereference: H [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assignment 'H=fopen("alphabet.h","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:43:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:44:11: warning: If resource allocation fails, then there is a possible null pointer dereference: H [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assignment 'H=fopen("alphabet.h","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:44:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:45:11: warning: If resource allocation fails, then there is a possible null pointer dereference: H [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assignment 'H=fopen("alphabet.h","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:45:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:47:11: warning: If resource allocation fails, then there is a possible null pointer dereference: C [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assignment 'C=fopen("alphabet.c","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:47:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:48:11: warning: If resource allocation fails, then there is a possible null pointer dereference: C [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assignment 'C=fopen("alphabet.c","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:48:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:49:11: warning: If resource allocation fails, then there is a possible null pointer dereference: C [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assignment 'C=fopen("alphabet.c","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:49:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:50:11: warning: If resource allocation fails, then there is a possible null pointer dereference: C [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assignment 'C=fopen("alphabet.c","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:50:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:52:11: warning: If resource allocation fails, then there is a possible null pointer dereference: H [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assignment 'H=fopen("alphabet.h","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:52:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:53:11: warning: If resource allocation fails, then there is a possible null pointer dereference: C [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assignment 'C=fopen("alphabet.c","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:53:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:55:13: warning: If resource allocation fails, then there is a possible null pointer dereference: C [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assignment 'C=fopen("alphabet.c","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:55:13: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:56:11: warning: If resource allocation fails, then there is a possible null pointer dereference: C [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assignment 'C=fopen("alphabet.c","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:56:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:58:11: warning: If resource allocation fails, then there is a possible null pointer dereference: H [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assignment 'H=fopen("alphabet.h","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:58:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:59:11: warning: If resource allocation fails, then there is a possible null pointer dereference: C [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assignment 'C=fopen("alphabet.c","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:59:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:61:13: warning: If resource allocation fails, then there is a possible null pointer dereference: C [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assignment 'C=fopen("alphabet.c","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:61:13: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:62:11: warning: If resource allocation fails, then there is a possible null pointer dereference: C [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assignment 'C=fopen("alphabet.c","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:62:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:64:11: warning: If resource allocation fails, then there is a possible null pointer dereference: H [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assignment 'H=fopen("alphabet.h","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:64:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:65:11: warning: If resource allocation fails, then there is a possible null pointer dereference: C [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assignment 'C=fopen("alphabet.c","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:65:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:67:13: warning: If resource allocation fails, then there is a possible null pointer dereference: C [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assignment 'C=fopen("alphabet.c","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:67:13: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:68:11: warning: If resource allocation fails, then there is a possible null pointer dereference: C [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assignment 'C=fopen("alphabet.c","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:68:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:70:11: warning: If resource allocation fails, then there is a possible null pointer dereference: H [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assignment 'H=fopen("alphabet.h","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:70:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:71:11: warning: If resource allocation fails, then there is a possible null pointer dereference: C [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assignment 'C=fopen("alphabet.c","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:71:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:73:13: warning: If resource allocation fails, then there is a possible null pointer dereference: C [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assignment 'C=fopen("alphabet.c","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:73:13: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:74:11: warning: If resource allocation fails, then there is a possible null pointer dereference: C [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assignment 'C=fopen("alphabet.c","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:74:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:76:11: warning: If resource allocation fails, then there is a possible null pointer dereference: H [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:32:18: note: Assignment 'H=fopen("alphabet.h","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:76:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/alphabet-generate.c:77:11: warning: If resource allocation fails, then there is a possible null pointer dereference: C [nullPointerOutOfResources] kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assuming allocation function fails kmer-code-2013-trunk/libbio/alphabet-generate.c:31:18: note: Assignment 'C=fopen("alphabet.c","w")', assigned value is 0 kmer-code-2013-trunk/libbio/alphabet-generate.c:77:11: note: Null pointer dereference kmer-code-2013-trunk/libbio/halign.c:65:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libbio/halign.c:101:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libbio/halign.c:257:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libbio/halign.c:458:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libbio/halign.c:66:9: warning: Identical condition 'x>M', second condition is always false [identicalConditionAfterEarlyExit] kmer-code-2013-trunk/libbio/halign.c:63:8: note: If condition 'x>M' is true, the function will return/exit kmer-code-2013-trunk/libbio/halign.c:66:9: note: Testing identical condition 'x>M' kmer-code-2013-trunk/libbio/halign.c:394:20: style:inconclusive: Function 'halign' argument 1 names different: declaration 'string1' definition 'seq1'. [funcArgNamesDifferent] kmer-code-2013-trunk/libbio/bio.h:34:20: note: Function 'halign' argument 1 names different: declaration 'string1' definition 'seq1'. kmer-code-2013-trunk/libbio/halign.c:394:20: note: Function 'halign' argument 1 names different: declaration 'string1' definition 'seq1'. kmer-code-2013-trunk/libbio/halign.c:395:20: style:inconclusive: Function 'halign' argument 2 names different: declaration 'string2' definition 'seq2'. [funcArgNamesDifferent] kmer-code-2013-trunk/libbio/bio.h:35:20: note: Function 'halign' argument 2 names different: declaration 'string2' definition 'seq2'. kmer-code-2013-trunk/libbio/halign.c:395:20: note: Function 'halign' argument 2 names different: declaration 'string2' definition 'seq2'. kmer-code-2013-trunk/libbio/halign.c:32:16: style: struct member 'edit_script_list::offset1' is never used. [unusedStructMember] kmer-code-2013-trunk/libbio/halign.c:32:25: style: struct member 'edit_script_list::offset2' is never used. [unusedStructMember] kmer-code-2013-trunk/libbio/halign.c:33:16: style: struct member 'edit_script_list::len1' is never used. [unusedStructMember] kmer-code-2013-trunk/libbio/halign.c:33:22: style: struct member 'edit_script_list::len2' is never used. [unusedStructMember] kmer-code-2013-trunk/libbio/halign.c:34:16: style: struct member 'edit_script_list::score' is never used. [unusedStructMember] kmer-code-2013-trunk/libbio/halign.c:35:16: style: struct member 'edit_script_list::first' is never used. [unusedStructMember] kmer-code-2013-trunk/libbio/halign.c:36:16: style: struct member 'edit_script_list::script' is never used. [unusedStructMember] kmer-code-2013-trunk/libbio/mers.h:39:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bitsToLetter [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libbio/kmertiny.H:23:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint64ZERO [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libbio/kmertiny.H:144:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bitsToLetter [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libbio/kmer.H:67:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable letterToBits [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libbio/kmer.C:70:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libbio/kmer.C:494:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libbio/merCovering.H:24:7: performance: Variable '_lo' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/merCovering.H:25:7: performance: Variable '_hi' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/merCovering.H:40:5: performance: Variable '_width' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/merCovering.H:41:5: performance: Variable '_pieces' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/merList.H:9:5: performance: Variable '_ptrsMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/merList.H:10:5: performance: Variable '_ptrsLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/merList.H:13:5: performance: Variable '_mersWid' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/kmer.C:4:3: performance: Variable '_style' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/kmer.C:6:3: performance: Variable '_merSize' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/kmer.C:8:3: performance: Variable '_merSizeValidIs' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/kmer.C:9:3: performance: Variable '_merSizeValidZero' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/kmer.C:15:3: performance: Variable '_compression' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/kmer.C:16:3: performance: Variable '_compressionIndex' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/kmer.C:17:3: performance: Variable '_compressionFirstIndex' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/kmer.C:19:3: performance: Variable '_compressionCurrentLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/kmer.C:21:3: performance: Variable '_templateSpan' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/kmer.C:22:3: performance: Variable '_templateLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/kmer.C:24:3: performance: Variable '_templatePos' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/kmer.C:25:3: performance: Variable '_templateMer' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/kmer.C:26:3: performance: Variable '_templateFirst' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libbio/merCovering.H:66:17: style:inconclusive: Technically the member function 'merCovering::sumOfLengths' can be const. [functionConst] kmer-code-2013-trunk/libbio/merCovering.H:75:17: style:inconclusive: Technically the member function 'merCovering::numberOfPieces' can be const. [functionConst] kmer-code-2013-trunk/libbio/merList.H:46:9: style:inconclusive: Technically the member function 'merList::getMer' can be const. [functionConst] kmer-code-2013-trunk/libbio/kmer.C:493:14: performance:inconclusive: Technically the member function 'kMerBuilder::addBaseCompressedSpaced' can be static (but you may consider moving to unnamed namespace). [functionStatic] kmer-code-2013-trunk/libbio/kmer.H:63:8: note: Technically the member function 'kMerBuilder::addBaseCompressedSpaced' can be static (but you may consider moving to unnamed namespace). kmer-code-2013-trunk/libbio/kmer.C:493:14: note: Technically the member function 'kMerBuilder::addBaseCompressedSpaced' can be static (but you may consider moving to unnamed namespace). kmer-code-2013-trunk/libbio/kmer.H:97:17: style:inconclusive: Technically the member function 'kMerBuilder::theFMer' can be const. [functionConst] kmer-code-2013-trunk/libbio/kmer.H:98:17: style:inconclusive: Technically the member function 'kMerBuilder::theRMer' can be const. [functionConst] kmer-code-2013-trunk/libbio/kmer.H:101:17: style:inconclusive: Technically the member function 'kMerBuilder::merSize' can be const. [functionConst] kmer-code-2013-trunk/libbio/kmer.H:102:17: style:inconclusive: Technically the member function 'kMerBuilder::templateSpan' can be const. [functionConst] kmer-code-2013-trunk/libbio/kmer.H:104:17: style:inconclusive: Technically the member function 'kMerBuilder::baseSpan' can be const. [functionConst] kmer-code-2013-trunk/libbio/merList.H:11:5: warning: Class 'merList' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libbio/merList.H:11:5: warning: Class 'merList' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libbio/kmer.C:141:5: warning: Class 'kMerBuilder' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libbio/kmer.C:141:5: warning: Class 'kMerBuilder' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libbio/merCovering.H:38:3: style: Class 'merCovering' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libbio/kmertiny.H:4:3: style: Class 'kMerTiny' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libbio/kmer.H:50:3: style: Class 'kMerBuilder' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libbio/kmertiny.H:142:29: style:inconclusive: Function 'merToString' argument 1 names different: declaration 'instr' definition 'str'. [funcArgNamesDifferent] kmer-code-2013-trunk/libbio/kmertiny.H:104:30: note: Function 'merToString' argument 1 names different: declaration 'instr' definition 'str'. kmer-code-2013-trunk/libbio/kmertiny.H:142:29: note: Function 'merToString' argument 1 names different: declaration 'instr' definition 'str'. kmer-code-2013-trunk/libbio/kmer.C:3:54: style: Parameter 'tm' can be declared as pointer to const. However it seems that 'kMerBuilder' is a callback function, if 'tm' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kmer-code-2013-trunk/libbio/kmer.H:48:7: note: You might need to cast the function pointer here kmer-code-2013-trunk/libbio/kmer.C:3:54: note: Parameter 'tm' can be declared as pointer to const kmer-code-2013-trunk/libbio/test/halign-test.C:42:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libbio/test/halign-test.C:12:6: style: Variable 's1' is reassigned a value before the old one has been used. [redundantAssignment] kmer-code-2013-trunk/libbio/test/halign-test.C:9:6: note: s1 is assigned kmer-code-2013-trunk/libbio/test/halign-test.C:12:6: note: s1 is overwritten kmer-code-2013-trunk/libbio/test/halign-test.C:13:6: style: Variable 's2' is reassigned a value before the old one has been used. [redundantAssignment] kmer-code-2013-trunk/libbio/test/halign-test.C:10:6: note: s2 is assigned kmer-code-2013-trunk/libbio/test/halign-test.C:13:6: note: s2 is overwritten kmer-code-2013-trunk/libbio/test/test-bigmer-msf.C:48:19: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libbio/test/test-setbits.C:19:46: error: There is an unknown macro here somewhere. Configuration is required. If uint64HEX is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libkmer/driver-existDB.C:53:29: error: There is an unknown macro here somewhere. Configuration is required. If uint64HEX is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libkmer/positionDB.H:127:34: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libkmer/existDB-create-from-fasta.C:136:65: error: There is an unknown macro here somewhere. Configuration is required. If uint64FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libkmer/existDB-create-from-meryl.C:27:69: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libkmer/existDB-create-from-sequence.C:136:68: error: There is an unknown macro here somewhere. Configuration is required. If uint64FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libkmer/existDB-state.C:169:39: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libkmer/existDB.C:44:50: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libkmer/test/test-maskonly.C:75:41: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libkmer/test/test-rebuild.C:17:31: error: There is an unknown macro here somewhere. Configuration is required. If uint64FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libmeryl/libmeryl.C:134:75: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libseq/fastaFile.C:151:59: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libseq/fastaStdin.C:43:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/fastaStdin.C:81:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/fastaStdin.C:96:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/fastaStdin.C:121:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/fastaStdin.C:156:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/fastaStdin.C:165:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/fastaStdin.C:209:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable whitespaceSymbol [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/seqFile.H:16:3: warning: Member variable 'seqFile::_filename' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/libseq/seqFile.H:16:3: warning: Member variable 'seqFile::_typename' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/libseq/seqFile.H:16:3: warning: Member variable 'seqFile::_randomAccessSupported' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/libseq/seqFile.H:17:3: warning:inconclusive: Member variable 'seqFile::_filename' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/libseq/seqFile.H:17:3: warning:inconclusive: Member variable 'seqFile::_typename' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/libseq/seqFile.H:17:3: warning:inconclusive: Member variable 'seqFile::_randomAccessSupported' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/libseq/fastaStdin.C:17:5: warning: Class 'fastaStdin' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libseq/fastaStdin.C:17:5: warning: Class 'fastaStdin' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libseq/fastaStdin.H:12:3: style: Class 'fastaStdin' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libseq/fastaStdin.H:16:4: style: The destructor '~fastaStdin' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:20:12: note: Virtual destructor in base class kmer-code-2013-trunk/libseq/fastaStdin.H:16:4: note: Destructor in derived class kmer-code-2013-trunk/libseq/fastaStdin.H:19:23: style: The function 'openFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:23:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastaStdin.H:19:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastaStdin.H:22:23: style: The function 'getNumberOfSequences' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:31:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastaStdin.H:22:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastaStdin.H:25:23: style: The function 'find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:34:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastaStdin.H:25:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastaStdin.H:27:23: style: The function 'getSequenceLength' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:36:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastaStdin.H:27:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastaStdin.H:28:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:37:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastaStdin.H:28:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastaStdin.H:31:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:40:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastaStdin.H:31:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastaStdin.C:110:13: style: Variable 'ret' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libseq/fastaStdin.C:110:9: style: Variable 'ret' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libseq/fastqFile.C:141:59: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libseq/fastqStdin.C:43:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/fastqStdin.C:81:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/fastqStdin.C:96:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/fastqStdin.C:121:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/fastqStdin.C:156:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/fastqStdin.C:165:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/fastqStdin.C:209:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable whitespaceSymbol [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/fastqStdin.C:17:5: warning: Class 'fastqStdin' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libseq/fastqStdin.C:17:5: warning: Class 'fastqStdin' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libseq/fastqStdin.H:12:3: style: Class 'fastqStdin' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libseq/fastqStdin.H:16:4: style: The destructor '~fastqStdin' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:20:12: note: Virtual destructor in base class kmer-code-2013-trunk/libseq/fastqStdin.H:16:4: note: Destructor in derived class kmer-code-2013-trunk/libseq/fastqStdin.H:19:23: style: The function 'openFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:23:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastqStdin.H:19:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastqStdin.H:22:23: style: The function 'getNumberOfSequences' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:31:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastqStdin.H:22:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastqStdin.H:25:23: style: The function 'find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:34:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastqStdin.H:25:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastqStdin.H:27:23: style: The function 'getSequenceLength' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:36:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastqStdin.H:27:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastqStdin.H:28:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:37:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastqStdin.H:28:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastqStdin.H:31:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:40:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastqStdin.H:31:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastqStdin.C:110:13: style: Variable 'ret' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libseq/fastqStdin.C:110:9: style: Variable 'ret' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libseq/merStream.C:11:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint64ZERO [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/merStream.C:53:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint64ZERO [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/merStream.C:72:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint64ZERO [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/merStream.C:11:3: performance: Variable '_beg' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libseq/merStream.C:12:3: performance: Variable '_end' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libseq/seqStream.H:32:21: style:inconclusive: Technically the member function 'seqStream::eof' can be const. [functionConst] kmer-code-2013-trunk/libseq/seqStream.H:68:21: style:inconclusive: Technically the member function 'seqStream::seqPos' can be const. [functionConst] kmer-code-2013-trunk/libseq/seqStream.H:69:21: style:inconclusive: Technically the member function 'seqStream::seqIID' can be const. [functionConst] kmer-code-2013-trunk/libseq/seqStream.H:70:21: style:inconclusive: Technically the member function 'seqStream::strPos' can be const. [functionConst] kmer-code-2013-trunk/libseq/seqStream.H:72:21: style:inconclusive: Technically the member function 'seqStream::numberOfSequences' can be const. [functionConst] kmer-code-2013-trunk/libseq/seqStream.H:77:21: style:inconclusive: Technically the member function 'seqStream::lengthOf' can be const. [functionConst] kmer-code-2013-trunk/libseq/seqStream.H:78:21: style:inconclusive: Technically the member function 'seqStream::IIDOf' can be const. [functionConst] kmer-code-2013-trunk/libseq/seqStream.H:79:21: style:inconclusive: Technically the member function 'seqStream::startOf' can be const. [functionConst] kmer-code-2013-trunk/libseq/merStream.C:21:26: warning: Class 'merStream' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libseq/merStream.C:21:26: warning: Class 'merStream' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libseq/seqStream.H:18:3: style: Class 'seqStream' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libseq/selftest.C:16:26: error: syntax error [syntaxError] kmer-code-2013-trunk/libseq/seqCache.C:171:75: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libseq/seqFactory.C:36:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/seqFactory.C:53:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/seqCache.H:11:5: performance: Variable '_idx' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libseq/seqCache.H:15:5: performance: Variable '_headerLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libseq/seqCache.H:18:5: performance: Variable '_seqLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libseq/seqFactory.C:13:3: performance: Variable '_filesNum' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libseq/seqFactory.C:14:3: performance: Variable '_filesMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libseq/seqFactory.C:15:3: warning: Class 'seqFactory' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libseq/seqFactory.C:15:3: warning: Class 'seqFactory' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libseq/fastaFile.H:27:3: style: Class 'fastaFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libseq/fastqFile.H:27:3: style: Class 'fastqFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libseq/seqCache.H:67:3: style: Class 'seqCache' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libseq/seqStore.H:72:3: style: Class 'seqStore' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libseq/fastaFile.H:31:4: style: The destructor '~fastaFile' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:20:12: note: Virtual destructor in base class kmer-code-2013-trunk/libseq/fastaFile.H:31:4: note: Destructor in derived class kmer-code-2013-trunk/libseq/fastaFile.H:34:23: style: The function 'openFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:23:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastaFile.H:34:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastaFile.H:37:23: style: The function 'find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:34:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastaFile.H:37:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastaFile.H:39:23: style: The function 'getSequenceLength' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:36:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastaFile.H:39:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastaFile.H:40:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:37:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastaFile.H:40:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastaFile.H:43:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:40:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastaFile.H:43:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastqFile.H:31:4: style: The destructor '~fastqFile' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:20:12: note: Virtual destructor in base class kmer-code-2013-trunk/libseq/fastqFile.H:31:4: note: Destructor in derived class kmer-code-2013-trunk/libseq/fastqFile.H:34:23: style: The function 'openFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:23:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastqFile.H:34:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastqFile.H:37:23: style: The function 'find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:34:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastqFile.H:37:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastqFile.H:39:23: style: The function 'getSequenceLength' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:36:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastqFile.H:39:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastqFile.H:40:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:37:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastqFile.H:40:23: note: Function in derived class kmer-code-2013-trunk/libseq/fastqFile.H:43:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:40:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/fastqFile.H:43:23: note: Function in derived class kmer-code-2013-trunk/libseq/seqStore.H:76:4: style: The destructor '~seqStore' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:20:12: note: Virtual destructor in base class kmer-code-2013-trunk/libseq/seqStore.H:76:4: note: Destructor in derived class kmer-code-2013-trunk/libseq/seqStore.H:79:23: style: The function 'openFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:23:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/seqStore.H:79:23: note: Function in derived class kmer-code-2013-trunk/libseq/seqStore.H:82:23: style: The function 'find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:34:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/seqStore.H:82:23: note: Function in derived class kmer-code-2013-trunk/libseq/seqStore.H:84:23: style: The function 'getSequenceLength' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:36:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/seqStore.H:84:23: note: Function in derived class kmer-code-2013-trunk/libseq/seqStore.H:85:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:37:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/seqStore.H:85:23: note: Function in derived class kmer-code-2013-trunk/libseq/seqStore.H:88:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:40:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/seqStore.H:88:23: note: Function in derived class kmer-code-2013-trunk/libseq/seqStore.C:129:58: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libseq/seqStream.C:236:61: error: There is an unknown macro here somewhere. Configuration is required. If uint64FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libseq/sffFile.C:68:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint16 [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/sffFile.C:101:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/sffFile.C:160:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint16 [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/sffFile.C:192:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/sffFile.C:17:3: warning: Class 'sffFile' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libseq/sffFile.C:17:3: warning: Class 'sffFile' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libseq/sffFile.H:64:3: style: Class 'sffFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libseq/sffFile.H:68:4: style: The destructor '~sffFile' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:20:12: note: Virtual destructor in base class kmer-code-2013-trunk/libseq/sffFile.H:68:4: note: Destructor in derived class kmer-code-2013-trunk/libseq/sffFile.H:71:17: style: The function 'openFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:23:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/sffFile.H:71:17: note: Function in derived class kmer-code-2013-trunk/libseq/sffFile.H:74:17: style: The function 'find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:34:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/sffFile.H:74:17: note: Function in derived class kmer-code-2013-trunk/libseq/sffFile.H:79:17: style: The function 'getSequenceLength' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:36:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/sffFile.H:79:17: note: Function in derived class kmer-code-2013-trunk/libseq/sffFile.H:81:17: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:37:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/sffFile.H:81:17: note: Function in derived class kmer-code-2013-trunk/libseq/sffFile.H:84:17: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kmer-code-2013-trunk/libseq/seqFile.H:40:25: note: Virtual function in base class kmer-code-2013-trunk/libseq/sffFile.H:84:17: note: Function in derived class kmer-code-2013-trunk/libseq/sffFile.C:111:5: error: Resource leak: F [resourceLeak] kmer-code-2013-trunk/libseq/sffFile.C:115:19: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources] kmer-code-2013-trunk/libseq/sffFile.C:108:18: note: Assuming allocation function fails kmer-code-2013-trunk/libseq/sffFile.C:108:18: note: Assignment 'F=fopen(name,"r")', assigned value is 0 kmer-code-2013-trunk/libseq/sffFile.C:109:7: note: Assuming condition is false kmer-code-2013-trunk/libseq/sffFile.C:115:19: note: Null pointer dereference kmer-code-2013-trunk/libseq/sffFile.C:117:10: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources] kmer-code-2013-trunk/libseq/sffFile.C:108:18: note: Assuming allocation function fails kmer-code-2013-trunk/libseq/sffFile.C:108:18: note: Assignment 'F=fopen(name,"r")', assigned value is 0 kmer-code-2013-trunk/libseq/sffFile.C:109:7: note: Assuming condition is false kmer-code-2013-trunk/libseq/sffFile.C:117:10: note: Null pointer dereference kmer-code-2013-trunk/libseq/sffFile.C:11:30: style:inconclusive: Function 'sffFile' argument 1 names different: declaration 'filename' definition 'name'. [funcArgNamesDifferent] kmer-code-2013-trunk/libseq/sffFile.H:64:23: note: Function 'sffFile' argument 1 names different: declaration 'filename' definition 'name'. kmer-code-2013-trunk/libseq/sffFile.C:11:30: note: Function 'sffFile' argument 1 names different: declaration 'filename' definition 'name'. kmer-code-2013-trunk/libseq/test-correctSequence.H:33:60: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libseq/test/test-merstream-speed.C:18:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libseq/test/test-merstream-speed.C:27:16: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources] kmer-code-2013-trunk/libseq/test/test-merstream-speed.C:25:12: note: Assuming allocation function fails kmer-code-2013-trunk/libseq/test/test-merstream-speed.C:25:12: note: Assignment 'F=fopen(argv[1],"r")', assigned value is 0 kmer-code-2013-trunk/libseq/test/test-merstream-speed.C:27:16: note: Null pointer dereference kmer-code-2013-trunk/libsim4/sim4core/exon.H:70:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:156:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4core/sim4parameters.H:126:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4core/sim4.H:211:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4core/sim4.H:220:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4core/sim4.H:488:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4core/mspManager.H:113:5: style: Obsolescent function 'bzero' called. It is recommended to use 'memset' instead. [prohibitedbzeroCalled] kmer-code-2013-trunk/libsim4/sim4core/sim4b1_s.H:16:3: warning:inconclusive: Member variable 'mss_t::type' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/libsim4/sim4core/sim4b1_s.H:16:3: warning:inconclusive: Member variable 'mss_t::masknum' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/libsim4/sim4core/sim4b1_s.H:16:3: warning:inconclusive: Member variable 'mss_t::seedLength' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/libsim4/sim4core/sim4b1_s.H:16:3: warning:inconclusive: Member variable 'mss_t::matchedLength' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/libsim4/sim4core/sim4b1_s.H:16:3: warning:inconclusive: Member variable 'mss_t::shifts' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/libsim4/sim4core/exon.H:123:5: performance: Variable '_listLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libsim4/sim4core/exon.H:124:5: performance: Variable '_listMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libsim4/sim4core/exon.H:127:5: performance: Variable '_curLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libsim4/sim4core/exon.H:128:5: performance: Variable '_curMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:52:5: performance: Variable '_estFrom' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:53:5: performance: Variable '_estTo' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:54:5: performance: Variable '_genFrom' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:55:5: performance: Variable '_genTo' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:56:5: performance: Variable '_numMatches' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:57:5: performance: Variable '_numMatchesN' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:58:5: performance: Variable '_percentIdentity' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:59:5: performance: Variable '_intronOrientation' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libsim4/sim4core/mspManager.H:41:10: performance:inconclusive: Technically the member function 'mspManager::transitionFunction' can be static (but you may consider moving to unnamed namespace). [functionStatic] kmer-code-2013-trunk/libsim4/sim4core/mspManager.H:79:17: style:inconclusive: Technically the member function 'mspManager::tooManyMSPs' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4core/mspManager.H:80:17: style:inconclusive: Technically the member function 'mspManager::numberOfMSPs' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4core/sim4parameters.H:134:19: style:inconclusive: Technically the member function 'sim4parameters::getOutputFormat' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:68:10: style:inconclusive: Technically the member function 'sim4command::externalSeedsExist' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:69:10: style:inconclusive: Technically the member function 'sim4command::numberOfExternalSeeds' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:70:10: style:inconclusive: Technically the member function 'sim4command::externalSeedESTPosition' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:71:10: style:inconclusive: Technically the member function 'sim4command::externalSeedGENPosition' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:72:10: style:inconclusive: Technically the member function 'sim4command::externalSeedLength' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:86:10: style:inconclusive: Technically the member function 'sim4command::doForward' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:87:10: style:inconclusive: Technically the member function 'sim4command::doReverse' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:100:19: style:inconclusive: Technically the member function 'sim4command::getGENidx' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:101:19: style:inconclusive: Technically the member function 'sim4command::getGENlo' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:102:19: style:inconclusive: Technically the member function 'sim4command::getGENhi' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.H:19:17: style:inconclusive: Technically the member function 'sim4polishList::length' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4core/sim4.H:252:7: style:inconclusive: Technically the member function 'Sim4::snake' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4core/sim4.H:263:7: style:inconclusive: Technically the member function 'Sim4::rsnake' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4core/sim4.H:378:9: performance:inconclusive: Technically the member function 'Sim4::find_previous' can be static (but you may consider moving to unnamed namespace). [functionStatic] kmer-code-2013-trunk/libsim4/sim4core/sim4.H:487:8: performance:inconclusive: Technically the member function 'Sim4::fatal' can be static (but you may consider moving to unnamed namespace). [functionStatic] kmer-code-2013-trunk/libsim4/sim4core/sim4.H:519:1: performance:inconclusive: Technically the member function 'Sim4::script_flip_list' can be static (but you may consider moving to unnamed namespace). [functionStatic] kmer-code-2013-trunk/libsim4/sim4core/sim4.H:532:9: performance:inconclusive: Technically the member function 'Sim4::computePercentIdentity' can be static (but you may consider moving to unnamed namespace). [functionStatic] kmer-code-2013-trunk/libsim4/sim4core/sim4.H:644:10: performance:inconclusive: Technically the member function 'Sim4::ckfree' can be static (but you may consider moving to unnamed namespace). [functionStatic] kmer-code-2013-trunk/libsim4/sim4core/exon.H:125:5: warning: Class 'exonManager' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libsim4/sim4core/exon.H:125:5: warning: Class 'exonManager' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libsim4/sim4core/sim4b1_s.H:17:3: style: Class 'mss_t' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:161:3: style: Class 'sim4polish' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.H:13:3: style: Class 'sim4polishList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libsim4/sim4core/sim4.H:544:3: style: Class 'Sim4' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:17:10: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:65:14: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:66:14: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:68:22: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:69:22: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:80:21: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:81:24: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:82:38: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:87:28: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:88:24: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:89:38: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:108:12: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:109:12: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:117:13: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:118:14: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:178:42: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:179:33: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:180:47: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:185:49: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:186:33: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:187:47: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:196:40: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:197:33: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:198:47: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:203:47: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:204:33: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:205:47: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:331:14: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:332:14: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:334:22: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:335:22: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:345:21: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:346:27: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:347:41: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:351:28: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:352:27: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:353:41: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:371:12: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:372:12: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:380:13: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:381:14: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:444:45: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:445:34: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:446:48: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:451:52: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:452:34: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:453:48: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:463:42: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:464:34: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:465:48: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:470:49: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:471:34: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:472:48: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:43:24: style: Parameter 's1' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:311:24: style: Parameter 's1' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:311:34: style: Parameter 's2' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libsim4/sim4core/sim4.H:378:41: style: Parameter 'target' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libsim4/sim4core/sim4parameters.H:73:29: style: Parameter 'z' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libsim4/sim4core/exon.H:67:25: style: Parameter 'label' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libsim4/sim4core/align.C:153:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4core/align.C:339:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4core/align.C:802:7: performance:inconclusive: Technically the member function 'Sim4::Flip_script' can be static (but you may consider moving to unnamed namespace). [functionStatic] kmer-code-2013-trunk/libsim4/sim4core/sim4.H:243:8: note: Technically the member function 'Sim4::Flip_script' can be static (but you may consider moving to unnamed namespace). kmer-code-2013-trunk/libsim4/sim4core/align.C:802:7: note: Technically the member function 'Sim4::Flip_script' can be static (but you may consider moving to unnamed namespace). kmer-code-2013-trunk/libsim4/sim4core/align.C:820:7: performance:inconclusive: Technically the member function 'Sim4::align_reverse' can be static (but you may consider moving to unnamed namespace). [functionStatic] kmer-code-2013-trunk/libsim4/sim4core/sim4.H:249:8: note: Technically the member function 'Sim4::align_reverse' can be static (but you may consider moving to unnamed namespace). kmer-code-2013-trunk/libsim4/sim4core/align.C:820:7: note: Technically the member function 'Sim4::align_reverse' can be static (but you may consider moving to unnamed namespace). kmer-code-2013-trunk/libsim4/sim4core/align.C:619:29: style: Condition 'j2-i2score==g->score' is always true [knownConditionTrueFalse] kmer-code-2013-trunk/libsim4/sim4core/util.C:392:28: note: Assuming that condition 'c->score>g->score' is not redundant kmer-code-2013-trunk/libsim4/sim4core/util.C:390:21: note: Assuming that condition 'g->score>c->score' is not redundant kmer-code-2013-trunk/libsim4/sim4core/util.C:394:28: note: Condition 'c->score==g->score' is always true kmer-code-2013-trunk/libsim4/sim4core/util.C:346:10: warning: Either the condition 'Glist==0L' is redundant or there is possible null pointer dereference: Glist. [nullPointerRedundantCheck] kmer-code-2013-trunk/libsim4/sim4core/util.C:350:14: note: Assuming that condition 'Glist==0L' is not redundant kmer-code-2013-trunk/libsim4/sim4core/util.C:346:10: note: Null pointer dereference kmer-code-2013-trunk/libsim4/sim4core/util.C:347:10: warning: Either the condition 'Clist==0L' is redundant or there is possible null pointer dereference: Clist. [nullPointerRedundantCheck] kmer-code-2013-trunk/libsim4/sim4core/util.C:350:31: note: Assuming that condition 'Clist==0L' is not redundant kmer-code-2013-trunk/libsim4/sim4core/util.C:347:10: note: Null pointer dereference kmer-code-2013-trunk/libsim4/sim4core/util.C:348:10: warning: Either the condition 'oris==0L' is redundant or there is possible null pointer dereference: oris. [nullPointerRedundantCheck] kmer-code-2013-trunk/libsim4/sim4core/util.C:350:47: note: Assuming that condition 'oris==0L' is not redundant kmer-code-2013-trunk/libsim4/sim4core/util.C:348:10: note: Null pointer dereference kmer-code-2013-trunk/libsim4/sim4core/util.C:750:14: warning: Either the condition 't1' is redundant or there is possible null pointer dereference: t1. [nullPointerRedundantCheck] kmer-code-2013-trunk/libsim4/sim4core/util.C:747:17: note: Assuming that condition 't1' is not redundant kmer-code-2013-trunk/libsim4/sim4core/util.C:750:14: note: Null pointer dereference kmer-code-2013-trunk/libsim4/sim4core/util.C:342:11: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/util.C:343:11: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/util.C:344:11: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/util.C:362:20: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/util.C:363:20: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/util.C:371:27: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/util.C:372:27: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/util.C:585:20: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/util.C:586:20: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/util.C:593:25: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/util.C:594:25: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4core/util.C:226:15: style: Variable 'head' is reassigned a value before the old one has been used. [redundantAssignment] kmer-code-2013-trunk/libsim4/sim4core/util.C:224:8: note: head is assigned kmer-code-2013-trunk/libsim4/sim4core/util.C:226:15: note: head is overwritten kmer-code-2013-trunk/libsim4/sim4core/util.C:756:10: style: Variable 't0' is reassigned a value before the old one has been used. [redundantAssignment] kmer-code-2013-trunk/libsim4/sim4core/util.C:748:16: note: t0 is assigned kmer-code-2013-trunk/libsim4/sim4core/util.C:756:10: note: t0 is overwritten kmer-code-2013-trunk/libsim4/sim4core/util.C:775:45: style: Variable 't1' is reassigned a value before the old one has been used. [redundantAssignment] kmer-code-2013-trunk/libsim4/sim4core/util.C:767:13: note: t1 is assigned kmer-code-2013-trunk/libsim4/sim4core/util.C:775:45: note: t1 is overwritten kmer-code-2013-trunk/libsim4/sim4core/util.C:141:7: style: The scope of the variable 'diff' can be reduced. [variableScope] kmer-code-2013-trunk/libsim4/sim4core/util.C:323:29: style:inconclusive: Function 'sync_slide_intron' argument 1 names different: declaration 'w' definition 'in_w'. [funcArgNamesDifferent] kmer-code-2013-trunk/libsim4/sim4core/sim4.H:344:32: note: Function 'sync_slide_intron' argument 1 names different: declaration 'w' definition 'in_w'. kmer-code-2013-trunk/libsim4/sim4core/util.C:323:29: note: Function 'sync_slide_intron' argument 1 names different: declaration 'w' definition 'in_w'. kmer-code-2013-trunk/libsim4/sim4core/util.C:509:20: style:inconclusive: Function 'wobble' argument 5 names different: declaration 'seq1' definition 'seq'. [funcArgNamesDifferent] kmer-code-2013-trunk/libsim4/sim4core/sim4.H:346:67: note: Function 'wobble' argument 5 names different: declaration 'seq1' definition 'seq'. kmer-code-2013-trunk/libsim4/sim4core/util.C:509:20: note: Function 'wobble' argument 5 names different: declaration 'seq1' definition 'seq'. kmer-code-2013-trunk/libsim4/sim4core/util.C:573:24: style:inconclusive: Function 'slide_intron' argument 1 names different: declaration 'w' definition 'in_w'. [funcArgNamesDifferent] kmer-code-2013-trunk/libsim4/sim4core/sim4.H:343:27: note: Function 'slide_intron' argument 1 names different: declaration 'w' definition 'in_w'. kmer-code-2013-trunk/libsim4/sim4core/util.C:573:24: note: Function 'slide_intron' argument 1 names different: declaration 'w' definition 'in_w'. kmer-code-2013-trunk/libsim4/sim4core/util.C:266:31: style: Parameter 's2' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libsim4/sim4core/util.C:299:41: style: Parameter 'rblock' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libsim4/sim4core/util.C:323:54: style: Parameter 'last' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libsim4/sim4core/util.C:325:31: style: Variable 'cell' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libsim4/sim4core/util.C:573:49: style: Parameter 'last' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libsim4/sim4core/util.C:603:15: style: Variable 's' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libsim4/sim4core/util.C:800:45: style: Parameter 'rblock' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-compare.C:249:59: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-copy.C:9:46: style: Parameter 'orig' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-copy.C:44:40: style: Parameter 'orig' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-deleteexon.C:10:10: style: The scope of the variable 'ed' can be reduced. [variableScope] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-deleteexon.C:10:15: style: The scope of the variable 'gd' can be reduced. [variableScope] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-exons.C:32:69: style: Parameter 'e' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-polishtostring.C:58:28: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-read.C:46:75: error: There is an unknown macro here somewhere. Configuration is required. If uint64FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-stringtopolish.C:42:34: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-updatescores.C:52:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IUPACidentity [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-updatescores.C:179:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IUPACidentity [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-updatescores.C:117:13: performance:inconclusive: Technically the member function 'sim4polish::s4p_percentIdentityApprox' can be static (but you may consider moving to unnamed namespace). [functionStatic] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:223:10: note: Technically the member function 'sim4polish::s4p_percentIdentityApprox' can be static (but you may consider moving to unnamed namespace). kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-updatescores.C:117:13: note: Technically the member function 'sim4polish::s4p_percentIdentityApprox' can be static (but you may consider moving to unnamed namespace). kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-updatescores.C:106:13: style:inconclusive: Technically the member function 'sim4polish::s4p_percentCoverageApprox' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:224:10: note: Technically the member function 'sim4polish::s4p_percentCoverageApprox' can be const. kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-updatescores.C:106:13: note: Technically the member function 'sim4polish::s4p_percentCoverageApprox' can be const. kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-updatescores.C:137:13: style:inconclusive: Technically the member function 'sim4polish::s4p_percentIdentityExact' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:228:10: note: Technically the member function 'sim4polish::s4p_percentIdentityExact' can be const. kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-updatescores.C:137:13: note: Technically the member function 'sim4polish::s4p_percentIdentityExact' can be const. kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-updatescores.C:131:13: style:inconclusive: Technically the member function 'sim4polish::s4p_percentCoverageExact' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:229:10: note: Technically the member function 'sim4polish::s4p_percentCoverageExact' can be const. kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-updatescores.C:131:13: note: Technically the member function 'sim4polish::s4p_percentCoverageExact' can be const. kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-updatescores.C:151:11: style: Variable 'est' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-updatescores.C:152:11: style: Variable 'gen' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:39:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:79:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:91:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:103:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:114:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:124:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:142:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:167:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:214:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:234:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:13:3: performance: Variable 'exPos' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:14:3: performance: Variable 'exMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:15:3: performance: Variable 'exAli' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:16:3: warning: Class 'sim4polishBuilder' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:16:3: warning: Class 'sim4polishBuilder' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:223:30: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:224:30: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:77:40: style: Parameter 'defline' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:89:40: style: Parameter 'defline' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishFile.C:120:57: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.C:12:3: performance: Variable 'len' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.C:13:3: performance: Variable 'max' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.C:18:3: performance: Variable 'len' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.C:19:3: performance: Variable 'max' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishReader.H:22:19: style:inconclusive: Technically the member function 'sim4polishReader::getsim4polishStyle' can be const. [functionConst] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.C:20:3: warning: Class 'sim4polishList' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.C:20:3: warning: Class 'sim4polishList' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishReader.H:14:3: style: Class 'sim4polishReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishReader.C:42:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishReader.C:18:5: warning: Class 'sim4polishReader' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishReader.C:18:5: warning: Class 'sim4polishReader' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.C:25:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.C:101:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.C:141:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.C:155:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.C:81:19: performance:inconclusive: Technically the member function 'sim4polishWriter::s4p_putHeaderS4DB' can be static (but you may consider moving to unnamed namespace). [functionStatic] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.H:21:8: note: Technically the member function 'sim4polishWriter::s4p_putHeaderS4DB' can be static (but you may consider moving to unnamed namespace). kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.C:81:19: note: Technically the member function 'sim4polishWriter::s4p_putHeaderS4DB' can be static (but you may consider moving to unnamed namespace). kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.C:86:19: performance:inconclusive: Technically the member function 'sim4polishWriter::s4p_putHeaderATAC' can be static (but you may consider moving to unnamed namespace). [functionStatic] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.H:23:8: note: Technically the member function 'sim4polishWriter::s4p_putHeaderATAC' can be static (but you may consider moving to unnamed namespace). kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.C:86:19: note: Technically the member function 'sim4polishWriter::s4p_putHeaderATAC' can be static (but you may consider moving to unnamed namespace). kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.C:36:5: warning: Class 'sim4polishWriter' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.C:36:5: warning: Class 'sim4polishWriter' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libutil/speedCounter.H:23:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/speedCounter.H:40:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/speedCounter.H:53:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/bitPackedArray.H:222:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/bitPackedFile.H:32:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/logMsg.H:63:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/logMsg.H:84:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/logMsg.H:95:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/bigQueue.C:331:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/unaryEncoding.h:43:3: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg] kmer-code-2013-trunk/libutil/bigQueue.H:44:3: warning: Member variable 'bigQueue::_inputFile' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/libutil/bigQueue.H:56:3: warning: Member variable 'bigQueue::_inputFile' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/libutil/bigQueue.H:68:3: warning: Member variable 'bigQueue::_inputFile' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/libutil/uint32List.H:47:11: style:inconclusive: Technically the member function 'uint32List::length' can be const. [functionConst] kmer-code-2013-trunk/libutil/readBuffer.H:11:20: style:inconclusive: Technically the member function 'readBuffer::eof' can be const. [functionConst] kmer-code-2013-trunk/libutil/readBuffer.H:20:20: style:inconclusive: Technically the member function 'readBuffer::tell' can be const. [functionConst] kmer-code-2013-trunk/libutil/readBuffer.H:22:20: style:inconclusive: Technically the member function 'readBuffer::filename' can be const. [functionConst] kmer-code-2013-trunk/libutil/splitToWords.H:104:11: style:inconclusive: Technically the member function 'splitToWords::numWords' can be const. [functionConst] kmer-code-2013-trunk/libutil/bitPackedArray.H:239:11: style:inconclusive: Technically the member function 'bitArray::get' can be const. [functionConst] kmer-code-2013-trunk/libutil/bitPackedArray.H:61:12: note: Technically the member function 'bitArray::get' can be const. kmer-code-2013-trunk/libutil/bitPackedArray.H:239:11: note: Technically the member function 'bitArray::get' can be const. kmer-code-2013-trunk/libutil/recordFile.H:25:14: style:inconclusive: Technically the member function 'recordFile::numRecords' can be const. [functionConst] kmer-code-2013-trunk/libutil/intervalList.H:460:27: style:inconclusive: Technically the member function 'intervalList::overlapping' can be const. [functionConst] kmer-code-2013-trunk/libutil/intervalList.H:109:13: note: Technically the member function 'intervalList::overlapping' can be const. kmer-code-2013-trunk/libutil/intervalList.H:460:27: note: Technically the member function 'intervalList::overlapping' can be const. kmer-code-2013-trunk/libutil/intervalList.H:127:13: style:inconclusive: Technically the member function 'intervalList::numberOfIntervals' can be const. [functionConst] kmer-code-2013-trunk/libutil/bigQueue.C:330:11: performance:inconclusive: Technically the member function 'bigQueue::save' can be static (but you may consider moving to unnamed namespace). [functionStatic] kmer-code-2013-trunk/libutil/bigQueue.H:102:11: note: Technically the member function 'bigQueue::save' can be static (but you may consider moving to unnamed namespace). kmer-code-2013-trunk/libutil/bigQueue.C:330:11: note: Technically the member function 'bigQueue::save' can be static (but you may consider moving to unnamed namespace). kmer-code-2013-trunk/libutil/uint32List.H:17:5: warning: Class 'uint32List' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libutil/uint32List.H:17:5: warning: Class 'uint32List' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libutil/bitPackedArray.H:88:5: warning: Class 'bitPackedHeap' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libutil/bitPackedArray.H:88:5: warning: Class 'bitPackedHeap' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libutil/logMsg.H:20:5: warning: Class 'logMsg' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libutil/logMsg.H:20:5: warning: Class 'logMsg' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libutil/bigQueue.C:88:12: warning: Class 'bigQueue' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libutil/bigQueue.C:88:12: warning: Class 'bigQueue' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libutil/uint32List.H:14:3: style: Class 'uint32List' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libutil/readBuffer.H:7:3: style: Class 'readBuffer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libutil/readBuffer.H:8:3: style: Class 'readBuffer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libutil/splitToWords.H:14:3: style: Class 'splitToWords' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libutil/bitPackedArray.H:26:3: style: Class 'bitPackedArray' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libutil/bitPackedArray.H:58:3: style: Class 'bitArray' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libutil/bitPackedArray.H:87:3: style: Class 'bitPackedHeap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libutil/bitPackedFile.H:17:3: style: Class 'bitPackedFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libutil/intervalList.H:48:3: style: Class 'intervalList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libutil/logMsg.H:17:3: style: Class 'logMsg' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libutil/bigQueue.C:211:33: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libutil/bigQueue.C:230:24: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libutil/bigQueue.C:266:36: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libutil/bitPacking.h:193:10: style: The scope of the variable 'b1' can be reduced. [variableScope] kmer-code-2013-trunk/libutil/bitPacking.h:245:10: style: The scope of the variable 'b1' can be reduced. [variableScope] kmer-code-2013-trunk/libutil/bitPackedArray.H:116:13: style: The scope of the variable 'cval' can be reduced. [variableScope] kmer-code-2013-trunk/libutil/bitPackedArray.H:167:13: style: The scope of the variable 'pidx' can be reduced. [variableScope] kmer-code-2013-trunk/libutil/bitPackedArray.H:168:13: style: The scope of the variable 'pval' can be reduced. [variableScope] kmer-code-2013-trunk/libutil/bitPackedFile.H:87:31: style:inconclusive: Function 'getBits' argument 1 names different: declaration 'size' definition 'siz'. [funcArgNamesDifferent] kmer-code-2013-trunk/libutil/bitPackedFile.H:20:29: note: Function 'getBits' argument 1 names different: declaration 'size' definition 'siz'. kmer-code-2013-trunk/libutil/bitPackedFile.H:87:31: note: Function 'getBits' argument 1 names different: declaration 'size' definition 'siz'. kmer-code-2013-trunk/libutil/bitPackedFile.H:107:44: style:inconclusive: Function 'putBits' argument 2 names different: declaration 'size' definition 'siz'. [funcArgNamesDifferent] kmer-code-2013-trunk/libutil/bitPackedFile.H:23:42: note: Function 'putBits' argument 2 names different: declaration 'size' definition 'siz'. kmer-code-2013-trunk/libutil/bitPackedFile.H:107:44: note: Function 'putBits' argument 2 names different: declaration 'size' definition 'siz'. kmer-code-2013-trunk/libutil/intervalList.H:187:64: style:inconclusive: Function 'add' argument 3 names different: declaration 'value' definition 'val'. [funcArgNamesDifferent] kmer-code-2013-trunk/libutil/intervalList.H:101:50: note: Function 'add' argument 3 names different: declaration 'value' definition 'val'. kmer-code-2013-trunk/libutil/intervalList.H:187:64: note: Function 'add' argument 3 names different: declaration 'value' definition 'val'. kmer-code-2013-trunk/libutil/intervalList.H:341:39: style:inconclusive: Function 'invert' argument 1 names different: declaration 'lo' definition 'invlo'. [funcArgNamesDifferent] kmer-code-2013-trunk/libutil/intervalList.H:123:25: note: Function 'invert' argument 1 names different: declaration 'lo' definition 'invlo'. kmer-code-2013-trunk/libutil/intervalList.H:341:39: note: Function 'invert' argument 1 names different: declaration 'lo' definition 'invlo'. kmer-code-2013-trunk/libutil/intervalList.H:341:51: style:inconclusive: Function 'invert' argument 2 names different: declaration 'hi' definition 'invhi'. [funcArgNamesDifferent] kmer-code-2013-trunk/libutil/intervalList.H:123:34: note: Function 'invert' argument 2 names different: declaration 'hi' definition 'invhi'. kmer-code-2013-trunk/libutil/intervalList.H:341:51: note: Function 'invert' argument 2 names different: declaration 'hi' definition 'invhi'. kmer-code-2013-trunk/libutil/intervalList.H:460:49: style:inconclusive: Function 'overlapping' argument 1 names different: declaration 'lo' definition 'rangelo'. [funcArgNamesDifferent] kmer-code-2013-trunk/libutil/intervalList.H:109:35: note: Function 'overlapping' argument 1 names different: declaration 'lo' definition 'rangelo'. kmer-code-2013-trunk/libutil/intervalList.H:460:49: note: Function 'overlapping' argument 1 names different: declaration 'lo' definition 'rangelo'. kmer-code-2013-trunk/libutil/intervalList.H:461:49: style:inconclusive: Function 'overlapping' argument 2 names different: declaration 'hi' definition 'rangehi'. [funcArgNamesDifferent] kmer-code-2013-trunk/libutil/intervalList.H:110:35: note: Function 'overlapping' argument 2 names different: declaration 'hi' definition 'rangehi'. kmer-code-2013-trunk/libutil/intervalList.H:461:49: note: Function 'overlapping' argument 2 names different: declaration 'hi' definition 'rangehi'. kmer-code-2013-trunk/libutil/intervalList.H:544:59: style:inconclusive: Function 'depth' argument 1 names different: declaration 'A' definition 'IL'. [funcArgNamesDifferent] kmer-code-2013-trunk/libutil/intervalList.H:125:45: note: Function 'depth' argument 1 names different: declaration 'A' definition 'IL'. kmer-code-2013-trunk/libutil/intervalList.H:544:59: note: Function 'depth' argument 1 names different: declaration 'A' definition 'IL'. kmer-code-2013-trunk/libutil/bigQueue.C:26:32: style: Parameter 'tmppath' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/bigQueue.C:27:32: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/bitPacking.h:107:25: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/bitPacking.h:181:26: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/bitPacking.h:184:26: style: Parameter 'sizs' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/bitPacking.h:241:26: style: Parameter 'sizs' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/fibonacciEncoding.h:121:35: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/splitToWords.H:67:20: style: Variable 'cmdI' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/bitPacking.h:193:14: style: Variable 'b1' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/bitPacking.h:245:14: style: Variable 'b1' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/unaryEncoding.h:39:9: style: Variable 'siz' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/unaryEncoding.h:43:7: style: Variable 'pos' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/bitPackedArray.H:116:18: style: Variable 'cval' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/bitPackedArray.H:167:18: style: Variable 'pidx' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/bitPackedArray.H:168:18: style: Variable 'pval' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/bitPackedArray.C:35:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/bitPackedArray.C:73:5: style: Obsolescent function 'bzero' called. It is recommended to use 'memset' instead. [prohibitedbzeroCalled] kmer-code-2013-trunk/libutil/bitPackedArray.C:99:5: style: Obsolescent function 'bzero' called. It is recommended to use 'memset' instead. [prohibitedbzeroCalled] kmer-code-2013-trunk/libutil/bitPackedArray.C:18:3: warning: Class 'bitPackedArray' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libutil/bitPackedArray.C:18:3: warning: Class 'bitPackedArray' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libutil/bitPackedArray.C:85:3: warning: Class 'bitArray' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libutil/bitPackedArray.C:85:3: warning: Class 'bitArray' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libutil/bitPackedFile.C:54:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/bitPackedFile.C:203:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/bitPackedFile.C:322:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/bitPackedFile.C:334:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/bitPackedFile.C:420:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/bitPackedFile.C:16:3: warning: Class 'bitPackedFile' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libutil/bitPackedFile.C:16:3: warning: Class 'bitPackedFile' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libutil/bitPackedFile.C:403:28: style:inconclusive: Function 'seek' argument 1 names different: declaration 'pos' definition 'bitpos'. [funcArgNamesDifferent] kmer-code-2013-trunk/libutil/bitPackedFile.H:27:26: note: Function 'seek' argument 1 names different: declaration 'pos' definition 'bitpos'. kmer-code-2013-trunk/libutil/bitPackedFile.C:403:28: note: Function 'seek' argument 1 names different: declaration 'pos' definition 'bitpos'. kmer-code-2013-trunk/libutil/bitPackedFile.C:92:11: style: Variable 't' can be declared as const array [constVariable] kmer-code-2013-trunk/libutil/bzipBuffer.C:17:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _filename [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/bzipBuffer.C:68:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _bzip2in [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/bzipBuffer.C:77:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _bzip2streamEnd [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/bzipBuffer.C:165:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/file.c:58:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PATH_MAX [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/file.c:107:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/file.c:181:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/file.c:308:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/file.c:334:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/file.c:412:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/file.c:263:12: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory] kmer-code-2013-trunk/libutil/file.c:262:23: note: Assuming allocation function fails kmer-code-2013-trunk/libutil/file.c:262:9: note: Assignment 'p=(char*)malloc(sizeof(char)*(strlen(path)+1))', assigned value is 0 kmer-code-2013-trunk/libutil/file.c:263:12: note: Null pointer dereference kmer-code-2013-trunk/libutil/file.c:264:17: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory] kmer-code-2013-trunk/libutil/file.c:262:23: note: Assuming allocation function fails kmer-code-2013-trunk/libutil/file.c:262:9: note: Assignment 'p=(char*)malloc(sizeof(char)*(strlen(path)+1))', assigned value is 0 kmer-code-2013-trunk/libutil/file.c:264:17: note: Null pointer dereference kmer-code-2013-trunk/libutil/file.c:57:20: style: Parameter 'path' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/file.c:154:17: style: Parameter 'addr' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/file.c:171:16: style: Parameter 'srcName' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/file.c:174:22: style: Variable 'bytesRead' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/file.c:300:20: style: Variable 'towrite' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/file.c:301:20: style: Variable 'written' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/file.c:325:20: style: Variable 'toread' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/file.c:326:20: style: Variable 'written' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/file.c:327:20: style: Variable 'failed' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/file.c:382:19: style: Variable 'isRW' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/file.c:398:14: style: Variable 'isRW' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/file.c:403:14: style: Variable 'isRW' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/kazlib/dict.c:398:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/kazlib/dict.c:1107:23: style: The comparison 'dnode_red == 0' is always true. [knownConditionTrueFalse] kmer-code-2013-trunk/libutil/kazlib/dict.c:1107:43: style: The comparison 'dnode_black == 1' is always true. [knownConditionTrueFalse] kmer-code-2013-trunk/libutil/kazlib/dict.c:1232:6: style: 'continue' is redundant since it is the last statement in a loop. [redundantContinue] kmer-code-2013-trunk/libutil/kazlib/dict.c:452:14: style: Variable 'nil' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/dict.c:499:14: style: Variable 'nil' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/dict.c:535:14: style: Variable 'nil' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/dict.c:871:14: style: Variable 'nil' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/dict.c:887:14: style: Variable 'nil' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/dict.c:905:14: style: Variable 'nil' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/dict.c:931:14: style: Variable 'nil' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/dict.c:962:32: style: Parameter 'dict' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/dict.c:967:26: style: Parameter 'dict' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/dict.c:972:25: style: Parameter 'dict' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/dict.c:1019:26: style: Parameter 'dnode' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/dict.c:1024:35: style: Parameter 'dnode' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/dict.c:1034:33: style: Parameter 'dnode' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/drivers/dict-main.c:87:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/kazlib/drivers/dict-main.c:164:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/kazlib/drivers/dict-main.c:40:30: style: Parameter 'str' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/drivers/dict-main.c:49:32: style: Parameter 'c' can be declared as pointer to const. However it seems that 'new_node' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kmer-code-2013-trunk/libutil/kazlib/drivers/dict-main.c:264:25: note: You might need to cast the function pointer here kmer-code-2013-trunk/libutil/kazlib/drivers/dict-main.c:49:32: note: Parameter 'c' can be declared as pointer to const kmer-code-2013-trunk/libutil/kazlib/drivers/dict-main.c:60:31: style: Parameter 'n' can be declared as pointer to const. However it seems that 'del_node' is a callback function, if 'n' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kmer-code-2013-trunk/libutil/kazlib/drivers/dict-main.c:264:35: note: You might need to cast the function pointer here kmer-code-2013-trunk/libutil/kazlib/drivers/dict-main.c:60:31: note: Parameter 'n' can be declared as pointer to const kmer-code-2013-trunk/libutil/kazlib/drivers/dict-main.c:60:40: style: Parameter 'c' can be declared as pointer to const. However it seems that 'del_node' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kmer-code-2013-trunk/libutil/kazlib/drivers/dict-main.c:264:35: note: You might need to cast the function pointer here kmer-code-2013-trunk/libutil/kazlib/drivers/dict-main.c:60:40: note: Parameter 'c' can be declared as pointer to const kmer-code-2013-trunk/libutil/kazlib/drivers/dict-main.c:74:11: style: Variable 'help' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/drivers/dict-main.c:141:11: style: Variable 'help' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/drivers/except-main.c:12:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/kazlib/drivers/except-main.c:4:27: style: Parameter 'arg' can be declared as pointer to const. However it seems that 'cleanup' is a callback function, if 'arg' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kmer-code-2013-trunk/libutil/kazlib/drivers/except-main.c:21:25: note: You might need to cast the function pointer here kmer-code-2013-trunk/libutil/kazlib/drivers/except-main.c:4:27: note: Parameter 'arg' can be declared as pointer to const kmer-code-2013-trunk/libutil/kazlib/drivers/hash-main.c:61:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HASHCOUNT_T_MAX [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/kazlib/drivers/hash-main.c:34:30: style: Parameter 'str' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/drivers/hash-main.c:43:32: style: Parameter 'c' can be declared as pointer to const. However it seems that 'new_node' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kmer-code-2013-trunk/libutil/kazlib/drivers/hash-main.c:177:25: note: You might need to cast the function pointer here kmer-code-2013-trunk/libutil/kazlib/drivers/hash-main.c:43:32: note: Parameter 'c' can be declared as pointer to const kmer-code-2013-trunk/libutil/kazlib/drivers/hash-main.c:54:31: style: Parameter 'n' can be declared as pointer to const. However it seems that 'del_node' is a callback function, if 'n' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kmer-code-2013-trunk/libutil/kazlib/drivers/hash-main.c:177:35: note: You might need to cast the function pointer here kmer-code-2013-trunk/libutil/kazlib/drivers/hash-main.c:54:31: note: Parameter 'n' can be declared as pointer to const kmer-code-2013-trunk/libutil/kazlib/drivers/hash-main.c:54:40: style: Parameter 'c' can be declared as pointer to const. However it seems that 'del_node' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kmer-code-2013-trunk/libutil/kazlib/drivers/hash-main.c:177:35: note: You might need to cast the function pointer here kmer-code-2013-trunk/libutil/kazlib/drivers/hash-main.c:54:40: note: Parameter 'c' can be declared as pointer to const kmer-code-2013-trunk/libutil/kazlib/drivers/hash-main.c:68:11: style: Variable 'help' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/drivers/list-main.c:52:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LISTCOUNT_T_MAX [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/kazlib/drivers/list-main.c:40:30: style: Parameter 'str' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/drivers/list-main.c:57:11: style: Variable 'help' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/drivers/sfx-main.c:12:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/kazlib/except.c:206:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/kazlib/except.c:206:5: warning: %ld in format string (no. 2) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint] kmer-code-2013-trunk/libutil/kazlib/except.c:206:5: warning: %ld in format string (no. 3) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint] kmer-code-2013-trunk/libutil/kazlib/except.c:204:41: style: Parameter 'except' can be declared as pointer to const. However it seems that 'unhandled_catcher' is a callback function, if 'except' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kmer-code-2013-trunk/libutil/kazlib/except.c:134:45: note: You might need to cast the function pointer here kmer-code-2013-trunk/libutil/kazlib/except.c:204:41: note: Parameter 'except' can be declared as pointer to const kmer-code-2013-trunk/libutil/kazlib/except.c:312:38: style: Parameter 'ex' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/except.c:317:29: style: Parameter 'ex' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/hash.c:685:25: style: Parameter 'hash' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/hash.c:720:25: style: Parameter 'hash' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/hash.c:731:26: style: Parameter 'hash' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/hash.c:788:26: style: Parameter 'node' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/hash.c:794:35: style: Parameter 'node' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/hash.c:800:32: style: Parameter 'hash' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/hash.c:806:31: style: Parameter 'hash' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/hash.c:813:26: style: Variable 'randbox' can be declared as const array [constVariable] kmer-code-2013-trunk/libutil/kazlib/list.c:492:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable compare [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/kazlib/list.c:532:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable compare [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/kazlib/list.c:99:46: style: Variable 'nil' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/list.c:119:52: style: Variable 'nil' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/list.c:207:52: style: Variable 'nil' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/list.c:306:36: style: Parameter 'list_pool' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/list.c:306:51: style: Parameter 'node' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/list.c:368:42: style: Parameter 'node' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/list.c:370:18: style: Variable 'nil' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/list.c:482:14: style: Variable 'd_nil' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/list.c:482:39: style: Variable 's_nil' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/list.c:558:28: style: Variable 'nil' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/list.c:598:26: style: Parameter 'list' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/list.c:608:25: style: Parameter 'list' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/list.c:617:37: style: Parameter 'list_pool' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/list.c:666:32: style: Parameter 'list' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/list.c:703:26: style: Parameter 'lnode' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/list.c:739:33: style: Parameter 'lnode' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/list.c:747:45: style: Variable 'nil' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/sfx.c:1121:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/kazlib/sfx.c:1121:2: warning: %ld in format string (no. 2) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint] kmer-code-2013-trunk/libutil/kazlib/sfx.c:1124:2: warning: %ld in format string (no. 2) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint] kmer-code-2013-trunk/libutil/kazlib/sfx.c:1127:2: warning: %ld in format string (no. 2) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint] kmer-code-2013-trunk/libutil/kazlib/sfx.c:1099:12: style: Variable 'result' is reassigned a value before the old one has been used. [redundantAssignment] kmer-code-2013-trunk/libutil/kazlib/sfx.c:1096:9: note: result is assigned kmer-code-2013-trunk/libutil/kazlib/sfx.c:1099:12: note: result is overwritten kmer-code-2013-trunk/libutil/kazlib/sfx.c:76:56: style: Parameter 'orig' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/sfx.c:94:43: style: Parameter 'ctx' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/sfx.c:122:48: style: Parameter 'expr' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/kazlib/sfx.c:1061:15: style: Variable 'cache_entry' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/kazlib/sfx.c:254:5: error: Uninitialized variable: ex [legacyUninitvar] kmer-code-2013-trunk/libutil/kazlib/sfx.c:994:5: error: Uninitialized variable: ex [legacyUninitvar] kmer-code-2013-trunk/libutil/md5.c:330:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/md5.c:362:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/md5.c:342:3: warning: If memory allocation fails, then there is a possible null pointer dereference: m [nullPointerOutOfMemory] kmer-code-2013-trunk/libutil/md5.c:331:24: note: Assuming allocation function fails kmer-code-2013-trunk/libutil/md5.c:331:9: note: Assignment 'm=(struct md5_s*)malloc(sizeof(struct md5_s))', assigned value is 0 kmer-code-2013-trunk/libutil/md5.c:332:9: note: Assuming condition is false kmer-code-2013-trunk/libutil/md5.c:342:3: note: Null pointer dereference kmer-code-2013-trunk/libutil/md5.c:369:3: warning: If memory allocation fails, then there is a possible null pointer dereference: m [nullPointerOutOfMemory] kmer-code-2013-trunk/libutil/md5.c:363:32: note: Assuming allocation function fails kmer-code-2013-trunk/libutil/md5.c:363:7: note: Assignment 'm=(struct md5_increment_s*)malloc(sizeof(struct md5_increment_s))', assigned value is 0 kmer-code-2013-trunk/libutil/md5.c:364:7: note: Assuming condition is false kmer-code-2013-trunk/libutil/md5.c:369:3: note: Null pointer dereference kmer-code-2013-trunk/libutil/md5.c:267:52: style: Parameter 'input' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/md5.c:312:20: style: Parameter 'm' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/mt19937ar/mt19937ar-test.c:19:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu32 [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/mt19937ar/mt19937ar.c:129:18: style:inconclusive: Function 'mtRandom32' argument 1 names different: declaration 'mt' definition 'ctx'. [funcArgNamesDifferent] kmer-code-2013-trunk/libutil/util.h:283:33: note: Function 'mtRandom32' argument 1 names different: declaration 'mt' definition 'ctx'. kmer-code-2013-trunk/libutil/mt19937ar/mt19937ar.c:129:18: note: Function 'mtRandom32' argument 1 names different: declaration 'mt' definition 'ctx'. kmer-code-2013-trunk/libutil/mt19937ar/mt19937ar.c:94:21: style: Parameter 'init_key' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/mt19937ar/mt19937ar.c:186:6: style: Variable 'y2' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/mt19937ar/tt800.c:57:1: portability: Omitted return type of function 'main' defaults to int, this is not supported by ISO C99 and later standards. [returnImplicitInt] kmer-code-2013-trunk/libutil/mt19937ar/tt800.c:29:26: style: Variable 'mag01' can be declared as const array [constVariable] kmer-code-2013-trunk/libutil/palloc.c:37:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/palloc.c:63:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/palloc.c:100:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/palloc.c:136:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/palloc.c:228:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/palloc.c:37:5: portability: %zd in format string (no. 1) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint] kmer-code-2013-trunk/libutil/palloc.c:100:5: portability: %zd in format string (no. 1) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint] kmer-code-2013-trunk/libutil/palloc.c:100:5: portability: %zd in format string (no. 2) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint] kmer-code-2013-trunk/libutil/palloc.c:136:7: portability: %zd in format string (no. 1) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint] kmer-code-2013-trunk/libutil/palloc.c:171:7: portability: %zd in format string (no. 1) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint] kmer-code-2013-trunk/libutil/palloc.c:189:7: portability: %zd in format string (no. 2) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint] kmer-code-2013-trunk/libutil/palloc.c:189:7: portability: %zd in format string (no. 3) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint] kmer-code-2013-trunk/libutil/palloc.c:189:7: portability: %zd in format string (no. 4) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint] kmer-code-2013-trunk/libutil/palloc.c:208:5: portability: %zd in format string (no. 2) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint] kmer-code-2013-trunk/libutil/palloc.c:208:5: portability: %zd in format string (no. 3) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint] kmer-code-2013-trunk/libutil/palloc.c:229:3: portability: %zd in format string (no. 1) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint] kmer-code-2013-trunk/libutil/palloc.c:231:5: portability: %zd in format string (no. 2) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint] kmer-code-2013-trunk/libutil/qsort_mt.c:153:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/readBuffer.C:27:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/readBuffer.C:67:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/readBuffer.C:127:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/readBuffer.C:149:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/readBuffer.C:225:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/readBuffer.C:69:3: warning: Class 'readBuffer' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libutil/readBuffer.C:69:3: warning: Class 'readBuffer' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libutil/readBuffer.C:45:15: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libutil/readBuffer.C:181:20: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libutil/readBuffer.C:248:20: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libutil/readBuffer.C:218:12: style: The scope of the variable 'bAct' can be reduced. [variableScope] kmer-code-2013-trunk/libutil/readBuffer.C:64:30: style:inconclusive: Function 'readBuffer' argument 1 names different: declaration 'F' definition 'file'. [funcArgNamesDifferent] kmer-code-2013-trunk/libutil/readBuffer.H:8:20: note: Function 'readBuffer' argument 1 names different: declaration 'F' definition 'file'. kmer-code-2013-trunk/libutil/readBuffer.C:64:30: note: Function 'readBuffer' argument 1 names different: declaration 'F' definition 'file'. kmer-code-2013-trunk/libutil/readBuffer.C:218:20: style: Variable 'bAct' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/recordFile.C:47:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/recordFile.C:146:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/recordFile.C:185:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/recordFile.C:224:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/recordFile.C:22:3: warning: Class 'recordFile' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/libutil/recordFile.C:22:3: warning: Class 'recordFile' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/libutil/recordFile.C:253:23: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libutil/recordFile.C:303:17: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libutil/recordFile.C:249:13: style: The scope of the variable 'len' can be reduced. [variableScope] kmer-code-2013-trunk/libutil/recordFile.C:298:13: style: The scope of the variable 'len' can be reduced. [variableScope] kmer-code-2013-trunk/libutil/recordFile.C:249:17: style: Variable 'len' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/recordFile.C:298:17: style: Variable 'len' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/sweatShop.C:127:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/sweatShop.C:162:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/sweatShop.C:258:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/sweatShop.C:390:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/sweatShop.C:468:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/sweatShop.C:81:12: warning: Member variable 'sweatShop::_stateMutex' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/libutil/sweatShop.C:16:3: warning: Member variable 'sweatShopWorker::threadID' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/libutil/sweatShop.C:184:12: style: Unused private function: 'sweatShop::loader' [unusedPrivateFunction] kmer-code-2013-trunk/libutil/sweatShop.H:43:11: note: Unused private function: 'sweatShop::loader' kmer-code-2013-trunk/libutil/sweatShop.C:184:12: note: Unused private function: 'sweatShop::loader' kmer-code-2013-trunk/libutil/sweatShop.C:235:12: style: Unused private function: 'sweatShop::worker' [unusedPrivateFunction] kmer-code-2013-trunk/libutil/sweatShop.H:44:11: note: Unused private function: 'sweatShop::worker' kmer-code-2013-trunk/libutil/sweatShop.C:235:12: note: Unused private function: 'sweatShop::worker' kmer-code-2013-trunk/libutil/sweatShop.C:310:12: style: Unused private function: 'sweatShop::writer' [unusedPrivateFunction] kmer-code-2013-trunk/libutil/sweatShop.H:45:11: note: Unused private function: 'sweatShop::writer' kmer-code-2013-trunk/libutil/sweatShop.C:310:12: note: Unused private function: 'sweatShop::writer' kmer-code-2013-trunk/libutil/sweatShop.C:356:12: style: Unused private function: 'sweatShop::status' [unusedPrivateFunction] kmer-code-2013-trunk/libutil/sweatShop.H:46:11: note: Unused private function: 'sweatShop::status' kmer-code-2013-trunk/libutil/sweatShop.C:356:12: note: Unused private function: 'sweatShop::status' kmer-code-2013-trunk/libutil/sweatShop.C:38:3: style: Class 'sweatShopState' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/libutil/sweatShop.C:57:19: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libutil/sweatShop.C:63:25: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libutil/sweatShop.C:69:19: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libutil/sweatShop.C:75:19: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libutil/sweatShop.C:171:19: style: Variable '_loaderP' is reassigned a value before the old one has been used. [redundantAssignment] kmer-code-2013-trunk/libutil/sweatShop.C:167:19: note: _loaderP is assigned kmer-code-2013-trunk/libutil/sweatShop.C:171:19: note: _loaderP is overwritten kmer-code-2013-trunk/libutil/sweatShop.C:242:11: style: The scope of the variable 'err' can be reduced. [variableScope] kmer-code-2013-trunk/libutil/sweatShop.C:311:32: style: Variable 'deleteState' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/sweatShop.C:363:21: style: Variable 'thisTime' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/sweatShop.C:368:21: style: Variable 'cpuPerSec' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/test/atomic.C:44:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PTHREAD_SCOPE_SYSTEM [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/test/atomic.C:55:5: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'signed int'. [invalidPrintfArgType_sint] kmer-code-2013-trunk/libutil/test/atomic.C:59:3: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'signed int'. [invalidPrintfArgType_sint] kmer-code-2013-trunk/libutil/test/atomic.C:26:21: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libutil/test/atomic.C:51:59: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libutil/test/endianess.c:12:10: error: No pair for character ("). Can't process file. File is either invalid or unicode, which is currently not supported. [syntaxError] kmer-code-2013-trunk/libutil/test/order.C:58:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/test/tcat.C:67:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/test/tcat.C:40:22: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libutil/test/test-bigQueue.C:53:13: warning: If resource allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfResources] kmer-code-2013-trunk/libutil/test/test-bigQueue.C:44:20: note: Assuming allocation function fails kmer-code-2013-trunk/libutil/test/test-bigQueue.C:44:20: note: Assignment 'out=fopen("junk-bigQueue-out-1","w")', assigned value is 0 kmer-code-2013-trunk/libutil/test/test-bigQueue.C:53:13: note: Null pointer dereference kmer-code-2013-trunk/libutil/test/test-bigQueue.C:58:10: warning: If resource allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfResources] kmer-code-2013-trunk/libutil/test/test-bigQueue.C:44:20: note: Assuming allocation function fails kmer-code-2013-trunk/libutil/test/test-bigQueue.C:44:20: note: Assignment 'out=fopen("junk-bigQueue-out-1","w")', assigned value is 0 kmer-code-2013-trunk/libutil/test/test-bigQueue.C:58:10: note: Null pointer dereference kmer-code-2013-trunk/libutil/test/test-bigQueue.C:66:13: warning: If resource allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfResources] kmer-code-2013-trunk/libutil/test/test-bigQueue.C:59:14: note: Assuming allocation function fails kmer-code-2013-trunk/libutil/test/test-bigQueue.C:59:14: note: Assignment 'out=fopen("junk-bigQueue-out-2","w")', assigned value is 0 kmer-code-2013-trunk/libutil/test/test-bigQueue.C:66:13: note: Null pointer dereference kmer-code-2013-trunk/libutil/test/test-bigQueue.C:71:10: warning: If resource allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfResources] kmer-code-2013-trunk/libutil/test/test-bigQueue.C:59:14: note: Assuming allocation function fails kmer-code-2013-trunk/libutil/test/test-bigQueue.C:59:14: note: Assignment 'out=fopen("junk-bigQueue-out-2","w")', assigned value is 0 kmer-code-2013-trunk/libutil/test/test-bigQueue.C:71:10: note: Null pointer dereference kmer-code-2013-trunk/libutil/test/test-bigQueue.C:21:18: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libutil/test/test-bigQueue.C:22:18: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libutil/test/test-bigQueue.C:64:18: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/libutil/test/test-bigQueue.C:21:12: style: Variable 'A' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/test/test-bigQueue.C:22:12: style: Variable 'B' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/test/test-bigQueue.C:64:14: style: Variable 't' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/libutil/test/test-bitPackedArray.C:67:35: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libutil/test/test-bitPackedFile.C:65:70: error: There is an unknown macro here somewhere. Configuration is required. If uint64HEX is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libutil/test/test-bitPacking.C:79:40: error: There is an unknown macro here somewhere. Configuration is required. If uint64HEX is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libutil/test/test-bzipBuffer.C:20:42: error: There is an unknown macro here somewhere. Configuration is required. If uint64HEX is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libutil/test/test-freeDiskSpace.c:8:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/test/test-intervalList.C:172:40: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libutil/test/test-logMsg.C:26:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/test/test-md5.c:23:25: style: Parameter 'ans' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/libutil/test/test-mmap.c:43:47: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libutil/test/test-palloc.c:32:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/test/test-readBuffer.C:27:42: error: There is an unknown macro here somewhere. Configuration is required. If uint64HEX is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libutil/test/test-recordFile.C:53:31: error: There is an unknown macro here somewhere. Configuration is required. If uint64HEX is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libutil/test/test-types.c:13:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint32 [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/test/test-types.c:19:10: style: Condition 'u3<0' is always true [knownConditionTrueFalse] kmer-code-2013-trunk/libutil/test/test-types.c:8:18: note: Assignment 'u3=-1', assigned value is -1 kmer-code-2013-trunk/libutil/test/test-types.c:19:10: note: Condition 'u3<0' is always true kmer-code-2013-trunk/libutil/test/test-types.c:22:10: style: Condition 's3>0' is always false [knownConditionTrueFalse] kmer-code-2013-trunk/libutil/test/test-types.c:9:17: note: Assignment 's3=-1', assigned value is -1 kmer-code-2013-trunk/libutil/test/test-types.c:22:10: note: Condition 's3>0' is always false kmer-code-2013-trunk/libutil/unaryEncodingTester.C:25:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/unaryEncodingTester.C:59:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/unaryEncodingTester.C:94:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/unaryEncodingTester.C:128:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/unaryEncodingTester.C:157:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/unaryEncodingTester.C:18:11: style: The scope of the variable 'val' can be reduced. [variableScope] kmer-code-2013-trunk/libutil/unaryEncodingTester.C:52:11: style: The scope of the variable 'val' can be reduced. [variableScope] kmer-code-2013-trunk/libutil/unaryEncodingTester.C:87:11: style: The scope of the variable 'val' can be reduced. [variableScope] kmer-code-2013-trunk/libutil/unaryEncodingTester.C:121:11: style: The scope of the variable 'val' can be reduced. [variableScope] kmer-code-2013-trunk/libutil/unaryEncodingTester.C:18:15: style: Variable 'val' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/unaryEncodingTester.C:52:15: style: Variable 'val' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/unaryEncodingTester.C:87:15: style: Variable 'val' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/unaryEncodingTester.C:121:15: style: Variable 'val' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/libutil/util.c:31:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/util.c:49:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/util.c:68:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/util.c:98:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/util.c:110:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/libutil/util.c:80:12: warning: If memory allocation fails, then there is a possible null pointer dereference: rslt [nullPointerOutOfMemory] kmer-code-2013-trunk/libutil/util.c:69:18: note: Assuming allocation function fails kmer-code-2013-trunk/libutil/util.c:69:18: note: Assignment 'rslt=malloc(size)', assigned value is 0 kmer-code-2013-trunk/libutil/util.c:70:9: note: Assuming condition is false kmer-code-2013-trunk/libutil/util.c:80:12: note: Null pointer dereference kmer-code-2013-trunk/meryl/args.C:26:72: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:439:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:721:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:769:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:804:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:862:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:279:15: warning: 'operator=' should check for assignment to self to avoid problems with dynamic memory. [operatorEqToSelf] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:128:11: style:inconclusive: Technically the member function 'splitToWords::numWords' can be const. [functionConst] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:182:15: style:inconclusive: Technically the member function 'intervalList::numberOfIntervals' can be const. [functionConst] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:484:15: style:inconclusive: Technically the member function 'intervalList::overlapping' can be const. [functionConst] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:201:15: note: Technically the member function 'intervalList::overlapping' can be const. kmer-code-2013-trunk/meryl/asmMerQC-regions.C:484:15: note: Technically the member function 'intervalList::overlapping' can be const. kmer-code-2013-trunk/meryl/asmMerQC-regions.C:224:23: style:inconclusive: Technically the member function 'intervalList::lo' can be const. [functionConst] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:225:23: style:inconclusive: Technically the member function 'intervalList::hi' can be const. [functionConst] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:249:15: style:inconclusive: Technically the member function 'intervalDepth::numberOfIntervals' can be const. [functionConst] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:253:23: style:inconclusive: Technically the member function 'intervalDepth::lo' can be const. [functionConst] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:254:23: style:inconclusive: Technically the member function 'intervalDepth::hi' can be const. [functionConst] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:255:23: style:inconclusive: Technically the member function 'intervalDepth::de' can be const. [functionConst] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:269:3: warning: Class 'intervalList' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:656:3: warning: Class 'intervalDepth' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:656:3: warning: Class 'intervalDepth' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:38:3: style: Class 'splitToWords' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:245:3: style: Class 'intervalDepth' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:955:13: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:955:13: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:955:13: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:955:13: warning: %u in format string (no. 4) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:958:15: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:958:15: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:958:15: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:958:15: warning: %u in format string (no. 4) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:982:13: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:982:13: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:982:13: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:982:13: warning: %u in format string (no. 4) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:985:15: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:985:15: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:985:15: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:985:15: warning: %u in format string (no. 4) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:994:9: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:994:9: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:730:21: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:724:18: note: Assuming allocation function fails kmer-code-2013-trunk/meryl/asmMerQC-regions.C:724:18: note: Assignment 'F=std::fopen(depthname,"r")', assigned value is 0 kmer-code-2013-trunk/meryl/asmMerQC-regions.C:725:7: note: Assuming condition is false kmer-code-2013-trunk/meryl/asmMerQC-regions.C:730:21: note: Null pointer dereference kmer-code-2013-trunk/meryl/asmMerQC-regions.C:731:16: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:724:18: note: Assuming allocation function fails kmer-code-2013-trunk/meryl/asmMerQC-regions.C:724:18: note: Assignment 'F=std::fopen(depthname,"r")', assigned value is 0 kmer-code-2013-trunk/meryl/asmMerQC-regions.C:725:7: note: Assuming condition is false kmer-code-2013-trunk/meryl/asmMerQC-regions.C:731:16: note: Null pointer dereference kmer-code-2013-trunk/meryl/asmMerQC-regions.C:778:28: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:772:18: note: Assuming allocation function fails kmer-code-2013-trunk/meryl/asmMerQC-regions.C:772:18: note: Assignment 'F=std::fopen(depthname,"r")', assigned value is 0 kmer-code-2013-trunk/meryl/asmMerQC-regions.C:773:7: note: Assuming condition is false kmer-code-2013-trunk/meryl/asmMerQC-regions.C:778:28: note: Null pointer dereference kmer-code-2013-trunk/meryl/asmMerQC-regions.C:779:16: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:772:18: note: Assuming allocation function fails kmer-code-2013-trunk/meryl/asmMerQC-regions.C:772:18: note: Assignment 'F=std::fopen(depthname,"r")', assigned value is 0 kmer-code-2013-trunk/meryl/asmMerQC-regions.C:773:7: note: Assuming condition is false kmer-code-2013-trunk/meryl/asmMerQC-regions.C:779:16: note: Null pointer dereference kmer-code-2013-trunk/meryl/asmMerQC-regions.C:813:21: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:807:18: note: Assuming allocation function fails kmer-code-2013-trunk/meryl/asmMerQC-regions.C:807:18: note: Assignment 'F=std::fopen(depthname,"r")', assigned value is 0 kmer-code-2013-trunk/meryl/asmMerQC-regions.C:808:7: note: Assuming condition is false kmer-code-2013-trunk/meryl/asmMerQC-regions.C:813:21: note: Null pointer dereference kmer-code-2013-trunk/meryl/asmMerQC-regions.C:814:16: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:807:18: note: Assuming allocation function fails kmer-code-2013-trunk/meryl/asmMerQC-regions.C:807:18: note: Assignment 'F=std::fopen(depthname,"r")', assigned value is 0 kmer-code-2013-trunk/meryl/asmMerQC-regions.C:808:7: note: Assuming condition is false kmer-code-2013-trunk/meryl/asmMerQC-regions.C:814:16: note: Null pointer dereference kmer-code-2013-trunk/meryl/asmMerQC-regions.C:337:22: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:338:22: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:620:23: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:621:23: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:847:9: style: The scope of the variable 'showDepthIntersect' can be reduced. [variableScope] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:848:9: style: The scope of the variable 'showVariantIntersect' can be reduced. [variableScope] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:849:9: style: The scope of the variable 'showVarDepthIntersect' can be reduced. [variableScope] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:484:45: style:inconclusive: Function 'overlapping' argument 1 names different: declaration 'lo' definition 'rangelo'. [funcArgNamesDifferent] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:201:45: note: Function 'overlapping' argument 1 names different: declaration 'lo' definition 'rangelo'. kmer-code-2013-trunk/meryl/asmMerQC-regions.C:484:45: note: Function 'overlapping' argument 1 names different: declaration 'lo' definition 'rangelo'. kmer-code-2013-trunk/meryl/asmMerQC-regions.C:485:45: style:inconclusive: Function 'overlapping' argument 2 names different: declaration 'hi' definition 'rangehi'. [funcArgNamesDifferent] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:202:45: note: Function 'overlapping' argument 2 names different: declaration 'hi' definition 'rangehi'. kmer-code-2013-trunk/meryl/asmMerQC-regions.C:485:45: note: Function 'overlapping' argument 2 names different: declaration 'hi' definition 'rangehi'. kmer-code-2013-trunk/meryl/asmMerQC-regions.C:279:39: style: Parameter 'src' can be declared as reference to const [constParameterReference] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:91:20: style: Variable 'cmdI' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:337:18: style: Variable 'A' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:338:18: style: Variable 'B' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:620:19: style: Variable 'A' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:621:19: style: Variable 'B' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:717:17: style: Parameter 'depthname' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:766:21: style: Parameter 'depthname' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:801:19: style: Parameter 'depthname' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:847:31: style: Variable 'showDepthIntersect' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:848:31: style: Variable 'showVariantIntersect' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:849:31: style: Variable 'showVarDepthIntersect' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:856:26: style: Variable 'showDepthIntersect' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:858:28: style: Variable 'showVariantIntersect' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:860:29: style: Variable 'showVarDepthIntersect' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:760:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:1004:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] kmer-code-2013-trunk/meryl/binaryOp.C:43:50: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/meryl/build-threads.C:22:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint32ZERO [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/meryl/build-threads.C:48:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint64ZERO [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/meryl/meryl.H:28:3: style: Class 'merylArgs' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/meryl/build-threads.C:23:22: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/meryl/build-threads.C:69:57: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/meryl/build.C:153:30: error: There is an unknown macro here somewhere. Configuration is required. If uint64FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/meryl/compare-counts.C:225:37: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/meryl/dump.C:17:26: error: There is an unknown macro here somewhere. Configuration is required. If uint64FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/meryl/estimate.C:54:31: error: There is an unknown macro here somewhere. Configuration is required. If uint64FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/meryl/kmer-mask.C:754:32: error: There is an unknown macro here somewhere. Configuration is required. If uint64FMTW is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/meryl/mapMers-depth.C:49:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/meryl/mapMers.C:135:15: error: There is an unknown macro here somewhere. Configuration is required. If uint64FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/meryl/maskMers.C:148:42: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/meryl/merge.C:14:74: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/meryl/merge.listmerge.C:221:74: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/meryl/merge.qsort.C:188:74: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/meryl/mervin.C:237:21: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/meryl/meryl.C:64:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/meryl/simple.C:98:30: error: There is an unknown macro here somewhere. Configuration is required. If uint64FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/meryl/test/kmerlite.H:20:34: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/meryl/test/stupidcount.C:23:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/meryl/unaryOp.C:13:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/seagen/aHit.C:20:23: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/seagen/hitMatrix.H:128:53: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/seagen/encodedQuery.C:142:79: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/seagen/hitReader.H:62:72: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/seagen/filtertest.C:180:40: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/seagen/hitConverter.C:10:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/seagen/hitConverter.C:36:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/seagen/hitConverter.C:61:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/seagen/misc/dumpCrapSeqs.C:19:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/seagen/misc/dumpCrapSeqs.C:15:18: style: The scope of the variable 'Q' can be reduced. [variableScope] kmer-code-2013-trunk/seagen/misc/dumpCrapSeqs.C:15:20: style: Variable 'Q' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/seagen/misc/f.C:25:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/seagen/misc/f.C:33:12: style: The scope of the variable 'file' can be reduced. [variableScope] kmer-code-2013-trunk/seagen/misc/f.C:36:12: style: The scope of the variable 'isBINARY' can be reduced. [variableScope] kmer-code-2013-trunk/seagen/misc/h.C:24:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/seagen/misc/h.C:32:12: style: The scope of the variable 'file' can be reduced. [variableScope] kmer-code-2013-trunk/seagen/misc/h.C:35:12: style: The scope of the variable 'isBINARY' can be reduced. [variableScope] kmer-code-2013-trunk/seagen/sortHits.C:27:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/seagen/sortHits.C:81:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/seagen/sortHits.C:117:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint32ZERO [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/seagen/sortHits.C:172:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/seagen/sortHits.C:28:5: warning: Class 'aHitReader' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/seagen/sortHits.C:28:5: warning: Class 'aHitReader' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/seagen/sortHits.C:110:12: warning: Class 'aHitTemporary' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/seagen/sortHits.C:110:12: warning: Class 'aHitTemporary' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/seagen/sortHits.C:26:3: style: Class 'aHitReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kmer-code-2013-trunk/seagen/sortHits.C:153:14: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/seagen/sortHits.C:154:14: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/seagen/sortHits.C:26:20: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/seagen/sortHits.C:72:23: style: Parameter 'hits' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/seagen/sortHits.C:153:10: style: Variable 'A' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/seagen/sortHits.C:154:10: style: Variable 'B' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/seagen/test/encodedQueryTest.C:10:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/seagen/test/intervalList-test.C:18:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/seagen/test/intervalList-test.C:93:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/seatac/filterObj.H:148:84: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/seatac/heavychains.H:67:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/seatac/heavychains.H:85:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint32ZERO [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/seatac/heavychains.H:407:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/seatac/filter-heavychains.C:147:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/seatac/heavychains.H:229:3: warning: Member variable 'Interval::lo' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/seatac/heavychains.H:229:3: warning: Member variable 'Interval::hi' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/seatac/heavychains.H:229:3: warning: Member variable 'Interval::S' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/seatac/heavychains.H:304:3: warning: Member variable 'DPTree::MaxJump' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/seatac/heavychains.H:249:5: warning: Member variable 'kd_node::Xy' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/seatac/heavychains.H:249:5: warning: Member variable 'kd_node::start' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/seatac/heavychains.H:249:5: warning: Member variable 'kd_node::stop' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/seatac/heavychains.H:249:5: warning: Member variable 'kd_node::intv' is not initialized in the constructor. [uninitMemberVar] kmer-code-2013-trunk/seatac/heavychains.H:52:5: performance: Variable 'beVerbose' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] kmer-code-2013-trunk/seatac/heavychains.H:107:16: style:inconclusive: Technically the member function 'StrandPair::sequenceIID1' can be const. [functionConst] kmer-code-2013-trunk/seatac/heavychains.H:371:10: style:inconclusive: Technically the member function 'DPTree::matchScore' can be const. [functionConst] kmer-code-2013-trunk/seatac/filter-heavychains.C:173:8: style:inconclusive: Technically the member function 'StrandPairManager::process' can be const. [functionConst] kmer-code-2013-trunk/seatac/filter-heavychains.C:178:10: style:inconclusive: Technically the member function 'StrandPairManager::print' can be const. [functionConst] kmer-code-2013-trunk/seatac/filter-heavychains.C:184:8: style:inconclusive: Technically the member function 'StrandPairManager::addStats' can be const. [functionConst] kmer-code-2013-trunk/seatac/heavychains.H:60:5: warning: Class 'StrandPair' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/seatac/heavychains.H:60:5: warning: Class 'StrandPair' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/seatac/heavychains.H:308:5: warning: Class 'DPTree' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/seatac/heavychains.H:308:5: warning: Class 'DPTree' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/seatac/filter-heavychains.C:94:14: warning: Class 'StrandPairManager' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] kmer-code-2013-trunk/seatac/filter-heavychains.C:94:14: warning: Class 'StrandPairManager' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] kmer-code-2013-trunk/seatac/filter-heavychains.C:227:10: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/seatac/filter-heavychains.C:245:4: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/seatac/filter-heavychains.C:250:4: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/seatac/filter-heavychains.C:256:11: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/seatac/filter-heavychains.C:294:10: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/seatac/filter-heavychains.C:309:4: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/seatac/filter-heavychains.C:309:39: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/seatac/filter-heavychains.C:314:4: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/seatac/heavychains.H:372:12: style: The scope of the variable 'score' can be reduced. [variableScope] kmer-code-2013-trunk/seatac/filter-heavychains.C:74:28: style: Parameter 'assemblyid1' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/seatac/filter-heavychains.C:75:28: style: Parameter 'assemblyid2' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/seatac/heavychains.H:48:21: style: Parameter 'assemblyid1' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/seatac/heavychains.H:49:21: style: Parameter 'assemblyid2' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/seatac/heavychains.H:125:22: style: Parameter 'm' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/seatac/heavychains.H:164:19: style: Parameter 'assemblyid1' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/seatac/heavychains.H:165:19: style: Parameter 'assemblyid2' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/seatac/heavychains.H:182:24: style: Parameter 'sp' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/seatac/heavychains.H:372:18: style: Variable 'score' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/seatac/filter-nop.C:67:28: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/seatac/heavychains-driver.C:54:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/seatac/heavychains-driver.C:98:19: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf] kmer-code-2013-trunk/seatac/heavychains.H:53:26: warning: Possible null pointer dereference: assemblyid1 [nullPointer] kmer-code-2013-trunk/seatac/heavychains-driver.C:30:25: note: Assignment 'assemblyId1=0L', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:38:14: note: Assuming condition is false kmer-code-2013-trunk/seatac/heavychains-driver.C:68:46: note: Calling function 'StrandPair', 2nd argument 'assemblyId1' value is 0 kmer-code-2013-trunk/seatac/heavychains.H:53:26: note: Null pointer dereference kmer-code-2013-trunk/seatac/heavychains.H:54:26: warning: Possible null pointer dereference: assemblyid2 [nullPointer] kmer-code-2013-trunk/seatac/heavychains-driver.C:31:25: note: Assignment 'assemblyId2=0L', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:38:14: note: Assuming condition is false kmer-code-2013-trunk/seatac/heavychains-driver.C:68:59: note: Calling function 'StrandPair', 3rd argument 'assemblyId2' value is 0 kmer-code-2013-trunk/seatac/heavychains.H:54:26: note: Null pointer dereference kmer-code-2013-trunk/seatac/heavychains.H:169:26: warning: Possible null pointer dereference: assemblyid1 [nullPointer] kmer-code-2013-trunk/seatac/heavychains-driver.C:30:25: note: Assignment 'assemblyId1=0L', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:38:14: note: Assuming condition is false kmer-code-2013-trunk/seatac/heavychains-driver.C:69:44: note: Calling function 'TheStats', 2nd argument 'assemblyId1' value is 0 kmer-code-2013-trunk/seatac/heavychains.H:169:26: note: Null pointer dereference kmer-code-2013-trunk/seatac/heavychains.H:170:26: warning: Possible null pointer dereference: assemblyid2 [nullPointer] kmer-code-2013-trunk/seatac/heavychains-driver.C:31:25: note: Assignment 'assemblyId2=0L', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:38:14: note: Assuming condition is false kmer-code-2013-trunk/seatac/heavychains-driver.C:69:57: note: Calling function 'TheStats', 3rd argument 'assemblyId2' value is 0 kmer-code-2013-trunk/seatac/heavychains.H:170:26: note: Null pointer dereference kmer-code-2013-trunk/seatac/heavychains.H:192:13: warning: If resource allocation fails, then there is a possible null pointer dereference: outfile [nullPointerOutOfResources] kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assuming allocation function fails kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assignment 'outF=std::fopen(outFileName,"w")', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:176:12: note: Calling function 'show', 1st argument 'outF' value is 0 kmer-code-2013-trunk/seatac/heavychains.H:192:13: note: Null pointer dereference kmer-code-2013-trunk/seatac/heavychains.H:193:13: warning: If resource allocation fails, then there is a possible null pointer dereference: outfile [nullPointerOutOfResources] kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assuming allocation function fails kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assignment 'outF=std::fopen(outFileName,"w")', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:176:12: note: Calling function 'show', 1st argument 'outF' value is 0 kmer-code-2013-trunk/seatac/heavychains.H:193:13: note: Null pointer dereference kmer-code-2013-trunk/seatac/heavychains.H:194:13: warning: If resource allocation fails, then there is a possible null pointer dereference: outfile [nullPointerOutOfResources] kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assuming allocation function fails kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assignment 'outF=std::fopen(outFileName,"w")', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:176:12: note: Calling function 'show', 1st argument 'outF' value is 0 kmer-code-2013-trunk/seatac/heavychains.H:194:13: note: Null pointer dereference kmer-code-2013-trunk/seatac/heavychains.H:195:13: warning: If resource allocation fails, then there is a possible null pointer dereference: outfile [nullPointerOutOfResources] kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assuming allocation function fails kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assignment 'outF=std::fopen(outFileName,"w")', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:176:12: note: Calling function 'show', 1st argument 'outF' value is 0 kmer-code-2013-trunk/seatac/heavychains.H:195:13: note: Null pointer dereference kmer-code-2013-trunk/seatac/heavychains.H:196:13: warning: If resource allocation fails, then there is a possible null pointer dereference: outfile [nullPointerOutOfResources] kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assuming allocation function fails kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assignment 'outF=std::fopen(outFileName,"w")', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:176:12: note: Calling function 'show', 1st argument 'outF' value is 0 kmer-code-2013-trunk/seatac/heavychains.H:196:13: note: Null pointer dereference kmer-code-2013-trunk/seatac/heavychains.H:197:13: warning: If resource allocation fails, then there is a possible null pointer dereference: outfile [nullPointerOutOfResources] kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assuming allocation function fails kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assignment 'outF=std::fopen(outFileName,"w")', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:176:12: note: Calling function 'show', 1st argument 'outF' value is 0 kmer-code-2013-trunk/seatac/heavychains.H:197:13: note: Null pointer dereference kmer-code-2013-trunk/seatac/heavychains.H:198:13: warning: If resource allocation fails, then there is a possible null pointer dereference: outfile [nullPointerOutOfResources] kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assuming allocation function fails kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assignment 'outF=std::fopen(outFileName,"w")', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:176:12: note: Calling function 'show', 1st argument 'outF' value is 0 kmer-code-2013-trunk/seatac/heavychains.H:198:13: note: Null pointer dereference kmer-code-2013-trunk/seatac/heavychains.H:199:13: warning: If resource allocation fails, then there is a possible null pointer dereference: outfile [nullPointerOutOfResources] kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assuming allocation function fails kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assignment 'outF=std::fopen(outFileName,"w")', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:176:12: note: Calling function 'show', 1st argument 'outF' value is 0 kmer-code-2013-trunk/seatac/heavychains.H:199:13: note: Null pointer dereference kmer-code-2013-trunk/seatac/heavychains.H:200:13: warning: If resource allocation fails, then there is a possible null pointer dereference: outfile [nullPointerOutOfResources] kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assuming allocation function fails kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assignment 'outF=std::fopen(outFileName,"w")', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:176:12: note: Calling function 'show', 1st argument 'outF' value is 0 kmer-code-2013-trunk/seatac/heavychains.H:200:13: note: Null pointer dereference kmer-code-2013-trunk/seatac/heavychains.H:201:13: warning: If resource allocation fails, then there is a possible null pointer dereference: outfile [nullPointerOutOfResources] kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assuming allocation function fails kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assignment 'outF=std::fopen(outFileName,"w")', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:176:12: note: Calling function 'show', 1st argument 'outF' value is 0 kmer-code-2013-trunk/seatac/heavychains.H:201:13: note: Null pointer dereference kmer-code-2013-trunk/seatac/heavychains-driver.C:58:22: warning: Possible null pointer dereference: inFileName [nullPointer] kmer-code-2013-trunk/seatac/heavychains-driver.C:34:25: note: Assignment 'inFileName=0L', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:38:14: note: Assuming condition is false kmer-code-2013-trunk/seatac/heavychains-driver.C:58:22: note: Null pointer dereference kmer-code-2013-trunk/seatac/heavychains-driver.C:59:22: warning: Possible null pointer dereference: outFileName [nullPointer] kmer-code-2013-trunk/seatac/heavychains-driver.C:35:25: note: Assignment 'outFileName=0L', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:38:14: note: Assuming condition is false kmer-code-2013-trunk/seatac/heavychains-driver.C:59:22: note: Null pointer dereference kmer-code-2013-trunk/seatac/heavychains-driver.C:61:11: warning: If resource allocation fails, then there is a possible null pointer dereference: outF [nullPointerOutOfResources] kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assuming allocation function fails kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assignment 'outF=std::fopen(outFileName,"w")', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:61:11: note: Null pointer dereference kmer-code-2013-trunk/seatac/heavychains-driver.C:85:39: warning: If resource allocation fails, then there is a possible null pointer dereference: inpF [nullPointerOutOfResources] kmer-code-2013-trunk/seatac/heavychains-driver.C:58:21: note: Assuming allocation function fails kmer-code-2013-trunk/seatac/heavychains-driver.C:58:21: note: Assignment 'inpF=std::fopen(inFileName,"r")', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:85:39: note: Null pointer dereference kmer-code-2013-trunk/seatac/heavychains-driver.C:182:10: warning: If resource allocation fails, then there is a possible null pointer dereference: outF [nullPointerOutOfResources] kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assuming allocation function fails kmer-code-2013-trunk/seatac/heavychains-driver.C:59:21: note: Assignment 'outF=std::fopen(outFileName,"w")', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:182:10: note: Null pointer dereference kmer-code-2013-trunk/seatac/heavychains-driver.C:82:11: style: The scope of the variable 'tmp_filled' can be reduced. [variableScope] kmer-code-2013-trunk/seatac/heavychains-driver.C:34:10: style: Variable 'inFileName' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/seatac/heavychains-driver.C:35:10: style: Variable 'outFileName' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/seatac/heavychains.C:96:55: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4db/sim4th.C:327:28: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:99:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:284:10: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: junkF [nullPointerOutOfResources] kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:125:24: note: Assuming allocation function fails kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:125:24: note: Assignment 'junkF=fopen("spl.junkfirst","w")', assigned value is 0 kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:284:10: note: Null pointer dereference kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:285:10: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: junkL [nullPointerOutOfResources] kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:126:24: note: Assuming allocation function fails kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:126:24: note: Assignment 'junkL=fopen("spl.junklast","w")', assigned value is 0 kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:285:10: note: Null pointer dereference kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:286:10: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: junkB [nullPointerOutOfResources] kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:127:24: note: Assuming allocation function fails kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:127:24: note: Assignment 'junkB=fopen("spl.junkboth","w")', assigned value is 0 kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:286:10: note: Null pointer dereference kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:287:10: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: splGap [nullPointerOutOfResources] kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:128:24: note: Assuming allocation function fails kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:128:24: note: Assignment 'splGap=fopen("spl.splitGap","w")', assigned value is 0 kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:287:10: note: Null pointer dereference kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:288:10: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: good [nullPointerOutOfResources] kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:129:24: note: Assuming allocation function fails kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:129:24: note: Assignment 'good=fopen("spl.good","w")', assigned value is 0 kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:288:10: note: Null pointer dereference kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:289:10: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: flank [nullPointerOutOfResources] kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:130:24: note: Assuming allocation function fails kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:130:24: note: Assignment 'flank=fopen("spl.flanking","w")', assigned value is 0 kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:289:10: note: Null pointer dereference kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:77:16: style: The scope of the variable 'splitFile' can be reduced. [variableScope] kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:78:16: style: The scope of the variable 'intronLimit' can be reduced. [variableScope] kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:135:9: style: The scope of the variable 'exA' can be reduced. [variableScope] kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:136:9: style: The scope of the variable 'exB' can be reduced. [variableScope] kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:77:16: style: Variable 'splitFile' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:77:26: style: Variable 'splitFile' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:78:28: style: Variable 'intronLimit' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:100:17: style: Variable 'splitFile' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:106:19: style: Variable 'intronLimit' is assigned a value that is never used. [unreadVariable] kmer-code-2013-trunk/sim4dbutils/cleanPolishes.C:178:60: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4dbutils/comparePolishes.C:308:40: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4dbutils/convertPolishes.C:20:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/sim4dbutils/convertPolishes.C:37:12: style: The comparison 'GOOD == 0L' is always true. [knownConditionTrueFalse] kmer-code-2013-trunk/sim4dbutils/convertPolishes.C:12:36: note: 'GOOD' is assigned value '0L' here. kmer-code-2013-trunk/sim4dbutils/convertPolishes.C:37:12: note: The comparison 'GOOD == 0L' is always true. kmer-code-2013-trunk/sim4dbutils/convertToAtac.C:279:41: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4dbutils/convertToExtent.C:43:27: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4dbutils/coveragehack.C:201:37: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4dbutils/depthOfPolishes.C:103:34: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4dbutils/detectChimera.C:129:43: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4dbutils/filterPolishes.C:178:36: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4dbutils/fixPolishesIID.C:46:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sim4polishStyleDefault [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/sim4dbutils/fixPolishesIID.C:106:12: style: The scope of the variable 'cd' can be reduced. [variableScope] kmer-code-2013-trunk/sim4dbutils/fixPolishesIID.C:107:12: style: The scope of the variable 'gd' can be reduced. [variableScope] kmer-code-2013-trunk/sim4dbutils/headPolishes.C:16:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sim4polishStyleDefault [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/sim4dbutils/headPolishes.C:47:9: style: The comparison 'W == 0L' is always true. [knownConditionTrueFalse] kmer-code-2013-trunk/sim4dbutils/headPolishes.C:14:27: note: 'W' is assigned value '0L' here. kmer-code-2013-trunk/sim4dbutils/headPolishes.C:47:9: note: The comparison 'W == 0L' is always true. kmer-code-2013-trunk/sim4dbutils/mappedCoverage.C:94:27: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4dbutils/mergePolishes.C:35:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sim4polishStyleDefault [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/sim4dbutils/mergePolishes.C:119:21: style: Array index 'first' is used before limits check. [arrayIndexThenCheck] kmer-code-2013-trunk/sim4dbutils/mergePolishes.C:84:15: warning: If resource allocation fails, then there is a possible null pointer dereference: O [nullPointerOutOfResources] kmer-code-2013-trunk/sim4dbutils/mergePolishes.C:76:26: note: Assuming allocation function fails kmer-code-2013-trunk/sim4dbutils/mergePolishes.C:76:26: note: Assignment 'O=fopen(otSeqName,"w")', assigned value is 0 kmer-code-2013-trunk/sim4dbutils/mergePolishes.C:84:15: note: Null pointer dereference kmer-code-2013-trunk/sim4dbutils/mergePolishes.C:93:10: warning: If resource allocation fails, then there is a possible null pointer dereference: O [nullPointerOutOfResources] kmer-code-2013-trunk/sim4dbutils/mergePolishes.C:76:26: note: Assuming allocation function fails kmer-code-2013-trunk/sim4dbutils/mergePolishes.C:76:26: note: Assignment 'O=fopen(otSeqName,"w")', assigned value is 0 kmer-code-2013-trunk/sim4dbutils/mergePolishes.C:93:10: note: Null pointer dereference kmer-code-2013-trunk/sim4dbutils/mergePolishes.C:41:28: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/sim4dbutils/mergePolishes.C:42:28: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/sim4dbutils/mergePolishes.C:49:21: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/sim4dbutils/mergePolishes.C:50:21: style: C-style pointer casting [cstyleCast] kmer-code-2013-trunk/sim4dbutils/mergePolishes.C:16:81: style: Parameter 'numSeqs' can be declared as pointer to const [constParameterPointer] kmer-code-2013-trunk/sim4dbutils/mergePolishes.C:26:23: style: Variable 'otSeqName' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/sim4dbutils/parseSNP.C:229:26: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:546:31: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4dbutils/pickBestPolish.C:35:30: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4dbutils/pickUniquePolish-nhgri.C:139:31: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4dbutils/pickUniquePolish.C:125:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _estFrom [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/sim4dbutils/pickUniquePolish.C:178:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIM4_MATCH_FORWARD [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/sim4dbutils/pickUniquePolish.C:279:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint32ZERO [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/sim4dbutils/plotCoverageVsIdentity.C:32:28: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4dbutils/plotIntronSize.C:24:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/sim4dbutils/plotIntronSize.C:52:7: warning: Uninitialized variable: all [uninitvar] kmer-code-2013-trunk/sim4dbutils/plotIntronSize.C:30:14: note: Assuming condition is false kmer-code-2013-trunk/sim4dbutils/plotIntronSize.C:52:7: note: Uninitialized variable: all kmer-code-2013-trunk/sim4dbutils/plotIntronSize.C:52:14: warning: Uninitialized variable: big [uninitvar] kmer-code-2013-trunk/sim4dbutils/plotIntronSize.C:30:14: note: Assuming condition is false kmer-code-2013-trunk/sim4dbutils/plotIntronSize.C:52:14: note: Uninitialized variable: big kmer-code-2013-trunk/sim4dbutils/realignPolishes.C:160:30: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4dbutils/removeDuplicate.C:28:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _genFrom [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/sim4dbutils/removeDuplicate.C:75:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint32ZERO [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/sim4dbutils/removeRedundant.C:107:29: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4dbutils/reportAlignmentDifferences.C:12:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/sim4dbutils/reportAlignmentDifferences.C:11:13: style: Variable 'outPrefix' can be declared as pointer to const [constVariablePointer] kmer-code-2013-trunk/sim4dbutils/s4p_overlap.C:20:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _genTo [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/sim4dbutils/sortPolishes.C:87:29: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4dbutils/summarizePolishes.C:167:36: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/sim4dbutils/trimExons.C:26:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/sim4dbutils/trimSequencesBasedOnMatches.C:18:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/sim4dbutils/trimSequencesBasedOnMatches.C:34:7: error: fprintf format string requires 2 parameters but only 1 is given. [wrongPrintfScanfArgNum] kmer-code-2013-trunk/sim4dbutils/uniqPolishes.C:33:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint32ZERO [valueFlowBailoutIncompleteVar] kmer-code-2013-trunk/sim4dbutils/vennPolishes.C:115:45: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/snapper/snapper2.H:421:53: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/tapper/tapperTag.H:204:93: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/trie/trie.C:190:26: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMT is a macro then please configure it. [unknownMacro] kmer-code-2013-trunk/libutil/splitToWords.H:5:1: error: The one definition rule is violated, different classes/structs have the same name 'splitToWords' [ctuOneDefinitionRuleViolation] kmer-code-2013-trunk/meryl/asmMerQC-regions.C:29:1: note: The one definition rule is violated, different classes/structs have the same name 'splitToWords' kmer-code-2013-trunk/libutil/splitToWords.H:5:1: note: The one definition rule is violated, different classes/structs have the same name 'splitToWords' kmer-code-2013-trunk/seatac/heavychains.H:53:26: error: Null pointer dereference: assemblyid1 [ctunullpointer] kmer-code-2013-trunk/seatac/heavychains-driver.C:30:25: note: Assignment 'assemblyId1=0L', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:38:14: note: Assuming condition is false kmer-code-2013-trunk/seatac/heavychains-driver.C:68:34: note: Calling function StrandPair, 2nd argument is null kmer-code-2013-trunk/seatac/heavychains.H:53:26: note: Dereferencing argument assemblyid1 that is null kmer-code-2013-trunk/seatac/heavychains.H:54:26: error: Null pointer dereference: assemblyid2 [ctunullpointer] kmer-code-2013-trunk/seatac/heavychains-driver.C:31:25: note: Assignment 'assemblyId2=0L', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:38:14: note: Assuming condition is false kmer-code-2013-trunk/seatac/heavychains-driver.C:68:34: note: Calling function StrandPair, 3rd argument is null kmer-code-2013-trunk/seatac/heavychains.H:54:26: note: Dereferencing argument assemblyid2 that is null kmer-code-2013-trunk/seatac/heavychains.H:169:26: error: Null pointer dereference: assemblyid1 [ctunullpointer] kmer-code-2013-trunk/seatac/heavychains-driver.C:30:25: note: Assignment 'assemblyId1=0L', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:38:14: note: Assuming condition is false kmer-code-2013-trunk/seatac/heavychains-driver.C:69:32: note: Calling function TheStats, 2nd argument is null kmer-code-2013-trunk/seatac/heavychains.H:169:26: note: Dereferencing argument assemblyid1 that is null kmer-code-2013-trunk/seatac/heavychains.H:170:26: error: Null pointer dereference: assemblyid2 [ctunullpointer] kmer-code-2013-trunk/seatac/heavychains-driver.C:31:25: note: Assignment 'assemblyId2=0L', assigned value is 0 kmer-code-2013-trunk/seatac/heavychains-driver.C:38:14: note: Assuming condition is false kmer-code-2013-trunk/seatac/heavychains-driver.C:69:32: note: Calling function TheStats, 3rd argument is null kmer-code-2013-trunk/seatac/heavychains.H:170:26: note: Dereferencing argument assemblyid2 that is null diff: 2.18.0 kmer-code-2013-trunk/ESTmapper/terminate.C:32:7: warning: Class 'iidReaderWriter' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/ESTmapper/terminate.C:32:7: warning: Class 'iidReaderWriter' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/ESTmapper/terminate.C:32:7: warning: Class 'iidReaderWriter' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/ESTmapper/terminate.C:32:7: warning: Class 'iidReaderWriter' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/atac-driver/matchExtender/match.H:43:5: warning: Class 'match_s' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/atac-driver/matchExtender/match.H:43:5: warning: Class 'match_s' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/atac-driver/matchExtender/match.H:43:5: warning: Class 'match_s' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/atac-driver/matchExtender/match.H:43:5: warning: Class 'match_s' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libbio/kmer.C:141:5: warning: Class 'kMerBuilder' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libbio/kmer.C:141:5: warning: Class 'kMerBuilder' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libbio/kmer.C:141:5: warning: Class 'kMerBuilder' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libbio/kmer.C:141:5: warning: Class 'kMerBuilder' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libbio/merList.H:11:5: warning: Class 'merList' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libbio/merList.H:11:5: warning: Class 'merList' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libbio/merList.H:11:5: warning: Class 'merList' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libbio/merList.H:11:5: warning: Class 'merList' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libseq/fastaStdin.C:17:5: warning: Class 'fastaStdin' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libseq/fastaStdin.C:17:5: warning: Class 'fastaStdin' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libseq/fastaStdin.C:17:5: warning: Class 'fastaStdin' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libseq/fastaStdin.C:17:5: warning: Class 'fastaStdin' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libseq/fastqStdin.C:17:5: warning: Class 'fastqStdin' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libseq/fastqStdin.C:17:5: warning: Class 'fastqStdin' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libseq/fastqStdin.C:17:5: warning: Class 'fastqStdin' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libseq/fastqStdin.C:17:5: warning: Class 'fastqStdin' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] head kmer-code-2013-trunk/libseq/merStream.C:21:26: warning: Class 'merStream' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] head kmer-code-2013-trunk/libseq/merStream.C:21:26: warning: Class 'merStream' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libseq/seqFactory.C:15:3: warning: Class 'seqFactory' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libseq/seqFactory.C:15:3: warning: Class 'seqFactory' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libseq/seqFactory.C:15:3: warning: Class 'seqFactory' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libseq/seqFactory.C:15:3: warning: Class 'seqFactory' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libseq/sffFile.C:17:3: warning: Class 'sffFile' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libseq/sffFile.C:17:3: warning: Class 'sffFile' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libseq/sffFile.C:17:3: warning: Class 'sffFile' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libseq/sffFile.C:17:3: warning: Class 'sffFile' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libsim4/sim4core/exon.H:125:5: warning: Class 'exonManager' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libsim4/sim4core/exon.H:125:5: warning: Class 'exonManager' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libsim4/sim4core/exon.H:125:5: warning: Class 'exonManager' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libsim4/sim4core/exon.H:125:5: warning: Class 'exonManager' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libsim4/sim4core/mspManager.C:19:3: warning: Class 'mspManager' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libsim4/sim4core/mspManager.C:19:3: warning: Class 'mspManager' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libsim4/sim4core/mspManager.C:19:3: warning: Class 'mspManager' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libsim4/sim4core/mspManager.C:19:3: warning: Class 'mspManager' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] head kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:120:12: warning: Class 'sim4command' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] head kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:120:12: warning: Class 'sim4command' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:16:3: warning: Class 'sim4polishBuilder' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:16:3: warning: Class 'sim4polishBuilder' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:16:3: warning: Class 'sim4polishBuilder' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:16:3: warning: Class 'sim4polishBuilder' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.C:20:3: warning: Class 'sim4polishList' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.C:20:3: warning: Class 'sim4polishList' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.C:20:3: warning: Class 'sim4polishList' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.C:20:3: warning: Class 'sim4polishList' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libsim4/sim4polish/sim4polishReader.C:18:5: warning: Class 'sim4polishReader' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libsim4/sim4polish/sim4polishReader.C:18:5: warning: Class 'sim4polishReader' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libsim4/sim4polish/sim4polishReader.C:18:5: warning: Class 'sim4polishReader' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libsim4/sim4polish/sim4polishReader.C:18:5: warning: Class 'sim4polishReader' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.C:36:5: warning: Class 'sim4polishWriter' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.C:36:5: warning: Class 'sim4polishWriter' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.C:36:5: warning: Class 'sim4polishWriter' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.C:36:5: warning: Class 'sim4polishWriter' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] head kmer-code-2013-trunk/libutil/bigQueue.C:88:12: warning: Class 'bigQueue' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] head kmer-code-2013-trunk/libutil/bigQueue.C:88:12: warning: Class 'bigQueue' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libutil/bitPackedArray.C:18:3: warning: Class 'bitPackedArray' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libutil/bitPackedArray.C:18:3: warning: Class 'bitPackedArray' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libutil/bitPackedArray.C:18:3: warning: Class 'bitPackedArray' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libutil/bitPackedArray.C:18:3: warning: Class 'bitPackedArray' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libutil/bitPackedArray.C:85:3: warning: Class 'bitArray' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libutil/bitPackedArray.C:85:3: warning: Class 'bitArray' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libutil/bitPackedArray.C:85:3: warning: Class 'bitArray' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libutil/bitPackedArray.C:85:3: warning: Class 'bitArray' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libutil/bitPackedArray.H:88:5: warning: Class 'bitPackedHeap' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libutil/bitPackedArray.H:88:5: warning: Class 'bitPackedHeap' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libutil/bitPackedArray.H:88:5: warning: Class 'bitPackedHeap' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libutil/bitPackedArray.H:88:5: warning: Class 'bitPackedHeap' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libutil/bitPackedFile.C:16:3: warning: Class 'bitPackedFile' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libutil/bitPackedFile.C:16:3: warning: Class 'bitPackedFile' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libutil/bitPackedFile.C:16:3: warning: Class 'bitPackedFile' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libutil/bitPackedFile.C:16:3: warning: Class 'bitPackedFile' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libutil/logMsg.H:20:5: warning: Class 'logMsg' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libutil/logMsg.H:20:5: warning: Class 'logMsg' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libutil/logMsg.H:20:5: warning: Class 'logMsg' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libutil/logMsg.H:20:5: warning: Class 'logMsg' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libutil/readBuffer.C:69:3: warning: Class 'readBuffer' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libutil/readBuffer.C:69:3: warning: Class 'readBuffer' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libutil/readBuffer.C:69:3: warning: Class 'readBuffer' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libutil/readBuffer.C:69:3: warning: Class 'readBuffer' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libutil/recordFile.C:22:3: warning: Class 'recordFile' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libutil/recordFile.C:22:3: warning: Class 'recordFile' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libutil/recordFile.C:22:3: warning: Class 'recordFile' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libutil/recordFile.C:22:3: warning: Class 'recordFile' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/libutil/uint32List.H:17:5: warning: Class 'uint32List' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/libutil/uint32List.H:17:5: warning: Class 'uint32List' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/libutil/uint32List.H:17:5: warning: Class 'uint32List' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/libutil/uint32List.H:17:5: warning: Class 'uint32List' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/meryl/asmMerQC-regions.C:269:3: warning: Class 'intervalList' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/meryl/asmMerQC-regions.C:269:3: warning: Class 'intervalList' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/meryl/asmMerQC-regions.C:656:3: warning: Class 'intervalDepth' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/meryl/asmMerQC-regions.C:656:3: warning: Class 'intervalDepth' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/meryl/asmMerQC-regions.C:656:3: warning: Class 'intervalDepth' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/meryl/asmMerQC-regions.C:656:3: warning: Class 'intervalDepth' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] head kmer-code-2013-trunk/seagen/sortHits.C:110:12: warning: Class 'aHitTemporary' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] head kmer-code-2013-trunk/seagen/sortHits.C:110:12: warning: Class 'aHitTemporary' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/seagen/sortHits.C:28:5: warning: Class 'aHitReader' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/seagen/sortHits.C:28:5: warning: Class 'aHitReader' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/seagen/sortHits.C:28:5: warning: Class 'aHitReader' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/seagen/sortHits.C:28:5: warning: Class 'aHitReader' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] head kmer-code-2013-trunk/seatac/filter-heavychains.C:94:14: warning: Class 'StrandPairManager' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] head kmer-code-2013-trunk/seatac/filter-heavychains.C:94:14: warning: Class 'StrandPairManager' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/seatac/heavychains.H:308:5: warning: Class 'DPTree' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/seatac/heavychains.H:308:5: warning: Class 'DPTree' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/seatac/heavychains.H:308:5: warning: Class 'DPTree' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/seatac/heavychains.H:308:5: warning: Class 'DPTree' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] 2.18.0 kmer-code-2013-trunk/seatac/heavychains.H:60:5: warning: Class 'StrandPair' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] head kmer-code-2013-trunk/seatac/heavychains.H:60:5: warning: Class 'StrandPair' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] 2.18.0 kmer-code-2013-trunk/seatac/heavychains.H:60:5: warning: Class 'StrandPair' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] head kmer-code-2013-trunk/seatac/heavychains.H:60:5: warning: Class 'StrandPair' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] DONE