2025-11-23 17:52
ftp://ftp.de.debian.org/debian/pool/main/r/r-bioc-cner/r-bioc-cner_1.42.0+dfsg.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j4
platform: Linux-5.4.0-216-generic-x86_64-with-glibc2.29
python: 3.8.10
client-version: 1.3.69
compiler: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
cppcheck: head 2.18.0
head-info: cb76e52 (2025-11-22 14:47:37 +0100)
count: 736 723
elapsed-time: 10.4 12.4
head-timing-info:

old-timing-info:

head results:
CNEr/inst/obsolete/alignment.c:57:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
CNEr/inst/obsolete/alignment.c:34:19: style: Variable 'cpStartTarget' is assigned a value that is never used. [unreadVariable]
CNEr/inst/obsolete/alignment.c:35:17: style: Variable 'cpEndTarget' is assigned a value that is never used. [unreadVariable]
CNEr/inst/obsolete/alignment.c:47:23: style: Variable 'cpStartTarget' is assigned a value that is never used. [unreadVariable]
CNEr/inst/obsolete/alignment.c:51:21: style: Variable 'cpEndTarget' is assigned a value that is never used. [unreadVariable]
CNEr/inst/obsolete/alignment.c:29:62: style: Unused variable: cpStartQuery [unusedVariable]
CNEr/inst/obsolete/alignment.c:29:76: style: Unused variable: cpEndQuery [unusedVariable]
CNEr/inst/obsolete/src/ceScan.c:129:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
CNEr/inst/obsolete/src/ceScan.c:147:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
CNEr/inst/obsolete/src/ceScan.c:567:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
CNEr/inst/obsolete/src/ceScan.c:589:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PATH_LEN [valueFlowBailoutIncompleteVar]
CNEr/inst/obsolete/src/ceScanBranch1.c:103:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
CNEr/inst/obsolete/src/ceScanBranch2.c:103:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
CNEr/inst/obsolete/src/ceScanBranch1.c:120:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
CNEr/inst/obsolete/src/ceScanBranch2.c:120:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
CNEr/inst/obsolete/src/ceScanBranch1.c:599:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
CNEr/inst/obsolete/src/ceScanBranch2.c:597:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
CNEr/inst/obsolete/src/ceScanBranch1.c:615:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PATH_LEN [valueFlowBailoutIncompleteVar]
CNEr/inst/obsolete/src/ceScanBranch2.c:613:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PATH_LEN [valueFlowBailoutIncompleteVar]
CNEr/inst/obsolete/src/ceScanBranch1.c:797:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PATH_LEN [valueFlowBailoutIncompleteVar]
CNEr/inst/obsolete/src/ceScanBranch2.c:793:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PATH_LEN [valueFlowBailoutIncompleteVar]
CNEr/inst/obsolete/src/ceScanBranch1.c:918:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NamesSymbol [valueFlowBailoutIncompleteVar]
CNEr/inst/obsolete/src/ceScanBranch2.c:853:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/common.h:1212:40: style: Parameter 'buf' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScan.c:236:37: style: Parameter 'hel' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScan.c:240:17: style: Variable 'ranges' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScan.c:290:17: style: Variable 'arrayEl' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScan.c:356:45: style: Parameter 'axt' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScan.c:381:86: style: Parameter 'profile' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScan.c:381:100: style: Parameter 'tPosList' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScan.c:381:115: style: Parameter 'qPosList' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScan.c:456:17: style: Variable 'tFilter' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScan.c:457:17: style: Variable 'qFilter' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScan.c:305:27: style: Variable 'arrayEl' is assigned a value that is never used. [unreadVariable]
CNEr/inst/obsolete/src/ceScanBranch2.c:356:10: warning: If memory allocation fails, then there is a possible null pointer dereference: holdCigar [nullPointerOutOfMemory]
CNEr/inst/obsolete/src/ceScanBranch2.c:354:36: note: Assuming allocation function fails
CNEr/inst/obsolete/src/ceScanBranch2.c:354:21: note: Assignment 'holdCigar=(char*)malloc(sizeof(char)*1000)', assigned value is 0
CNEr/inst/obsolete/src/ceScanBranch2.c:356:10: note: Null pointer dereference
CNEr/inst/obsolete/src/ceScanBranch2.c:710:12: warning: If memory allocation fails, then there is a possible null pointer dereference: tName [nullPointerOutOfMemory]
CNEr/inst/obsolete/src/ceScanBranch2.c:709:34: note: Assuming allocation function fails
CNEr/inst/obsolete/src/ceScanBranch2.c:709:19: note: Assignment 'tName=(char*)malloc(sizeof(char)*strlen(CHAR(STRING_ELT(tNames,i))))', assigned value is 0
CNEr/inst/obsolete/src/ceScanBranch2.c:710:12: note: Null pointer dereference
CNEr/src/io.c:13:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NA_STRING [valueFlowBailoutIncompleteVar]
CNEr/inst/obsolete/src/ceScanBranch2.c:734:12: warning: If memory allocation fails, then there is a possible null pointer dereference: name [nullPointerOutOfMemory]
CNEr/inst/obsolete/src/ceScanBranch2.c:733:33: note: Assuming allocation function fails
CNEr/inst/obsolete/src/ceScanBranch2.c:733:18: note: Assignment 'name=(char*)malloc(sizeof(char)*strlen(CHAR(STRING_ELT(names,i))))', assigned value is 0
CNEr/inst/obsolete/src/ceScanBranch2.c:734:12: note: Null pointer dereference
CNEr/inst/obsolete/src/ceScanBranch2.c:205:37: style: Parameter 'hel' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:209:17: style: Variable 'ranges' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:258:17: style: Variable 'arrayEl' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:302:45: style: Parameter 'axt' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:326:52: style: Parameter 'axt' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:361:86: style: Parameter 'profile' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:361:100: style: Parameter 'tPosList' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:361:115: style: Parameter 'qPosList' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:403:80: style: Parameter 'profile' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:403:94: style: Parameter 'tPosList' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:403:109: style: Parameter 'qPosList' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:485:17: style: Variable 'tFilter' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:486:17: style: Variable 'qFilter' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:610:76: style: Parameter 'winSize' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:610:90: style: Parameter 'minScore' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:610:105: style: Parameter 'nThresholds' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:610:140: style: Parameter 'nrAxtFiles' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:632:36: style: Parameter 'hel' can be declared as pointer to const. However it seems that 'freeRangeArray' is a callback function, if 'hel' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
CNEr/inst/obsolete/src/ceScanBranch2.c:647:27: note: You might need to cast the function pointer here
CNEr/inst/obsolete/src/ceScanBranch2.c:632:36: note: Parameter 'hel' can be declared as pointer to const
CNEr/inst/obsolete/src/ceScanBranch2.c:697:14: style: Variable 'p_tStarts' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:697:26: style: Variable 'p_tEnds' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:755:11: style: Variable 'p_axtqStart' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:755:25: style: Variable 'p_axtqEnd' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:755:37: style: Variable 'p_axttStart' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:755:51: style: Variable 'p_axttEnd' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:755:63: style: Variable 'p_score' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:755:73: style: Variable 'p_symCount' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:797:8: style: Variable 'p_winSize' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:797:20: style: Variable 'p_minScore' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:72:7: style: struct member 'slAllCNE::minScore' is never used. [unusedStructMember]
CNEr/inst/obsolete/src/ceScanBranch2.c:73:7: style: struct member 'slAllCNE::winSize' is never used. [unusedStructMember]
CNEr/inst/obsolete/src/ceScanBranch1.c:356:10: warning: If memory allocation fails, then there is a possible null pointer dereference: holdCigar [nullPointerOutOfMemory]
CNEr/inst/obsolete/src/ceScanBranch1.c:354:36: note: Assuming allocation function fails
CNEr/inst/obsolete/src/ceScanBranch1.c:354:21: note: Assignment 'holdCigar=(char*)malloc(sizeof(char)*1000)', assigned value is 0
CNEr/inst/obsolete/src/ceScanBranch1.c:356:10: note: Null pointer dereference
CNEr/inst/obsolete/src/ceScanBranch1.c:712:12: warning: If memory allocation fails, then there is a possible null pointer dereference: tName [nullPointerOutOfMemory]
CNEr/inst/obsolete/src/ceScanBranch1.c:711:34: note: Assuming allocation function fails
CNEr/inst/obsolete/src/ceScanBranch1.c:711:19: note: Assignment 'tName=(char*)malloc(sizeof(char)*strlen(CHAR(STRING_ELT(tNames,i))))', assigned value is 0
CNEr/inst/obsolete/src/ceScanBranch1.c:712:12: note: Null pointer dereference
CNEr/inst/obsolete/src/ceScanBranch1.c:737:12: warning: If memory allocation fails, then there is a possible null pointer dereference: name [nullPointerOutOfMemory]
CNEr/inst/obsolete/src/ceScanBranch1.c:736:33: note: Assuming allocation function fails
CNEr/inst/obsolete/src/ceScanBranch1.c:736:18: note: Assignment 'name=(char*)malloc(sizeof(char)*strlen(CHAR(STRING_ELT(names,i))))', assigned value is 0
CNEr/inst/obsolete/src/ceScanBranch1.c:737:12: note: Null pointer dereference
CNEr/inst/obsolete/src/ceScanBranch2.c:74:17: style: struct member 'slAllCNE::CNE' is never used. [unusedStructMember]
CNEr/inst/obsolete/src/ceScanBranch1.c:205:37: style: Parameter 'hel' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:209:17: style: Variable 'ranges' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:258:17: style: Variable 'arrayEl' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:302:45: style: Parameter 'axt' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:326:52: style: Parameter 'axt' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:273:27: style: Variable 'arrayEl' is assigned a value that is never used. [unreadVariable]
CNEr/inst/obsolete/src/ceScanBranch1.c:361:86: style: Parameter 'profile' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:361:100: style: Parameter 'tPosList' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:361:115: style: Parameter 'qPosList' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:403:80: style: Parameter 'profile' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:403:94: style: Parameter 'tPosList' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:403:109: style: Parameter 'qPosList' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:487:17: style: Variable 'tFilter' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:488:17: style: Variable 'qFilter' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:612:76: style: Parameter 'winSize' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:612:90: style: Parameter 'minScore' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:612:105: style: Parameter 'nThresholds' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:612:140: style: Parameter 'nrAxtFiles' can be declared as pointer to const [constParameterPointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:634:36: style: Parameter 'hel' can be declared as pointer to const. However it seems that 'freeRangeArray' is a callback function, if 'hel' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
CNEr/inst/obsolete/src/ceScanBranch1.c:649:27: note: You might need to cast the function pointer here
CNEr/inst/obsolete/src/ceScanBranch1.c:634:36: note: Parameter 'hel' can be declared as pointer to const
CNEr/inst/obsolete/src/ceScanBranch1.c:699:14: style: Variable 'p_tStarts' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:611:10: style: Unused variable: n [unusedVariable]
CNEr/inst/obsolete/src/ceScanBranch1.c:699:26: style: Variable 'p_tEnds' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:613:8: style: Unused variable: rest [unusedVariable]
CNEr/inst/obsolete/src/ceScanBranch1.c:759:11: style: Variable 'p_axtqStart' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:666:23: style: Unused variable: thresholds [unusedVariable]
CNEr/inst/obsolete/src/ceScanBranch1.c:759:25: style: Variable 'p_axtqEnd' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:667:17: style: Unused variable: CNE [unusedVariable]
CNEr/inst/obsolete/src/ceScanBranch1.c:759:37: style: Variable 'p_axttStart' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:759:51: style: Variable 'p_axttEnd' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:759:63: style: Variable 'p_score' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:759:73: style: Variable 'p_symCount' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:801:8: style: Variable 'p_winSize' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch1.c:801:20: style: Variable 'p_minScore' can be declared as pointer to const [constVariablePointer]
CNEr/inst/obsolete/src/ceScanBranch2.c:713:11: style: Variable 'hel' is assigned a value that is never used. [unreadVariable]
CNEr/inst/obsolete/src/ceScanBranch2.c:793:8: style: Unused variable: path [unusedVariable]
CNEr/inst/obsolete/src/ceScanBranch2.c:827:16: style: Variable 'nrThresholds' is assigned a value that is never used. [unreadVariable]
CNEr/inst/obsolete/src/ceScanBranch2.c:823:41: style: Unused variable: curThresholds [unusedVariable]
CNEr/inst/obsolete/src/ceScanBranch2.c:824:17: style: Unused variable: CNE [unusedVariable]
CNEr/inst/obsolete/src/ceScanBranch2.c:828:7: style: Unused variable: i [unusedVariable]
CNEr/inst/obsolete/src/ceScanBranch1.c:72:7: style: struct member 'slAllCNE::minScore' is never used. [unusedStructMember]
CNEr/src/ceScan.c:886:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
CNEr/inst/obsolete/src/ceScanBranch1.c:73:7: style: struct member 'slAllCNE::winSize' is never used. [unusedStructMember]
CNEr/src/ceScan.c:941:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
CNEr/inst/obsolete/src/ceScanBranch1.c:74:17: style: struct member 'slAllCNE::CNE' is never used. [unusedStructMember]
CNEr/inst/obsolete/src/ceScanBranch1.c:273:27: style: Variable 'arrayEl' is assigned a value that is never used. [unreadVariable]
CNEr/inst/obsolete/src/ceScanBranch1.c:613:10: style: Unused variable: n [unusedVariable]
CNEr/inst/obsolete/src/ceScanBranch1.c:615:8: style: Unused variable: rest [unusedVariable]
CNEr/inst/obsolete/src/ceScanBranch1.c:668:23: style: Unused variable: thresholds [unusedVariable]
CNEr/inst/obsolete/src/ceScanBranch1.c:669:17: style: Unused variable: CNE [unusedVariable]
CNEr/inst/obsolete/src/ceScanBranch1.c:715:11: style: Variable 'hel' is assigned a value that is never used. [unreadVariable]
CNEr/inst/obsolete/src/ceScanBranch1.c:797:8: style: Unused variable: path [unusedVariable]
CNEr/inst/obsolete/src/ceScanBranch1.c:849:17: style: Variable 'curThresholds' is assigned a value that is never used. [unreadVariable]
CNEr/inst/obsolete/src/ceScanBranch1.c:832:125: style: Unused variable: cigarWidth [unusedVariable]
CNEr/src/ucsc/_portimpl.c:52:36: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/_cheapcgi.c:26:15: warning: %x in format string (no. 1) requires 'unsigned int *' but the argument type is 'signed int *'. [invalidScanfArgType_int]
CNEr/src/ucsc/_cheapcgi.c:45:27: style: Variable 'in' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/base64.c:68:27: style: Redundant initialization for 'c'. The initialized value is overwritten before it is read. [redundantInitialization]
CNEr/src/ucsc/base64.c:67:12: note: c is initialized
CNEr/src/ucsc/base64.c:68:27: note: c is overwritten
CNEr/src/ucsc/base64.c:101:9: style: Local variable 'i' shadows outer variable [shadowVariable]
CNEr/src/ucsc/base64.c:95:8: note: Shadowed declaration
CNEr/src/ucsc/base64.c:101:9: note: Shadow variable
CNEr/src/ucsc/base64.c:15:6: style: Variable 'b64' can be declared as const array [constVariable]
CNEr/src/ucsc/base64.c:21:16: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/base64.c:91:6: style: Variable 'b64' can be declared as const array [constVariable]
CNEr/src/ucsc/base64.c:97:7: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/base64.c:20:10: style: Variable 'word' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/base64.c:96:10: style: Variable 'word' is assigned a value that is never used. [unreadVariable]
CNEr/src/io.c:94:26: style: Unused variable: curAxt [unusedVariable]
CNEr/src/ceScan.c:311:10: warning: If memory allocation fails, then there is a possible null pointer dereference: holdCigar [nullPointerOutOfMemory]
CNEr/src/ceScan.c:310:36: note: Assuming allocation function fails
CNEr/src/ceScan.c:310:21: note: Assignment 'holdCigar=(char*)malloc(sizeof(char)*1000)', assigned value is 0
CNEr/src/ceScan.c:311:10: note: Null pointer dereference
CNEr/src/ceScan.c:718:12: warning: If memory allocation fails, then there is a possible null pointer dereference: tName [nullPointerOutOfMemory]
CNEr/src/ceScan.c:716:34: note: Assuming allocation function fails
CNEr/src/ceScan.c:716:19: note: Assignment 'tName=(char*)malloc(sizeof(char)*(strlen(CHAR(STRING_ELT(tNames,i)))+1))', assigned value is 0
CNEr/src/ceScan.c:718:12: note: Null pointer dereference
CNEr/src/ceScan.c:741:12: warning: If memory allocation fails, then there is a possible null pointer dereference: name [nullPointerOutOfMemory]
CNEr/src/ceScan.c:739:33: note: Assuming allocation function fails
CNEr/src/ceScan.c:739:18: note: Assignment 'name=(char*)malloc(sizeof(char)*(strlen(CHAR(STRING_ELT(names,i)))+1))', assigned value is 0
CNEr/src/ceScan.c:741:12: note: Null pointer dereference
CNEr/src/ceScan.c:150:17: style: Variable 'ranges' can be declared as pointer to const [constVariablePointer]
CNEr/src/ceScan.c:202:17: style: Variable 'arrayEl' can be declared as pointer to const [constVariablePointer]
CNEr/src/ceScan.c:248:45: style: Parameter 'axt' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:273:52: style: Parameter 'axt' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:319:31: style: Parameter 'profile' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:319:45: style: Parameter 'tPosList' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:319:60: style: Parameter 'qPosList' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:369:31: style: Parameter 'profile' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:369:45: style: Parameter 'tPosList' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:369:60: style: Parameter 'qPosList' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/bits.c:65:22: style: Parameter 'orig' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:471:17: style: Variable 'tFilter' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/bits.c:97:38: style: Parameter 'orig' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:472:17: style: Variable 'qFilter' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/bits.c:143:26: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:611:10: style: Parameter 'winSize' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/bits.c:149:25: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:611:24: style: Parameter 'minScore' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/bits.c:250:28: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:611:39: style: Parameter 'nThresholds' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/bits.c:261:23: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:612:27: style: Parameter 'nrAxtFiles' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/bits.c:261:32: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:702:14: style: Variable 'p_tStarts' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/bits.c:274:27: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:702:26: style: Variable 'p_tEnds' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/bits.c:285:22: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:736:11: style: Variable 'p_sizes' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/bits.c:285:31: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:765:11: style: Variable 'p_axtqStart' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/bits.c:298:28: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:765:25: style: Variable 'p_axtqEnd' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/bits.c:308:23: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:765:37: style: Variable 'p_axttStart' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/bits.c:308:32: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
CNEr/src/ceScan.c:765:51: style: Variable 'p_axttEnd' can be declared as pointer to const [constVariablePointer]
CNEr/src/ceScan.c:766:8: style: Variable 'p_score' can be declared as pointer to const [constVariablePointer]
CNEr/src/ceScan.c:766:18: style: Variable 'p_symCount' can be declared as pointer to const [constVariablePointer]
CNEr/src/ceScan.c:824:8: style: Variable 'p_winSize' can be declared as pointer to const [constVariablePointer]
CNEr/src/ceScan.c:824:20: style: Variable 'p_minScore' can be declared as pointer to const [constVariablePointer]
CNEr/src/ceScan.c:217:27: style: Variable 'arrayEl' is assigned a value that is never used. [unreadVariable]
CNEr/src/ceScan.c:613:10: style: Unused variable: n [unusedVariable]
CNEr/src/ceScan.c:615:8: style: Unused variable: rest [unusedVariable]
CNEr/src/ceScan.c:673:23: style: Unused variable: thresholds [unusedVariable]
CNEr/src/ceScan.c:674:17: style: Unused variable: CNE [unusedVariable]
CNEr/src/ceScan.c:721:11: style: Variable 'hel' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/axt.c:116:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
CNEr/src/ceScan.c:865:17: style: Unused variable: CNE [unusedVariable]
CNEr/src/ceScan.c:868:7: style: Unused variable: nrCNE [unusedVariable]
CNEr/src/ceScan.c:868:28: style: Unused variable: i [unusedVariable]
CNEr/src/ceScan.c:898:20: style: Variable 'nrThresholds' is assigned a value that is never used. [unreadVariable]
CNEr/src/ceScan.c:898:7: style: Variable 'nrThresholds' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/binRange.c:127:10: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
CNEr/src/ucsc/binRange.c:128:8: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
CNEr/src/ucsc/binRange.c:196:52: style: Parameter 'bk' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/binRange.c:229:47: style: Parameter 'bk' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/binRange.c:232:20: style: Variable 'el' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/binRange.c:260:44: style: Parameter 'bk' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/binRange.c:261:8: style: Parameter 'oldVal' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/binRange.c:309:58: style: Parameter 'bk' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/binRange.c:344:70: style: Parameter 'val' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/chain.c:636:5: warning: Either the condition 'chain==NULL' is redundant or there is possible null pointer dereference: chain. [nullPointerRedundantCheck]
CNEr/src/ucsc/chain.c:634:11: note: Assuming that condition 'chain==NULL' is not redundant
CNEr/src/ucsc/chain.c:636:5: note: Null pointer dereference
CNEr/src/ucsc/chain.c:367:19: style: Local variable 'old' shadows outer variable [shadowVariable]
CNEr/src/ucsc/chain.c:351:14: note: Shadowed declaration
CNEr/src/ucsc/chain.c:367:19: note: Shadow variable
CNEr/src/ucsc/chain.c:94:54: style: Parameter 'qSym' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/chain.c:94:66: style: Parameter 'tSym' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/chain.c:630:42: style: Parameter 'chain' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:280:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/cheapcgi.c:530:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/cheapcgi.c:2093:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/axt.c:186:55: style: Parameter 'q' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/axt.c:186:64: style: Parameter 't' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/axt.c:196:64: style: Parameter 'qSym' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/axt.c:196:76: style: Parameter 'tSym' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/axt.c:244:77: style: Parameter 'qSym' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/axt.c:244:89: style: Parameter 'tSym' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/axt.c:334:11: style: Variable 'tSymEnd' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/axt.c:390:7: style: Variable 'tSym' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/axt.c:618:12: style: Variable 'letter' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/axt.c:636:12: style: Variable 's' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/axt.c:706:12: style: Variable 'trans' can be declared as const array [constVariable]
CNEr/src/ucsc/axt.c:768:71: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/axt.c:861:65: style: Parameter 'axt' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/axt.c:908:33: style: Parameter 'ss' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/axt.c:974:34: style: Parameter 'axt' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/axt.c:993:32: style: Parameter 'axt' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dlist.c:191:28: style: Parameter 'list' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dlist.c:292:55: style: Parameter 'val' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnaseq.c:28:43: style:inconclusive: Function 'cloneDnaSeq' argument 1 names different: declaration 'seq' definition 'orig'. [funcArgNamesDifferent]
CNEr/src/ucsc/dnaseq.h:33:43: note: Function 'cloneDnaSeq' argument 1 names different: declaration 'seq' definition 'orig'.
CNEr/src/ucsc/dnaseq.c:28:43: note: Function 'cloneDnaSeq' argument 1 names different: declaration 'seq' definition 'orig'.
CNEr/src/ucsc/dnaseq.c:86:70: style:inconclusive: Function 'translateSeqN' argument 3 names different: declaration 'size' definition 'inSize'. [funcArgNamesDifferent]
CNEr/src/ucsc/dnaseq.h:44:70: note: Function 'translateSeqN' argument 3 names different: declaration 'size' definition 'inSize'.
CNEr/src/ucsc/dnaseq.c:86:70: note: Function 'translateSeqN' argument 3 names different: declaration 'size' definition 'inSize'.
CNEr/src/ucsc/dnaseq.c:14:52: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnaseq.c:72:7: style: Variable 'poly' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/dnaseq.c:131:55: style: Parameter 'letters' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnaseq.c:152:7: style: Variable 'poly' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/common.c:2417:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/common.c:2571:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_WRONLY [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/common.c:2609:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/common.c:2692:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/common.c:3083:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/common.c:3307:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/dystring.c:196:64: warning: Either the condition 'orig==NULL' is redundant or there is possible null pointer dereference: orig. [nullPointerRedundantCheck]
CNEr/src/ucsc/dystring.c:200:10: note: Assuming that condition 'orig==NULL' is not redundant
CNEr/src/ucsc/dystring.c:196:64: note: Null pointer dereference
CNEr/src/ucsc/dystring.c:72:49: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dystring.c:130:7: style: Variable 's' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/dystring.c:139:50: style: Parameter 'format' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dystring.c:192:49: style: Parameter 'in' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dystring.c:235:68: style: Parameter 'text' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dystring.c:148:5: error: va_list 'argscp' used before va_start() was called. [va_list_usedBeforeStarted]
CNEr/src/ucsc/dystring.c:157:64: error: va_list 'argscp' used before va_start() was called. [va_list_usedBeforeStarted]
CNEr/src/ucsc/dystring.c:158:5: error: va_list 'argscp' used before va_start() was called. [va_list_usedBeforeStarted]
CNEr/src/ucsc/errabort.c:54:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/errabort.c:127:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/errabort.c:211:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/errabort.c:249:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/errabort.c:304:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PTHREAD_MUTEX_INITIALIZER [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/errabort.c:105:13: style: Condition 'strings==NULL' is always true [knownConditionTrueFalse]
CNEr/src/ucsc/errabort.c:93:18: note: Assignment 'strings=NULL', assigned value is 0
CNEr/src/ucsc/errabort.c:105:13: note: Condition 'strings==NULL' is always true
CNEr/src/ucsc/errabort.c:50:33: style: Parameter 'format' can be declared as pointer to const. However it seems that 'defaultVaWarn' is a callback function, if 'format' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
CNEr/src/ucsc/errabort.c:326:26: note: You might need to cast the function pointer here
CNEr/src/ucsc/errabort.c:50:33: note: Parameter 'format' can be declared as pointer to const
CNEr/src/ucsc/errabort.c:60:32: style: Parameter 'format' can be declared as pointer to const. However it seems that 'silentVaWarn' is a callback function, if 'format' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
CNEr/src/ucsc/errabort.c:276:17: note: You might need to cast the function pointer here
CNEr/src/ucsc/errabort.c:60:32: note: Parameter 'format' can be declared as pointer to const
CNEr/src/ucsc/errabort.c:291:28: style: Variable 'ptav' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:2079:6: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
CNEr/src/ucsc/cheapcgi.c:2080:17: style: Obsolete function 'asctime' called. It is recommended to use 'strftime' instead. [prohibitedasctimeCalled]
CNEr/src/ucsc/cheapcgi.c:851:13: warning: %x in format string (no. 1) requires 'unsigned int *' but the argument type is 'signed int *'. [invalidScanfArgType_int]
CNEr/src/ucsc/cheapcgi.c:325:3: warning: Either the condition '!s' is redundant or there is possible null pointer dereference: s. [nullPointerRedundantCheck]
CNEr/src/ucsc/cheapcgi.c:323:6: note: Assuming that condition '!s' is not redundant
CNEr/src/ucsc/cheapcgi.c:325:3: note: Null pointer dereference
CNEr/src/ucsc/cheapcgi.c:329:3: warning: Either the condition '!s' is redundant or there is possible null pointer dereference: s. [nullPointerRedundantCheck]
CNEr/src/ucsc/cheapcgi.c:327:6: note: Assuming that condition '!s' is not redundant
CNEr/src/ucsc/cheapcgi.c:329:3: note: Null pointer dereference
CNEr/src/ucsc/cheapcgi.c:487:12: warning: Either the condition 'dataPt==NULL' is redundant or there is possible null pointer dereference: dataPt++. [nullPointerRedundantCheck]
CNEr/src/ucsc/cheapcgi.c:484:16: note: Assuming that condition 'dataPt==NULL' is not redundant
CNEr/src/ucsc/cheapcgi.c:487:12: note: Null pointer dereference
CNEr/src/ucsc/cheapcgi.c:599:12: warning: Either the condition 'dataPt==NULL' is redundant or there is possible null pointer dereference: dataPt++. [nullPointerRedundantCheck]
CNEr/src/ucsc/cheapcgi.c:595:16: note: Assuming that condition 'dataPt==NULL' is not redundant
CNEr/src/ucsc/cheapcgi.c:599:12: note: Null pointer dereference
CNEr/src/ucsc/cheapcgi.c:487:12: warning: Either the condition 'dataPt==NULL' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
CNEr/src/ucsc/cheapcgi.c:484:16: note: Assuming that condition 'dataPt==NULL' is not redundant
CNEr/src/ucsc/cheapcgi.c:487:12: note: Null pointer addition
CNEr/src/ucsc/cheapcgi.c:599:12: warning: Either the condition 'dataPt==NULL' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
CNEr/src/ucsc/cheapcgi.c:595:16: note: Assuming that condition 'dataPt==NULL' is not redundant
CNEr/src/ucsc/cheapcgi.c:599:12: note: Null pointer addition
CNEr/src/ucsc/hash.c:614:50: debug: Function::addArguments found argument 'freeFunc' with varid 0. [varid0]
CNEr/src/ucsc/cheapcgi.c:359:75: style: Local variable 'ct' shadows outer variable [shadowVariable]
CNEr/src/ucsc/cheapcgi.c:301:18: note: Shadowed declaration
CNEr/src/ucsc/cheapcgi.c:359:75: note: Shadow variable
CNEr/src/ucsc/cheapcgi.c:35:16: style: Variable 'v' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:135:14: style: Variable 'clientBrowserExtra' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:136:14: style: Variable 'clientOsExtra' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:255:7: style: Variable 's' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:359:75: style: Variable 'ct' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:389:8: style: Variable 'lastPathSep' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:530:11: style: Variable 'val' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:548:7: style: Variable 'qs' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:554:7: style: Variable 'cl' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:754:16: style: Variable 'var' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:787:25: style: Variable 'in' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:870:25: style: Variable 'in' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:916:25: style: Variable 'in' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:1103:33: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1103:45: style: Parameter 'value' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1103:58: style: Parameter 'msg' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1111:37: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1111:49: style: Parameter 'value' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1111:62: style: Parameter 'msg' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1111:73: style: Parameter 'onClick' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1125:33: style: Parameter 'command' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1125:48: style: Parameter 'value' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1131:39: style: Parameter 'command' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1131:54: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1131:66: style: Parameter 'value' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1139:34: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1139:46: style: Parameter 'value' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1148:29: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1197:26: style: Parameter 'text' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1203:33: style: Parameter 'text' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1203:45: style: Parameter 'msg' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1211:25: style: Parameter 'text' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1217:31: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1217:43: style: Parameter 'value' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1226:38: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1226:50: style: Parameter 'value' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1227:47: style: Parameter 'command' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1254:50: style: Parameter 'moreHtml' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1324:81: style: Parameter 'id' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1325:50: style: Parameter 'moreHtml' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1370:39: style: Parameter 'varName' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1370:54: style: Parameter 'initialVal' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1379:37: style: Parameter 'varName' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1379:52: style: Parameter 'initialVal' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1380:16: style: Parameter 'script' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1404:40: style: Parameter 'varName' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1404:55: style: Parameter 'initialVal' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1404:84: style: Parameter 'extra' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1421:26: style: Parameter 'varName' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1430:33: style: Parameter 'varName' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1430:64: style: Parameter 'title' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1431:33: style: Parameter 'min' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1431:44: style: Parameter 'max' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1506:29: style: Parameter 'varName' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1515:36: style: Parameter 'varName' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1515:70: style: Parameter 'title' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1516:36: style: Parameter 'min' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1516:47: style: Parameter 'max' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1582:55: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1583:44: style: Parameter 'class' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1583:57: style: Parameter 'style' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1583:69: style: Parameter 'javascript' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1587:7: style: Variable 'selString' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:1643:7: style: Variable 'selString' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:1695:32: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1696:61: style: Parameter 'extraAttribs' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1700:7: style: Variable 'selString' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:1802:36: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1802:48: style: Parameter 'menu' can be declared as const array [constParameter]
CNEr/src/ucsc/cheapcgi.c:1808:7: style: Variable 'selString' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:1823:44: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1823:56: style: Parameter 'text' can be declared as const array [constParameter]
CNEr/src/ucsc/cheapcgi.c:1824:71: style: Parameter 'extra' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1828:7: style: Variable 'selString' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:1849:38: style: Parameter 'varName' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1849:53: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1849:66: style: Parameter 'extra' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:1905:37: style: Parameter 'val' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/cheapcgi.c:2072:7: style: Variable 'ip' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:2074:7: style: Variable 'requestUri' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:2075:7: style: Variable 'hgsid' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:2076:7: style: Variable 'cgiFileName' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:2078:12: style: Variable 'tm' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/cheapcgi.c:361:8: style: Variable 'ct' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/cheapcgi.c:1736:17: style: Variable 'checked' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/dnautil.c:607:27: style:inconclusive: Function 'aaFilteredSize' argument 1 names different: declaration 'rawDna' definition 'raw'. [funcArgNamesDifferent]
CNEr/src/ucsc/dnautil.h:157:27: note: Function 'aaFilteredSize' argument 1 names different: declaration 'rawDna' definition 'raw'.
CNEr/src/ucsc/dnautil.c:607:27: note: Function 'aaFilteredSize' argument 1 names different: declaration 'rawDna' definition 'raw'.
CNEr/src/ucsc/dnautil.c:199:21: style: Parameter 'dna' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:267:25: style: Parameter 'dna' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:288:21: style: Parameter 'start' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:477:24: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:477:32: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:525:24: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:551:32: style: Parameter 'raw' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:551:42: style: Parameter 'filter' can be declared as const array [constParameter]
CNEr/src/ucsc/dnautil.c:564:26: style: Parameter 'in' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:564:46: style: Parameter 'filter' can be declared as const array [constParameter]
CNEr/src/ucsc/dnautil.c:588:25: style: Parameter 'in' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:646:28: style: Parameter 'dna' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:659:28: style: Parameter 'dna' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:674:23: style: Parameter 'in' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:689:22: style: Parameter 'in' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:704:21: style: Parameter 'in' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:719:24: style: Parameter 'tiles' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:737:24: style: Parameter 'tiles' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:767:35: style: Parameter 'iStart' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:767:48: style: Parameter 'iEnd' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:802:30: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:802:39: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:1005:21: style: Parameter 'poly' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:1020:24: style: Parameter 'poly' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/dnautil.c:971:11: style: Variable 'pastPoly' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/hash.c:266:8: warning: Either the condition 'hel==NULL' is redundant or there is possible null pointer dereference: hel. [nullPointerRedundantCheck]
CNEr/src/ucsc/hash.c:264:9: note: Assuming that condition 'hel==NULL' is not redundant
CNEr/src/ucsc/hash.c:266:8: note: Null pointer dereference
CNEr/src/ucsc/hash.c:305:8: warning: Either the condition 'hel==NULL' is redundant or there is possible null pointer dereference: hel. [nullPointerRedundantCheck]
CNEr/src/ucsc/hash.c:303:9: note: Assuming that condition 'hel==NULL' is not redundant
CNEr/src/ucsc/hash.c:305:8: note: Null pointer dereference
CNEr/src/ucsc/hash.c:312:31: error: Pointer addition with NULL pointer. [nullPointerArithmetic]
CNEr/src/ucsc/hash.c:311:12: note: Assignment 'pt=NULL', assigned value is 0
CNEr/src/ucsc/hash.c:312:31: note: Null pointer addition
CNEr/src/ucsc/hash.c:524:5: style: 'continue' is redundant since it is the last statement in a loop. [redundantContinue]
CNEr/src/ucsc/hash.c:547:9: style: 'continue' is redundant since it is the last statement in a loop. [redundantContinue]
CNEr/src/ucsc/hash.c:404:20: style: Local variable 'hel' shadows outer variable [shadowVariable]
CNEr/src/ucsc/hash.c:390:16: note: Shadowed declaration
CNEr/src/ucsc/hash.c:404:20: note: Shadow variable
CNEr/src/ucsc/hash.c:44:7: style: Variable 'keyStr' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/hash.c:58:16: style: Variable 'us' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/hash.c:263:16: style: Variable 'hel' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/hash.c:272:16: style: Variable 'hel' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/hash.c:292:16: style: Variable 'hel' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/hash.c:302:16: style: Variable 'hel' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/hash.c:332:35: style: Parameter 'hash' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/hash.c:404:20: style: Variable 'hel' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/hash.c:427:35: style: Parameter 'hash' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/hash.c:439:36: style: Parameter 'hash' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/hash.c:468:48: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/hash.c:480:44: style: Parameter 'hash' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/hash.c:643:37: style: Parameter 'hel' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/hash.c:663:46: style: Parameter 'label' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/internet.c:45:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AF_INET [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/internet.c:67:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AF_INET [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/internet.c:89:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AF_INET [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/internet.c:109:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AF_INET [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/internet.c:148:42: style: Parameter 'unpackedIp' can be declared as const array [constParameter]
CNEr/src/ucsc/internet.c:148:71: style: Parameter 'subnet' can be declared as const array [constParameter]
CNEr/src/ucsc/localmem.c:39:1: warning: Either the condition 'mb==NULL' is redundant or there is possible null pointer dereference: mb. [nullPointerRedundantCheck]
CNEr/src/ucsc/localmem.c:37:8: note: Assuming that condition 'mb==NULL' is not redundant
CNEr/src/ucsc/localmem.c:39:1: note: Null pointer dereference
CNEr/src/ucsc/localmem.c:40:1: warning: Either the condition 'mb==NULL' is redundant or there is possible null pointer dereference: mb. [nullPointerRedundantCheck]
CNEr/src/ucsc/localmem.c:37:8: note: Assuming that condition 'mb==NULL' is not redundant
CNEr/src/ucsc/localmem.c:40:1: note: Null pointer dereference
CNEr/src/ucsc/localmem.c:41:1: warning: Either the condition 'mb==NULL' is redundant or there is possible null pointer dereference: mb. [nullPointerRedundantCheck]
CNEr/src/ucsc/localmem.c:37:8: note: Assuming that condition 'mb==NULL' is not redundant
CNEr/src/ucsc/localmem.c:41:1: note: Null pointer dereference
CNEr/src/ucsc/localmem.c:39:23: warning: Either the condition 'mb==NULL' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
CNEr/src/ucsc/localmem.c:37:8: note: Assuming that condition 'mb==NULL' is not redundant
CNEr/src/ucsc/localmem.c:39:23: note: Null pointer addition
CNEr/src/ucsc/localmem.c:40:24: warning: Either the condition 'mb==NULL' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
CNEr/src/ucsc/localmem.c:37:8: note: Assuming that condition 'mb==NULL' is not redundant
CNEr/src/ucsc/localmem.c:40:24: note: Null pointer addition
CNEr/src/ucsc/localmem.c:80:17: style: Variable 'mb' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/localmem.c:130:39: style: Parameter 'pt' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/localmem.c:138:43: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/localmem.c:166:7: style: Variable 'endFirstWord' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/localmem.c:191:46: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/localmem.c:122:23: portability: 'pt' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
CNEr/src/ucsc/linefile.c:106:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/linefile.c:286:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/linefile.c:300:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/linefile.c:312:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/linefile.c:636:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/memalloc.c:93:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/memalloc.c:116:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/memalloc.c:138:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/memalloc.c:160:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/memalloc.c:189:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/memalloc.c:190:8: warning: Either the condition '(pt=mhStack->alloc(size))==NULL' is redundant or there is possible null pointer dereference: pt. [nullPointerRedundantCheck]
CNEr/src/ucsc/memalloc.c:187:33: note: Assuming that condition '(pt=mhStack->alloc(size))==NULL' is not redundant
CNEr/src/ucsc/memalloc.c:190:8: note: Null pointer dereference
CNEr/src/ucsc/memalloc.c:479:9: warning: Either the condition 'mt==NULL' is redundant or there is possible null pointer dereference: mt. [nullPointerRedundantCheck]
CNEr/src/ucsc/memalloc.c:474:8: note: Assuming that condition 'mt==NULL' is not redundant
CNEr/src/ucsc/memalloc.c:479:9: note: Null pointer dereference
CNEr/src/ucsc/memalloc.c:194:37: style:inconclusive: Function 'needMoreMem' argument 2 names different: declaration 'copySize' definition 'oldSize'. [funcArgNamesDifferent]
CNEr/src/ucsc/common.h:213:37: note: Function 'needMoreMem' argument 2 names different: declaration 'copySize' definition 'oldSize'.
CNEr/src/ucsc/memalloc.c:194:37: note: Function 'needMoreMem' argument 2 names different: declaration 'copySize' definition 'oldSize'.
CNEr/src/ucsc/memalloc.c:216:18: style:inconclusive: Function 'freez' argument 1 names different: declaration 'ppt' definition 'vpt'. [funcArgNamesDifferent]
CNEr/src/ucsc/common.h:229:18: note: Function 'freez' argument 1 names different: declaration 'ppt' definition 'vpt'.
CNEr/src/ucsc/memalloc.c:216:18: note: Function 'freez' argument 1 names different: declaration 'ppt' definition 'vpt'.
CNEr/src/ucsc/memalloc.c:287:10: style: Local variable 'maxAlloc' shadows outer variable [shadowVariable]
CNEr/src/ucsc/memalloc.c:75:15: note: Shadowed declaration
CNEr/src/ucsc/memalloc.c:287:10: note: Shadow variable
CNEr/src/ucsc/memalloc.c:333:29: style: Variable 'cmb' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/memalloc.c:401:24: style: struct member 'memTracker::next' is never used. [unusedStructMember]
CNEr/src/ucsc/linefile.c:1143:21: style: Condition 'chunkSize>0' is always true [knownConditionTrueFalse]
CNEr/src/ucsc/linefile.c:1112:18: note: Assuming that condition 'chunkSize==0' is not redundant
CNEr/src/ucsc/linefile.c:1143:21: note: Condition 'chunkSize>0' is always true
CNEr/src/ucsc/linefile.c:1054:8: style: Variable 'code' is reassigned a value before the old one has been used. [redundantAssignment]
CNEr/src/ucsc/linefile.c:1053:8: note: code is assigned
CNEr/src/ucsc/linefile.c:1054:8: note: code is overwritten
CNEr/src/ucsc/linefile.c:16:35: style: Parameter 'm' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/linefile.c:100:33: style: Parameter 'fileName' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/linefile.c:125:7: style: Variable 'testName' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/linefile.c:171:39: style: Parameter 'fileName' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/linefile.c:184:41: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/linefile.c:199:45: style: Parameter 'fileOrUrl' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/linefile.c:240:49: style: Parameter 'lf' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/linefile.c:240:59: style: Parameter 'seqName' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/linefile.c:323:45: style: Parameter 'lf' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/linefile.c:323:55: style: Parameter 'where' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/linefile.c:807:7: style: Variable 's' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/linefile.c:824:11: style: Variable 'clippedText' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/linefile.c:980:65: style: Parameter 'start' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/linefile.c:1096:13: style: Variable 'csword' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/linefile.c:104:17: style: Variable 'bytesread' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/linefile.c:109:19: style: Variable 'bytesread' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/mime.c:260:6: warning: Either the condition '!val' is redundant or there is possible null pointer dereference: val. [nullPointerRedundantCheck]
CNEr/src/ucsc/mime.c:258:9: note: Assuming that condition '!val' is not redundant
CNEr/src/ucsc/mime.c:260:6: note: Null pointer dereference
CNEr/src/ucsc/mime.c:261:8: warning: Either the condition '!val' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
CNEr/src/ucsc/mime.c:258:9: note: Assuming that condition '!val' is not redundant
CNEr/src/ucsc/mime.c:261:8: note: Null pointer addition
CNEr/src/ucsc/mime.c:545:9: style: Redundant initialization for 'c1'. The initialized value is overwritten before it is read. [redundantInitialization]
CNEr/src/ucsc/mime.c:528:10: note: c1 is initialized
CNEr/src/ucsc/mime.c:545:9: note: c1 is overwritten
CNEr/src/ucsc/mime.c:311:7: style: Variable 'h' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/mime.c:313:7: style: Variable 'puncChars' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/mime.c:340:7: style: Variable 'puncChars' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/mime.c:94:15: style: Variable 'bytesRead' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/mime.c:600:19: style: Variable 'toobig' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/mime.c:632:13: style: Variable 'toobig' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/obscure.c:192:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/obscure.c:216:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/obscure.c:671:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/obscure.c:703:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/common.c:3224:11: style: Array index 'slen' is used before limits check. [arrayIndexThenCheck]
CNEr/src/ucsc/common.c:2420:26: warning: Either the condition 'mode' is redundant or there is possible null pointer dereference: mode. [nullPointerRedundantCheck]
CNEr/src/ucsc/common.c:2423:9: note: Assuming that condition 'mode' is not redundant
CNEr/src/ucsc/common.c:2420:26: note: Null pointer dereference
CNEr/src/ucsc/common.c:3096:5: warning: Either the condition 'buf==NULL' is redundant or there is possible null pointer dereference: buf. [nullPointerRedundantCheck]
CNEr/src/ucsc/common.c:3091:17: note: Assuming that condition 'buf==NULL' is not redundant
CNEr/src/ucsc/common.c:3096:5: note: Null pointer dereference
CNEr/src/ucsc/common.c:224:23: style:inconclusive: Function 'slPopHead' argument 1 names different: declaration 'listPt' definition 'vListPt'. [funcArgNamesDifferent]
CNEr/src/ucsc/common.h:395:23: note: Function 'slPopHead' argument 1 names different: declaration 'listPt' definition 'vListPt'.
CNEr/src/ucsc/common.c:224:23: note: Function 'slPopHead' argument 1 names different: declaration 'listPt' definition 'vListPt'.
CNEr/src/ucsc/common.c:237:23: style:inconclusive: Function 'slPopTail' argument 1 names different: declaration 'listPt' definition 'vListPt'. [funcArgNamesDifferent]
CNEr/src/ucsc/common.h:398:23: note: Function 'slPopTail' argument 1 names different: declaration 'listPt' definition 'vListPt'.
CNEr/src/ucsc/common.c:237:23: note: Function 'slPopTail' argument 1 names different: declaration 'listPt' definition 'vListPt'.
CNEr/src/ucsc/common.c:260:19: style:inconclusive: Function 'slCat' argument 1 names different: declaration 'a' definition 'va'. [funcArgNamesDifferent]
CNEr/src/ucsc/common.h:401:19: note: Function 'slCat' argument 1 names different: declaration 'a' definition 'va'.
CNEr/src/ucsc/common.c:260:19: note: Function 'slCat' argument 1 names different: declaration 'a' definition 'va'.
CNEr/src/ucsc/common.c:260:29: style:inconclusive: Function 'slCat' argument 2 names different: declaration 'b' definition 'vb'. [funcArgNamesDifferent]
CNEr/src/ucsc/common.h:401:28: note: Function 'slCat' argument 2 names different: declaration 'b' definition 'vb'.
CNEr/src/ucsc/common.c:260:29: note: Function 'slCat' argument 2 names different: declaration 'b' definition 'vb'.
CNEr/src/ucsc/common.c:1571:40: style:inconclusive: Function 'replaceChars' argument 2 names different: declaration 'oldStr' definition 'old'. [funcArgNamesDifferent]
CNEr/src/ucsc/common.h:842:40: note: Function 'replaceChars' argument 2 names different: declaration 'oldStr' definition 'old'.
CNEr/src/ucsc/common.c:1571:40: note: Function 'replaceChars' argument 2 names different: declaration 'oldStr' definition 'old'.
CNEr/src/ucsc/common.c:1571:51: style:inconclusive: Function 'replaceChars' argument 3 names different: declaration 'newStr' definition 'new'. [funcArgNamesDifferent]
CNEr/src/ucsc/common.h:842:54: note: Function 'replaceChars' argument 3 names different: declaration 'newStr' definition 'new'.
CNEr/src/ucsc/common.c:1571:51: note: Function 'replaceChars' argument 3 names different: declaration 'newStr' definition 'new'.
CNEr/src/ucsc/common.c:14:22: style: Parameter 'pt' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:55:27: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:55:36: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:157:16: style: Variable 'pt' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/common.c:182:39: style: Parameter 'el' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:390:16: style: Variable 'toRemove' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/common.c:526:18: style: Variable 'el' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/common.c:543:18: style: Variable 'el' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/common.c:592:32: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:610:33: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:667:56: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:670:16: style: Variable 'el' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/common.c:688:45: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:693:16: style: Variable 'el' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/common.c:827:16: style: Variable 'el' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/common.c:880:54: style: Parameter 'val' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:946:32: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1002:54: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1015:16: style: Variable 'el' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/common.c:1027:7: style: Variable 's' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/common.c:1316:25: style: Parameter 's1' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1316:35: style: Parameter 's2' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1333:33: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1333:42: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1367:30: style: Parameter 'firstWord' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1367:47: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1392:34: style: Parameter 'word' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1421:23: style: Parameter 'needle' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/net.c:51:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_NONBLOCK [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/common.c:1434:40: style: Parameter 'end' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/net.c:314:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIG_IGN [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/common.c:1455:24: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/net.c:597:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EINTR [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/common.c:1455:38: style: Parameter 'end' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/net.c:1149:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EIO [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/common.c:1467:21: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/net.c:1231:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/common.c:1498:40: style: Parameter 'limit' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/net.c:1968:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/common.c:1508:22: style: Parameter 'needle' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1508:46: style: Parameter 'haystack' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1571:40: style: Parameter 'old' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1571:51: style: Parameter 'new' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1613:44: style: Parameter 'oldStr' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1613:58: style: Parameter 'newStr' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1662:7: style: Variable 'in' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/common.c:1697:33: style: Parameter 'strip' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1722:21: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1734:22: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1745:23: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1756:29: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1791:31: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1860:21: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1860:30: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:1890:32: style: Parameter 'sep' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:2133:7: style: Variable 'in' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/common.c:2151:7: style: Variable 'in' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/common.c:2196:29: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:2223:7: style: Variable 'endFirstWord' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/common.c:2333:7: style: Variable 'e' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/common.c:2396:21: style: Parameter 'pt' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:2411:38: style: Parameter 'mode' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:2437:34: style: Parameter 'buf' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:2551:7: style: Variable 'success' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/common.c:2604:32: style: Parameter 'buf' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:2635:23: style: Parameter 'head' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:2635:35: style: Parameter 'suffix' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:2646:23: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:2654:25: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:3046:38: style: Parameter 'src' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:3128:42: style: Parameter 'needle' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:3144:7: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/common.c:3315:21: style: Parameter 'path' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/common.c:3373:11: style: Variable 'tz' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/common.c:3417:35: style: Parameter 'tp' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/obscure.c:436:9: warning: Either the condition 'val==NULL' is redundant or there is possible null pointer dereference: val++. [nullPointerRedundantCheck]
CNEr/src/ucsc/obscure.c:432:13: note: Assuming that condition 'val==NULL' is not redundant
CNEr/src/ucsc/obscure.c:436:9: note: Null pointer dereference
CNEr/src/ucsc/obscure.c:246:10: error: Pointer addition with NULL pointer. [nullPointerArithmetic]
CNEr/src/ucsc/obscure.c:245:12: note: Assignment 'pt=NULL', assigned value is 0
CNEr/src/ucsc/obscure.c:246:10: note: Null pointer addition
CNEr/src/ucsc/obscure.c:262:10: error: Pointer addition with NULL pointer. [nullPointerArithmetic]
CNEr/src/ucsc/obscure.c:261:12: note: Assignment 'pt=NULL', assigned value is 0
CNEr/src/ucsc/obscure.c:262:10: note: Null pointer addition
CNEr/src/ucsc/obscure.c:436:9: warning: Either the condition 'val==NULL' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
CNEr/src/ucsc/obscure.c:432:13: note: Assuming that condition 'val==NULL' is not redundant
CNEr/src/ucsc/obscure.c:436:9: note: Null pointer addition
CNEr/src/ucsc/obscure.c:16:27: style: Parameter 'fileName' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/obscure.c:253:7: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/obscure.c:253:18: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/obscure.c:269:7: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/obscure.c:269:18: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/obscure.c:372:20: style: Parameter 'in' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/obscure.c:639:25: style: Parameter 'position' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/obscure.c:714:31: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/kxTok.c:14:58: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/kxTok.c:39:29: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/common.c:1038:8: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/common.c:1967:17: style: Variable 'quoting' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/osunix.c:133:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REG_NOSUB [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/osunix.c:165:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/osunix.c:206:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/osunix.c:501:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ICANON [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/osunix.c:554:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/options.c:62:24: warning: Either the condition 'val==NULL' is redundant or there is possible null pointer dereference: val. [nullPointerRedundantCheck]
CNEr/src/ucsc/options.c:60:13: note: Assuming that condition 'val==NULL' is not redundant
CNEr/src/ucsc/options.c:62:24: note: Null pointer dereference
CNEr/src/ucsc/options.c:63:11: warning: Either the condition 'val==NULL' is redundant or there is possible null pointer dereference: val. [nullPointerRedundantCheck]
CNEr/src/ucsc/options.c:60:13: note: Assuming that condition 'val==NULL' is not redundant
CNEr/src/ucsc/options.c:63:11: note: Null pointer dereference
CNEr/src/ucsc/options.c:70:25: warning: Either the condition 'val==NULL' is redundant or there is possible null pointer dereference: val. [nullPointerRedundantCheck]
CNEr/src/ucsc/options.c:68:13: note: Assuming that condition 'val==NULL' is not redundant
CNEr/src/ucsc/options.c:70:25: note: Null pointer dereference
CNEr/src/ucsc/options.c:71:11: warning: Either the condition 'val==NULL' is redundant or there is possible null pointer dereference: val. [nullPointerRedundantCheck]
CNEr/src/ucsc/options.c:68:13: note: Assuming that condition 'val==NULL' is not redundant
CNEr/src/ucsc/options.c:71:11: note: Null pointer dereference
CNEr/src/ucsc/options.c:78:35: warning: Either the condition 'val==NULL' is redundant or there is possible null pointer dereference: val. [nullPointerRedundantCheck]
CNEr/src/ucsc/options.c:76:13: note: Assuming that condition 'val==NULL' is not redundant
CNEr/src/ucsc/options.c:78:35: note: Null pointer dereference
CNEr/src/ucsc/options.c:79:11: warning: Either the condition 'val==NULL' is redundant or there is possible null pointer dereference: val. [nullPointerRedundantCheck]
CNEr/src/ucsc/options.c:76:13: note: Assuming that condition 'val==NULL' is not redundant
CNEr/src/ucsc/options.c:79:11: note: Null pointer dereference
CNEr/src/ucsc/options.c:86:35: warning: Either the condition 'val==NULL' is redundant or there is possible null pointer dereference: val. [nullPointerRedundantCheck]
CNEr/src/ucsc/options.c:84:13: note: Assuming that condition 'val==NULL' is not redundant
CNEr/src/ucsc/options.c:86:35: note: Null pointer dereference
CNEr/src/ucsc/options.c:87:11: warning: Either the condition 'val==NULL' is redundant or there is possible null pointer dereference: val. [nullPointerRedundantCheck]
CNEr/src/ucsc/options.c:84:13: note: Assuming that condition 'val==NULL' is not redundant
CNEr/src/ucsc/options.c:87:11: note: Null pointer dereference
CNEr/src/ucsc/options.c:26:48: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/options.c:96:91: style: Parameter 'spec' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/options.c:142:11: style: Variable 's' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/options.c:319:24: style: Variable 'spec' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/options.c:62:15: style: Variable 'discardMe' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/options.c:70:15: style: Variable 'discardMe' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/options.c:78:15: style: Variable 'discardMe' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/options.c:86:15: style: Variable 'discardMe' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/oswin9x.c:21:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _O_RDONLY [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/oswin9x.c:58:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLOCKS_PER_SEC [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/oswin9x.c:72:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _MAX_PATH [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/oswin9x.c:186:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _A_SUBDIR [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/oswin9x.c:156:28: warning: Either the condition 'dir==NULL' is redundant or there is possible null pointer dereference: dir. [nullPointerRedundantCheck]
CNEr/src/ucsc/oswin9x.c:160:11: note: Assuming that condition 'dir==NULL' is not redundant
CNEr/src/ucsc/oswin9x.c:156:28: note: Null pointer dereference
CNEr/src/ucsc/oswin9x.c:181:17: style: Variable 'fileName' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/oswin9x.c:103:9: style: Variable 'dir' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/oswin9x.c:184:22: style: Variable 'fileName' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/osunix.c:475:21: portability: Non reentrant function 'getpwuid' called. For threadsafe applications it is recommended to use the reentrant replacement function 'getpwuid_r'. [prohibitedgetpwuidCalled]
CNEr/src/ucsc/osunix.c:604:15: style: Obsolescent function 'utime' called. It is recommended to use 'utimensat' instead. [prohibitedutimeCalled]
CNEr/src/ucsc/osunix.c:257:19: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
CNEr/src/ucsc/osunix.c:255:15: note: outer condition: hostName==NULL
CNEr/src/ucsc/osunix.c:257:19: note: identical inner condition: hostName==NULL
CNEr/src/ucsc/osunix.c:279:5: style: Condition '!gotIt' is always true [knownConditionTrueFalse]
CNEr/src/ucsc/osunix.c:277:17: note: Assignment 'gotIt=0', assigned value is 0
CNEr/src/ucsc/osunix.c:279:5: note: Condition '!gotIt' is always true
CNEr/src/ucsc/osunix.c:71:1: warning: Possible null pointer dereference: nullPt [nullPointer]
CNEr/src/ucsc/osunix.c:70:23: note: Assignment 'nullPt=NULL', assigned value is 0
CNEr/src/ucsc/osunix.c:71:1: note: Null pointer dereference
CNEr/src/ucsc/osunix.c:478:8: warning: Either the condition 'pw==NULL' is redundant or there is possible null pointer dereference: pw. [nullPointerRedundantCheck]
CNEr/src/ucsc/osunix.c:476:8: note: Assuming that condition 'pw==NULL' is not redundant
CNEr/src/ucsc/osunix.c:478:8: note: Null pointer dereference
CNEr/src/ucsc/osunix.c:365:29: warning: Either the condition 'excess==NULL' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
CNEr/src/ucsc/osunix.c:366:16: note: Assuming that condition 'excess==NULL' is not redundant
CNEr/src/ucsc/osunix.c:365:29: note: Null pointer addition
CNEr/src/ucsc/osunix.c:23:22: style:inconclusive: Function 'fileSize' argument 1 names different: declaration 'fileName' definition 'pathname'. [funcArgNamesDifferent]
CNEr/src/ucsc/common.h:1303:22: note: Function 'fileSize' argument 1 names different: declaration 'fileName' definition 'pathname'.
CNEr/src/ucsc/osunix.c:23:22: note: Function 'fileSize' argument 1 names different: declaration 'fileName' definition 'pathname'.
CNEr/src/ucsc/osunix.c:91:34: style: Parameter 'newDir' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/osunix.c:97:41: style: Parameter 'pattern' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/osunix.c:124:46: style: Parameter 'regEx' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/osunix.c:175:47: style: Parameter 'pattern' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/osunix.c:181:16: style: Variable 'de' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/osunix.c:334:7: style: Variable 's' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/osunix.c:365:11: style: Variable 'excessEnd' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/osunix.c:401:7: style: Variable 's' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/osunix.c:475:16: style: Variable 'pw' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/osunix.c:543:24: style: Parameter 'format' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/osunix.c:163:10: style: Variable 'err' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/osunix.c:282:11: style: Variable 'gotIt' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/pipeline.c:181:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIG_IGN [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/pipeline.c:306:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIG_IGN [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/pipeline.c:395:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/pipeline.c:404:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_WRONLY [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/pipeline.c:590:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/portimpl.c:92:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S_IRWXU [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/pipeline.c:218:83: style: Parameter 'otherEndBuf' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/pipeline.c:529:37: style: Parameter 'pl' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/pipeline.c:535:33: style: Parameter 'pl' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/pipeline.c:668:10: style: Variable 'word' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/pipeline.c:45:22: style: struct member 'pipeline::next' is never used. [unusedStructMember]
CNEr/src/ucsc/pipeline.c:367:2: style: Variable 'l' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/portimpl.c:21:11: style: Variable 's' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/servBrcMcw.c:18:7: style: Variable 'tname' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/servCrunx.c:17:7: style: Variable 'tname' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/servCrunx.c:19:7: style: Variable 'tempDirHtml' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/servcis.c:18:7: style: Variable 'tname' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/servcl.c:17:7: style: Variable 'tname' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/servpws.c:14:54: style: Parameter 'base' can be declared as pointer to const. However it seems that '_makeTempName' is a callback function, if 'base' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
CNEr/src/ucsc/servpws.c:40:5: note: You might need to cast the function pointer here
CNEr/src/ucsc/servpws.c:14:54: note: Parameter 'base' can be declared as pointer to const
CNEr/src/ucsc/servpws.c:14:66: style: Parameter 'suffix' can be declared as pointer to const. However it seems that '_makeTempName' is a callback function, if 'suffix' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
CNEr/src/ucsc/servpws.c:40:5: note: You might need to cast the function pointer here
CNEr/src/ucsc/servpws.c:14:66: note: Parameter 'suffix' can be declared as pointer to const
CNEr/src/ucsc/servmsII.c:14:54: style: Parameter 'base' can be declared as pointer to const. However it seems that '_makeTempName' is a callback function, if 'base' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
CNEr/src/ucsc/servmsII.c:41:5: note: You might need to cast the function pointer here
CNEr/src/ucsc/servmsII.c:14:54: note: Parameter 'base' can be declared as pointer to const
CNEr/src/ucsc/servmsII.c:14:66: style: Parameter 'suffix' can be declared as pointer to const. However it seems that '_makeTempName' is a callback function, if 'suffix' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
CNEr/src/ucsc/servmsII.c:41:5: note: You might need to cast the function pointer here
CNEr/src/ucsc/servmsII.c:14:66: note: Parameter 'suffix' can be declared as pointer to const
CNEr/src/ucsc/sqlNum.c:117:7: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/sqlNum.c:175:7: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/verbose.c:25:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/verbose.c:76:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/verbose.c:118:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/verbose.c:129:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/verbose.c:19:37: style: Parameter 'format' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/verbose.c:81:15: style: Variable 'emacs' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/verbose.c:82:15: style: Variable 'term' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/wildcmp.c:112:28: style: Parameter 'wildCard' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/wildcmp.c:112:44: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/udc.c:480:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_WRONLY [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/udc.c:522:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDWR [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/udc.c:806:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/udc.c:862:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
CNEr/src/ucsc/sqlList.c:1274:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
CNEr/src/ucsc/sqlList.c:1278:11: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
CNEr/src/ucsc/sqlList.c:585:52: style:inconclusive: Function 'sqlUnsignedArray' argument 3 names different: declaration 'maxArraySize' definition 'arraySize'. [funcArgNamesDifferent]
CNEr/src/ucsc/sqlList.h:12:52: note: Function 'sqlUnsignedArray' argument 3 names different: declaration 'maxArraySize' definition 'arraySize'.
CNEr/src/ucsc/sqlList.c:585:52: note: Function 'sqlUnsignedArray' argument 3 names different: declaration 'maxArraySize' definition 'arraySize'.
CNEr/src/ucsc/sqlList.c:665:45: style:inconclusive: Function 'sqlSignedArray' argument 3 names different: declaration 'maxArraySize' definition 'arraySize'. [funcArgNamesDifferent]
CNEr/src/ucsc/sqlList.h:13:45: note: Function 'sqlSignedArray' argument 3 names different: declaration 'maxArraySize' definition 'arraySize'.
CNEr/src/ucsc/sqlList.c:665:45: note: Function 'sqlSignedArray' argument 3 names different: declaration 'maxArraySize' definition 'arraySize'.
CNEr/src/ucsc/sqlList.c:765:50: style:inconclusive: Function 'sqlLongLongStaticArray' argument 2 names different: declaration 'array' definition 'retArray'. [funcArgNamesDifferent]
CNEr/src/ucsc/sqlList.h:32:50: note: Function 'sqlLongLongStaticArray' argument 2 names different: declaration 'array' definition 'retArray'.
CNEr/src/ucsc/sqlList.c:765:50: note: Function 'sqlLongLongStaticArray' argument 2 names different: declaration 'array' definition 'retArray'.
CNEr/src/utils.c:55:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INTSXP [valueFlowBailoutIncompleteVar]
CNEr/src/utils.c:81:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INTSXP [valueFlowBailoutIncompleteVar]
CNEr/src/utils.c:24:8: style: Variable 'p_start' can be declared as pointer to const [constVariablePointer]
CNEr/src/utils.c:24:18: style: Variable 'p_end' can be declared as pointer to const [constVariablePointer]
CNEr/src/utils.c:49:22: style: Variable '_binFirstShift' is assigned a value that is never used. [unreadVariable]
CNEr/src/utils.c:50:21: style: Variable '_binNextShift' is assigned a value that is never used. [unreadVariable]
CNEr/src/utils.c:49:7: style: Variable '_binFirstShift' is assigned a value that is never used. [unreadVariable]
CNEr/src/utils.c:50:7: style: Variable '_binNextShift' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/udc.c:433:6: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
CNEr/src/ucsc/udc.c:533:7: warning: Either the condition 'fd<0' is redundant or fstat() argument nr 1 can have invalid value. The value is -1 but the valid values are '0:'. [invalidFunctionArg]
CNEr/src/ucsc/udc.c:523:8: note: Assuming that condition 'fd<0' is not redundant
CNEr/src/ucsc/udc.c:533:7: note: Invalid argument
CNEr/src/ucsc/udc.c:962:6: warning: %X in format string (no. 1) requires 'unsigned int *' but the argument type is 'signed int *'. [invalidScanfArgType_int]
CNEr/src/ucsc/udc.c:668:23: warning: Either the condition 'bits==NULL' is redundant or there is possible null pointer dereference: bits. [nullPointerRedundantCheck]
CNEr/src/ucsc/udc.c:664:14: note: Assuming that condition 'bits==NULL' is not redundant
CNEr/src/ucsc/udc.c:668:23: note: Null pointer dereference
CNEr/src/ucsc/udc.c:560:12: style: Variable 'reserved64' is reassigned a value before the old one has been used. [redundantAssignment]
CNEr/src/ucsc/udc.c:559:12: note: reserved64 is assigned
CNEr/src/ucsc/udc.c:560:12: note: reserved64 is overwritten
CNEr/src/ucsc/udc.c:561:12: style: Variable 'reserved64' is reassigned a value before the old one has been used. [redundantAssignment]
CNEr/src/ucsc/udc.c:560:12: note: reserved64 is assigned
CNEr/src/ucsc/udc.c:561:12: note: reserved64 is overwritten
CNEr/src/ucsc/udc.c:562:12: style: Variable 'reserved64' is reassigned a value before the old one has been used. [redundantAssignment]
CNEr/src/ucsc/udc.c:561:12: note: reserved64 is assigned
CNEr/src/ucsc/udc.c:562:12: note: reserved64 is overwritten
CNEr/src/ucsc/udc.c:131:12: style: Checking if unsigned expression 'rd' is less than zero. [unsignedLessThanZero]
CNEr/src/ucsc/udc.c:371:23: style: Checking if unsigned expression 'retInfo->size' is less than zero. [unsignedLessThanZero]
CNEr/src/ucsc/udc.c:255:40: style: Parameter 'url' can be declared as pointer to const. However it seems that 'udcDataViaTransparent' is a callback function, if 'url' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
CNEr/src/ucsc/udc.c:609:23: note: You might need to cast the function pointer here
CNEr/src/ucsc/udc.c:255:40: note: Parameter 'url' can be declared as pointer to const
CNEr/src/ucsc/udc.c:255:76: style: Parameter 'buffer' can be declared as pointer to const. However it seems that 'udcDataViaTransparent' is a callback function, if 'buffer' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
CNEr/src/ucsc/udc.c:609:23: note: You might need to cast the function pointer here
CNEr/src/ucsc/udc.c:255:76: note: Parameter 'buffer' can be declared as pointer to const
CNEr/src/ucsc/udc.c:256:23: style: Parameter 'ci' can be declared as pointer to const. However it seems that 'udcDataViaTransparent' is a callback function, if 'ci' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
CNEr/src/ucsc/udc.c:609:23: note: You might need to cast the function pointer here
CNEr/src/ucsc/udc.c:256:23: note: Parameter 'ci' can be declared as pointer to const
CNEr/src/ucsc/udc.c:265:44: style: Parameter 'url' can be declared as pointer to const. However it seems that 'udcInfoViaTransparent' is a callback function, if 'url' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
CNEr/src/ucsc/udc.c:610:23: note: You might need to cast the function pointer here
CNEr/src/ucsc/udc.c:265:44: note: Parameter 'url' can be declared as pointer to const
CNEr/src/ucsc/udc.c:265:75: style: Parameter 'retInfo' can be declared as pointer to const. However it seems that 'udcInfoViaTransparent' is a callback function, if 'retInfo' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
CNEr/src/ucsc/udc.c:610:23: note: You might need to cast the function pointer here
CNEr/src/ucsc/udc.c:265:75: note: Parameter 'retInfo' can be declared as pointer to const
CNEr/src/ucsc/udc.c:312:7: style: Variable 'fileName' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/udc.c:366:7: style: Variable 'sizeString' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/udc.c:463:49: style: Parameter 'file' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/udc.c:463:61: style: Parameter 'fileName' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/udc.c:703:7: style: Variable 's' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/udc.c:757:11: style: Variable 'afterHost' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/udc.c:1074:19: style: Variable 'bitmap' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/udc.c:1471:32: style: Parameter 'file' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/udc.c:1586:38: style: Parameter 'udc' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/udc.c:680:19: style: int result is assigned to long long variable. If the variable is long long to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
CNEr/src/ucsc/udc.c:1166:18: style: int result is assigned to long long variable. If the variable is long long to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
CNEr/src/ucsc/udc.c:1167:16: style: int result is assigned to long long variable. If the variable is long long to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
CNEr/src/ucsc/udc.c:71:25: style: struct member 'udcProtocol::next' is never used. [unusedStructMember]
CNEr/src/ucsc/udc.c:79:21: style: struct member 'udcFile::next' is never used. [unusedStructMember]
CNEr/src/ucsc/udc.c:103:23: style: struct member 'udcBitmap::next' is never used. [unusedStructMember]
CNEr/src/ucsc/net.c:1838:10: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
CNEr/src/ucsc/net.c:2249:10: style: Obsolescent function 'utime' called. It is recommended to use 'utimensat' instead. [prohibitedutimeCalled]
CNEr/src/ucsc/net.c:301:12: warning: Either the condition '(socket=dup(socket))<0' is redundant or fdopen() argument nr 1 can have invalid value. The value is -1 but the valid values are '0:'. [invalidFunctionArg]
CNEr/src/ucsc/net.c:299:28: note: Assuming that condition '(socket=dup(socket))<0' is not redundant
CNEr/src/ucsc/net.c:301:12: note: Invalid argument
CNEr/src/ucsc/net.c:1259:25: warning: Either the condition 'sd<0' is redundant or read() argument nr 1 can have invalid value. The value is -1 but the valid values are '0:'. [invalidFunctionArg]
CNEr/src/ucsc/net.c:1268:8: note: Assuming that condition 'sd<0' is not redundant
CNEr/src/ucsc/net.c:1270:36: note: Calling function 'netSlurpFile', 1st argument 'sd' value is -1
CNEr/src/ucsc/net.c:1259:25: note: Invalid argument
CNEr/src/ucsc/net.c:1271:7: warning: Either the condition 'sd<0' is redundant or close() argument nr 1 can have invalid value. The value is -1 but the valid values are '0:'. [invalidFunctionArg]
CNEr/src/ucsc/net.c:1268:8: note: Assuming that condition 'sd<0' is not redundant
CNEr/src/ucsc/net.c:1271:7: note: Invalid argument
CNEr/src/ucsc/udc.c:558:12: style: Variable 'reserved32' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/udc.c:562:12: style: Variable 'reserved64' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/net.c:434:3: style: Variable 's' is reassigned a value before the old one has been used. [redundantAssignment]
CNEr/src/ucsc/net.c:433:3: note: s is assigned
CNEr/src/ucsc/net.c:434:3: note: s is overwritten
CNEr/src/ucsc/net.c:1160:11: style: Variable 'word' is reassigned a value before the old one has been used. [redundantAssignment]
CNEr/src/ucsc/net.c:1159:11: note: word is assigned
CNEr/src/ucsc/net.c:1160:11: note: word is overwritten
CNEr/src/ucsc/net.c:1748:10: style: Variable 'word' is reassigned a value before the old one has been used. [redundantAssignment]
CNEr/src/ucsc/net.c:1744:10: note: word is assigned
CNEr/src/ucsc/net.c:1748:10: note: word is overwritten
CNEr/src/ucsc/net.c:2397:37: style: Checking if unsigned expression 'netReadAll(sd,buf,length)' is less than zero. [unsignedLessThanZero]
CNEr/src/ucsc/net.c:2426:35: style: Checking if unsigned expression 'netReadAll(sd,s,length)' is less than zero. [unsignedLessThanZero]
CNEr/src/ucsc/net.c:2459:35: style: Checking if unsigned expression 'netReadAll(sd,s,length)' is less than zero. [unsignedLessThanZero]
CNEr/src/ucsc/net.c:459:11: style: Local variable 't' shadows outer variable [shadowVariable]
CNEr/src/ucsc/net.c:423:11: note: Shadowed declaration
CNEr/src/ucsc/net.c:459:11: note: Shadow variable
CNEr/src/ucsc/net.c:1734:7: style: Local variable 'fileSize' shadows outer function [shadowFunction]
CNEr/src/ucsc/common.h:1303:7: note: Shadowed declaration
CNEr/src/ucsc/net.c:1734:7: note: Shadow variable
CNEr/src/ucsc/net.c:1789:7: style: Local variable 'fileSize' shadows outer function [shadowFunction]
CNEr/src/ucsc/common.h:1303:7: note: Shadowed declaration
CNEr/src/ucsc/net.c:1789:7: note: Shadow variable
CNEr/src/ucsc/net.c:373:8: style: Variable 's' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/net.c:386:34: style: Parameter 'url' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/net.c:398:8: style: Variable 'y' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/net.c:400:8: style: Variable 'z' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/net.c:621:7: style: Variable 'startLastLine' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/net.c:736:7: style: Variable 'from' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/net.c:1206:11: style: Variable 'rangeString' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/net.c:1210:8: style: Variable 'slash' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/net.c:1275:37: style: Parameter 'x' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/net.c:1285:11: style: Variable 'y' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/net.c:1287:11: style: Variable 'z' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/net.c:1370:8: style: Variable 'version' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/net.c:1657:78: style: Parameter 'url' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/net.c:1657:105: style: Parameter 'dateString' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/net.c:1667:22: style: Variable 'pc' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/net.c:1806:11: style: Variable 'sizeString' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/net.c:1817:11: style: Variable 'ds' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/net.c:1834:17: style: Variable 'ts' can be declared as pointer to const [constVariablePointer]
CNEr/src/ucsc/net.c:2303:37: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/net.c:2325:41: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/net.c:2351:41: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/net.c:2522:34: style: Parameter 'lf' can be declared as pointer to const [constParameterPointer]
CNEr/src/ucsc/net.c:1313:6: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/net.c:1315:11: style: Variable 'nread' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/net.c:1371:10: style: Variable 'version' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/net.c:1883:7: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/net.c:1987:19: style: Variable 'readCount' is assigned a value that is never used. [unreadVariable]
CNEr/src/ucsc/net.c:2599:9: style: Variable 'done' is assigned a value that is never used. [unreadVariable]
diff:
head CNEr/src/ucsc/binRange.c:232:20: style: Variable 'el' can be declared as pointer to const [constVariablePointer]
head CNEr/src/ucsc/cheapcgi.c:35:16: style: Variable 'v' can be declared as pointer to const [constVariablePointer]
head CNEr/src/ucsc/common.c:157:16: style: Variable 'pt' can be declared as pointer to const [constVariablePointer]
head CNEr/src/ucsc/common.c:2333:7: style: Variable 'e' can be declared as pointer to const [constVariablePointer]
head CNEr/src/ucsc/common.c:526:18: style: Variable 'el' can be declared as pointer to const [constVariablePointer]
head CNEr/src/ucsc/common.c:543:18: style: Variable 'el' can be declared as pointer to const [constVariablePointer]
head CNEr/src/ucsc/common.c:670:16: style: Variable 'el' can be declared as pointer to const [constVariablePointer]
head CNEr/src/ucsc/common.c:693:16: style: Variable 'el' can be declared as pointer to const [constVariablePointer]
head CNEr/src/ucsc/common.c:827:16: style: Variable 'el' can be declared as pointer to const [constVariablePointer]
head CNEr/src/ucsc/hash.c:643:37: style: Parameter 'hel' can be declared as pointer to const [constParameterPointer]
head CNEr/src/ucsc/net.c:1667:22: style: Variable 'pc' can be declared as pointer to const [constVariablePointer]
head CNEr/src/ucsc/options.c:142:11: style: Variable 's' can be declared as pointer to const [constVariablePointer]
head CNEr/src/ucsc/osunix.c:181:16: style: Variable 'de' can be declared as pointer to const [constVariablePointer]


DONE