2025-05-05 15:20
ftp://ftp.de.debian.org/debian/pool/main/l/lutefisk/lutefisk_1.0.7+dfsg.orig.tar.gz
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 -j1
platform: Linux-6.8.0-59-generic-x86_64-with-glibc2.39
python: 3.12.3
client-version: 1.3.67
compiler: g++ (Ubuntu 14.2.0-4ubuntu2~24.04) 14.2.0
cppcheck: head 2.17.0
head-info: fcc0493 (2025-05-05 13:08:11 +0200)
count: 460 433
elapsed-time: 56.8 56.4
head-timing-info:

old-timing-info:

head results:
lutefisk-1.0.7+dfsg.orig/src/ListRoutines.c:65:15: style: Variable 'object' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:297:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REAL_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:356:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REAL_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:359:3: warning: If memory allocation fails, then there is a possible null pointer dereference: workSpace [nullPointerOutOfMemory]
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:356:31: note: Assuming allocation function fails
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:356:14: note: Assignment 'workSpace=(REAL_4*)malloc((n*2)*sizeof(REAL_4))', assigned value is 0
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:359:3: note: Null pointer dereference
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:379:33: style:inconclusive: Function 'FastFourier' argument 1 names different: declaration 'data' definition 'array'. [funcArgNamesDifferent]
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:63:33: note: Function 'FastFourier' argument 1 names different: declaration 'data' definition 'array'.
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:379:33: note: Function 'FastFourier' argument 1 names different: declaration 'data' definition 'array'.
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:440:28: style:inconclusive: Function 'twofft' argument 1 names different: declaration 'data1' definition 'array1'. [funcArgNamesDifferent]
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:64:27: note: Function 'twofft' argument 1 names different: declaration 'data1' definition 'array1'.
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:440:28: note: Function 'twofft' argument 1 names different: declaration 'data1' definition 'array1'.
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:440:44: style:inconclusive: Function 'twofft' argument 2 names different: declaration 'data2' definition 'array2'. [funcArgNamesDifferent]
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:64:43: note: Function 'twofft' argument 2 names different: declaration 'data2' definition 'array2'.
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:440:44: note: Function 'twofft' argument 2 names different: declaration 'data2' definition 'array2'.
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:479:28: style:inconclusive: Function 'realft' argument 1 names different: declaration 'data' definition 'array'. [funcArgNamesDifferent]
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:65:27: note: Function 'realft' argument 1 names different: declaration 'data' definition 'array'.
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:479:28: note: Function 'realft' argument 1 names different: declaration 'data' definition 'array'.
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:440:28: style: Parameter 'array1' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskFourier.c:440:44: style: Parameter 'array2' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:195:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mOverZ [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:235:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:424:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:1252:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:1706:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:68:23: style: Array index 'i' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:88:22: style: Array index 'i' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:531:13: style: Array index 'i' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:579:13: style: Array index 'i' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:1361:23: style: Array index 'i' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:140:24: style: Variable 'nextMassPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:224:27: style: Parameter 'tagNode' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:224:43: style: Parameter 'tagNodeIntensity' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:226:19: style: Variable 'subsequencePtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:410:36: style: Parameter 'tagNode' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:410:52: style: Parameter 'tagNodeIntensity' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:1213:27: style: Parameter 'tagNode' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:1213:60: style: Parameter 'tagNodeIntensity' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:1513:11: style: Variable 'tagMassPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:1681:19: style: Variable 'firstTagPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:1965:13: style: Variable 'n3' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:1965:18: style: Variable 'n4' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:1980:35: style: Parameter 'peptide' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:153:9: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:280:17: style: Variable 'subsequencePtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:918:20: style: Variable 'totalIntensity' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:996:10: style: Variable 'charge' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:1363:10: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetAutoTag.c:1737:14: style: Variable 'firstTagPtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2301:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REAL_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2539:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REAL_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2907:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable intensity [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:771:28: style: The if condition is the same as the previous if condition [duplicateCondition]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:744:28: note: First condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:771:28: note: Second condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1473:32: style: Condition 'currPtr->mOverZ<=y1Arg+gParam.fragmentErr' is always true [knownConditionTrueFalse]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1462:32: note: Assuming that condition 'currPtr->mOverZ>y1Arg+gParam.fragmentErr' is not redundant
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1473:32: note: Condition 'currPtr->mOverZ<=y1Arg+gParam.fragmentErr' is always true
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1515:32: style: Condition 'currPtr->mOverZ<=y1Lys+gParam.fragmentErr' is always true [knownConditionTrueFalse]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1511:32: note: Assuming that condition 'currPtr->mOverZ>y1Lys+gParam.fragmentErr' is not redundant
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1515:32: note: Condition 'currPtr->mOverZ<=y1Lys+gParam.fragmentErr' is always true
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1537:33: style: Condition 'currPtr->mOverZ<=immoniumIons[i]+gParam.fragmentErr' is always true [knownConditionTrueFalse]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1532:32: note: Assuming that condition 'currPtr->mOverZ>immoniumIons[i]+gParam.fragmentErr' is not redundant
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1537:33: note: Condition 'currPtr->mOverZ<=immoniumIons[i]+gParam.fragmentErr' is always true
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3796:41: style: Condition 'currPtr->mOverZ>=precurMin2W-tolerance' is always true [knownConditionTrueFalse]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3792:33: note: Assuming that condition 'currPtr->mOverZ>precurMin2W-tolerance' is not redundant
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3796:41: note: Condition 'currPtr->mOverZ>=precurMin2W-tolerance' is always true
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:4478:1: portability: %d in format string (no. 1) requires 'int' but the argument type is 'tMSDataList * {aka tMSDataList *}'. [invalidPrintfArgType_sint]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1239:21: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1331:17: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1618:9: style: Variable 'ptrOfNoReturn' is assigned an expression that holds the same value. [redundantAssignment]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1606:19: note: ptrOfNoReturn is assigned '&inPeakList->mass[inPeakList->numObjects]' here.
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1618:9: note: Variable 'ptrOfNoReturn' is assigned an expression that holds the same value.
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2349:5: style: Variable 'ptrOfNoReturn' is assigned an expression that holds the same value. [redundantAssignment]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2328:19: note: ptrOfNoReturn is assigned '&inMSDataList->mass[inMSDataList->numObjects]' here.
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2349:5: note: Variable 'ptrOfNoReturn' is assigned an expression that holds the same value.
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2593:5: style: Variable 'ptrOfNoReturn' is assigned an expression that holds the same value. [redundantAssignment]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2564:19: note: ptrOfNoReturn is assigned '&inMSDataList->mass[inMSDataList->numObjects]' here.
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2593:5: note: Variable 'ptrOfNoReturn' is assigned an expression that holds the same value.
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:4462:35: style: Variable 'prevIntensity' is reassigned a value before the old one has been used. [redundantAssignment]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:4452:31: note: prevIntensity is assigned
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:4462:35: note: prevIntensity is overwritten
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:44:9: style: Statements following 'return' will never be executed. [unreachableCode]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:4240:40: style:inconclusive: Function 'LowMassIonRemoval' argument 1 names different: declaration 'peakList' definition 'inMSDataList'. [funcArgNamesDifferent]
lutefisk-1.0.7+dfsg.orig/src/LutefiskPrototypes.h:120:39: note: Function 'LowMassIonRemoval' argument 1 names different: declaration 'peakList' definition 'inMSDataList'.
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:4240:40: note: Function 'LowMassIonRemoval' argument 1 names different: declaration 'peakList' definition 'inMSDataList'.
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:41:37: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:710:38: style: Parameter 'peakList' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:712:16: style: Variable 'lowMassIons' can be declared as const array [constVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1419:14: style: Variable 'ptrOfNoReturn' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1587:14: style: Variable 'ptrOfNoReturn' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1779:17: style: Variable 'previousPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1780:14: style: Variable 'ptrOfNoReturn' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1781:14: style: Variable 'currPeakPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1782:14: style: Variable 'peakPtrOfNoReturn' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2018:18: style: Variable 'previousPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2019:18: style: Variable 'ptrOfNoReturn' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2218:18: style: Variable 'currPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2219:18: style: Variable 'prevPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2220:18: style: Variable 'ptrOfNoReturn' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2298:26: style: Variable 'ptrOfNoReturn' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2535:22: style: Variable 'ptrOfNoReturn' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2781:22: style: Variable 'ptrOfNoReturn' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3024:14: style: Variable 'n3' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3024:19: style: Variable 'n4' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3051:14: style: Variable 'n3' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3051:19: style: Variable 'n4' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3082:18: style: Variable 'ptrOfNoReturn' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3359:18: style: Variable 'ptrOfNoReturn' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3515:18: style: Variable 'ptrOfNoReturn' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3575:18: style: Variable 'windowStartPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3576:18: style: Variable 'ptrOfNoReturn' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3760:18: style: Variable 'currPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3761:18: style: Variable 'ptrOfNoReturn' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3856:22: style: Variable 'ptrOfNoReturn' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3884:22: style: Variable 'ptrOfNoReturn' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3973:18: style: Variable 'ptrOfNoReturn' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:4197:18: style: Variable 'currPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:4198:18: style: Variable 'ptrOfNoReturn' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:4242:12: style: Variable 'lowMassIons' can be declared as const array [constVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:4250:18: style: Variable 'currPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:4251:18: style: Variable 'ptrOfNoReturn' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:4599:30: style: Parameter 'inList' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:4177:9: warning: Uninitialized variable: nextToLastPtr [uninitvar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:4171:29: note: Assuming condition is false
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:4177:9: note: Uninitialized variable: nextToLastPtr
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:86:27: style: Variable 'generalQuality' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:87:27: style: Variable 'lowMassQuality' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:88:28: style: Variable 'highMassQuality' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:89:20: style: Variable 'quality' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:573:24: style: Variable 'quality' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:573:16: style: Variable 'quality' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1898:24: style: Variable 'firstDataPoint' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1899:17: style: Variable 'dataNum' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1900:21: style: Variable 'calcDataNum' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:1901:19: style: Variable 'intensity' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2018:30: style: Variable 'previousPtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2018:18: style: Variable 'previousPtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3080:29: style: Variable 'isotopePtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3081:30: style: Variable 'isotope2Ptr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3575:33: style: Variable 'windowStartPtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3575:18: style: Variable 'windowStartPtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:4162:18: style: Variable 'firstPtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:4202:25: style: Variable 'noise' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:4584:22: style: Variable 'mass[ionNum]' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:4585:27: style: Variable 'intensity[ionNum]' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:146:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REAL_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:506:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:662:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLOCKS_PER_SEC [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:1117:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:568:25: style: Array index 'l' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:1203:21: style: Array index 'i' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:1351:14: style: Array index 'position' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:986:23: style: Condition 'currPtr->mOverZ>=yLys-gParam.fragmentErr' is always true [knownConditionTrueFalse]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:980:22: note: Assuming that condition 'currPtr->mOverZ>=yLys-gParam.fragmentErr' is not redundant
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:982:23: note: Assuming condition is false
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:986:23: note: Condition 'currPtr->mOverZ>=yLys-gParam.fragmentErr' is always true
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:992:21: style: Condition 'currPtr->mOverZ<=yArg+gParam.fragmentErr' is always true [knownConditionTrueFalse]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:982:23: note: Assuming that condition 'currPtr->mOverZ>yArg+gParam.fragmentErr' is not redundant
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:992:21: note: Condition 'currPtr->mOverZ<=yArg+gParam.fragmentErr' is always true
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:2115:14: style: Variable 'keepGoing' is reassigned a value before the old one has been used. [redundantAssignment]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:2107:16: note: keepGoing is assigned
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:2115:14: note: keepGoing is overwritten
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:854:42: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:1223:42: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:1468:50: style: Parameter 'peptide' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:1530:35: style: Parameter 'mass' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:1782:42: style: Parameter 'mass' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:2132:37: style: Parameter 'nodeMass' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:2063:14: warning: Uninitialized variable: newNode [uninitvar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:2032:16: note: Assuming condition is false
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:2063:14: note: Uninitialized variable: newNode
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:1507:12: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:1507:7: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:2062:11: style: Variable 'oldNode' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:315:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SCHAR [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2500:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REAL_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:1430:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:1435:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2485:13: style: Condition 'big_endian' is always false [knownConditionTrueFalse]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2479:18: note: Assignment 'big_endian=0', assigned value is 0
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2485:13: note: Condition 'big_endian' is always false
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2502:9: portability: %d in format string (no. 1) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2507:9: portability: %d in format string (no. 1) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2512:9: portability: %d in format string (no. 1) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2517:9: portability: %d in format string (no. 1) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2522:9: portability: %d in format string (no. 1) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2527:9: portability: %d in format string (no. 1) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2532:9: portability: %d in format string (no. 1) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2537:9: portability: %d in format string (no. 1) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:753:21: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:757:21: note: Found duplicate branches for 'if' and 'else'.
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:753:21: note: Found duplicate branches for 'if' and 'else'.
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2250:19: style: Variable 'gGapListIndex' is reassigned a value before the old one has been used. [redundantAssignment]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2212:19: note: gGapListIndex is assigned
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2250:19: note: gGapListIndex is overwritten
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:245:42: style: Variable 'firstRawDataPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:1406:14: style: Variable 'setting' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:1407:14: style: Variable 'value' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2205:20: style: Variable 'currPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2206:20: style: Variable 'nextPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2482:16: style: Variable 'test' can be declared as const array [constVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:245:58: style: Variable 'firstRawDataPtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:246:39: style: Variable 'firstSequencePtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:247:37: style: Variable 'theTime' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:245:42: style: Variable 'firstRawDataPtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:247:29: style: Variable 'theTime' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:1404:33: style: Variable 'Leu' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:1404:46: style: Variable 'Ile' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:1404:59: style: Variable 'Gln' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:1404:72: style: Variable 'Lys' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2205:20: style: Variable 'currPtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2206:20: style: Variable 'nextPtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2732:11: style: Variable 'water' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:2733:12: style: Variable 'ammonia' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:1119:13: style: Array index 'cycle' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:1119:29: style: Array index 'cycle' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:188:11: style: The if condition is the same as the previous if condition [duplicateCondition]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:182:11: note: First condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:188:11: note: Second condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:337:11: style: The if condition is the same as the previous if condition [duplicateCondition]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:331:11: note: First condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:337:11: note: Second condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:512:11: style: The if condition is the same as the previous if condition [duplicateCondition]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:506:11: note: First condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:512:11: note: Second condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:649:11: style: The if condition is the same as the previous if condition [duplicateCondition]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:643:11: note: First condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:649:11: note: Second condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:790:11: style: The if condition is the same as the previous if condition [duplicateCondition]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:784:11: note: First condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:790:11: note: Second condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:912:11: style: The if condition is the same as the previous if condition [duplicateCondition]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:906:11: note: First condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:912:11: note: Second condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:1586:11: style: The if condition is the same as the previous if condition [duplicateCondition]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:1580:11: note: First condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:1586:11: note: Second condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:1735:11: style: The if condition is the same as the previous if condition [duplicateCondition]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:1729:11: note: First condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:1735:11: note: Second condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:1911:11: style: The if condition is the same as the previous if condition [duplicateCondition]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:1905:11: note: First condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:1911:11: note: Second condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:2046:11: style: The if condition is the same as the previous if condition [duplicateCondition]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:2040:11: note: First condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:2046:11: note: Second condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:2187:11: style: The if condition is the same as the previous if condition [duplicateCondition]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:2181:11: note: First condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:2187:11: note: Second condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:2440:11: style: The if condition is the same as the previous if condition [duplicateCondition]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:2434:11: note: First condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:2440:11: note: Second condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:489:85: style: Parameter 'ionPresent' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:1888:82: style: Parameter 'ionPresent' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:1496:13: warning: Uninitialized variable: oldValue [uninitvar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:1486:30: note: Assuming condition is false
lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:1496:13: note: Uninitialized variable: oldValue
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:47:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REAL_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:155:19: error: Array 'lowMassIons[25][3]' accessed at index lowMassIons[*][3], which is out of bounds. [arrayIndexOutOfBounds]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:153:17: note: Assuming that condition 'j<4' is not redundant
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:155:19: note: Array index out of bounds
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:585:8: style: The if condition is the same as the previous if condition [duplicateCondition]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:544:8: note: First condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:585:8: note: Second condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:840:8: style: The if condition is the same as the previous if condition [duplicateCondition]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:808:8: note: First condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:840:8: note: Second condition
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:84:15: style: Condition 'probScore>1' is always false [knownConditionTrueFalse]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:44:21: note: Assignment 'probScore=0', assigned value is 0
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:48:16: note: Assuming condition is false
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:84:15: note: Condition 'probScore>1' is always false
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:570:18: style: Condition 'mass[k]>aIon-gParam.fragmentErr' is always true [knownConditionTrueFalse]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:548:20: note: Assuming that condition 'mass[k]>aIon-gParam.fragmentErr' is not redundant
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:570:18: note: Condition 'mass[k]>aIon-gParam.fragmentErr' is always true
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:824:18: style: Condition 'mass[k]>yIonMin18-gParam.fragmentErr' is always true [knownConditionTrueFalse]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:812:20: note: Assuming that condition 'mass[k]>yIonMin18-gParam.fragmentErr' is not redundant
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:824:18: note: Condition 'mass[k]>yIonMin18-gParam.fragmentErr' is always true
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:40:35: warning: Function 'LutefiskProbScorer' argument order different: declaration 'sequence, seqLength, fragNum, fragMOverZ, argPresent' definition 'sequence, seqLength, ionFound, fragNum, fragMOverZ' [funcArgOrderDifferent]
lutefisk-1.0.7+dfsg.orig/src/LutefiskPrototypes.h:373:36: note: Function 'LutefiskProbScorer' argument order different: declaration 'sequence, seqLength, fragNum, fragMOverZ, argPresent' definition 'sequence, seqLength, ionFound, fragNum, fragMOverZ'
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:40:35: note: Function 'LutefiskProbScorer' argument order different: declaration 'sequence, seqLength, fragNum, fragMOverZ, argPresent' definition 'sequence, seqLength, ionFound, fragNum, fragMOverZ'
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:105:33: warning: Function 'FindImmoniumIons' argument order different: declaration 'mass, ionCount, probScore, randomProb, sequence, seqLength, ' definition 'ionFound, mass, ionCount, score, randomProb, sequence, seqLength' [funcArgOrderDifferent]
lutefisk-1.0.7+dfsg.orig/src/LutefiskPrototypes.h:374:34: note: Function 'FindImmoniumIons' argument order different: declaration 'mass, ionCount, probScore, randomProb, sequence, seqLength, ' definition 'ionFound, mass, ionCount, score, randomProb, sequence, seqLength'
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:105:33: note: Function 'FindImmoniumIons' argument order different: declaration 'mass, ionCount, probScore, randomProb, sequence, seqLength, ' definition 'ionFound, mass, ionCount, score, randomProb, sequence, seqLength'
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:193:33: warning: Function 'FindInternalIons' argument order different: declaration 'mass, ionCount, probScore, randomProb, sequence, seqLength, , ' definition 'ionFound, mass, ionCount, score, randomProb, ionRank, sequence, seqLength' [funcArgOrderDifferent]
lutefisk-1.0.7+dfsg.orig/src/LutefiskPrototypes.h:376:34: note: Function 'FindInternalIons' argument order different: declaration 'mass, ionCount, probScore, randomProb, sequence, seqLength, , ' definition 'ionFound, mass, ionCount, score, randomProb, ionRank, sequence, seqLength'
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:193:33: note: Function 'FindInternalIons' argument order different: declaration 'mass, ionCount, probScore, randomProb, sequence, seqLength, , ' definition 'ionFound, mass, ionCount, score, randomProb, ionRank, sequence, seqLength'
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:477:26: warning: Function 'FindBIons' argument order different: declaration 'mass, ionCount, probScore, randomProb, sequence, seqLength, argPresent, , ' definition 'ionFound, mass, ionCount, sequenceNum, probScore, randomProb, intensity, sequence, seqLength' [funcArgOrderDifferent]
lutefisk-1.0.7+dfsg.orig/src/LutefiskPrototypes.h:379:28: note: Function 'FindBIons' argument order different: declaration 'mass, ionCount, probScore, randomProb, sequence, seqLength, argPresent, , ' definition 'ionFound, mass, ionCount, sequenceNum, probScore, randomProb, intensity, sequence, seqLength'
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:477:26: note: Function 'FindBIons' argument order different: declaration 'mass, ionCount, probScore, randomProb, sequence, seqLength, argPresent, , ' definition 'ionFound, mass, ionCount, sequenceNum, probScore, randomProb, intensity, sequence, seqLength'
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:744:26: warning: Function 'FindYIons' argument order different: declaration 'mass, ionCount, probScore, randomProb, sequence, seqLength, argPresent, , ' definition 'ionFound, mass, ionCount, sequenceNum, probScore, randomProb, intensity, sequence, seqLength' [funcArgOrderDifferent]
lutefisk-1.0.7+dfsg.orig/src/LutefiskPrototypes.h:381:28: note: Function 'FindYIons' argument order different: declaration 'mass, ionCount, probScore, randomProb, sequence, seqLength, argPresent, , ' definition 'ionFound, mass, ionCount, sequenceNum, probScore, randomProb, intensity, sequence, seqLength'
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:744:26: note: Function 'FindYIons' argument order different: declaration 'mass, ionCount, probScore, randomProb, sequence, seqLength, argPresent, , ' definition 'ionFound, mass, ionCount, sequenceNum, probScore, randomProb, intensity, sequence, seqLength'
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:105:50: style: Parameter 'mass' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:106:30: style: Parameter 'randomProb' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:106:49: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:108:9: style: Variable 'lowMassIons' can be declared as const array [constVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:193:50: style: Parameter 'mass' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:194:29: style: Parameter 'randomProb' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:194:64: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:306:29: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:357:49: style: Parameter 'mass' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:428:44: style: Parameter 'mass' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:477:43: style: Parameter 'mass' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:478:14: style: Parameter 'randomProb' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:478:34: style: Parameter 'intensity' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:478:52: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:744:43: style: Parameter 'mass' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:745:14: style: Parameter 'randomProb' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:745:34: style: Parameter 'intensity' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:745:52: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:42:12: style: Unused variable: j [unusedVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:311:15: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:311:10: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:312:10: style: Unused variable: weirdMass [unusedVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:480:19: style: Variable 'ionsInARow' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:480:8: style: Variable 'ionsInARow' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:747:19: style: Variable 'ionsInARow' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:747:8: style: Variable 'ionsInARow' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:778:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:2789:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3629:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:6840:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REAL_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8630:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8833:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:9970:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REAL_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:574:22: error: Array 'databaseSequences[50][60]' accessed at index databaseSequences[*][257], which is out of bounds. [arrayIndexOutOfBounds]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:572:17: note: Assuming that condition 'i<258' is not redundant
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:574:22: note: Array index out of bounds
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:575:17: error: Array 'gDatabaseSeq[50][60]' accessed at index gDatabaseSeq[*][257], which is out of bounds. [arrayIndexOutOfBounds]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:572:17: note: Assuming that condition 'i<258' is not redundant
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:575:17: note: Array index out of bounds
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:713:24: style: Array index 'k' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1440:13: style: Array index 'cycle' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1440:29: style: Array index 'cycle' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8058:22: style: Array index 'k' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4085:22: style: Condition 'currPtr->mOverZ<=(argYIon+gToleranceWide)' is always true [knownConditionTrueFalse]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4075:22: note: Assuming that condition 'currPtr->mOverZ>argYIon+gToleranceWide' is not redundant
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4079:52: note: Assuming condition is false
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4085:22: note: Condition 'currPtr->mOverZ<=(argYIon+gToleranceWide)' is always true
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:6175:64: style: Condition 'currPtr->rank==0' is always true [knownConditionTrueFalse]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:6173:65: note: Assuming that condition 'currPtr->rank==0' is not redundant
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:6175:64: note: Condition 'currPtr->rank==0' is always true
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8349:65: style: Condition 'fragMOverZ[i]>=precurMin2WMinErr' is always true [knownConditionTrueFalse]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8347:21: note: Assuming that condition 'fragMOverZ[i]>=precurMin2WMinErr' is not redundant
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8349:65: note: Condition 'fragMOverZ[i]>=precurMin2WMinErr' is always true
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8351:24: style: Condition 'fragMOverZ[i]<=precurMin2APlusErr' is always true [knownConditionTrueFalse]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8345:20: note: Assuming that condition 'fragMOverZ[i]<=precurMin2APlusErr' is not redundant
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8351:24: note: Condition 'fragMOverZ[i]<=precurMin2APlusErr' is always true
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:304:3: error: Memory leak: string [memleak]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:9392:4: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:9396:4: note: Found duplicate branches for 'if' and 'else'.
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:9392:4: note: Found duplicate branches for 'if' and 'else'.
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8194:16: style: The comparison 'argPresent == 0' is always true. [knownConditionTrueFalse]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8178:20: note: 'argPresent' is assigned value '0' here.
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8194:16: note: The comparison 'argPresent == 0' is always true.
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1584:16: style: Variable 'gGapListIndex' is reassigned a value before the old one has been used. [redundantAssignment]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1535:16: note: gGapListIndex is assigned
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1584:16: note: gGapListIndex is overwritten
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3966:9: style: Variable 'i' is reassigned a value before the old one has been used. [redundantAssignment]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3960:5: note: i is assigned
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3966:9: note: i is overwritten
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:2955:4: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3043:4: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1116:77: style:inconclusive: Function 'GoodSequence' argument 3 names different: declaration 'peptideCorrection' definition 'aaCorrection'. [funcArgNamesDifferent]
lutefisk-1.0.7+dfsg.orig/src/LutefiskPrototypes.h:283:79: note: Function 'GoodSequence' argument 3 names different: declaration 'peptideCorrection' definition 'aaCorrection'.
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1116:77: note: Function 'GoodSequence' argument 3 names different: declaration 'peptideCorrection' definition 'aaCorrection'.
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8740:50: style:inconclusive: Function 'ScoreSequences' argument 1 names different: declaration 'finalSequencePtr' definition 'firstSequencePtr'. [funcArgNamesDifferent]
lutefisk-1.0.7+dfsg.orig/src/LutefiskPrototypes.h:208:50: note: Function 'ScoreSequences' argument 1 names different: declaration 'finalSequencePtr' definition 'firstSequencePtr'.
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8740:50: note: Function 'ScoreSequences' argument 1 names different: declaration 'finalSequencePtr' definition 'firstSequencePtr'.
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:11579:9: style: Local variable 'fp' shadows outer variable [shadowVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:11543:8: note: Shadowed declaration
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:11579:9: note: Shadow variable
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:286:28: style: Parameter 'peptide' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:678:51: style: Parameter 'fragMOverZ' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:679:12: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:749:13: style: Parameter 'fragIntensity' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1060:67: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1116:61: style: Parameter 'peptide' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1116:77: style: Parameter 'aaCorrection' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1188:19: style: Variable 'stopPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1191:19: style: Variable 'checkPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1192:19: style: Variable 'testPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1653:33: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:2213:47: style: Parameter 'byError' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:2725:47: style: Parameter 'fragMOverZ' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:2779:61: style: Parameter 'fragMOverZ' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:2780:17: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:2781:18: style: Parameter 'bFound' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:2894:34: style: Variable 'correctPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:2976:29: style: Variable 'correctPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3062:35: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3200:35: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3328:28: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3353:25: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3391:26: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3438:43: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3438:60: style: Parameter 'fragMOverZ' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3438:79: style: Parameter 'fragIntensity' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3439:16: style: Parameter 'ionFound' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3439:34: style: Parameter 'ionFoundTemplate' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3441:16: style: Parameter 'yFound' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3441:32: style: Parameter 'bFound' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3442:15: style: Parameter 'charSequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3442:37: style: Parameter 'byError' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3442:53: style: Parameter 'ionType' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3613:65: style: Parameter 'fragMOverZ' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3944:63: style: Parameter 'ionFoundTemplate' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4107:33: style: Parameter 'fragIntensity' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4107:56: style: Parameter 'ionFound' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4169:58: style: Parameter 'fragMOverZ' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:5032:44: style: Parameter 'currPtr' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:5064:41: style: Parameter 'currPtr' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:6273:18: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:6273:35: style: Parameter 'charSequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:6336:58: style: Parameter 'ionFound' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:6373:54: style: Parameter 'ionFound' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:6500:48: style: Parameter 'fragMOverZ' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:6500:67: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:6501:31: style: Parameter 'lowMassIons' can be declared as const array [constParameter]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:6766:51: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:6825:50: style: Parameter 'highMZFrags' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:6825:70: style: Parameter 'highMZInts' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8022:44: style: Parameter 'fragMOverZ' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8023:12: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8173:54: style: Parameter 'fragMOverZ' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8174:12: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8311:56: style: Parameter 'fragMOverZ' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8311:75: style: Parameter 'fragIntensity' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8379:55: style: Parameter 'fragMOverZ' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8470:58: style: Parameter 'fragMOverZ' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8471:13: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8564:44: style: Parameter 'fragMOverZ' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:9530:32: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:9530:81: style: Parameter 'fragMOverZ' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:9836:42: style: Parameter 'ionFoundTemplate' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:10045:32: style: Parameter 'mass' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:10046:34: style: Parameter 'randomProb' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:10046:53: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:10199:32: style: Parameter 'mass' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:10200:33: style: Parameter 'randomProb' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:10200:52: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:10313:29: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:10420:49: style: Parameter 'mass' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:10496:25: style: Parameter 'mass' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:10497:14: style: Parameter 'randomProb' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:11049:25: style: Parameter 'mass' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:11050:14: style: Parameter 'randomProb' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:11797:51: style: Parameter 'fragMOverZ' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:2959:5: warning: Uninitialized variable: test [uninitvar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:2923:16: note: Assuming condition is false
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:2959:5: note: Uninitialized variable: test
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8698:4: warning: Uninitialized variable: destroyPtr [uninitvar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8688:20: note: Assuming condition is false
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8698:4: note: Uninitialized variable: destroyPtr
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:310:8: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1189:26: style: Variable 'newPtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1191:28: style: Variable 'checkPtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1192:27: style: Variable 'testPtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1194:17: style: Variable 'p' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1194:24: style: Variable 'q' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1248:11: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1191:19: style: Variable 'checkPtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1192:19: style: Variable 'testPtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1194:15: style: Variable 'p' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1194:22: style: Variable 'q' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1784:19: style: Variable 'lcqBIonIntensity' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:2662:23: style: Variable 'intensityDiff' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:2696:22: style: Variable 'confidenceLimitLow' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:2917:14: style: Variable 'lowestScore' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:2953:5: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:2961:4: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3006:14: style: Variable 'lowestScore' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3041:5: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3049:4: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:3554:24: style: Variable 'lowMassIonConversion' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4111:18: style: Variable 'numScore' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4111:9: style: Variable 'numScore' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4181:26: style: Variable 'monoToAvYSwitch' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4182:26: style: Variable 'avToMonoBSwitch' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4294:9: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4315:13: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4355:10: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4364:13: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4181:10: style: Variable 'monoToAvYSwitch' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4182:10: style: Variable 'avToMonoBSwitch' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4473:22: style: Variable 'peptideString' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4475:22: style: Variable 'peptideLength' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4478:28: style: Variable 'theTime' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4478:20: style: Variable 'theTime' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:7169:26: style: Variable 'monoToAvYSwitch' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:7170:26: style: Variable 'avToMonoBSwitch' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:7244:11: style: Variable 'bOrYIon' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:7381:16: style: Variable 'bOrYIon' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:7719:16: style: Variable 'bOrYIon' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:7169:10: style: Variable 'monoToAvYSwitch' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:7170:10: style: Variable 'avToMonoBSwitch' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8746:34: style: Variable 'averageBYScore' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8746:54: style: Variable 'highestBYScore' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8750:37: style: Variable 'realSeqLengthNoFudgingAtAll' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8755:19: style: Variable 'probScore' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8757:25: style: Variable 'aSequenceFound' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8850:18: style: Variable 'aSequenceFound' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8870:12: style: Variable 'precursor' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8887:18: style: Variable 'aSequenceFound' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8985:19: style: Variable 'aSequenceFound' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8997:19: style: Variable 'aSequenceFound' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:9011:18: style: Variable 'aSequenceFound' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:9023:18: style: Variable 'aSequenceFound' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:9276:4: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:9408:18: style: Variable 'aSequenceFound' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:9421:18: style: Variable 'aSequenceFound' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:9432:18: style: Variable 'aSequenceFound' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:9458:18: style: Variable 'aSequenceFound' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8746:19: style: Variable 'averageBYScore' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8746:39: style: Variable 'highestBYScore' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8758:10: style: Unused variable: test [unusedVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:9841:30: style: Variable 'previousPtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:9984:4: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:10318:15: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:10318:10: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:11560:16: style: Variable 'length' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:206:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:977:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:1834:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:2241:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:310:18: style: Array index 'i' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:994:21: style: Array index 'i' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:1188:25: style: Array index 'i' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:1221:22: style: Array index 'i' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:1512:20: style: Array index 'testValue' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:1558:25: style: Array index 'j' is used before limits check. [arrayIndexThenCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:76:5: warning: Either the condition 'newSubsequencePtr==0' is redundant or there is possible null pointer dereference: newSubsequencePtr. [nullPointerRedundantCheck]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:76:58: note: Assuming that condition 'newSubsequencePtr==0' is not redundant
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:76:5: note: Null pointer dereference
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:72:54: style: Variable 'lastPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:189:50: style: Parameter 'sequenceNode' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:550:29: style: Variable 'correctPtr' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:629:25: style: Parameter 'peptide' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:629:62: style: Parameter 'aaPresentMass' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:960:9: style: Parameter 'lastNode' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:967:9: style: Parameter 'sequenceNode' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:1144:20: style: Variable 'n3' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:1145:20: style: Variable 'n4' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:1283:9: style: Parameter 'oneEdgeNodes' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:1722:49: style: Parameter 'peptide' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:1775:44: style: Parameter 'peptide' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:1817:47: style: Parameter 'sequenceNode' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:119:11: style: Variable 'lastPtr' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:559:4: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:572:14: style: Variable 'lowestScore' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:619:4: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:840:10: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:840:8: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:1458:40: style: Variable 'z' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:1458:39: style: Variable 'z' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:2193:14: style: Variable 'finalSeqNum' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSummedNode.c:127:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSummedNode.c:57:48: style: Parameter 'sequenceNodeN' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSummedNode.c:58:13: style: Parameter 'sequenceNodeC' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSummedNode.c:58:34: style: Parameter 'evidence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSummedNode.c:220:30: style: Parameter 'sequenceNode' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSummedNode.c:261:66: style: Parameter 'evidence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSummedNode.c:262:39: style: Parameter 'sequenceNodeC' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSummedNode.c:263:13: style: Parameter 'sequenceNodeN' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSummedNode.c:309:63: style: Parameter 'evidence' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSummedNode.c:310:34: style: Parameter 'sequenceNodeC' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSummedNode.c:311:13: style: Parameter 'sequenceNodeN' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSummedNode.c:378:55: style: Parameter 'sequenceNodeC' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSummedNode.c:379:15: style: Parameter 'sequenceNodeN' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSummedNode.c:314:10: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskSummedNode.c:314:8: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskXCorr.c:510:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REAL_4 [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/LutefiskXCorr.c:520:6: style: Condition '!spectrum2' is always false [knownConditionTrueFalse]
lutefisk-1.0.7+dfsg.orig/src/LutefiskXCorr.c:244:40: style: Variable 'pSeq' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskXCorr.c:480:11: style: Variable 'pSeq' can be declared as pointer to const [constVariablePointer]
lutefisk-1.0.7+dfsg.orig/src/LutefiskXCorr.c:484:12: style: Variable 'tolerance' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskXCorr.c:495:12: style: Variable 'offset' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskXCorr.c:681:18: style: Variable 'AionMass' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskXCorr.c:693:18: style: Variable 'AionMass' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskXCorr.c:704:20: style: Variable 'AionMass' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskXCorr.c:712:20: style: Variable 'AionMass' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskXCorr.c:752:18: style: Variable 'YionMass' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskXCorr.c:812:18: style: Variable 'YionMass' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskXCorr.c:826:18: style: Variable 'YionMass' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/LutefiskXCorr.c:860:21: style: Variable 'fragmentMass' is assigned a value that is never used. [unreadVariable]
lutefisk-1.0.7+dfsg.orig/src/getopt.c:28:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
lutefisk-1.0.7+dfsg.orig/src/getopt.c:19:45: style: Parameter 'opts' can be declared as pointer to const [constParameterPointer]
lutefisk-1.0.7+dfsg.orig/src/getopt.c:23:24: style: Variable 'cp' can be declared as pointer to const [constVariablePointer]
diff:
head lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:2018:18: style: Variable 'previousPtr' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:3575:18: style: Variable 'windowStartPtr' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskGetCID.c:573:16: style: Variable 'quality' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskHaggis.c:1507:7: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:245:42: style: Variable 'firstRawDataPtr' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskMain.c:247:29: style: Variable 'theTime' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskMakeGraph.c:1119:29: style: Array index 'cycle' is used before limits check. [arrayIndexThenCheck]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:311:10: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:480:8: style: Variable 'ionsInARow' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskProbScorer.c:747:8: style: Variable 'ionsInARow' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:10318:10: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1191:19: style: Variable 'checkPtr' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1192:19: style: Variable 'testPtr' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1194:15: style: Variable 'p' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1194:22: style: Variable 'q' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:1440:29: style: Array index 'cycle' is used before limits check. [arrayIndexThenCheck]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4111:9: style: Variable 'numScore' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4181:10: style: Variable 'monoToAvYSwitch' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4182:10: style: Variable 'avToMonoBSwitch' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:4478:20: style: Variable 'theTime' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:7169:10: style: Variable 'monoToAvYSwitch' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:7170:10: style: Variable 'avToMonoBSwitch' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8746:19: style: Variable 'averageBYScore' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskScore.c:8746:39: style: Variable 'highestBYScore' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:1458:39: style: Variable 'z' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskSubseqMaker.c:840:8: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
head lutefisk-1.0.7+dfsg.orig/src/LutefiskSummedNode.c:314:8: style: Variable 'i' is assigned a value that is never used. [unreadVariable]


DONE