2026-05-03 05:22
ftp://ftp.de.debian.org/debian/pool/main/libm/libmuscle/libmuscle_3.7+4565.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=openmp  --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-6.8.0-111-generic-x86_64-with-glibc2.39
python: 3.12.3
client-version: 1.3.70
compiler: g++ (Ubuntu 14.2.0-4ubuntu2~24.04.1) 14.2.0
cppcheck: head 2.20.0
head-info: e5c4a73 (2026-05-01 11:10:43 +0200)
count: 562 562
elapsed-time: 7.0 6.0
head-timing-info:

old-timing-info:

head results:
libmuscle-3.7+4565/libMUSCLE/aligngivenpath.cpp:112:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_GL [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/aligngivenpath.cpp:661:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ProfPos [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/aligngivenpath.cpp:306:12: style: Local variable 'uColCountA' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/aligngivenpath.cpp:269:17: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/aligngivenpath.cpp:306:12: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/aligngivenpath.cpp:316:12: style: Local variable 'uColCountB' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/aligngivenpath.cpp:270:17: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/aligngivenpath.cpp:316:12: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/aligngivenpath.cpp:668:18: style: Local variable 'uPrefixLengthA' shadows outer argument [shadowArgument]
libmuscle-3.7+4565/libMUSCLE/aligngivenpath.cpp:646:31: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/aligngivenpath.cpp:668:18: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/aligngivenpath.cpp:669:18: style: Local variable 'uPrefixLengthB' shadows outer argument [shadowArgument]
libmuscle-3.7+4565/libMUSCLE/aligngivenpath.cpp:647:31: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/aligngivenpath.cpp:669:18: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/aligngivenpath.cpp:188:26: style: Variable 'uLengthA' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/aligngivenpath.cpp:189:26: style: Variable 'uLengthB' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/aligngivenpathsw.cpp:178:12: style: Local variable 'uColCountA' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/aligngivenpathsw.cpp:141:17: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/aligngivenpathsw.cpp:178:12: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/aligngivenpathsw.cpp:188:12: style: Local variable 'uColCountB' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/aligngivenpathsw.cpp:142:17: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/aligngivenpathsw.cpp:188:12: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/aligngivenpathsw.cpp:60:26: style: Variable 'uLengthA' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/aligngivenpathsw.cpp:61:26: style: Variable 'uLengthB' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/aligntwomsas.cpp:21:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_scoreGapOpen [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/aligntwomsas.cpp:33:5: style: Variable 'r' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/aligntwoprofs.cpp:21:5: style: Variable 'r' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/aln.cpp:22:5: error: There is an unknown macro here somewhere. Configuration is required. If MUSCLE_MAJOR_VERSION is a macro then please configure it. [unknownMacro]
libmuscle-3.7+4565/libMUSCLE/alpha.cpp:117:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AX_GAP [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/alpha.cpp:125:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NX_A [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/alpha.cpp:145:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NX_A [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/alpha.cpp:166:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AX_A [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/anchoredpp.cpp:224:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uInsane [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/anchoredpp.cpp:277:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SCORE [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/anchoredpp.cpp:45:7: style: The scope of the variable 'bLeftTermGap' can be reduced. [variableScope]
libmuscle-3.7+4565/libMUSCLE/anchoredpp.cpp:60:7: style: The scope of the variable 'bRightTermGap' can be reduced. [variableScope]
libmuscle-3.7+4565/libMUSCLE/anchoredpp.cpp:121:7: style: The scope of the variable 'bLeftTermGap' can be reduced. [variableScope]
libmuscle-3.7+4565/libMUSCLE/anchoredpp.cpp:136:7: style: The scope of the variable 'bRightTermGap' can be reduced. [variableScope]
libmuscle-3.7+4565/libMUSCLE/anchoredpp.cpp:41:7: style: Variable 'bGapping1' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/anchoredpp.cpp:42:7: style: Variable 'bGapping2' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/anchoredpp.cpp:486:12: style: Unused variable: uId [unusedVariable]
libmuscle-3.7+4565/libMUSCLE/anchors.cpp:63:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MINUS_INFINITY [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/anchors.cpp:158:5: style: Variable 'uAnchorCol' is assigned an expression that holds the same value. [redundantAssignment]
libmuscle-3.7+4565/libMUSCLE/anchors.cpp:144:26: note: uBestColIndex is assigned 'BestCols[n]' here.
libmuscle-3.7+4565/libMUSCLE/anchors.cpp:149:39: note: Assuming condition is false
libmuscle-3.7+4565/libMUSCLE/anchors.cpp:158:5: note: Variable 'uAnchorCol' is assigned an expression that holds the same value.
libmuscle-3.7+4565/libMUSCLE/anchors.cpp:108:12: style: Parameter 'BestCols' can be declared as const array [constParameter]
libmuscle-3.7+4565/libMUSCLE/anchors.cpp:164:27: style: Variable 'uWindowCenter' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/bittraceback.cpp:22:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BIT_xM [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/bittraceback.cpp:64:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BIT_xM [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/bittraceback.cpp:163:8: style: Local variable 'Bits' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/bittraceback.cpp:149:7: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/bittraceback.cpp:163:8: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/bittraceback.cpp:149:7: style: Variable 'Bits' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:12:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Nodes [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:24:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Nodes [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:31:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrSet [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:125:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:169:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_JoinStyle [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:248:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Nodes [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:286:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uInsane [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:297:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_CentroidStyle [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:373:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uClusterCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:404:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:439:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:446:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uLeafCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:482:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uLeafCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:492:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uLeafCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:505:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uTriangularMatrixSize [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:512:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_dDist [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:518:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_dDist [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:556:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:563:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrClusterList [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:570:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Nodes [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:578:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:599:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:613:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_JoinStyle [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:641:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uInsane [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:186:31: style: Variable 'uClusterCount' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:206:31: style: Variable 'uClusterCount' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/clust.cpp:362:22: style: Variable 'dDistLR' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/cluster.cpp:94:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrLeft [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/cluster.cpp:110:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrLeft [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/cluster.cpp:124:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrLeft [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/cluster.cpp:168:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrLeft [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/cluster.cpp:194:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrDisjoints [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/cluster.cpp:209:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrDisjoints [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/cluster.cpp:218:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrDisjoints [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/cluster.cpp:225:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Nodes [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/cluster.cpp:230:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrDisjoints [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/cluster.cpp:239:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Nodes [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/cluster.cpp:246:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uLeafCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/cluster.cpp:269:18: style: Variable 'dMaxDist' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/color.cpp:172:8: style: Local variable 'c' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/color.cpp:150:6: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/color.cpp:172:8: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/cons.cpp:34:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAX_ALPHA [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/diaglist.cpp:12:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/diaglist.cpp:29:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/diaglist.cpp:36:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/diaglist.cpp:84:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/diaglist.cpp:222:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/diaglist.cpp:313:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Diags [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/diaglist.cpp:323:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/diaglist.cpp:188:2: style:inconclusive: Statements following 'return' will never be executed. [unreachableCode]
libmuscle-3.7+4565/libMUSCLE/diaglist.cpp:311:2: style: Statements following 'return' will never be executed. [unreachableCode]
libmuscle-3.7+4565/libMUSCLE/diffobjscore.cpp:78:27: style: Variable 'uSeqCount' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/diffpaths.cpp:25:22: style: Variable 'Edge1' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/diffpaths.cpp:26:22: style: Variable 'Edge2' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/difftrees.cpp:227:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_NEIGHBOR [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/difftreese.cpp:132:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NODE_CHANGED [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/distcalc.cpp:12:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrDF [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/distcalc.cpp:38:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrMSA [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/distcalc.cpp:46:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Distance [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/distfunc.cpp:9:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Dists [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/distfunc.cpp:18:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Names [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/distfunc.cpp:30:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Dists [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/distfunc.cpp:35:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/distfunc.cpp:40:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/distfunc.cpp:56:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Dists [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/distfunc.cpp:62:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/distfunc.cpp:68:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/distfunc.cpp:73:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/distfunc.cpp:79:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/distfunc.cpp:85:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/distfunc.cpp:91:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/distfunc.cpp:97:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/distpwkimura.cpp:12:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQWEIGHT_Henikoff [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/domuscle.cpp:36:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Undefined [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/domuscle.cpp:79:37: warning:inconclusive: Either the condition '0==uSeqCount' is redundant or there is division by zero at line 79. [zerodivcond]
libmuscle-3.7+4565/libMUSCLE/domuscle.cpp:90:8: note: Assuming that condition '0==uSeqCount' is not redundant
libmuscle-3.7+4565/libMUSCLE/domuscle.cpp:79:37: note: Division by zero
libmuscle-3.7+4565/libMUSCLE/dosp.cpp:17:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Undefined [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/dosp.cpp:56:22: style: C-style reference casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/dpreglist.cpp:9:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/dpreglist.cpp:20:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/dpreglist.cpp:28:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/dpreglist.cpp:72:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPREGIONTYPE_Rect [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/dpreglist.cpp:84:40: style: Variable 'uDiagLengthMinusCaps' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/edgelist.cpp:8:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNode1 [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/edgelist.cpp:21:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNode1 [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/edgelist.cpp:31:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/edgelist.cpp:40:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/edgelist.cpp:45:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/edgelist.cpp:66:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCacheSize [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/edgelist.cpp:83:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/estring.cpp:190:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cType [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/estring.cpp:245:7: style: Local variable 'cPrevEdgeType' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/estring.cpp:191:7: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/estring.cpp:245:7: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/estring.cpp:306:7: style: Local variable 'cPrevEdgeType' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/estring.cpp:191:7: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/estring.cpp:306:7: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/fasta.cpp:18:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uInsane [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/fasta.cpp:17:21: style: Variable 'uSeqCount' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/fasta.cpp:18:21: style: Variable 'uColCount' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/fasta2.cpp:34:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/fasta2.cpp:72:15: style: Variable 'BufferLength' is reassigned a value before the old one has been used. [redundantAssignment]
libmuscle-3.7+4565/libMUSCLE/fasta2.cpp:69:2: note: BufferLength is assigned
libmuscle-3.7+4565/libMUSCLE/fasta2.cpp:72:15: note: BufferLength is overwritten
libmuscle-3.7+4565/libMUSCLE/fasta2.cpp:39:7: style: Local variable 'c' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/fasta2.cpp:33:6: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/fasta2.cpp:39:7: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/fasta2.cpp:56:7: style: Local variable 'c' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/fasta2.cpp:33:6: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/fasta2.cpp:56:7: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/fasta2.cpp:78:7: style: Local variable 'c' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/fasta2.cpp:33:6: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/fasta2.cpp:78:7: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:25:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LINKAGE_Undefined [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:74:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLUSTER_NeighborJoining [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:56:10: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:51:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:51:17: note: Assignment 'f=fopen(FileName,"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:56:10: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:59:11: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:51:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:51:17: note: Assignment 'f=fopen(FileName,"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:59:11: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:61:12: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:51:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:51:17: note: Assignment 'f=fopen(FileName,"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:61:12: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:62:11: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:51:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:51:17: note: Assignment 'f=fopen(FileName,"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:62:11: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:64:9: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:51:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:51:17: note: Assignment 'f=fopen(FileName,"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/fastclust.cpp:64:9: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/fastdistjones.cpp:133:10: warning: If memory allocation fails, then there is a possible null pointer dereference: SeqList [nullPointerOutOfMemory]
libmuscle-3.7+4565/libMUSCLE/fastdistjones.cpp:124:53: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/fastdistjones.cpp:124:28: note: Assignment 'SeqList=(unsigned short*)malloc(uSeqListBytes)', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/fastdistjones.cpp:129:9: note: Assuming condition is false
libmuscle-3.7+4565/libMUSCLE/fastdistjones.cpp:133:10: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/fastdistjones.cpp:34:23: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/fastdistjones.cpp:43:17: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/fastdistjones.cpp:124:28: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/fastdistkbit.cpp:20:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AX_Y [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/fastdistkmer.cpp:87:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable byte [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/fastdistkmer.cpp:238:14: style: Variable 'KD' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/fastdistmafft.cpp:199:19: style: Local variable 'uTupleCount' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/fastdistmafft.cpp:165:18: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/fastdistmafft.cpp:199:19: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/fastdistmafft.cpp:200:20: style: Local variable 'L' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/fastdistmafft.cpp:166:19: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/fastdistmafft.cpp:200:20: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/fastdistmafft.cpp:241:22: style: Variable 'pName1' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/fastdistnuc.cpp:100:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_DNA [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/fastdistnuc.cpp:184:19: style: Local variable 'uTupleCount' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/fastdistnuc.cpp:150:18: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/fastdistnuc.cpp:184:19: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/fastdistnuc.cpp:185:20: style: Local variable 'L' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/fastdistnuc.cpp:151:19: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/fastdistnuc.cpp:185:20: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/fastdistnuc.cpp:226:22: style: Variable 'pName1' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/fastscorepath2.cpp:44:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_scoreGapClose [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/finddiags.cpp:35:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uResidueGroup [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/finddiags.cpp:61:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Amino [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/finddiagsn.cpp:35:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uResidueGroup [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/finddiagsn.cpp:47:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_DNA [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/finddiagsn.cpp:22:17: style: Unsigned expression 'Letter' can't be negative so it is unnecessary to test it. [unsignedPositive]
libmuscle-3.7+4565/libMUSCLE/glbaligndiag.cpp:65:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Amino [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/glbaligndiag.cpp:26:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:40:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uLength [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:128:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GapOpenA [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:226:9: style: Local variable 'scoreSum' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:193:8: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:226:9: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:227:13: style: Local variable 'ptrSortOrderAi' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:194:12: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:227:13: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:228:19: style: Local variable 'ptrSortOrderAEnd' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:195:18: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:228:19: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:229:11: style: Local variable 'ptrFreqsAi' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:196:10: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:229:11: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:272:24: style: Local variable 'ptrSortOrderAi' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:194:12: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:272:24: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:382:10: style: Local variable 'd' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:320:9: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:382:10: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:383:10: style: Local variable 'DNew' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:321:9: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:383:10: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:196:10: style: Variable 'ptrFreqsAi' can be declared as pointer to const [constVariablePointer]
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:229:11: style: Variable 'ptrFreqsAi' can be declared as pointer to const [constVariablePointer]
libmuscle-3.7+4565/libMUSCLE/glbalignle.cpp:281:11: style: Variable 'ptrNSBR' can be declared as pointer to const [constVariablePointer]
libmuscle-3.7+4565/libMUSCLE/glbalignsimple.cpp:106:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MINUS_INFINITY [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/glbalignsimple.cpp:277:13: style: Redundant initialization for 'cEdgeType'. The initialized value is overwritten before it is read. [redundantInitialization]
libmuscle-3.7+4565/libMUSCLE/glbalignsimple.cpp:272:17: note: cEdgeType is initialized
libmuscle-3.7+4565/libMUSCLE/glbalignsimple.cpp:277:13: note: cEdgeType is overwritten
libmuscle-3.7+4565/libMUSCLE/glbalignsimple.cpp:92:9: style: Variable 'DPL_' can be declared as pointer to const [constVariablePointer]
libmuscle-3.7+4565/libMUSCLE/glbalignsimple.cpp:92:9: style: Variable 'DPL_' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:34:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uLength [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:111:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GapOpenA [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:240:3: style: Variable 'ptrMCurr_j' is assigned an expression that holds the same value. [redundantAssignment]
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:216:21: note: ptrMCurr_j is assigned 'MCurr' here.
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:230:10: note: Assuming condition is false
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:240:3: note: Variable 'ptrMCurr_j' is assigned an expression that holds the same value.
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:188:9: style: Local variable 'scoreSum' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:164:8: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:188:9: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:189:13: style: Local variable 'ptrSortOrderAi' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:165:12: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:189:13: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:190:19: style: Local variable 'ptrSortOrderAEnd' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:166:18: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:190:19: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:191:11: style: Local variable 'ptrFreqsAi' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:167:10: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:191:11: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:223:24: style: Local variable 'ptrSortOrderAi' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:165:12: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:223:24: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:321:10: style: Local variable 'd' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:259:9: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:321:10: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:322:10: style: Local variable 'DNew' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:260:9: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:322:10: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:167:10: style: Variable 'ptrFreqsAi' can be declared as pointer to const [constVariablePointer]
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:191:11: style: Variable 'ptrFreqsAi' can be declared as pointer to const [constVariablePointer]
libmuscle-3.7+4565/libMUSCLE/glbalignsp.cpp:232:11: style: Variable 'ptrNSBR' can be declared as pointer to const [constVariablePointer]
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:32:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uLength [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:66:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uLength [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:138:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_DNA [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:275:3: style: Variable 'ptrMCurr_j' is assigned an expression that holds the same value. [redundantAssignment]
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:251:21: note: ptrMCurr_j is assigned 'MCurr' here.
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:265:10: note: Assuming condition is false
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:275:3: note: Variable 'ptrMCurr_j' is assigned an expression that holds the same value.
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:223:9: style: Local variable 'scoreSum' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:199:8: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:223:9: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:224:13: style: Local variable 'ptrSortOrderAi' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:200:12: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:224:13: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:225:19: style: Local variable 'ptrSortOrderAEnd' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:201:18: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:225:19: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:226:11: style: Local variable 'ptrFreqsAi' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:202:10: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:226:11: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:258:24: style: Local variable 'ptrSortOrderAi' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:200:12: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:258:24: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:356:10: style: Local variable 'd' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:294:9: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:356:10: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:357:10: style: Local variable 'DNew' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:295:9: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:357:10: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:202:10: style: Variable 'ptrFreqsAi' can be declared as pointer to const [constVariablePointer]
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:226:11: style: Variable 'ptrFreqsAi' can be declared as pointer to const [constVariablePointer]
libmuscle-3.7+4565/libMUSCLE/glbalignspn.cpp:267:11: style: Variable 'ptrNSBR' can be declared as pointer to const [constVariablePointer]
libmuscle-3.7+4565/libMUSCLE/glbalignss.cpp:45:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uLength [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/glbalignss.cpp:100:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AX_X [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/glbalignss.cpp:114:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AX_X [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/glbalignss.cpp:127:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPrev [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/glbalignss.cpp:265:10: style: Local variable 'd' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignss.cpp:208:9: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignss.cpp:265:10: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignss.cpp:266:10: style: Local variable 'DNew' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignss.cpp:209:9: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/glbalignss.cpp:266:10: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/glbalignss.cpp:182:13: style: Variable 'ptrLettersB' can be declared as pointer to const [constVariablePointer]
libmuscle-3.7+4565/libMUSCLE/glbalignss.cpp:122:31: style: Variable 'uPrefixCountA' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignss.cpp:123:31: style: Variable 'uPrefixCountB' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/glbalignss.cpp:180:24: style: Variable 'ptrRowA' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/glbalndimer.cpp:20:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MINUS_INFINITY [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/glbalndimer.cpp:161:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MINUS_INFINITY [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/glbalndimer.cpp:335:17: style: Variable 'uPrefixCountA' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/globals.cpp:62:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _SH_DENYNO [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/globals.cpp:98:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/globals.cpp:125:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/globals.cpp:82:30: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
libmuscle-3.7+4565/libMUSCLE/globals.cpp:83:22: style: Obsolete function 'asctime' called. It is recommended to use 'strftime' instead. [prohibitedasctimeCalled]
libmuscle-3.7+4565/libMUSCLE/globals.cpp:269:13: style: Same expression ''.'==c' found multiple times in chain of '||' operators. [duplicateExpression]
libmuscle-3.7+4565/libMUSCLE/globals.cpp:82:13: style: Variable 'ptmCurrentTime' can be declared as pointer to const [constVariablePointer]
libmuscle-3.7+4565/libMUSCLE/globals.cpp:75:2: error: va_list 'ArgList' was opened but not closed by va_end(). [va_end_missing]
libmuscle-3.7+4565/libMUSCLE/globals.cpp:115:2: error: va_list 'ArgList' was opened but not closed by va_end(). [va_end_missing]
libmuscle-3.7+4565/libMUSCLE/globals.cpp:127:2: error: va_list 'ArgList' was opened but not closed by va_end(). [va_end_missing]
libmuscle-3.7+4565/libMUSCLE/globalsother.cpp:34:34: style: Parameter 'argv' can be declared as const array [constParameter]
libmuscle-3.7+4565/libMUSCLE/henikoffweight.cpp:27:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAX_ALPHA [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/henikoffweight.cpp:64:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Weights [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/henikoffweightpb.cpp:30:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAX_ALPHA [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/henikoffweightpb.cpp:87:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Weights [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/henikoffweightpb.cpp:99:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Weights [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/henikoffweightpb.cpp:43:16: style: Local variable 'uLetter' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/henikoffweightpb.cpp:32:11: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/henikoffweightpb.cpp:43:16: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/henikoffweightpb.cpp:60:12: style: Local variable 'uLetter' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/henikoffweightpb.cpp:32:11: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/henikoffweightpb.cpp:60:12: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/html.cpp:90:6: style: The scope of the variable 'CurrentColor' can be reduced. [variableScope]
libmuscle-3.7+4565/libMUSCLE/html.cpp:90:19: style: Variable 'CurrentColor' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/hydro.cpp:11:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Amino [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/intmath.cpp:9:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MINUS_INFINITY [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/intmath.cpp:24:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MINUS_INFINITY [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/intmath.cpp:35:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MINUS_INFINITY [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/intmath.cpp:43:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INTSCALE [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/intmath.cpp:48:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INTSCALE [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/intmath.cpp:53:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INTSCALE [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/intmath.cpp:80:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MINUS_INFINITY [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/intmath.cpp:135:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MINUS_INFINITY [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/local.cpp:42:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Undefined [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/main.cpp:38:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MUSCLE_LONG_VERSION [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/makerootmsa.cpp:91:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_NEIGHBOR [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/makerootmsa.cpp:145:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_NEIGHBOR [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/makerootmsa.cpp:167:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uInsane [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/makerootmsa.cpp:20:17: style: Variable 'uSeqLength' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/makerootmsa.cpp:95:22: style: Variable 'Path' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/makerootmsa.cpp:169:32: style: Variable 'uTreeNodeCount' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/makerootmsab.cpp:28:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MINUS_INFINITY [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/makerootmsab.cpp:58:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Prof [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/makerootmsab.cpp:37:20: warning: Assert statement modifies 'uLengthOut'. [assignmentInAssert]
libmuscle-3.7+4565/libMUSCLE/mhack.cpp:20:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Amino [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/mhack.cpp:42:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Amino [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:16:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:37:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:64:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:124:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:145:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:162:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uColCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:180:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:190:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:209:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:236:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:329:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uColCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:356:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:365:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:372:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:433:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_SeqIndexToId [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:453:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:466:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:472:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:528:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Weights [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:590:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Weights [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:597:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAX_ALPHA [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:668:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:687:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_IdToSeqIndex [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:695:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:708:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:716:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BTInsane [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:745:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:756:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_IdToSeqIndex [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:798:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uSeqCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:826:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Amino [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:161:8: style: Local variable 'c' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/msa.cpp:157:7: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/msa.cpp:161:8: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/msa2.cpp:27:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FCOUNT [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa2.cpp:407:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQWEIGHT_ClustalW [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa2.cpp:437:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_NEIGHBOR [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/msa2.cpp:57:20: style: Local variable 'uLetter' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/msa2.cpp:40:19: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/msa2.cpp:57:20: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/msa2.cpp:78:20: style: Local variable 'uLetter' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/msa2.cpp:40:19: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/msa2.cpp:78:20: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/msa2.cpp:479:30: style: Variable 'uColCountCat' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/msf.cpp:74:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_DNA [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/muscle.cpp:17:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Undefined [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/muscle.cpp:60:37: warning:inconclusive: Either the condition '0==uSeqCount' is redundant or there is division by zero at line 60. [zerodivcond]
libmuscle-3.7+4565/libMUSCLE/muscle.cpp:72:8: note: Assuming that condition '0==uSeqCount' is not redundant
libmuscle-3.7+4565/libMUSCLE/muscle.cpp:60:37: note: Division by zero
libmuscle-3.7+4565/libMUSCLE/nwsmall.cpp:386:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BIT_MM [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/nwsmall.cpp:407:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BIT_MD [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/nwsmall.cpp:425:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BIT_MI [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/nwsmall.cpp:526:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MINUS_INFINITY [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/nwsmall.cpp:635:6: style: Variable 'Iij' is reassigned a value before the old one has been used. [redundantAssignment]
libmuscle-3.7+4565/libMUSCLE/nwsmall.cpp:610:3: note: Iij is assigned
libmuscle-3.7+4565/libMUSCLE/nwsmall.cpp:635:6: note: Iij is overwritten
libmuscle-3.7+4565/libMUSCLE/objscore.cpp:22:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJSCORE_SPM [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/objscore.cpp:48:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
libmuscle-3.7+4565/libMUSCLE/objscore2.cpp:349:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_bAllGaps [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/objscore2.cpp:413:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PPSCORE_LE [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/objscore2.cpp:69:7: style: The scope of the variable 'bLeftTermGap' can be reduced. [variableScope]
libmuscle-3.7+4565/libMUSCLE/objscore2.cpp:84:7: style: The scope of the variable 'bRightTermGap' can be reduced. [variableScope]
libmuscle-3.7+4565/libMUSCLE/objscore2.cpp:142:7: style: The scope of the variable 'bLeftTermGap' can be reduced. [variableScope]
libmuscle-3.7+4565/libMUSCLE/objscore2.cpp:157:7: style: The scope of the variable 'bRightTermGap' can be reduced. [variableScope]
libmuscle-3.7+4565/libMUSCLE/objscore2.cpp:65:7: style: Variable 'bGapping1' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/objscore2.cpp:66:7: style: Variable 'bGapping2' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/objscore2.cpp:316:28: style: Variable 'uColCount2' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/onexception.cpp:13:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/options.cpp:154:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/options.cpp:188:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/options.cpp:198:9: style: Variable 'Value' can be declared as pointer to const [constVariablePointer]
libmuscle-3.7+4565/libMUSCLE/outweights.cpp:16:11: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/outweights.cpp:8:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/outweights.cpp:8:17: note: Assignment 'f=fopen(FileName,"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/outweights.cpp:16:11: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/outweights.cpp:18:9: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/outweights.cpp:8:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/outweights.cpp:8:17: note: Assignment 'f=fopen(FileName,"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/outweights.cpp:18:9: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/params.cpp:164:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MUSCLE_LONG_VERSION [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/params.cpp:229:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SCORE [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/params.cpp:258:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DISTANCE_Kmer6_6 [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/params.cpp:275:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DISTANCE_Kmer6_6 [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/params.cpp:300:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fInsane [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/params.cpp:330:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DISTANCE_Kmer4_6 [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/params.cpp:428:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DISTANCE_Opts [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/params.cpp:440:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PPSCORE_SP [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/params.cpp:520:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQWEIGHT_ClustalW [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/params.cpp:642:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJSCORE_Opts [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/params.cpp:428:39: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/params.cpp:429:39: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/params.cpp:431:40: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/params.cpp:432:40: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/params.cpp:642:39: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/params.cpp:643:39: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/params.cpp:645:38: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/params.cpp:646:38: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/params.cpp:648:39: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/params.cpp:649:39: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/params.cpp:651:37: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/params.cpp:652:37: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/params.cpp:654:38: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/params.cpp:655:38: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/params.cpp:657:32: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/params.cpp:658:32: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/params.cpp:660:37: style: C-style pointer casting [cstyleCast]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:24:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:78:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:158:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:164:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:173:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:191:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCacheCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:275:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:301:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNeighbor1 [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:324:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:332:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:339:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:346:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:356:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:420:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:499:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:545:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_bRooted [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:584:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:599:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:663:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:715:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:729:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_NEIGHBOR [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:761:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uRootNodeIndex [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:772:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uRootNodeIndex [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:785:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:824:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:859:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:929:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNeighbor1 [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:945:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_bHasHeight [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:968:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:984:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNeighbor1 [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:1033:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:1092:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy.cpp:667:21: style: Variable 'dEdgeLength' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/phy2.cpp:11:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uInsane [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy2.cpp:45:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uInsane [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy2.cpp:89:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_NEIGHBOR [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy2.cpp:205:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_NEIGHBOR [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy3.cpp:66:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_NEIGHBOR [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy3.cpp:83:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_NEIGHBOR [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy3.cpp:193:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_NEIGHBOR [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy3.cpp:264:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_NEIGHBOR [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy3.cpp:357:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_NEIGHBOR [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy3.cpp:466:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ROOT_Pseudo [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy3.cpp:11:2: warning: Member variable 'EdgeInfo::m_uNode1' is not initialized in the constructor. [uninitMemberVar]
libmuscle-3.7+4565/libMUSCLE/phy3.cpp:11:2: warning: Member variable 'EdgeInfo::m_uNode2' is not initialized in the constructor. [uninitMemberVar]
libmuscle-3.7+4565/libMUSCLE/phy3.cpp:11:2: warning: Member variable 'EdgeInfo::m_dMaxDistToLeaf' is not initialized in the constructor. [uninitMemberVar]
libmuscle-3.7+4565/libMUSCLE/phy3.cpp:11:2: warning: Member variable 'EdgeInfo::m_dTotalDistToLeaves' is not initialized in the constructor. [uninitMemberVar]
libmuscle-3.7+4565/libMUSCLE/phy3.cpp:11:2: warning: Member variable 'EdgeInfo::m_uMaxStep' is not initialized in the constructor. [uninitMemberVar]
libmuscle-3.7+4565/libMUSCLE/phy3.cpp:11:2: warning: Member variable 'EdgeInfo::m_uMostDistantLeaf' is not initialized in the constructor. [uninitMemberVar]
libmuscle-3.7+4565/libMUSCLE/phy3.cpp:11:2: warning: Member variable 'EdgeInfo::m_uLeafCount' is not initialized in the constructor. [uninitMemberVar]
libmuscle-3.7+4565/libMUSCLE/phy3.cpp:127:25: style: Variable 'dThisDist' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/phy3.cpp:169:17: style: Variable 'uLeafCount' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/phy3.cpp:192:9: style: Variable 'dAllMaxDist' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/phy3.cpp:193:11: style: Variable 'uMaxFrom' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/phy3.cpp:194:11: style: Variable 'uMaxTo' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/phy4.cpp:178:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phy4.cpp:78:37: error:inconclusive: Array 'Subfams[0]' accessed at index -1, which is out of bounds. [negativeIndex]
libmuscle-3.7+4565/libMUSCLE/phy4.cpp:50:26: note: Assignment 'iParentSubscript=-1', assigned value is -1
libmuscle-3.7+4565/libMUSCLE/phy4.cpp:52:20: note: Assuming condition is false
libmuscle-3.7+4565/libMUSCLE/phy4.cpp:78:37: note: Negative array index
libmuscle-3.7+4565/libMUSCLE/phy4.cpp:83:9: error:inconclusive: Array 'Subfams[0]' accessed at index -1, which is out of bounds. [negativeIndex]
libmuscle-3.7+4565/libMUSCLE/phy4.cpp:50:26: note: Assignment 'iParentSubscript=-1', assigned value is -1
libmuscle-3.7+4565/libMUSCLE/phy4.cpp:52:20: note: Assuming condition is false
libmuscle-3.7+4565/libMUSCLE/phy4.cpp:83:9: note: Negative array index
libmuscle-3.7+4565/libMUSCLE/phyfromclust.cpp:9:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uCacheCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phyfromclust.cpp:51:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phyfromfile.cpp:58:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NTT_Lparen [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phyfromfile.cpp:159:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NTT_Semicolon [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phyfromfile.cpp:186:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NTT_String [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phytofile.cpp:9:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/phytofile.cpp:19:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uRootNodeIndex [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/posgap.cpp:136:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Amino [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/ppscore.cpp:47:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Undefined [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/profile.cpp:37:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Undefined [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/profile.cpp:120:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Undefined [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/profilefrommsa.cpp:161:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAX_ALPHA [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/profilefrommsa.cpp:188:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RESIDUE_GROUP_MULTIPLE [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/profilefrommsa.cpp:211:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RESIDUE_GROUP_MULTIPLE [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/profilefrommsa.cpp:255:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ProfPos [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/profilefrommsa.cpp:252:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
libmuscle-3.7+4565/libMUSCLE/profilefrommsa.cpp:248:27: style: Variable 'uSeqCount' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/profilefrommsa.cpp:257:33: style: Variable 'uHydrophobicRunLength' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/progalign.cpp:190:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_NEIGHBOR [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/progalign.cpp:194:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
libmuscle-3.7+4565/libMUSCLE/progalign.cpp:43:28: style: Variable 'uIterCount' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/progress.cpp:30:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/progress.cpp:142:2: error: va_list 'ArgList' was opened but not closed by va_end(). [va_end_missing]
libmuscle-3.7+4565/libMUSCLE/progressivealign.cpp:69:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_NEIGHBOR [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/progressivealign.cpp:77:12: style: Variable 'ProgNodes' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/pwpath.cpp:11:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uArraySize [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/pwpath.cpp:23:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Edges [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/pwpath.cpp:31:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Edges [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/pwpath.cpp:43:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uArraySize [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/pwpath.cpp:61:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uArraySize [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/pwpath.cpp:71:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uEdgeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/pwpath.cpp:82:11: style: The scope of the variable 'uStartA' can be reduced. [variableScope]
libmuscle-3.7+4565/libMUSCLE/pwpath.cpp:83:11: style: The scope of the variable 'uStartB' can be reduced. [variableScope]
libmuscle-3.7+4565/libMUSCLE/pwpath.cpp:215:16: style: Local variable 'uEdgeIndex' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/pwpath.cpp:214:11: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/pwpath.cpp:215:16: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/pwpath.cpp:214:22: style: Variable 'uEdgeIndex' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/readmx.cpp:86:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAX_ALPHA [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/readmx.cpp:116:9: style: Variable 'maxp' can be declared as pointer to const [constVariablePointer]
libmuscle-3.7+4565/libMUSCLE/readmx.cpp:123:10: style: Variable 'Value' can be declared as pointer to const [constVariablePointer]
libmuscle-3.7+4565/libMUSCLE/realigndiffs.cpp:64:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_NEIGHBOR [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/realigndiffs.cpp:116:12: style: Variable 'ProgNodes' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/realigndiffse.cpp:61:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NODE_CHANGED [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/realigndiffse.cpp:132:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
libmuscle-3.7+4565/libMUSCLE/refine.cpp:30:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Undefined [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/refinehoriz.cpp:173:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable g_uTreeSplitNode1 [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/refinesubfams.cpp:154:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_NEIGHBOR [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/refinesubfams.cpp:65:17: style: Variable 'uNodeCount' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/refinetreee.cpp:38:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NODE_CHANGED [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/refinevert.cpp:24:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uBestColRight [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/refinevert.cpp:47:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uBestColLeft [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/refinew.cpp:105:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/refinew.cpp:259:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Undefined [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/refinew.cpp:109:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
libmuscle-3.7+4565/libMUSCLE/refinew.cpp:109:4: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
libmuscle-3.7+4565/libMUSCLE/refinew.cpp:197:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
libmuscle-3.7+4565/libMUSCLE/refinew.cpp:201:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
libmuscle-3.7+4565/libMUSCLE/refinew.cpp:205:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
libmuscle-3.7+4565/libMUSCLE/refinew.cpp:151:19: style: Local variable 'uSeqCount' shadows outer variable [shadowVariable]
libmuscle-3.7+4565/libMUSCLE/refinew.cpp:77:17: note: Shadowed declaration
libmuscle-3.7+4565/libMUSCLE/refinew.cpp:151:19: note: Shadow variable
libmuscle-3.7+4565/libMUSCLE/refinew.cpp:25:30: style: Variable 'uColCountCat' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/refinew.cpp:151:29: style: Variable 'uSeqCount' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/refinew.cpp:155:32: style: Variable 'uColCountCat' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/refinew.cpp:192:22: style: Variable 'uOutCols' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/savebest.cpp:29:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/savebest.cpp:70:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_Success [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/scoredist.cpp:77:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Amino [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/scoredist.cpp:97:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQWEIGHT_Henikoff [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/scoregaps.cpp:53:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uInsane [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/scorehistory.cpp:11:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uNodeCount [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/scorehistory.cpp:26:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uIters [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/scorehistory.cpp:41:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uIters [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/scorehistory.cpp:74:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uIters [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/scorehistory.cpp:100:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_bScoreSet [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/scorepp.cpp:96:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PPSCORE_SP [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/seq.cpp:13:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrName [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/seq.cpp:21:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrName [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/seq.cpp:50:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrName [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/seq.cpp:116:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrName [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/seq.cpp:127:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrName [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/seq.cpp:141:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrName [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/seq.cpp:302:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrName [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/seq.cpp:316:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrName [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/seqvect.cpp:242:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Amino [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/seqvect.cpp:203:19: error: Null pointer dereference: (Seq*)0 [nullPointer]
libmuscle-3.7+4565/libMUSCLE/seqvect.cpp:203:9: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
libmuscle-3.7+4565/libMUSCLE/setblosumweights.cpp:63:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Weights [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/setblosumweights.cpp:132:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BLOSUM_DIST [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/setgscweights.cpp:126:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_Weights [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/setnewhandler.cpp:16:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/spfast.cpp:254:27: style: Variable 'uSeqCount' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/sptest.cpp:51:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PPSCORE_SV [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/subfam.cpp:211:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Undefined [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/subfam.cpp:277:37: warning:inconclusive: Either the condition '0==uSeqCount' is redundant or there is division by zero at line 277. [zerodivcond]
libmuscle-3.7+4565/libMUSCLE/subfam.cpp:291:8: note: Assuming that condition '0==uSeqCount' is not redundant
libmuscle-3.7+4565/libMUSCLE/subfam.cpp:277:37: note: Division by zero
libmuscle-3.7+4565/libMUSCLE/subfam.cpp:407:12: style: Variable 'ProgNodes' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/subfam.cpp:408:15: style: Variable 'NodeInSubFam' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/subfam.cpp:409:15: style: Variable 'NodeIsSubFam' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/subfam.cpp:410:10: style: Variable 'SubFams' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/subfams.cpp:19:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uInsane [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/subfams.cpp:46:25: style: Checking if unsigned expression 'i' is less than zero. [unsignedLessThanZero]
libmuscle-3.7+4565/libMUSCLE/subfams.cpp:42:46: style: Parameter 'DF' can be declared as reference to const [constParameterReference]
libmuscle-3.7+4565/libMUSCLE/subfams.cpp:65:29: style: Parameter 'DF' can be declared as reference to const [constParameterReference]
libmuscle-3.7+4565/libMUSCLE/sw.cpp:16:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MINUS_INFINITY [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/sw.cpp:61:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MINUS_INFINITY [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/termgaps.cpp:21:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MINUS_INFINITY [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/termgaps.cpp:11:19: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
libmuscle-3.7+4565/libMUSCLE/termgaps.cpp:12:18: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
libmuscle-3.7+4565/libMUSCLE/textfile.cpp:13:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/textfile.cpp:31:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrFile [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/textfile.cpp:49:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrFile [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/textfile.cpp:81:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uLineNr [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/textfile.cpp:102:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrFile [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/textfile.cpp:109:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrFile [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/textfile.cpp:122:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrFile [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/textfile.cpp:172:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_uLineNr [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/textfile.cpp:244:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrFile [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/textfile.cpp:252:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_ptrFile [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/textfile.cpp:261:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_cPushedBack [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/textfile.cpp:320:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_bLastCharWasEOL [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/textfile.cpp:133:2: error: va_list 'ArgList' was opened but not closed by va_end(). [va_end_missing]
libmuscle-3.7+4565/libMUSCLE/threewaywt.cpp:151:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_NEIGHBOR [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/threewaywt.cpp:250:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_NEIGHBOR [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/tomhydro.cpp:83:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALPHA_Amino [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/traceback.cpp:40:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cInsane [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/traceback.cpp:22:17: style: Variable 'uPrefixCountA' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/traceback.cpp:23:17: style: Variable 'uPrefixCountB' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/tracebackopt.cpp:47:19: style: Condition 'iDelta<0' is always true [knownConditionTrueFalse]
libmuscle-3.7+4565/libMUSCLE/tracebackopt.cpp:25:9: note: Assuming that condition '0==iDelta' is not redundant
libmuscle-3.7+4565/libMUSCLE/tracebackopt.cpp:47:19: note: Condition 'iDelta<0' is always true
libmuscle-3.7+4565/libMUSCLE/tracebacksw.cpp:65:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MINUS_INFINITY [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/tracebacksw.cpp:23:17: style: Variable 'uPrefixCountA' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/tracebacksw.cpp:24:17: style: Variable 'uPrefixCountB' is assigned a value that is never used. [unreadVariable]
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:65:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LINKAGE_Undefined [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:94:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLUSTER_NeighborJoining [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:19:11: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:12:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:12:17: note: Assignment 'f=fopen(FileName,"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:19:11: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:21:12: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:12:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:12:17: note: Assignment 'f=fopen(FileName,"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:21:12: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:22:11: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:12:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:12:17: note: Assignment 'f=fopen(FileName,"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:22:11: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:24:9: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:12:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:12:17: note: Assignment 'f=fopen(FileName,"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:24:9: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:49:10: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:44:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:44:17: note: Assignment 'f=fopen(FileName,"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:49:10: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:53:11: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:44:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:44:17: note: Assignment 'f=fopen(FileName,"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:53:11: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:56:12: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:44:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:44:17: note: Assignment 'f=fopen(FileName,"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:56:12: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:57:11: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:44:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:44:17: note: Assignment 'f=fopen(FileName,"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:57:11: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:59:9: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:44:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:44:17: note: Assignment 'f=fopen(FileName,"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/treefrommsa.cpp:59:9: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/typetostr.cpp:26:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MINUS_INFINITY [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/typetostr.cpp:43:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MINUS_INFINITY [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/typetostr.cpp:15:2: warning: %d in format string (no. 1) requires 'int' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
libmuscle-3.7+4565/libMUSCLE/typetostr.cpp:15:2: warning: %d in format string (no. 2) requires 'int' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
libmuscle-3.7+4565/libMUSCLE/typetostr.cpp:15:2: warning: %d in format string (no. 3) requires 'int' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
libmuscle-3.7+4565/libMUSCLE/upgma2.cpp:76:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uInsane [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/upgma2.cpp:152:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BIG_DIST [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/upgma2.cpp:396:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LINKAGE_Avg [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/usage.cpp:13:24: error: There is an unknown macro here somewhere. Configuration is required. If MUSCLE_LONG_VERSION is a macro then please configure it. [unknownMacro]
libmuscle-3.7+4565/libMUSCLE/writescorefile.cpp:55:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
libmuscle-3.7+4565/libMUSCLE/writescorefile.cpp:62:11: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/writescorefile.cpp:53:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/writescorefile.cpp:53:17: note: Assignment 'f=fopen(g_pstrScoreFileName.get(),"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/writescorefile.cpp:62:11: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/writescorefile.cpp:66:12: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/writescorefile.cpp:53:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/writescorefile.cpp:53:17: note: Assignment 'f=fopen(g_pstrScoreFileName.get(),"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/writescorefile.cpp:66:12: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/writescorefile.cpp:68:11: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/writescorefile.cpp:53:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/writescorefile.cpp:53:17: note: Assignment 'f=fopen(g_pstrScoreFileName.get(),"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/writescorefile.cpp:68:11: note: Null pointer dereference
libmuscle-3.7+4565/libMUSCLE/writescorefile.cpp:70:9: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
libmuscle-3.7+4565/libMUSCLE/writescorefile.cpp:53:17: note: Assuming allocation function fails
libmuscle-3.7+4565/libMUSCLE/writescorefile.cpp:53:17: note: Assignment 'f=fopen(g_pstrScoreFileName.get(),"w")', assigned value is 0
libmuscle-3.7+4565/libMUSCLE/writescorefile.cpp:70:9: note: Null pointer dereference
diff:


DONE