2024-04-24 14:16
ftp://ftp.de.debian.org/debian/pool/main/f/fasttree/fasttree_2.1.11.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 -D__GNUC__ --platform=unix64 -j1
platform: Linux-5.15.0-105-generic-x86_64-with-glibc2.35
python: 3.10.12
client-version: 1.3.56
compiler: g++ (Ubuntu 12.3.0-1ubuntu1~22.04) 12.3.0
cppcheck: head 2.14.0
head-info: 9fab9b9 (2024-04-24 10:46:48 +0200)
count: 336 336
elapsed-time: 114.0 113.0
head-timing-info:

old-timing-info:

head results:
FastTree-2.1.11/fasttree.c:1682:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:2544:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:2631:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:2783:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:3151:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:3186:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:3224:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:3254:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:3263:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:3345:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:3607:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable node [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:3676:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:3921:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:3973:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:4132:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:4409:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:4513:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:4548:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:4645:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:4653:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:4707:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:4728:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:4756:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:4818:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:4923:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:5359:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:5468:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:5616:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:5724:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:5793:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:5917:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:5959:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:6001:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:6046:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:6131:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:6246:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:6334:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:6612:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:6750:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:6832:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:6980:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:7298:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:7577:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:7625:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:7763:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:8154:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:8348:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:8403:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:8455:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:8523:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:8787:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:8813:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:8987:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:9460:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:9503:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:10050:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
FastTree-2.1.11/fasttree.c:1701:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1720:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1725:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1736:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1739:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1747:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1752:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1761:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1764:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1775:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1786:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1791:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1794:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1797:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1826:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1829:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1836:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1847:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1862:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1865:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1876:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1895:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:1900:27: style: Array index 'iArg' is used before limits check. [arrayIndexThenCheck]
FastTree-2.1.11/fasttree.c:9554:10: warning: Buffer 'matrix' is too small, the function 'CreateTransitionMatrix' expects a bigger buffer in 1st argument [argumentSize]
FastTree-2.1.11/fasttree.c:9554:10: note: Function 'CreateTransitionMatrix' is called
FastTree-2.1.11/fasttree.c:9557:58: note: Declaration of 1st function argument.
FastTree-2.1.11/fasttree.c:9526:10: note: Passing buffer 'matrix' to function that is declared here
FastTree-2.1.11/fasttree.c:9554:10: note: Buffer 'matrix' is too small, the function 'CreateTransitionMatrix' expects a bigger buffer in 1st argument
FastTree-2.1.11/fasttree.c:4692:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
FastTree-2.1.11/fasttree.c:4693:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
FastTree-2.1.11/fasttree.c:4695:77: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
FastTree-2.1.11/fasttree.c:10077:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
FastTree-2.1.11/fasttree.c:10083:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
FastTree-2.1.11/fasttree.c:10090:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
FastTree-2.1.11/fasttree.c:6102:40: warning: Invalid log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
FastTree-2.1.11/fasttree.c:6097:20: note: Assignment 'rellk=0', assigned value is 0
FastTree-2.1.11/fasttree.c:6098:27: note: Assuming condition is false
FastTree-2.1.11/fasttree.c:6102:40: note: Invalid argument
FastTree-2.1.11/fasttree.c:3430:20: style: Condition 'node==root' is always true [knownConditionTrueFalse]
FastTree-2.1.11/fasttree.c:3427:13: note: Assuming that condition 'node!=root' is not redundant
FastTree-2.1.11/fasttree.c:3430:20: note: Condition 'node==root' is always true
FastTree-2.1.11/fasttree.c:4105:54: style: Condition 'nOn1>0' is always false [knownConditionTrueFalse]
FastTree-2.1.11/fasttree.c:4105:23: note: Assuming that condition 'nOn1>0' is not redundant
FastTree-2.1.11/fasttree.c:4105:54: note: Condition 'nOn1>0' is always false
FastTree-2.1.11/fasttree.c:4106:54: style: Condition 'nOn2>0' is always false [knownConditionTrueFalse]
FastTree-2.1.11/fasttree.c:4106:23: note: Assuming that condition 'nOn2>0' is not redundant
FastTree-2.1.11/fasttree.c:4106:54: note: Condition 'nOn2>0' is always false
FastTree-2.1.11/fasttree.c:4110:28: style: Condition 'nOn==1' is always true [knownConditionTrueFalse]
FastTree-2.1.11/fasttree.c:4110:16: note: Assuming that condition 'nSplit==1' is not redundant
FastTree-2.1.11/fasttree.c:4108:16: note: nSplit is assigned '(code1==-1?1:0)+(code2==-1?1:0)+(code3==-1?1:0)' here.
FastTree-2.1.11/fasttree.c:4109:59: note: Assignment 'nOn=(code1==1?1:0)+(code2==1?1:0)+(code3==1?1:0)', assigned value is symbolic=nSplit
FastTree-2.1.11/fasttree.c:4110:28: note: Condition 'nOn==1' is always true
FastTree-2.1.11/fasttree.c:4415:47: style: Condition 'f' is always true [knownConditionTrueFalse]
FastTree-2.1.11/fasttree.c:6479:51: style: Condition 'verbose>2' is always true [knownConditionTrueFalse]
FastTree-2.1.11/fasttree.c:6479:16: note: Assuming that condition 'verbose>2' is not redundant
FastTree-2.1.11/fasttree.c:6479:51: note: Condition 'verbose>2' is always true
FastTree-2.1.11/fasttree.c:2577:5: warning: fprintf format string requires 0 parameters but 1 is given. [wrongPrintfScanfArgNum]
FastTree-2.1.11/fasttree.c:4693:11: style: Redundant initialization for 'field'. The initialized value is overwritten before it is read. [redundantInitialization]
FastTree-2.1.11/fasttree.c:4692:17: note: field is initialized
FastTree-2.1.11/fasttree.c:4693:11: note: field is overwritten
FastTree-2.1.11/fasttree.c:9663:3: style: Statements following 'return' will never be executed. [unreachableCode]
FastTree-2.1.11/fasttree.c:2525:39: style:inconclusive: Function 'ProgressReport' argument 2 names different: declaration 'iArg1' definition 'i1'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1479:39: note: Function 'ProgressReport' argument 2 names different: declaration 'iArg1' definition 'i1'.
FastTree-2.1.11/fasttree.c:2525:39: note: Function 'ProgressReport' argument 2 names different: declaration 'iArg1' definition 'i1'.
FastTree-2.1.11/fasttree.c:2525:47: style:inconclusive: Function 'ProgressReport' argument 3 names different: declaration 'iArg2' definition 'i2'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1479:50: note: Function 'ProgressReport' argument 3 names different: declaration 'iArg2' definition 'i2'.
FastTree-2.1.11/fasttree.c:2525:47: note: Function 'ProgressReport' argument 3 names different: declaration 'iArg2' definition 'i2'.
FastTree-2.1.11/fasttree.c:2525:55: style:inconclusive: Function 'ProgressReport' argument 4 names different: declaration 'iArg3' definition 'i3'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1479:61: note: Function 'ProgressReport' argument 4 names different: declaration 'iArg3' definition 'i3'.
FastTree-2.1.11/fasttree.c:2525:55: note: Function 'ProgressReport' argument 4 names different: declaration 'iArg3' definition 'i3'.
FastTree-2.1.11/fasttree.c:2525:63: style:inconclusive: Function 'ProgressReport' argument 5 names different: declaration 'iArg4' definition 'i4'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1479:72: note: Function 'ProgressReport' argument 5 names different: declaration 'iArg4' definition 'i4'.
FastTree-2.1.11/fasttree.c:2525:63: note: Function 'ProgressReport' argument 5 names different: declaration 'iArg4' definition 'i4'.
FastTree-2.1.11/fasttree.c:2575:32: style:inconclusive: Function 'LogTree' argument 2 names different: declaration 'round' definition 'i'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1480:32: note: Function 'LogTree' argument 2 names different: declaration 'round' definition 'i'.
FastTree-2.1.11/fasttree.c:2575:32: note: Function 'LogTree' argument 2 names different: declaration 'round' definition 'i'.
FastTree-2.1.11/fasttree.c:2575:59: style:inconclusive: Function 'LogTree' argument 3 names different: declaration 'fp' definition 'fpLog'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1480:63: note: Function 'LogTree' argument 3 names different: declaration 'fp' definition 'fpLog'.
FastTree-2.1.11/fasttree.c:2575:59: note: Function 'LogTree' argument 3 names different: declaration 'fp' definition 'fpLog'.
FastTree-2.1.11/fasttree.c:2584:36: style:inconclusive: Function 'InitNJ' argument 2 names different: declaration 'nSeqs' definition 'nSeq'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:947:36: note: Function 'InitNJ' argument 2 names different: declaration 'nSeqs' definition 'nSeq'.
FastTree-2.1.11/fasttree.c:2584:36: note: Function 'InitNJ' argument 2 names different: declaration 'nSeqs' definition 'nSeq'.
FastTree-2.1.11/fasttree.c:3097:66: style:inconclusive: Function 'ExhaustiveNJSearch' argument 3 names different: declaration 'bestjoin' definition 'join'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1200:66: note: Function 'ExhaustiveNJSearch' argument 3 names different: declaration 'bestjoin' definition 'join'.
FastTree-2.1.11/fasttree.c:3097:66: note: Function 'ExhaustiveNJSearch' argument 3 names different: declaration 'bestjoin' definition 'join'.
FastTree-2.1.11/fasttree.c:3125:63: style:inconclusive: Function 'FastNJSearch' argument 3 names different: declaration 'visible' definition 'besthits'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1203:63: note: Function 'FastNJSearch' argument 3 names different: declaration 'visible' definition 'besthits'.
FastTree-2.1.11/fasttree.c:3125:63: note: Function 'FastNJSearch' argument 3 names different: declaration 'visible' definition 'besthits'.
FastTree-2.1.11/fasttree.c:3125:91: style:inconclusive: Function 'FastNJSearch' argument 4 names different: declaration 'bestjoin' definition 'join'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1203:90: note: Function 'FastNJSearch' argument 4 names different: declaration 'bestjoin' definition 'join'.
FastTree-2.1.11/fasttree.c:3125:91: note: Function 'FastNJSearch' argument 4 names different: declaration 'bestjoin' definition 'join'.
FastTree-2.1.11/fasttree.c:3583:92: style:inconclusive: Function 'PrintNJ' argument 6 names different: declaration 'bQuoteNames' definition 'bQuote'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1556:99: note: Function 'PrintNJ' argument 6 names different: declaration 'bQuoteNames' definition 'bQuote'.
FastTree-2.1.11/fasttree.c:3583:92: note: Function 'PrintNJ' argument 6 names different: declaration 'bQuoteNames' definition 'bQuote'.
FastTree-2.1.11/fasttree.c:3947:22: style:inconclusive: Function 'SeqToProfile' argument 4 names different: declaration 'constraintSeqs' definition 'constraintSeq'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1067:22: note: Function 'SeqToProfile' argument 4 names different: declaration 'constraintSeqs' definition 'constraintSeq'.
FastTree-2.1.11/fasttree.c:3947:22: note: Function 'SeqToProfile' argument 4 names different: declaration 'constraintSeqs' definition 'constraintSeq'.
FastTree-2.1.11/fasttree.c:4016:26: style:inconclusive: Function 'SeqDist' argument 4 names different: declaration 'distance_matrix' definition 'dmat'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1081:38: note: Function 'SeqDist' argument 4 names different: declaration 'distance_matrix' definition 'dmat'.
FastTree-2.1.11/fasttree.c:4016:26: note: Function 'SeqDist' argument 4 names different: declaration 'distance_matrix' definition 'dmat'.
FastTree-2.1.11/fasttree.c:4092:68: style:inconclusive: Function 'JoinConstraintPenaltyPiece' argument 4 names different: declaration 'iConstraint' definition 'iC'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1045:68: note: Function 'JoinConstraintPenaltyPiece' argument 4 names different: declaration 'iConstraint' definition 'iC'.
FastTree-2.1.11/fasttree.c:4092:68: note: Function 'JoinConstraintPenaltyPiece' argument 4 names different: declaration 'iConstraint' definition 'iC'.
FastTree-2.1.11/fasttree.c:4117:89: style:inconclusive: Function 'QuartetConstraintPenalties' argument 3 names different: declaration 'd' definition 'penalty'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1104:89: note: Function 'QuartetConstraintPenalties' argument 3 names different: declaration 'd' definition 'penalty'.
FastTree-2.1.11/fasttree.c:4117:89: note: Function 'QuartetConstraintPenalties' argument 3 names different: declaration 'd' definition 'penalty'.
FastTree-2.1.11/fasttree.c:4152:66: style:inconclusive: Function 'QuartetConstraintPenaltiesPiece' argument 2 names different: declaration 'iConstraint' definition 'iC'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1117:66: note: Function 'QuartetConstraintPenaltiesPiece' argument 2 names different: declaration 'iConstraint' definition 'iC'.
FastTree-2.1.11/fasttree.c:4152:66: note: Function 'QuartetConstraintPenaltiesPiece' argument 2 names different: declaration 'iConstraint' definition 'iC'.
FastTree-2.1.11/fasttree.c:4152:84: style:inconclusive: Function 'QuartetConstraintPenaltiesPiece' argument 3 names different: declaration 'penalty' definition 'piece'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1117:93: note: Function 'QuartetConstraintPenaltiesPiece' argument 3 names different: declaration 'penalty' definition 'piece'.
FastTree-2.1.11/fasttree.c:4152:84: note: Function 'QuartetConstraintPenaltiesPiece' argument 3 names different: declaration 'penalty' definition 'piece'.
FastTree-2.1.11/fasttree.c:4229:26: style:inconclusive: Function 'LogCorrect' argument 1 names different: declaration 'distance' definition 'dist'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1122:26: note: Function 'LogCorrect' argument 1 names different: declaration 'distance' definition 'dist'.
FastTree-2.1.11/fasttree.c:4229:26: note: Function 'LogCorrect' argument 1 names different: declaration 'distance' definition 'dist'.
FastTree-2.1.11/fasttree.c:4296:35: style:inconclusive: Function 'ProfileDist' argument 4 names different: declaration 'distance_matrix' definition 'dmat'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1078:35: note: Function 'ProfileDist' argument 4 names different: declaration 'distance_matrix' definition 'dmat'.
FastTree-2.1.11/fasttree.c:4296:35: note: Function 'ProfileDist' argument 4 names different: declaration 'distance_matrix' definition 'dmat'.
FastTree-2.1.11/fasttree.c:4360:25: style:inconclusive: Function 'AverageProfile' argument 5 names different: declaration 'distance_matrix' definition 'dmat'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1131:25: note: Function 'AverageProfile' argument 5 names different: declaration 'distance_matrix' definition 'dmat'.
FastTree-2.1.11/fasttree.c:4360:25: note: Function 'AverageProfile' argument 5 names different: declaration 'distance_matrix' definition 'dmat'.
FastTree-2.1.11/fasttree.c:4361:13: style:inconclusive: Function 'AverageProfile' argument 6 names different: declaration 'weight1' definition 'bionjWeight'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1132:13: note: Function 'AverageProfile' argument 6 names different: declaration 'weight1' definition 'bionjWeight'.
FastTree-2.1.11/fasttree.c:4361:13: note: Function 'AverageProfile' argument 6 names different: declaration 'weight1' definition 'bionjWeight'.
FastTree-2.1.11/fasttree.c:4437:66: style:inconclusive: Function 'NormalizeFreq' argument 2 names different: declaration 'distance_matrix' definition 'dmat'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1187:66: note: Function 'NormalizeFreq' argument 2 names different: declaration 'distance_matrix' definition 'dmat'.
FastTree-2.1.11/fasttree.c:4437:66: note: Function 'NormalizeFreq' argument 2 names different: declaration 'distance_matrix' definition 'dmat'.
FastTree-2.1.11/fasttree.c:4468:28: style:inconclusive: Function 'OutProfile' argument 5 names different: declaration 'distance_matrix' definition 'dmat'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1156:28: note: Function 'OutProfile' argument 5 names different: declaration 'distance_matrix' definition 'dmat'.
FastTree-2.1.11/fasttree.c:4468:28: note: Function 'OutProfile' argument 5 names different: declaration 'distance_matrix' definition 'dmat'.
FastTree-2.1.11/fasttree.c:4532:28: style:inconclusive: Function 'UpdateOutProfile' argument 8 names different: declaration 'distance_matrix' definition 'dmat'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1161:28: note: Function 'UpdateOutProfile' argument 8 names different: declaration 'distance_matrix' definition 'dmat'.
FastTree-2.1.11/fasttree.c:4532:28: note: Function 'UpdateOutProfile' argument 8 names different: declaration 'distance_matrix' definition 'dmat'.
FastTree-2.1.11/fasttree.c:4649:82: style:inconclusive: Function 'ReadMatrix' argument 3 names different: declaration 'check_codes' definition 'checkCodes'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:929:82: note: Function 'ReadMatrix' argument 3 names different: declaration 'check_codes' definition 'checkCodes'.
FastTree-2.1.11/fasttree.c:4649:82: note: Function 'ReadMatrix' argument 3 names different: declaration 'check_codes' definition 'checkCodes'.
FastTree-2.1.11/fasttree.c:4844:40: style:inconclusive: Function 'PosteriorProfile' argument 1 names different: declaration 'profile1' definition 'p1'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1137:40: note: Function 'PosteriorProfile' argument 1 names different: declaration 'profile1' definition 'p1'.
FastTree-2.1.11/fasttree.c:4844:40: note: Function 'PosteriorProfile' argument 1 names different: declaration 'profile1' definition 'p1'.
FastTree-2.1.11/fasttree.c:4844:55: style:inconclusive: Function 'PosteriorProfile' argument 2 names different: declaration 'profile2' definition 'p2'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1137:61: note: Function 'PosteriorProfile' argument 2 names different: declaration 'profile2' definition 'p2'.
FastTree-2.1.11/fasttree.c:4844:55: note: Function 'PosteriorProfile' argument 2 names different: declaration 'profile2' definition 'p2'.
FastTree-2.1.11/fasttree.c:5199:29: style:inconclusive: Function 'PairLogLk' argument 1 names different: declaration 'p1' definition 'pA'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1368:35: note: Function 'PairLogLk' argument 1 names different: declaration 'p1' definition 'pA'.
FastTree-2.1.11/fasttree.c:5199:29: note: Function 'PairLogLk' argument 1 names different: declaration 'p1' definition 'pA'.
FastTree-2.1.11/fasttree.c:5199:44: style:inconclusive: Function 'PairLogLk' argument 2 names different: declaration 'p2' definition 'pB'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1368:56: note: Function 'PairLogLk' argument 2 names different: declaration 'p2' definition 'pB'.
FastTree-2.1.11/fasttree.c:5199:44: note: Function 'PairLogLk' argument 2 names different: declaration 'p2' definition 'pB'.
FastTree-2.1.11/fasttree.c:5631:26: style:inconclusive: Function 'MLQuartetNNI' argument 7 names different: declaration 'length' definition 'len'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1314:26: note: Function 'MLQuartetNNI' argument 7 names different: declaration 'length' definition 'len'.
FastTree-2.1.11/fasttree.c:5631:26: note: Function 'MLQuartetNNI' argument 7 names different: declaration 'length' definition 'len'.
FastTree-2.1.11/fasttree.c:5870:58: style:inconclusive: Function 'SetMLGtr' argument 2 names different: declaration 'gtrfreq' definition 'freq_in'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1362:58: note: Function 'SetMLGtr' argument 2 names different: declaration 'gtrfreq' definition 'freq_in'.
FastTree-2.1.11/fasttree.c:5870:58: note: Function 'SetMLGtr' argument 2 names different: declaration 'gtrfreq' definition 'freq_in'.
FastTree-2.1.11/fasttree.c:6292:17: style:inconclusive: Function 'NNI' argument 6 names different: declaration 'maxDeltaCriterion' definition 'dMaxDelta'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:974:17: note: Function 'NNI' argument 6 names different: declaration 'maxDeltaCriterion' definition 'dMaxDelta'.
FastTree-2.1.11/fasttree.c:6292:17: note: Function 'NNI' argument 6 names different: declaration 'maxDeltaCriterion' definition 'dMaxDelta'.
FastTree-2.1.11/fasttree.c:6578:8: style:inconclusive: Function 'FindSPRSteps' argument 2 names different: declaration 'node' definition 'nodeMove'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1424:8: note: Function 'FindSPRSteps' argument 2 names different: declaration 'node' definition 'nodeMove'.
FastTree-2.1.11/fasttree.c:6578:8: note: Function 'FindSPRSteps' argument 2 names different: declaration 'node' definition 'nodeMove'.
FastTree-2.1.11/fasttree.c:6579:8: style:inconclusive: Function 'FindSPRSteps' argument 3 names different: declaration 'parent' definition 'nodeAround'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1425:8: note: Function 'FindSPRSteps' argument 3 names different: declaration 'parent' definition 'nodeAround'.
FastTree-2.1.11/fasttree.c:6579:8: note: Function 'FindSPRSteps' argument 3 names different: declaration 'parent' definition 'nodeAround'.
FastTree-2.1.11/fasttree.c:7393:32: style:inconclusive: Function 'SplitSupport' argument 1 names different: declaration 'p1' definition 'pA'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1054:32: note: Function 'SplitSupport' argument 1 names different: declaration 'p1' definition 'pA'.
FastTree-2.1.11/fasttree.c:7393:32: note: Function 'SplitSupport' argument 1 names different: declaration 'p1' definition 'pA'.
FastTree-2.1.11/fasttree.c:7393:47: style:inconclusive: Function 'SplitSupport' argument 2 names different: declaration 'p2' definition 'pB'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1054:47: note: Function 'SplitSupport' argument 2 names different: declaration 'p2' definition 'pB'.
FastTree-2.1.11/fasttree.c:7393:47: note: Function 'SplitSupport' argument 2 names different: declaration 'p2' definition 'pB'.
FastTree-2.1.11/fasttree.c:7393:62: style:inconclusive: Function 'SplitSupport' argument 3 names different: declaration 'p3' definition 'pC'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1054:62: note: Function 'SplitSupport' argument 3 names different: declaration 'p3' definition 'pC'.
FastTree-2.1.11/fasttree.c:7393:62: note: Function 'SplitSupport' argument 3 names different: declaration 'p3' definition 'pC'.
FastTree-2.1.11/fasttree.c:7393:77: style:inconclusive: Function 'SplitSupport' argument 4 names different: declaration 'p4' definition 'pD'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1054:77: note: Function 'SplitSupport' argument 4 names different: declaration 'p4' definition 'pD'.
FastTree-2.1.11/fasttree.c:7393:77: note: Function 'SplitSupport' argument 4 names different: declaration 'p4' definition 'pD'.
FastTree-2.1.11/fasttree.c:7497:32: style:inconclusive: Function 'SHSupport' argument 2 names different: declaration 'nBoostrap' definition 'nBootstrap'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1063:32: note: Function 'SHSupport' argument 2 names different: declaration 'nBoostrap' definition 'nBootstrap'.
FastTree-2.1.11/fasttree.c:7497:32: note: Function 'SHSupport' argument 2 names different: declaration 'nBoostrap' definition 'nBootstrap'.
FastTree-2.1.11/fasttree.c:7539:77: style:inconclusive: Function 'SetDistCriterion' argument 3 names different: declaration 'join' definition 'hit'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1022:80: note: Function 'SetDistCriterion' argument 3 names different: declaration 'join' definition 'hit'.
FastTree-2.1.11/fasttree.c:7539:77: note: Function 'SetDistCriterion' argument 3 names different: declaration 'join' definition 'hit'.
FastTree-2.1.11/fasttree.c:7989:40: style:inconclusive: Function 'ActiveAncestor' argument 2 names different: declaration 'node' definition 'iNode'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1040:40: note: Function 'ActiveAncestor' argument 2 names different: declaration 'node' definition 'iNode'.
FastTree-2.1.11/fasttree.c:7989:40: note: Function 'ActiveAncestor' argument 2 names different: declaration 'node' definition 'iNode'.
FastTree-2.1.11/fasttree.c:7997:77: style:inconclusive: Function 'UpdateBestHit' argument 3 names different: declaration 'join' definition 'hit'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1031:77: note: Function 'UpdateBestHit' argument 3 names different: declaration 'join' definition 'hit'.
FastTree-2.1.11/fasttree.c:7997:77: note: Function 'UpdateBestHit' argument 3 names different: declaration 'join' definition 'hit'.
FastTree-2.1.11/fasttree.c:8356:13: style:inconclusive: Function 'UpdateTopVisible' argument 3 names different: declaration 'iNode' definition 'iIn'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1280:13: note: Function 'UpdateTopVisible' argument 3 names different: declaration 'iNode' definition 'iIn'.
FastTree-2.1.11/fasttree.c:8356:13: note: Function 'UpdateTopVisible' argument 3 names different: declaration 'iNode' definition 'iIn'.
FastTree-2.1.11/fasttree.c:8497:25: style:inconclusive: Function 'TopHitNJSearch' argument 4 names different: declaration 'bestjoin' definition 'join'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1219:25: note: Function 'TopHitNJSearch' argument 4 names different: declaration 'bestjoin' definition 'join'.
FastTree-2.1.11/fasttree.c:8497:25: note: Function 'TopHitNJSearch' argument 4 names different: declaration 'bestjoin' definition 'join'.
FastTree-2.1.11/fasttree.c:8607:31: style:inconclusive: Function 'NGaps' argument 2 names different: declaration 'node' definition 'iNode'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1448:25: note: Function 'NGaps' argument 2 names different: declaration 'node' definition 'iNode'.
FastTree-2.1.11/fasttree.c:8607:31: note: Function 'NGaps' argument 2 names different: declaration 'node' definition 'iNode'.
FastTree-2.1.11/fasttree.c:8692:14: style:inconclusive: Function 'TransferBestHits' argument 7 names different: declaration 'updateDistance' definition 'updateDistances'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1260:14: note: Function 'TransferBestHits' argument 7 names different: declaration 'updateDistance' definition 'updateDistances'.
FastTree-2.1.11/fasttree.c:8692:14: note: Function 'TransferBestHits' argument 7 names different: declaration 'updateDistance' definition 'updateDistances'.
FastTree-2.1.11/fasttree.c:8762:21: style:inconclusive: Function 'pnorm' argument 1 names different: declaration 'z' definition 'x'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1530:21: note: Function 'pnorm' argument 1 names different: declaration 'z' definition 'x'.
FastTree-2.1.11/fasttree.c:8762:21: note: Function 'pnorm' argument 1 names different: declaration 'z' definition 'x'.
FastTree-2.1.11/fasttree.c:9384:27: style:inconclusive: Function 'TraversePostorder' argument 1 names different: declaration 'lastnode' definition 'node'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1604:27: note: Function 'TraversePostorder' argument 1 names different: declaration 'lastnode' definition 'node'.
FastTree-2.1.11/fasttree.c:9384:27: note: Function 'TraversePostorder' argument 1 names different: declaration 'lastnode' definition 'node'.
FastTree-2.1.11/fasttree.c:9433:73: style:inconclusive: Function 'GetUpProfile' argument 3 names different: declaration 'node' definition 'outnode'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1612:73: note: Function 'GetUpProfile' argument 3 names different: declaration 'node' definition 'outnode'.
FastTree-2.1.11/fasttree.c:9433:73: note: Function 'GetUpProfile' argument 3 names different: declaration 'node' definition 'outnode'.
FastTree-2.1.11/fasttree.c:9507:49: style:inconclusive: Function 'PathToRoot' argument 3 names different: declaration 'depth' definition 'outDepth'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1637:49: note: Function 'PathToRoot' argument 3 names different: declaration 'depth' definition 'outDepth'.
FastTree-2.1.11/fasttree.c:9507:49: note: Function 'PathToRoot' argument 3 names different: declaration 'depth' definition 'outDepth'.
FastTree-2.1.11/fasttree.c:9525:40: style:inconclusive: Function 'CreateGTR' argument 1 names different: declaration 'gtrrates' definition 'r'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:940:40: note: Function 'CreateGTR' argument 1 names different: declaration 'gtrrates' definition 'r'.
FastTree-2.1.11/fasttree.c:9525:40: note: Function 'CreateGTR' argument 1 names different: declaration 'gtrrates' definition 'r'.
FastTree-2.1.11/fasttree.c:9525:72: style:inconclusive: Function 'CreateGTR' argument 2 names different: declaration 'gtrfreq' definition 'f'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:940:79: note: Function 'CreateGTR' argument 2 names different: declaration 'gtrfreq' definition 'f'.
FastTree-2.1.11/fasttree.c:9525:72: note: Function 'CreateGTR' argument 2 names different: declaration 'gtrfreq' definition 'f'.
FastTree-2.1.11/fasttree.c:10003:43: style:inconclusive: Function 'vector_add_mult' argument 1 names different: declaration 'f' definition 'fTot'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1501:43: note: Function 'vector_add_mult' argument 1 names different: declaration 'f' definition 'fTot'.
FastTree-2.1.11/fasttree.c:10003:43: note: Function 'vector_add_mult' argument 1 names different: declaration 'f' definition 'fTot'.
FastTree-2.1.11/fasttree.c:10003:66: style:inconclusive: Function 'vector_add_mult' argument 2 names different: declaration 'add' definition 'fAdd'. [funcArgNamesDifferent]
FastTree-2.1.11/fasttree.c:1501:63: note: Function 'vector_add_mult' argument 2 names different: declaration 'add' definition 'fAdd'.
FastTree-2.1.11/fasttree.c:10003:66: note: Function 'vector_add_mult' argument 2 names different: declaration 'add' definition 'fAdd'.
FastTree-2.1.11/fasttree.c:2099:9: style: Local variable 'i' shadows outer variable [shadowVariable]
FastTree-2.1.11/fasttree.c:1957:9: note: Shadowed declaration
FastTree-2.1.11/fasttree.c:2099:9: note: Shadow variable
FastTree-2.1.11/fasttree.c:2115:11: style: Local variable 'i' shadows outer variable [shadowVariable]
FastTree-2.1.11/fasttree.c:2099:9: note: Shadowed declaration
FastTree-2.1.11/fasttree.c:2115:11: note: Shadow variable
FastTree-2.1.11/fasttree.c:2221:6: style: Local variable 'i' shadows outer variable [shadowVariable]
FastTree-2.1.11/fasttree.c:2099:9: note: Shadowed declaration
FastTree-2.1.11/fasttree.c:2221:6: note: Shadow variable
FastTree-2.1.11/fasttree.c:4776:9: style: Local variable 'j' shadows outer variable [shadowVariable]
FastTree-2.1.11/fasttree.c:4752:9: note: Shadowed declaration
FastTree-2.1.11/fasttree.c:4776:9: note: Shadow variable
FastTree-2.1.11/fasttree.c:6149:10: style: Local variable 'gammaLogLk' shadows outer variable [shadowVariable]
FastTree-2.1.11/fasttree.c:854:6: note: Shadowed declaration
FastTree-2.1.11/fasttree.c:6149:10: note: Shadow variable
FastTree-2.1.11/fasttree.c:6459:6: style: Local variable 'i' shadows outer variable [shadowVariable]
FastTree-2.1.11/fasttree.c:6327:7: note: Shadowed declaration
FastTree-2.1.11/fasttree.c:6459:6: note: Shadow variable
FastTree-2.1.11/fasttree.c:7804:12: style: Local variable 'close' shadows outer variable [shadowVariable]
FastTree-2.1.11/fasttree.c:7720:10: note: Shadowed declaration
FastTree-2.1.11/fasttree.c:7804:12: note: Shadow variable
FastTree-2.1.11/fasttree.c:8273:11: style: Local variable 'iNode' shadows outer variable [shadowVariable]
FastTree-2.1.11/fasttree.c:8234:9: note: Shadowed declaration
FastTree-2.1.11/fasttree.c:8273:11: note: Shadow variable
FastTree-2.1.11/fasttree.c:8321:9: style: Local variable 'i' shadows outer variable [shadowVariable]
FastTree-2.1.11/fasttree.c:8099:7: note: Shadowed declaration
FastTree-2.1.11/fasttree.c:8321:9: note: Shadow variable
FastTree-2.1.11/fasttree.c:8476:11: style: Local variable 'iNode' shadows outer variable [shadowVariable]
FastTree-2.1.11/fasttree.c:8430:7: note: Shadowed declaration
FastTree-2.1.11/fasttree.c:8476:11: note: Shadow variable
FastTree-2.1.11/fasttree.c:2525:27: style: Parameter 'format' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:2575:20: style: Parameter 'format' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:3223:26: style: Parameter 'err' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:3223:37: style: Parameter 'token' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:3548:14: style: Variable 'last' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:3611:14: style: Variable 'last' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:3946:10: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:4015:29: style: Parameter 'codes1' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:4015:52: style: Parameter 'codes2' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:4198:41: style: Parameter 'profiles' can be declared as const array [constParameter]
FastTree-2.1.11/fasttree.c:4649:23: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:4692:11: style: Variable 'field' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:4704:23: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:4723:45: style: Parameter 'prefix' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:4889:18: style: Variable 'f1' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:4890:18: style: Variable 'f2' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:4968:16: style: Variable 'fGap' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:4980:18: style: Variable 'expeigen1' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:4981:18: style: Variable 'expeigen2' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:4982:18: style: Variable 'f1' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:4983:18: style: Variable 'f2' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:5047:16: style: Variable 'fGap' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:5168:45: style: Parameter 'rates' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:5176:29: style: Parameter 'pSame' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:5176:45: style: Parameter 'rates' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:5184:62: style: Parameter 'transmat' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:5224:18: style: Variable 'fA' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:5225:18: style: Variable 'fB' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:5276:16: style: Variable 'fGap' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:5280:18: style: Variable 'expeigen' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:5288:18: style: Variable 'fA' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:5289:18: style: Variable 'fB' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:5327:16: style: Variable 'fGap' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:5431:22: style: Parameter 'branch_lengths' can be declared as const array [constParameter]
FastTree-2.1.11/fasttree.c:5853:17: style: Variable 'codes' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:5870:58: style: Parameter 'freq_in' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:5884:22: style: Variable 'codes' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:5982:66: style: Parameter 'rates' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:6456:9: style: Variable 'length2' can be declared as const array [constVariable]
FastTree-2.1.11/fasttree.c:6555:33: style: Parameter 'NJ' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:6573:53: style: Parameter 'NJ' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:7468:10: style: Variable 'colw' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:7473:15: style: Variable 'd' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:7474:15: style: Variable 'w' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:7497:49: style: Parameter 'col' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:7497:61: style: Parameter 'loglk' can be declared as const array [constParameter]
FastTree-2.1.11/fasttree.c:7497:79: style: Parameter 'site_likelihoods' can be declared as const array [constParameter]
FastTree-2.1.11/fasttree.c:7666:31: style: Parameter 'NJ' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:7798:18: style: Variable 'closehit' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:7898:22: style: Variable 'lNode' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:7964:20: style: Variable 'l' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:8027:10: style: Variable 'v' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:8051:16: style: Variable 'hit' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:8056:18: style: Variable 'saved' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:8356:31: style: Parameter 'hit' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:8461:16: style: Variable 'v' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:8607:23: style: Parameter 'NJ' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:8698:16: style: Variable 'old' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:8729:12: style: Variable 'hit' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:8802:22: style: Parameter 'data' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:9106:67: style: Parameter 'x' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:9281:41: style: Parameter 'hash' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:9372:33: style: Parameter 'NJ' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:9421:56: style: Parameter 'NJ' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:9426:30: style: Parameter 'NJ' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:9486:68: style: Parameter 'NJ' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:9520:32: style: Parameter 'NJ' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:9525:40: style: Parameter 'r' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:9558:23: style: Parameter 'stat' can be declared as const array [constParameter]
FastTree-2.1.11/fasttree.c:9878:39: style: Parameter 'f1' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:9878:60: style: Parameter 'f2' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:9895:48: style: Parameter 'f1' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:9895:69: style: Parameter 'f2' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:9919:49: style: Parameter 'f1' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:9919:70: style: Parameter 'f2' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:9919:91: style: Parameter 'f3' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:9940:51: style: Parameter 'f1' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:9940:72: style: Parameter 'f2' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:9940:93: style: Parameter 'fBy' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:9966:39: style: Parameter 'f1' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:10003:66: style: Parameter 'fAdd' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:10043:57: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
FastTree-2.1.11/fasttree.c:10077:11: style: Variable 'field' can be declared as pointer to const [constVariablePointer]
FastTree-2.1.11/fasttree.c:2902:27: style: float result is assigned to double variable. If the variable is double to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
FastTree-2.1.11/fasttree.c:4307:16: style: float result is assigned to double variable. If the variable is double to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
FastTree-2.1.11/fasttree.c:4551:25: style: float result is assigned to double variable. If the variable is double to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
FastTree-2.1.11/fasttree.c:7419:21: style: float result is assigned to double variable. If the variable is double to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
FastTree-2.1.11/fasttree.c:7420:21: style: float result is assigned to double variable. If the variable is double to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
FastTree-2.1.11/fasttree.c:7421:21: style: float result is assigned to double variable. If the variable is double to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
FastTree-2.1.11/fasttree.c:7422:21: style: float result is assigned to double variable. If the variable is double to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
FastTree-2.1.11/fasttree.c:7423:21: style: float result is assigned to double variable. If the variable is double to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
FastTree-2.1.11/fasttree.c:7424:21: style: float result is assigned to double variable. If the variable is double to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
FastTree-2.1.11/fasttree.c:7615:14: style: float result is assigned to double variable. If the variable is double to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
FastTree-2.1.11/fasttree.c:2249:12: style: Variable 'nni_stats' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:2317:13: style: Variable 'tmatAsDist' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:2339:16: style: Variable 'oldlength' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:2409:12: style: Variable 'nni_stats' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:2438:10: style: Variable 'rates' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:2439:15: style: Variable 'site_loglk' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:2512:18: style: Variable 'uniqConstraints' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:2513:19: style: Variable 'constraints' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:2514:14: style: Variable 'unique' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:2516:15: style: Variable 'hashnames' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:2517:9: style: Variable 'aln' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:2970:22: style: Variable 'activeProfiles' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:3044:32: style: Variable 'visible' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:3045:38: style: Variable 'besthitNew' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:3046:11: style: Variable 'tophits' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:3519:7: style: Variable 'map' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:3520:9: style: Variable 'stack' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:3521:12: style: Variable 'children' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:3522:10: style: Variable 'parent' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:3533:13: style: Variable 'traversal' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:3580:9: style: Variable 'stack' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:3665:9: style: Variable 'stack' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:4963:12: style: Variable 'PSame1' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:4964:12: style: Variable 'PSame2' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:4965:12: style: Variable 'PDiff1' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:4966:12: style: Variable 'PDiff2' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:5143:20: style: Variable 'expeigenRates1' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:5144:20: style: Variable 'expeigenRates2' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:5270:11: style: Variable 'pSame' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:5271:11: style: Variable 'pDiff' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:5423:19: style: Variable 'expeigenRates' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:5455:7: style: Variable 'pAB' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:5456:7: style: Variable 'pCD' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:5523:11: style: Variable 'pAB' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:5524:11: style: Variable 'pCD' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:5543:8: style: Variable 'pBCD' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:5558:8: style: Variable 'pACD' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:5559:7: style: Variable 'pCD' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:5577:8: style: Variable 'pABD' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:5611:8: style: Variable 'pABC' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:5612:7: style: Variable 'pAB' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:5748:16: style: Variable 'traversal2' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:5817:11: style: Variable 'pAB' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:5820:13: style: Variable 'traversal' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:5825:21: style: Variable 'site_likelihood' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:6051:14: style: Variable 'site_loglk' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:6107:9: style: Variable 'dRate' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:6169:21: style: Variable 'gamma_loglk_sites' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:6244:7: style: Variable 'pB' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:6256:13: style: Variable 'traversal' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:6257:14: style: Variable 'upProfiles' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:6272:13: style: Variable 'traversal' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:6287:13: style: Variable 'traversal' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:6543:13: style: Variable 'traversal' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:6551:14: style: Variable 'upProfiles' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:6809:9: style: Variable 'steps' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:6810:14: style: Variable 'upProfiles' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:6811:12: style: Variable 'nodeList' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:6958:13: style: Variable 'traversal' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:6959:14: style: Variable 'upProfiles' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:7033:13: style: Variable 'traversal' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:7034:14: style: Variable 'upProfiles' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:7035:7: style: Variable 'col' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:7267:13: style: Variable 'traversal' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:7268:14: style: Variable 'upProfiles' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:7270:9: style: Variable 'col' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:7388:13: style: Variable 'traversal' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:7389:14: style: Variable 'upProfiles' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:7824:16: style: Variable 'besthitsClose' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:7866:21: style: Variable 'besthitsClose2' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:7871:18: style: Variable 'besthitsSeed' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:7872:22: style: Variable 'besthitsNeighbor' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:8300:16: style: Variable 'bothList' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:8307:19: style: Variable 'uniqueList2' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:9348:14: style: Variable 'hashseqs' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:9784:19: style: Variable 'iter' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:9784:40: style: Variable 'm' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:9785:19: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:9785:41: style: Variable 'g' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:9785:48: style: Variable 'p' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:9785:55: style: Variable 'r' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:9785:62: style: Variable 's' is assigned a value that is never used. [unreadVariable]
FastTree-2.1.11/fasttree.c:9435:7: error: Null pointer dereference: upProfiles [ctunullpointer]
FastTree-2.1.11/fasttree.c:6352:11: note: Calling function SetupABCD, 4th argument is null
FastTree-2.1.11/fasttree.c:7095:16: note: Calling function GetUpProfile, 1st argument is null
FastTree-2.1.11/fasttree.c:9435:7: note: Dereferencing argument upProfiles that is null
diff:


DONE