2026-07-26 20:47
ftp://ftp.de.debian.org/debian/pool/main/c/clearcut/clearcut_1.0.9+git20211013.b799afe.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j16
platform: Linux-7.0.0-28-generic-x86_64-with-glibc2.39
python: 3.12.3
client-version: 1.4.0
compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
cppcheck: head 2.21.0
head-info: 6640862 (2026-07-26 07:32:28 -0400)
count: 88 88
elapsed-time: 0.5 0.2
head-timing-info:

old-timing-info:

head results:
clearcut-1.0.9+git20211013.b799afe/common.h:93:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FLT_EPSILON [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/fasta.c:334:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/fasta.c:734:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/getopt_long.c:152:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/getopt_long.c:355:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/dmat.c:348:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/dmat.c:459:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/dmat.c:797:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/prng.c:81:34: style: Parameter 'init_key' can be declared as const array [constParameter]
clearcut-1.0.9+git20211013.b799afe/prng.c:110:26: style: Variable 'mag01' can be declared as const array [constVariable]
clearcut-1.0.9+git20211013.b799afe/dist.c:101:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/dist.c:132:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/dist.c:286:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FLT_EPSILON [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/dist.c:435:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FLT_EPSILON [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/getopt_long.c:81:17: style: Parameter 'arg' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/getopt_long.c:117:22: style: Parameter 'arg' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/getopt_long.c:117:42: style: Parameter 'longopts' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/getopt_long.c:141:26: style: Parameter 'arg' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/getopt_long.c:209:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
clearcut-1.0.9+git20211013.b799afe/getopt_long.c:384:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
clearcut-1.0.9+git20211013.b799afe/fasta.c:468:2: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
clearcut-1.0.9+git20211013.b799afe/fasta.c:398:7: error: Common realloc mistake: 'buf' nulled but not freed upon failure [memleakOnRealloc]
clearcut-1.0.9+git20211013.b799afe/fasta.c:359:3: warning: If memory allocation fails, then there is a possible null pointer dereference: alignment [nullPointerOutOfMemory]
clearcut-1.0.9+git20211013.b799afe/fasta.c:355:37: note: Assuming allocation function fails
clearcut-1.0.9+git20211013.b799afe/fasta.c:355:15: note: Assignment 'alignment=(struct NJ_alignment*)calloc(1,sizeof(struct NJ_alignment))', assigned value is 0
clearcut-1.0.9+git20211013.b799afe/fasta.c:359:3: note: Null pointer dereference
clearcut-1.0.9+git20211013.b799afe/fasta.c:298:24: style: Parameter 'nj_args' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/fasta.c:302:9: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
clearcut-1.0.9+git20211013.b799afe/fasta.c:630:34: style: Parameter 'alignment' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/fasta.c:726:34: style: Parameter 'alignment' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/fasta.c:746:31: style: Parameter 'alignment' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:95:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:306:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:426:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:521:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:937:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1115:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1241:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1481:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1831:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1951:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:2124:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/dist.c:143:5: error: Memory leak: dmat [memleak]
clearcut-1.0.9+git20211013.b799afe/dist.c:122:26: style: Parameter 'nj_args' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/dist.c:515:31: style: Parameter 'alignment' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/dmat.c:239:8: style: The if condition is the same as the previous if condition [duplicateCondition]
clearcut-1.0.9+git20211013.b799afe/dmat.c:232:8: note: First condition
clearcut-1.0.9+git20211013.b799afe/dmat.c:239:8: note: Second condition
clearcut-1.0.9+git20211013.b799afe/dist.c:277:9: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
clearcut-1.0.9+git20211013.b799afe/dmat.c:859:6: style: Condition 'fp' is always true [knownConditionTrueFalse]
clearcut-1.0.9+git20211013.b799afe/dmat.c:163:22: style: Parameter 'token' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/dmat.c:435:35: style: Parameter 'nj_args' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/dmat.c:781:27: style: Parameter 'nj_args' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/dmat.c:782:10: style: Parameter 'dmat' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/cmdargs.c:252:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1853:6: style: Condition 'perm' is always true [knownConditionTrueFalse]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1646:3: warning: If memory allocation fails, then there is a possible null pointer dereference: vertex [nullPointerOutOfMemory]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1643:31: note: Assuming allocation function fails
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1643:12: note: Assignment 'vertex=(struct NJ_VERTEX*)calloc(1,sizeof(struct NJ_VERTEX))', assigned value is 0
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1646:3: note: Null pointer dereference
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1647:3: warning: If memory allocation fails, then there is a possible null pointer dereference: vertex [nullPointerOutOfMemory]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1643:31: note: Assuming allocation function fails
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1643:12: note: Assignment 'vertex=(struct NJ_VERTEX*)calloc(1,sizeof(struct NJ_VERTEX))', assigned value is 0
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1647:3: note: Null pointer dereference
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1647:26: warning: If memory allocation fails, then there is a possible null pointer dereference: vertex [nullPointerOutOfMemory]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1643:31: note: Assuming allocation function fails
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1643:12: note: Assignment 'vertex=(struct NJ_VERTEX*)calloc(1,sizeof(struct NJ_VERTEX))', assigned value is 0
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1647:26: note: Null pointer dereference
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1650:3: warning: If memory allocation fails, then there is a possible null pointer dereference: vertex [nullPointerOutOfMemory]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1643:31: note: Assuming allocation function fails
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1643:12: note: Assignment 'vertex=(struct NJ_VERTEX*)calloc(1,sizeof(struct NJ_VERTEX))', assigned value is 0
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1650:3: note: Null pointer dereference
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1651:3: warning: If memory allocation fails, then there is a possible null pointer dereference: vertex [nullPointerOutOfMemory]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1643:31: note: Assuming allocation function fails
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1643:12: note: Assignment 'vertex=(struct NJ_VERTEX*)calloc(1,sizeof(struct NJ_VERTEX))', assigned value is 0
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1651:3: note: Null pointer dereference
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1656:5: warning: If memory allocation fails, then there is a possible null pointer dereference: vertex [nullPointerOutOfMemory]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1643:31: note: Assuming allocation function fails
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1643:12: note: Assignment 'vertex=(struct NJ_VERTEX*)calloc(1,sizeof(struct NJ_VERTEX))', assigned value is 0
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1656:5: note: Null pointer dereference
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1658:5: warning: If memory allocation fails, then there is a possible null pointer dereference: vertex [nullPointerOutOfMemory]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1643:31: note: Assuming allocation function fails
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1643:12: note: Assignment 'vertex=(struct NJ_VERTEX*)calloc(1,sizeof(struct NJ_VERTEX))', assigned value is 0
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1658:5: note: Null pointer dereference
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1659:5: warning: If memory allocation fails, then there is a possible null pointer dereference: vertex [nullPointerOutOfMemory]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1643:31: note: Assuming allocation function fails
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1643:12: note: Assignment 'vertex=(struct NJ_VERTEX*)calloc(1,sizeof(struct NJ_VERTEX))', assigned value is 0
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1659:5: note: Null pointer dereference
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1661:5: warning: If memory allocation fails, then there is a possible null pointer dereference: vertex [nullPointerOutOfMemory]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1643:31: note: Assuming allocation function fails
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1643:12: note: Assignment 'vertex=(struct NJ_VERTEX*)calloc(1,sizeof(struct NJ_VERTEX))', assigned value is 0
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1661:5: note: Null pointer dereference
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1698:3: warning: Either the condition 'vertex' is redundant or there is possible null pointer dereference: vertex. [nullPointerRedundantCheck]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1390:6: note: Assuming that condition 'vertex' is not redundant
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1380:29: note: Calling function 'NJ_decompose', 2nd argument 'vertex' value is 0
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1698:3: note: Null pointer dereference
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1709:3: warning: Either the condition 'vertex' is redundant or there is possible null pointer dereference: vertex. [nullPointerRedundantCheck]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1390:6: note: Assuming that condition 'vertex' is not redundant
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1380:29: note: Calling function 'NJ_decompose', 2nd argument 'vertex' value is 0
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1709:3: note: Null pointer dereference
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1714:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_node [nullPointerOutOfMemory]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1712:31: note: Assuming allocation function fails
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1712:14: note: Assignment 'new_node=(struct NJ_TREE*)calloc(1,sizeof(struct NJ_TREE))', assigned value is 0
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1714:3: note: Null pointer dereference
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1714:21: warning: Either the condition 'vertex' is redundant or there is possible null pointer dereference: vertex. [nullPointerRedundantCheck]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1390:6: note: Assuming that condition 'vertex' is not redundant
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1380:29: note: Calling function 'NJ_decompose', 2nd argument 'vertex' value is 0
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1714:21: note: Null pointer dereference
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1715:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_node [nullPointerOutOfMemory]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1712:31: note: Assuming allocation function fails
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1712:14: note: Assignment 'new_node=(struct NJ_TREE*)calloc(1,sizeof(struct NJ_TREE))', assigned value is 0
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1715:3: note: Null pointer dereference
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1715:21: warning: Either the condition 'vertex' is redundant or there is possible null pointer dereference: vertex. [nullPointerRedundantCheck]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1390:6: note: Assuming that condition 'vertex' is not redundant
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1380:29: note: Calling function 'NJ_decompose', 2nd argument 'vertex' value is 0
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1715:21: note: Null pointer dereference
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1716:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_node [nullPointerOutOfMemory]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1712:31: note: Assuming allocation function fails
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1712:14: note: Assignment 'new_node=(struct NJ_TREE*)calloc(1,sizeof(struct NJ_TREE))', assigned value is 0
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1716:3: note: Null pointer dereference
clearcut-1.0.9+git20211013.b799afe/clearcut.c:299:10: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:299:16: style: Variable 'r2' can be declared as pointer to const [constVariablePointer]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:419:16: style: Variable 'r2' can be declared as pointer to const [constVariablePointer]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:681:27: style: Parameter 'dmat' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:796:19: style: Parameter 'nj_args' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:805:22: style: Variable 'r2' can be declared as pointer to const [constVariablePointer]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:928:10: style: Variable 'vptr' can be declared as pointer to const [constVariablePointer]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1413:32: style: Parameter 'dmat' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1592:19: style: Variable 'val' can be declared as pointer to const [constVariablePointer]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1637:22: style: Parameter 'dmat' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1741:28: style: Parameter 'vertex' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1768:18: style: Parameter 'dmat' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1792:26: style: Parameter 'dmat' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1920:32: style: Parameter 'perm' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1943:19: style: Parameter 'src' can be declared as pointer to const [constParameterPointer]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:2121:10: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:2122:10: style: Variable 'r2' can be declared as pointer to const [constVariablePointer]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:314:12: style: Variable 'p' is assigned a value that is never used. [unreadVariable]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:433:12: style: Variable 'p' is assigned a value that is never used. [unreadVariable]
clearcut-1.0.9+git20211013.b799afe/clearcut.c:1125:9: style: Variable 'min' is assigned a value that is never used. [unreadVariable]
clearcut-1.0.9+git20211013.b799afe/cmdargs.c:406:24: style: Parameter 'nj_args' can be declared as pointer to const [constParameterPointer]
diff:


DONE