2025-07-11 08:01
ftp://ftp.de.debian.org/debian/pool/main/r/r-cran-seqinr/r-cran-seqinr_4.2-36.orig.tar.gz
cppcheck-options: --library=posix --library=gnu --library=bsd  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j3
platform: Linux-6.8.0-63-generic-x86_64-with-glibc2.39
python: 3.12.3
client-version: 1.3.67
compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
cppcheck: head 2.17.0
head-info: 8f3d36a (2025-07-08 11:07:56 +0200)
count: 63 63
elapsed-time: 2.5 3.2
head-timing-info:

old-timing-info:

head results:
seqinr/src/getzlibsock.c:28:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
seqinr/src/fastacc.c:8:8: style: Variable 'pbits_in_char' can be declared as pointer to const [constVariablePointer]
seqinr/src/fastacc.c:8:24: style: Variable 'pnoc' can be declared as pointer to const [constVariablePointer]
seqinr/src/fastacc.c:9:18: style: Variable 'ptarget' can be declared as pointer to const [constVariablePointer]
seqinr/src/fastacc.c:9:28: style: Variable 'pdatabase' can be declared as pointer to const [constVariablePointer]
seqinr/src/getzlibsock.c:192:7: style: The if condition is the same as the previous if condition [duplicateCondition]
seqinr/src/getzlibsock.c:190:7: note: First condition
seqinr/src/getzlibsock.c:192:7: note: Second condition
seqinr/src/getzlibsock.c:197:6: style: The if condition is the same as the previous if condition [duplicateCondition]
seqinr/src/getzlibsock.c:195:8: note: First condition
seqinr/src/getzlibsock.c:197:6: note: Second condition
seqinr/src/getzlibsock.c:29:13: style: Variable 'ans2' is assigned a value that is never used. [unreadVariable]
seqinr/src/getzlibsock.c:61:10: style: Variable 'nprotect' is assigned a value that is never used. [unreadVariable]
seqinr/src/getzlibsock.c:87:10: style: Variable 'nprotect' is assigned a value that is never used. [unreadVariable]
seqinr/src/getzlibsock.c:119:11: style: Variable 'nprotect' is assigned a value that is never used. [unreadVariable]
seqinr/src/getzlibsock.c:138:10: style: Variable 'nprotect' is assigned a value that is never used. [unreadVariable]
seqinr/src/packagename_init.c:41:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
seqinr/src/util.c:19:9: style: Variable 'string' can be declared as pointer to const [constVariablePointer]
seqinr/src/util.c:53:9: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
seqinr/src/util.c:54:15: style: Variable 'dna' can be declared as const array [constVariable]
seqinr/src/zsockr.c:53:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Z_NULL [valueFlowBailoutIncompleteVar]
seqinr/src/zsockr.c:103:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
seqinr/src/zsockr.c:129:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
seqinr/src/alignment.c:146:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VECSXP [valueFlowBailoutIncompleteVar]
seqinr/src/alignment.c:452:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VECSXP [valueFlowBailoutIncompleteVar]
seqinr/src/alignment.c:574:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VECSXP [valueFlowBailoutIncompleteVar]
seqinr/src/alignment.c:676:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VECSXP [valueFlowBailoutIncompleteVar]
seqinr/src/alignment.c:779:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VECSXP [valueFlowBailoutIncompleteVar]
seqinr/src/zsockr.c:52:8: style: Condition 'big==NULL' is always false [knownConditionTrueFalse]
seqinr/src/zsockr.c:145:7: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
seqinr/src/kaks.c:872:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
seqinr/src/alignment.c:55:25: error: Memory leak: seq [memleak]
seqinr/src/alignment.c:57:26: error: Memory leak: seq [memleak]
seqinr/src/alignment.c:57:26: error: Memory leak: seqname [memleak]
seqinr/src/alignment.c:878:3: error: Common realloc mistake: 'seq' nulled but not freed upon failure [memleakOnRealloc]
seqinr/src/alignment.c:879:3: error: Common realloc mistake: 'seqname' nulled but not freed upon failure [memleakOnRealloc]
seqinr/src/alignment.c:880:3: error: Common realloc mistake: 'comments' nulled but not freed upon failure [memleakOnRealloc]
seqinr/src/alignment.c:111:34: warning: Either the condition '(fic=fopen(fic_name,"r"))==NULL' is redundant or there is possible null pointer dereference: fic. [nullPointerRedundantCheck]
seqinr/src/alignment.c:104:35: note: Assuming that condition '(fic=fopen(fic_name,"r"))==NULL' is not redundant
seqinr/src/alignment.c:111:34: note: Null pointer dereference
seqinr/src/alignment.c:158:5: warning: If memory allocation fails, then there is a possible null pointer dereference: aln [nullPointerOutOfMemory]
seqinr/src/alignment.c:154:34: note: Assuming allocation function fails
seqinr/src/alignment.c:154:9: note: Assignment 'aln=(struct SEQMASE*)calloc(nb_seq+1,sizeof(struct SEQMASE))', assigned value is 0
seqinr/src/alignment.c:158:5: note: Null pointer dereference
seqinr/src/alignment.c:159:5: warning: If memory allocation fails, then there is a possible null pointer dereference: aln [nullPointerOutOfMemory]
seqinr/src/alignment.c:154:34: note: Assuming allocation function fails
seqinr/src/alignment.c:154:9: note: Assignment 'aln=(struct SEQMASE*)calloc(nb_seq+1,sizeof(struct SEQMASE))', assigned value is 0
seqinr/src/alignment.c:159:5: note: Null pointer dereference
seqinr/src/alignment.c:160:5: warning: If memory allocation fails, then there is a possible null pointer dereference: aln [nullPointerOutOfMemory]
seqinr/src/alignment.c:154:34: note: Assuming allocation function fails
seqinr/src/alignment.c:154:9: note: Assignment 'aln=(struct SEQMASE*)calloc(nb_seq+1,sizeof(struct SEQMASE))', assigned value is 0
seqinr/src/alignment.c:160:5: note: Null pointer dereference
seqinr/src/alignment.c:310:5: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory]
seqinr/src/alignment.c:307:24: note: Assuming allocation function fails
seqinr/src/alignment.c:307:9: note: Assignment 'seq=(char**)malloc(totseqs*sizeof(char*))', assigned value is 0
seqinr/src/alignment.c:310:5: note: Null pointer dereference
seqinr/src/alignment.c:316:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ndiff [nullPointerOutOfMemory]
seqinr/src/alignment.c:313:25: note: Assuming allocation function fails
seqinr/src/alignment.c:313:11: note: Assignment 'ndiff=(int**)malloc(MAXNSEQS*sizeof(int*))', assigned value is 0
seqinr/src/alignment.c:316:5: note: Null pointer dereference
seqinr/src/alignment.c:322:5: warning: If memory allocation fails, then there is a possible null pointer dereference: dist [nullPointerOutOfMemory]
seqinr/src/alignment.c:319:27: note: Assuming allocation function fails
seqinr/src/alignment.c:319:10: note: Assignment 'dist=(double**)malloc(MAXNSEQS*sizeof(double*))', assigned value is 0
seqinr/src/alignment.c:322:5: note: Null pointer dereference
seqinr/src/alignment.c:331:26: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory]
seqinr/src/alignment.c:307:24: note: Assuming allocation function fails
seqinr/src/alignment.c:307:9: note: Assignment 'seq=(char**)malloc(totseqs*sizeof(char*))', assigned value is 0
seqinr/src/alignment.c:331:26: note: Null pointer dereference
seqinr/src/alignment.c:334:5: warning: If memory allocation fails, then there is a possible null pointer dereference: dist [nullPointerOutOfMemory]
seqinr/src/alignment.c:319:27: note: Assuming allocation function fails
seqinr/src/alignment.c:319:10: note: Assignment 'dist=(double**)malloc(MAXNSEQS*sizeof(double*))', assigned value is 0
seqinr/src/alignment.c:334:5: note: Null pointer dereference
seqinr/src/alignment.c:461:34: warning: If resource allocation fails, then there is a possible null pointer dereference: in [nullPointerOutOfResources]
seqinr/src/alignment.c:454:10: note: Assuming allocation function fails
seqinr/src/alignment.c:454:10: note: Assignment 'in=fopen(fname,"r")', assigned value is 0
seqinr/src/alignment.c:461:34: note: Null pointer dereference
seqinr/src/alignment.c:582:31: warning: If resource allocation fails, then there is a possible null pointer dereference: in [nullPointerOutOfResources]
seqinr/src/alignment.c:577:11: note: Assuming allocation function fails
seqinr/src/alignment.c:577:11: note: Assignment 'in=fopen(fname,"r")', assigned value is 0
seqinr/src/alignment.c:582:31: note: Null pointer dereference
seqinr/src/alignment.c:685:35: warning: Either the condition '(in=fopen(fname,"r"))==NULL' is redundant or there is possible null pointer dereference: in. [nullPointerRedundantCheck]
seqinr/src/alignment.c:680:31: note: Assuming that condition '(in=fopen(fname,"r"))==NULL' is not redundant
seqinr/src/alignment.c:685:35: note: Null pointer dereference
seqinr/src/alignment.c:83:9: style: Variable 'fic_name' can be declared as pointer to const [constVariablePointer]
seqinr/src/alignment.c:271:7: style: Variable 'mat_pos' can be declared as const array [constVariable]
seqinr/src/alignment.c:275:7: style: Variable 'matp' can be declared as const array [constVariable]
seqinr/src/alignment.c:443:9: style: Variable 'fname' can be declared as pointer to const [constVariablePointer]
seqinr/src/alignment.c:564:9: style: Variable 'fname' can be declared as pointer to const [constVariablePointer]
seqinr/src/alignment.c:566:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
seqinr/src/alignment.c:667:9: style: Variable 'fname' can be declared as pointer to const [constVariablePointer]
seqinr/src/alignment.c:670:20: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
seqinr/src/alignment.c:670:24: style: Variable 'i' can be declared as pointer to const [constVariablePointer]
seqinr/src/alignment.c:769:9: style: Variable 'fname' can be declared as pointer to const [constVariablePointer]
seqinr/src/kaks.c:393:15: style: Parameter 'cod' can be declared as pointer to const [constParameterPointer]
seqinr/src/kaks.c:623:18: style: Parameter 'cod1' can be declared as pointer to const [constParameterPointer]
seqinr/src/kaks.c:623:30: style: Parameter 'cod2' can be declared as pointer to const [constParameterPointer]
seqinr/src/kaks.c:764:76: style: Parameter 'aa' can be declared as pointer to const [constParameterPointer]
seqinr/src/kaks.c:764:98: style: Parameter 'pos' can be declared as pointer to const [constParameterPointer]
seqinr/src/kaks.c:811:76: style: Parameter 'aa' can be declared as pointer to const [constParameterPointer]
seqinr/src/kaks.c:797:39: warning: Uninitialized variable: n [uninitvar]
seqinr/src/kaks.c:796:30: note: Assuming condition is false
seqinr/src/kaks.c:797:39: note: Uninitialized variable: n
seqinr/src/kaks.c:871:40: style: Unused variable: pos [unusedVariable]
diff:


DONE