2024-03-25 07:56 ftp://ftp.de.debian.org/debian/pool/main/p/python-biopython/python-biopython_1.83+dfsg.orig.tar.xz cppcheck-options: --library=posix --library=gnu --showtime=top5 --check-library --inconclusive --enable=style,information --inline-suppr --disable=missingInclude --suppress=unmatchedSuppression --template=daca2 --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=valueFlowBailoutIncompleteVar -D__GNUC__ --platform=unix64 -j4 platform: Linux-6.1.0-0.deb11.6-amd64-x86_64-with-glibc2.31 python: 3.9.2 client-version: 1.3.45 compiler: g++ (Debian 10.2.1-6) 10.2.1 20210110 cppcheck: head 2.13.0 head-info: fd7bd50 (2024-03-25 07:57:46 +0100) count: 151 149 elapsed-time: 2.5 2.7 head-timing-info: Tokenizer::simplifyTokens1::ValueFlow: 1.83802s (avg. 1.83802s - 1 result(s)) valueFlowAfterAssign(tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 0.735146s (avg. 0.245049s - 3 result(s)) valueFlowCondition(SymbolicConditionHandler{}, tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 0.378096s (avg. 0.126032s - 3 result(s)) valueFlowSymbolic(tokenlist, symboldatabase, errorLogger, settings): 0.278497s (avg. 0.278497s - 1 result(s)) valueFlowUninit(tokenlist, errorLogger, settings): 0.134923s (avg. 0.0449743s - 3 result(s)) Overall time: 2.36985s old-timing-info: Tokenizer::simplifyTokens1::ValueFlow: 2.44417s (avg. 2.44417s - 1 result(s)) valueFlowCondition(SymbolicConditionHandler{}, tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 0.665739s (avg. 0.166435s - 4 result(s)) valueFlowConditionExpressions(tokenlist, symboldatabase, errorLogger, *settings): 0.608254s (avg. 0.608254s - 1 result(s)) valueFlowAfterAssign(tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 0.51033s (avg. 0.127582s - 4 result(s)) valueFlowCondition(SimpleConditionHandler{}, tokenlist, symboldatabase, errorLogger, settings, skippedFunctions): 0.195637s (avg. 0.0489093s - 4 result(s)) Overall time: 2.62109s head results: biopython-biopython-183/Bio/Cluster/clustermodule.c:149:21: portability: Casting between const char * and double * which have an incompatible binary data representation. [invalidPointerCast] biopython-biopython-183/Bio/Cluster/clustermodule.c:2281:15: style: Local variable 'mean' shadows outer function [shadowFunction] biopython-biopython-183/Bio/Cluster/cluster.h:86:8: note: Shadowed declaration biopython-biopython-183/Bio/Cluster/clustermodule.c:2281:15: note: Shadow variable biopython-biopython-183/Bio/Cluster/clustermodule.c:277:10: style: Variable 'p' can be declared as pointer to const [constVariablePointer] biopython-biopython-183/Bio/Cluster/clustermodule.c:681:21: style: Parameter 'self' can be declared as pointer to const. However it seems that 'PyNode_repr' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Cluster/clustermodule.c:783:15: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Cluster/clustermodule.c:681:21: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Cluster/clustermodule.c:874:17: style: Variable 'p' can be declared as pointer to const [constVariablePointer] biopython-biopython-183/Bio/Cluster/clustermodule.c:958:23: style: Parameter 'self' can be declared as pointer to const. However it seems that 'PyTree_length' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Cluster/clustermodule.c:1014:14: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Cluster/clustermodule.c:958:23: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Cluster/clustermodule.c:1050:20: style: Parameter 'self' can be declared as pointer to const. However it seems that 'PyTree_cut' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Cluster/clustermodule.c:1133:26: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Cluster/clustermodule.c:1050:20: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Cluster/clustermodule.c:1198:22: style: Parameter 'self' can be declared as pointer to const. However it seems that 'py_version' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Cluster/clustermodule.c:2368:31: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Cluster/clustermodule.c:1198:22: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/PDB/ccealignmodule.c:555:31: debug: Function::addArguments found argument 'self' with varid 0. [varid0] biopython-biopython-183/Bio/Align/_codonaligner.c:49:42: style: Parameter 'self' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/Align/_codonaligner.c:274:36: style: Parameter 'self' can be declared as pointer to const. However it seems that 'PathGenerator_reset' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_codonaligner.c:284:19: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_codonaligner.c:274:36: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_codonaligner.c:580:45: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_frameshift_minus_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_codonaligner.c:745:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_codonaligner.c:580:45: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_codonaligner.c:604:44: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_frameshift_plus_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_codonaligner.c:749:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_codonaligner.c:604:44: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_codonaligner.c:628:43: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_frameshift_two_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_codonaligner.c:757:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_codonaligner.c:628:43: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_codonaligner.c:652:43: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_frameshift_one_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_codonaligner.c:753:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_codonaligner.c:652:43: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_codonaligner.c:676:39: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_frameshift_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_codonaligner.c:761:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_codonaligner.c:676:39: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_codonaligner.c:775:24: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_codonaligner.c:1070:19: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_codonaligner.c:775:24: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_codonaligner.c:777:11: style: Variable 'sA' can be declared as pointer to const [constVariablePointer] biopython-biopython-183/Bio/Align/_codonaligner.c:889:24: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_align' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_codonaligner.c:1075:19: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_codonaligner.c:889:24: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_codonaligner.c:891:11: style: Variable 'sA' can be declared as pointer to const [constVariablePointer] biopython-biopython-183/Bio/Align/_codonaligner.c:239:9: warning: Uninitialized variable: path [uninitvar] biopython-biopython-183/Bio/Align/_codonaligner.c:200:19: note: Assuming condition is false biopython-biopython-183/Bio/Align/_codonaligner.c:239:9: note: Uninitialized variable: path biopython-biopython-183/Bio/Align/_codonaligner.c:194:15: style: Variable 'trace' is assigned a value that is never used. [unreadVariable] biopython-biopython-183/Bio/PDB/ccealignmodule.c:297:34: style: Same expression on both sides of '-'. [duplicateExpression] biopython-biopython-183/Bio/PDB/ccealignmodule.c:296:33: note: 'curPathLength' is assigned value '1' here. biopython-biopython-183/Bio/PDB/ccealignmodule.c:297:34: note: Same expression on both sides of '-'. biopython-biopython-183/Bio/PDB/ccealignmodule.c:444:30: style: Local variable 'i' shadows outer variable [shadowVariable] biopython-biopython-183/Bio/PDB/ccealignmodule.c:215:9: note: Shadowed declaration biopython-biopython-183/Bio/PDB/ccealignmodule.c:444:30: note: Shadow variable biopython-biopython-183/Bio/PDB/ccealignmodule.c:468:21: style: Local variable 'i' shadows outer variable [shadowVariable] biopython-biopython-183/Bio/PDB/ccealignmodule.c:215:9: note: Shadowed declaration biopython-biopython-183/Bio/PDB/ccealignmodule.c:468:21: note: Shadow variable biopython-biopython-183/Bio/PDB/ccealignmodule.c:515:13: style: Local variable 'j' shadows outer variable [shadowVariable] biopython-biopython-183/Bio/PDB/ccealignmodule.c:215:12: note: Shadowed declaration biopython-biopython-183/Bio/PDB/ccealignmodule.c:515:13: note: Shadow variable biopython-biopython-183/Bio/PDB/ccealignmodule.c:377:31: style: Variable 'score1' is assigned a value that is never used. [unreadVariable] biopython-biopython-183/Bio/PDB/ccealignmodule.c:377:45: style: Variable 'score2' is assigned a value that is never used. [unreadVariable] biopython-biopython-183/Bio/PDB/ccealignmodule.c:411:30: style: Variable 'done' is assigned a value that is never used. [unreadVariable] biopython-biopython-183/Bio/PDB/ccealignmodule.c:423:26: style: Variable 'done' is assigned a value that is never used. [unreadVariable] biopython-biopython-183/Bio/PDB/ccealignmodule.c:424:34: style: Variable 'curPathLength' is assigned a value that is never used. [unreadVariable] biopython-biopython-183/Bio/SeqIO/_twoBitIO.c:292:9: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg] biopython-biopython-183/Bio/SeqIO/_twoBitIO.c:429:9: warning: Either the condition '!full_sequence' is redundant or there is possible null pointer dereference: full_sequence. [nullPointerRedundantCheck] biopython-biopython-183/Bio/SeqIO/_twoBitIO.c:430:13: note: Assuming that condition '!full_sequence' is not redundant biopython-biopython-183/Bio/SeqIO/_twoBitIO.c:429:9: note: Null pointer dereference biopython-biopython-183/Bio/SeqIO/_twoBitIO.c:291:14: style: Variable 'bytes' is assigned a value that is never used. [unreadVariable] biopython-biopython-183/Bio/SeqIO/_twoBitIO.c:292:15: style: Variable 'bytes' is assigned a value that is never used. [unreadVariable] biopython-biopython-183/Bio/PDB/kdtrees.c:87:24: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Point_getradius' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/PDB/kdtrees.c:95:24: note: You might need to cast the function pointer here biopython-biopython-183/Bio/PDB/kdtrees.c:87:24: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/PDB/kdtrees.c:195:30: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Neighbor_getradius' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/PDB/kdtrees.c:204:24: note: You might need to cast the function pointer here biopython-biopython-183/Bio/PDB/kdtrees.c:195:30: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/PDB/kdtrees.c:284:31: style: Parameter 'node' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/PDB/kdtrees.c:327:36: style: Parameter 'region' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/PDB/kdtrees.c:327:52: style: Parameter 'coord' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/PDB/kdtrees.c:443:35: style: Parameter 'coord1' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/PDB/kdtrees.c:443:51: style: Parameter 'coord2' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/PDB/kdtrees.c:478:31: style: Parameter 'self' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/PDB/kdtrees.c:509:55: style: Parameter 'node' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/PDB/kdtrees.c:530:72: style: Parameter 'node1' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/PDB/kdtrees.c:530:85: style: Parameter 'node2' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/PDB/kdtrees.c:1120:13: style: Variable 'coords' can be declared as pointer to const [constVariablePointer] biopython-biopython-183/Bio/PDB/kdtrees.c:424:12: style: struct member 'Radius::value' is never used. [unusedStructMember] biopython-biopython-183/Bio/PDB/kdtrees.c:447:25: style: Variable 'dif' is assigned a value that is never used. [unreadVariable] biopython-biopython-183/Bio/motifs/_pwm.c:25:9: style: Same expression on both sides of '/='. [duplicateExpression] biopython-biopython-183/Bio/motifs/_pwm.c:15:63: style: Parameter 'matrix' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/cpairwise2module.c:318:54: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck] biopython-biopython-183/Bio/cpairwise2module.c:322:54: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck] biopython-biopython-183/Bio/cpairwise2module.c:329:46: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck] biopython-biopython-183/Bio/cpairwise2module.c:39:38: style: Parameter 'sequenceA' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/cpairwise2module.c:39:55: style: Parameter 'sequenceB' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/Cluster/cluster.c:710:31: error: Array 'w[0]' accessed at index -1, which is out of bounds. [negativeIndex] biopython-biopython-183/Bio/Cluster/cluster.c:705:31: note: Assuming that condition 'l>=0' is not redundant biopython-biopython-183/Bio/Cluster/cluster.c:706:27: note: Assignment 'l1=l-1', assigned value is -1 biopython-biopython-183/Bio/Cluster/cluster.c:707:46: note: Assuming condition is false biopython-biopython-183/Bio/Cluster/cluster.c:710:31: note: Negative array index biopython-biopython-183/Bio/Cluster/cluster.c:912:31: error: Array 'w[0]' accessed at index -1, which is out of bounds. [negativeIndex] biopython-biopython-183/Bio/Cluster/cluster.c:907:31: note: Assuming that condition 'l>=0' is not redundant biopython-biopython-183/Bio/Cluster/cluster.c:908:27: note: Assignment 'l1=l-1', assigned value is -1 biopython-biopython-183/Bio/Cluster/cluster.c:909:46: note: Assuming condition is false biopython-biopython-183/Bio/Cluster/cluster.c:912:31: note: Negative array index biopython-biopython-183/Bio/Align/_pairwisealigner.c:5998:5: style: Variable 'temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:5998:5: note: temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:5998:5: note: temp is overwritten biopython-biopython-183/Bio/Align/_pairwisealigner.c:6009:5: style: Variable 'temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6009:5: note: temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:6009:5: note: temp is overwritten biopython-biopython-183/Bio/Align/_pairwisealigner.c:6020:5: style: Variable 'temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6020:5: note: temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:6020:5: note: temp is overwritten biopython-biopython-183/Bio/Align/_pairwisealigner.c:6030:5: style: Variable 'temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6030:5: note: temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:6030:5: note: temp is overwritten biopython-biopython-183/Bio/Align/_pairwisealigner.c:6042:5: style: Variable 'temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6042:5: note: temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:6042:5: note: temp is overwritten biopython-biopython-183/Bio/Align/_pairwisealigner.c:6053:5: style: Variable 'temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6053:5: note: temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:6053:5: note: temp is overwritten biopython-biopython-183/Bio/Align/_pairwisealigner.c:6065:5: style: Variable 'temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6065:5: note: temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:6065:5: note: temp is overwritten biopython-biopython-183/Bio/Align/_pairwisealigner.c:6076:5: style: Variable 'temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6076:5: note: temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:6076:5: note: temp is overwritten biopython-biopython-183/Bio/Align/_pairwisealigner.c:6110:5: style: Variable 'M_temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6110:5: note: M_temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:6110:5: note: M_temp is overwritten biopython-biopython-183/Bio/Align/_pairwisealigner.c:6120:5: style: Variable 'M_temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6120:5: note: M_temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:6120:5: note: M_temp is overwritten biopython-biopython-183/Bio/Align/_pairwisealigner.c:6132:5: style: Variable 'Ix_temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6132:5: note: Ix_temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:6132:5: note: Ix_temp is overwritten biopython-biopython-183/Bio/Align/_pairwisealigner.c:6132:5: style: Variable 'Iy_temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6132:5: note: Iy_temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:6132:5: note: Iy_temp is overwritten biopython-biopython-183/Bio/Align/_pairwisealigner.c:6143:5: style: Variable 'Ix_temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6143:5: note: Ix_temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:6143:5: note: Ix_temp is overwritten biopython-biopython-183/Bio/Align/_pairwisealigner.c:6143:5: style: Variable 'Iy_temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6143:5: note: Iy_temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:6143:5: note: Iy_temp is overwritten biopython-biopython-183/Bio/Align/_pairwisealigner.c:6155:5: style: Variable 'M_temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6155:5: note: M_temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:6155:5: note: M_temp is overwritten biopython-biopython-183/Bio/Align/_pairwisealigner.c:6155:5: style: Variable 'Ix_temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6155:5: note: Ix_temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:6155:5: note: Ix_temp is overwritten biopython-biopython-183/Bio/Align/_pairwisealigner.c:6155:5: style: Variable 'Iy_temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6155:5: note: Iy_temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:6155:5: note: Iy_temp is overwritten biopython-biopython-183/Bio/Align/_pairwisealigner.c:6166:5: style: Variable 'M_temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6166:5: note: M_temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:6166:5: note: M_temp is overwritten biopython-biopython-183/Bio/Align/_pairwisealigner.c:6166:5: style: Variable 'Ix_temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6166:5: note: Ix_temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:6166:5: note: Ix_temp is overwritten biopython-biopython-183/Bio/Align/_pairwisealigner.c:6166:5: style: Variable 'Iy_temp' is reassigned a value before the old one has been used. [redundantAssignment] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6166:5: note: Iy_temp is assigned biopython-biopython-183/Bio/Align/_pairwisealigner.c:6166:5: note: Iy_temp is overwritten biopython-biopython-183/Bio/Cluster/cluster.c:3835:5: error: Common realloc mistake: 'result' nulled but not freed upon failure [memleakOnRealloc] biopython-biopython-183/Bio/Cluster/cluster.c:233:20: style:inconclusive: Function 'mean' argument 2 names different: declaration 'x' definition 'a'. [funcArgNamesDifferent] biopython-biopython-183/Bio/Cluster/cluster.h:86:27: note: Function 'mean' argument 2 names different: declaration 'x' definition 'a'. biopython-biopython-183/Bio/Cluster/cluster.c:233:20: note: Function 'mean' argument 2 names different: declaration 'x' definition 'a'. biopython-biopython-183/Bio/Cluster/cluster.c:1014:9: style:inconclusive: Function 'pca' argument 1 names different: declaration 'm' definition 'nrows'. [funcArgNamesDifferent] biopython-biopython-183/Bio/Cluster/cluster.h:82:13: note: Function 'pca' argument 1 names different: declaration 'm' definition 'nrows'. biopython-biopython-183/Bio/Cluster/cluster.c:1014:9: note: Function 'pca' argument 1 names different: declaration 'm' definition 'nrows'. biopython-biopython-183/Bio/Cluster/cluster.c:1014:20: style:inconclusive: Function 'pca' argument 2 names different: declaration 'n' definition 'ncolumns'. [funcArgNamesDifferent] biopython-biopython-183/Bio/Cluster/cluster.h:82:20: note: Function 'pca' argument 2 names different: declaration 'n' definition 'ncolumns'. biopython-biopython-183/Bio/Cluster/cluster.c:1014:20: note: Function 'pca' argument 2 names different: declaration 'n' definition 'ncolumns'. biopython-biopython-183/Bio/Cluster/cluster.c:2840:29: style:inconclusive: Function 'kcluster' argument 2 names different: declaration 'ngenes' definition 'nrows'. [funcArgNamesDifferent] biopython-biopython-183/Bio/Cluster/cluster.h:52:34: note: Function 'kcluster' argument 2 names different: declaration 'ngenes' definition 'nrows'. biopython-biopython-183/Bio/Cluster/cluster.c:2840:29: note: Function 'kcluster' argument 2 names different: declaration 'ngenes' definition 'nrows'. biopython-biopython-183/Bio/Cluster/cluster.c:2840:40: style:inconclusive: Function 'kcluster' argument 3 names different: declaration 'ndata' definition 'ncolumns'. [funcArgNamesDifferent] biopython-biopython-183/Bio/Cluster/cluster.h:52:46: note: Function 'kcluster' argument 3 names different: declaration 'ndata' definition 'ncolumns'. biopython-biopython-183/Bio/Cluster/cluster.c:2840:40: note: Function 'kcluster' argument 3 names different: declaration 'ndata' definition 'ncolumns'. biopython-biopython-183/Bio/Cluster/cluster.c:3010:49: style:inconclusive: Function 'kmedoids' argument 3 names different: declaration 'distance' definition 'distmatrix'. [funcArgNamesDifferent] biopython-biopython-183/Bio/Cluster/cluster.h:55:54: note: Function 'kmedoids' argument 3 names different: declaration 'distance' definition 'distmatrix'. biopython-biopython-183/Bio/Cluster/cluster.c:3010:49: note: Function 'kmedoids' argument 3 names different: declaration 'distance' definition 'distmatrix'. biopython-biopython-183/Bio/Cluster/cluster.c:3199:20: style:inconclusive: Function 'distancematrix' argument 1 names different: declaration 'ngenes' definition 'nrows'. [funcArgNamesDifferent] biopython-biopython-183/Bio/Cluster/cluster.h:43:25: note: Function 'distancematrix' argument 1 names different: declaration 'ngenes' definition 'nrows'. biopython-biopython-183/Bio/Cluster/cluster.c:3199:20: note: Function 'distancematrix' argument 1 names different: declaration 'ngenes' definition 'nrows'. biopython-biopython-183/Bio/Cluster/cluster.c:3199:31: style:inconclusive: Function 'distancematrix' argument 2 names different: declaration 'ndata' definition 'ncolumns'. [funcArgNamesDifferent] biopython-biopython-183/Bio/Cluster/cluster.h:43:37: note: Function 'distancematrix' argument 2 names different: declaration 'ndata' definition 'ncolumns'. biopython-biopython-183/Bio/Cluster/cluster.c:3199:31: note: Function 'distancematrix' argument 2 names different: declaration 'ndata' definition 'ncolumns'. biopython-biopython-183/Bio/Cluster/cluster.c:3200:12: style:inconclusive: Function 'distancematrix' argument 5 names different: declaration 'weight' definition 'weights'. [funcArgNamesDifferent] biopython-biopython-183/Bio/Cluster/cluster.h:44:11: note: Function 'distancematrix' argument 5 names different: declaration 'weight' definition 'weights'. biopython-biopython-183/Bio/Cluster/cluster.c:3200:12: note: Function 'distancematrix' argument 5 names different: declaration 'weight' definition 'weights'. biopython-biopython-183/Bio/Cluster/cluster.c:3200:58: style:inconclusive: Function 'distancematrix' argument 8 names different: declaration 'distances' definition 'matrix'. [funcArgNamesDifferent] biopython-biopython-183/Bio/Cluster/cluster.h:44:54: note: Function 'distancematrix' argument 8 names different: declaration 'distances' definition 'matrix'. biopython-biopython-183/Bio/Cluster/cluster.c:3200:58: note: Function 'distancematrix' argument 8 names different: declaration 'distances' definition 'matrix'. biopython-biopython-183/Bio/Cluster/cluster.c:4572:47: style:inconclusive: Function 'somcluster' argument 7 names different: declaration 'nxnodes' definition 'nxgrid'. [funcArgNamesDifferent] biopython-biopython-183/Bio/Cluster/cluster.h:77:45: note: Function 'somcluster' argument 7 names different: declaration 'nxnodes' definition 'nxgrid'. biopython-biopython-183/Bio/Cluster/cluster.c:4572:47: note: Function 'somcluster' argument 7 names different: declaration 'nxnodes' definition 'nxgrid'. biopython-biopython-183/Bio/Cluster/cluster.c:4572:59: style:inconclusive: Function 'somcluster' argument 8 names different: declaration 'nynodes' definition 'nygrid'. [funcArgNamesDifferent] biopython-biopython-183/Bio/Cluster/cluster.h:77:58: note: Function 'somcluster' argument 8 names different: declaration 'nynodes' definition 'nygrid'. biopython-biopython-183/Bio/Cluster/cluster.c:4572:59: note: Function 'somcluster' argument 8 names different: declaration 'nynodes' definition 'nygrid'. biopython-biopython-183/Bio/Cluster/cluster.c:66:48: style: Parameter 'index' can be declared as const array [constParameter] biopython-biopython-183/Bio/Cluster/cluster.c:233:20: style: Parameter 'a' can be declared as const array [constParameter] biopython-biopython-183/Bio/Cluster/cluster.c:2249:36: style: Parameter 'clusterid' can be declared as const array [constParameter] biopython-biopython-183/Bio/Cluster/cluster.c:2361:36: style: Parameter 'clusterid' can be declared as const array [constParameter] biopython-biopython-183/Bio/Cluster/cluster.c:2561:9: style: Parameter 'clusterid' can be declared as const array [constParameter] biopython-biopython-183/Bio/Cluster/cluster.c:4688:42: style: Parameter 'index1' can be declared as const array [constParameter] biopython-biopython-183/Bio/Cluster/cluster.c:4688:56: style: Parameter 'index2' can be declared as const array [constParameter] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6312:13: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6316:13: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6334:13: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6338:13: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6360:13: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6364:13: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6385:13: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6389:13: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak] biopython-biopython-183/Bio/Align/_pairwisealigner.c:80:42: style: Parameter 'self' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/Align/_pairwisealigner.c:170:53: style: Parameter 'self' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/Align/_pairwisealigner.c:213:51: style: Parameter 'self' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/Align/_pairwisealigner.c:1942:27: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_mode' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3808:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:1942:27: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:2197:37: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_open_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3840:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:2197:37: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:2242:39: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_extend_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3844:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:2242:39: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:2287:41: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_internal_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3848:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:2287:41: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:2327:46: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_internal_open_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3852:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:2327:46: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:2363:48: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_internal_extend_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3856:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:2363:48: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:2400:36: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_end_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3860:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:2400:36: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:2448:41: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_end_open_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3864:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:2448:41: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:2488:43: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_end_extend_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3868:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:2488:43: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:2528:37: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_left_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3872:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:2528:37: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:2568:38: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_right_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3884:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:2568:38: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:2608:42: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_left_open_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3876:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:2608:42: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:2644:44: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_left_extend_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3880:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:2644:44: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:2680:43: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_right_open_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3888:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:2680:43: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:2716:45: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_right_extend_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3892:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:2716:45: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:2752:44: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_target_open_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3896:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:2752:44: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:2786:46: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_target_extend_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3900:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:2786:46: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:2872:43: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_query_open_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3908:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:2872:43: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:2906:45: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_query_extend_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3912:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:2906:45: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:3041:48: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_target_internal_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3940:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:3041:48: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:3074:43: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_target_end_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3920:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:3074:43: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:3110:48: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_target_end_open_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3924:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:3110:48: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:3143:50: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_target_end_extend_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3928:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:3143:50: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:3223:44: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_target_left_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3952:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:3223:44: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:3303:45: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_target_right_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3964:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:3303:45: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:3335:42: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_query_end_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3968:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:3335:42: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:3371:47: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_query_end_open_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3972:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:3371:47: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:3403:49: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_query_end_extend_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3976:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:3403:49: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:3485:47: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_query_internal_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:3988:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:3485:47: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:3566:43: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_query_left_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:4000:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:3566:43: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:3646:44: style: Parameter 'self' can be declared as pointer to const. However it seems that 'Aligner_get_query_right_gap_score' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_pairwisealigner.c:4012:17: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_pairwisealigner.c:3646:44: note: Parameter 'self' can be declared as pointer to const biopython-biopython-183/Bio/Align/_pairwisealigner.c:5990:48: style: Parameter 'self' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6013:46: style: Parameter 'self' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6034:48: style: Parameter 'self' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6057:46: style: Parameter 'self' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6080:45: style: Parameter 'self' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6103:44: style: Parameter 'self' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6124:45: style: Parameter 'self' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6147:44: style: Parameter 'self' can be declared as pointer to const [constParameterPointer] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6715:15: style: Variable 'substitution_matrix' can be declared as pointer to const [constVariablePointer] biopython-biopython-183/Bio/Align/_pairwisealigner.c:6814:15: style: Variable 'substitution_matrix' can be declared as pointer to const [constVariablePointer] biopython-biopython-183/Bio/Align/_pairwisealigner.c:754:15: style: Variable 'trace' is assigned a value that is never used. [unreadVariable] diff: head biopython-biopython-183/Bio/Align/_codonaligner.c:274:36: style: Parameter 'self' can be declared as pointer to const. However it seems that 'PathGenerator_reset' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Align/_codonaligner.c:284:19: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Align/_codonaligner.c:274:36: note: Parameter 'self' can be declared as pointer to const head biopython-biopython-183/Bio/Cluster/clustermodule.c:1198:22: style: Parameter 'self' can be declared as pointer to const. However it seems that 'py_version' is a callback function, if 'self' is declared with const you might also need to cast function pointer(s). [constParameterCallback] biopython-biopython-183/Bio/Cluster/clustermodule.c:2368:31: note: You might need to cast the function pointer here biopython-biopython-183/Bio/Cluster/clustermodule.c:1198:22: note: Parameter 'self' can be declared as pointer to const DONE