2025-05-05 09:15 ftp://ftp.de.debian.org/debian/pool/main/k/kma/kma_1.4.21.orig.tar.xz cppcheck-options: --library=posix --library=gnu --library=bsd --library=zlib --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-6.8.0-1022-oracle-aarch64-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: b78787f (2025-05-05 09:36:05 +0200) count: 936 931 elapsed-time: 1371.5 1397.3 head-timing-info: old-timing-info: head results: kma-1.4.21/ankers.c:41:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/ankers.c:63:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/ankers.c:195:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/ankers.c:30:23: style: Parameter 'out_Tem' can be declared as pointer to const. However it seems that 'print_ankers' is a callback function, if 'out_Tem' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/ankers.c:28:87: note: You might need to cast the function pointer here kma-1.4.21/ankers.c:30:23: note: Parameter 'out_Tem' can be declared as pointer to const kma-1.4.21/ankers.c:52:30: style: Parameter 'out_Tem' can be declared as pointer to const [constParameterPointer] kma-1.4.21/alnfrags.c:2153:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable excludeOut [valueFlowBailoutIncompleteVar] kma-1.4.21/assembly.c:278:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable excludeOut [valueFlowBailoutIncompleteVar] kma-1.4.21/assembly.c:784:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable excludeOut [valueFlowBailoutIncompleteVar] kma-1.4.21/assembly.c:1276:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/assembly.c:1410:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/assembly.c:1525:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alnToMatDense [valueFlowBailoutIncompleteVar] kma-1.4.21/assembly.c:1697:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable excludeOut [valueFlowBailoutIncompleteVar] kma-1.4.21/align.c:750:62: style: Parameter 'qseq' can be declared as pointer to const [constParameterPointer] kma-1.4.21/align.c:772:29: style: Parameter 'src' can be declared as pointer to const [constParameterPointer] kma-1.4.21/align.c:999:28: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] kma-1.4.21/align.c:231:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/align.c:233:21: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/align.c:527:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/align.c:762:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/align.c:794:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/align.c:796:21: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/align.c:1009:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/align.c:1011:21: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/align.c:1011:7: style: Variable 'mask' is assigned a value that is never used. [unreadVariable] kma-1.4.21/align.c:1012:6: style: Variable 'key' is assigned a value that is never used. [unreadVariable] kma-1.4.21/alnfrags.c:74:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:176:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:236:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:399:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:409:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:454:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:487:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:518:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:577:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:735:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:745:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:789:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:822:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:853:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:910:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:1033:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:1043:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:1083:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:1208:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:1269:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:1433:6: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:1443:6: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:1508:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:1548:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:1581:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:1646:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:1810:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:1820:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:1886:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:1926:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:1959:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:2021:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:2123:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:2140:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:2211:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:2284:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/alnfrags.c:142:14: style: Variable 'read_score' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/alnfrags.c:137:15: note: read_score is assigned kma-1.4.21/alnfrags.c:142:14: note: read_score is overwritten kma-1.4.21/alnfrags.c:160:5: style: Variable 'bestScore' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/alnfrags.c:159:20: note: Assuming that condition 'score==bestScore' is not redundant kma-1.4.21/alnfrags.c:160:5: note: Variable 'bestScore' is assigned an expression that holds the same value. kma-1.4.21/alnfrags.c:1003:5: style: Variable 'bestScore' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/alnfrags.c:1002:20: note: Assuming that condition 'score==bestScore' is not redundant kma-1.4.21/alnfrags.c:1003:5: note: Variable 'bestScore' is assigned an expression that holds the same value. kma-1.4.21/alnfrags.c:1158:14: style: Variable 'read_score' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/alnfrags.c:1144:15: note: read_score is assigned kma-1.4.21/alnfrags.c:1158:14: note: read_score is overwritten kma-1.4.21/alnfrags.c:1158:14: style: Variable 'read_score' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/alnfrags.c:1151:16: note: read_score is assigned kma-1.4.21/alnfrags.c:1158:14: note: read_score is overwritten kma-1.4.21/alnfrags.c:42:55: style: Parameter 'matched_templates' can be declared as pointer to const [constParameterPointer] kma-1.4.21/alnfrags.c:45:30: style: Variable 'qBoundPtr' can be declared as pointer to const [constVariablePointer] kma-1.4.21/alnfrags.c:187:336: style: Parameter 'qseq_rr' can be declared as pointer to const [constParameterPointer] kma-1.4.21/alnfrags.c:527:322: style: Parameter 'qseq_rr' can be declared as pointer to const [constParameterPointer] kma-1.4.21/alnfrags.c:862:320: style: Parameter 'qseq_rr' can be declared as pointer to const [constParameterPointer] kma-1.4.21/alnfrags.c:1055:30: style: Variable 'qBoundPtr' can be declared as pointer to const [constVariablePointer] kma-1.4.21/alnfrags.c:1220:332: style: Parameter 'qseq_rr' can be declared as pointer to const. However it seems that 'alnFragsUnionPE' is a callback function, if 'qseq_rr' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/alnfrags.c:40:355: note: You might need to cast the function pointer here kma-1.4.21/alnfrags.c:1220:332: note: Parameter 'qseq_rr' can be declared as pointer to const kma-1.4.21/alnfrags.c:1596:334: style: Parameter 'qseq_rr' can be declared as pointer to const [constParameterPointer] kma-1.4.21/alnfrags.c:1974:332: style: Parameter 'qseq_rr' can be declared as pointer to const [constParameterPointer] kma-1.4.21/alnfrags.c:1248:11: style: Variable 'bestHits' is assigned a value that is never used. [unreadVariable] kma-1.4.21/alnfrags.c:1625:11: style: Variable 'bestHits' is assigned a value that is never used. [unreadVariable] kma-1.4.21/alnfrags.c:2208:13: style: Variable 'read_score' is assigned a value that is never used. [unreadVariable] kma-1.4.21/chain.c:62:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/compdna.c:41:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/compdna.c:77:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/compdna.c:300:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/compdna.c:310:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/compdna.c:326:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/compdna.c:369:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/compdna.c:69:14: style: Variable 'dest->size' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/compdna.c:65:13: note: dest->size is assigned kma-1.4.21/compdna.c:69:14: note: dest->size is overwritten kma-1.4.21/compdna.c:287:8: style: Variable 'i' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/compdna.c:284:4: note: i is assigned kma-1.4.21/compdna.c:287:8: note: i is overwritten kma-1.4.21/compdna.c:287:15: style: Variable 'j' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/compdna.c:285:4: note: j is assigned kma-1.4.21/compdna.c:287:15: note: j is overwritten kma-1.4.21/compdna.c:99:50: style: Parameter 'seq' can be declared as pointer to const. However it seems that 'compDNA' is a callback function, if 'seq' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/compdna.c:63:24: note: You might need to cast the function pointer here kma-1.4.21/compdna.c:99:50: note: Parameter 'seq' can be declared as pointer to const kma-1.4.21/compdna.c:132:17: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] kma-1.4.21/compdna.c:298:24: style: Parameter 'compressor' can be declared as pointer to const [constParameterPointer] kma-1.4.21/compkmers.c:36:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/compkmers.c:42:48: style: Parameter 'qseq' can be declared as pointer to const [constParameterPointer] kma-1.4.21/compress.c:45:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/compress.c:115:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/compress.c:647:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/compress.c:1012:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/compress.c:1093:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/chain.c:169:14: style: Condition 'gap=(points->qStart[j]-qEnd)' is always true [knownConditionTrueFalse] kma-1.4.21/chain.c:137:12: note: Assuming that condition 'qEndqStart[j]' is not redundant kma-1.4.21/chain.c:169:14: note: Condition 'gap=(points->qStart[j]-qEnd)' is always true kma-1.4.21/chain.c:190:14: style: Condition 'gap=tGap' is always true [knownConditionTrueFalse] kma-1.4.21/chain.c:186:13: note: Assuming that condition 'tEndqStart[j]-qEnd)' is always true [knownConditionTrueFalse] kma-1.4.21/chain.c:320:12: note: Assuming that condition 'qEndqStart[j]' is not redundant kma-1.4.21/chain.c:353:14: note: Condition 'gap=(points->qStart[j]-qEnd)' is always true kma-1.4.21/chain.c:403:14: style: Condition 'gap=tGap' is always true [knownConditionTrueFalse] kma-1.4.21/chain.c:399:13: note: Assuming that condition 'tEndn' is always false [knownConditionTrueFalse] kma-1.4.21/dist.c:550:11: note: j_end is assigned '(Dist->nn:(j+chunk)' here. kma-1.4.21/dist.c:551:22: note: Condition 'j_end==Dist->n' is always false kma-1.4.21/dist.c:673:9: warning: Possible null pointer dereference: thread [nullPointer] kma-1.4.21/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0 kma-1.4.21/dist.c:822:9: note: Assuming condition is false kma-1.4.21/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0 kma-1.4.21/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0 kma-1.4.21/dist.c:673:9: note: Null pointer dereference kma-1.4.21/dist.c:674:11: warning: Possible null pointer dereference: thread [nullPointer] kma-1.4.21/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0 kma-1.4.21/dist.c:822:9: note: Assuming condition is false kma-1.4.21/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0 kma-1.4.21/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0 kma-1.4.21/dist.c:674:11: note: Null pointer dereference kma-1.4.21/dist.c:675:15: warning: Possible null pointer dereference: thread [nullPointer] kma-1.4.21/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0 kma-1.4.21/dist.c:822:9: note: Assuming condition is false kma-1.4.21/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0 kma-1.4.21/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0 kma-1.4.21/dist.c:675:15: note: Null pointer dereference kma-1.4.21/dist.c:676:6: warning: Possible null pointer dereference: thread [nullPointer] kma-1.4.21/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0 kma-1.4.21/dist.c:822:9: note: Assuming condition is false kma-1.4.21/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0 kma-1.4.21/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0 kma-1.4.21/dist.c:676:6: note: Null pointer dereference kma-1.4.21/dist.c:677:11: warning: Possible null pointer dereference: thread [nullPointer] kma-1.4.21/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0 kma-1.4.21/dist.c:822:9: note: Assuming condition is false kma-1.4.21/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0 kma-1.4.21/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0 kma-1.4.21/dist.c:677:11: note: Null pointer dereference kma-1.4.21/dist.c:678:11: warning: Possible null pointer dereference: thread [nullPointer] kma-1.4.21/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0 kma-1.4.21/dist.c:822:9: note: Assuming condition is false kma-1.4.21/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0 kma-1.4.21/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0 kma-1.4.21/dist.c:678:11: note: Null pointer dereference kma-1.4.21/dist.c:679:13: warning: Possible null pointer dereference: thread [nullPointer] kma-1.4.21/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0 kma-1.4.21/dist.c:822:9: note: Assuming condition is false kma-1.4.21/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0 kma-1.4.21/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0 kma-1.4.21/dist.c:679:13: note: Null pointer dereference kma-1.4.21/dist.c:680:14: warning: Possible null pointer dereference: thread [nullPointer] kma-1.4.21/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0 kma-1.4.21/dist.c:822:9: note: Assuming condition is false kma-1.4.21/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0 kma-1.4.21/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0 kma-1.4.21/dist.c:680:14: note: Null pointer dereference kma-1.4.21/dist.c:681:7: warning: Possible null pointer dereference: thread [nullPointer] kma-1.4.21/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0 kma-1.4.21/dist.c:822:9: note: Assuming condition is false kma-1.4.21/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0 kma-1.4.21/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0 kma-1.4.21/dist.c:681:7: note: Null pointer dereference kma-1.4.21/dist.c:682:9: warning: Possible null pointer dereference: thread [nullPointer] kma-1.4.21/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0 kma-1.4.21/dist.c:822:9: note: Assuming condition is false kma-1.4.21/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0 kma-1.4.21/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0 kma-1.4.21/dist.c:682:9: note: Null pointer dereference kma-1.4.21/dist.c:683:18: warning: Possible null pointer dereference: thread [nullPointer] kma-1.4.21/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0 kma-1.4.21/dist.c:822:9: note: Assuming condition is false kma-1.4.21/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0 kma-1.4.21/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0 kma-1.4.21/dist.c:683:18: note: Null pointer dereference kma-1.4.21/dist.c:846:2: warning: Possible null pointer dereference: thread [nullPointer] kma-1.4.21/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0 kma-1.4.21/dist.c:822:9: note: Assuming condition is false kma-1.4.21/dist.c:846:2: note: Null pointer dereference kma-1.4.21/dist.c:850:18: warning: Possible null pointer dereference: thread [nullPointer] kma-1.4.21/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0 kma-1.4.21/dist.c:822:9: note: Assuming condition is false kma-1.4.21/dist.c:850:18: note: Null pointer dereference kma-1.4.21/dist.c:174:31: style: Variable 'values_j' can be declared as pointer to const [constVariablePointer] kma-1.4.21/dist.c:176:30: style: Variable 'values_sj' can be declared as pointer to const [constVariablePointer] kma-1.4.21/dist.c:233:31: style: Variable 'values_j' can be declared as pointer to const [constVariablePointer] kma-1.4.21/dist.c:235:30: style: Variable 'values_sj' can be declared as pointer to const [constVariablePointer] kma-1.4.21/dist.c:343:24: style: Variable 'name' can be declared as pointer to const [constVariablePointer] kma-1.4.21/dist.c:485:33: style: Variable 'name' can be declared as pointer to const [constVariablePointer] kma-1.4.21/dist.c:773:44: style: Parameter 'outputfilename' can be declared as pointer to const [constParameterPointer] kma-1.4.21/dist.c:898:8: style: Variable 'arg' can be declared as pointer to const [constVariablePointer] kma-1.4.21/dist.c:59:33: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/dist.c:767:12: style: Variable 'outfileM' is assigned a value that is never used. [unreadVariable] kma-1.4.21/dist.c:1008:12: style: Variable 'file_len' is assigned a value that is never used. [unreadVariable] kma-1.4.21/hashmap.c:51:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/hashmap.c:97:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/hashmap.c:132:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/hashmap.c:155:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/hashmap.c:214:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/hashmap.c:312:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/hashmap.c:258:37: style: Parameter 'templates' can be declared as pointer to const [constParameterPointer] kma-1.4.21/hashmap.c:307:18: style: Variable 'hu_values' can be declared as pointer to const [constVariablePointer] kma-1.4.21/hashmapcci.c:69:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/hashmapcci.c:438:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cciLock [valueFlowBailoutIncompleteVar] kma-1.4.21/hashmapcci.c:489:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/hashmapcci.c:528:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/hashmapindex.c:64:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/hashmapindex.c:403:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/hashmapindex.c:377:15: warning: Possible null pointer dereference: src [nullPointer] kma-1.4.21/hashmapindex.c:365:30: note: Assignment 'src=0', assigned value is 0 kma-1.4.21/hashmapindex.c:377:15: note: Null pointer dereference kma-1.4.21/hashmapindex.c:378:17: warning: Possible null pointer dereference: src [nullPointer] kma-1.4.21/hashmapindex.c:365:30: note: Assignment 'src=0', assigned value is 0 kma-1.4.21/hashmapindex.c:378:17: note: Null pointer dereference kma-1.4.21/hashmapindex.c:298:40: style: Parameter 'src' can be declared as pointer to const [constParameterPointer] kma-1.4.21/hashmapindex.c:426:32: style: Parameter 'template_index' can be declared as pointer to const. However it seems that 'alignClean' is a callback function, if 'template_index' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/hashmapindex.c:38:40: note: You might need to cast the function pointer here kma-1.4.21/hashmapindex.c:426:32: note: Parameter 'template_index' can be declared as pointer to const kma-1.4.21/hashmapindex.c:243:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/hashmapindex.c:316:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/hashmapcci.c:452:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/hashmapcci.c:459:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/hashmapcci.c:517:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/hashmapcci.c:541:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/hashmapcci.c:594:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/hashmapcci.c:488:8: style: Condition '0len>>5)+1)*sizeof(unsigned long)', assigned value is greater than 7 kma-1.4.21/hashmapcci.c:488:8: note: Condition '0len>>5)+1)*sizeof(unsigned long)', assigned value is greater than 7 kma-1.4.21/hashmapcci.c:527:13: note: Condition 'check<0' is always false kma-1.4.21/hashmapcci.c:129:18: style: Variable 'chain' can be declared as pointer to const [constVariablePointer] kma-1.4.21/hashmapcci.c:612:34: style: Parameter 'src' can be declared as pointer to const [constParameterPointer] kma-1.4.21/hashmapcci.c:497:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/hashmapcci.c:597:13: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/hashmapcci.c:243:7: style: Variable 'next' is assigned a value that is never used. [unreadVariable] kma-1.4.21/hashmapcci.c:270:2: style: Variable 'newchain' is assigned a value that is never used. [unreadVariable] kma-1.4.21/hashmapcci.c:453:10: style: Variable 'pos' is assigned a value that is never used. [unreadVariable] kma-1.4.21/hashmapkma.c:185:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/hashmapkma.c:282:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/hashmapkma.c:464:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/hashmapkma.c:604:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/hashmapkmers.c:42:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/hashmapkmers.c:67:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/hashtable.c:85:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/hashmapkma.c:122:18: style: Variable 'str1' can be declared as pointer to const [constVariablePointer] kma-1.4.21/hashmapkma.c:196:33: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/hashmapkma.c:292:33: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/hashmapkma.c:474:33: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/hashmapkma.c:614:33: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/hashmapkma.c:444:12: style: Variable 'seekSize' is assigned a value that is never used. [unreadVariable] kma-1.4.21/hashmapkma.c:588:12: style: Variable 'seekSize' is assigned a value that is never used. [unreadVariable] kma-1.4.21/hashtable.c:327:3: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg] kma-1.4.21/hashtable.c:59:18: style: Variable 'values_s' can be declared as pointer to const [constVariablePointer] kma-1.4.21/hashtable.c:127:18: style: Variable 'value_s' can be declared as pointer to const [constVariablePointer] kma-1.4.21/hashtable.c:73:11: style: Variable 'kmerNode' is assigned a value that is never used. [unreadVariable] kma-1.4.21/hashtable.c:144:11: style: Variable 'kmerNode' is assigned a value that is never used. [unreadVariable] kma-1.4.21/hashtable.c:147:13: style: Variable 'decon_node' is assigned a value that is never used. [unreadVariable] kma-1.4.21/hashtable.c:323:15: style: Variable 'deConTable' is assigned a value that is never used. [unreadVariable] kma-1.4.21/hashtable.c:327:14: style: Variable 'deConTable' is assigned a value that is never used. [unreadVariable] kma-1.4.21/conclave.c:65:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/conclave.c:237:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/conclave.c:413:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/conclave.c:776:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/index.c:45:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] kma-1.4.21/index.c:95:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/index.c:410:5: error: Common realloc mistake: 'deconfiles' nulled but not freed upon failure [memleakOnRealloc] kma-1.4.21/index.c:436:5: error: Common realloc mistake: 'deconfiles' nulled but not freed upon failure [memleakOnRealloc] kma-1.4.21/index.c:88:17: style: Variable 'update' can be declared as pointer to const [constVariablePointer] kma-1.4.21/index.c:520:21: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/index.c:537:22: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/index.c:104:12: style: Variable 'templates' is assigned a value that is never used. [unreadVariable] kma-1.4.21/conclave.c:113:38: style: Array index 'tmp_template' is used before limits check. [arrayIndexThenCheck] kma-1.4.21/conclave.c:284:38: style: Array index 'tmp_template' is used before limits check. [arrayIndexThenCheck] kma-1.4.21/conclave.c:448:38: style: Array index 'tmp_template' is used before limits check. [arrayIndexThenCheck] kma-1.4.21/conclave.c:642:39: style: Array index 'tmp_template' is used before limits check. [arrayIndexThenCheck] kma-1.4.21/conclave.c:811:38: style: Array index 'tmp_template' is used before limits check. [arrayIndexThenCheck] kma-1.4.21/conclave.c:1005:39: style: Array index 'tmp_template' is used before limits check. [arrayIndexThenCheck] kma-1.4.21/conclave.c:109:8: style: Variable 'bestScore' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/conclave.c:105:26: note: Assuming that condition 'tmp_score==bestScore' is not redundant kma-1.4.21/conclave.c:109:8: note: Variable 'bestScore' is assigned an expression that holds the same value. kma-1.4.21/conclave.c:116:8: style: Variable 'bestScore' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/conclave.c:105:26: note: Assuming that condition 'tmp_score==bestScore' is not redundant kma-1.4.21/conclave.c:116:8: note: Variable 'bestScore' is assigned an expression that holds the same value. kma-1.4.21/conclave.c:272:7: style: Variable 'bestScore' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/conclave.c:260:15: note: tmp_score is assigned '1.0*alignment_scores[tmp_template]/template_lengths[tmp_template]' here. kma-1.4.21/conclave.c:272:7: note: Variable 'bestScore' is assigned an expression that holds the same value. kma-1.4.21/conclave.c:280:8: style: Variable 'bestScore' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/conclave.c:268:25: note: Assuming that condition 'tmp_score==bestScore' is not redundant kma-1.4.21/conclave.c:280:8: note: Variable 'bestScore' is assigned an expression that holds the same value. kma-1.4.21/conclave.c:287:8: style: Variable 'bestScore' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/conclave.c:268:25: note: Assuming that condition 'tmp_score==bestScore' is not redundant kma-1.4.21/conclave.c:287:8: note: Variable 'bestScore' is assigned an expression that holds the same value. kma-1.4.21/conclave.c:446:8: style: Variable 'bestScore' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/conclave.c:442:26: note: Assuming that condition 'tmp_score==bestScore' is not redundant kma-1.4.21/conclave.c:446:8: note: Variable 'bestScore' is assigned an expression that holds the same value. kma-1.4.21/conclave.c:451:8: style: Variable 'bestScore' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/conclave.c:442:26: note: Assuming that condition 'tmp_score==bestScore' is not redundant kma-1.4.21/conclave.c:451:8: note: Variable 'bestScore' is assigned an expression that holds the same value. kma-1.4.21/conclave.c:638:9: style: Variable 'bestScore' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/conclave.c:634:27: note: Assuming that condition 'tmp_score==bestScore' is not redundant kma-1.4.21/conclave.c:638:9: note: Variable 'bestScore' is assigned an expression that holds the same value. kma-1.4.21/conclave.c:645:9: style: Variable 'bestScore' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/conclave.c:634:27: note: Assuming that condition 'tmp_score==bestScore' is not redundant kma-1.4.21/conclave.c:645:9: note: Variable 'bestScore' is assigned an expression that holds the same value. kma-1.4.21/conclave.c:803:7: style: Variable 'bestScore' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/conclave.c:793:15: note: tmp_score is assigned '1.0*alignment_scores[tmp_template]/template_lengths[tmp_template]' here. kma-1.4.21/conclave.c:803:7: note: Variable 'bestScore' is assigned an expression that holds the same value. kma-1.4.21/conclave.c:809:8: style: Variable 'bestScore' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/conclave.c:799:25: note: Assuming that condition 'tmp_score==bestScore' is not redundant kma-1.4.21/conclave.c:809:8: note: Variable 'bestScore' is assigned an expression that holds the same value. kma-1.4.21/conclave.c:814:8: style: Variable 'bestScore' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/conclave.c:799:25: note: Assuming that condition 'tmp_score==bestScore' is not redundant kma-1.4.21/conclave.c:814:8: note: Variable 'bestScore' is assigned an expression that holds the same value. kma-1.4.21/conclave.c:993:8: style: Variable 'bestScore' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/conclave.c:981:16: note: tmp_score is assigned '1.0*alignment_scores[tmp_template]/template_lengths[tmp_template]' here. kma-1.4.21/conclave.c:993:8: note: Variable 'bestScore' is assigned an expression that holds the same value. kma-1.4.21/conclave.c:1001:9: style: Variable 'bestScore' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/conclave.c:989:26: note: Assuming that condition 'tmp_score==bestScore' is not redundant kma-1.4.21/conclave.c:1001:9: note: Variable 'bestScore' is assigned an expression that holds the same value. kma-1.4.21/conclave.c:1008:9: style: Variable 'bestScore' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/conclave.c:989:26: note: Assuming that condition 'tmp_score==bestScore' is not redundant kma-1.4.21/conclave.c:1008:9: note: Variable 'bestScore' is assigned an expression that holds the same value. kma-1.4.21/conclave.c:33:40: style: Parameter 'src' can be declared as pointer to const [constParameterPointer] kma-1.4.21/conclave.c:43:178: style: Parameter 'alignment_scores' can be declared as pointer to const. However it seems that 'runConClave' is a callback function, if 'alignment_scores' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/conclave.c:30:181: note: You might need to cast the function pointer here kma-1.4.21/conclave.c:43:178: note: Parameter 'alignment_scores' can be declared as pointer to const kma-1.4.21/conclave.c:43:211: style: Parameter 'uniq_alignment_scores' can be declared as pointer to const. However it seems that 'runConClave' is a callback function, if 'uniq_alignment_scores' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/conclave.c:30:181: note: You might need to cast the function pointer here kma-1.4.21/conclave.c:43:211: note: Parameter 'uniq_alignment_scores' can be declared as pointer to const kma-1.4.21/conclave.c:43:239: style: Parameter 'template_lengths' can be declared as pointer to const. However it seems that 'runConClave' is a callback function, if 'template_lengths' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/conclave.c:30:181: note: You might need to cast the function pointer here kma-1.4.21/conclave.c:43:239: note: Parameter 'template_lengths' can be declared as pointer to const kma-1.4.21/conclave.c:215:181: style: Parameter 'alignment_scores' can be declared as pointer to const [constParameterPointer] kma-1.4.21/conclave.c:215:214: style: Parameter 'uniq_alignment_scores' can be declared as pointer to const [constParameterPointer] kma-1.4.21/conclave.c:215:242: style: Parameter 'template_lengths' can be declared as pointer to const [constParameterPointer] kma-1.4.21/conclave.c:386:179: style: Parameter 'alignment_scores' can be declared as pointer to const. However it seems that 'runConClave2' is a callback function, if 'alignment_scores' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/conclave.c:31:213: note: You might need to cast the function pointer here kma-1.4.21/conclave.c:386:179: note: Parameter 'alignment_scores' can be declared as pointer to const kma-1.4.21/conclave.c:386:240: style: Parameter 'template_lengths' can be declared as pointer to const. However it seems that 'runConClave2' is a callback function, if 'template_lengths' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/conclave.c:31:213: note: You might need to cast the function pointer here kma-1.4.21/conclave.c:386:240: note: Parameter 'template_lengths' can be declared as pointer to const kma-1.4.21/conclave.c:749:182: style: Parameter 'alignment_scores' can be declared as pointer to const [constParameterPointer] kma-1.4.21/conclave.c:749:243: style: Parameter 'template_lengths' can be declared as pointer to const [constParameterPointer] kma-1.4.21/kmapipe.c:68:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/kmapipe.c:161:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/kmapipe.c:99:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/kmapipe.c:108:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/kmapipe.c:127:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/kmapipe.c:180:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/kmapipe.c:219:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/kmapipe.c:229:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/kmapipe.c:243:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/kmapipe.c:257:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/kmapipe.c:109:33: warning: Either the condition '!src' is redundant or there is possible null pointer dereference: src. [nullPointerRedundantCheck] kma-1.4.21/kmapipe.c:110:7: note: Assuming that condition '!src' is not redundant kma-1.4.21/kmapipe.c:109:33: note: Null pointer dereference kma-1.4.21/kmapipe.c:119:8: warning: Either the condition '!src' is redundant or there is possible null pointer dereference: src. [nullPointerRedundantCheck] kma-1.4.21/kmapipe.c:129:7: note: Assuming that condition '!src' is not redundant kma-1.4.21/kmapipe.c:119:8: note: Null pointer dereference kma-1.4.21/kmapipe.c:128:33: warning: Either the condition '!src' is redundant or there is possible null pointer dereference: src. [nullPointerRedundantCheck] kma-1.4.21/kmapipe.c:129:7: note: Assuming that condition '!src' is not redundant kma-1.4.21/kmapipe.c:128:33: note: Null pointer dereference kma-1.4.21/kmapipe.c:230:33: warning: Either the condition '!src' is redundant or there is possible null pointer dereference: src. [nullPointerRedundantCheck] kma-1.4.21/kmapipe.c:231:7: note: Assuming that condition '!src' is not redundant kma-1.4.21/kmapipe.c:230:33: note: Null pointer dereference kma-1.4.21/kmapipe.c:242:25: warning: Either the condition '!src' is redundant or there is possible null pointer dereference: src. [nullPointerRedundantCheck] kma-1.4.21/kmapipe.c:260:7: note: Assuming that condition '!src' is not redundant kma-1.4.21/kmapipe.c:242:25: note: Null pointer dereference kma-1.4.21/kmapipe.c:258:8: warning: Either the condition '!src' is redundant or there is possible null pointer dereference: src. [nullPointerRedundantCheck] kma-1.4.21/kmapipe.c:260:7: note: Assuming that condition '!src' is not redundant kma-1.4.21/kmapipe.c:258:8: note: Null pointer dereference kma-1.4.21/kmapipe.c:259:33: warning: Either the condition '!src' is redundant or there is possible null pointer dereference: src. [nullPointerRedundantCheck] kma-1.4.21/kmapipe.c:260:7: note: Assuming that condition '!src' is not redundant kma-1.4.21/kmapipe.c:259:33: note: Null pointer dereference kma-1.4.21/kmerlink.c:41:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/kmerlink.c:45:52: style: Parameter 'node' can be declared as pointer to const [constParameterPointer] kma-1.4.21/kmers.c:65:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/kmers.c:76:5: style: Suspicious condition (assignment + comparison); Clarify expression with parentheses. [clarifyCondition] kma-1.4.21/kmers.c:141:12: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast] kma-1.4.21/kmers.c:143:18: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast] kma-1.4.21/kmers.c:145:18: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast] kma-1.4.21/kmers.c:146:16: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast] kma-1.4.21/kmers.c:147:8: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast] kma-1.4.21/kmers.c:148:17: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast] kma-1.4.21/kmers.c:149:21: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast] kma-1.4.21/kmeranker.c:77:11: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast] kma-1.4.21/kmeranker.c:518:14: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast] kma-1.4.21/kmeranker.c:519:13: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast] kma-1.4.21/kmeranker.c:512:34: style:inconclusive: Function 'chooseChain' argument 1 names different: declaration 'bestScore' definition 'best_score'. [funcArgNamesDifferent] kma-1.4.21/kmeranker.h:57:34: note: Function 'chooseChain' argument 1 names different: declaration 'bestScore' definition 'best_score'. kma-1.4.21/kmeranker.c:512:34: note: Function 'chooseChain' argument 1 names different: declaration 'bestScore' definition 'best_score'. kma-1.4.21/kmeranker.c:512:63: style:inconclusive: Function 'chooseChain' argument 2 names different: declaration 'bestScore_r' definition 'best_score_r'. [funcArgNamesDifferent] kma-1.4.21/kmeranker.h:57:62: note: Function 'chooseChain' argument 2 names different: declaration 'bestScore_r' definition 'best_score_r'. kma-1.4.21/kmeranker.c:512:63: note: Function 'chooseChain' argument 2 names different: declaration 'bestScore_r' definition 'best_score_r'. kma-1.4.21/kmeranker.c:33:27: style: Parameter 'src' can be declared as pointer to const. However it seems that 'ankerScore' is a callback function, if 'src' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/kmeranker.c:26:38: note: You might need to cast the function pointer here kma-1.4.21/kmeranker.c:33:27: note: Parameter 'src' can be declared as pointer to const kma-1.4.21/kmeranker.c:37:30: style: Parameter 'src' can be declared as pointer to const [constParameterPointer] kma-1.4.21/kmeranker.c:60:13: style: Variable 'bests' can be declared as pointer to const [constVariablePointer] kma-1.4.21/kmmap.c:42:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/kmmap.c:202:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/loadupdate.c:163:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/loadupdate.c:39:14: style: Parameter 'templatefilename' can be declared as pointer to const [constParameterPointer] kma-1.4.21/loadupdate.c:39:38: style: Parameter 'outputfilename' can be declared as pointer to const [constParameterPointer] kma-1.4.21/main.c:70:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/main.c:55:13: style: Condition '--argc' is always true [knownConditionTrueFalse] kma-1.4.21/kmmap.c:51:23: warning: If memory allocation fails, then there is a possible null pointer dereference: uptr++ [nullPointerOutOfMemory] kma-1.4.21/kmmap.c:44:13: note: Assuming allocation function fails kma-1.4.21/kmmap.c:44:13: note: Assignment 'data=mmap(0,Size,PROT_READ,MAP_SHARED,fd,0)', assigned value is 0 kma-1.4.21/kmmap.c:50:7: note: uptr is assigned '(unsigned int*)data' here. kma-1.4.21/kmmap.c:51:23: note: Null pointer dereference kma-1.4.21/kmmap.c:51:23: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory] kma-1.4.21/kmmap.c:44:13: note: Assuming allocation function fails kma-1.4.21/kmmap.c:44:13: note: Assignment 'data=mmap(0,Size,PROT_READ,MAP_SHARED,fd,0)', assigned value is 0 kma-1.4.21/kmmap.c:50:7: note: uptr is assigned '(unsigned int*)data' here. kma-1.4.21/kmmap.c:51:23: note: Null pointer addition kma-1.4.21/kmmap.c:63:33: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/matrix.c:73:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/matrix.c:104:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] kma-1.4.21/matrix.c:139:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/matrix.c:168:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MS_SYNC [valueFlowBailoutIncompleteVar] kma-1.4.21/matrix.c:49:2: style: Variable '*ptr' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/matrix.c:47:6: note: src is assigned '*ptr' here. kma-1.4.21/matrix.c:49:2: note: Variable '*ptr' is assigned an expression that holds the same value. kma-1.4.21/matrix.c:176:20: style: Variable 'src' can be declared as pointer to const [constVariablePointer] kma-1.4.21/makeindex.c:208:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/makeindex.c:38:60: style: Parameter 'name' can be declared as pointer to const. However it seems that 'biasPrint' is a callback function, if 'name' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/makeindex.c:35:59: note: You might need to cast the function pointer here kma-1.4.21/makeindex.c:38:60: note: Parameter 'name' can be declared as pointer to const kma-1.4.21/makeindex.c:42:62: style: Parameter 'name' can be declared as pointer to const [constParameterPointer] kma-1.4.21/makeindex.c:46:23: style: Parameter 'qseq' can be declared as pointer to const. However it seems that 'lenCheck' is a callback function, if 'qseq' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/makeindex.c:36:43: note: You might need to cast the function pointer here kma-1.4.21/makeindex.c:46:23: note: Parameter 'qseq' can be declared as pointer to const kma-1.4.21/makeindex.c:54:17: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] kma-1.4.21/makeindex.c:87:17: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] kma-1.4.21/mt1.c:53:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/mt1.c:69:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/mt1.c:110:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/nw.c:253:8: style: Variable 'E_ptr' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/nw.c:230:8: note: E_ptr is assigned kma-1.4.21/nw.c:253:8: note: E_ptr is overwritten kma-1.4.21/nw.c:582:8: style: Variable 'E_ptr' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/nw.c:559:8: note: E_ptr is assigned kma-1.4.21/nw.c:582:8: note: E_ptr is overwritten kma-1.4.21/nw.c:852:8: style: Variable 'E_ptr' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/nw.c:830:8: note: E_ptr is assigned kma-1.4.21/nw.c:852:8: note: E_ptr is overwritten kma-1.4.21/nw.c:1147:8: style: Variable 'E_ptr' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/nw.c:1125:8: note: E_ptr is assigned kma-1.4.21/nw.c:1147:8: note: E_ptr is overwritten kma-1.4.21/nw.c:30:17: style: Variable 'query' can be declared as pointer to const [constVariablePointer] kma-1.4.21/nw.c:315:17: style: Variable 'query' can be declared as pointer to const [constVariablePointer] kma-1.4.21/nw.c:647:17: style: Variable 'query' can be declared as pointer to const [constVariablePointer] kma-1.4.21/nw.c:898:17: style: Variable 'query' can be declared as pointer to const [constVariablePointer] kma-1.4.21/nw.c:90:18: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment] kma-1.4.21/nw.c:99:18: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment] kma-1.4.21/nw.c:381:18: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment] kma-1.4.21/nw.c:390:18: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment] kma-1.4.21/nw.c:689:18: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment] kma-1.4.21/nw.c:698:18: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment] kma-1.4.21/nw.c:946:18: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment] kma-1.4.21/nw.c:955:18: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment] kma-1.4.21/mt1.c:455:3: warning: %ld in format string (no. 2) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint] kma-1.4.21/mt1.c:455:3: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] kma-1.4.21/mt1.c:115:20: warning: Either the condition 'outputfilename' is redundant or there is possible null pointer dereference: outputfilename. [nullPointerRedundantCheck] kma-1.4.21/mt1.c:122:5: note: Assuming that condition 'outputfilename' is not redundant kma-1.4.21/mt1.c:115:20: note: Null pointer dereference kma-1.4.21/mt1.c:46:25: style: Parameter 'header' can be declared as pointer to const [constParameterPointer] kma-1.4.21/mt1.c:46:40: style: Parameter 'qseq' can be declared as pointer to const [constParameterPointer] kma-1.4.21/mt1.c:61:30: style: Parameter 'header' can be declared as pointer to const [constParameterPointer] kma-1.4.21/mt1.c:61:45: style: Parameter 'qseq' can be declared as pointer to const [constParameterPointer] kma-1.4.21/mt1.c:61:71: style: Parameter 'header_r' can be declared as pointer to const [constParameterPointer] kma-1.4.21/pherror.c:31:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/pherror.c:41:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/pherror.c:58:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/pherror.c:76:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/pherror.c:59:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/pherror.c:58:20: style: Condition 'nmemb==0' is always true [knownConditionTrueFalse] kma-1.4.21/pherror.c:55:9: note: Assuming that condition '0<(nmemb=read(fileno(stream),ptr,size))' is not redundant kma-1.4.21/pherror.c:58:20: note: Condition 'nmemb==0' is always true kma-1.4.21/pherror.c:58:35: style: Condition 'nmemb==-1' is always false [knownConditionTrueFalse] kma-1.4.21/pherror.c:58:20: note: Assuming that condition 'nmemb==0' is not redundant kma-1.4.21/pherror.c:58:35: note: Condition 'nmemb==-1' is always false kma-1.4.21/printconsensus.c:24:49: style: Parameter 'header' can be declared as pointer to const [constParameterPointer] kma-1.4.21/qc.c:73:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/qc.c:241:8: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/qc.c:241:8: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/qc.c:241:8: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/qc.c:241:8: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/qc.c:243:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/qc.c:243:9: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/qc.c:243:9: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/qc.c:243:9: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/qc.c:251:7: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/qc.c:251:7: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/qc.c:251:7: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/qc.c:251:7: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/qc.c:254:8: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/qc.c:254:8: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/qc.c:254:8: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/qc.c:254:8: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/qc.c:170:12: style: Variable 'dist' can be declared as pointer to const [constVariablePointer] kma-1.4.21/qc.c:205:5: style: Variable 'p' is assigned a value that is never used. [unreadVariable] kma-1.4.21/qseqs.c:48:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/nw2p.c:257:7: style: Variable 'e' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/nw2p.c:223:7: note: e is assigned kma-1.4.21/nw2p.c:257:7: note: e is overwritten kma-1.4.21/nw2p.c:257:7: style: Variable 'e' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/nw2p.c:226:7: note: e is assigned kma-1.4.21/nw2p.c:257:7: note: e is overwritten kma-1.4.21/nw2p.c:257:7: style: Variable 'e' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/nw2p.c:236:8: note: e is assigned kma-1.4.21/nw2p.c:257:7: note: e is overwritten kma-1.4.21/nw2p.c:257:7: style: Variable 'e' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/nw2p.c:246:8: note: e is assigned kma-1.4.21/nw2p.c:257:7: note: e is overwritten kma-1.4.21/nw2p.c:340:8: style: Variable 'E_ptr' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/nw2p.c:317:8: note: E_ptr is assigned kma-1.4.21/nw2p.c:340:8: note: E_ptr is overwritten kma-1.4.21/nw2p.c:704:8: style: Variable 'E_ptr' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/nw2p.c:681:8: note: E_ptr is assigned kma-1.4.21/nw2p.c:704:8: note: E_ptr is overwritten kma-1.4.21/nw2p.c:974:8: style: Variable 'E_ptr' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/nw2p.c:952:8: note: E_ptr is assigned kma-1.4.21/nw2p.c:974:8: note: E_ptr is overwritten kma-1.4.21/nw2p.c:1269:8: style: Variable 'E_ptr' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/nw2p.c:1247:8: note: E_ptr is assigned kma-1.4.21/nw2p.c:1269:8: note: E_ptr is overwritten kma-1.4.21/nw2p.c:31:17: style: Variable 'query' can be declared as pointer to const [constVariablePointer] kma-1.4.21/nw2p.c:437:17: style: Variable 'query' can be declared as pointer to const [constVariablePointer] kma-1.4.21/nw2p.c:769:17: style: Variable 'query' can be declared as pointer to const [constVariablePointer] kma-1.4.21/nw2p.c:1020:17: style: Variable 'query' can be declared as pointer to const [constVariablePointer] kma-1.4.21/nw2p.c:99:18: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment] kma-1.4.21/nw2p.c:111:18: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment] kma-1.4.21/nw2p.c:503:18: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment] kma-1.4.21/nw2p.c:512:18: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment] kma-1.4.21/nw2p.c:811:18: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment] kma-1.4.21/nw2p.c:820:18: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment] kma-1.4.21/nw2p.c:1068:18: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment] kma-1.4.21/nw2p.c:1077:18: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment] kma-1.4.21/nw2p.c:267:8: style: Variable 'Q2' is assigned a value that is never used. [unreadVariable] kma-1.4.21/qualcheck.c:112:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/qualcheck.c:236:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/runinput.c:398:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/runinput.c:498:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/runinput.c:639:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/runinput.c:746:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/runinput.c:781:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/runinput.c:805:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/qualcheck.c:313:14: style: Condition 'thisKlen>=MinKlen' is always true [knownConditionTrueFalse] kma-1.4.21/qualcheck.c:287:14: note: Assuming that condition 'thisKlen=MinKlen' is always true kma-1.4.21/qualcheck.c:182:3: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/qualcheck.c:315:4: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/qualcheck.c:31:26: style: Parameter 'templates' can be declared as pointer to const. However it seems that 'lengthCheck' is a callback function, if 'templates' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/qualcheck.c:29:94: note: You might need to cast the function pointer here kma-1.4.21/qualcheck.c:31:26: note: Parameter 'templates' can be declared as pointer to const kma-1.4.21/qualcheck.c:81:126: style: Parameter 'header' can be declared as pointer to const [constParameterPointer] kma-1.4.21/qualcheck.c:190:103: style: Parameter 'template_ulengths' can be declared as pointer to const [constParameterPointer] kma-1.4.21/qualcheck.c:190:129: style: Parameter 'header' can be declared as pointer to const [constParameterPointer] kma-1.4.21/qualcheck.c:326:86: style: Parameter 'values' can be declared as pointer to const. However it seems that 'updateScoreAndTemplate' is a callback function, if 'values' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/qualcheck.c:223:33: note: You might need to cast the function pointer here kma-1.4.21/qualcheck.c:326:86: note: Parameter 'values' can be declared as pointer to const kma-1.4.21/qualcheck.c:343:18: style: Variable 'values' can be declared as pointer to const [constVariablePointer] kma-1.4.21/qualcheck.c:356:44: style: Parameter 'values' can be declared as pointer to const. However it seems that 'addUscore' is a callback function, if 'values' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/qualcheck.c:224:20: note: You might need to cast the function pointer here kma-1.4.21/qualcheck.c:356:44: note: Parameter 'values' can be declared as pointer to const kma-1.4.21/qualcheck.c:369:18: style: Variable 'values' can be declared as pointer to const [constVariablePointer] kma-1.4.21/qualcheck.c:39:19: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/qualcheck.c:99:19: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/qualcheck.c:100:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/qualcheck.c:211:19: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/qualcheck.c:212:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/runinput.c:336:14: style: Unsigned expression 'end' can't be negative so it is unnecessary to test it. [unsignedPositive] kma-1.4.21/runinput.c:331:10: note: Assignment 'start=0', assigned value is 0 kma-1.4.21/runinput.c:336:14: note: Unsigned positive kma-1.4.21/runinput.c:34:54: style: Parameter 'qual' can be declared as pointer to const [constParameterPointer] kma-1.4.21/runinput.c:56:29: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer] kma-1.4.21/runinput.c:97:24: style: Variable 'qptr' can be declared as pointer to const [constVariablePointer] kma-1.4.21/runinput.c:130:33: style: Variable 'sptr3' can be declared as pointer to const [constVariablePointer] kma-1.4.21/runinput.c:130:41: style: Variable 'qptr3' can be declared as pointer to const [constVariablePointer] kma-1.4.21/runinput.c:318:17: style: Variable 'sptr' can be declared as pointer to const [constVariablePointer] kma-1.4.21/runinput.c:732:21: style: Parameter 'header' can be declared as pointer to const [constParameterPointer] kma-1.4.21/runinput.c:765:22: style: Parameter 'header' can be declared as pointer to const. However it seems that 'printFsa' is a callback function, if 'header' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/runinput.c:31:66: note: You might need to cast the function pointer here kma-1.4.21/runinput.c:765:22: note: Parameter 'header' can be declared as pointer to const kma-1.4.21/runinput.c:789:27: style: Parameter 'header' can be declared as pointer to const. However it seems that 'printFsa_pair' is a callback function, if 'header' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/runinput.c:32:95: note: You might need to cast the function pointer here kma-1.4.21/runinput.c:789:27: note: Parameter 'header' can be declared as pointer to const kma-1.4.21/runinput.c:789:68: style: Parameter 'header_r' can be declared as pointer to const. However it seems that 'printFsa_pair' is a callback function, if 'header_r' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/runinput.c:32:95: note: You might need to cast the function pointer here kma-1.4.21/runinput.c:789:68: note: Parameter 'header_r' can be declared as pointer to const kma-1.4.21/sam.c:102:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] kma-1.4.21/sam.c:204:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] kma-1.4.21/sam.c:197:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/sam.c:33:17: style: Variable 's' can be declared as pointer to const [constVariablePointer] kma-1.4.21/sam.c:34:17: style: Variable 't' can be declared as pointer to const [constVariablePointer] kma-1.4.21/sam.c:34:21: style: Variable 'q' can be declared as pointer to const [constVariablePointer] kma-1.4.21/sam.c:100:58: style: Parameter 'template_lengths' can be declared as pointer to const [constParameterPointer] kma-1.4.21/sam.c:100:95: style: Parameter 'cmd' can be declared as pointer to const [constParameterPointer] kma-1.4.21/sam.c:114:79: style: Parameter 'rname' can be declared as pointer to const [constParameterPointer] kma-1.4.21/sam.c:120:16: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] kma-1.4.21/sam.c:120:24: style: Variable 'rnext' can be declared as pointer to const [constVariablePointer] kma-1.4.21/sam.c:120:32: style: Variable 'qual' can be declared as pointer to const [constVariablePointer] kma-1.4.21/sam.c:121:17: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] kma-1.4.21/runkma.c:78:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/runkma.c:114:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] kma-1.4.21/runkma.c:180:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/runkma.c:969:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/savekmers.c:73:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/savekmers.c:98:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable excludeOut [valueFlowBailoutIncompleteVar] kma-1.4.21/savekmers.c:3903:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/savekmers.c:4850:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/savekmers.c:5114:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/savekmers.c:5169:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/savekmers.c:5986:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/runkma.c:1147:5: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint] kma-1.4.21/runkma.c:1161:3: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint] kma-1.4.21/runkma.c:213:20: warning: Either the condition 'outputfilename' is redundant or there is possible null pointer dereference: outputfilename. [nullPointerRedundantCheck] kma-1.4.21/runkma.c:223:5: note: Assuming that condition 'outputfilename' is not redundant kma-1.4.21/runkma.c:213:20: note: Null pointer dereference kma-1.4.21/runkma.c:991:20: warning: Either the condition 'outputfilename' is redundant or there is possible null pointer dereference: outputfilename. [nullPointerRedundantCheck] kma-1.4.21/runkma.c:1007:5: note: Assuming that condition 'outputfilename' is not redundant kma-1.4.21/runkma.c:991:20: note: Null pointer dereference kma-1.4.21/runkma.c:1088:8: style: Variable 't_len' is assigned a value that is never used. [unreadVariable] kma-1.4.21/runkma.c:1089:13: style: Variable 'read_score' is assigned a value that is never used. [unreadVariable] kma-1.4.21/runkma.c:1179:11: style: Variable 'header_r' is assigned a value that is never used. [unreadVariable] kma-1.4.21/runkma.c:1186:9: style: Variable 'qseq_r' is assigned a value that is never used. [unreadVariable] kma-1.4.21/runkma.c:1445:8: style: Variable 'depth' is assigned a value that is never used. [unreadVariable] kma-1.4.21/runkma.c:1446:7: style: Variable 'q_id' is assigned a value that is never used. [unreadVariable] kma-1.4.21/runkma.c:1447:8: style: Variable 'cover' is assigned a value that is never used. [unreadVariable] kma-1.4.21/runkma.c:1448:10: style: Variable 'q_cover' is assigned a value that is never used. [unreadVariable] kma-1.4.21/seq2fasta.c:39:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/seq2fasta.c:81:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/seq2fasta.c:139:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/seq2fasta.c:193:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/seq2fasta.c:215:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/seq2fasta.c:254:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/seq2fasta.c:51:39: style: Parameter 'template_lengths' can be declared as pointer to const [constParameterPointer] kma-1.4.21/seq2fasta.c:101:42: style: Parameter 'template_lengths' can be declared as pointer to const [constParameterPointer] kma-1.4.21/seq2fasta.c:171:20: style: Variable 'intStr' can be declared as pointer to const [constVariablePointer] kma-1.4.21/seq2fasta.c:233:11: style: Variable 'file_len' is assigned a value that is never used. [unreadVariable] kma-1.4.21/seqparse.c:37:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] kma-1.4.21/seqparse.c:97:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/seqparse.c:204:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/seqparse.c:257:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/seqparse.c:422:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/seqparse.c:399:13: style: Variable 'src->bytes' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/seqparse.c:395:14: note: src->bytes is assigned kma-1.4.21/seqparse.c:399:13: note: src->bytes is overwritten kma-1.4.21/seqparse.c:545:13: style: Variable 'src->bytes' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/seqparse.c:541:14: note: src->bytes is assigned kma-1.4.21/seqparse.c:545:13: note: src->bytes is overwritten kma-1.4.21/seqparse.c:32:18: style: Variable 'check' can be declared as pointer to const [constVariablePointer] kma-1.4.21/seqparse.c:66:69: style: Parameter 'trans' can be declared as pointer to const [constParameterPointer] kma-1.4.21/seqparse.c:161:57: style: Parameter 'trans' can be declared as pointer to const [constParameterPointer] kma-1.4.21/seqparse.c:241:81: style: Parameter 'trans' can be declared as pointer to const [constParameterPointer] kma-1.4.21/seqparse.c:405:69: style: Parameter 'trans' can be declared as pointer to const [constParameterPointer] kma-1.4.21/seqparse.c:554:17: style: Variable 'buff' can be declared as pointer to const [constVariablePointer] kma-1.4.21/shm.c:59:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/shm.c:181:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/shm.c:273:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/shm.c:297:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/shm.c:315:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/shm.c:339:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/shm.c:357:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/shm.c:386:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/shm.c:399:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] kma-1.4.21/shm.c:444:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/shm.c:44:37: style: Parameter 'dest' can be declared as pointer to const [constParameterPointer] kma-1.4.21/shm.c:416:30: style: Parameter 'argv' can be declared as const array [constParameter] kma-1.4.21/shm.c:418:40: style: Variable 'template_lengths' can be declared as pointer to const [constVariablePointer] kma-1.4.21/shm.c:420:17: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] kma-1.4.21/shm.c:421:27: style: Variable 'template_names' can be declared as pointer to const [constVariablePointer] kma-1.4.21/shm.c:69:21: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/shm.c:191:21: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/sparse.c:91:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/sparse.c:149:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/sparse.c:273:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/sparse.c:365:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/sparse.c:371:5: style: Suspicious condition (assignment + comparison); Clarify expression with parentheses. [clarifyCondition] kma-1.4.21/sparse.c:626:5: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/sparse.c:773:5: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/sparse.c:58:29: warning: Shifting 64-bit value by 64 bits is undefined behaviour. See condition at line 68. [shiftTooManyBits] kma-1.4.21/sparse.c:68:5: note: Assuming that condition 'prefix_len' is not redundant kma-1.4.21/sparse.c:58:29: note: Shift kma-1.4.21/spltdb.c:66:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/spltdb.c:208:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/spltdb.c:364:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/spltdb.c:409:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ptrInfo [valueFlowBailoutIncompleteVar] kma-1.4.21/spltdb.c:586:8: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled] kma-1.4.21/spltdb.c:615:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/spltdb.c:1067:5: style: Condition 'progress' is always false [knownConditionTrueFalse] kma-1.4.21/spltdb.c:1065:13: note: Assignment 'progress=0', assigned value is 0 kma-1.4.21/spltdb.c:1067:5: note: Condition 'progress' is always false kma-1.4.21/spltdb.c:713:5: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint] kma-1.4.21/spltdb.c:801:3: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint] kma-1.4.21/spltdb.c:806:3: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] kma-1.4.21/spltdb.c:54:30: style: Parameter 'out_Tem' can be declared as pointer to const [constParameterPointer] kma-1.4.21/spltdb.c:196:37: style: Parameter 'out_Tem' can be declared as pointer to const [constParameterPointer] kma-1.4.21/spltdb.c:422:13: style: Variable 'tm' can be declared as pointer to const [constVariablePointer] kma-1.4.21/spltdb.c:613:5: style: Variable 'j' is assigned a value that is never used. [unreadVariable] kma-1.4.21/spltdb.c:829:11: style: Variable 'header_r' is assigned a value that is never used. [unreadVariable] kma-1.4.21/spltdb.c:836:9: style: Variable 'qseq_r' is assigned a value that is never used. [unreadVariable] kma-1.4.21/spltdb.c:1060:8: style: Variable 'depth' is assigned a value that is never used. [unreadVariable] kma-1.4.21/spltdb.c:1061:7: style: Variable 'q_id' is assigned a value that is never used. [unreadVariable] kma-1.4.21/spltdb.c:1062:8: style: Variable 'cover' is assigned a value that is never used. [unreadVariable] kma-1.4.21/spltdb.c:1063:10: style: Variable 'q_cover' is assigned a value that is never used. [unreadVariable] kma-1.4.21/stdnuc.c:278:38: style: Parameter 'compressor' can be declared as pointer to const [constParameterPointer] kma-1.4.21/stdnuc.c:287:48: style: Parameter 'Pos' can be declared as pointer to const. However it seems that 'getHmer' is a callback function, if 'Pos' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/stdnuc.c:405:16: note: You might need to cast the function pointer here kma-1.4.21/stdnuc.c:287:48: note: Parameter 'Pos' can be declared as pointer to const kma-1.4.21/stdnuc.c:312:58: style: Parameter 'kmersize' can be declared as pointer to const. However it seems that 'getMmer' is a callback function, if 'kmersize' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/stdnuc.c:411:15: note: You might need to cast the function pointer here kma-1.4.21/stdnuc.c:312:58: note: Parameter 'kmersize' can be declared as pointer to const kma-1.4.21/stdnuc.c:336:59: style: Parameter 'kmersize' can be declared as pointer to const. However it seems that 'getMmerR' is a callback function, if 'kmersize' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/stdnuc.c:412:16: note: You might need to cast the function pointer here kma-1.4.21/stdnuc.c:336:59: note: Parameter 'kmersize' can be declared as pointer to const kma-1.4.21/stdnuc.c:438:17: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer] kma-1.4.21/stdnuc.c:453:23: style: Variable 'comp' can be declared as const array [constVariable] kma-1.4.21/stdnuc.c:468:46: style: Parameter 'trans' can be declared as pointer to const [constParameterPointer] kma-1.4.21/stdstat.c:204:28: style: Parameter 'src' can be declared as pointer to const [constParameterPointer] kma-1.4.21/stdstat.c:241:31: style: Parameter 'qual' can be declared as pointer to const [constParameterPointer] kma-1.4.21/tmp.c:61:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/tmp.c:36:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/tmp.c:69:6: style: Variable 'fd' is assigned a value that is never used. [unreadVariable] kma-1.4.21/trim.c:52:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/trim.c:100:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/trim.c:146:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/trim.c:206:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] kma-1.4.21/trim.c:28:26: style: Parameter 'header' can be declared as pointer to const. However it seems that 'printTrimFsa' is a callback function, if 'header' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/trim.c:378:18: note: You might need to cast the function pointer here kma-1.4.21/trim.c:28:26: note: Parameter 'header' can be declared as pointer to const kma-1.4.21/trim.c:28:54: style: Parameter 'qual' can be declared as pointer to const. However it seems that 'printTrimFsa' is a callback function, if 'qual' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/trim.c:378:18: note: You might need to cast the function pointer here kma-1.4.21/trim.c:28:54: note: Parameter 'qual' can be declared as pointer to const kma-1.4.21/trim.c:70:31: style: Parameter 'header' can be declared as pointer to const. However it seems that 'printTrimFsa_pair' is a callback function, if 'header' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/trim.c:380:23: note: You might need to cast the function pointer here kma-1.4.21/trim.c:70:31: note: Parameter 'header' can be declared as pointer to const kma-1.4.21/trim.c:70:59: style: Parameter 'qual' can be declared as pointer to const. However it seems that 'printTrimFsa_pair' is a callback function, if 'qual' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/trim.c:380:23: note: You might need to cast the function pointer here kma-1.4.21/trim.c:70:59: note: Parameter 'qual' can be declared as pointer to const kma-1.4.21/trim.c:70:72: style: Parameter 'header_r' can be declared as pointer to const. However it seems that 'printTrimFsa_pair' is a callback function, if 'header_r' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/trim.c:380:23: note: You might need to cast the function pointer here kma-1.4.21/trim.c:70:72: note: Parameter 'header_r' can be declared as pointer to const kma-1.4.21/trim.c:70:104: style: Parameter 'qual_r' can be declared as pointer to const. However it seems that 'printTrimFsa_pair' is a callback function, if 'qual_r' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/trim.c:380:23: note: You might need to cast the function pointer here kma-1.4.21/trim.c:70:104: note: Parameter 'qual_r' can be declared as pointer to const kma-1.4.21/tsv.c:46:2: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg] kma-1.4.21/tsv.c:107:2: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg] kma-1.4.21/tsv.c:86:2: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/tsv.c:89:2: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/tsv.c:49:55: style: Parameter 'template_name' can be declared as pointer to const [constParameterPointer] kma-1.4.21/tsv.c:49:77: style: Parameter 'aligned_assem' can be declared as pointer to const [constParameterPointer] kma-1.4.21/tsv.c:46:2: style: Variable 'flag' is assigned a value that is never used. [unreadVariable] kma-1.4.21/tsv.c:107:2: style: Variable 'flag' is assigned a value that is never used. [unreadVariable] kma-1.4.21/update.c:40:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/update.c:88:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/update.c:237:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] kma-1.4.21/update.c:272:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/update.c:251:33: style: Parameter 'argv' can be declared as const array [constParameter] kma-1.4.21/update.c:96:21: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/update.c:97:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] kma-1.4.21/updateindex.c:179:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/updateindex.c:196:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/updateindex.c:189:4: warning: Either the condition '!template_lengths' is redundant or there is possible null pointer dereference: template_lengths. [nullPointerRedundantCheck] kma-1.4.21/updateindex.c:195:6: note: Assuming that condition '!template_lengths' is not redundant kma-1.4.21/updateindex.c:189:4: note: Null pointer dereference kma-1.4.21/updateindex.c:190:24: warning: Either the condition '!template_ulengths' is redundant or there is possible null pointer dereference: template_ulengths. [nullPointerRedundantCheck] kma-1.4.21/updateindex.c:195:49: note: Assuming that condition '!template_ulengths' is not redundant kma-1.4.21/updateindex.c:190:24: note: Null pointer dereference kma-1.4.21/updateindex.c:191:5: warning: Either the condition '!template_ulengths' is redundant or there is possible null pointer dereference: template_ulengths. [nullPointerRedundantCheck] kma-1.4.21/updateindex.c:195:49: note: Assuming that condition '!template_ulengths' is not redundant kma-1.4.21/updateindex.c:191:5: note: Null pointer dereference kma-1.4.21/updateindex.c:192:4: warning: Either the condition '!template_slengths' is redundant or there is possible null pointer dereference: template_slengths. [nullPointerRedundantCheck] kma-1.4.21/updateindex.c:195:27: note: Assuming that condition '!template_slengths' is not redundant kma-1.4.21/updateindex.c:192:4: note: Null pointer dereference kma-1.4.21/updateindex.c:192:33: warning: Either the condition '!template_slengths' is redundant or there is possible null pointer dereference: template_slengths. [nullPointerRedundantCheck] kma-1.4.21/updateindex.c:195:27: note: Assuming that condition '!template_slengths' is not redundant kma-1.4.21/updateindex.c:192:33: note: Null pointer dereference kma-1.4.21/updateindex.c:192:54: warning: Either the condition '!template_ulengths' is redundant or there is possible null pointer dereference: template_ulengths. [nullPointerRedundantCheck] kma-1.4.21/updateindex.c:195:49: note: Assuming that condition '!template_ulengths' is not redundant kma-1.4.21/updateindex.c:192:54: note: Null pointer dereference kma-1.4.21/updateindex.c:193:4: warning: Either the condition '!template_ulengths' is redundant or there is possible null pointer dereference: template_ulengths. [nullPointerRedundantCheck] kma-1.4.21/updateindex.c:195:49: note: Assuming that condition '!template_ulengths' is not redundant kma-1.4.21/updateindex.c:193:4: note: Null pointer dereference kma-1.4.21/updateindex.c:193:33: warning: Either the condition '!template_ulengths' is redundant or there is possible null pointer dereference: template_ulengths. [nullPointerRedundantCheck] kma-1.4.21/updateindex.c:195:49: note: Assuming that condition '!template_ulengths' is not redundant kma-1.4.21/updateindex.c:193:33: note: Null pointer dereference kma-1.4.21/updateindex.c:193:54: warning: Either the condition '!template_ulengths' is redundant or there is possible null pointer dereference: template_ulengths. [nullPointerRedundantCheck] kma-1.4.21/updateindex.c:195:49: note: Assuming that condition '!template_ulengths' is not redundant kma-1.4.21/updateindex.c:193:54: note: Null pointer dereference kma-1.4.21/updateindex.c:194:4: warning: Either the condition '!template_lengths' is redundant or there is possible null pointer dereference: template_lengths. [nullPointerRedundantCheck] kma-1.4.21/updateindex.c:195:6: note: Assuming that condition '!template_lengths' is not redundant kma-1.4.21/updateindex.c:194:4: note: Null pointer dereference kma-1.4.21/updateindex.c:194:32: warning: Either the condition '!template_lengths' is redundant or there is possible null pointer dereference: template_lengths. [nullPointerRedundantCheck] kma-1.4.21/updateindex.c:195:6: note: Assuming that condition '!template_lengths' is not redundant kma-1.4.21/updateindex.c:194:32: note: Null pointer dereference kma-1.4.21/updateindex.c:194:52: warning: Either the condition '!template_ulengths' is redundant or there is possible null pointer dereference: template_ulengths. [nullPointerRedundantCheck] kma-1.4.21/updateindex.c:195:49: note: Assuming that condition '!template_ulengths' is not redundant kma-1.4.21/updateindex.c:194:52: note: Null pointer dereference kma-1.4.21/updateindex.c:37:48: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] kma-1.4.21/updateindex.c:83:69: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] kma-1.4.21/updateindex.c:169:28: style: Parameter 'qseq' can be declared as pointer to const. However it seems that 'updateAnnots' is a callback function, if 'qseq' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/updateindex.c:31:96: note: You might need to cast the function pointer here kma-1.4.21/updateindex.c:169:28: note: Parameter 'qseq' can be declared as pointer to const kma-1.4.21/updateindex.c:184:35: style: Parameter 'qseq' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updateindex.c:92:29: warning: Shifting 64-bit value by 64 bits is undefined behaviour. See condition at line 116. [shiftTooManyBits] kma-1.4.21/updateindex.c:116:7: note: Assuming that condition 'prefix_len' is not redundant kma-1.4.21/updateindex.c:91:17: note: prefix_shifter is assigned '64-(prefix_len<<1)' here. kma-1.4.21/updateindex.c:92:29: note: Shift kma-1.4.21/updatescores.c:37:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/updatescores.c:75:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/updatescores.c:195:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/updatescores.c:290:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/updatescores.c:380:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/updatescores.c:473:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/updatescores.c:501:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/updatescores.c:539:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] kma-1.4.21/updatescores.c:26:39: style: Parameter 'qseq' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:26:85: style: Parameter 'start' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:26:97: style: Parameter 'end' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:26:124: style: Parameter 'header' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:64:42: style: Parameter 'qseq' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:64:74: style: Parameter 'qseq_r' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:64:123: style: Parameter 'start' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:64:135: style: Parameter 'end' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:64:162: style: Parameter 'header' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:64:177: style: Parameter 'header_r' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:109:43: style: Parameter 'qseq' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:109:160: style: Parameter 'Scores' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:109:173: style: Parameter 'Lengths' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:109:189: style: Parameter 'header' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:203:34: style: Parameter 'qseq' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:203:160: style: Parameter 'Scores' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:203:173: style: Parameter 'Lengths' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:203:189: style: Parameter 'header' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:300:37: style: Parameter 'qseq' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:300:141: style: Parameter 'Scores' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:300:156: style: Parameter 'header' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:390:37: style: Parameter 'qseq' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:390:69: style: Parameter 'qseq_r' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:390:176: style: Parameter 'Scores' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:390:191: style: Parameter 'header' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:390:206: style: Parameter 'header_r' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:490:39: style: Parameter 'qseq' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:490:85: style: Parameter 'start' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:490:97: style: Parameter 'end' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:490:124: style: Parameter 'header' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:528:42: style: Parameter 'qseq' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:528:74: style: Parameter 'qseq_r' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:528:123: style: Parameter 'start' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:528:135: style: Parameter 'end' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:528:162: style: Parameter 'header' can be declared as pointer to const [constParameterPointer] kma-1.4.21/updatescores.c:528:177: style: Parameter 'header_r' can be declared as pointer to const [constParameterPointer] kma-1.4.21/valueshash.c:38:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/valueshash.c:60:35: style: Parameter 'values' can be declared as pointer to const [constParameterPointer] kma-1.4.21/valueshash.c:77:18: style: Variable 'values' can be declared as pointer to const [constVariablePointer] kma-1.4.21/valueshash.c:88:26: style: Parameter 'values' can be declared as pointer to const [constParameterPointer] kma-1.4.21/valueshash.c:93:18: style: Variable 'values' can be declared as pointer to const [constVariablePointer] kma-1.4.21/valueshash.c:98:25: style: Parameter 's1' can be declared as pointer to const [constParameterPointer] kma-1.4.21/valueshash.c:98:39: style: Parameter 's2' can be declared as pointer to const [constParameterPointer] kma-1.4.21/valueshash.c:115:18: style: Variable 's1' can be declared as pointer to const [constVariablePointer] kma-1.4.21/valueshash.c:115:23: style: Variable 's2' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:176:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:2151:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:2434:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3044:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3048:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3057:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3345:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3349:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3358:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3450:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3466:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3508:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3536:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3562:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3625:6: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3641:6: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3696:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3703:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3735:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3766:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3825:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3841:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:4855:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:5119:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:5821:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:5827:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:6539:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/savekmers.c:3851:12: style: Condition 'hitCounter' is always true [knownConditionTrueFalse] kma-1.4.21/savekmers.c:5283:11: style: Condition 'last' is always true [knownConditionTrueFalse] kma-1.4.21/savekmers.c:5399:11: style: Condition 'last' is always true [knownConditionTrueFalse] kma-1.4.21/savekmers.c:6237:12: style: Condition 'last' is always true [knownConditionTrueFalse] kma-1.4.21/savekmers.c:6028:5: warning: Possible null pointer dereference: Sizes [nullPointer] kma-1.4.21/savekmers.c:5949:22: note: Assignment 'Sizes=0', assigned value is 0 kma-1.4.21/savekmers.c:6028:5: note: Null pointer dereference kma-1.4.21/savekmers.c:306:16: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast] kma-1.4.21/savekmers.c:376:16: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast] kma-1.4.21/savekmers.c:1327:15: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast] kma-1.4.21/savekmers.c:1521:15: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast] kma-1.4.21/savekmers.c:1771:15: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast] kma-1.4.21/savekmers.c:1832:15: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast] kma-1.4.21/savekmers.c:4535:15: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast] kma-1.4.21/savekmers.c:4873:15: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast] kma-1.4.21/savekmers.c:5159:15: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast] kma-1.4.21/savekmers.c:5160:12: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast] kma-1.4.21/savekmers.c:5977:15: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast] kma-1.4.21/savekmers.c:5978:12: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast] kma-1.4.21/savekmers.c:2040:7: style: Variable 'end' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/savekmers.c:1959:6: note: end is assigned kma-1.4.21/savekmers.c:2040:7: note: end is overwritten kma-1.4.21/savekmers.c:2430:6: style: Variable 'end' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/savekmers.c:2191:6: note: end is assigned kma-1.4.21/savekmers.c:2430:6: note: end is overwritten kma-1.4.21/savekmers.c:4444:8: style: Variable 'bestHits' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/savekmers.c:4440:24: note: *regionTemplates is assigned 'bestHits' here. kma-1.4.21/savekmers.c:4444:8: note: Variable 'bestHits' is assigned an expression that holds the same value. kma-1.4.21/savekmers.c:5293:8: style: Variable 'last' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/savekmers.c:5267:16: note: Assuming that condition 'values==last' is not redundant kma-1.4.21/savekmers.c:5293:8: note: Variable 'last' is assigned an expression that holds the same value. kma-1.4.21/savekmers.c:5472:5: style: Variable 'rc' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/savekmers.c:5346:5: note: rc is assigned kma-1.4.21/savekmers.c:5472:5: note: rc is overwritten kma-1.4.21/savekmers.c:5409:8: style: Variable 'last' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/savekmers.c:5383:16: note: Assuming that condition 'values==last' is not redundant kma-1.4.21/savekmers.c:5409:8: note: Variable 'last' is assigned an expression that holds the same value. kma-1.4.21/savekmers.c:6247:9: style: Variable 'last' is assigned an expression that holds the same value. [redundantAssignment] kma-1.4.21/savekmers.c:6222:17: note: Assuming that condition 'values==last' is not redundant kma-1.4.21/savekmers.c:6247:9: note: Variable 'last' is assigned an expression that holds the same value. kma-1.4.21/savekmers.c:3866:182: style:inconclusive: Function 'save_kmers_HMM' argument 9 names different: declaration 'header' definition 'headerOrg'. [funcArgNamesDifferent] kma-1.4.21/savekmers.h:86:182: note: Function 'save_kmers_HMM' argument 9 names different: declaration 'header' definition 'headerOrg'. kma-1.4.21/savekmers.c:3866:182: note: Function 'save_kmers_HMM' argument 9 names different: declaration 'header' definition 'headerOrg'. kma-1.4.21/savekmers.c:535:50: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation] kma-1.4.21/savekmers.c:596:53: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation] kma-1.4.21/savekmers.c:1104:49: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation] kma-1.4.21/savekmers.c:1165:52: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation] kma-1.4.21/savekmers.c:2253:49: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation] kma-1.4.21/savekmers.c:2314:52: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation] kma-1.4.21/savekmers.c:2544:49: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation] kma-1.4.21/savekmers.c:2605:52: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation] kma-1.4.21/savekmers.c:2855:49: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation] kma-1.4.21/savekmers.c:2916:52: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation] kma-1.4.21/savekmers.c:5538:49: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation] kma-1.4.21/savekmers.c:6355:48: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation] kma-1.4.21/savekmers.c:300:60: style: Variable 'Templates' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:370:60: style: Variable 'Templates' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:415:28: style: Parameter 'bestTemplates' can be declared as pointer to const [constParameterPointer] kma-1.4.21/savekmers.c:436:48: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:698:18: style: Variable 'values_s' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:699:48: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:831:18: style: Variable 'values_s' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:832:69: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:1008:48: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:1254:25: style: Parameter 'bestTemplates' can be declared as pointer to const [constParameterPointer] kma-1.4.21/savekmers.c:1254:45: style: Parameter 'bestTemplates_r' can be declared as pointer to const [constParameterPointer] kma-1.4.21/savekmers.c:1275:29: style: Parameter 'bestTemplates' can be declared as pointer to const. However it seems that 'getSecondBestForce' is a callback function, if 'bestTemplates' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/savekmers.c:45:62: note: You might need to cast the function pointer here kma-1.4.21/savekmers.c:1275:29: note: Parameter 'bestTemplates' can be declared as pointer to const kma-1.4.21/savekmers.c:1275:49: style: Parameter 'bestTemplates_r' can be declared as pointer to const. However it seems that 'getSecondBestForce' is a callback function, if 'bestTemplates_r' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/savekmers.c:45:62: note: You might need to cast the function pointer here kma-1.4.21/savekmers.c:1275:49: note: Parameter 'bestTemplates_r' can be declared as pointer to const kma-1.4.21/savekmers.c:1275:119: style: Parameter 'regionScores' can be declared as pointer to const. However it seems that 'getSecondBestForce' is a callback function, if 'regionScores' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/savekmers.c:45:62: note: You might need to cast the function pointer here kma-1.4.21/savekmers.c:1275:119: note: Parameter 'regionScores' can be declared as pointer to const kma-1.4.21/savekmers.c:1324:60: style: Variable 'Templates' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:1383:22: style: Parameter 'bestTemplates' can be declared as pointer to const [constParameterPointer] kma-1.4.21/savekmers.c:1383:42: style: Parameter 'bestTemplates_r' can be declared as pointer to const [constParameterPointer] kma-1.4.21/savekmers.c:1415:47: style: Parameter 'bestTemplates_r' can be declared as pointer to const. However it seems that 'getSecondBestPen' is a callback function, if 'bestTemplates_r' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/savekmers.c:46:70: note: You might need to cast the function pointer here kma-1.4.21/savekmers.c:1415:47: note: Parameter 'bestTemplates_r' can be declared as pointer to const kma-1.4.21/savekmers.c:1415:117: style: Parameter 'regionScores' can be declared as pointer to const. However it seems that 'getSecondBestPen' is a callback function, if 'regionScores' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/savekmers.c:46:70: note: You might need to cast the function pointer here kma-1.4.21/savekmers.c:1415:117: note: Parameter 'regionScores' can be declared as pointer to const kma-1.4.21/savekmers.c:1514:118: style: Parameter 'regionScores' can be declared as pointer to const [constParameterPointer] kma-1.4.21/savekmers.c:1648:20: style: Parameter 'bestTemplates' can be declared as pointer to const. However it seems that 'getF_Best' is a callback function, if 'bestTemplates' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/savekmers.c:47:46: note: You might need to cast the function pointer here kma-1.4.21/savekmers.c:1648:20: note: Parameter 'bestTemplates' can be declared as pointer to const kma-1.4.21/savekmers.c:1648:40: style: Parameter 'bestTemplates_r' can be declared as pointer to const. However it seems that 'getF_Best' is a callback function, if 'bestTemplates_r' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/savekmers.c:47:46: note: You might need to cast the function pointer here kma-1.4.21/savekmers.c:1648:40: note: Parameter 'bestTemplates_r' can be declared as pointer to const kma-1.4.21/savekmers.c:1682:40: style: Parameter 'bestTemplates_r' can be declared as pointer to const. However it seems that 'getR_Best' is a callback function, if 'bestTemplates_r' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/savekmers.c:48:46: note: You might need to cast the function pointer here kma-1.4.21/savekmers.c:1682:40: note: Parameter 'bestTemplates_r' can be declared as pointer to const kma-1.4.21/savekmers.c:1768:60: style: Variable 'Templates' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:1829:60: style: Variable 'Templates' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:1930:18: style: Variable 'values_s' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:1931:69: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:2167:48: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:2449:48: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:3073:18: style: Variable 'values_s' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:3074:48: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:3877:12: style: Variable 'values' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:3878:18: style: Variable 'values_s' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:4523:88: style: Parameter 'template_lengths' can be declared as pointer to const. However it seems that 'ankerAndClean' is a callback function, if 'template_lengths' is declared with const you might also need to cast function pointer(s). [constParameterCallback] kma-1.4.21/savekmers.c:39:142: note: You might need to cast the function pointer here kma-1.4.21/savekmers.c:4523:88: note: Parameter 'template_lengths' can be declared as pointer to const kma-1.4.21/savekmers.c:4528:17: style: Variable 'Templates' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:4529:12: style: Variable 'values' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:4530:18: style: Variable 'values_s' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:4867:63: style: Variable 'Templates' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:4868:15: style: Variable 'values' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:4869:18: style: Variable 'values_s' can be declared as pointer to const [constVariablePointer] kma-1.4.21/savekmers.c:845:29: warning: Shifting 64-bit value by 64 bits is undefined behaviour. See condition at line 869. [shiftTooManyBits] kma-1.4.21/savekmers.c:869:5: note: Assuming that condition 'prefix_len' is not redundant kma-1.4.21/savekmers.c:844:22: note: Assignment 'prefix_shifter=64-(prefix_len<<1)', assigned value is 64 kma-1.4.21/savekmers.c:845:29: note: Shift kma-1.4.21/savekmers.c:1945:29: warning: Shifting 64-bit value by 64 bits is undefined behaviour. See condition at line 1960. [shiftTooManyBits] kma-1.4.21/savekmers.c:1960:5: note: Assuming that condition 'prefix_len' is not redundant kma-1.4.21/savekmers.c:1944:22: note: Assignment 'prefix_shifter=64-(prefix_len<<1)', assigned value is 64 kma-1.4.21/savekmers.c:1945:29: note: Shift kma-1.4.21/savekmers.c:815:9: style: Variable 'reps' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:868:6: style: Variable 'end' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:1043:6: style: Variable 'end' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:2510:7: style: Variable 'end' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:2821:7: style: Variable 'end' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:3040:7: style: Variable 'end' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:3124:7: style: Variable 'end' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:3183:8: style: Variable 'reps' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:3245:7: style: Variable 'end' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:3305:8: style: Variable 'reps' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:3341:7: style: Variable 'end' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:3408:17: style: Variable 'hitCounter' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:4010:8: style: Variable 'end' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:4030:14: style: Variable 'bestScore' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:4247:11: style: Variable 'Ms' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:4263:11: style: Variable 'Ms' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:5184:21: style: Variable 'DB_size' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:5659:12: style: Variable 'ties_len' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:5661:18: style: Variable 'best_score_len' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:5663:20: style: Variable 'best_score_len_r' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:5703:11: style: Variable 'score' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:5743:11: style: Variable 'score' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:5822:7: style: Variable 'i' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:5828:7: style: Variable 'i' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:6000:21: style: Variable 'DB_size' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:6461:14: style: Variable 'hitCounter' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:6481:12: style: Variable 'ties_len' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:6489:10: style: Variable 'score' is assigned a value that is never used. [unreadVariable] kma-1.4.21/savekmers.c:6540:6: style: Variable 'i' is assigned a value that is never used. [unreadVariable] kma-1.4.21/xml.c:64:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] kma-1.4.21/xml.c:77:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] kma-1.4.21/xml.c:103:16: portability: Undefined behaviour, pointer arithmetic 'counts-1' is out of bounds. [pointerOutOfBounds] kma-1.4.21/xml.c:119:16: portability: Undefined behaviour, pointer arithmetic 'counts-1' is out of bounds. [pointerOutOfBounds] kma-1.4.21/xml.c:200:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] kma-1.4.21/xml.c:40:2: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/xml.c:136:2: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint] kma-1.4.21/xml.c:211:2: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] kma-1.4.21/xml.c:55:10: warning: Either the condition 'out' is redundant or there is possible null pointer dereference: out. [nullPointerRedundantCheck] kma-1.4.21/xml.c:77:5: note: Assuming that condition 'out' is not redundant kma-1.4.21/xml.c:76:9: note: Calling function 'capXML', 1st argument 'out' value is 0 kma-1.4.21/xml.c:55:10: note: Null pointer dereference kma-1.4.21/xml.c:56:10: warning: Either the condition 'out' is redundant or there is possible null pointer dereference: out. [nullPointerRedundantCheck] kma-1.4.21/xml.c:77:5: note: Assuming that condition 'out' is not redundant kma-1.4.21/xml.c:76:9: note: Calling function 'capXML', 1st argument 'out' value is 0 kma-1.4.21/xml.c:56:10: note: Null pointer dereference kma-1.4.21/xml.c:95:17: style: Variable 'qPtr' can be declared as pointer to const [constVariablePointer] kma-1.4.21/xml.c:154:11: style: Variable 'bases' can be declared as const array [constVariable] kma-1.4.21/vcf.c:143:35: error: Array 'assembly[pos].counts[6]' accessed at index 8, which is out of bounds. [arrayIndexOutOfBounds] kma-1.4.21/vcf.c:138:10: note: Assignment 'nuc='-'', assigned value is 45 kma-1.4.21/vcf.c:142:20: note: Assignment 'bestNuc=nuc2num[nuc]', assigned value is 8 kma-1.4.21/vcf.c:143:35: note: Array index out of bounds kma-1.4.21/vcf.c:153:18: error: Array 'bases[6]' accessed at index 8, which is out of bounds. [arrayIndexOutOfBounds] kma-1.4.21/vcf.c:138:10: note: Assignment 'nuc='-'', assigned value is 45 kma-1.4.21/vcf.c:142:20: note: Assignment 'bestNuc=nuc2num[nuc]', assigned value is 8 kma-1.4.21/vcf.c:146:17: note: Assuming condition is false kma-1.4.21/vcf.c:153:18: note: Array index out of bounds kma-1.4.21/vcf.c:187:29: warning: Either the condition 'bestNuc=='-'' is redundant or the array 'assembly[pos].counts[6]' is accessed at index 8, which is out of bounds. [arrayIndexOutOfBoundsCond] kma-1.4.21/vcf.c:244:16: note: Assuming that condition 'bestNuc=='-'' is not redundant kma-1.4.21/vcf.c:183:20: note: Assignment 'nucNum=nuc2num[bestNuc]', assigned value is 8 kma-1.4.21/vcf.c:187:29: note: Array index out of bounds kma-1.4.21/vcf.c:145:9: style: Variable 'i' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/vcf.c:135:4: note: i is assigned kma-1.4.21/vcf.c:145:9: note: i is overwritten kma-1.4.21/vcf.c:46:43: style: Parameter 'templateFilename' can be declared as pointer to const [constParameterPointer] kma-1.4.21/vcf.c:97:22: style: Parameter 'template_name' can be declared as pointer to const [constParameterPointer] kma-1.4.21/vcf.c:97:52: style: Parameter 'template_seq' can be declared as pointer to const [constParameterPointer] kma-1.4.21/vcf.c:135:6: error: Uninitialized variable: i [uninitvar] kma-1.4.21/vcf.c:152:10: style: Variable 'nucNum' is assigned a value that is never used. [unreadVariable] kma-1.4.21/vcf.c:157:11: style: Variable 'nucNum' is assigned a value that is never used. [unreadVariable] kma-1.4.21/vcf.c:169:12: style: Variable 'nucNum' is assigned a value that is never used. [unreadVariable] kma-1.4.21/kma.c:104:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] kma-1.4.21/kma.c:277:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] kma-1.4.21/kma.c:1621:162: warning: Result of operator '|' is always true if one operand is non-zero. Did you intend to use '&'? [badBitmaskCheck] kma-1.4.21/kma.c:360:6: error: Common realloc mistake: 'templatefilenames' nulled but not freed upon failure [memleakOnRealloc] kma-1.4.21/kma.c:370:6: error: Common realloc mistake: 'templatefilenames' nulled but not freed upon failure [memleakOnRealloc] kma-1.4.21/kma.c:1250:11: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast] kma-1.4.21/kma.c:1251:27: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast] kma-1.4.21/kma.c:1251:45: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast] kma-1.4.21/kma.c:834:20: style: Opposite expression on both sides of '<'. [oppositeExpression] kma-1.4.21/kma.c:844:20: style: Opposite expression on both sides of '<'. [oppositeExpression] kma-1.4.21/kma.c:854:19: style: Opposite expression on both sides of '<'. [oppositeExpression] kma-1.4.21/kma.c:865:20: style: Opposite expression on both sides of '<'. [oppositeExpression] kma-1.4.21/kma.c:876:20: style: Opposite expression on both sides of '<'. [oppositeExpression] kma-1.4.21/kma.c:897:11: style: Opposite expression on both sides of '<'. [oppositeExpression] kma-1.4.21/kma.c:908:11: style: Opposite expression on both sides of '<'. [oppositeExpression] kma-1.4.21/kma.c:1123:21: style: Variable 'significantBase' is reassigned a value before the old one has been used. [redundantAssignment] kma-1.4.21/kma.c:1119:22: note: significantBase is assigned kma-1.4.21/kma.c:1123:21: note: significantBase is overwritten kma-1.4.21/kma.c:1500:46: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] diff: head kma-1.4.21/kma.c:1251:45: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast] 2.17.0 kma-1.4.21/kmmap.c:51:23: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory] kma-1.4.21/kmmap.c:44:13: note: Assuming allocation function fails kma-1.4.21/kmmap.c:44:13: note: Assignment 'data=mmap(0,Size,PROT_READ,MAP_SHARED,fd,0)', assigned value is 0 kma-1.4.21/kmmap.c:50:7: note: uptr is assigned '(unsigned int*)data' here. kma-1.4.21/kmmap.c:51:23: note: Null pointer addition head kma-1.4.21/kmmap.c:51:23: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory] kma-1.4.21/kmmap.c:44:13: note: Assuming allocation function fails kma-1.4.21/kmmap.c:44:13: note: Assignment 'data=mmap(0,Size,PROT_READ,MAP_SHARED,fd,0)', assigned value is 0 kma-1.4.21/kmmap.c:50:7: note: uptr is assigned '(unsigned int*)data' here. kma-1.4.21/kmmap.c:51:23: note: Null pointer addition head kma-1.4.21/updateindex.c:192:33: warning: Either the condition '!template_slengths' is redundant or there is possible null pointer dereference: template_slengths. [nullPointerRedundantCheck] kma-1.4.21/updateindex.c:195:27: note: Assuming that condition '!template_slengths' is not redundant kma-1.4.21/updateindex.c:192:33: note: Null pointer dereference head kma-1.4.21/updateindex.c:193:33: warning: Either the condition '!template_ulengths' is redundant or there is possible null pointer dereference: template_ulengths. [nullPointerRedundantCheck] kma-1.4.21/updateindex.c:195:49: note: Assuming that condition '!template_ulengths' is not redundant kma-1.4.21/updateindex.c:193:33: note: Null pointer dereference head kma-1.4.21/updateindex.c:193:54: warning: Either the condition '!template_ulengths' is redundant or there is possible null pointer dereference: template_ulengths. [nullPointerRedundantCheck] kma-1.4.21/updateindex.c:195:49: note: Assuming that condition '!template_ulengths' is not redundant kma-1.4.21/updateindex.c:193:54: note: Null pointer dereference head kma-1.4.21/updateindex.c:194:32: warning: Either the condition '!template_lengths' is redundant or there is possible null pointer dereference: template_lengths. [nullPointerRedundantCheck] kma-1.4.21/updateindex.c:195:6: note: Assuming that condition '!template_lengths' is not redundant kma-1.4.21/updateindex.c:194:32: note: Null pointer dereference DONE