2025-06-25 16:06
ftp://ftp.de.debian.org/debian/pool/main/w/wise/wise_2.4.1.orig.tar.gz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=gtk  --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 -j1
platform: Linux-6.8.0-62-generic-x86_64-with-glibc2.39
python: 3.12.3
client-version: 1.3.67
compiler: g++ (Ubuntu 14.2.0-4ubuntu2~24.04) 14.2.0
cppcheck: head 2.17.0
head-info: 129055d (2025-06-24 18:36:34 +0200)
count: 5105 5058
elapsed-time: 341.3 349.1
head-timing-info:

old-timing-info:

head results:
wise-2.4.1/src/HMMer2/aligneval.c:104:7: style: Condition '!make_alilist(calc1,calc2,&tlist1,&len1)' is always false [knownConditionTrueFalse]
wise-2.4.1/src/HMMer2/aligneval.c:104:21: note: Calling function 'make_alilist' returns 1
wise-2.4.1/src/HMMer2/aligneval.c:104:7: note: Condition '!make_alilist(calc1,calc2,&tlist1,&len1)' is always false
wise-2.4.1/src/HMMer2/aligneval.c:105:7: style: Condition '!make_alilist(calc2,calc1,&tlist2,&len2)' is always false [knownConditionTrueFalse]
wise-2.4.1/src/HMMer2/aligneval.c:105:21: note: Calling function 'make_alilist' returns 1
wise-2.4.1/src/HMMer2/aligneval.c:105:7: note: Condition '!make_alilist(calc2,calc1,&tlist2,&len2)' is always false
wise-2.4.1/src/HMMer2/aligneval.c:106:7: style: Condition '!make_alilist(known1,known2,&klist1,&len1)' is always false [knownConditionTrueFalse]
wise-2.4.1/src/HMMer2/aligneval.c:106:21: note: Calling function 'make_alilist' returns 1
wise-2.4.1/src/HMMer2/aligneval.c:106:7: note: Condition '!make_alilist(known1,known2,&klist1,&len1)' is always false
wise-2.4.1/src/HMMer2/aligneval.c:107:7: style: Condition '!make_alilist(known2,known1,&klist2,&len2)' is always false [knownConditionTrueFalse]
wise-2.4.1/src/HMMer2/aligneval.c:107:21: note: Calling function 'make_alilist' returns 1
wise-2.4.1/src/HMMer2/aligneval.c:107:7: note: Condition '!make_alilist(known2,known1,&klist2,&len2)' is always false
wise-2.4.1/src/HMMer2/aligneval.c:108:7: style: Condition '!compare_lists(klist1,klist2,tlist1,tlist2,len1,len2,&score)' is always false [knownConditionTrueFalse]
wise-2.4.1/src/HMMer2/aligneval.c:108:22: note: Calling function 'compare_lists' returns 1
wise-2.4.1/src/HMMer2/aligneval.c:108:7: note: Condition '!compare_lists(klist1,klist2,tlist1,tlist2,len1,len2,&score)' is always false
wise-2.4.1/src/HMMer2/aligneval.c:142:7: style: Condition '!make_ref_alilist(ref,known1,known2,calc1,calc2,&tlist1,&len1)' is always false [knownConditionTrueFalse]
wise-2.4.1/src/HMMer2/aligneval.c:142:25: note: Calling function 'make_ref_alilist' returns 1
wise-2.4.1/src/HMMer2/aligneval.c:142:7: note: Condition '!make_ref_alilist(ref,known1,known2,calc1,calc2,&tlist1,&len1)' is always false
wise-2.4.1/src/HMMer2/aligneval.c:143:7: style: Condition '!make_ref_alilist(ref,known2,known1,calc2,calc1,&tlist2,&len2)' is always false [knownConditionTrueFalse]
wise-2.4.1/src/HMMer2/aligneval.c:143:25: note: Calling function 'make_ref_alilist' returns 1
wise-2.4.1/src/HMMer2/aligneval.c:143:7: note: Condition '!make_ref_alilist(ref,known2,known1,calc2,calc1,&tlist2,&len2)' is always false
wise-2.4.1/src/HMMer2/aligneval.c:144:7: style: Condition '!make_ref_alilist(ref,known1,known2,known1,known2,&klist1,&len1)' is always false [knownConditionTrueFalse]
wise-2.4.1/src/HMMer2/aligneval.c:144:25: note: Calling function 'make_ref_alilist' returns 1
wise-2.4.1/src/HMMer2/aligneval.c:144:7: note: Condition '!make_ref_alilist(ref,known1,known2,known1,known2,&klist1,&len1)' is always false
wise-2.4.1/src/HMMer2/aligneval.c:145:7: style: Condition '!make_ref_alilist(ref,known2,known1,known2,known1,&klist2,&len2)' is always false [knownConditionTrueFalse]
wise-2.4.1/src/HMMer2/aligneval.c:145:25: note: Calling function 'make_ref_alilist' returns 1
wise-2.4.1/src/HMMer2/aligneval.c:145:7: note: Condition '!make_ref_alilist(ref,known2,known1,known2,known1,&klist2,&len2)' is always false
wise-2.4.1/src/HMMer2/aligneval.c:146:7: style: Condition '!compare_lists(klist1,klist2,tlist1,tlist2,len1,len2,&score)' is always false [knownConditionTrueFalse]
wise-2.4.1/src/HMMer2/aligneval.c:146:22: note: Calling function 'compare_lists' returns 1
wise-2.4.1/src/HMMer2/aligneval.c:146:7: note: Condition '!compare_lists(klist1,klist2,tlist1,tlist2,len1,len2,&score)' is always false
wise-2.4.1/src/HMMer2/aligneval.c:224:23: style:inconclusive: Function 'make_ref_alilist' argument 1 names different: declaration 'refcoords' definition 'ref'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/aligneval.c:65:34: note: Function 'make_ref_alilist' argument 1 names different: declaration 'refcoords' definition 'ref'.
wise-2.4.1/src/HMMer2/aligneval.c:224:23: note: Function 'make_ref_alilist' argument 1 names different: declaration 'refcoords' definition 'ref'.
wise-2.4.1/src/HMMer2/aligneval.c:170:20: style: Parameter 's1' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/aligneval.c:170:30: style: Parameter 's2' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/aligneval.c:224:34: style: Parameter 'k1' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/aligneval.c:225:10: style: Parameter 's1' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/aligneval.c:225:20: style: Parameter 's2' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/aligneval.c:295:20: style: Parameter 'k1' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/aligneval.c:295:29: style: Parameter 'k2' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/aligneval.c:295:38: style: Parameter 't1' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/aligneval.c:295:47: style: Parameter 't2' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/aligneval.c:401:24: style: Parameter 's1' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/aligneval.c:401:34: style: Parameter 's2' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/alignio.c:317:3: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/alignio.c:321:3: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/alignio.c:165:50: style: Parameter 'ainfo' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/alignio.c:202:25: style: Parameter 'aseq' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/alignio.c:202:47: style: Parameter 'ss' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/alignio.c:240:27: style: Parameter 'aseq' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/alignio.c:240:49: style: Parameter 'ss' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/alignio.c:299:29: style: Parameter 'name1' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/alignio.c:300:29: style: Parameter 'name2' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/alignio.c:143:18: warning: Uninitialized variable: aseq [uninitvar]
wise-2.4.1/src/HMMer2/alignio.c:118:17: note: Assuming condition is false
wise-2.4.1/src/HMMer2/alignio.c:143:18: note: Uninitialized variable: aseq
wise-2.4.1/src/HMMer2/alignio.c:520:7: style: Variable 'pex' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/HMMer2/alphabet.c:237:36: style:inconclusive: Boolean expression '!ainfo->sqinfo[idx].flags' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
wise-2.4.1/src/HMMer2/alphabet.c:237:36: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
wise-2.4.1/src/HMMer2/alphabet.c:259:37: style:inconclusive: Function 'P7CountSymbol' argument 2 names different: declaration 'sym' definition 'symidx'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/funcs.h:33:50: note: Function 'P7CountSymbol' argument 2 names different: declaration 'sym' definition 'symidx'.
wise-2.4.1/src/HMMer2/alphabet.c:259:37: note: Function 'P7CountSymbol' argument 2 names different: declaration 'sym' definition 'symidx'.
wise-2.4.1/src/HMMer2/alphabet.c:146:9: style: Variable 's' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/alphabet.c:170:24: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/alphabet.c:190:26: style: Parameter 'dsq' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/alphabet.c:385:34: style: Parameter 'syms' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/cluster.c:147:17: style:inconclusive: Function 'Cluster' argument 1 names different: declaration 'mx' definition 'dmx'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/sqfuncs.h:53:28: note: Function 'Cluster' argument 1 names different: declaration 'mx' definition 'dmx'.
wise-2.4.1/src/HMMer2/cluster.c:147:17: note: Function 'Cluster' argument 1 names different: declaration 'mx' definition 'dmx'.
wise-2.4.1/src/HMMer2/cluster.c:458:40: style: Parameter 'ainfo' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/cluster.c:521:29: style: Parameter 'ainfo' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/cluster.c:521:52: style: Parameter 'tree' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/core_algorithms.c:413:52: style:inconclusive: Function 'P7ViterbiTrace' argument 3 names different: declaration 'L' definition 'N'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/funcs.h:50:65: note: Function 'P7ViterbiTrace' argument 3 names different: declaration 'L' definition 'N'.
wise-2.4.1/src/HMMer2/core_algorithms.c:413:52: note: Function 'P7ViterbiTrace' argument 3 names different: declaration 'L' definition 'N'.
wise-2.4.1/src/HMMer2/core_algorithms.c:191:17: style: Parameter 'dsq' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/core_algorithms.c:413:43: style: Parameter 'dsq' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/core_algorithms.c:836:24: style: Parameter 'dsq' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/core_algorithms.c:1251:23: style: Parameter 'dsq' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/core_algorithms.c:1421:42: style: Parameter 'dsq' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/core_algorithms.c:958:12: warning: Uninitialized variable: cur [uninitvar]
wise-2.4.1/src/HMMer2/core_algorithms.c:883:17: note: Assuming condition is false
wise-2.4.1/src/HMMer2/core_algorithms.c:958:12: note: Uninitialized variable: cur
wise-2.4.1/src/HMMer2/core_algorithms.c:794:7: style: Variable 'tpos' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/HMMer2/dayhoff.c:115:20: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/dayhoff.c:122:20: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/dayhoff.c:143:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/dayhoff.c:156:11: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/dayhoff.c:133:10: warning: Either the condition '(pam=(int**)calloc(27,sizeof(int*)))==NULL' is redundant or there is possible null pointer dereference: pam. [nullPointerRedundantCheck]
wise-2.4.1/src/HMMer2/dayhoff.c:130:51: note: Assuming that condition '(pam=(int**)calloc(27,sizeof(int*)))==NULL' is not redundant
wise-2.4.1/src/HMMer2/dayhoff.c:133:10: note: Null pointer dereference
wise-2.4.1/src/HMMer2/debug.c:46:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/HMMer2/debug.c:73:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/HMMer2/debug.c:40:53: style:inconclusive: Function 'VerboseWorry' argument 4 names different: declaration 'fmt' definition 'format'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/funcs.h:63:65: note: Function 'VerboseWorry' argument 4 names different: declaration 'fmt' definition 'format'.
wise-2.4.1/src/HMMer2/debug.c:40:53: note: Function 'VerboseWorry' argument 4 names different: declaration 'fmt' definition 'format'.
wise-2.4.1/src/HMMer2/debug.c:40:31: style: Parameter 'file' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/debug.c:71:13: style: Parameter 'file' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/debug.c:113:73: style: Parameter 'dsq' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/debug.c:181:42: style: Parameter 'pri' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/debug.c:375:32: style: Parameter 't1' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/debug.c:375:54: style: Parameter 't2' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/file.c:154:7: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/file.c:161:11: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/file.c:50:19: style:inconclusive: Function 'FileDirname' argument 1 names different: declaration 'filename' definition 'file'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/sqfuncs.h:70:32: note: Function 'FileDirname' argument 1 names different: declaration 'filename' definition 'file'.
wise-2.4.1/src/HMMer2/file.c:50:19: note: Function 'FileDirname' argument 1 names different: declaration 'filename' definition 'file'.
wise-2.4.1/src/HMMer2/file.c:50:19: style: Parameter 'file' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/file.c:53:9: style: Variable 'lastslash' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/file.c:83:16: style: Parameter 'file' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/file.c:86:9: style: Variable 'lastslash' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/file.c:110:18: style: Parameter 'dir' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/file.c:110:29: style: Parameter 'file' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/file.c:144:19: style: Parameter 'fname' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/file.c:144:32: style: Parameter 'env' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/file.c:148:9: style: Variable 's' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/file.c:175:18: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/file.c:164:10: warning: Uninitialized variable: fp [uninitvar]
wise-2.4.1/src/HMMer2/file.c:155:12: note: Assuming condition is false
wise-2.4.1/src/HMMer2/file.c:164:10: note: Uninitialized variable: fp
wise-2.4.1/src/HMMer2/gnuregex.c:4579:26: debug: Function::addArguments found argument 's2' with varid 0. [varid0]
wise-2.4.1/src/HMMer2/gnuregex.c:4454:24: debug: Function::addArguments found argument 'end' with varid 0. [varid0]
wise-2.4.1/src/HMMer2/gnuregex.c:4491:25: debug: Function::addArguments found argument 'end' with varid 0. [varid0]
wise-2.4.1/src/HMMer2/gnuregex.c:4345:25: debug: Function::addArguments found argument 'end' with varid 0. [varid0]
wise-2.4.1/src/HMMer2/gnuregex.c:4352:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/HMMer2/gnuregex.c:4460:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/HMMer2/gnuregex.c:4520:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/HMMer2/gnuregex.c:4583:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable s2 [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/HMMer2/gnuregex.c:1154:26: error: Memory leak: compile_stack.stack [memleak]
wise-2.4.1/src/HMMer2/gnuregex.c:2581:11: error: Memory leak: fail_stack.stack [memleak]
wise-2.4.1/src/HMMer2/gnuregex.c:4824:9: error: Memory leak: regs.start [memleak]
wise-2.4.1/src/HMMer2/gnuregex.c:4824:9: error: Memory leak: regs.end [memleak]
wise-2.4.1/src/HMMer2/gnuregex.c:4064:13: style: Variable 'reg_dummy[this_reg]' is reassigned a value before the old one has been used. [redundantAssignment]
wise-2.4.1/src/HMMer2/gnuregex.c:4064:13: note: reg_dummy[this_reg] is assigned
wise-2.4.1/src/HMMer2/gnuregex.c:4064:13: note: reg_dummy[this_reg] is overwritten
wise-2.4.1/src/HMMer2/gnuregex.c:2147:34: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
wise-2.4.1/src/HMMer2/gnuregex.c:2150:32: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
wise-2.4.1/src/HMMer2/gnuregex.c:2217:40: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
wise-2.4.1/src/HMMer2/gnuregex.c:1176:15: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1191:16: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1284:17: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1309:13: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1323:17: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1333:11: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1345:6: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1351:13: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1359:13: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1595:19: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1625:19: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1669:21: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1685:15: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1713:15: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1800:22: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1819:22: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1913:15: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1919:15: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1924:15: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1928:15: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1932:15: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1936:15: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1940:15: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1944:15: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:1962:15: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:2010:8: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:2014:4: style: Variable 'old_buffer' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:2119:11: style: Parameter 'pattern' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/gnuregex.c:2119:21: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/gnuregex.c:2122:9: style: Variable 'prev' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:2138:15: style: Parameter 'pend' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/gnuregex.c:2141:9: style: Variable 'next' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:2143:9: style: Variable 'next_next' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:2188:20: style: Parameter 'pend' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/gnuregex.c:2874:18: style: Variable 'fastmap' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:2875:18: style: Variable 'translate' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:2916:23: style: Variable 'd' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:3161:16: style: Variable 'end2' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:3168:13: style: Variable 'dend' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:3773:26: style: Variable 'dend2' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:4060:28: style: Variable 'pdummy' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:4061:19: style: Variable 'sdummy' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:4581:12: style: Parameter 'translate' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/gnuregex.c:4583:27: style: Variable 'p1' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:4583:37: style: Variable 'p2' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:4866:9: style: Variable 'msg' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/gnuregex.c:4064:13: style: Variable 'sdummy' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/HMMer2/gnuregex.c:4064:13: style: Variable 'pdummy' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/HMMer2/gnuregex.c:3758:19: style: Unused variable: destination [unusedVariable]
wise-2.4.1/src/HMMer2/gnuregex.c:3905:11: style: Unused variable: destination [unusedVariable]
wise-2.4.1/src/HMMer2/gnuregex.c:3958:11: style: Unused variable: destination [unusedVariable]
wise-2.4.1/src/HMMer2/gnuregex.c:4097:11: style: Unused variable: destination [unusedVariable]
wise-2.4.1/src/HMMer2/gnuregex.c:4110:11: style: Unused variable: destination [unusedVariable]
wise-2.4.1/src/HMMer2/histogram.c:1018:29: warning: Invalid log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
wise-2.4.1/src/HMMer2/histogram.c:1012:14: note: Assignment 'p=0.0', assigned value is 0.0
wise-2.4.1/src/HMMer2/histogram.c:1017:18: note: Assuming condition is false
wise-2.4.1/src/HMMer2/histogram.c:1018:29: note: Invalid argument
wise-2.4.1/src/HMMer2/histogram.c:648:11: style: The if condition is the same as the previous if condition [duplicateCondition]
wise-2.4.1/src/HMMer2/histogram.c:634:11: note: First condition
wise-2.4.1/src/HMMer2/histogram.c:648:11: note: Second condition
wise-2.4.1/src/HMMer2/histogram.c:708:11: style:inconclusive: Function 'ExtremeValueSetHistogram' argument 4 names different: declaration 'low' definition 'lowbound'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/funcs.h:99:16: note: Function 'ExtremeValueSetHistogram' argument 4 names different: declaration 'low' definition 'lowbound'.
wise-2.4.1/src/HMMer2/histogram.c:708:11: note: Function 'ExtremeValueSetHistogram' argument 4 names different: declaration 'low' definition 'lowbound'.
wise-2.4.1/src/HMMer2/histogram.c:708:27: style:inconclusive: Function 'ExtremeValueSetHistogram' argument 5 names different: declaration 'high' definition 'highbound'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/funcs.h:99:27: note: Function 'ExtremeValueSetHistogram' argument 5 names different: declaration 'high' definition 'highbound'.
wise-2.4.1/src/HMMer2/histogram.c:708:27: note: Function 'ExtremeValueSetHistogram' argument 5 names different: declaration 'high' definition 'highbound'.
wise-2.4.1/src/HMMer2/histogram.c:1164:32: style:inconclusive: Function 'EVDMaxLikelyFit' argument 2 names different: declaration 'y' definition 'c'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/funcs.h:108:46: note: Function 'EVDMaxLikelyFit' argument 2 names different: declaration 'y' definition 'c'.
wise-2.4.1/src/HMMer2/histogram.c:1164:32: note: Function 'EVDMaxLikelyFit' argument 2 names different: declaration 'y' definition 'c'.
wise-2.4.1/src/HMMer2/histogram.c:364:50: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/histogram.c:1045:19: style: Parameter 'x' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/histogram.c:1045:27: style: Parameter 'y' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/histogram.c:1102:19: style: Parameter 'x' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/histogram.c:1102:27: style: Parameter 'y' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/histogram.c:222:15: warning: Uninitialized variable: lowbound [uninitvar]
wise-2.4.1/src/HMMer2/histogram.c:211:36: note: Assuming condition is false
wise-2.4.1/src/HMMer2/histogram.c:222:15: note: Uninitialized variable: lowbound
wise-2.4.1/src/HMMer2/histogram.c:1251:25: warning: Uninitialized variable: total [uninitvar]
wise-2.4.1/src/HMMer2/histogram.c:1245:17: note: Assuming condition is false
wise-2.4.1/src/HMMer2/histogram.c:1251:25: note: Uninitialized variable: total
wise-2.4.1/src/HMMer2/histogram.c:1249:7: error: Uninitialized variable: total [legacyUninitvar]
wise-2.4.1/src/HMMer2/hmmalign.c:101:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/HMMer2/hmmbuild.c:241:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/HMMer2/hmmbuild.c:553:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/HMMer2/hmmbuild.c:718:29: style:inconclusive: Function 'position_average_score' argument 2 names different: declaration 'seq' definition 'dsq'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/hmmbuild.c:122:64: note: Function 'position_average_score' argument 2 names different: declaration 'seq' definition 'dsq'.
wise-2.4.1/src/HMMer2/hmmbuild.c:718:29: note: Function 'position_average_score' argument 2 names different: declaration 'seq' definition 'dsq'.
wise-2.4.1/src/HMMer2/hmmbuild.c:615:11: style: Parameter 'ainfo' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/hmmbuild.c:655:48: style: Parameter 'hmm' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/hmmbuild.c:719:29: style: Parameter 'wgt' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/hmmbuild.c:799:25: style: Parameter 'pernode' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/hmmbuild.c:744:6: style: Variable 'pos' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/HMMer2/hmmcalibrate.c:130:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/HMMer2/hmmcalibrate.c:76:12: style: Variable 'mode' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/hmmconvert.c:108:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/HMMer2/hmmconvert.c:70:12: style: Variable 'mode' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/hmmemit.c:103:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/HMMer2/hmmio.c:582:11: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:588:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:593:11: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:595:11: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:602:6: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:606:8: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:612:11: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:614:11: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:634:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:636:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:637:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:645:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:648:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:653:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:657:11: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:663:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:666:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:669:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:671:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1264:10: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1268:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1457:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1462:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1486:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1490:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1511:24: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1512:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1523:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1533:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1537:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1541:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1547:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1560:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1564:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1568:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1574:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1587:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1591:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:1595:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/hmmio.c:922:43: style: Condition 'k==hmm->M' is always false [knownConditionTrueFalse]
wise-2.4.1/src/HMMer2/hmmio.c:922:13: note: Assuming that condition 'k<hmm->M' is not redundant
wise-2.4.1/src/HMMer2/hmmio.c:922:43: note: Condition 'k==hmm->M' is always false
wise-2.4.1/src/HMMer2/hmmio.c:929:43: style: Condition 'k==hmm->M' is always false [knownConditionTrueFalse]
wise-2.4.1/src/HMMer2/hmmio.c:929:13: note: Assuming that condition 'k<hmm->M' is not redundant
wise-2.4.1/src/HMMer2/hmmio.c:929:43: note: Condition 'k==hmm->M' is always false
wise-2.4.1/src/HMMer2/hmmio.c:477:12: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:480:10: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:481:10: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:485:12: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:486:12: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:491:10: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:492:10: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:493:10: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:498:12: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:500:12: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:502:12: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:749:18: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:752:15: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:753:15: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:757:17: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:758:17: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:761:16: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:762:16: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:768:16: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:769:16: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:770:16: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:774:18: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:776:18: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:778:18: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:784:16: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:785:14: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:786:14: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:791:13: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:794:15: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:795:11: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:796:11: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:798:13: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1366:19: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1369:20: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1377:19: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1378:19: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1379:19: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1380:19: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1383:18: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1384:18: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1385:18: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1387:20: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1395:19: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1396:19: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1397:19: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1399:18: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1400:18: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1401:18: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1409:19: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1410:19: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1411:19: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1412:19: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1415:18: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1416:18: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1417:18: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:1419:20: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
wise-2.4.1/src/HMMer2/hmmio.c:181:47: style:inconclusive: Function 'HMMFileOpenFseek' argument 3 names different: declaration 'pos' definition 'byte_pos'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/funcs.h:121:63: note: Function 'HMMFileOpenFseek' argument 3 names different: declaration 'pos' definition 'byte_pos'.
wise-2.4.1/src/HMMer2/hmmio.c:181:47: note: Function 'HMMFileOpenFseek' argument 3 names different: declaration 'pos' definition 'byte_pos'.
wise-2.4.1/src/HMMer2/hmmio.c:434:50: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
wise-2.4.1/src/HMMer2/hmmio.c:439:50: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
wise-2.4.1/src/HMMer2/hmmio.c:1050:24: style: Parameter 'hmmfp' can be declared as pointer to const. However it seems that 'read_asc11hmm' is a callback function, if 'hmmfp' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise-2.4.1/src/HMMer2/hmmio.c:307:21: note: You might need to cast the function pointer here
wise-2.4.1/src/HMMer2/hmmio.c:1050:24: note: Parameter 'hmmfp' can be declared as pointer to const
wise-2.4.1/src/HMMer2/hmmio.c:1082:24: style: Parameter 'hmmfp' can be declared as pointer to const. However it seems that 'read_asc10hmm' is a callback function, if 'hmmfp' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise-2.4.1/src/HMMer2/hmmio.c:310:21: note: You might need to cast the function pointer here
wise-2.4.1/src/HMMer2/hmmio.c:1082:24: note: Parameter 'hmmfp' can be declared as pointer to const
wise-2.4.1/src/HMMer2/hmmio.c:1140:18: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/hmmio.c:1188:34: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/hmmio.c:1257:27: style: Parameter 'pfx' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/hmmio.c:1260:9: style: Variable 'sptr' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/hmmio.c:1450:9: style: Variable 'statetype' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/hmmio.c:1451:9: style: Variable 's' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/hmmpfam.c:142:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FLT_MAX [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/HMMer2/hmmpfam.c:229:32: warning: Either the condition 'hmm==NULL' is redundant or there is possible null pointer dereference: hmm. [nullPointerRedundantCheck]
wise-2.4.1/src/HMMer2/hmmpfam.c:223:10: note: Assuming that condition 'hmm==NULL' is not redundant
wise-2.4.1/src/HMMer2/hmmpfam.c:229:32: note: Null pointer dereference
wise-2.4.1/src/HMMer2/hmmsearch.c:137:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FLT_MAX [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/HMMer2/hmmsearch.c:198:61: warning: Either the condition 'hmm==NULL' is redundant or there is possible null pointer dereference: hmm. [nullPointerRedundantCheck]
wise-2.4.1/src/HMMer2/hmmsearch.c:189:11: note: Assuming that condition 'hmm==NULL' is not redundant
wise-2.4.1/src/HMMer2/hmmsearch.c:198:61: note: Null pointer dereference
wise-2.4.1/src/HMMer2/hmmsearch.c:256:36: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
wise-2.4.1/src/HMMer2/hmmsearch.c:500:33: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
wise-2.4.1/src/HMMer2/interleaved.c:216:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/interleaved.c:220:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/interleaved.c:223:67: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/interleaved.c:224:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/interleaved.c:338:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/interleaved.c:340:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/interleaved.c:165:82: error: Invalid strncmp() argument nr 3. A non-boolean value is required. [invalidFunctionArgBool]
wise-2.4.1/src/HMMer2/interleaved.c:240:82: error: Invalid strncmp() argument nr 3. A non-boolean value is required. [invalidFunctionArgBool]
wise-2.4.1/src/HMMer2/interleaved.c:296:30: error: Resource leak: fp [resourceLeak]
wise-2.4.1/src/HMMer2/interleaved.c:454:26: style:inconclusive: Function 'ReadAlignment' argument 4 names different: declaration 'ainfo' definition 'ret_ainfo'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/sqfuncs.h:92:79: note: Function 'ReadAlignment' argument 4 names different: declaration 'ainfo' definition 'ret_ainfo'.
wise-2.4.1/src/HMMer2/interleaved.c:454:26: note: Function 'ReadAlignment' argument 4 names different: declaration 'ainfo' definition 'ret_ainfo'.
wise-2.4.1/src/HMMer2/interleaved.c:385:77: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
wise-2.4.1/src/HMMer2/interleaved.c:94:14: style: Variable 's2' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/interleaved.c:160:35: style: Parameter 'expected_name' can be declared as pointer to const. However it seems that 'dataline_clustal' is a callback function, if 'expected_name' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise-2.4.1/src/HMMer2/interleaved.c:468:65: note: You might need to cast the function pointer here
wise-2.4.1/src/HMMer2/interleaved.c:160:35: note: Parameter 'expected_name' can be declared as pointer to const
wise-2.4.1/src/HMMer2/interleaved.c:235:31: style: Parameter 'expected_name' can be declared as pointer to const. However it seems that 'dataline_MSF' is a callback function, if 'expected_name' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise-2.4.1/src/HMMer2/interleaved.c:458:57: note: You might need to cast the function pointer here
wise-2.4.1/src/HMMer2/interleaved.c:235:31: note: Parameter 'expected_name' can be declared as pointer to const
wise-2.4.1/src/HMMer2/masks.c:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
wise-2.4.1/src/HMMer2/masks.c:97:9: style: Condition 's0>0' is always true [knownConditionTrueFalse]
wise-2.4.1/src/HMMer2/masks.c:79:18: note: Assignment 'pcut=0.01', assigned value is 0.01
wise-2.4.1/src/HMMer2/masks.c:86:11: note: Assuming condition is false
wise-2.4.1/src/HMMer2/masks.c:96:35: note: Assignment 's0=-log(pcut*H/(noff*K))/lambda', assigned value is 13.8253295521
wise-2.4.1/src/HMMer2/masks.c:97:9: note: Condition 's0>0' is always true
wise-2.4.1/src/HMMer2/masks.c:156:71: style: Parameter 'dsq' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/mathsupport.c:109:17: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
wise-2.4.1/src/HMMer2/mathsupport.c:111:17: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
wise-2.4.1/src/HMMer2/mathsupport.c:141:6: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
wise-2.4.1/src/HMMer2/mathsupport.c:85:24: style: Parameter 'hmm' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/mathsupport.c:195:18: style: Parameter 'cvec' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/mathsupport.c:195:38: style: Parameter 'alpha' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/mathsupport.c:235:24: style: Parameter 'alpha' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/mathsupport.c:328:29: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/mathsupport.c:328:46: style: Parameter 'alpha' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/misc.c:62:28: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/misc.c:68:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/misc.c:37:24: style: Parameter 'banner' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/modelmakers.c:315:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FLT_MAX [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/HMMer2/modelmakers.c:520:25: style: Array index 'apos' is used before limits check. [arrayIndexThenCheck]
wise-2.4.1/src/HMMer2/modelmakers.c:730:40: style:inconclusive: Function 'trace_doctor' argument 2 names different: declaration 'M' definition 'mlen'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/modelmakers.c:56:52: note: Function 'trace_doctor' argument 2 names different: declaration 'M' definition 'mlen'.
wise-2.4.1/src/HMMer2/modelmakers.c:730:40: note: Function 'trace_doctor' argument 2 names different: declaration 'M' definition 'mlen'.
wise-2.4.1/src/HMMer2/modelmakers.c:220:10: style: Parameter 'null' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/modelmakers.c:427:40: style: Parameter 'insopt' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/modelmakers.c:428:18: style: Parameter 'wgt' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/modelmakers.c:468:44: style: Parameter 'wgt' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/modelmakers.c:582:55: style: Parameter 'matassign' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/modelmakers.c:824:42: style: Parameter 'matassign' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/modelmakers.c:850:22: style: Parameter 'matassign' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/modelmakers.c:362:11: warning: Uninitialized variable: j [uninitvar]
wise-2.4.1/src/HMMer2/modelmakers.c:304:22: note: Assuming condition is false
wise-2.4.1/src/HMMer2/modelmakers.c:362:11: note: Uninitialized variable: j
wise-2.4.1/src/HMMer2/modelmakers.c:377:12: warning: Uninitialized variable: first [uninitvar]
wise-2.4.1/src/HMMer2/modelmakers.c:359:17: note: Assuming condition is false
wise-2.4.1/src/HMMer2/modelmakers.c:377:12: note: Uninitialized variable: first
wise-2.4.1/src/HMMer2/modelmakers.c:273:9: style: Variable 't_me' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/HMMer2/msf.c:41:11: style: Parameter 'ainfo' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/plan7.c:344:46: style: Parameter 'null' can be declared as const array [constParameter]
wise-2.4.1/src/HMMer2/plan7.c:787:42: style: Parameter 'aacode' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/plan7.c:793:10: style: Variable 'tripnull' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/plan7.c:918:30: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/plan7.c:918:40: style: Parameter 'null' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/plan7.c:816:34: error: Uninitialized variable: tripnull [uninitvar]
wise-2.4.1/src/HMMer2/plan9.c:117:13: style: The if condition is the same as the previous if condition [duplicateCondition]
wise-2.4.1/src/HMMer2/plan9.c:115:13: note: First condition
wise-2.4.1/src/HMMer2/plan9.c:117:13: note: Second condition
wise-2.4.1/src/HMMer2/prior.c:203:54: style:inconclusive: Function 'PAMPrior' argument 3 names different: declaration 'pamwgt' definition 'wt'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/funcs.h:219:66: note: Function 'PAMPrior' argument 3 names different: declaration 'pamwgt' definition 'wt'.
wise-2.4.1/src/HMMer2/prior.c:203:54: note: Function 'PAMPrior' argument 3 names different: declaration 'pamwgt' definition 'wt'.
wise-2.4.1/src/HMMer2/prior.c:379:56: style: Parameter 'pri' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/prior.c:380:25: style: Parameter 'eq' can be declared as const array [constParameter]
wise-2.4.1/src/HMMer2/prior.c:510:16: style: Variable 'defmq' can be declared as const array [constVariable]
wise-2.4.1/src/HMMer2/revcomp.c:46:31: style: Array index 'idx' is used before limits check. [arrayIndexThenCheck]
wise-2.4.1/src/HMMer2/revcomp.c:31:9: style: Variable 'bckp' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/selex.c:111:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/selex.c:148:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/selex.c:175:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/selex.c:195:22: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/selex.c:253:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/selex.c:256:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/selex.c:266:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/selex.c:271:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/selex.c:277:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/selex.c:282:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/selex.c:287:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/selex.c:291:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/selex.c:295:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/selex.c:300:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/selex.c:366:20: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/selex.c:379:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/selex.c:728:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/selex.c:732:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/selex.c:763:31: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/selex.c:64:52: style:inconclusive: Function 'ReadSELEX' argument 3 names different: declaration 'ret_aliinfo' definition 'ainfo'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/sqfuncs.h:106:64: note: Function 'ReadSELEX' argument 3 names different: declaration 'ret_aliinfo' definition 'ainfo'.
wise-2.4.1/src/HMMer2/selex.c:64:52: note: Function 'ReadSELEX' argument 3 names different: declaration 'ret_aliinfo' definition 'ainfo'.
wise-2.4.1/src/HMMer2/selex.c:609:14: style: Variable 's2' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/selex.c:701:21: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/selex.c:215:38: warning: Uninitialized variable: num [uninitvar]
wise-2.4.1/src/HMMer2/selex.c:116:10: note: Assuming condition is false
wise-2.4.1/src/HMMer2/selex.c:215:38: note: Uninitialized variable: num
wise-2.4.1/src/HMMer2/sqerror.c:39:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/HMMer2/sqerror.c:64:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/HMMer2/sqio.c:777:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/HMMer2/sqio.c:649:48: style:inconclusive: Boolean expression '*V->sbuffer!='\0'' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
wise-2.4.1/src/HMMer2/sqio.c:333:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:344:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:385:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:411:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:443:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:455:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:461:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:553:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:555:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:592:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:602:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:607:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:641:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:644:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:667:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:686:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:697:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:699:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:701:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:703:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:705:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:710:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/HMMer2/sqio.c:391:49: style: Redundant condition: The condition '*V->sbuffer != '\0'' is redundant since '*V->sbuffer == ';'' is sufficient. [redundantCondition]
wise-2.4.1/src/HMMer2/sqio.c:537:46: style: Redundant condition: The condition '*V->sbuffer != 0' is redundant since '*V->sbuffer == '>'' is sufficient. [redundantCondition]
wise-2.4.1/src/HMMer2/sqio.c:562:46: style: Redundant condition: The condition '*V->sbuffer != 0' is redundant since '*V->sbuffer == '>'' is sufficient. [redundantCondition]
wise-2.4.1/src/HMMer2/sqio.c:1033:11: style: Condition 'sp==NULL' is always false [knownConditionTrueFalse]
wise-2.4.1/src/HMMer2/sqio.c:1664:20: style: Condition 'cmp>0' is always true [knownConditionTrueFalse]
wise-2.4.1/src/HMMer2/sqio.c:1661:20: note: Assuming that condition 'cmp==0' is not redundant
wise-2.4.1/src/HMMer2/sqio.c:1664:20: note: Condition 'cmp>0' is always true
wise-2.4.1/src/HMMer2/sqio.c:896:17: style:inconclusive: Function 'ReadSeq' argument 1 names different: declaration 'fp' definition 'V'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/sqfuncs.h:142:30: note: Function 'ReadSeq' argument 1 names different: declaration 'fp' definition 'V'.
wise-2.4.1/src/HMMer2/sqio.c:896:17: note: Function 'ReadSeq' argument 1 names different: declaration 'fp' definition 'V'.
wise-2.4.1/src/HMMer2/sqio.c:1259:26: style:inconclusive: Function 'WriteSeq' argument 2 names different: declaration 'outfmt' definition 'outform'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/sqfuncs.h:147:39: note: Function 'WriteSeq' argument 2 names different: declaration 'outfmt' definition 'outform'.
wise-2.4.1/src/HMMer2/sqio.c:1259:26: note: Function 'WriteSeq' argument 2 names different: declaration 'outfmt' definition 'outform'.
wise-2.4.1/src/HMMer2/sqio.c:1641:45: style:inconclusive: Function 'GSIGetOffset' argument 3 names different: declaration 'sqfile' definition 'ret_seqfile'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/sqfuncs.h:151:58: note: Function 'GSIGetOffset' argument 3 names different: declaration 'sqfile' definition 'ret_seqfile'.
wise-2.4.1/src/HMMer2/sqio.c:1641:45: note: Function 'GSIGetOffset' argument 3 names different: declaration 'sqfile' definition 'ret_seqfile'.
wise-2.4.1/src/HMMer2/sqio.c:1642:12: style:inconclusive: Function 'GSIGetOffset' argument 4 names different: declaration 'fmt' definition 'ret_format'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/sqfuncs.h:152:11: note: Function 'GSIGetOffset' argument 4 names different: declaration 'fmt' definition 'ret_format'.
wise-2.4.1/src/HMMer2/sqio.c:1642:12: note: Function 'GSIGetOffset' argument 4 names different: declaration 'fmt' definition 'ret_format'.
wise-2.4.1/src/HMMer2/sqio.c:267:16: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sqio.c:314:14: style: Parameter 's' can be declared as pointer to const. However it seems that 'endPIR' is a callback function, if 's' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise-2.4.1/src/HMMer2/sqio.c:350:15: note: You might need to cast the function pointer here
wise-2.4.1/src/HMMer2/sqio.c:314:14: note: Parameter 's' can be declared as pointer to const
wise-2.4.1/src/HMMer2/sqio.c:368:13: style: Parameter 's' can be declared as pointer to const. However it seems that 'endIG' is a callback function, if 's' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise-2.4.1/src/HMMer2/sqio.c:388:19: note: You might need to cast the function pointer here
wise-2.4.1/src/HMMer2/sqio.c:368:13: note: Parameter 's' can be declared as pointer to const
wise-2.4.1/src/HMMer2/sqio.c:493:18: style: Parameter 's' can be declared as pointer to const. However it seems that 'endGCGdata' is a callback function, if 's' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise-2.4.1/src/HMMer2/sqio.c:535:20: note: You might need to cast the function pointer here
wise-2.4.1/src/HMMer2/sqio.c:493:18: note: Parameter 's' can be declared as pointer to const
wise-2.4.1/src/HMMer2/sqio.c:542:18: style: Parameter 's' can be declared as pointer to const. However it seems that 'endPearson' is a callback function, if 's' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise-2.4.1/src/HMMer2/sqio.c:560:15: note: You might need to cast the function pointer here
wise-2.4.1/src/HMMer2/sqio.c:542:18: note: Parameter 's' can be declared as pointer to const
wise-2.4.1/src/HMMer2/sqio.c:568:15: style: Parameter 's' can be declared as pointer to const. However it seems that 'endEMBL' is a callback function, if 's' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise-2.4.1/src/HMMer2/sqio.c:612:15: note: You might need to cast the function pointer here
wise-2.4.1/src/HMMer2/sqio.c:568:15: note: Parameter 's' can be declared as pointer to const
wise-2.4.1/src/HMMer2/sqio.c:628:16: style: Parameter 's' can be declared as pointer to const. However it seems that 'endZuker' is a callback function, if 's' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise-2.4.1/src/HMMer2/sqio.c:647:15: note: You might need to cast the function pointer here
wise-2.4.1/src/HMMer2/sqio.c:628:16: note: Parameter 's' can be declared as pointer to const
wise-2.4.1/src/HMMer2/sqio.c:1166:19: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sqio.c:1566:15: style: Parameter 'gsifile' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sqio.c:1641:34: style: Parameter 'key' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sqio.c:1428:11: style: Variable 's[l]' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/HMMer2/sqio.c:1429:11: style: Variable 'ss[l]' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/HMMer2/sre_math.c:635:13: warning: Invalid log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
wise-2.4.1/src/HMMer2/sre_math.c:631:10: note: Assignment 'sum=0.0', assigned value is 0.0
wise-2.4.1/src/HMMer2/sre_math.c:632:17: note: Assuming condition is false
wise-2.4.1/src/HMMer2/sre_math.c:635:13: note: Invalid argument
wise-2.4.1/src/HMMer2/sre_math.c:651:13: warning: Invalid log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
wise-2.4.1/src/HMMer2/sre_math.c:647:10: note: Assignment 'sum=0.0', assigned value is 0.0
wise-2.4.1/src/HMMer2/sre_math.c:648:17: note: Assuming condition is false
wise-2.4.1/src/HMMer2/sre_math.c:651:13: note: Invalid argument
wise-2.4.1/src/HMMer2/sre_math.c:246:14: style:inconclusive: Function 'Gammln' argument 1 names different: declaration 'xx' definition 'x'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/sqfuncs.h:168:28: note: Function 'Gammln' argument 1 names different: declaration 'xx' definition 'x'.
wise-2.4.1/src/HMMer2/sre_math.c:246:14: note: Function 'Gammln' argument 1 names different: declaration 'xx' definition 'x'.
wise-2.4.1/src/HMMer2/sre_math.c:585:24: style:inconclusive: Function 'DChoose' argument 2 names different: declaration 'n' definition 'N'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/sqfuncs.h:192:38: note: Function 'DChoose' argument 2 names different: declaration 'n' definition 'N'.
wise-2.4.1/src/HMMer2/sre_math.c:585:24: note: Function 'DChoose' argument 2 names different: declaration 'n' definition 'N'.
wise-2.4.1/src/HMMer2/sre_math.c:601:23: style:inconclusive: Function 'FChoose' argument 2 names different: declaration 'n' definition 'N'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/sqfuncs.h:193:37: note: Function 'FChoose' argument 2 names different: declaration 'n' definition 'N'.
wise-2.4.1/src/HMMer2/sre_math.c:601:23: note: Function 'FChoose' argument 2 names different: declaration 'n' definition 'N'.
wise-2.4.1/src/HMMer2/sre_math.c:164:16: style: Parameter 'x' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:164:26: style: Parameter 'y' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:207:24: style: Parameter 'x' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:207:34: style: Parameter 'y' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:207:44: style: Parameter 'var' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:251:17: style: Variable 'cof' can be declared as const array [constVariable]
wise-2.4.1/src/HMMer2/sre_math.c:356:14: style: Parameter 'vec' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:365:13: style: Parameter 'vec' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:375:28: style: Parameter 'vec2' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:382:26: style: Parameter 'vec2' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:390:29: style: Parameter 'vec2' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:397:27: style: Parameter 'vec2' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:405:14: style: Parameter 'vec1' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:405:28: style: Parameter 'vec2' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:415:13: style: Parameter 'vec1' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:415:26: style: Parameter 'vec2' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:431:14: style: Parameter 'vec' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:441:13: style: Parameter 'vec' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:585:17: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:601:16: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:623:17: style: Parameter 'logp' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_math.c:639:16: style: Parameter 'logp' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_string.c:40:14: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_string.c:176:16: style: Parameter 'rexp' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_string.c:176:28: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_string.c:254:28: style: Parameter 's2' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_string.c:282:28: style: Parameter 's2' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_string.c:312:36: style: Parameter 's2' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/sre_string.c:351:22: style: Parameter 'alphabet' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/stack.c:43:3: warning: Either the condition '(stack=(struct intstack_s*)malloc(sizeof(struct intstack_s)))==NULL' is redundant or there is possible null pointer dereference: stack. [nullPointerRedundantCheck]
wise-2.4.1/src/HMMer2/stack.c:41:74: note: Assuming that condition '(stack=(struct intstack_s*)malloc(sizeof(struct intstack_s)))==NULL' is not redundant
wise-2.4.1/src/HMMer2/stack.c:43:3: note: Null pointer dereference
wise-2.4.1/src/HMMer2/stack.c:53:3: warning: Either the condition '(new=(struct intstack_s*)malloc(sizeof(struct intstack_s)))==NULL' is redundant or there is possible null pointer dereference: new. [nullPointerRedundantCheck]
wise-2.4.1/src/HMMer2/stack.c:51:72: note: Assuming that condition '(new=(struct intstack_s*)malloc(sizeof(struct intstack_s)))==NULL' is not redundant
wise-2.4.1/src/HMMer2/stack.c:53:3: note: Null pointer dereference
wise-2.4.1/src/HMMer2/stack.c:55:3: warning: Either the condition '(new=(struct intstack_s*)malloc(sizeof(struct intstack_s)))==NULL' is redundant or there is possible null pointer dereference: new. [nullPointerRedundantCheck]
wise-2.4.1/src/HMMer2/stack.c:51:72: note: Assuming that condition '(new=(struct intstack_s*)malloc(sizeof(struct intstack_s)))==NULL' is not redundant
wise-2.4.1/src/HMMer2/stack.c:55:3: note: Null pointer dereference
wise-2.4.1/src/HMMer2/tophits.c:171:40: style:inconclusive: Function 'RegisterHit' argument 2 names different: declaration 'sortkey' definition 'key'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/funcs.h:238:54: note: Function 'RegisterHit' argument 2 names different: declaration 'sortkey' definition 'key'.
wise-2.4.1/src/HMMer2/tophits.c:171:40: note: Function 'RegisterHit' argument 2 names different: declaration 'sortkey' definition 'key'.
wise-2.4.1/src/HMMer2/tophits.c:246:33: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/tophits.c:272:17: style: Variable 'h1' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/tophits.c:273:17: style: Variable 'h2' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/HMMer2/trace.c:767:30: style: Array index 'i' is used before limits check. [arrayIndexThenCheck]
wise-2.4.1/src/HMMer2/trace.c:767:24: warning: Either the condition 'ali->aseq!=NULL' is redundant or there is possible null pointer dereference: ali->aseq. [nullPointerRedundantCheck]
wise-2.4.1/src/HMMer2/trace.c:786:23: note: Assuming that condition 'ali->aseq!=NULL' is not redundant
wise-2.4.1/src/HMMer2/trace.c:767:24: note: Null pointer dereference
wise-2.4.1/src/HMMer2/trace.c:343:74: style:inconclusive: Function 'P7Traces2Alignment' argument 5 names different: declaration 'M' definition 'mlen'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/funcs.h:269:87: note: Function 'P7Traces2Alignment' argument 5 names different: declaration 'M' definition 'mlen'.
wise-2.4.1/src/HMMer2/trace.c:343:74: note: Function 'P7Traces2Alignment' argument 5 names different: declaration 'M' definition 'mlen'.
wise-2.4.1/src/HMMer2/trace.c:156:41: style: Parameter 'dsq' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/trace.c:282:41: style: Parameter 'dsq' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/trace.c:343:55: style: Parameter 'wgt' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/trace.c:613:15: style: Parameter 'dsq' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/trace.c:754:44: style: Parameter 'ali' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/trace.c:892:37: style: Parameter 'tr' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/types.c:74:14: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/HMMer2/weight.c:174:7: style: Condition '!simple_diffmx(aseq,ainfo->nseq,&dmx)' is always false [knownConditionTrueFalse]
wise-2.4.1/src/HMMer2/weight.c:174:22: note: Calling function 'simple_diffmx' returns 1
wise-2.4.1/src/HMMer2/weight.c:174:7: note: Condition '!simple_diffmx(aseq,ainfo->nseq,&dmx)' is always false
wise-2.4.1/src/HMMer2/weight.c:288:39: style: Variable 'min' is assigned an expression that holds the same value. [redundantAssignment]
wise-2.4.1/src/HMMer2/weight.c:284:18: note: Assuming that condition 'dist==min' is not redundant
wise-2.4.1/src/HMMer2/weight.c:288:39: note: Variable 'min' is assigned an expression that holds the same value.
wise-2.4.1/src/HMMer2/weight.c:382:22: style:inconclusive: Function 'BlosumWeights' argument 1 names different: declaration 'aseq' definition 'aseqs'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/sqfuncs.h:244:34: note: Function 'BlosumWeights' argument 1 names different: declaration 'aseq' definition 'aseqs'.
wise-2.4.1/src/HMMer2/weight.c:382:22: note: Function 'BlosumWeights' argument 1 names different: declaration 'aseq' definition 'aseqs'.
wise-2.4.1/src/HMMer2/weight.c:382:49: style:inconclusive: Function 'BlosumWeights' argument 3 names different: declaration 'blosumlevel' definition 'maxid'. [funcArgNamesDifferent]
wise-2.4.1/src/HMMer2/sqfuncs.h:244:60: note: Function 'BlosumWeights' argument 3 names different: declaration 'blosumlevel' definition 'maxid'.
wise-2.4.1/src/HMMer2/weight.c:382:49: note: Function 'BlosumWeights' argument 3 names different: declaration 'blosumlevel' definition 'maxid'.
wise-2.4.1/src/api/examples/revcomp.c:10:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/api/examples/sw.c:14:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
commandline.dy:314:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
commandline.dy:75:67: style: Parameter 'tag' can be declared as pointer to const [constParameterPointer]
commandline.dy:310:10: style: Variable 'temp' can be declared as pointer to const [constVariablePointer]
commandline.dy:135:12: style: Variable 'arg' is assigned a value that is never used. [unreadVariable]
linesubs.dy:36:10: style: Variable 'run2' can be declared as pointer to const [constVariablePointer]
linesubs.dy:84:37: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/base/wiseconfig.c:151:7: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/base/wiseconfig.c:165:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/base/wiseconfig.c:207:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/base/wiseconfig.c:213:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/base/wiseconfig.c:250:10: warning: If memory allocation fails, then there is a possible null pointer dereference: runner [nullPointerOutOfMemory]
wise-2.4.1/src/base/wiseconfig.c:246:26: note: Assuming allocation function fails
wise-2.4.1/src/base/wiseconfig.c:246:10: note: Assignment 'runner=(char*)malloc(sizeof(char)*(strlen(base)+strlen(string)+1))', assigned value is 0
wise-2.4.1/src/base/wiseconfig.c:250:10: note: Null pointer dereference
wise-2.4.1/src/base/wiseconfig.c:251:10: warning: If memory allocation fails, then there is a possible null pointer dereference: runner [nullPointerOutOfMemory]
wise-2.4.1/src/base/wiseconfig.c:246:26: note: Assuming allocation function fails
wise-2.4.1/src/base/wiseconfig.c:246:10: note: Assignment 'runner=(char*)malloc(sizeof(char)*(strlen(base)+strlen(string)+1))', assigned value is 0
wise-2.4.1/src/base/wiseconfig.c:251:10: note: Null pointer dereference
wise-2.4.1/src/base/wiseconfig.c:258:10: warning: If memory allocation fails, then there is a possible null pointer dereference: runner [nullPointerOutOfMemory]
wise-2.4.1/src/base/wiseconfig.c:255:26: note: Assuming allocation function fails
wise-2.4.1/src/base/wiseconfig.c:255:10: note: Assignment 'runner=(char*)malloc(sizeof(char)*(strlen(string)+1))', assigned value is 0
wise-2.4.1/src/base/wiseconfig.c:258:10: note: Null pointer dereference
wise-2.4.1/src/base/wiseconfig.c:260:27: warning: If memory allocation fails, then there is a possible null pointer dereference: runner [nullPointerOutOfMemory]
wise-2.4.1/src/base/wiseconfig.c:246:26: note: Assuming allocation function fails
wise-2.4.1/src/base/wiseconfig.c:246:10: note: Assignment 'runner=(char*)malloc(sizeof(char)*(strlen(base)+strlen(string)+1))', assigned value is 0
wise-2.4.1/src/base/wiseconfig.c:260:27: note: Null pointer dereference
wise-2.4.1/src/base/wiseconfig.c:260:19: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
wise-2.4.1/src/base/wiseconfig.c:246:26: note: Assuming allocation function fails
wise-2.4.1/src/base/wiseconfig.c:246:10: note: Assignment 'runner=(char*)malloc(sizeof(char)*(strlen(base)+strlen(string)+1))', assigned value is 0
wise-2.4.1/src/base/wiseconfig.c:260:19: note: Null pointer addition
wise-2.4.1/src/base/wiseconfig.c:246:9: style: Variable 'runner' is reassigned a value before the old one has been used. [redundantAssignment]
wise-2.4.1/src/base/wiseconfig.c:240:9: note: runner is assigned
wise-2.4.1/src/base/wiseconfig.c:246:9: note: runner is overwritten
wise-2.4.1/src/base/wiseconfig.c:155:45: style:inconclusive: Function 'config_number_from_key' argument 2 names different: declaration 'pass' definition 'passed'. [funcArgNamesDifferent]
wise-2.4.1/src/base/wiseconfig.h:38:45: note: Function 'config_number_from_key' argument 2 names different: declaration 'pass' definition 'passed'.
wise-2.4.1/src/base/wiseconfig.c:155:45: note: Function 'config_number_from_key' argument 2 names different: declaration 'pass' definition 'passed'.
wise-2.4.1/src/base/wiseconfig.c:94:31: style: Parameter 'key' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/base/wiseconfig.c:157:9: style: Variable 'runner' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/base/wiseconfig.c:229:34: style: Parameter 'base' can be declared as pointer to const [constParameterPointer]
wiseerror.dy:143:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable error_msg_call [valueFlowBailoutIncompleteVar]
wiseerror.dy:173:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable error_msg_call [valueFlowBailoutIncompleteVar]
wiseerror.dy:211:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable error_msg_call [valueFlowBailoutIncompleteVar]
wiseerror.dy:552:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wiseerror.dy:584:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wiseerror.dy:614:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wiseerror.dy:668:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wiseerror.dy:663:17: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
wiseerror.dy:665:7: style: Obsolescent function 'asctime_r' called. It is recommended to use 'strftime' instead. [prohibitedasctime_rCalled]
wiseerror.dy:473:14: style: The comparison 'type == 8' is always true. [knownConditionTrueFalse]
wiseerror.dy:466:14: note: 'type' is assigned value '8' here.
wiseerror.dy:473:14: note: The comparison 'type == 8' is always true.
wiseerror.dy:525:14: style: The comparison 'type == 2' is always true. [knownConditionTrueFalse]
wiseerror.dy:518:14: note: 'type' is assigned value '2' here.
wiseerror.dy:525:14: note: The comparison 'type == 2' is always true.
wiseerror.dy:551:14: style: The comparison 'type == 1' is always true. [knownConditionTrueFalse]
wiseerror.dy:544:14: note: 'type' is assigned value '1' here.
wiseerror.dy:551:14: note: The comparison 'type == 1' is always true.
wiseerror.dy:648:15: style: Variable 'loctime' can be declared as pointer to const [constVariablePointer]
wiseerror.dy:207:16: style: Unused variable: j [unusedVariable]
wiseerror.dy:208:16: style: Unused variable: count [unusedVariable]
wiseerror.dy:141:17: error: va_list 'ap' was opened but not closed by va_end(). [va_end_missing]
wiseerror.dy:475:9: error: va_list 'ap' was opened but not closed by va_end(). [va_end_missing]
wiseerror.dy:501:9: error: va_list 'ap' was opened but not closed by va_end(). [va_end_missing]
wiseerror.dy:527:9: error: va_list 'ap' was opened but not closed by va_end(). [va_end_missing]
wiseerror.dy:555:9: error: va_list 'ap' was opened but not closed by va_end(). [va_end_missing]
wiseerror.dy:590:9: error: va_list 'ap' was opened but not closed by va_end(). [va_end_missing]
wisefile.dy:80:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wisefile.dy:284:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
wisefile.dy:137:28: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
wisefile.dy:157:26: style: Parameter 'from' can be declared as pointer to const [constParameterPointer]
wisefile.dy:157:38: style: Parameter 'to' can be declared as pointer to const [constParameterPointer]
wisefile.dy:180:10: style: Variable 'runner' can be declared as pointer to const [constVariablePointer]
wisefile.dy:213:26: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
wisefile.dy:367:43: style: Parameter 'env' can be declared as pointer to const [constParameterPointer]
wisefile.dy:188:9: style: Variable 'runner' is assigned a value that is never used. [unreadVariable]
wisememman.dy:163:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable elsize [valueFlowBailoutIncompleteVar]
wisememman.dy:215:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
wisestreaminterface.dy:105:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wisestreaminterface.dy:104:15: note: Assuming allocation function fails
wisestreaminterface.dy:104:15: note: Assignment 'out=malloc(sizeof(struct Wise2ReadStreamInterface))', assigned value is 0
wisestreaminterface.dy:105:3: note: Null pointer dereference
wisestreaminterface.dy:106:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wisestreaminterface.dy:104:15: note: Assuming allocation function fails
wisestreaminterface.dy:104:15: note: Assignment 'out=malloc(sizeof(struct Wise2ReadStreamInterface))', assigned value is 0
wisestreaminterface.dy:106:3: note: Null pointer dereference
wisestreaminterface.dy:107:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wisestreaminterface.dy:104:15: note: Assuming allocation function fails
wisestreaminterface.dy:104:15: note: Assignment 'out=malloc(sizeof(struct Wise2ReadStreamInterface))', assigned value is 0
wisestreaminterface.dy:107:3: note: Null pointer dereference
wisestreaminterface.dy:108:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wisestreaminterface.dy:104:15: note: Assuming allocation function fails
wisestreaminterface.dy:104:15: note: Assignment 'out=malloc(sizeof(struct Wise2ReadStreamInterface))', assigned value is 0
wisestreaminterface.dy:108:3: note: Null pointer dereference
wisestreaminterface.dy:201:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wisestreaminterface.dy:200:15: note: Assuming allocation function fails
wisestreaminterface.dy:200:15: note: Assignment 'out=malloc(sizeof(struct Wise2WriteStreamInterface))', assigned value is 0
wisestreaminterface.dy:201:3: note: Null pointer dereference
wisestreaminterface.dy:202:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wisestreaminterface.dy:200:15: note: Assuming allocation function fails
wisestreaminterface.dy:200:15: note: Assignment 'out=malloc(sizeof(struct Wise2WriteStreamInterface))', assigned value is 0
wisestreaminterface.dy:202:3: note: Null pointer dereference
wisestreaminterface.dy:203:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wisestreaminterface.dy:200:15: note: Assuming allocation function fails
wisestreaminterface.dy:200:15: note: Assignment 'out=malloc(sizeof(struct Wise2WriteStreamInterface))', assigned value is 0
wisestreaminterface.dy:203:3: note: Null pointer dereference
wisestreaminterface.dy:204:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wisestreaminterface.dy:200:15: note: Assuming allocation function fails
wisestreaminterface.dy:200:15: note: Assignment 'out=malloc(sizeof(struct Wise2WriteStreamInterface))', assigned value is 0
wisestreaminterface.dy:204:3: note: Null pointer dereference
wisestreaminterface.dy:150:50: style: Parameter 'string' can be declared as pointer to const. However it seems that 'Wise2_write_buffer_FILE_impl' is a callback function, if 'string' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wisestreaminterface.dy:201:23: note: You might need to cast the function pointer here
wisestreaminterface.dy:150:50: note: Parameter 'string' can be declared as pointer to const
wisestreaminterface.dy:182:9: error: va_list 'ap' was opened but not closed by va_end(). [va_end_missing]
wisestring.dy:41:46: style: Parameter 'qstr' can be declared as pointer to const [constParameterPointer]
wisestring.dy:44:10: style: Variable 'stop' can be declared as pointer to const [constVariablePointer]
wisestring.dy:80:34: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
wisestring.dy:113:33: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
wisestring.dy:139:54: style: Parameter 'punc' can be declared as pointer to const [constParameterPointer]
wisestring.dy:139:66: style: Parameter 'space' can be declared as pointer to const [constParameterPointer]
wisestring.dy:273:52: style: Parameter 'whitespace' can be declared as pointer to const [constParameterPointer]
wisestring.dy:308:45: style: Parameter 'space' can be declared as pointer to const [constParameterPointer]
wisestring.dy:412:43: style: Parameter 'space' can be declared as pointer to const [constParameterPointer]
wisestring.dy:545:32: style: Parameter 'se' can be declared as pointer to const [constParameterPointer]
wisestring.dy:610:10: style: Variable 'st' can be declared as pointer to const [constVariablePointer]
wisestring.dy:650:10: style: Variable 'st' can be declared as pointer to const [constVariablePointer]
wisestring.dy:682:38: style: Parameter 'key' can be declared as pointer to const [constParameterPointer]
wisestring.dy:682:49: style: Parameter 'sub' can be declared as pointer to const [constParameterPointer]
wisestring.dy:686:10: style: Variable 'stop' can be declared as pointer to const [constVariablePointer]
wisestring.dy:815:50: style: Parameter 'parsestr' can be declared as pointer to const [constParameterPointer]
wisestring.dy:815:66: style: Parameter 'strpair' can be declared as pointer to const [constParameterPointer]
wisestring.dy:877:46: style: Parameter 'quote' can be declared as pointer to const [constParameterPointer]
wisestring.dy:1032:44: style: Parameter 'space' can be declared as pointer to const [constParameterPointer]
wisestring.dy:1103:27: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
wisestring.dy:833:6: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/contig/testoverlap.c:21:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/corba/corba_singleton.c:18:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/corba/hspscan_corba_wrapper.c:42:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/corba/hspscan_corba_wrapper.c:112:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/corba/hspscan_corba_wrapper.c:99:97: style:inconclusive: Function 'new_corba_HSPScan' argument 3 names different: declaration 'client_side_compmat' definition 'client_side_mat'. [funcArgNamesDifferent]
wise-2.4.1/src/corba/hspscan_corba_wrapper.h:19:103: note: Function 'new_corba_HSPScan' argument 3 names different: declaration 'client_side_compmat' definition 'client_side_mat'.
wise-2.4.1/src/corba/hspscan_corba_wrapper.c:99:97: note: Function 'new_corba_HSPScan' argument 3 names different: declaration 'client_side_compmat' definition 'client_side_mat'.
wise-2.4.1/src/corba/hspscan_corba_wrapper.c:39:7: style: Unused variable: i [unusedVariable]
wise-2.4.1/src/corba/hspscan_server_impl.c:156:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/corba/hspscan_server_impl.c:267:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/corba/hspscan_server_impl.c:309:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/corba/hspscan_server_impl.c:341:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/corba/hspscan_server_impl.c:384:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/corba/hspscan_server_impl.c:405:27: style: The if condition is the same as the previous if condition [duplicateCondition]
wise-2.4.1/src/corba/hspscan_server_impl.c:401:27: note: First condition
wise-2.4.1/src/corba/hspscan_server_impl.c:405:27: note: Second condition
wise-2.4.1/src/corba/hspscan_server_impl.c:409:27: style: The if condition is the same as the previous if condition [duplicateCondition]
wise-2.4.1/src/corba/hspscan_server_impl.c:405:27: note: First condition
wise-2.4.1/src/corba/hspscan_server_impl.c:409:27: note: Second condition
wise-2.4.1/src/corba/hspscan_server_impl.c:177:75: style: Parameter 'servant' can be declared as pointer to const. However it seems that 'impl_Wise2HSP_HSP_ts_iterator_is_more' is a callback function, if 'servant' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise-2.4.1/src/corba/hspscan_server_impl.c:67:17: note: You might need to cast the function pointer here
wise-2.4.1/src/corba/hspscan_server_impl.c:177:75: note: Parameter 'servant' can be declared as pointer to const
wise-2.4.1/src/corba/hspscan_server_impl.c:178:31: style: Parameter 'ev' can be declared as pointer to const. However it seems that 'impl_Wise2HSP_HSP_ts_iterator_is_more' is a callback function, if 'ev' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise-2.4.1/src/corba/hspscan_server_impl.c:67:17: note: You might need to cast the function pointer here
wise-2.4.1/src/corba/hspscan_server_impl.c:178:31: note: Parameter 'ev' can be declared as pointer to const
wise-2.4.1/src/corba/hspscan_server_impl.c:338:7: style: Unused variable: size [unusedVariable]
wise-2.4.1/src/corba/hspscan_server_impl.c:375:25: style: Unused variable: corba_hspm [unusedVariable]
wise-2.4.1/src/corba/hspscan_server_impl.c:380:8: style: Unused variable: size [unusedVariable]
wise-2.4.1/src/corba/hspscan_server_impl.c:381:8: style: Unused variable: i [unusedVariable]
wise-2.4.1/src/corba/scanwise_protein_index.c:98:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/corba/scanwise_protein_index.c:107:10: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: ofp [nullPointerOutOfResources]
wise-2.4.1/src/corba/scanwise_protein_index.c:103:14: note: Assuming allocation function fails
wise-2.4.1/src/corba/scanwise_protein_index.c:103:14: note: Assignment 'ofp=fopen(ior_file,"w")', assigned value is 0
wise-2.4.1/src/corba/scanwise_protein_index.c:107:10: note: Null pointer dereference
wise-2.4.1/src/corba/scanwise_protein_index.c:156:11: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: ofp [nullPointerOutOfResources]
wise-2.4.1/src/corba/scanwise_protein_index.c:151:14: note: Assuming allocation function fails
wise-2.4.1/src/corba/scanwise_protein_index.c:151:14: note: Assignment 'ofp=fopen(ior_file,"w")', assigned value is 0
wise-2.4.1/src/corba/scanwise_protein_index.c:156:11: note: Null pointer dereference
wise-2.4.1/src/corba/scanwise_protein_index.c:157:10: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: ofp [nullPointerOutOfResources]
wise-2.4.1/src/corba/scanwise_protein_index.c:151:14: note: Assuming allocation function fails
wise-2.4.1/src/corba/scanwise_protein_index.c:151:14: note: Assignment 'ofp=fopen(ior_file,"w")', assigned value is 0
wise-2.4.1/src/corba/scanwise_protein_index.c:157:10: note: Null pointer dereference
wise-2.4.1/src/corba/scanwise_protein_index.c:65:29: style: Variable 'objref' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/corba/scanwise_protein_index.c:71:10: style: Variable 'oc_file' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/corba/scanwise_protein_index.c:66:13: style: Variable 'count' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/corba/scanwise_protein_index.c:53:7: style: Unused variable: i [unusedVariable]
wise-2.4.1/src/corba/scanwise_protein_index.c:55:29: style: Unused variable: oid [unusedVariable]
wise-2.4.1/src/corba/scanwise_protein_index.c:59:14: style: Unused variable: seq [unusedVariable]
wise-2.4.1/src/corba/scanwise_protein_index.c:60:7: style: Unused variable: ret [unusedVariable]
wise-2.4.1/src/corba/scanwise_protein_index.c:66:7: style: Variable 'count' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/corba/test_client.c:44:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/corba/test_server.c:64:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/corba/test_server.c:62:21: style: Condition 'is_array==1&&0' is always false [knownConditionTrueFalse]
wise-2.4.1/src/corba/test_server.c:80:11: warning: If resource allocation fails, then there is a possible null pointer dereference: ofp [nullPointerOutOfResources]
wise-2.4.1/src/corba/test_server.c:79:14: note: Assuming allocation function fails
wise-2.4.1/src/corba/test_server.c:79:14: note: Assignment 'ofp=fopen("hsp.ior","w")', assigned value is 0
wise-2.4.1/src/corba/test_server.c:80:11: note: Null pointer dereference
wise-2.4.1/src/corba/test_server.c:81:10: warning: If resource allocation fails, then there is a possible null pointer dereference: ofp [nullPointerOutOfResources]
wise-2.4.1/src/corba/test_server.c:79:14: note: Assuming allocation function fails
wise-2.4.1/src/corba/test_server.c:79:14: note: Assignment 'ofp=fopen("hsp.ior","w")', assigned value is 0
wise-2.4.1/src/corba/test_server.c:81:10: note: Null pointer dereference
wise-2.4.1/src/corba/test_server.c:29:29: style: Variable 'objref' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/corba/test_server.c:47:9: style: Variable 'count' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/corba/test_server.c:19:29: style: Unused variable: oid [unusedVariable]
wise-2.4.1/src/corba/test_wrapper.c:38:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/corba/test_wrapper.c:17:7: style: Unused variable: ret [unusedVariable]
assembly.dy:104:10: style: Variable 'base' can be declared as pointer to const [constVariablePointer]
assembly.dy:228:78: style: Parameter 'aop' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/dnaindex/assembly/badkmer.c:14:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VERSION_NUMBER [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dnaindex/assembly/badkmer.c:68:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dnaindex/assembly/badkmer.c:89:7: style: Condition 'show_stats_before' is always false [knownConditionTrueFalse]
wise-2.4.1/src/dnaindex/assembly/badkmer.c:39:31: note: Assignment 'show_stats_before=0', assigned value is 0
wise-2.4.1/src/dnaindex/assembly/badkmer.c:67:12: note: Assuming condition is false
wise-2.4.1/src/dnaindex/assembly/badkmer.c:89:7: note: Condition 'show_stats_before' is always false
wise-2.4.1/src/dnaindex/assembly/badkmer.c:45:22: style: Variable 'aseq' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/dnaindex/assembly/badkmer.c:85:8: style: Variable 'load' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/dnaindex/assembly/pathwise.c:15:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VERSION_NUMBER [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dnaindex/assembly/pathwise.c:98:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dnaindex/assembly/pathwise.c:123:8: style: Variable 'load' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/dnaindex/assembly/test_assemblygraph.c:38:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dnaindex/assembly/test_assemblygraph.c:13:14: style: Unused variable: assem [unusedVariable]
wise-2.4.1/src/dnaindex/assembly/test_basegraph.c:33:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dnaindex/assembly/test_basegraph.c:55:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dnaindex/assembly/test_graphtangle.c:50:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable state [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dnaindex/assembly/test_graphtangle.c:120:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dnaindex/assembly/test_graphtangle.c:54:7: warning: %d in format string (no. 1) requires 'int' but the argument type is 'BaseNode *'. [invalidPrintfArgType_sint]
wise-2.4.1/src/dnaindex/assembly/test_graphtangle.c:72:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'BaseNode *'. [invalidPrintfArgType_sint]
wise-2.4.1/src/dnaindex/assembly/test_graphtangle.c:88:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'BaseNode *'. [invalidPrintfArgType_sint]
assembly_sanger_project.dy:25:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
assembly_sanger_project.dy:146:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQUENCE_DNA [valueFlowBailoutIncompleteVar]
assembly_sanger_project.dy:84:7: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
assembly_sanger_project.dy:124:4: error: Common realloc mistake: 'seqstr' nulled but not freed upon failure [memleakOnRealloc]
assembly_sanger_project.dy:130:3: warning: If memory allocation fails, then there is a possible null pointer dereference: seqstr [nullPointerOutOfMemory]
assembly_sanger_project.dy:78:18: note: Assuming allocation function fails
assembly_sanger_project.dy:78:18: note: Assignment 'seqstr=malloc(sizeof(char)*1028)', assigned value is 0
assembly_sanger_project.dy:82:32: note: Assuming condition is false
assembly_sanger_project.dy:130:3: note: Null pointer dereference
assembly_sanger_project.dy:27:10: style: Variable 'run' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/dnaindex/bigseqwise.c:57:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dnaindex/bigseqwise.c:40:25: style: Variable 'reference' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/dnaindex/bigseqwise.c:97:13: style: Variable 'reference' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/dnaindex/chhash.c:28:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dnaindex/chhash.c:121:13: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
comparapath.dy:119:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
comparapath.dy:180:7: warning: %ld in format string (no. 4) requires 'long' but the argument type is 'ComparaHead *'. [invalidPrintfArgType_sint]
comparapath.dy:180:7: portability: %ld in format string (no. 5) requires 'long' but the argument type is 'ComparaHead * {aka ComparaHead *}'. [invalidPrintfArgType_sint]
comparapath.dy:180:7: portability: %ld in format string (no. 6) requires 'long' but the argument type is 'ComparaHead * {aka ComparaHead *}'. [invalidPrintfArgType_sint]
comparapath.dy:180:7: warning: %ld in format string (no. 7) requires 'long' but the argument type is 'ComparaHead *'. [invalidPrintfArgType_sint]
comparapath.dy:538:2: portability: %ld in format string (no. 2) requires 'long' but the argument type is 'kmer_t {aka signed long long}'. [invalidPrintfArgType_sint]
comparapath.dy:538:2: portability: %ld in format string (no. 3) requires 'long' but the argument type is 'kmer_t {aka signed long long}'. [invalidPrintfArgType_sint]
comparapath.dy:538:2: portability: %ld in format string (no. 4) requires 'long' but the argument type is 'kmer_t {aka signed long long}'. [invalidPrintfArgType_sint]
comparapath.dy:573:2: portability: %ld in format string (no. 1) requires 'long' but the argument type is 'kmer_t {aka signed long long}'. [invalidPrintfArgType_sint]
comparapath.dy:342:9: warning: Either the condition 'chead==NULL' is redundant or there is possible null pointer dereference: current. [nullPointerRedundantCheck]
comparapath.dy:346:15: note: Assuming that condition 'chead==NULL' is not redundant
comparapath.dy:344:13: note: Assignment to 'chead=current'
comparapath.dy:342:9: note: Null pointer dereference
comparapath.dy:615:2: warning: Either the condition 'chead==NULL' is redundant or there is possible null pointer dereference: chead. [nullPointerRedundantCheck]
comparapath.dy:611:12: note: Assuming that condition 'chead==NULL' is not redundant
comparapath.dy:615:2: note: Null pointer dereference
comparapath.dy:674:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
comparapath.dy:673:15: note: Assuming allocation function fails
comparapath.dy:673:15: note: Assignment 'out=malloc(sizeof(struct ComparaIndex))', assigned value is 0
comparapath.dy:674:3: note: Null pointer dereference
comparapath.dy:677:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
comparapath.dy:673:15: note: Assuming allocation function fails
comparapath.dy:673:15: note: Assignment 'out=malloc(sizeof(struct ComparaIndex))', assigned value is 0
comparapath.dy:677:3: note: Null pointer dereference
comparapath.dy:678:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
comparapath.dy:673:15: note: Assuming allocation function fails
comparapath.dy:673:15: note: Assignment 'out=malloc(sizeof(struct ComparaIndex))', assigned value is 0
comparapath.dy:678:3: note: Null pointer dereference
comparapath.dy:679:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
comparapath.dy:673:15: note: Assuming allocation function fails
comparapath.dy:673:15: note: Assignment 'out=malloc(sizeof(struct ComparaIndex))', assigned value is 0
comparapath.dy:679:3: note: Null pointer dereference
comparapath.dy:680:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
comparapath.dy:673:15: note: Assuming allocation function fails
comparapath.dy:673:15: note: Assignment 'out=malloc(sizeof(struct ComparaIndex))', assigned value is 0
comparapath.dy:680:3: note: Null pointer dereference
comparapath.dy:681:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
comparapath.dy:673:15: note: Assuming allocation function fails
comparapath.dy:673:15: note: Assignment 'out=malloc(sizeof(struct ComparaIndex))', assigned value is 0
comparapath.dy:681:3: note: Null pointer dereference
comparapath.dy:691:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
comparapath.dy:689:15: note: Assuming allocation function fails
comparapath.dy:689:15: note: Assignment 'out=malloc(sizeof(struct ComparaLinkStart))', assigned value is 0
comparapath.dy:691:3: note: Null pointer dereference
comparapath.dy:692:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
comparapath.dy:689:15: note: Assuming allocation function fails
comparapath.dy:689:15: note: Assignment 'out=malloc(sizeof(struct ComparaLinkStart))', assigned value is 0
comparapath.dy:692:3: note: Null pointer dereference
comparapath.dy:753:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
comparapath.dy:752:44: note: Assuming allocation function fails
comparapath.dy:752:9: note: Assignment 'out=(struct ComparaHeadBlockAllocator*)malloc(sizeof(struct ComparaHeadBlockAllocator))', assigned value is 0
comparapath.dy:753:3: note: Null pointer dereference
comparapath.dy:754:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
comparapath.dy:752:44: note: Assuming allocation function fails
comparapath.dy:752:9: note: Assignment 'out=(struct ComparaHeadBlockAllocator*)malloc(sizeof(struct ComparaHeadBlockAllocator))', assigned value is 0
comparapath.dy:754:3: note: Null pointer dereference
comparapath.dy:755:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
comparapath.dy:752:44: note: Assuming allocation function fails
comparapath.dy:752:9: note: Assignment 'out=(struct ComparaHeadBlockAllocator*)malloc(sizeof(struct ComparaHeadBlockAllocator))', assigned value is 0
comparapath.dy:755:3: note: Null pointer dereference
comparapath.dy:756:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
comparapath.dy:752:44: note: Assuming allocation function fails
comparapath.dy:752:9: note: Assignment 'out=(struct ComparaHeadBlockAllocator*)malloc(sizeof(struct ComparaHeadBlockAllocator))', assigned value is 0
comparapath.dy:756:3: note: Null pointer dereference
comparapath.dy:758:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
comparapath.dy:752:44: note: Assuming allocation function fails
comparapath.dy:752:9: note: Assignment 'out=(struct ComparaHeadBlockAllocator*)malloc(sizeof(struct ComparaHeadBlockAllocator))', assigned value is 0
comparapath.dy:758:3: note: Null pointer dereference
comparapath.dy:759:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
comparapath.dy:752:44: note: Assuming allocation function fails
comparapath.dy:752:9: note: Assignment 'out=(struct ComparaHeadBlockAllocator*)malloc(sizeof(struct ComparaHeadBlockAllocator))', assigned value is 0
comparapath.dy:759:3: note: Null pointer dereference
comparapath.dy:137:17: style: Variable 'prev' can be declared as pointer to const [constVariablePointer]
comparapath.dy:254:40: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
comparapath.dy:266:40: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
comparapath.dy:298:17: style: Variable 'chead' can be declared as pointer to const [constVariablePointer]
comparapath.dy:335:16: style: Variable 'chead' can be declared as pointer to const [constVariablePointer]
comparapath.dy:453:150: style: Parameter 'tag' can be declared as pointer to const [constParameterPointer]
comparapath.dy:490:144: style: Parameter 'skipflag' can be declared as pointer to const [constParameterPointer]
comparapath.dy:503:17: style: Variable 'revhead' can be declared as pointer to const [constVariablePointer]
comparapath.dy:246:96: warning: Uninitialized variable: last_pos [uninitvar]
comparapath.dy:154:36: note: Assuming condition is false
comparapath.dy:246:96: note: Uninitialized variable: last_pos
compressed_protein_index.dy:105:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SeqLookupResultStruct [valueFlowBailoutIncompleteVar]
compressed_protein_index.dy:211:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SeqLookupResultStruct [valueFlowBailoutIncompleteVar]
compressed_protein_index.dy:39:94: style: Parameter 'prev' can be declared as pointer to const. However it seems that 'Wise2_get_next_CompressedProteinClient' is a callback function, if 'prev' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
compressed_protein_index.dy:119:20: note: You might need to cast the function pointer here
compressed_protein_index.dy:39:94: note: Parameter 'prev' can be declared as pointer to const
compressed_protein_index.dy:63:29: style: Variable 'cl' can be declared as pointer to const [constVariablePointer]
compressed_protein_index.dy:73:67: style: Parameter 'data' can be declared as pointer to const. However it seems that 'Wise2_free_SeqLookupResultInterface_CompressedProteinClient' is a callback function, if 'data' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
compressed_protein_index.dy:121:20: note: You might need to cast the function pointer here
compressed_protein_index.dy:73:67: note: Parameter 'data' can be declared as pointer to const
compressed_protein_index.dy:127:27: style: Variable 'h' can be declared as pointer to const [constVariablePointer]
compressed_protein_index.dy:219:57: style: Parameter 'data' can be declared as pointer to const. However it seems that 'Wise2_add_direct_number_CompressedProteinIndex' is a callback function, if 'data' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
compressed_protein_index.dy:174:28: note: You might need to cast the function pointer here
compressed_protein_index.dy:219:57: note: Parameter 'data' can be declared as pointer to const
compressed_protein_index.dy:219:88: style: Parameter 'target' can be declared as pointer to const. However it seems that 'Wise2_add_direct_number_CompressedProteinIndex' is a callback function, if 'target' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
compressed_protein_index.dy:174:28: note: You might need to cast the function pointer here
compressed_protein_index.dy:219:88: note: Parameter 'target' can be declared as pointer to const
compressed_protein_index.dy:226:64: style: Parameter 'data' can be declared as pointer to const [constParameterPointer]
compressed_protein_index.dy:234:87: style: Parameter 'para' can be declared as pointer to const. However it seems that 'Wise2_add_seq_CompressedProteinIndex' is a callback function, if 'para' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
compressed_protein_index.dy:172:21: note: You might need to cast the function pointer here
compressed_protein_index.dy:234:87: note: Parameter 'para' can be declared as pointer to const
dnamapping.dy:119:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASE_N [valueFlowBailoutIncompleteVar]
dnamapping.dy:29:5: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
dnamapping.dy:26:15: note: Assuming allocation function fails
dnamapping.dy:26:15: note: Assignment 'out=calloc(len,sizeof(char))', assigned value is 0
dnamapping.dy:29:5: note: Null pointer dereference
dnamapping.dy:21:39: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
dnamapping.dy:163:46: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
dnanumber.dy:84:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASE_N [valueFlowBailoutIncompleteVar]
dnanumber.dy:132:3: error: Found an exit path from function with non-void return type that has missing return statement [missingReturn]
dnanumber.dy:45:7: style: Unused variable: power [unusedVariable]
eulerindex.dy:150:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
eulerindex.dy:197:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
eulerindex.dy:235:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
eulerindex.dy:281:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
eulerindex.dy:358:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
eulerindex.dy:461:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
eulerindex.dy:484:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
eulerindex.dy:575:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
eulerindex.dy:382:27: style: Variable 'can_untangle_right[i]' is reassigned a value before the old one has been used. [redundantAssignment]
eulerindex.dy:379:29: note: can_untangle_right[i] is assigned
eulerindex.dy:382:27: note: can_untangle_right[i] is overwritten
eulerindex.dy:178:10: style: Variable 'dna' can be declared as pointer to const [constVariablePointer]
eulerindex.dy:233:15: style: Variable 'prev' can be declared as pointer to const [constVariablePointer]
eulerindex.dy:140:15: style: Unused variable: node [unusedVariable]
eulerindex.dy:444:16: style: Variable 'resolved' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/dnaindex/findbad_kmer.c:77:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dnaindex/findbad_kmer.c:61:20: style: Variable 'sps' can be declared as pointer to const [constVariablePointer]
kmer_assembly.dy:75:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_assembly.dy:164:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_assembly.dy:365:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_assembly.dy:103:26: style: The if condition is the same as the previous if condition [duplicateCondition]
kmer_assembly.dy:99:26: note: First condition
kmer_assembly.dy:103:26: note: Second condition
kmer_assembly.dy:296:3: portability: %ld in format string (no. 1) requires 'long' but the argument type is 'kmer_t {aka signed long long}'. [invalidPrintfArgType_sint]
kmer_assembly.dy:302:5: portability: %ld in format string (no. 3) requires 'long' but the argument type is 'kmer_t {aka signed long long}'. [invalidPrintfArgType_sint]
kmer_assembly.dy:309:5: portability: %ld in format string (no. 3) requires 'long' but the argument type is 'kmer_t {aka signed long long}'. [invalidPrintfArgType_sint]
kmer_assembly.dy:365:3: portability: %ld in format string (no. 2) requires 'long' but the argument type is 'KmerAssemblyLink * {aka KmerAssemblyLink *}'. [invalidPrintfArgType_sint]
kmer_assembly.dy:367:5: error: fprintf format string requires 2 parameters but only 1 is given. [wrongPrintfScanfArgNum]
kmer_assembly.dy:329:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_assembly.dy:327:36: note: Assuming allocation function fails
kmer_assembly.dy:327:9: note: Assignment 'out=(struct KmerAssemblyIndex*)malloc(sizeof(struct KmerAssemblyIndex))', assigned value is 0
kmer_assembly.dy:329:3: note: Null pointer dereference
kmer_assembly.dy:330:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_assembly.dy:327:36: note: Assuming allocation function fails
kmer_assembly.dy:327:9: note: Assignment 'out=(struct KmerAssemblyIndex*)malloc(sizeof(struct KmerAssemblyIndex))', assigned value is 0
kmer_assembly.dy:330:3: note: Null pointer dereference
kmer_assembly.dy:341:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_assembly.dy:339:36: note: Assuming allocation function fails
kmer_assembly.dy:339:9: note: Assignment 'out=(struct KmerAssemblyLink*)malloc(sizeof(struct KmerAssemblyLink))', assigned value is 0
kmer_assembly.dy:341:3: note: Null pointer dereference
kmer_assembly.dy:342:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_assembly.dy:339:36: note: Assuming allocation function fails
kmer_assembly.dy:339:9: note: Assignment 'out=(struct KmerAssemblyLink*)malloc(sizeof(struct KmerAssemblyLink))', assigned value is 0
kmer_assembly.dy:342:3: note: Null pointer dereference
kmer_assembly.dy:343:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_assembly.dy:339:36: note: Assuming allocation function fails
kmer_assembly.dy:339:9: note: Assignment 'out=(struct KmerAssemblyLink*)malloc(sizeof(struct KmerAssemblyLink))', assigned value is 0
kmer_assembly.dy:343:3: note: Null pointer dereference
kmer_assembly.dy:345:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_assembly.dy:339:36: note: Assuming allocation function fails
kmer_assembly.dy:339:9: note: Assignment 'out=(struct KmerAssemblyLink*)malloc(sizeof(struct KmerAssemblyLink))', assigned value is 0
kmer_assembly.dy:345:3: note: Null pointer dereference
kmer_assembly.dy:346:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_assembly.dy:339:36: note: Assuming allocation function fails
kmer_assembly.dy:339:9: note: Assignment 'out=(struct KmerAssemblyLink*)malloc(sizeof(struct KmerAssemblyLink))', assigned value is 0
kmer_assembly.dy:346:3: note: Null pointer dereference
kmer_assembly.dy:347:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_assembly.dy:339:36: note: Assuming allocation function fails
kmer_assembly.dy:339:9: note: Assignment 'out=(struct KmerAssemblyLink*)malloc(sizeof(struct KmerAssemblyLink))', assigned value is 0
kmer_assembly.dy:347:3: note: Null pointer dereference
kmer_assembly.dy:348:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_assembly.dy:339:36: note: Assuming allocation function fails
kmer_assembly.dy:339:9: note: Assignment 'out=(struct KmerAssemblyLink*)malloc(sizeof(struct KmerAssemblyLink))', assigned value is 0
kmer_assembly.dy:348:3: note: Null pointer dereference
kmer_assembly.dy:392:50: style: Parameter 'kai' can be declared as pointer to const [constParameterPointer]
kmer_assembly_contig.dy:84:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_assembly_contig.dy:159:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_assembly_contig.dy:261:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_assembly_contig.dy:34:111: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
kmer_assembly_contig.dy:221:102: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
kmer_assembly_contig.dy:66:27: style: Unused variable: final [unusedVariable]
kmer_assembly_error.dy:37:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_assembly_error.dy:93:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_assembly_error.dy:149:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_assembly_error.dy:259:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_assembly_error.dy:337:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_assembly_error.dy:499:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_assembly_error.dy:228:22: style: The if condition is the same as the previous if condition [duplicateCondition]
kmer_assembly_error.dy:223:22: note: First condition
kmer_assembly_error.dy:228:22: note: Second condition
kmer_assembly_error.dy:93:7: portability: %ld in format string (no. 1) requires 'long' but the argument type is 'kmer_t {aka signed long long}'. [invalidPrintfArgType_sint]
kmer_assembly_error.dy:105:7: portability: %ld in format string (no. 1) requires 'long' but the argument type is 'kmer_t {aka signed long long}'. [invalidPrintfArgType_sint]
kmer_assembly_error.dy:351:2: warning: %d in format string (no. 2) requires 'int' but the argument type is 'signed int *'. [invalidPrintfArgType_sint]
kmer_assembly_error.dy:14:123: style: Parameter 'start_labels' can be declared as pointer to const [constParameterPointer]
kmer_assembly_error.dy:57:125: style: Parameter 'start_labels' can be declared as pointer to const [constParameterPointer]
kmer_assembly_error.dy:125:23: style: Variable 'sps' can be declared as pointer to const [constVariablePointer]
kmer_assembly_error.dy:206:10: style: Variable 'alphabet' can be declared as pointer to const [constVariablePointer]
kmer_assembly_error.dy:208:8: style: Unused variable: next [unusedVariable]
kmer_assembly_untangler.dy:120:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_assembly_untangler.dy:217:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_assembly_untangler.dy:287:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
kmer_assembly_untangler.dy:308:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_assembly_untangler.dy:333:109: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
kmer_assembly_untangler.dy:372:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_assembly_untangler.dy:437:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_assembly_untangler.dy:746:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_assembly_untangler.dy:120:7: portability: %ld in format string (no. 1) requires 'long' but the argument type is 'kmer_t {aka signed long long}'. [invalidPrintfArgType_sint]
kmer_assembly_untangler.dy:141:7: portability: %ld in format string (no. 1) requires 'long' but the argument type is 'kmer_t {aka signed long long}'. [invalidPrintfArgType_sint]
kmer_assembly_untangler.dy:141:7: portability: %ld in format string (no. 2) requires 'long' but the argument type is 'kmer_t {aka signed long long}'. [invalidPrintfArgType_sint]
kmer_assembly_untangler.dy:157:7: portability: %ld in format string (no. 1) requires 'long' but the argument type is 'kmer_t {aka signed long long}'. [invalidPrintfArgType_sint]
kmer_assembly_untangler.dy:159:7: portability: %ld in format string (no. 1) requires 'long' but the argument type is 'kmer_t {aka signed long long}'. [invalidPrintfArgType_sint]
kmer_assembly_untangler.dy:444:5: portability: %ld in format string (no. 1) requires 'long' but the argument type is 'kmer_t {aka signed long long}'. [invalidPrintfArgType_sint]
kmer_assembly_untangler.dy:746:5: portability: %ld in format string (no. 4) requires 'long' but the argument type is 'kmer_t {aka signed long long}'. [invalidPrintfArgType_sint]
kmer_assembly_untangler.dy:746:5: portability: %ld in format string (no. 6) requires 'long' but the argument type is 'kmer_t {aka signed long long}'. [invalidPrintfArgType_sint]
kmer_assembly_untangler.dy:38:71: style: Parameter 'kap' can be declared as pointer to const [constParameterPointer]
kmer_assembly_untangler.dy:301:66: style: Parameter 'res' can be declared as pointer to const [constParameterPointer]
kmer_assembly_untangler.dy:301:89: style: Parameter 'current' can be declared as pointer to const [constParameterPointer]
kmer_assembly_untangler.dy:321:67: style: Parameter 'res' can be declared as pointer to const [constParameterPointer]
kmer_assembly_untangler.dy:321:90: style: Parameter 'rightside' can be declared as pointer to const [constParameterPointer]
kmer_assembly_untangler.dy:599:52: style: Parameter 'kai' can be declared as pointer to const [constParameterPointer]
kmer_assembly_untangler.dy:599:91: style: Parameter 'start_label' can be declared as pointer to const [constParameterPointer]
kmer_assembly_untangler.dy:660:110: style: Parameter 'start_label' can be declared as pointer to const [constParameterPointer]
kmer_assembly_untangler.dy:717:116: style: Parameter 'start_label' can be declared as pointer to const [constParameterPointer]
kmer_assembly_untangler.dy:384:25: warning: Uninitialized variables: newpath.dynamite_hard_link, newpath.stack, newpath.stack_len, newpath.max_stack, newpath.right_tail, newpath.left_tail [uninitvar]
kmer_assembly_untangler.dy:370:67: note: Assuming condition is false
kmer_assembly_untangler.dy:384:25: note: Uninitialized variables: newpath.dynamite_hard_link, newpath.stack, newpath.stack_len, newpath.max_stack, newpath.right_tail, newpath.left_tail
kmer_direct.dy:48:3: error: Memory leak: kdi.index [memleak]
kmer_direct.dy:30:3: warning: If memory allocation fails, then there is a possible null pointer dereference: kdi [nullPointerOutOfMemory]
kmer_direct.dy:29:15: note: Assuming allocation function fails
kmer_direct.dy:29:15: note: Assignment 'kdi=malloc(sizeof(struct KmerDirectIndex))', assigned value is 0
kmer_direct.dy:30:3: note: Null pointer dereference
kmer_direct.dy:31:7: warning: If memory allocation fails, then there is a possible null pointer dereference: kdi [nullPointerOutOfMemory]
kmer_direct.dy:29:15: note: Assuming allocation function fails
kmer_direct.dy:29:15: note: Assignment 'kdi=malloc(sizeof(struct KmerDirectIndex))', assigned value is 0
kmer_direct.dy:31:7: note: Null pointer dereference
kmer_direct.dy:35:3: warning: If memory allocation fails, then there is a possible null pointer dereference: kdi [nullPointerOutOfMemory]
kmer_direct.dy:29:15: note: Assuming allocation function fails
kmer_direct.dy:29:15: note: Assignment 'kdi=malloc(sizeof(struct KmerDirectIndex))', assigned value is 0
kmer_direct.dy:31:18: note: Assuming condition is false
kmer_direct.dy:35:3: note: Null pointer dereference
kmer_direct.dy:39:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_direct.dy:37:15: note: Assuming allocation function fails
kmer_direct.dy:37:15: note: Assignment 'out=malloc(sizeof(struct KmerIndexInterface))', assigned value is 0
kmer_direct.dy:39:3: note: Null pointer dereference
kmer_direct.dy:40:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_direct.dy:37:15: note: Assuming allocation function fails
kmer_direct.dy:37:15: note: Assignment 'out=malloc(sizeof(struct KmerIndexInterface))', assigned value is 0
kmer_direct.dy:40:3: note: Null pointer dereference
kmer_direct.dy:41:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_direct.dy:37:15: note: Assuming allocation function fails
kmer_direct.dy:37:15: note: Assignment 'out=malloc(sizeof(struct KmerIndexInterface))', assigned value is 0
kmer_direct.dy:41:3: note: Null pointer dereference
kmer_direct.dy:42:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_direct.dy:37:15: note: Assuming allocation function fails
kmer_direct.dy:37:15: note: Assignment 'out=malloc(sizeof(struct KmerIndexInterface))', assigned value is 0
kmer_direct.dy:42:3: note: Null pointer dereference
kmer_direct.dy:44:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_direct.dy:37:15: note: Assuming allocation function fails
kmer_direct.dy:37:15: note: Assignment 'out=malloc(sizeof(struct KmerIndexInterface))', assigned value is 0
kmer_direct.dy:44:3: note: Null pointer dereference
kmer_direct.dy:45:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_direct.dy:37:15: note: Assuming allocation function fails
kmer_direct.dy:37:15: note: Assignment 'out=malloc(sizeof(struct KmerIndexInterface))', assigned value is 0
kmer_direct.dy:45:3: note: Null pointer dereference
kmer_glib_index.dy:40:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_glib_index.dy:38:15: note: Assuming allocation function fails
kmer_glib_index.dy:38:15: note: Assignment 'out=malloc(sizeof(struct KmerIndexInterface))', assigned value is 0
kmer_glib_index.dy:40:3: note: Null pointer dereference
kmer_glib_index.dy:41:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_glib_index.dy:38:15: note: Assuming allocation function fails
kmer_glib_index.dy:38:15: note: Assignment 'out=malloc(sizeof(struct KmerIndexInterface))', assigned value is 0
kmer_glib_index.dy:41:3: note: Null pointer dereference
kmer_glib_index.dy:42:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_glib_index.dy:38:15: note: Assuming allocation function fails
kmer_glib_index.dy:38:15: note: Assignment 'out=malloc(sizeof(struct KmerIndexInterface))', assigned value is 0
kmer_glib_index.dy:42:3: note: Null pointer dereference
kmer_glib_index.dy:43:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_glib_index.dy:38:15: note: Assuming allocation function fails
kmer_glib_index.dy:38:15: note: Assignment 'out=malloc(sizeof(struct KmerIndexInterface))', assigned value is 0
kmer_glib_index.dy:43:3: note: Null pointer dereference
kmer_glib_index.dy:45:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_glib_index.dy:38:15: note: Assuming allocation function fails
kmer_glib_index.dy:38:15: note: Assignment 'out=malloc(sizeof(struct KmerIndexInterface))', assigned value is 0
kmer_glib_index.dy:45:3: note: Null pointer dereference
kmer_glib_index.dy:46:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_glib_index.dy:38:15: note: Assuming allocation function fails
kmer_glib_index.dy:38:15: note: Assignment 'out=malloc(sizeof(struct KmerIndexInterface))', assigned value is 0
kmer_glib_index.dy:46:3: note: Null pointer dereference
kmer_glib_index.dy:133:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_glib_index.dy:132:15: note: Assuming allocation function fails
kmer_glib_index.dy:132:15: note: Assignment 'out=malloc(sizeof(struct KmerGlibIndex))', assigned value is 0
kmer_glib_index.dy:133:3: note: Null pointer dereference
kmer_glib_index.dy:134:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_glib_index.dy:132:15: note: Assuming allocation function fails
kmer_glib_index.dy:132:15: note: Assignment 'out=malloc(sizeof(struct KmerGlibIndex))', assigned value is 0
kmer_glib_index.dy:134:3: note: Null pointer dereference
kmer_glib_index.dy:135:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_glib_index.dy:132:15: note: Assuming allocation function fails
kmer_glib_index.dy:132:15: note: Assignment 'out=malloc(sizeof(struct KmerGlibIndex))', assigned value is 0
kmer_glib_index.dy:135:3: note: Null pointer dereference
kmer_glib_index.dy:136:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_glib_index.dy:132:15: note: Assuming allocation function fails
kmer_glib_index.dy:132:15: note: Assignment 'out=malloc(sizeof(struct KmerGlibIndex))', assigned value is 0
kmer_glib_index.dy:136:3: note: Null pointer dereference
kmer_hash.dy:263:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_hash.dy:318:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
kmer_hash.dy:318:3: portability: %lx in format string (no. 1) requires 'unsigned long' but the argument type is 'kmer_t {aka signed long long}'. [invalidPrintfArgType_uint]
kmer_hash.dy:319:3: portability: %lx in format string (no. 1) requires 'unsigned long' but the argument type is 'kmer_t {aka signed long long}'. [invalidPrintfArgType_uint]
kmer_hash.dy:118:5: error: Memory leak: khi [memleak]
kmer_hash.dy:133:3: error: Memory leak: khi.bucket [memleak]
kmer_hash.dy:115:3: warning: If memory allocation fails, then there is a possible null pointer dereference: khi [nullPointerOutOfMemory]
kmer_hash.dy:114:15: note: Assuming allocation function fails
kmer_hash.dy:114:15: note: Assignment 'khi=malloc(sizeof(struct KmerHashIndex))', assigned value is 0
kmer_hash.dy:115:3: note: Null pointer dereference
kmer_hash.dy:116:7: warning: If memory allocation fails, then there is a possible null pointer dereference: khi [nullPointerOutOfMemory]
kmer_hash.dy:114:15: note: Assuming allocation function fails
kmer_hash.dy:114:15: note: Assignment 'khi=malloc(sizeof(struct KmerHashIndex))', assigned value is 0
kmer_hash.dy:116:7: note: Null pointer dereference
kmer_hash.dy:120:3: warning: If memory allocation fails, then there is a possible null pointer dereference: khi [nullPointerOutOfMemory]
kmer_hash.dy:114:15: note: Assuming allocation function fails
kmer_hash.dy:114:15: note: Assignment 'khi=malloc(sizeof(struct KmerHashIndex))', assigned value is 0
kmer_hash.dy:116:19: note: Assuming condition is false
kmer_hash.dy:120:3: note: Null pointer dereference
kmer_hash.dy:121:3: warning: If memory allocation fails, then there is a possible null pointer dereference: khi [nullPointerOutOfMemory]
kmer_hash.dy:114:15: note: Assuming allocation function fails
kmer_hash.dy:114:15: note: Assignment 'khi=malloc(sizeof(struct KmerHashIndex))', assigned value is 0
kmer_hash.dy:116:19: note: Assuming condition is false
kmer_hash.dy:121:3: note: Null pointer dereference
kmer_hash.dy:125:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_hash.dy:123:15: note: Assuming allocation function fails
kmer_hash.dy:123:15: note: Assignment 'out=malloc(sizeof(struct KmerIndexInterface))', assigned value is 0
kmer_hash.dy:125:3: note: Null pointer dereference
kmer_hash.dy:126:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_hash.dy:123:15: note: Assuming allocation function fails
kmer_hash.dy:123:15: note: Assignment 'out=malloc(sizeof(struct KmerIndexInterface))', assigned value is 0
kmer_hash.dy:126:3: note: Null pointer dereference
kmer_hash.dy:127:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_hash.dy:123:15: note: Assuming allocation function fails
kmer_hash.dy:123:15: note: Assignment 'out=malloc(sizeof(struct KmerIndexInterface))', assigned value is 0
kmer_hash.dy:127:3: note: Null pointer dereference
kmer_hash.dy:128:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_hash.dy:123:15: note: Assuming allocation function fails
kmer_hash.dy:123:15: note: Assignment 'out=malloc(sizeof(struct KmerIndexInterface))', assigned value is 0
kmer_hash.dy:128:3: note: Null pointer dereference
kmer_hash.dy:130:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_hash.dy:123:15: note: Assuming allocation function fails
kmer_hash.dy:123:15: note: Assignment 'out=malloc(sizeof(struct KmerIndexInterface))', assigned value is 0
kmer_hash.dy:130:3: note: Null pointer dereference
kmer_hash.dy:131:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
kmer_hash.dy:123:15: note: Assuming allocation function fails
kmer_hash.dy:123:15: note: Assignment 'out=malloc(sizeof(struct KmerIndexInterface))', assigned value is 0
kmer_hash.dy:131:3: note: Null pointer dereference
kmer_hash.dy:167:8: style: Redundant initialization for 'hash'. The initialized value is overwritten before it is read. [redundantInitialization]
kmer_hash.dy:142:15: note: hash is initialized
kmer_hash.dy:167:8: note: hash is overwritten
kmer_hash.dy:252:7: style: Unused variable: i [unusedVariable]
wise-2.4.1/src/dnaindex/kmer_stat.c:21:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dnaindex/kwise.c:78:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
largeseqreader.dy:44:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
largeseqreader.dy:90:2: error: Common realloc mistake: 'seqbuffer' nulled but not freed upon failure [memleakOnRealloc]
largeseqreader.dy:93:2: error: Common realloc mistake: 'seqbuffer' nulled but not freed upon failure [memleakOnRealloc]
largeseqreader.dy:100:3: warning: If memory allocation fails, then there is a possible null pointer dereference: seqbuffer [nullPointerOutOfMemory]
largeseqreader.dy:71:21: note: Assuming allocation function fails
largeseqreader.dy:71:21: note: Assignment 'seqbuffer=calloc(4096,sizeof(char))', assigned value is 0
largeseqreader.dy:74:25: note: Assuming condition is false
largeseqreader.dy:100:3: note: Null pointer dereference
largeseqreader.dy:44:7: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
linkindex.dy:239:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
linkindex.dy:466:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
linkindex.dy:69:5: portability: %d in format string (no. 1) requires 'int' but the argument type is 'Wise2_LinkStream * {aka Wise2_LinkStream *}'. [invalidPrintfArgType_sint]
linkindex.dy:102:7: portability: %d in format string (no. 1) requires 'int' but the argument type is 'Wise2_LinkStream * {aka Wise2_LinkStream *}'. [invalidPrintfArgType_sint]
linkindex.dy:102:7: portability: %d in format string (no. 2) requires 'int' but the argument type is 'Wise2_LinkStream * {aka Wise2_LinkStream *}'. [invalidPrintfArgType_sint]
linkindex.dy:289:7: portability: %d in format string (no. 2) requires 'int' but the argument type is 'Wise2_LinkEdge * {aka Wise2_LinkEdge *}'. [invalidPrintfArgType_sint]
linkindex.dy:289:7: portability: %d in format string (no. 3) requires 'int' but the argument type is 'Wise2_LinkEdge * {aka Wise2_LinkEdge *}'. [invalidPrintfArgType_sint]
linkindex.dy:315:4: portability: %d in format string (no. 3) requires 'int' but the argument type is 'Wise2_LinkNumber * {aka Wise2_LinkNumber *}'. [invalidPrintfArgType_sint]
linkindex.dy:466:5: portability: %d in format string (no. 1) requires 'int' but the argument type is 'Wise2_LinkStream * {aka Wise2_LinkStream *}'. [invalidPrintfArgType_sint]
linkindex.dy:466:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'Wise2_LinkEdge * {aka Wise2_LinkEdge *}'. [invalidPrintfArgType_sint]
linkindex.dy:466:5: portability: %d in format string (no. 3) requires 'int' but the argument type is 'Wise2_LinkEdge * {aka Wise2_LinkEdge *}'. [invalidPrintfArgType_sint]
linkindex.dy:466:5: portability: %d in format string (no. 4) requires 'int' but the argument type is 'Wise2_LinkStream * {aka Wise2_LinkStream *}'. [invalidPrintfArgType_sint]
linkindex.dy:466:5: portability: %d in format string (no. 5) requires 'int' but the argument type is 'Wise2_LinkStream * {aka Wise2_LinkStream *}'. [invalidPrintfArgType_sint]
linkindex.dy:466:5: portability: %d in format string (no. 7) requires 'int' but the argument type is 'Wise2_LinkStream * {aka Wise2_LinkStream *}'. [invalidPrintfArgType_sint]
linkindex.dy:466:5: portability: %d in format string (no. 8) requires 'int' but the argument type is 'Wise2_LinkStream * {aka Wise2_LinkStream *}'. [invalidPrintfArgType_sint]
linkindex.dy:466:5: portability: %d in format string (no. 10) requires 'int' but the argument type is 'Wise2_LinkStream * {aka Wise2_LinkStream *}'. [invalidPrintfArgType_sint]
linkindex.dy:516:7: portability: %d in format string (no. 4) requires 'int' but the argument type is 'Wise2_LinkNumber * {aka Wise2_LinkNumber *}'. [invalidPrintfArgType_sint]
linkindex.dy:205:3: warning: Either the condition 'runner!=NULL' is redundant or there is possible null pointer dereference: runner. [nullPointerRedundantCheck]
linkindex.dy:165:17: note: Assuming that condition 'runner!=NULL' is not redundant
linkindex.dy:205:3: note: Null pointer dereference
linkindex.dy:530:17: warning: Either the condition 'lna->array[dns->seq[i].number]==NULL' is redundant or there is possible null pointer dereference: lna->array[dns->seq[i].number]. [nullPointerRedundantCheck]
linkindex.dy:540:40: note: Assuming that condition 'lna->array[dns->seq[i].number]==NULL' is not redundant
linkindex.dy:530:17: note: Null pointer dereference
linkindex.dy:537:20: warning: Either the condition 'lna->array[dns->seq[i].number]==NULL' is redundant or there is possible null pointer dereference: lna->array[dns->seq[i].number]. [nullPointerRedundantCheck]
linkindex.dy:540:40: note: Assuming that condition 'lna->array[dns->seq[i].number]==NULL' is not redundant
linkindex.dy:537:20: note: Null pointer dereference
linkindex.dy:313:20: style: Local variable 'stream' shadows outer variable [shadowVariable]
linkindex.dy:229:16: note: Shadowed declaration
linkindex.dy:313:20: note: Shadow variable
linkindex.dy:59:16: style: Variable 'prev' can be declared as pointer to const [constVariablePointer]
linkindex.dy:463:65: style: Parameter 'l_two' can be declared as pointer to const [constParameterPointer]
linkindex.dy:545:23: style: Variable 'edge' can be declared as pointer to const [constVariablePointer]
linkindex.dy:507:20: style: Variable 'seen_end' is assigned a value that is never used. [unreadVariable]
linkindex.dy:506:11: style: Unused variable: k [unusedVariable]
linkindex.dy:507:11: style: Variable 'seen_end' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/dnaindex/make_shotgun.c:16:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
shotgun.dy:37:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
shotgun.dy:50:7: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: seqstr [nullPointerOutOfMemory]
shotgun.dy:42:18: note: Assuming allocation function fails
shotgun.dy:42:18: note: Assignment 'seqstr=calloc(shot->read_length+1,sizeof(char))', assigned value is 0
shotgun.dy:50:7: note: Null pointer dereference
shotgun.dy:53:5: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: seqstr [nullPointerOutOfMemory]
shotgun.dy:42:18: note: Assuming allocation function fails
shotgun.dy:42:18: note: Assignment 'seqstr=calloc(shot->read_length+1,sizeof(char))', assigned value is 0
shotgun.dy:53:5: note: Null pointer dereference
shotgun.dy:27:43: style: Parameter 'shot' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/dnaindex/test_compara.c:16:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dnaindex/test_compara.c:72:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dnaindex/test_compara.c:9:17: style: Parameter 'tv1' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/dnaindex/test_compara.c:10:17: style: Parameter 'tv2' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/dnaindex/test_compara.c:30:23: style: Variable 'hloi' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/dnaindex/test_compara.c:34:22: style: Variable 't' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/dnaindex/test_compara.c:47:8: style: Variable 'hloi' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/dnaindex/test_compara.c:65:5: style: Variable 't' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/dnaindex/test_compara.c:27:7: style: Unused variable: i [unusedVariable]
wise-2.4.1/src/dnaindex/test_compara.c:29:13: style: Unused variable: hl [unusedVariable]
wise-2.4.1/src/dnaindex/test_euler.c:13:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dnaindex/test_kmer.c:32:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dnaindex/test_linkindex.c:7:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
vectorindex.dy:46:3: style: Obsolescent function 'bzero' called. It is recommended to use 'memset' instead. [prohibitedbzeroCalled]
vectorindex.dy:46:9: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
vectorindex.dy:44:15: note: Assuming allocation function fails
vectorindex.dy:44:15: note: Assignment 'out=malloc(sizeof(struct KmerVectorPosition))', assigned value is 0
vectorindex.dy:46:9: note: Null pointer dereference
api.dy:507:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
api.dy:1104:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
api.dy:1165:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
api.dy:1104:10: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
api.dy:1106:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
api.dy:1165:9: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
api.dy:1167:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
api.dy:47:22: style: Variable 'obj' can be declared as pointer to const [constVariablePointer]
api.dy:112:48: style: Parameter 'module' can be declared as pointer to const [constParameterPointer]
api.dy:170:48: style: Parameter 'package' can be declared as pointer to const [constParameterPointer]
api.dy:170:77: style: Parameter 'objectname' can be declared as pointer to const [constParameterPointer]
api.dy:244:46: style: Parameter 'module' can be declared as pointer to const [constParameterPointer]
api.dy:290:47: style: Parameter 'package' can be declared as pointer to const [constParameterPointer]
api.dy:290:62: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
api.dy:319:47: style: Parameter 'package' can be declared as pointer to const [constParameterPointer]
api.dy:349:49: style: Parameter 'package_name' can be declared as pointer to const [constParameterPointer]
api.dy:354:22: style: Variable 'obj' can be declared as pointer to const [constVariablePointer]
api.dy:368:22: style: Variable 'obj' can be declared as pointer to const [constVariablePointer]
api.dy:405:46: style: Parameter 'package_name' can be declared as pointer to const [constParameterPointer]
api.dy:444:10: style: Variable 'temp' can be declared as pointer to const [constVariablePointer]
api.dy:551:65: style: Parameter 'package' can be declared as pointer to const [constParameterPointer]
api.dy:556:10: style: Variable 'listappend' can be declared as pointer to const [constVariablePointer]
api.dy:839:42: style: Parameter 'api' can be declared as pointer to const [constParameterPointer]
api.dy:839:53: style: Parameter 'package_name' can be declared as pointer to const [constParameterPointer]
api.dy:923:46: style: Parameter 'package_name' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/dyc/compugen.c:467:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dyc/compugen.c:524:60: error: Found an exit path from function with non-void return type that has missing return statement [missingReturn]
wise-2.4.1/src/dyc/compugen.c:1165:0: error: Found an exit path from function with non-void return type that has missing return statement [missingReturn]
wise-2.4.1/src/dyc/compugen.c:1052:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1052:3: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1052:15: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1052:15: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1052:27: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1052:27: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1054:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1054:3: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1054:15: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1054:15: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1054:27: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1054:27: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1054:45: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1054:45: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1054:61: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1054:61: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1054:73: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1054:73: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1056:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1056:3: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1056:20: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1056:20: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1056:37: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1056:37: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1056:50: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1056:50: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1056:62: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1056:62: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1056:73: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1056:73: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1056:84: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1056:84: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1084:5: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1081:28: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1081:8: note: Assignment 'out=(struct OneModel*)malloc(sizeof(struct OneModel))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1084:5: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1084:26: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1081:28: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1081:8: note: Assignment 'out=(struct OneModel*)malloc(sizeof(struct OneModel))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1084:26: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1084:51: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1081:28: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1081:8: note: Assignment 'out=(struct OneModel*)malloc(sizeof(struct OneModel))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1084:51: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1088:5: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1081:28: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1081:8: note: Assignment 'out=(struct OneModel*)malloc(sizeof(struct OneModel))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1088:5: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1092:5: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1081:28: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1081:8: note: Assignment 'out=(struct OneModel*)malloc(sizeof(struct OneModel))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1092:5: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1095:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1081:28: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1081:8: note: Assignment 'out=(struct OneModel*)malloc(sizeof(struct OneModel))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1095:3: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1097:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1081:28: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1081:8: note: Assignment 'out=(struct OneModel*)malloc(sizeof(struct OneModel))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1097:3: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1099:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1081:28: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1081:8: note: Assignment 'out=(struct OneModel*)malloc(sizeof(struct OneModel))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1099:3: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:1099:21: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/dyc/compugen.c:1081:28: note: Assuming allocation function fails
wise-2.4.1/src/dyc/compugen.c:1081:8: note: Assignment 'out=(struct OneModel*)malloc(sizeof(struct OneModel))', assigned value is 0
wise-2.4.1/src/dyc/compugen.c:1099:21: note: Null pointer dereference
wise-2.4.1/src/dyc/compugen.c:205:31: style: Parameter 'in_str' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/dyc/compugen.c:367:34: style: Parameter 'start_state_name' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/dyc/compugen.c:368:14: style: Parameter 'end_state_name' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/dyc/compugen.c:796:46: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/dyc/compugen.c:864:40: style: Parameter 'dy_func_name' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/dyc/compugen.c:1154:37: style: Parameter 'target_type' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/dyc/compugen.c:1182:46: style: Parameter 'state_name' can be declared as pointer to const [constParameterPointer]
dbmpi.dy:50:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dbmpi.dy:287:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dbmpi.dy:230:60: warning: Either the condition 'gm->ttype!=NULL' is redundant or there is possible null pointer dereference: gm->ttype. [nullPointerRedundantCheck]
dbmpi.dy:234:41: note: Assuming that condition 'gm->ttype!=NULL' is not redundant
dbmpi.dy:230:60: note: Null pointer dereference
dbthread.dy:563:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dbthread.dy:21:62: style: Parameter 'dpi' can be declared as pointer to const [constParameterPointer]
dbthread.dy:175:60: style: Parameter 'dpi' can be declared as pointer to const [constParameterPointer]
display.dy:116:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
display.dy:369:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
display.dy:428:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
display.dy:492:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
display.dy:574:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
display.dy:613:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
display.dy:718:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
display.dy:752:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
display.dy:373:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
display.dy:384:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
display.dy:432:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
display.dy:443:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
display.dy:496:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
display.dy:507:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
display.dy:524:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
display.dy:533:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
display.dy:554:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
display.dy:97:41: style: Parameter 'dfp' can be declared as pointer to const [constParameterPointer]
display.dy:97:59: style: Parameter 'a2d' can be declared as pointer to const [constParameterPointer]
display.dy:326:19: style: Variable 'temp' can be declared as pointer to const [constVariablePointer]
display.dy:342:71: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
display.dy:429:10: style: Variable 'runner' can be declared as pointer to const [constVariablePointer]
display.dy:810:53: style: Parameter 'a2dr' can be declared as pointer to const [constParameterPointer]
display.dy:833:47: style: Parameter 'a2df' can be declared as pointer to const [constParameterPointer]
display.dy:619:8: style: Variable 'base' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/dyc/docugen.c:133:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dyc/docugen.c:13:33: style: Parameter 'node' can be declared as pointer to const. However it seems that 'place_k_loop' is a callback function, if 'node' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise-2.4.1/src/dyc/docugen.c:211:69: note: You might need to cast the function pointer here
wise-2.4.1/src/dyc/docugen.c:13:33: note: Parameter 'node' can be declared as pointer to const
wise-2.4.1/src/dyc/docugen.c:15:19: style: Variable 'trans' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/dyc/docugen.c:246:11: style: Variable 'sc' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/dyc/docugen.c:206:11: style: Variable 'range' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/dyc/docugen.c:248:6: style: Variable 'sc' is assigned a value that is never used. [unreadVariable]
dy2om.dy:240:15: style: Variable 'su' can be declared as pointer to const [constVariablePointer]
dy2om.dy:556:41: style: Parameter 'ot' can be declared as pointer to const [constParameterPointer]
dy2om.dy:132:16: style: Unused variable: et [unusedVariable]
wise-2.4.1/src/dyc/dyc.c:108:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dyc/dyc.c:454:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dyc/dyc.c:690:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dyc/dyc.c:125:2: warning: Either the condition 'fi==NULL' is redundant or there is possible null pointer dereference: fi. [nullPointerRedundantCheck]
wise-2.4.1/src/dyc/dyc.c:126:9: note: Assuming that condition 'fi==NULL' is not redundant
wise-2.4.1/src/dyc/dyc.c:125:2: note: Null pointer dereference
wise-2.4.1/src/dyc/dyc.c:283:35: style: Parameter 'api' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/dyc/dyc.c:452:10: style: Variable 'rt' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/dyc/dyc.c:695:17: style: Variable 'doinfo' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/dyc/dyc.c:696:17: style: Variable 'no_config_mts' is assigned a value that is never used. [unreadVariable]
dyna2.dy:315:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
dyna2.dy:1274:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dyna2.dy:1305:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dyna2.dy:1581:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
dyna2.dy:1625:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
dyna2.dy:1655:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dyna2.dy:1893:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dyna2.dy:1630:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
dyna2.dy:1631:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
dyna2.dy:1632:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
dyna2.dy:1066:3: warning: Either the condition 'temp==NULL' is redundant or there is possible null pointer dereference: temp. [nullPointerRedundantCheck]
dyna2.dy:1068:12: note: Assuming that condition 'temp==NULL' is not redundant
dyna2.dy:1066:3: note: Null pointer dereference
dyna2.dy:1077:3: warning: Either the condition 'temp==NULL' is redundant or there is possible null pointer dereference: temp. [nullPointerRedundantCheck]
dyna2.dy:1079:12: note: Assuming that condition 'temp==NULL' is not redundant
dyna2.dy:1077:3: note: Null pointer dereference
dyna2.dy:1085:3: warning: Either the condition 'temp==NULL' is redundant or there is possible null pointer dereference: temp. [nullPointerRedundantCheck]
dyna2.dy:1087:12: note: Assuming that condition 'temp==NULL' is not redundant
dyna2.dy:1085:3: note: Null pointer dereference
dyna2.dy:692:56: style: Same expression on both sides of '&&'. [duplicateExpression]
dyna2.dy:1631:10: style: Variable 'runner' is reassigned a value before the old one has been used. [redundantAssignment]
dyna2.dy:1630:10: note: runner is assigned
dyna2.dy:1631:10: note: runner is overwritten
dyna2.dy:447:14: style: Local variable 'expr' shadows outer function [shadowFunction]
wise-2.4.1/src/dyc/dynfile.h:261:6: note: Shadowed declaration
dyna2.dy:447:14: note: Shadow variable
dyna2.dy:179:41: style: Parameter 'gm' can be declared as pointer to const [constParameterPointer]
dyna2.dy:195:58: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
dyna2.dy:781:22: style: Variable 'temp' can be declared as pointer to const [constVariablePointer]
dyna2.dy:796:22: style: Variable 'temp' can be declared as pointer to const [constVariablePointer]
dyna2.dy:1155:35: style: Parameter 'type' can be declared as pointer to const [constParameterPointer]
dyna2.dy:1163:30: style: Parameter 'type' can be declared as pointer to const [constParameterPointer]
dyna2.dy:1248:35: style: Parameter 'cell' can be declared as pointer to const [constParameterPointer]
dyna2.dy:1558:7: style: Variable 'out' is assigned a value that is never used. [unreadVariable]
dyna2.dy:1836:7: style: Variable 'out' is assigned a value that is never used. [unreadVariable]
dyna2.dy:2040:9: style: Variable 'out' is assigned a value that is never used. [unreadVariable]
dynadb.dy:23:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dynadb.dy:199:88: style: Parameter 'dpi' can be declared as pointer to const [constParameterPointer]
dynadebug.dy:169:5: warning: Redundant code: Found unused function. [constStatement]
dynadebug.dy:95:11: style: Unused variable: m [unusedVariable]
dynadebug.dy:215:10: style: Unused variable: arg_str [unusedVariable]
dynadebug.dy:216:10: style: Unused variable: chainstr [unusedVariable]
dynadebug.dy:218:9: style: Unused variable: l [unusedVariable]
dynafunc.dy:475:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dynafunc.dy:506:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dynafunc.dy:671:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FATAL [valueFlowBailoutIncompleteVar]
dynafunc.dy:1053:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WARNING [valueFlowBailoutIncompleteVar]
dynafunc.dy:2153:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dynafunc.dy:2360:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dynafunc.dy:25:76: style: Parameter 'dpi' can be declared as pointer to const [constParameterPointer]
dynafunc.dy:598:84: style: Parameter 'dpi' can be declared as pointer to const [constParameterPointer]
dynafunc.dy:1140:10: style: Variable 'matrix_tag' can be declared as pointer to const [constVariablePointer]
dynafunc.dy:1141:10: style: Variable 'special_tag' can be declared as pointer to const [constVariablePointer]
dynafunc.dy:2052:95: style: Parameter 'bestscore' can be declared as pointer to const [constParameterPointer]
dynafunc.dy:1140:21: style: Variable 'matrix_tag' is assigned a value that is never used. [unreadVariable]
dynafunc.dy:1141:22: style: Variable 'special_tag' is assigned a value that is never used. [unreadVariable]
dynafunc.dy:1140:10: style: Variable 'matrix_tag' is assigned a value that is never used. [unreadVariable]
dynafunc.dy:1141:10: style: Variable 'special_tag' is assigned a value that is never used. [unreadVariable]
dynashadow.dy:570:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dynashadow.dy:1855:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WARNING [valueFlowBailoutIncompleteVar]
dynashadow.dy:1921:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WARNING [valueFlowBailoutIncompleteVar]
dynashadow.dy:2163:3: warning: Redundant code: Found unused function. [constStatement]
dynashadow.dy:2261:3: warning: Redundant code: Found unused function. [constStatement]
dynashadow.dy:1798:14: style: Variable 'fi' can be declared as pointer to const [constVariablePointer]
dynashadow.dy:1799:6: style: Variable 'fi' is assigned a value that is never used. [unreadVariable]
dynfile.dy:622:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dynfile.dy:640:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dynfile.dy:719:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dynfile.dy:742:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dynfile.dy:764:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dynfile.dy:786:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dynfile.dy:810:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dynfile.dy:831:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dynfile.dy:855:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dynfile.dy:871:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dynfile.dy:897:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dynfile.dy:919:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dynfile.dy:937:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dynfile.dy:1149:3: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
dynfile.dy:56:47: style: Parameter 'mod_name' can be declared as pointer to const [constParameterPointer]
dynfile.dy:139:60: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
dynfile.dy:232:46: style: Parameter 'fi' can be declared as pointer to const [constParameterPointer]
dynfile.dy:378:43: style: Parameter 'one' can be declared as pointer to const. However it seems that 'compare_two_FuncInfo_alpha' is a callback function, if 'one' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
dynfile.dy:332:22: note: You might need to cast the function pointer here
dynfile.dy:378:43: note: Parameter 'one' can be declared as pointer to const
dynfile.dy:378:58: style: Parameter 'two' can be declared as pointer to const. However it seems that 'compare_two_FuncInfo_alpha' is a callback function, if 'two' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
dynfile.dy:332:22: note: You might need to cast the function pointer here
dynfile.dy:378:58: note: Parameter 'two' can be declared as pointer to const
dynfile.dy:399:41: style: Parameter 'one' can be declared as pointer to const. However it seems that 'compare_two_FuncInfo_pos' is a callback function, if 'one' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
dynfile.dy:335:22: note: You might need to cast the function pointer here
dynfile.dy:399:41: note: Parameter 'one' can be declared as pointer to const
dynfile.dy:399:56: style: Parameter 'two' can be declared as pointer to const. However it seems that 'compare_two_FuncInfo_pos' is a callback function, if 'two' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
dynfile.dy:335:22: note: You might need to cast the function pointer here
dynfile.dy:399:56: note: Parameter 'two' can be declared as pointer to const
dynfile.dy:481:19: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
dynfile.dy:555:19: style: Variable 'temp' can be declared as pointer to const [constVariablePointer]
dynfile.dy:568:19: style: Variable 'temp' can be declared as pointer to const [constVariablePointer]
dynfile.dy:1039:32: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
dynfile.dy:1149:7: style: Variable 'dfp' is assigned a value that is never used. [unreadVariable]
dynfile.dy:780:1: error: va_list 'ap' was opened but not closed by va_end(). [va_end_missing]
dynfile.dy:804:1: error: va_list 'ap' was opened but not closed by va_end(). [va_end_missing]
dynfile.dy:824:1: error: va_list 'ap' was opened but not closed by va_end(). [va_end_missing]
dynfile.dy:850:1: error: va_list 'ap' was opened but not closed by va_end(). [va_end_missing]
dynfile.dy:932:1: error: va_list 'ap' was opened but not closed by va_end(). [va_end_missing]
dynfile.dy:950:1: error: va_list 'ap' was opened but not closed by va_end(). [va_end_missing]
dyshatter.dy:92:13: style: Variable 'ai' can be declared as pointer to const [constVariablePointer]
dyshatter.dy:100:6: style: Variable 'ai' is assigned a value that is never used. [unreadVariable]
dyshatter.dy:95:7: style: Unused variable: j [unusedVariable]
exprtree.dy:114:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
exprtree.dy:199:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
friend.dy:24:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
friend.dy:24:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
friend.dy:25:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
friend.dy:25:10: style: Variable 'runner' is reassigned a value before the old one has been used. [redundantAssignment]
friend.dy:24:10: note: runner is assigned
friend.dy:25:10: note: runner is overwritten
friend.dy:39:49: style: Parameter 'fr' can be declared as pointer to const [constParameterPointer]
ftext.dy:28:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
ftext.dy:105:34: style: Parameter 'ft' can be declared as pointer to const [constParameterPointer]
ftext.dy:105:44: style: Parameter 'header' can be declared as pointer to const [constParameterPointer]
ftext.dy:105:79: style: Parameter 'blank_text' can be declared as pointer to const [constParameterPointer]
ftext.dy:111:8: style: Variable 'space' can be declared as const array [constVariable]
ftext.dy:154:26: style: Parameter 'ft' can be declared as pointer to const [constParameterPointer]
ftext.dy:238:29: style: Parameter 'pre' can be declared as pointer to const [constParameterPointer]
ftext.dy:238:42: style: Parameter 'fb' can be declared as pointer to const [constParameterPointer]
funcinfo.dy:447:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
funcinfo.dy:466:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
funcinfo.dy:503:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
funcinfo.dy:522:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
funcinfo.dy:627:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
funcinfo.dy:548:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
funcinfo.dy:560:13: warning: Either the condition 'ari!=NULL' is redundant or there is possible null pointer dereference: ari. [nullPointerRedundantCheck]
funcinfo.dy:563:18: note: Assuming that condition 'ari!=NULL' is not redundant
funcinfo.dy:560:13: note: Null pointer dereference
funcinfo.dy:343:8: style: Variable 'name' is reassigned a value before the old one has been used. [redundantAssignment]
funcinfo.dy:341:8: note: name is assigned
funcinfo.dy:343:8: note: name is overwritten
funcinfo.dy:156:27: style: Parameter 'fi' can be declared as pointer to const [constParameterPointer]
funcinfo.dy:190:35: style: Parameter 'one' can be declared as pointer to const. However it seems that 'compare_ArgInfo_pos' is a callback function, if 'one' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
funcinfo.dy:185:20: note: You might need to cast the function pointer here
funcinfo.dy:190:35: note: Parameter 'one' can be declared as pointer to const
funcinfo.dy:190:49: style: Parameter 'two' can be declared as pointer to const. However it seems that 'compare_ArgInfo_pos' is a callback function, if 'two' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
funcinfo.dy:185:20: note: You might need to cast the function pointer here
funcinfo.dy:190:49: note: Parameter 'two' can be declared as pointer to const
funcinfo.dy:433:53: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
input.dy:39:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
input.dy:77:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
input.dy:100:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
input.dy:131:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
input.dy:131:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
input.dy:136:10: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
input.dy:137:10: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
input.dy:126:10: style: Variable 'runner' can be declared as pointer to const [constVariablePointer]
kbestsearch.dy:65:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
kbestsearch.dy:274:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
kbestsearch.dy:114:9: style: Condition '0&&gm->qtype!=NULL' is always false [knownConditionTrueFalse]
kbestsearch.dy:466:22: style: Variable 'state' can be declared as pointer to const [constVariablePointer]
kbestsearch.dy:520:34: style: Parameter 'two' can be declared as pointer to const. However it seems that 'comp_Transition' is a callback function, if 'two' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
kbestsearch.dy:505:25: note: You might need to cast the function pointer here
kbestsearch.dy:520:34: note: Parameter 'two' can be declared as pointer to const
kbestsearch.dy:520:51: style: Parameter 'one' can be declared as pointer to const. However it seems that 'comp_Transition' is a callback function, if 'one' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
kbestsearch.dy:505:25: note: You might need to cast the function pointer here
kbestsearch.dy:520:51: note: Parameter 'one' can be declared as pointer to const
kbestsearch.dy:566:35: style: Parameter 'trans' can be declared as pointer to const [constParameterPointer]
labelmaster.dy:71:28: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
labelmaster.dy:95:56: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
labelmaster.dy:107:55: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
lex.yy.c:554:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
lex.yy.c:919:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
lex.yy.c:1110:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
lex.yy.c:1466:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
lex.yy.c:919:3: style: Redundant initialization for 'c'. The initialized value is overwritten before it is read. [redundantInitialization]
lex.yy.c:919:3: note: c is initialized
lex.yy.c:919:3: note: c is overwritten
calc.l:36:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
calc.l:45:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
calc.l:54:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
calc.l:63:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
calc.l:70:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
lex.yy.c:827:17: style: Variable 'source' can be declared as pointer to const [constVariablePointer]
lex.yy.c:1039:18: style: Variable 'source' can be declared as pointer to const [constVariablePointer]
lex.yy.c:1369:15: style: Parameter 'bytes' can be declared as pointer to const [constParameterPointer]
lex.yy.c:1463:6: style: Parameter 'msg' can be declared as const array [constParameter]
linkmap.dy:20:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
linkmap.dy:76:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lm [valueFlowBailoutIncompleteVar]
linkmap.c:292:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LinkSetLISTLENGTH [valueFlowBailoutIncompleteVar]
linkmap.c:343:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LinkSetLISTLENGTH [valueFlowBailoutIncompleteVar]
linkmap.dy:37:7: style: Variable 'c' is reassigned a value before the old one has been used. [redundantAssignment]
linkmap.dy:30:7: note: c is assigned
linkmap.dy:37:7: note: c is overwritten
linkmap.dy:18:48: style: Parameter 'startid' can be declared as pointer to const [constParameterPointer]
linkmap.dy:18:63: style: Parameter 'stopid' can be declared as pointer to const [constParameterPointer]
linkmap.dy:24:13: style: Variable 'lm' can be declared as pointer to const [constVariablePointer]
linkmap.dy:47:46: style: Parameter 'urlstub' can be declared as pointer to const [constParameterPointer]
linkmap.dy:70:36: style: Parameter 'word' can be declared as pointer to const [constParameterPointer]
linkmap.dy:70:51: style: Parameter 'ls' can be declared as pointer to const [constParameterPointer]
linkmap.dy:32:12: error: Uninitialized variable: buffer [uninitvar]
linkmap.dy:37:7: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
linkmap.dy:39:13: style: Variable 'lm' is assigned a value that is never used. [unreadVariable]
method.dy:334:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
method.dy:404:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
method.dy:510:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
method.dy:576:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
method.dy:133:54: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
method.dy:177:33: style: Parameter 'ma' can be declared as pointer to const [constParameterPointer]
method.dy:183:23: style: Parameter 'ty' can be declared as pointer to const [constParameterPointer]
method.dy:376:33: style: Parameter 'ty' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/dyc/module.c:231:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WARNING [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dyc/module.c:260:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WARNING [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dyc/module.c:295:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dyc/module.c:482:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WARNING [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dyc/module.c:565:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PEDANTIC [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dyc/module.c:600:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WARNING [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dyc/module.c:619:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WARNING [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dyc/module.c:320:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/dyc/module.c:321:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise-2.4.1/src/dyc/module.c:321:13: style: Variable 'runner' is reassigned a value before the old one has been used. [redundantAssignment]
wise-2.4.1/src/dyc/module.c:320:13: note: runner is assigned
wise-2.4.1/src/dyc/module.c:321:13: note: runner is overwritten
wise-2.4.1/src/dyc/module.c:293:44: style: Parameter 'fend' can be declared as pointer to const [constParameterPointer]
modulefunc.dy:104:10: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
modulefunc.dy:113:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
modulefunc.dy:120:10: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
modulefunc.dy:54:79: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
modulefunc.dy:90:43: style: Parameter 'mf' can be declared as pointer to const [constParameterPointer]
objectinfo.dy:21:83: debug: Function::addArguments found argument 'fgets_func' with varid 0. [varid0]
objectinfo.dy:27:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fgets_func [valueFlowBailoutIncompleteVar]
optimiser.dy:175:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cse [valueFlowBailoutIncompleteVar]
optimiser.dy:82:37: style: Parameter 'etr' can be declared as pointer to const. However it seems that 'cses_expr_placer' is a callback function, if 'etr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
optimiser.dy:66:54: note: You might need to cast the function pointer here
optimiser.dy:82:37: note: Parameter 'etr' can be declared as pointer to const
optimiser.dy:240:46: style: Parameter 'start' can be declared as pointer to const [constParameterPointer]
telegraph.dy:17:45: style: Parameter 'gm' can be declared as pointer to const [constParameterPointer]
type.dy:133:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
type.dy:440:62: style: Condition 'word!=NULL&&strcmp(word,sunit->no_accept)==0&&0' is always false [knownConditionTrueFalse]
type.dy:268:15: style: Variable 'su' can be declared as pointer to const [constVariablePointer]
type.dy:384:15: style: Variable 'sunit' can be declared as pointer to const [constVariablePointer]
wisec.dy:47:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
wisec.dy:217:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
wisec.dy:343:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WARNING [valueFlowBailoutIncompleteVar]
wisec.dy:718:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WARNING [valueFlowBailoutIncompleteVar]
wisec.dy:861:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WARNING [valueFlowBailoutIncompleteVar]
wisec.dy:1051:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WARNING [valueFlowBailoutIncompleteVar]
wisec.dy:1165:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
wisec.dy:1356:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
wisec.dy:232:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wisec.dy:1305:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wisec.dy:89:20: style: Variable 'mf' can be declared as pointer to const [constVariablePointer]
wisec.dy:215:10: style: Variable 'runner' can be declared as pointer to const [constVariablePointer]
wisec.dy:415:38: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
wisec.dy:432:40: style: Parameter 'se' can be declared as pointer to const [constParameterPointer]
wisec.dy:1163:33: style: Parameter 'element' can be declared as pointer to const [constParameterPointer]
wisec.dy:1184:33: style: Parameter 'se' can be declared as pointer to const [constParameterPointer]
wisec.dy:1274:36: style: Parameter 'sh' can be declared as pointer to const [constParameterPointer]
wisec.dy:1286:38: style: Parameter 'sh' can be declared as pointer to const [constParameterPointer]
wisec.dy:1300:10: style: Variable 'runner' can be declared as pointer to const [constVariablePointer]
wisec.dy:1530:41: style: Parameter 'se' can be declared as pointer to const [constParameterPointer]
wisec.dy:1305:14: style: Variable 'runner' is assigned a value that is never used. [unreadVariable]
wisec.dy:1361:17: style: Variable 'isfunc' is assigned a value that is never used. [unreadVariable]
calc.y:89:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
calc.y:707:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ETR_STATEMENT [valueFlowBailoutIncompleteVar]
calc.y:355:13: error: Array 'yyv[150]' accessed at index -1, which is out of bounds. [negativeIndex]
calc.y:356:13: error: Array 'yys[150]' accessed at index -1, which is out of bounds. [negativeIndex]
calc.y:364:2: style: Statements following 'goto' will never be executed. [unreachableCode]
calc.y:374:2: style: Label 'yynewstate' is not used. There is #if in function body so the label might be used in code that is removed by the preprocessor. [unusedLabelConfiguration]
calc.y:547:4: warning: Label 'yyerrlab' is not used. There is #if in function body so the label might be used in code that is removed by the preprocessor. Should this be a 'case' of the enclosing switch()? [unusedLabelSwitchConfiguration]
calc.y:554:14: style: Variable 'yy_state' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/dynamite_examples/dbsearch.c:7:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dynamite_examples/dbsearch.c:96:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_OK [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dynamite_examples/est2gen.c:84:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dynamite_examples/est2gen.c:71:25: style: Variable 'has_outputted' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/dynamite_examples/est2gen.c:62:9: style: Unused variable: cdna_open [unusedVariable]
wise-2.4.1/src/dynamite_examples/est2gen.c:62:19: style: Unused variable: cdna_ext [unusedVariable]
wise-2.4.1/src/dynamite_examples/est2gen.c:62:28: style: Unused variable: gen_open [unusedVariable]
wise-2.4.1/src/dynamite_examples/est2gen.c:62:37: style: Unused variable: gen_ext [unusedVariable]
wise-2.4.1/src/dynamite_examples/est2gen.c:62:45: style: Unused variable: intron_open [unusedVariable]
wise-2.4.1/src/dynamite_examples/est2gen.c:71:11: style: Variable 'has_outputted' is assigned a value that is never used. [unreadVariable]
estgendisplay.dy:98:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BC_RIGHT [valueFlowBailoutIncompleteVar]
estgendisplay.dy:81:46: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
estgendisplay.dy:23:10: style: Unused variable: temp [unusedVariable]
wise-2.4.1/src/dynamite_examples/psw.c:68:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dynamite_examples/psw.c:47:25: style: Variable 'has_outputted' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/dynamite_examples/psw.c:47:11: style: Variable 'has_outputted' is assigned a value that is never used. [unreadVariable]
seqaligndisplay.dy:97:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BC_RIGHT [valueFlowBailoutIncompleteVar]
seqaligndisplay.dy:84:43: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
seqaligndisplay.dy:23:10: style: Unused variable: temp [unusedVariable]
aln.dy:1037:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
aln.dy:1183:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
aln.dy:430:15: warning: Opposite inner 'if' condition leads to a dead code block. [oppositeInnerCondition]
aln.dy:429:14: note: outer condition: alc!=NULL
aln.dy:430:15: note: opposite inner condition: alc==NULL
aln.dy:1015:7: warning: fprintf format string requires 1 parameter but 2 are given. [wrongPrintfScanfArgNum]
aln.dy:1093:5: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
aln.dy:1189:3: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
aln.dy:300:10: style: Variable 'prev' is reassigned a value before the old one has been used. [redundantAssignment]
aln.dy:254:10: note: prev is assigned
aln.dy:300:10: note: prev is overwritten
aln.dy:300:10: style: Variable 'prev' is reassigned a value before the old one has been used. [redundantAssignment]
aln.dy:292:7: note: prev is assigned
aln.dy:300:10: note: prev is overwritten
aln.dy:563:38: style: Parameter 'alc' can be declared as pointer to const [constParameterPointer]
aln.dy:889:60: style: Parameter 'start' can be declared as pointer to const [constParameterPointer]
aln.dy:1161:34: style: Parameter 'alu' can be declared as pointer to const [constParameterPointer]
aln.dy:1180:41: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
aln.c:2287:46: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
aln.c:2334:36: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
aln.c:2378:39: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
aln.c:2422:38: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
aln.c:2469:38: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
aln.c:2513:47: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
aln.c:2557:36: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
aln.c:2601:34: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
aln.c:2645:36: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
aln.c:2689:44: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
aln.c:2733:41: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
aln.c:2777:44: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
aln.c:2821:44: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
aln.c:2865:50: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
aln.c:2909:48: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
aln.c:2953:46: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
aln.c:2997:48: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
aln.c:3041:46: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
aln.dy:1090:8: style: Variable 'base' is assigned a value that is never used. [unreadVariable]
alnconvert.dy:36:66: style: Parameter 'label1' can be declared as pointer to const [constParameterPointer]
alnconvert.dy:36:80: style: Parameter 'label2' can be declared as pointer to const [constParameterPointer]
alnrange.dy:63:31: style: Parameter 'alr' can be declared as pointer to const [constParameterPointer]
alnrange.dy:95:39: style: Parameter 'one' can be declared as pointer to const. However it seems that 'Wise2_compare_AlnRange_start' is a callback function, if 'one' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
alnrange.dy:80:24: note: You might need to cast the function pointer here
alnrange.dy:95:39: note: Parameter 'one' can be declared as pointer to const
alnrange.dy:95:54: style: Parameter 'two' can be declared as pointer to const. However it seems that 'Wise2_compare_AlnRange_start' is a callback function, if 'two' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
alnrange.dy:80:24: note: You might need to cast the function pointer here
alnrange.dy:95:54: note: Parameter 'two' can be declared as pointer to const
alnrange.c:510:39: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
alnrange.c:554:39: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
alnrange.c:598:43: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
alnrange.c:642:38: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
alnrange.c:686:38: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
alnrange.c:730:42: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
alnrange.c:774:43: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
alnrange.c:818:42: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
alnrange.c:862:44: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
alnrange.c:909:42: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
arrayseqlookup.dy:452:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
arrayseqlookup.dy:450:15: note: Assuming allocation function fails
arrayseqlookup.dy:450:15: note: Assignment 'out=malloc(sizeof(struct ArraySeqHead))', assigned value is 0
arrayseqlookup.dy:452:3: note: Null pointer dereference
arrayseqlookup.dy:453:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
arrayseqlookup.dy:450:15: note: Assuming allocation function fails
arrayseqlookup.dy:450:15: note: Assignment 'out=malloc(sizeof(struct ArraySeqHead))', assigned value is 0
arrayseqlookup.dy:453:3: note: Null pointer dereference
arrayseqlookup.dy:454:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
arrayseqlookup.dy:450:15: note: Assuming allocation function fails
arrayseqlookup.dy:450:15: note: Assignment 'out=malloc(sizeof(struct ArraySeqHead))', assigned value is 0
arrayseqlookup.dy:454:3: note: Null pointer dereference
arrayseqlookup.dy:77:55: style: Parameter 'asl' can be declared as pointer to const [constParameterPointer]
arrayseqlookup.dy:170:25: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
arrayseqlookup.dy:189:36: style: Parameter 'data' can be declared as pointer to const. However it seems that 'Wise2_free_arrayhead_results' is a callback function, if 'data' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
arrayseqlookup.dy:112:34: note: You might need to cast the function pointer here
arrayseqlookup.dy:189:36: note: Parameter 'data' can be declared as pointer to const
arrayseqlookup.dy:261:20: style: Variable 'cli' can be declared as pointer to const [constVariablePointer]
arrayseqlookup.dy:332:76: style: Parameter 'para' can be declared as pointer to const. However it seems that 'Wise2_add_seq_arraylookup' is a callback function, if 'para' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
arrayseqlookup.dy:58:24: note: You might need to cast the function pointer here
arrayseqlookup.dy:332:76: note: Parameter 'para' can be declared as pointer to const
arrayseqlookup.dy:401:24: style: Variable 'temp' can be declared as pointer to const [constVariablePointer]
arrayseqlookup.dy:410:10: style: Variable 'temp' is assigned a value that is never used. [unreadVariable]
asciibtcanvas.dy:213:20: style: Variable 'abd' can be declared as pointer to const [constVariablePointer]
cdna.dy:225:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
cdna.c:328:39: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
cdnadb.dy:75:34: style: Parameter 'hs' can be declared as pointer to const [constParameterPointer]
cdnadb.c:550:46: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
cdnadb.c:594:45: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
cdnadb.c:638:45: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
cdnadb.c:682:47: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
cdnadb.c:726:46: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
cdnadb.c:770:41: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
cdnadb.c:814:43: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
cdnadb.c:858:54: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
codon.dy:117:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
codon.dy:129:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
codon.dy:130:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
codon.dy:754:14: style: Variable 'codon[i]' is reassigned a value before the old one has been used. [redundantAssignment]
codon.dy:746:16: note: codon[i] is assigned
codon.dy:754:14: note: codon[i] is overwritten
codon.dy:121:10: style: Variable 'run2' can be declared as pointer to const [constVariablePointer]
codon.dy:261:43: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
codon.dy:291:41: style: Parameter 'ct' can be declared as pointer to const [constParameterPointer]
codon.dy:596:33: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
codon.dy:725:54: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
codon.c:782:44: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
codon.dy:431:7: style: Variable 'o' is assigned a value that is never used. [unreadVariable]
codon.dy:433:7: style: Variable 'w' is assigned a value that is never used. [unreadVariable]
codon.dy:435:7: style: Variable 't' is assigned a value that is never used. [unreadVariable]
codon.dy:754:14: style: Variable 'codon[i]' is assigned a value that is never used. [unreadVariable]
codonmapper.dy:56:58: style: Parameter 'codon' can be declared as pointer to const [constParameterPointer]
codonmapper.dy:133:43: style: Parameter 'cf' can be declared as pointer to const [constParameterPointer]
codonmapper.dy:228:61: style: Parameter 'ct' can be declared as pointer to const [constParameterPointer]
codonmapper.dy:256:64: style: Parameter 'protein_array' can be declared as pointer to const [constParameterPointer]
codonmapper.c:666:50: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
codonmapper.dy:481:18: style: Variable 'total_freq' is assigned a value that is never used. [unreadVariable]
codonmatrix.dy:49:68: style: Parameter 'cm' can be declared as pointer to const [constParameterPointer]
codonmatrix.dy:151:47: style: Parameter 'cms' can be declared as pointer to const [constParameterPointer]
complexconsensi.dy:247:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
complexconsensi.dy:285:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
complexconsensi.dy:285:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
complexconsensi.dy:286:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
complexconsensi.dy:50:55: style: Parameter 'ccw' can be declared as pointer to const [constParameterPointer]
complexconsensi.dy:71:26: style: Variable 'ccw' can be declared as pointer to const [constVariablePointer]
complexconsensi.dy:96:26: style: Variable 'ccw' can be declared as pointer to const [constVariablePointer]
complexconsensi.dy:282:10: style: Variable 'score' can be declared as pointer to const [constVariablePointer]
complexevalset.dy:168:35: style: Parameter 'data' can be declared as pointer to const. However it seems that 'Wise2_flat_negi_eval' is a callback function, if 'data' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
complexevalset.dy:150:24: note: You might need to cast the function pointer here
complexevalset.dy:168:35: note: Parameter 'data' can be declared as pointer to const
complexevalset.dy:168:47: style: Parameter 'seq' can be declared as pointer to const. However it seems that 'Wise2_flat_negi_eval' is a callback function, if 'seq' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
complexevalset.dy:150:24: note: You might need to cast the function pointer here
complexevalset.dy:168:47: note: Parameter 'seq' can be declared as pointer to const
complexevalset.dy:211:35: style: Parameter 'data' can be declared as pointer to const. However it seems that 'Wise2_flat_zero_eval' is a callback function, if 'data' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
complexevalset.dy:193:24: note: You might need to cast the function pointer here
complexevalset.dy:211:35: note: Parameter 'data' can be declared as pointer to const
complexevalset.dy:211:47: style: Parameter 'seq' can be declared as pointer to const. However it seems that 'Wise2_flat_zero_eval' is a callback function, if 'seq' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
complexevalset.dy:193:24: note: You might need to cast the function pointer here
complexevalset.dy:211:47: note: Parameter 'seq' can be declared as pointer to const
complexevalset.dy:259:36: style: Parameter 'data' can be declared as pointer to const. However it seems that 'Wise2_stupid_5SS_eval' is a callback function, if 'data' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
complexevalset.dy:240:24: note: You might need to cast the function pointer here
complexevalset.dy:259:36: note: Parameter 'data' can be declared as pointer to const
complexevalset.dy:259:48: style: Parameter 'seq' can be declared as pointer to const. However it seems that 'Wise2_stupid_5SS_eval' is a callback function, if 'seq' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
complexevalset.dy:240:24: note: You might need to cast the function pointer here
complexevalset.dy:259:48: note: Parameter 'seq' can be declared as pointer to const
complexevalset.dy:310:36: style: Parameter 'data' can be declared as pointer to const. However it seems that 'Wise2_stupid_3SS_eval' is a callback function, if 'data' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
complexevalset.dy:290:24: note: You might need to cast the function pointer here
complexevalset.dy:310:36: note: Parameter 'data' can be declared as pointer to const
complexevalset.dy:310:48: style: Parameter 'seq' can be declared as pointer to const. However it seems that 'Wise2_stupid_3SS_eval' is a callback function, if 'seq' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
complexevalset.dy:290:24: note: You might need to cast the function pointer here
complexevalset.dy:310:48: note: Parameter 'seq' can be declared as pointer to const
complexevalset.dy:529:38: style: Parameter 'data' can be declared as pointer to const. However it seems that 'Wise2_base_number_func' is a callback function, if 'data' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
complexevalset.dy:510:20: note: You might need to cast the function pointer here
complexevalset.dy:529:38: note: Parameter 'data' can be declared as pointer to const
complexevalset.dy:529:50: style: Parameter 'seq' can be declared as pointer to const. However it seems that 'Wise2_base_number_func' is a callback function, if 'seq' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
complexevalset.dy:510:20: note: You might need to cast the function pointer here
complexevalset.dy:529:50: note: Parameter 'seq' can be declared as pointer to const
complexevalset.dy:612:43: style: Parameter 'data' can be declared as pointer to const. However it seems that 'Wise2_aminoacid_number_func' is a callback function, if 'data' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
complexevalset.dy:593:20: note: You might need to cast the function pointer here
complexevalset.dy:612:43: note: Parameter 'data' can be declared as pointer to const
complexevalset.dy:612:55: style: Parameter 'seq' can be declared as pointer to const. However it seems that 'Wise2_aminoacid_number_func' is a callback function, if 'seq' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
complexevalset.dy:593:20: note: You might need to cast the function pointer here
complexevalset.dy:612:55: note: Parameter 'seq' can be declared as pointer to const
complexevalset.dy:480:9: style: Variable 'codon' is assigned a value that is never used. [unreadVariable]
complexsequence.dy:108:14: style: Variable 'rev' can be declared as pointer to const [constVariablePointer]
complexsequence.dy:360:77: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
complexsequence.dy:378:57: style: Parameter 'cses' can be declared as pointer to const [constParameterPointer]
complexsequence.c:850:51: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
complexsequence.c:894:57: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
complexsequence.c:938:65: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
complexsequence.c:982:82: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
complexsequence.c:1026:72: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
complexsequence.c:1070:73: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
complexsequence.c:1114:74: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
compmat.dy:130:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
compmat.dy:438:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
compmat.dy:541:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
compmat.dy:275:23: warning: Either the condition 'aa2>26' is redundant or the array 'cm->comp[26][26]' is accessed at index cm->comp[*][26], which is out of bounds. [arrayIndexOutOfBoundsCond]
compmat.dy:270:46: note: Assuming that condition 'aa2>26' is not redundant
compmat.dy:275:23: note: Array index out of bounds
compmat.dy:461:20: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
compmat.dy:461:66: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
compmat.dy:484:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
compmat.dy:484:83: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
compmat.dy:564:20: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
compmat.dy:564:66: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
compmat.dy:588:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
compmat.dy:588:83: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
compmat.dy:116:10: style: Variable 'aa_set' can be declared as const array [constVariable]
compmat.dy:155:44: style: Parameter 'cp' can be declared as pointer to const [constParameterPointer]
compmat.dy:186:44: style: Parameter 'cm' can be declared as pointer to const [constParameterPointer]
compmat.dy:214:42: style: Parameter 'cm' can be declared as pointer to const [constParameterPointer]
compmat.c:820:38: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
compmat.dy:377:21: warning: Uninitialized variable: minnumbers [uninitvar]
compmat.dy:362:29: note: Assuming condition is false
compmat.dy:377:21: note: Uninitialized variable: minnumbers
dbsearchimpl.dy:279:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
dbsearchimpl.dy:153:13: style: Condition 'num==-1' is always true [knownConditionTrueFalse]
dbsearchimpl.dy:152:11: note: Assignment 'num=-1', assigned value is -1
dbsearchimpl.dy:153:13: note: Condition 'num==-1' is always true
dbsearchimpl.dy:89:48: style: Parameter 'dbsi' can be declared as pointer to const [constParameterPointer]
dbsearchimpl.dy:117:56: style: Parameter 'dbsi' can be declared as pointer to const [constParameterPointer]
dbsearchimpl.c:382:45: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
dbsearchimpl.c:426:52: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
dbsearchimpl.c:470:54: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
dbsearchimpl.c:514:58: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
dbsearchimpl.c:558:55: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
dnaindexcons.dy:215:109: style: Parameter 'res_struct' can be declared as pointer to const [constParameterPointer]
dnaindexcons.dy:281:36: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
dnaindexcons.dy:286:10: style: Variable 'no' is assigned a value that is never used. [unreadVariable]
dnamatrix.dy:188:58: style: Parameter 'dpm' can be declared as pointer to const [constParameterPointer]
dnamatrix.dy:211:33: style: Parameter 'dcm' can be declared as pointer to const [constParameterPointer]
dnamatrix.dy:232:41: style: Parameter 'dpm' can be declared as pointer to const [constParameterPointer]
dpenvelope.dy:113:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
dpenvelope.dy:37:33: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
dpenvelope.dy:37:44: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
dpenvelope.dy:180:35: style: Parameter 'dpe' can be declared as pointer to const [constParameterPointer]
dpenvelope.dy:316:36: style: Parameter 'one' can be declared as pointer to const. However it seems that 'Wise2_compare_DPUnit_startj' is a callback function, if 'one' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
dpenvelope.dy:301:23: note: You might need to cast the function pointer here
dpenvelope.dy:316:36: note: Parameter 'one' can be declared as pointer to const
dpenvelope.dy:316:49: style: Parameter 'two' can be declared as pointer to const. However it seems that 'Wise2_compare_DPUnit_startj' is a callback function, if 'two' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
dpenvelope.dy:301:23: note: You might need to cast the function pointer here
dpenvelope.dy:316:49: note: Parameter 'two' can be declared as pointer to const
dprunimpl.dy:33:41: style: Parameter 'dpri' can be declared as pointer to const [constParameterPointer]
gene.dy:224:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
gene.dy:224:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gene.dy:238:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gene.dy:67:30: style: Parameter 'g' can be declared as pointer to const [constParameterPointer]
gene.dy:396:42: style: Parameter 'key' can be declared as pointer to const [constParameterPointer]
gene.dy:399:16: style: Variable 'tr' can be declared as pointer to const [constVariablePointer]
gene.dy:476:16: style: Variable 'ex' can be declared as pointer to const [constVariablePointer]
gene.dy:497:16: style: Variable 'ex' can be declared as pointer to const [constVariablePointer]
gene.c:819:30: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
gene.c:863:28: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
gene.c:907:43: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
gene.c:951:38: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
gene.c:998:35: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
gene.c:1042:32: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
gene.c:1086:32: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
gene.c:1130:35: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
gene.c:1174:37: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
gene.dy:439:9: warning: Uninitialized variable: tr [uninitvar]
gene.dy:425:14: note: Assuming condition is false
gene.dy:439:9: note: Uninitialized variable: tr
gene.dy:289:11: style: Variable 'base' is assigned a value that is never used. [unreadVariable]
genericindexresult.dy:43:24: style: Variable 'gir' can be declared as pointer to const [constVariablePointer]
genericindexresult.dy:60:42: style: Parameter 'data' can be declared as pointer to const [constParameterPointer]
genomic.dy:335:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
genomic.dy:276:27: style: Redundant condition: The condition '*run2' is redundant since '*run2 == 'N'' is sufficient. [redundantCondition]
genomic.c:758:45: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
genomic.c:805:37: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
genomic.c:849:48: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
genomic.c:893:46: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
genomic.c:937:50: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
genomicdb.dy:76:37: style: Parameter 'hs' can be declared as pointer to const [constParameterPointer]
genomicdb.c:556:52: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
genomicdb.c:600:51: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
genomicdb.c:644:53: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
genomicdb.c:688:52: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
genomicdb.c:732:47: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
genomicdb.c:776:48: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
genomicdb.c:820:60: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
genomicregion.dy:215:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
genomicregion.dy:738:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
genomicregion.dy:777:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
genomicregion.dy:839:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
genomicregion.dy:847:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
genomicregion.dy:749:10: warning: If resource allocation fails, then there is a possible null pointer dereference: ifp [nullPointerOutOfResources]
genomicregion.dy:743:14: note: Assuming allocation function fails
genomicregion.dy:743:14: note: Assignment 'ifp=popen(buffer,"r")', assigned value is 0
genomicregion.dy:749:10: note: Null pointer dereference
genomicregion.dy:757:10: warning: If resource allocation fails, then there is a possible null pointer dereference: ifp [nullPointerOutOfResources]
genomicregion.dy:753:14: note: Assuming allocation function fails
genomicregion.dy:753:14: note: Assignment 'ifp=popen(buffer,"r")', assigned value is 0
genomicregion.dy:757:10: note: Null pointer dereference
genomicregion.dy:790:10: warning: If resource allocation fails, then there is a possible null pointer dereference: ifp [nullPointerOutOfResources]
genomicregion.dy:782:14: note: Assuming allocation function fails
genomicregion.dy:782:14: note: Assignment 'ifp=popen(buffer,"r")', assigned value is 0
genomicregion.dy:790:10: note: Null pointer dereference
genomicregion.dy:902:23: warning: If resource allocation fails, then there is a possible null pointer dereference: ifp [nullPointerOutOfResources]
genomicregion.dy:782:14: note: Assuming allocation function fails
genomicregion.dy:782:14: note: Assignment 'ifp=popen(buffer,"r")', assigned value is 0
genomicregion.dy:786:54: note: Calling function 'Wise2_read_EMBL_FT_into_GenomicRegion', 4th argument 'ifp' value is 0
genomicregion.dy:902:23: note: Null pointer dereference
genomicregion.dy:461:24: style: Variable 'te->exon[j]->used' is reassigned a value before the old one has been used. [redundantAssignment]
genomicregion.dy:458:24: note: te->exon[j]->used is assigned
genomicregion.dy:461:24: note: te->exon[j]->used is overwritten
genomicregion.dy:567:24: style: Variable 'te->exon[j]->used' is reassigned a value before the old one has been used. [redundantAssignment]
genomicregion.dy:564:24: note: te->exon[j]->used is assigned
genomicregion.dy:567:24: note: te->exon[j]->used is overwritten
genomicregion.dy:126:59: style: Parameter 'sgro' can be declared as pointer to const [constParameterPointer]
genomicregion.dy:126:106: style: Parameter 'dividestr' can be declared as pointer to const [constParameterPointer]
genomicregion.dy:312:51: style: Parameter 'gog' can be declared as pointer to const [constParameterPointer]
genomicregion.dy:391:16: style: Variable 'tr' can be declared as pointer to const [constVariablePointer]
genomicregion.dy:499:16: style: Variable 'tr' can be declared as pointer to const [constVariablePointer]
genomicregion.dy:719:58: style: Parameter 'gr' can be declared as pointer to const [constParameterPointer]
genomicregion.dy:735:55: style: Parameter 'efetch' can be declared as pointer to const [constParameterPointer]
genomicregion.dy:774:52: style: Parameter 'srsquery' can be declared as pointer to const [constParameterPointer]
genomicregion.dy:1114:45: style: Parameter 'gr' can be declared as pointer to const [constParameterPointer]
genomicregion.dy:1114:55: style: Parameter 'seq_name' can be declared as pointer to const [constParameterPointer]
genomicregion.dy:1167:50: style: Parameter 'gr' can be declared as pointer to const [constParameterPointer]
genomicregion.dy:1167:60: style: Parameter 'seq_name' can be declared as pointer to const [constParameterPointer]
genomicregion.dy:1167:76: style: Parameter 'method' can be declared as pointer to const [constParameterPointer]
genomicregion.dy:1167:90: style: Parameter 'db' can be declared as pointer to const [constParameterPointer]
genomicregion.dy:1167:114: style: Parameter 'weblocation' can be declared as pointer to const [constParameterPointer]
genomicregion.dy:1218:55: style: Parameter 'seq_name' can be declared as pointer to const [constParameterPointer]
genomicregion.dy:1218:71: style: Parameter 'source' can be declared as pointer to const [constParameterPointer]
genomicregion.c:2053:47: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
genomicregion.c:2097:56: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
histogram.dy:1076:29: warning: Invalid log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
histogram.dy:1070:14: note: Assignment 'p=0.0', assigned value is 0.0
histogram.dy:1075:18: note: Assuming condition is false
histogram.dy:1076:29: note: Invalid argument
histogram.dy:630:11: style: The if condition is the same as the previous if condition [duplicateCondition]
histogram.dy:616:11: note: First condition
histogram.dy:630:11: note: Second condition
histogram.dy:85:42: style: Parameter 'his' can be declared as pointer to const [constParameterPointer]
histogram.dy:1107:24: style: Parameter 'x' can be declared as pointer to const [constParameterPointer]
histogram.dy:1107:32: style: Parameter 'y' can be declared as pointer to const [constParameterPointer]
histogram.dy:1170:24: style: Parameter 'x' can be declared as pointer to const [constParameterPointer]
histogram.dy:1170:32: style: Parameter 'y' can be declared as pointer to const [constParameterPointer]
histogram.dy:1484:20: style: Parameter 'x' can be declared as pointer to const [constParameterPointer]
histogram.dy:1484:30: style: Parameter 'y' can be declared as pointer to const [constParameterPointer]
histogram.dy:1720:17: style: Variable 'cof' can be declared as const array [constVariable]
histogram.dy:298:15: warning: Uninitialized variable: lowbound [uninitvar]
histogram.dy:287:36: note: Assuming condition is false
histogram.dy:298:15: note: Uninitialized variable: lowbound
histogram.dy:1325:25: warning: Uninitialized variable: total [uninitvar]
histogram.dy:1319:17: note: Assuming condition is false
histogram.dy:1325:25: note: Uninitialized variable: total
histogram.dy:1323:7: error: Uninitialized variable: total [legacyUninitvar]
hitlist.dy:261:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
hitlist.dy:347:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
hitlist.dy:403:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
hitlist.dy:496:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
hitlist.dy:714:9: warning: Either the condition 'alc!=NULL' is redundant or there is possible null pointer dereference: alc. [nullPointerRedundantCheck]
hitlist.dy:601:26: note: Assuming that condition 'alc!=NULL' is not redundant
hitlist.dy:714:9: note: Null pointer dereference
hitlist.dy:77:37: style: Parameter 'one' can be declared as pointer to const. However it seems that 'Wise2_compare_HitPair_score' is a callback function, if 'one' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hitlist.dy:61:19: note: You might need to cast the function pointer here
hitlist.dy:77:37: note: Parameter 'one' can be declared as pointer to const
hitlist.dy:77:51: style: Parameter 'two' can be declared as pointer to const. However it seems that 'Wise2_compare_HitPair_score' is a callback function, if 'two' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hitlist.dy:61:19: note: You might need to cast the function pointer here
hitlist.dy:77:51: note: Parameter 'two' can be declared as pointer to const
hitlist.dy:201:45: style: Parameter 'hsp' can be declared as pointer to const [constParameterPointer]
hitlist.dy:201:60: style: Parameter 'q' can be declared as pointer to const [constParameterPointer]
hitlist.dy:201:73: style: Parameter 't' can be declared as pointer to const [constParameterPointer]
hitlist.dy:256:10: style: Variable 'temp' can be declared as pointer to const [constVariablePointer]
hitlist.dy:311:57: style: Parameter 'hloi' can be declared as pointer to const [constParameterPointer]
hitlist.dy:393:21: style: Variable 'haln' can be declared as pointer to const [constVariablePointer]
hitlist.dy:590:64: style: Parameter 'qname' can be declared as pointer to const [constParameterPointer]
hitlist.dy:590:77: style: Parameter 'query' can be declared as pointer to const [constParameterPointer]
hitlist.dy:590:90: style: Parameter 'tname' can be declared as pointer to const [constParameterPointer]
hitlist.dy:590:103: style: Parameter 'target' can be declared as pointer to const [constParameterPointer]
hitlist.dy:594:15: style: Variable 'prev' can be declared as pointer to const [constVariablePointer]
hscore.dy:432:13: warning: Either the condition 'hs==NULL' is redundant or there is possible null pointer dereference: hs. [nullPointerRedundantCheck]
hscore.dy:427:10: note: Assuming that condition 'hs==NULL' is not redundant
hscore.dy:432:13: note: Null pointer dereference
hscore.dy:223:38: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
hscore.dy:423:33: style: Parameter 'hs' can be declared as pointer to const [constParameterPointer]
hscore.dy:468:44: style: Parameter 'one' can be declared as pointer to const. However it seems that 'Wise2_compare_DataScore_by_score' is a callback function, if 'one' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hscore.dy:451:18: note: You might need to cast the function pointer here
hscore.dy:468:44: note: Parameter 'one' can be declared as pointer to const
hscore.dy:468:60: style: Parameter 'two' can be declared as pointer to const. However it seems that 'Wise2_compare_DataScore_by_score' is a callback function, if 'two' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hscore.dy:451:18: note: You might need to cast the function pointer here
hscore.dy:468:60: note: Parameter 'two' can be declared as pointer to const
hscore.c:1222:48: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
hscore.c:1266:49: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
hscore.c:1310:40: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
hscore.c:1354:44: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
hscore.c:1398:42: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
hscore.c:1442:50: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
hsp.dy:64:22: style: Parameter 'test' can be declared as pointer to const [constParameterPointer]
hsp.dy:113:35: style: Parameter 'one' can be declared as pointer to const [constParameterPointer]
hsp.dy:113:48: style: Parameter 'two' can be declared as pointer to const [constParameterPointer]
hsp.dy:145:29: style: Parameter 'one' can be declared as pointer to const. However it seems that 'Wise2_compare_HSP_score' is a callback function, if 'one' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hsp.dy:130:19: note: You might need to cast the function pointer here
hsp.dy:145:29: note: Parameter 'one' can be declared as pointer to const
hsp.dy:145:39: style: Parameter 'two' can be declared as pointer to const. However it seems that 'Wise2_compare_HSP_score' is a callback function, if 'two' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hsp.dy:130:19: note: You might need to cast the function pointer here
hsp.dy:145:39: note: Parameter 'two' can be declared as pointer to const
hsp.dy:447:27: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
hsp.dy:473:21: style: Parameter 'hsp' can be declared as pointer to const [constParameterPointer]
hsp.dy:248:6: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
hsp.dy:251:6: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
hsp2hitscan.dy:123:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
hsp2hitscan.dy:239:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
hsp2hitscan.dy:105:108: style: Parameter 'para' can be declared as pointer to const [constParameterPointer]
hsp2hitscan.dy:218:10: style: Variable 'std_aa' can be declared as pointer to const [constVariablePointer]
hsp2hitscan.dy:224:7: style: Variable 'base' can be declared as const array [constVariable]
hsp2hitscan.dy:370:43: style: Parameter 'one' can be declared as pointer to const. However it seems that 'Wise2_compare_SeedHitSet_score' is a callback function, if 'one' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hsp2hitscan.dy:403:27: note: You might need to cast the function pointer here
hsp2hitscan.dy:370:43: note: Parameter 'one' can be declared as pointer to const
hsp2hitscan.dy:370:60: style: Parameter 'two' can be declared as pointer to const. However it seems that 'Wise2_compare_SeedHitSet_score' is a callback function, if 'two' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hsp2hitscan.dy:403:27: note: You might need to cast the function pointer here
hsp2hitscan.dy:370:60: note: Parameter 'two' can be declared as pointer to const
hsp2hitscan.dy:387:40: style: Parameter 'one' can be declared as pointer to const. However it seems that 'Wise2_compare_SeedHit_diagonal' is a callback function, if 'one' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hsp2hitscan.dy:417:22: note: You might need to cast the function pointer here
hsp2hitscan.dy:387:40: note: Parameter 'one' can be declared as pointer to const
hsp2hitscan.dy:387:54: style: Parameter 'two' can be declared as pointer to const. However it seems that 'Wise2_compare_SeedHit_diagonal' is a callback function, if 'two' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hsp2hitscan.dy:417:22: note: You might need to cast the function pointer here
hsp2hitscan.dy:387:54: note: Parameter 'two' can be declared as pointer to const
hsp2hitscan.dy:280:22: error: Uninitialized variable: base[j] [legacyUninitvar]
hsp2hitscan.dy:224:7: style: Variable 'base' is not assigned a value. [unassignedVariable]
hsp2hitscan.dy:225:7: style: Unused variable: start_base [unusedVariable]
hsp2hitscan.dy:226:18: style: Unused variable: head [unusedVariable]
hsp2hitscan.dy:236:9: style: Unused variable: k [unusedVariable]
hsphandler.dy:409:13: style: Variable 'eaten' is assigned a value that is never used. [unreadVariable]
hsphandler.dy:436:7: style: Unused variable: i [unusedVariable]
hsphandler.dy:437:7: style: Unused variable: j [unusedVariable]
hsplookupscan.dy:233:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMPILE_VERBOSITY_FLAG [valueFlowBailoutIncompleteVar]
hsplookupscan.dy:478:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
hsplookupscan.dy:332:13: style: Condition '1||has_seen==0' is always true [knownConditionTrueFalse]
hsplookupscan.dy:477:9: style: Condition 'trace' is always false [knownConditionTrueFalse]
hsplookupscan.dy:465:15: note: Assignment 'trace=0', assigned value is 0
hsplookupscan.dy:477:9: note: Condition 'trace' is always false
hsplookupscan.dy:482:11: style: Condition 'trace' is always false [knownConditionTrueFalse]
hsplookupscan.dy:465:15: note: Assignment 'trace=0', assigned value is 0
hsplookupscan.dy:482:11: note: Condition 'trace' is always false
hsplookupscan.dy:504:9: style: Condition 'trace' is always false [knownConditionTrueFalse]
hsplookupscan.dy:465:15: note: Assignment 'trace=0', assigned value is 0
hsplookupscan.dy:504:9: note: Condition 'trace' is always false
hsplookupscan.dy:36:38: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
hsplookupscan.dy:153:26: style: Parameter 'data' can be declared as pointer to const [constParameterPointer]
hsplookupscan.dy:153:41: style: Parameter 'user_data' can be declared as pointer to const [constParameterPointer]
hsplookupscan.dy:153:61: style: Parameter 'data2' can be declared as pointer to const [constParameterPointer]
hsplookupscan.dy:175:10: style: Variable 'std_aa' can be declared as pointer to const [constVariablePointer]
hsplookupscan.dy:576:96: style: Parameter 'para' can be declared as pointer to const. However it seems that 'Wise2_simple_HSPScan_scan_query' is a callback function, if 'para' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hsplookupscan.dy:89:21: note: You might need to cast the function pointer here
hsplookupscan.dy:576:96: note: Parameter 'para' can be declared as pointer to const
hsplookupscan.dy:41:10: style: Variable 'no' is assigned a value that is never used. [unreadVariable]
hsplookupscan.dy:509:17: style: Variable 'newseq[j]' is assigned a value that is never used. [unreadVariable]
hsplookupscan.dy:543:14: style: Variable 'newseq[j]' is assigned a value that is never used. [unreadVariable]
hsplookupthreaded.dy:280:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
hsplookupthreaded.dy:284:3: warning: %d in format string (no. 1) requires 'int' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
hsplookupthreaded.dy:256:4: error: Common realloc mistake: 'oph' nulled but not freed upon failure [memleakOnRealloc]
hsplookupthreaded.dy:257:4: error: Common realloc mistake: 'pos' nulled but not freed upon failure [memleakOnRealloc]
hsplookupthreaded.dy:203:5: warning: If memory allocation fails, then there is a possible null pointer dereference: position [nullPointerOutOfMemory]
hsplookupthreaded.dy:191:21: note: Assuming allocation function fails
hsplookupthreaded.dy:191:21: note: Assignment 'position=calloc(max_size,sizeof(int))', assigned value is 0
hsplookupthreaded.dy:203:5: note: Null pointer dereference
hsplookupthreaded.dy:204:5: warning: If memory allocation fails, then there is a possible null pointer dereference: seqnumber [nullPointerOutOfMemory]
hsplookupthreaded.dy:192:21: note: Assuming allocation function fails
hsplookupthreaded.dy:192:21: note: Assignment 'seqnumber=calloc(max_size,sizeof(int))', assigned value is 0
hsplookupthreaded.dy:204:5: note: Null pointer dereference
hsplookupthreaded.dy:297:28: warning: If memory allocation fails, then there is a possible null pointer dereference: oph [nullPointerOutOfMemory]
hsplookupthreaded.dy:234:15: note: Assuming allocation function fails
hsplookupthreaded.dy:234:15: note: Assignment 'oph=calloc(max_oph,sizeof(struct OrderedPosHolder))', assigned value is 0
hsplookupthreaded.dy:249:12: note: Assuming condition is false
hsplookupthreaded.dy:297:28: note: Null pointer dereference
hsplookupthreaded.dy:297:39: warning: If memory allocation fails, then there is a possible null pointer dereference: oph [nullPointerOutOfMemory]
hsplookupthreaded.dy:234:15: note: Assuming allocation function fails
hsplookupthreaded.dy:234:15: note: Assignment 'oph=calloc(max_oph,sizeof(struct OrderedPosHolder))', assigned value is 0
hsplookupthreaded.dy:249:12: note: Assuming condition is false
hsplookupthreaded.dy:297:39: note: Null pointer dereference
hsplookupthreaded.dy:297:56: warning: If memory allocation fails, then there is a possible null pointer dereference: oph [nullPointerOutOfMemory]
hsplookupthreaded.dy:234:15: note: Assuming allocation function fails
hsplookupthreaded.dy:234:15: note: Assignment 'oph=calloc(max_oph,sizeof(struct OrderedPosHolder))', assigned value is 0
hsplookupthreaded.dy:249:12: note: Assuming condition is false
hsplookupthreaded.dy:297:56: note: Null pointer dereference
hsplookupthreaded.dy:134:112: style: Parameter 'para' can be declared as pointer to const. However it seems that 'Wise2_one_off_ordered_HSPscan_scan_query_direct' is a callback function, if 'para' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hsplookupthreaded.dy:111:23: note: You might need to cast the function pointer here
hsplookupthreaded.dy:134:112: note: Parameter 'para' can be declared as pointer to const
hsplookupthreaded.dy:155:10: style: Variable 'std_aa' can be declared as pointer to const [constVariablePointer]
hsplookupthreaded.dy:718:10: style: Variable 'std_aa' can be declared as pointer to const [constVariablePointer]
hsplookupthreaded.dy:740:27: style: Variable 'asl' can be declared as pointer to const [constVariablePointer]
hsplookupthreaded.dy:189:12: 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]
hsplookupthreaded.dy:137:22: style: Unused variable: hsp_para [unusedVariable]
hspscaninterface.dy:61:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
hspscaninterface.dy:118:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
hspscaninterface.dy:117:26: style: Variable 'h' can be declared as pointer to const [constVariablePointer]
hspstream.dy:134:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
hspstream.dy:132:7: style: Unused variable: i [unusedVariable]
hspthreadeddb.dy:105:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PTHREAD_SCOPE_SYSTEM [valueFlowBailoutIncompleteVar]
hspthreadeddb.dy:178:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
hspthreadeddb.dy:245:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PTHREAD_SCOPE_SYSTEM [valueFlowBailoutIncompleteVar]
hspthreadeddb.dy:178:3: portability: %d in format string (no. 1) requires 'int' but the argument type is 'Wise2_HSPDatabaseSegment * {aka Wise2_HSPDatabaseSegment *}'. [invalidPrintfArgType_sint]
hsptwohitscan.dy:105:10: style: Variable 'std_aa' can be declared as pointer to const [constVariablePointer]
hsptwohitscan.dy:374:7: style: Unused variable: i [unusedVariable]
hsptwohitscan.dy:375:7: style: Unused variable: j [unusedVariable]
intallocator.dy:274:3: portability: %ld in format string (no. 2) requires 'long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
intallocator.dy:233:24: style: Variable 'h' can be declared as pointer to const [constVariablePointer]
intallocator.dy:272:24: style: Variable 'h' can be declared as pointer to const [constVariablePointer]
linkedlist_lookpos.dy:78:24: style: Variable 'posres' can be declared as pointer to const [constVariablePointer]
matrixdebug.dy:123:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
matrixdebug.dy:218:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
matrixdebug.dy:385:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
matrixdebug.dy:68:17: style: Variable 'prev' can be declared as pointer to const [constVariablePointer]
matrixdebug.dy:166:54: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
matrixdebug.dy:191:66: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
matrixdebug.dy:66:7: style: Unused variable: j [unusedVariable]
matrixdebug.dy:67:7: style: Unused variable: cum [unusedVariable]
packaln.dy:89:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
packaln.dy:124:44: style: Parameter 'pau' can be declared as pointer to const [constParameterPointer]
packaln.dy:168:24: style: Variable 'pau' can be declared as pointer to const [constVariablePointer]
packaln.c:634:34: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
packaln.c:678:36: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
packaln.c:722:40: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
packaln.c:766:40: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
packaln.c:810:44: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
packaln.c:854:44: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
pairbase.dy:359:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pairbase.dy:605:51: style: Parameter 'sc' can be declared as pointer to const [constParameterPointer]
pairbase.dy:632:61: style: Parameter 'sc' can be declared as pointer to const [constParameterPointer]
pairbase.dy:747:61: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
pairbase.dy:47:7: style: Unused variable: codon_a [unusedVariable]
pairbase.dy:48:7: style: Unused variable: codon_b [unusedVariable]
probability.dy:172:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
probability.dy:172:64: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
probability.dy:115:31: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
probability.dy:140:47: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
probability.dy:196:43: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
probability.dy:221:49: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
probability.dy:269:46: style: Parameter 'from' can be declared as pointer to const [constParameterPointer]
probability.dy:469:44: style: Parameter 'top' can be declared as pointer to const [constParameterPointer]
probability.dy:469:56: style: Parameter 'bottem' can be declared as pointer to const [constParameterPointer]
protein.c:323:45: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
proteindb.dy:61:37: style: Parameter 'hs' can be declared as pointer to const [constParameterPointer]
proteindb.c:441:52: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
proteindb.c:485:51: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
proteindb.c:529:55: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
proteindb.c:573:47: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
proteindb.c:617:60: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
proteindb.c:661:52: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
proteindb.c:705:47: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
proteinstreamedindex.dy:429:19: style: Condition 'in->index[i]==NULL' is always false [knownConditionTrueFalse]
proteinstreamedindex.dy:581:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
proteinstreamedindex.dy:580:15: note: Assuming allocation function fails
proteinstreamedindex.dy:580:15: note: Assignment 'out=malloc(sizeof(struct ProteinStreamedIndexPos))', assigned value is 0
proteinstreamedindex.dy:581:3: note: Null pointer dereference
proteinstreamedindex.dy:582:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
proteinstreamedindex.dy:580:15: note: Assuming allocation function fails
proteinstreamedindex.dy:580:15: note: Assignment 'out=malloc(sizeof(struct ProteinStreamedIndexPos))', assigned value is 0
proteinstreamedindex.dy:582:3: note: Null pointer dereference
proteinstreamedindex.dy:583:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
proteinstreamedindex.dy:580:15: note: Assuming allocation function fails
proteinstreamedindex.dy:580:15: note: Assignment 'out=malloc(sizeof(struct ProteinStreamedIndexPos))', assigned value is 0
proteinstreamedindex.dy:583:3: note: Null pointer dereference
proteinstreamedindex.dy:584:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
proteinstreamedindex.dy:580:15: note: Assuming allocation function fails
proteinstreamedindex.dy:580:15: note: Assignment 'out=malloc(sizeof(struct ProteinStreamedIndexPos))', assigned value is 0
proteinstreamedindex.dy:584:3: note: Null pointer dereference
proteinstreamedindex.dy:585:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
proteinstreamedindex.dy:580:15: note: Assuming allocation function fails
proteinstreamedindex.dy:580:15: note: Assignment 'out=malloc(sizeof(struct ProteinStreamedIndexPos))', assigned value is 0
proteinstreamedindex.dy:585:3: note: Null pointer dereference
proteinstreamedindex.dy:586:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
proteinstreamedindex.dy:580:15: note: Assuming allocation function fails
proteinstreamedindex.dy:580:15: note: Assignment 'out=malloc(sizeof(struct ProteinStreamedIndexPos))', assigned value is 0
proteinstreamedindex.dy:586:3: note: Null pointer dereference
proteinstreamedindex.dy:159:27: style: Variable 'client' can be declared as pointer to const [constVariablePointer]
proteinstreamedindex.dy:225:43: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
proteinstreamedindex.dy:351:104: style: Parameter 'para' can be declared as pointer to const [constParameterPointer]
proteinstreamedindex.dy:419:55: style: Parameter 'in' can be declared as pointer to const [constParameterPointer]
proteinstreamedindex.dy:230:10: style: Variable 'no' is assigned a value that is never used. [unreadVariable]
proteinstreamedindex.dy:378:9: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
pthreadpool.dy:58:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable max_work [valueFlowBailoutIncompleteVar]
randomdb.dy:110:10: style: Variable 'name' can be declared as pointer to const [constVariablePointer]
randomdb.c:357:66: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
randomdb.c:401:53: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
randomdb.c:445:66: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
randomdb.c:489:65: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
randomdb.c:533:50: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
randomdb.c:577:58: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
randomdb.c:621:45: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
randomdb.c:665:58: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
randomdb.c:709:60: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
randomdb.c:753:42: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
randommodel.dy:597:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
randommodel.dy:556:22: style: Same expression on both sides of '-'. [duplicateExpression]
randommodel.dy:192:47: style: Parameter 'rcs' can be declared as pointer to const [constParameterPointer]
randommodel.dy:214:53: style: Parameter 'rds' can be declared as pointer to const [constParameterPointer]
randommodel.dy:235:77: style: Parameter 'dis' can be declared as pointer to const [constParameterPointer]
randommodel.dy:235:98: style: Parameter 'rnd' can be declared as pointer to const [constParameterPointer]
randommodel.dy:267:59: style: Parameter 'codon' can be declared as const array [constParameter]
randommodel.dy:386:80: style: Parameter 'rmd' can be declared as pointer to const [constParameterPointer]
randommodel.dy:520:72: style: Parameter 'rm' can be declared as pointer to const [constParameterPointer]
randommodel.c:1161:52: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
randommodel.c:1205:46: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
searchstatlookup.dy:24:38: style: Parameter 'data' can be declared as pointer to const. However it seems that 'Wise2_bit_halfbit_lookup_ssi' is a callback function, if 'data' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
searchstatlookup.dy:91:22: note: You might need to cast the function pointer here
searchstatlookup.dy:24:38: note: Parameter 'data' can be declared as pointer to const
searchstatlookup.dy:45:57: style: Parameter 'a' can be declared as pointer to const. However it seems that 'Wise2_evalue_halfbit_lookup_ssi' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
searchstatlookup.dy:90:22: note: You might need to cast the function pointer here
searchstatlookup.dy:45:57: note: Parameter 'a' can be declared as pointer to const
searchstatlookup.dy:45:70: style: Parameter 'b' can be declared as pointer to const. However it seems that 'Wise2_evalue_halfbit_lookup_ssi' is a callback function, if 'b' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
searchstatlookup.dy:90:22: note: You might need to cast the function pointer here
searchstatlookup.dy:45:70: note: Parameter 'b' can be declared as pointer to const
searchstatlookup.dy:47:15: style: Variable 'l' can be declared as pointer to const [constVariablePointer]
seqalign.dy:87:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
seqalign.dy:332:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
seqalign.dy:509:18: style: Condition 'buffer[0]=='/'' is always false [knownConditionTrueFalse]
seqalign.dy:506:18: note: Assuming that condition 'buffer[0]!='#'' is not redundant
seqalign.dy:509:18: note: Condition 'buffer[0]=='/'' is always false
seqlookup.dy:276:37: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
seqlookup.dy:310:36: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
seqlookup.dy:343:31: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
seqlookup.dy:374:37: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
seqlookup.dy:281:10: style: Variable 'no' is assigned a value that is never used. [unreadVariable]
seqlookup.dy:315:10: style: Variable 'no' is assigned a value that is never used. [unreadVariable]
seqlookup.dy:348:10: style: Variable 'no' is assigned a value that is never used. [unreadVariable]
sequence.dy:663:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
sequence.dy:702:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
sequence.dy:795:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
sequence.dy:846:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
sequence.dy:1007:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
sequence.dy:231:12: warning: Either the condition '(no=(int)(toupper(seq->seq[i])-'A'))>26' is redundant or the array 'ch[26]' is accessed at index 26, which is out of bounds. [arrayIndexOutOfBoundsCond]
sequence.dy:229:47: note: Assuming that condition '(no=(int)(toupper(seq->seq[i])-'A'))>26' is not redundant
sequence.dy:231:12: note: Array index out of bounds
sequence.dy:234:19: style: Same expression on both sides of '-'. [duplicateExpression]
sequence.dy:216:34: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
sequence.dy:374:41: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
sequence.dy:636:40: style: Parameter 'datastring' can be declared as pointer to const [constParameterPointer]
sequence.dy:636:58: style: Parameter 'srsstring' can be declared as pointer to const [constParameterPointer]
sequence.dy:854:10: style: Variable 'temp' can be declared as pointer to const [constVariablePointer]
sequence.dy:1112:44: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
sequence.dy:1178:58: style: Parameter 'more' can be declared as pointer to const [constParameterPointer]
sequence.c:1722:40: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequence.c:1766:39: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequence.c:1810:36: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequence.c:1854:39: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequence.c:1898:39: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequence.c:1942:36: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequence.c:1986:38: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequence.c:2030:39: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequence.c:2074:42: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequence.c:2118:40: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequence.c:2165:42: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequence.dy:870:38: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
sequence.dy:873:9: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
sequence.dy:938:9: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
sequence.dy:853:23: style: Variable 'seen_weight' is assigned a value that is never used. [unreadVariable]
sequence.dy:853:11: style: Variable 'seen_weight' is assigned a value that is never used. [unreadVariable]
sequencedb.dy:561:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
sequencedb.dy:637:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
sequencedb.dy:570:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
sequencedb.dy:571:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
sequencedb.dy:637:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
sequencedb.dy:638:10: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
sequencedb.dy:639:10: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
sequencedb.dy:574:5: error: Null pointer dereference: out [nullPointer]
sequencedb.dy:559:22: note: Assignment 'out=NULL', assigned value is 0
sequencedb.dy:565:33: note: Assuming condition is false
sequencedb.dy:574:5: note: Null pointer dereference
sequencedb.dy:576:8: error: Null pointer dereference: out [nullPointer]
sequencedb.dy:559:22: note: Assignment 'out=NULL', assigned value is 0
sequencedb.dy:565:33: note: Assuming condition is false
sequencedb.dy:576:8: note: Null pointer dereference
sequencedb.dy:571:10: style: Variable 'runner' is reassigned a value before the old one has been used. [redundantAssignment]
sequencedb.dy:570:10: note: runner is assigned
sequencedb.dy:571:10: note: runner is overwritten
sequencedb.dy:76:54: style: Parameter 'sdb' can be declared as pointer to const [constParameterPointer]
sequencedb.dy:424:16: style: Variable 'fs' can be declared as pointer to const [constVariablePointer]
sequencedb.dy:605:27: style: Parameter 'word' can be declared as pointer to const [constParameterPointer]
sequencedb.dy:635:10: style: Variable 'run3' can be declared as pointer to const [constVariablePointer]
sequencedb.c:1027:44: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequencedb.c:1074:39: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequencedb.c:1118:51: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequencedb.c:1162:52: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequencedb.c:1206:48: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequencedb.c:1250:50: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequencedb.c:1294:48: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequencedb.c:1338:45: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequencedb.c:1382:43: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequencedb.c:1426:41: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
sequencestream.dy:191:52: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
shadowseqindex.dy:365:3: portability: %f in format string (no. 2) requires 'double' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_float]
shadowseqindex.dy:551:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
shadowseqindex.dy:549:15: note: Assuming allocation function fails
shadowseqindex.dy:549:15: note: Assignment 'out=malloc(sizeof(struct ShadowArraySeqHead))', assigned value is 0
shadowseqindex.dy:551:3: note: Null pointer dereference
shadowseqindex.dy:552:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
shadowseqindex.dy:549:15: note: Assuming allocation function fails
shadowseqindex.dy:549:15: note: Assignment 'out=malloc(sizeof(struct ShadowArraySeqHead))', assigned value is 0
shadowseqindex.dy:552:3: note: Null pointer dereference
shadowseqindex.dy:553:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
shadowseqindex.dy:549:15: note: Assuming allocation function fails
shadowseqindex.dy:549:15: note: Assignment 'out=malloc(sizeof(struct ShadowArraySeqHead))', assigned value is 0
shadowseqindex.dy:553:3: note: Null pointer dereference
shadowseqindex.dy:165:26: style: Variable 'client' can be declared as pointer to const [constVariablePointer]
shattermatrix.dy:34:9: style: Variable 'ret' can be declared as pointer to const [constVariablePointer]
shattermatrix.dy:157:7: style: Unused variable: j [unusedVariable]
singlenumberspace.dy:47:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
subseqhash.dy:77:42: style: Parameter 'data' can be declared as pointer to const. However it seems that 'Wise2_free_client_subseqhash_ghash' is a callback function, if 'data' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
subseqhash.dy:59:20: note: You might need to cast the function pointer here
subseqhash.dy:77:42: note: Parameter 'data' can be declared as pointer to const
subseqhash.dy:194:81: style: Parameter 'para' can be declared as pointer to const. However it seems that 'Wise2_add_seq_subseqhash_ghash' is a callback function, if 'para' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
subseqhash.dy:32:18: note: You might need to cast the function pointer here
subseqhash.dy:194:81: note: Parameter 'para' can be declared as pointer to const
subseqlookup.dy:189:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
subseqlookup.dy:88:18: style: Variable 'look' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/dynlibsrc/test_genomic.c:5:1: portability: Omitted return type of function 'main' defaults to int, this is not supported by ISO C99 and later standards. [returnImplicitInt]
wise-2.4.1/src/dynlibsrc/test_genomic.c:13:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dynlibsrc/test_hsp.c:29:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dynlibsrc/test_intallocator.c:46:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dynlibsrc/test_psi.c:15:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dynlibsrc/test_randomdb.c:4:1: portability: Omitted return type of function 'main' defaults to int, this is not supported by ISO C99 and later standards. [returnImplicitInt]
wise-2.4.1/src/dynlibsrc/test_randomdb.c:21:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dynlibsrc/test_seqhash.c:22:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dynlibsrc/test_seqhash.c:100:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dynlibsrc/test_seqhash.c:65:18: style: Unused variable: slp [unusedVariable]
wise-2.4.1/src/dynlibsrc/test_shadowindex.c:13:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dynlibsrc/testdb.c:14:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dynlibsrc/testpairbase.c:75:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/dynlibsrc/testpairbase.c:54:14: warning: Either the condition 'sa==NULL' is redundant or there is possible null pointer dereference: sa. [nullPointerRedundantCheck]
wise-2.4.1/src/dynlibsrc/testpairbase.c:47:10: note: Assuming that condition 'sa==NULL' is not redundant
wise-2.4.1/src/dynlibsrc/testpairbase.c:54:14: note: Null pointer dereference
wise-2.4.1/src/dynlibsrc/testpairbase.c:17:14: style: Variable 'sa' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/dynlibsrc/testpdb.c:14:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
transcript.c:1073:30: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
transcript.c:1117:28: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
transcript.c:1161:33: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
transcript.c:1205:33: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
transcript.c:1252:27: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
transcript.c:1296:30: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
transcript.c:1343:41: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
transcript.c:1387:46: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
transcript.c:1434:48: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
transcript.c:1478:44: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
transcript.dy:189:7: style: Unused variable: k [unusedVariable]
transcript.dy:190:23: style: Unused variable: sf [unusedVariable]
translation.dy:50:46: style: Parameter 't' can be declared as pointer to const [constParameterPointer]
translation.dy:156:36: style: Parameter 'ts' can be declared as pointer to const [constParameterPointer]
translation.c:254:44: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
translation.c:298:42: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
translation.c:342:54: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
translation.c:386:52: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/external/mott/gaplib.c:107:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/external/mott/gaplib.c:355:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/external/mott/gaplib.c:261:3: warning: If memory allocation fails, then there is a possible null pointer dereference: h [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/gaplib.c:255:32: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/gaplib.c:255:16: note: Assignment 'h=(double**)calloc(its,sizeof(double*))', assigned value is 0
wise-2.4.1/src/external/mott/gaplib.c:261:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/gaplib.c:262:3: warning: If memory allocation fails, then there is a possible null pointer dereference: h [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/gaplib.c:255:32: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/gaplib.c:255:16: note: Assignment 'h=(double**)calloc(its,sizeof(double*))', assigned value is 0
wise-2.4.1/src/external/mott/gaplib.c:262:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/gaplib.c:264:5: warning: If memory allocation fails, then there is a possible null pointer dereference: h [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/gaplib.c:255:32: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/gaplib.c:255:16: note: Assignment 'h=(double**)calloc(its,sizeof(double*))', assigned value is 0
wise-2.4.1/src/external/mott/gaplib.c:264:5: note: Null pointer dereference
wise-2.4.1/src/external/mott/gaplib.c:264:15: warning: If memory allocation fails, then there is a possible null pointer dereference: h [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/gaplib.c:255:32: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/gaplib.c:255:16: note: Assignment 'h=(double**)calloc(its,sizeof(double*))', assigned value is 0
wise-2.4.1/src/external/mott/gaplib.c:264:15: note: Null pointer dereference
wise-2.4.1/src/external/mott/gaplib.c:277:5: warning: If memory allocation fails, then there is a possible null pointer dereference: h [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/gaplib.c:255:32: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/gaplib.c:255:16: note: Assignment 'h=(double**)calloc(its,sizeof(double*))', assigned value is 0
wise-2.4.1/src/external/mott/gaplib.c:277:5: note: Null pointer dereference
wise-2.4.1/src/external/mott/gaplib.c:284:5: warning: If memory allocation fails, then there is a possible null pointer dereference: h [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/gaplib.c:255:32: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/gaplib.c:255:16: note: Assignment 'h=(double**)calloc(its,sizeof(double*))', assigned value is 0
wise-2.4.1/src/external/mott/gaplib.c:284:5: note: Null pointer dereference
wise-2.4.1/src/external/mott/gaplib.c:226:68: error: If memory allocation fails: overflow in pointer arithmetic, NULL pointer is subtracted. [nullPointerArithmeticOutOfMemory]
wise-2.4.1/src/external/mott/gaplib.c:226:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/gaplib.c:226:68: note: Null pointer subtraction
wise-2.4.1/src/external/mott/gaplib.c:254:56: error: If memory allocation fails: overflow in pointer arithmetic, NULL pointer is subtracted. [nullPointerArithmeticOutOfMemory]
wise-2.4.1/src/external/mott/gaplib.c:254:30: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/gaplib.c:254:56: note: Null pointer subtraction
wise-2.4.1/src/external/mott/gaplib.c:482:12: error: If memory allocation fails: overflow in pointer arithmetic, NULL pointer is subtracted. [nullPointerArithmeticOutOfMemory]
wise-2.4.1/src/external/mott/gaplib.c:481:26: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/gaplib.c:481:11: note: Assignment 't_ptr=(double*)calloc(hmax-hmin+1,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/gaplib.c:482:12: note: Null pointer subtraction
wise-2.4.1/src/external/mott/gaplib.c:517:15: error: If memory allocation fails: overflow in pointer arithmetic, NULL pointer is subtracted. [nullPointerArithmeticOutOfMemory]
wise-2.4.1/src/external/mott/gaplib.c:516:28: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/gaplib.c:516:13: note: Assignment 's_ptr=(double*)calloc(max-min+1,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/gaplib.c:517:15: note: Null pointer subtraction
wise-2.4.1/src/external/mott/gaplib.c:73:37: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/external/mott/gaplib.c:128:27: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/external/mott/gaplib.c:209:38: style: Parameter 'freq1' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/external/mott/gaplib.c:209:53: style: Parameter 'freq2' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/external/mott/gaplib.c:250:36: style: Parameter 'distribution' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/external/mott/gaplib.c:392:24: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/external/mott/gaplib.c:124:10: warning: Uninitialized variable: midpt [uninitvar]
wise-2.4.1/src/external/mott/gaplib.c:111:21: note: Assuming condition is false
wise-2.4.1/src/external/mott/gaplib.c:124:10: note: Uninitialized variable: midpt
wise-2.4.1/src/external/mott/gaplib.c:387:10: warning: Uninitialized variable: midpt [uninitvar]
wise-2.4.1/src/external/mott/gaplib.c:360:21: note: Assuming condition is false
wise-2.4.1/src/external/mott/gaplib.c:387:10: note: Uninitialized variable: midpt
wise-2.4.1/src/external/mott/gaplib.c:116:13: style: Variable 'fleft' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/external/mott/gaplib.c:120:14: style: Variable 'fright' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/external/mott/gaplib.c:503:8: style: Variable 'mean' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/external/mott/gaplib.c:504:8: style: Variable 'total' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/external/mott/gaplib.c:506:10: style: Variable 'mean' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/external/mott/gaplib.c:507:11: style: Variable 'total' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/external/mott/gaplib.c:548:12: style: Variable 'expect' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/external/mott/gaplib.c:549:11: style: Variable 'total' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/external/mott/gaplib.c:551:14: style: Variable 'expect' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/external/mott/gaplib.c:552:13: style: Variable 'total' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/external/mott/mott_api.c:234:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:234:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:235:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:235:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:236:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:236:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:237:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:237:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:238:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:238:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:239:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:239:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:240:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:240:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:241:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:241:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:242:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:242:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:243:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:243:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:244:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:244:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:245:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:245:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:246:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:246:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:247:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:247:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:248:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:248:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:249:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:249:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:250:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:250:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:251:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:251:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:252:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:252:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:253:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:253:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:255:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:255:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:256:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:256:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:257:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:257:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:258:3: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:258:3: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:262:10: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:262:10: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:265:5: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:265:5: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:265:24: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
wise-2.4.1/src/external/mott/mott_api.c:265:24: note: Null pointer dereference
wise-2.4.1/src/external/mott/mott_api.c:179:52: error: If memory allocation fails: overflow in pointer arithmetic, NULL pointer is subtracted. [nullPointerArithmeticOutOfMemory]
wise-2.4.1/src/external/mott/mott_api.c:179:22: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/mott_api.c:179:52: note: Null pointer subtraction
wise-2.4.1/src/external/mott/mott_api.c:162:31: style: Parameter 'freq1' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/external/mott/mott_api.c:162:46: style: Parameter 'freq2' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/external/mott/mott_api.c:194:43: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/external/mott/mott_api.c:150:9: style: Unused variable: n [unusedVariable]
wise-2.4.1/src/external/mott/mott_api.c:198:11: style: Variable 't' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/external/mott/wise2_mott_bridge.c:18:5: warning: If memory allocation fails, then there is a possible null pointer dereference: matrix [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/wise2_mott_bridge.c:16:18: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/wise2_mott_bridge.c:16:18: note: Assignment 'matrix=calloc(100,sizeof(int*))', assigned value is 0
wise-2.4.1/src/external/mott/wise2_mott_bridge.c:18:5: note: Null pointer dereference
wise-2.4.1/src/external/mott/wise2_mott_bridge.c:25:7: warning: If memory allocation fails, then there is a possible null pointer dereference: matrix [nullPointerOutOfMemory]
wise-2.4.1/src/external/mott/wise2_mott_bridge.c:16:18: note: Assuming allocation function fails
wise-2.4.1/src/external/mott/wise2_mott_bridge.c:16:18: note: Assignment 'matrix=calloc(100,sizeof(int*))', assigned value is 0
wise-2.4.1/src/external/mott/wise2_mott_bridge.c:25:7: note: Null pointer dereference
wise-2.4.1/src/external/mott/wise2_mott_bridge.c:53:37: style: Parameter 'data' can be declared as pointer to const. However it seems that 'calc_bits_Mott' is a callback function, if 'data' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise-2.4.1/src/external/mott/wise2_mott_bridge.c:75:22: note: You might need to cast the function pointer here
wise-2.4.1/src/external/mott/wise2_mott_bridge.c:53:37: note: Parameter 'data' can be declared as pointer to const
wise-2.4.1/src/external/mott/wise2_mott_bridge.c:58:39: style: Parameter 'data' can be declared as pointer to const. However it seems that 'attribution_Mott' is a callback function, if 'data' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise-2.4.1/src/external/mott/wise2_mott_bridge.c:76:22: note: You might need to cast the function pointer here
wise-2.4.1/src/external/mott/wise2_mott_bridge.c:58:39: note: Parameter 'data' can be declared as pointer to const
wise-2.4.1/src/external/mott/wise2_mott_bridge.c:63:35: style: Parameter 'data' can be declared as pointer to const. However it seems that 'free_data_noop' is a callback function, if 'data' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise-2.4.1/src/external/mott/wise2_mott_bridge.c:77:22: note: You might need to cast the function pointer here
wise-2.4.1/src/external/mott/wise2_mott_bridge.c:63:35: note: Parameter 'data' can be declared as pointer to const
abc.c:305:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
abc.c:585:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
abc.c:665:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
abc.c:828:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
abc.c:970:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
abc.c:989:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
abc.c:1140:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
abc.c:1180:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
abc.c:1264:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
abc.c:1295:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
abc.c:1335:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
abc.c:1818:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
abc.c:1904:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
abc.c:1951:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
abc.c:2066:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
abc.c:2279:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
abc.c:2402:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
abc.c:2482:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
abc.c:2572:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
abc.c:2713:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
abc.c:3308:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
abc.c:3437:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
abc.c:1135:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
abc.c:1809:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
abc.c:1803:15: note: 'hiddenj' is assigned value 'startj' here.
abc.c:1809:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
abc.c:1201:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
abc.c:1193:15: note: stopstate is assigned
abc.c:1201:15: note: stopstate is overwritten
abc.c:131:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
abc.c:132:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
abc.c:133:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
abc.c:166:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
abc.c:2558:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
abc.c:3059:34: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
abc.c:3480:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
abc.c:2572:11: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2573:11: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2584:17: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2586:21: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2588:16: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2592:23: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2613:10: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2615:11: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2625:59: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2626:57: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2640:17: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2642:21: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2644:16: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2648:23: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2651:16: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2655:23: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2658:16: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2662:23: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2665:16: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2669:23: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2672:16: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2676:23: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2683:10: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2685:11: style: Modulo of one is always equal to zero [moduloofone]
abc.c:2271:11: 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]
abc.c:2390:11: 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]
abc.c:2561:11: 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]
abc.c:63:41: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
abc.c:2878:41: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
abc.c:579:20: style: Variable 'target_pos' is assigned a value that is never used. [unreadVariable]
abc.c:679:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
abc.c:788:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
abc.c:882:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
abc.c:822:19: style: Unused variable: de [unusedVariable]
abc.c:1686:9: style: Unused variable: temp [unusedVariable]
aligngenemodel.dy:137:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
aligngenemodel.dy:357:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
aligngenemodel.dy:377:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
aligngenemodel.dy:416:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Probability [valueFlowBailoutIncompleteVar]
aligngenemodel.dy:446:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
aligngenemodel.dy:598:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
aligngenemodel.dy:738:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq [valueFlowBailoutIncompleteVar]
aligngenemodel.dy:785:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq [valueFlowBailoutIncompleteVar]
aligngenemodel.dy:843:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NMaskType_VARIABLE [valueFlowBailoutIncompleteVar]
aligngenemodel.dy:931:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
aligngenemodel.dy:983:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Score [valueFlowBailoutIncompleteVar]
aligngenemodel.dy:446:3: warning: %d in format string (no. 1) requires 'int' but the argument type is 'GenomicRegion *'. [invalidPrintfArgType_sint]
aligngenemodel.dy:451:3: warning: %d in format string (no. 1) requires 'int' but the argument type is 'GenomicRegion *'. [invalidPrintfArgType_sint]
aligngenemodel.dy:446:50: warning: Either the condition 'gr!=NULL' is redundant or there is possible null pointer dereference: gr. [nullPointerRedundantCheck]
aligngenemodel.dy:453:10: note: Assuming that condition 'gr!=NULL' is not redundant
aligngenemodel.dy:446:50: note: Null pointer dereference
aligngenemodel.dy:451:50: warning: Either the condition 'gr!=NULL' is redundant or there is possible null pointer dereference: gr. [nullPointerRedundantCheck]
aligngenemodel.dy:453:10: note: Assuming that condition 'gr!=NULL' is not redundant
aligngenemodel.dy:451:50: note: Null pointer dereference
aligngenemodel.dy:524:9: warning: If memory allocation fails, then there is a possible null pointer dereference: should_show [nullPointerOutOfMemory]
aligngenemodel.dy:448:23: note: Assuming allocation function fails
aligngenemodel.dy:448:23: note: Assignment 'should_show=calloc(agm->len,sizeof(int))', assigned value is 0
aligngenemodel.dy:524:9: note: Null pointer dereference
aligngenemodel.dy:122:39: style: Parameter 'sal' can be declared as pointer to const [constParameterPointer]
aligngenemodel.dy:122:86: style: Parameter 'agmp' can be declared as pointer to const [constParameterPointer]
aligngenemodel.dy:211:19: style: Variable 'col' is assigned a value that is never used. [unreadVariable]
aligngenemodel.dy:212:19: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
aligngenemodel.dy:242:19: style: Variable 'col' is assigned a value that is never used. [unreadVariable]
aligngenemodel.dy:243:19: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
aligngenemodel.dy:276:19: style: Variable 'col' is assigned a value that is never used. [unreadVariable]
aligngenemodel.dy:277:19: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
aligngenemodel.dy:444:7: style: Variable 'count' is assigned a value that is never used. [unreadVariable]
aligngenemodel.dy:731:19: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
aligngenemodel.dy:817:14: style: Unused variable: cp [unusedVariable]
aligngenemodel.dy:818:19: style: Unused variable: dm [unusedVariable]
wise-2.4.1/src/models/alignwise.c:21:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/alignwise.c:173:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/alignwise.c:14:33: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/alignwise.c:125:25: style: Variable 'show_trans' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/alignwise.c:127:25: style: Variable 'show_gene_raw' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/alignwise.c:96:7: style: Unused variable: i [unusedVariable]
wise-2.4.1/src/models/alignwise.c:125:11: style: Variable 'show_trans' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/alignwise.c:127:11: style: Variable 'show_gene_raw' is assigned a value that is never used. [unreadVariable]
alignwisedp.c:577:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
alignwisedp.c:703:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
alignwisedp.c:735:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
alignwisedp.c:1059:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
alignwisedp.c:1195:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
alignwisedp.c:1214:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
alignwisedp.c:1467:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
alignwisedp.c:1507:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
alignwisedp.c:1610:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
alignwisedp.c:1641:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
alignwisedp.c:1681:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
alignwisedp.c:2394:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
alignwisedp.c:2581:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
alignwisedp.c:2640:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
alignwisedp.c:2755:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
alignwisedp.c:3219:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
alignwisedp.c:3491:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
alignwisedp.c:3672:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
alignwisedp.c:3774:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
alignwisedp.c:4166:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
alignwisedp.c:5133:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
alignwisedp.c:5424:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
alignwisedp.c:1462:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
alignwisedp.c:2385:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
alignwisedp.c:2379:15: note: 'hiddenj' is assigned value 'startj' here.
alignwisedp.c:2385:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
alignwisedp.c:233:11: style: Variable 'SIG_0_3' can be declared as pointer to const [constVariablePointer]
alignwisedp.c:234:11: style: Variable 'SIG_0_6' can be declared as pointer to const [constVariablePointer]
alignwisedp.c:235:11: style: Variable 'SIG_0_5' can be declared as pointer to const [constVariablePointer]
alignwisedp.c:236:11: style: Variable 'SIG_0_4' can be declared as pointer to const [constVariablePointer]
alignwisedp.c:237:11: style: Variable 'SIG_0_8' can be declared as pointer to const [constVariablePointer]
alignwisedp.c:238:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
alignwisedp.c:239:11: style: Variable 'SIG_0_9' can be declared as pointer to const [constVariablePointer]
alignwisedp.c:240:11: style: Variable 'SIG_0_10' can be declared as pointer to const [constVariablePointer]
alignwisedp.c:273:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
alignwisedp.c:659:37: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
alignwisedp.c:3760:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
alignwisedp.c:4666:46: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
alignwisedp.c:5474:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
alignwisedp.c:1058:11: style: int result is assigned to long long variable. If the variable is long long to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
alignwisedp.c:3211:11: 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]
alignwisedp.c:3479:11: 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]
alignwisedp.c:3763:11: 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]
alignwisedp.c:165:47: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
alignwisedp.c:4485:47: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
alignwisedp.c:682:9: style: Unused variable: db_status [unusedVariable]
alignwisedp.c:749:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
alignwisedp.c:1021:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
alignwisedp.c:1113:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
alignwisedp.c:1053:19: style: Unused variable: de [unusedVariable]
alignwisedp.c:1495:19: style: Unused variable: pau [unusedVariable]
wise-2.4.1/src/models/amplimer_resolver.c:55:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/amplimer_resolver.c:134:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
bigdba.c:457:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
bigdba.c:528:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
bigdba.c:570:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
bigdba.c:886:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
bigdba.c:1052:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
bigdba.c:1071:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
bigdba.c:1335:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
bigdba.c:1375:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
bigdba.c:1459:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
bigdba.c:1490:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
bigdba.c:1530:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
bigdba.c:2283:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
bigdba.c:2503:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
bigdba.c:2560:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
bigdba.c:2675:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
bigdba.c:3297:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
bigdba.c:3614:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
bigdba.c:3828:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
bigdba.c:3928:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
bigdba.c:4274:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
bigdba.c:5282:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
bigdba.c:5556:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
bigdba.c:1330:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
bigdba.c:2274:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
bigdba.c:2268:15: note: 'hiddenj' is assigned value 'startj' here.
bigdba.c:2274:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
bigdba.c:1396:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
bigdba.c:1388:15: note: stopstate is assigned
bigdba.c:1396:15: note: stopstate is overwritten
bigdba.c:136:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
bigdba.c:137:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
bigdba.c:138:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
bigdba.c:171:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
bigdba.c:3914:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
bigdba.c:4790:60: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
bigdba.c:5604:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
bigdba.c:3928:11: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3929:11: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3930:11: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3931:11: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3932:11: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3933:11: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3934:11: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3945:17: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3947:21: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3949:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3953:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3956:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3960:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3963:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3967:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3974:10: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3976:11: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3985:17: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3987:21: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3989:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3993:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3996:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4000:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4003:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4007:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4014:10: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4016:11: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4025:17: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4027:21: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4029:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4033:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4036:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4040:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4043:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4047:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4054:10: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4056:11: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4065:17: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4067:21: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4069:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4073:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4076:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4080:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4083:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4087:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4094:10: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4096:11: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4105:17: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4107:21: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4109:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4113:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4116:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4120:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4123:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4127:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4134:10: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4136:11: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4145:17: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4147:21: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4149:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4153:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4156:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4160:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4163:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4167:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4170:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4174:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4177:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4181:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4202:10: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4204:11: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4213:17: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4215:21: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4217:16: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4221:23: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4228:10: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4230:11: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4240:72: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:4241:70: style: Modulo of one is always equal to zero [moduloofone]
bigdba.c:3289:11: 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]
bigdba.c:3602:11: 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]
bigdba.c:3917:11: 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]
bigdba.c:68:54: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
bigdba.c:4609:54: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
bigdba.c:507:9: style: Unused variable: db_status [unusedVariable]
bigdba.c:584:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
bigdba.c:838:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
bigdba.c:940:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
bigdba.c:880:19: style: Unused variable: de [unusedVariable]
bigdba.c:2116:9: style: Unused variable: temp [unusedVariable]
wise-2.4.1/src/models/cdnawise.c:104:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/cdnawise.c:104:10: style: Variable 'ofp' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/models/cdnawise.c:104:14: style: Variable 'ofp' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/cdnawise.c:58:7: style: Unused variable: i [unusedVariable]
wise-2.4.1/src/models/cdnawise.c:78:15: style: Unused variable: gs [unusedVariable]
wise-2.4.1/src/models/cdnawise.c:99:13: style: Unused variable: trans [unusedVariable]
wise-2.4.1/src/models/cdnawise.c:104:10: style: Variable 'ofp' is assigned a value that is never used. [unreadVariable]
cdnawise10.c:553:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
cdnawise10.c:841:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
cdnawise10.c:925:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
cdnawise10.c:1304:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
cdnawise10.c:1458:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
cdnawise10.c:1477:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
cdnawise10.c:1790:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
cdnawise10.c:1830:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
cdnawise10.c:1914:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
cdnawise10.c:1945:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
cdnawise10.c:1985:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
cdnawise10.c:2853:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
cdnawise10.c:3129:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
cdnawise10.c:3192:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
cdnawise10.c:3307:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
cdnawise10.c:4075:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
cdnawise10.c:4474:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
cdnawise10.c:4744:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
cdnawise10.c:4850:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
cdnawise10.c:5314:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
cdnawise10.c:6517:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
cdnawise10.c:6858:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
cdnawise10.c:1785:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
cdnawise10.c:2844:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
cdnawise10.c:2838:15: note: 'hiddenj' is assigned value 'startj' here.
cdnawise10.c:2844:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
cdnawise10.c:1851:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
cdnawise10.c:1843:15: note: stopstate is assigned
cdnawise10.c:1851:15: note: stopstate is overwritten
cdnawise10.c:141:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
cdnawise10.c:142:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
cdnawise10.c:143:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
cdnawise10.c:144:11: style: Variable 'SIG_3_3' can be declared as pointer to const [constVariablePointer]
cdnawise10.c:145:11: style: Variable 'SIG_0_6' can be declared as pointer to const [constVariablePointer]
cdnawise10.c:146:11: style: Variable 'SIG_0_5' can be declared as pointer to const [constVariablePointer]
cdnawise10.c:147:11: style: Variable 'SIG_0_4' can be declared as pointer to const [constVariablePointer]
cdnawise10.c:148:11: style: Variable 'SIG_0_3' can be declared as pointer to const [constVariablePointer]
cdnawise10.c:149:11: style: Variable 'SIG_3_8' can be declared as pointer to const [constVariablePointer]
cdnawise10.c:150:11: style: Variable 'SIG_0_8' can be declared as pointer to const [constVariablePointer]
cdnawise10.c:151:11: style: Variable 'SIG_3_9' can be declared as pointer to const [constVariablePointer]
cdnawise10.c:152:11: style: Variable 'SIG_0_9' can be declared as pointer to const [constVariablePointer]
cdnawise10.c:153:11: style: Variable 'SIG_3_10' can be declared as pointer to const [constVariablePointer]
cdnawise10.c:154:11: style: Variable 'SIG_0_10' can be declared as pointer to const [constVariablePointer]
cdnawise10.c:187:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
cdnawise10.c:4836:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
cdnawise10.c:5914:48: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
cdnawise10.c:6909:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
cdnawise10.c:4067:11: 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]
cdnawise10.c:4462:11: 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]
cdnawise10.c:4839:11: 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]
cdnawise10.c:73:48: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
cdnawise10.c:5733:48: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
cdnawise10.c:835:20: style: Variable 'target_pos' is assigned a value that is never used. [unreadVariable]
cdnawise10.c:939:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
cdnawise10.c:1260:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
cdnawise10.c:1358:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
cdnawise10.c:1298:19: style: Unused variable: de [unusedVariable]
cdnawise10.c:2658:9: style: Unused variable: temp [unusedVariable]
wise-2.4.1/src/models/clonewise.c:73:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/clonewise.c:133:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/clonewise.c:248:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/clonewise.c:64:27: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/clonewise.c:107:31: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/clonewise.c:110:15: style: Variable 'runner' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/models/clonewise.c:224:10: style: Variable 'divide_string' can be declared as pointer to const [constVariablePointer]
clonewisedp.c:420:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
clonewisedp.c:556:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
clonewisedp.c:593:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
clonewisedp.c:870:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
clonewisedp.c:1021:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
clonewisedp.c:1040:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
clonewisedp.c:1247:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
clonewisedp.c:1287:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
clonewisedp.c:1390:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
clonewisedp.c:1421:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
clonewisedp.c:1461:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
clonewisedp.c:2049:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
clonewisedp.c:2159:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
clonewisedp.c:2208:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
clonewisedp.c:2323:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
clonewisedp.c:2600:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
clonewisedp.c:2757:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
clonewisedp.c:2861:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
clonewisedp.c:2953:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
clonewisedp.c:3248:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
clonewisedp.c:4062:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
clonewisedp.c:4301:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
clonewisedp.c:1242:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
clonewisedp.c:2040:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
clonewisedp.c:2034:15: note: 'hiddenj' is assigned value 'startj' here.
clonewisedp.c:2040:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
clonewisedp.c:133:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
clonewisedp.c:134:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
clonewisedp.c:135:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
clonewisedp.c:168:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
clonewisedp.c:507:37: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
clonewisedp.c:2939:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
clonewisedp.c:3680:46: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
clonewisedp.c:4346:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
clonewisedp.c:2953:11: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:2954:11: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:2955:11: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:2966:17: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:2968:21: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:2970:16: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:2974:23: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:2977:16: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:2981:23: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:2984:16: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:2988:23: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:2991:16: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:2995:23: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3016:10: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3018:11: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3028:77: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3029:75: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3043:17: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3045:21: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3047:16: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3051:23: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3054:16: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3058:23: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3079:10: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3081:11: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3091:77: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3092:75: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3106:17: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3108:21: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3110:16: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3114:23: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3117:16: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3121:23: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3142:10: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3144:11: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3154:77: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:3155:75: style: Modulo of one is always equal to zero [moduloofone]
clonewisedp.c:869:11: style: int result is assigned to long long variable. If the variable is long long to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
clonewisedp.c:2592:11: 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]
clonewisedp.c:2745:11: 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]
clonewisedp.c:2942:11: 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]
clonewisedp.c:65:47: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
clonewisedp.c:3499:47: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
clonewisedp.c:535:9: style: Unused variable: db_status [unusedVariable]
clonewisedp.c:607:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
clonewisedp.c:827:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
clonewisedp.c:924:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
clonewisedp.c:864:19: style: Unused variable: de [unusedVariable]
clonewisedp.c:1275:19: style: Unused variable: pau [unusedVariable]
dba.c:420:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
dba.c:488:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
dba.c:527:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dba.c:807:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
dba.c:964:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
dba.c:983:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
dba.c:1219:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
dba.c:1259:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
dba.c:1343:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
dba.c:1374:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
dba.c:1414:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
dba.c:2101:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dba.c:2289:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dba.c:2344:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
dba.c:2459:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dba.c:2979:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dba.c:3250:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dba.c:3432:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dba.c:3530:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dba.c:3828:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dba.c:4735:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
dba.c:4976:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
dba.c:1214:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
dba.c:2092:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
dba.c:2086:15: note: 'hiddenj' is assigned value 'startj' here.
dba.c:2092:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
dba.c:1280:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
dba.c:1272:15: note: stopstate is assigned
dba.c:1280:15: note: stopstate is overwritten
dba.c:135:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
dba.c:136:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
dba.c:137:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
dba.c:170:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
dba.c:3516:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
dba.c:4302:54: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
dba.c:5023:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
dba.c:3530:11: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3531:11: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3532:11: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3533:11: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3534:11: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3535:11: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3546:17: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3548:21: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3550:16: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3554:23: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3557:16: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3561:23: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3564:16: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3568:23: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3575:10: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3577:11: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3586:17: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3588:21: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3590:16: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3594:23: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3597:16: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3601:23: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3604:16: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3608:23: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3615:10: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3617:11: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3626:17: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3628:21: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3630:16: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3634:23: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3637:16: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3641:23: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3644:16: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3648:23: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3655:10: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3657:11: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3666:17: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3668:21: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3670:16: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3674:23: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3677:16: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3681:23: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3684:16: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3688:23: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3695:10: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3697:11: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3706:17: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3708:21: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3710:16: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3714:23: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3717:16: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3721:23: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3724:16: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3728:23: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3731:16: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3735:23: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3756:10: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3758:11: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3767:17: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3769:21: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3771:16: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3775:23: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3782:10: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3784:11: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3794:69: style: Modulo of one is always equal to zero [moduloofone]
dba.c:3795:67: style: Modulo of one is always equal to zero [moduloofone]
dba.c:2971:11: 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]
dba.c:3238:11: 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]
dba.c:3519:11: 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]
dba.c:67:51: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
dba.c:4121:51: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
dba.c:467:9: style: Unused variable: db_status [unusedVariable]
dba.c:541:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
dba.c:762:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
dba.c:861:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
dba.c:801:19: style: Unused variable: de [unusedVariable]
dba.c:1942:9: style: Unused variable: temp [unusedVariable]
wise-2.4.1/src/models/dbac.c:183:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/dbac.c:395:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/dbac.c:513:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/dbac.c:413:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
wise-2.4.1/src/models/dbac.c:391:5: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory]
wise-2.4.1/src/models/dbac.c:388:15: note: Assuming allocation function fails
wise-2.4.1/src/models/dbac.c:388:15: note: Assignment 'seq=calloc(one->len,sizeof(char))', assigned value is 0
wise-2.4.1/src/models/dbac.c:391:5: note: Null pointer dereference
wise-2.4.1/src/models/dbac.c:51:32: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/dbac.c:51:47: style: Parameter 'one' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/dbac.c:51:62: style: Parameter 'two' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/dbac.c:75:33: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/dbac.c:75:48: style: Parameter 'x' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/dbac.c:75:61: style: Parameter 'y' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/dbac.c:78:12: style: Variable 'xa' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/models/dbac.c:78:17: style: Variable 'ya' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/models/dbac.c:84:10: style: Variable 'type' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/models/dbac.c:154:25: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/dbac.c:157:12: style: Variable 'xa' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/models/dbac.c:157:17: style: Variable 'ya' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/models/dbac.c:163:10: style: Variable 'type' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/models/dbac.c:174:10: style: Variable 'xstr' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/models/dbac.c:175:10: style: Variable 'ystr' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/models/dbac.c:371:48: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/dbac.c:460:19: style: Unused variable: dmat [unusedVariable]
wise-2.4.1/src/models/dbac.c:463:7: style: Unused variable: score [unusedVariable]
dbadisplay.dy:42:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
dbadisplay.dy:117:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
dbadisplay.dy:40:40: style: Parameter 'alc' can be declared as pointer to const [constParameterPointer]
dbadisplay.dy:90:66: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
dbadisplay.dy:106:17: style: Variable 'is_reversed' is assigned a value that is never used. [unreadVariable]
dbadisplay.dy:118:15: style: Variable 'end_alc' is assigned a value that is never used. [unreadVariable]
dnaalign.dy:195:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dnaalign.c:577:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
dnaalign.c:642:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
dnaalign.c:678:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dnaalign.c:906:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
dnaalign.c:1054:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
dnaalign.c:1073:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
dnaalign.c:1257:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
dnaalign.c:1297:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
dnaalign.c:1381:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
dnaalign.c:1412:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
dnaalign.c:1452:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
dnaalign.c:1968:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dnaalign.c:2056:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dnaalign.c:2105:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
dnaalign.c:2220:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dnaalign.c:2415:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dnaalign.c:2542:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dnaalign.c:2624:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dnaalign.c:2716:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dnaalign.c:2953:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dnaalign.c:3670:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
dnaalign.c:3862:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
dnaalign.c:1140:25: style: The if condition is the same as the previous if condition [duplicateCondition]
dnaalign.c:1136:25: note: First condition
dnaalign.c:1140:25: note: Second condition
dnaalign.c:1144:25: style: The if condition is the same as the previous if condition [duplicateCondition]
dnaalign.c:1140:25: note: First condition
dnaalign.c:1144:25: note: Second condition
dnaalign.c:1148:25: style: The if condition is the same as the previous if condition [duplicateCondition]
dnaalign.c:1144:25: note: First condition
dnaalign.c:1148:25: note: Second condition
dnaalign.c:1186:25: style: The if condition is the same as the previous if condition [duplicateCondition]
dnaalign.c:1180:25: note: First condition
dnaalign.c:1186:25: note: Second condition
dnaalign.c:1192:25: style: The if condition is the same as the previous if condition [duplicateCondition]
dnaalign.c:1186:25: note: First condition
dnaalign.c:1192:25: note: Second condition
dnaalign.c:1198:25: style: The if condition is the same as the previous if condition [duplicateCondition]
dnaalign.c:1192:25: note: First condition
dnaalign.c:1198:25: note: Second condition
dnaalign.c:1252:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
dnaalign.c:1959:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
dnaalign.c:1953:15: note: 'hiddenj' is assigned value 'startj' here.
dnaalign.c:1959:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
dnaalign.c:1318:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
dnaalign.c:1310:15: note: stopstate is assigned
dnaalign.c:1318:15: note: stopstate is overwritten
dnaalign.c:344:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
dnaalign.c:345:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
dnaalign.c:346:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
dnaalign.c:379:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
dnaalign.c:2702:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
dnaalign.c:3344:44: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
dnaalign.c:3906:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
dnaalign.c:2716:11: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2717:11: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2718:11: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2729:17: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2731:21: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2733:16: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2737:23: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2740:16: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2744:23: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2807:10: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2809:11: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2819:64: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2820:62: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2835:64: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2836:62: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2851:64: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2852:62: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2867:64: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2868:62: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2882:17: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2884:21: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2886:16: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2890:23: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2897:10: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2899:11: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2908:17: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2910:21: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2912:16: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2916:23: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2923:10: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2925:11: style: Modulo of one is always equal to zero [moduloofone]
dnaalign.c:2407:11: 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]
dnaalign.c:2530:11: 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]
dnaalign.c:2705:11: 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]
dnaalign.c:276:46: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
dnaalign.c:3163:46: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
dnaalign.c:621:9: style: Unused variable: db_status [unusedVariable]
dnaalign.c:692:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
dnaalign.c:864:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
dnaalign.c:960:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
dnaalign.c:900:19: style: Unused variable: de [unusedVariable]
dnaalign.c:1798:9: style: Unused variable: temp [unusedVariable]
dnahmm.dy:123:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
dnahmm.dy:169:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASE_N [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/dnal.c:53:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/dnal.c:68:23: warning: Either the condition 'alb==NULL' is redundant or there is possible null pointer dereference: alb. [nullPointerRedundantCheck]
wise-2.4.1/src/models/dnal.c:70:11: note: Assuming that condition 'alb==NULL' is not redundant
wise-2.4.1/src/models/dnal.c:68:23: note: Null pointer dereference
dnamatcher.dy:80:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
dnaprofile.dy:97:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
dnaprofile.dy:192:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASE_N [valueFlowBailoutIncompleteVar]
dnaprofile.dy:226:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
dnaprofile.dy:245:9: warning: Either the condition 'base_n<4' is redundant or the array 'count[4]' is accessed at index 4, which is out of bounds. [arrayIndexOutOfBoundsCond]
dnaprofile.dy:241:18: note: Assuming that condition 'base_n<4' is not redundant
dnaprofile.dy:245:9: note: Array index out of bounds
dnaprofile.dy:76:73: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
dnaprofile.dy:61:15: style: Variable 'prob' is assigned a value that is never used. [unreadVariable]
dnaprofile.dy:140:9: style: Unused variable: k [unusedVariable]
dnaprofiledp.dy:134:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INTEGER_FACTOR [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:123:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Score [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:183:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Score [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:632:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:762:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:796:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:995:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:1137:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:1156:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:1333:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:1373:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:1457:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:1488:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:1528:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:2071:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:2191:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:2242:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:2357:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:2654:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:2827:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:2941:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:3035:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:3230:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:3913:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:4078:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
dnaprofiledp.c:1328:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
dnaprofiledp.c:2062:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
dnaprofiledp.c:2056:15: note: 'hiddenj' is assigned value 'startj' here.
dnaprofiledp.c:2062:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
dnaprofiledp.c:1394:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
dnaprofiledp.c:1386:15: note: stopstate is assigned
dnaprofiledp.c:1394:15: note: stopstate is overwritten
dnaprofiledp.c:422:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
dnaprofiledp.c:423:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
dnaprofiledp.c:424:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
dnaprofiledp.c:457:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
dnaprofiledp.c:716:41: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
dnaprofiledp.c:3021:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
dnaprofiledp.c:3612:54: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
dnaprofiledp.c:4123:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
dnaprofiledp.c:3035:11: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3036:11: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3037:11: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3038:11: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3049:17: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3051:21: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3053:16: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3057:23: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3060:16: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3064:23: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3067:16: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3071:23: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3092:10: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3094:11: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3104:69: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3105:67: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3119:17: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3121:21: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3123:16: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3127:23: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3130:16: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3134:23: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3137:16: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3141:23: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3148:10: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3150:11: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3159:17: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3161:21: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3163:16: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3167:23: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3174:10: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3176:11: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3185:17: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3187:21: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3189:16: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3193:23: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3200:10: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:3202:11: style: Modulo of one is always equal to zero [moduloofone]
dnaprofiledp.c:994:11: style: int result is assigned to long long variable. If the variable is long long to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
dnaprofiledp.c:2646:11: 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]
dnaprofiledp.c:2815:11: 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]
dnaprofiledp.c:3024:11: 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]
dnaprofiledp.c:354:51: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
dnaprofiledp.c:3431:51: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
dnaprofiledp.c:259:9: style: Unused variable: j [unusedVariable]
dnaprofiledp.c:741:9: style: Unused variable: db_status [unusedVariable]
dnaprofiledp.c:810:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
dnaprofiledp.c:955:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
dnaprofiledp.c:1049:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
dnaprofiledp.c:989:19: style: Unused variable: de [unusedVariable]
dnaprofiledp.c:1929:9: style: Unused variable: temp [unusedVariable]
dnaprofileengine.dy:97:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
dnaprofileengine.dy:215:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
dnaprofileengine.dy:260:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NMaskType_VARIABLE [valueFlowBailoutIncompleteVar]
dnaprofileengine.dy:319:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq [valueFlowBailoutIncompleteVar]
dnaprofileengine.dy:356:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NMaskType_BANNED [valueFlowBailoutIncompleteVar]
dnaprofileengine.dy:489:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
dnaprofileengine.dy:541:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
dnaprofileengine.dy:612:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
dnaprofileengine.dy:72:3: error: Found an exit path from function with non-void return type that has missing return statement [missingReturn]
dnaprofileengine.dy:620:3: warning: %d in format string (no. 1) requires 'int' but the argument type is 'PackAln *'. [invalidPrintfArgType_sint]
dnaprofileengine.dy:66:68: style: Parameter 'in' can be declared as pointer to const [constParameterPointer]
dnaprofileengine.dy:70:20: style: Variable 'out' can be declared as pointer to const [constVariablePointer]
dnaprofileengine.dy:645:55: style: Parameter 'one' can be declared as pointer to const. However it seems that 'Wise2_compare_DnaProfileMatchPair' is a callback function, if 'one' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
dnaprofileengine.dy:642:35: note: You might need to cast the function pointer here
dnaprofileengine.dy:645:55: note: Parameter 'one' can be declared as pointer to const
dnaprofileengine.dy:645:81: style: Parameter 'two' can be declared as pointer to const. However it seems that 'Wise2_compare_DnaProfileMatchPair' is a callback function, if 'two' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
dnaprofileengine.dy:642:35: note: You might need to cast the function pointer here
dnaprofileengine.dy:645:81: note: Parameter 'two' can be declared as pointer to const
dnaprofileengine.dy:72:7: style: Variable 'out' is assigned a value that is never used. [unreadVariable]
dnaprofileengine.dy:68:7: style: Unused variable: i [unusedVariable]
dnaprofileengine.dy:69:8: style: Unused variable: name_buf [unusedVariable]
dnaprofileengine.dy:524:7: style: Unused variable: j [unusedVariable]
wise-2.4.1/src/models/dnawise.c:54:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/editdist.c:60:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
editdistdp.c:400:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
editdistdp.c:528:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
editdistdp.c:561:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
editdistdp.c:711:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
editdistdp.c:850:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
editdistdp.c:869:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
editdistdp.c:1002:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
editdistdp.c:1042:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
editdistdp.c:1126:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
editdistdp.c:1157:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
editdistdp.c:1197:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
editdistdp.c:1638:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
editdistdp.c:1691:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
editdistdp.c:1736:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
editdistdp.c:1851:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
editdistdp.c:1961:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
editdistdp.c:2037:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
editdistdp.c:2084:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
editdistdp.c:2172:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
editdistdp.c:2293:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
editdistdp.c:2836:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
editdistdp.c:2953:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
editdistdp.c:932:25: style: The if condition is the same as the previous if condition [duplicateCondition]
editdistdp.c:928:25: note: First condition
editdistdp.c:932:25: note: Second condition
editdistdp.c:997:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
editdistdp.c:1629:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
editdistdp.c:1623:15: note: 'hiddenj' is assigned value 'startj' here.
editdistdp.c:1629:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
editdistdp.c:1063:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
editdistdp.c:1055:15: note: stopstate is assigned
editdistdp.c:1063:15: note: stopstate is overwritten
editdistdp.c:239:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
editdistdp.c:240:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
editdistdp.c:241:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
editdistdp.c:274:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
editdistdp.c:483:40: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
editdistdp.c:2158:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
editdistdp.c:2615:52: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
editdistdp.c:2995:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
editdistdp.c:2172:11: style: Modulo of one is always equal to zero [moduloofone]
editdistdp.c:2183:17: style: Modulo of one is always equal to zero [moduloofone]
editdistdp.c:2185:21: style: Modulo of one is always equal to zero [moduloofone]
editdistdp.c:2187:16: style: Modulo of one is always equal to zero [moduloofone]
editdistdp.c:2191:23: style: Modulo of one is always equal to zero [moduloofone]
editdistdp.c:2194:16: style: Modulo of one is always equal to zero [moduloofone]
editdistdp.c:2198:23: style: Modulo of one is always equal to zero [moduloofone]
editdistdp.c:2247:10: style: Modulo of one is always equal to zero [moduloofone]
editdistdp.c:2249:11: style: Modulo of one is always equal to zero [moduloofone]
editdistdp.c:2259:68: style: Modulo of one is always equal to zero [moduloofone]
editdistdp.c:2260:66: style: Modulo of one is always equal to zero [moduloofone]
editdistdp.c:710:11: style: int result is assigned to long long variable. If the variable is long long to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
editdistdp.c:1953:11: 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]
editdistdp.c:2025:11: 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]
editdistdp.c:2161:11: 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]
editdistdp.c:171:50: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
editdistdp.c:2434:50: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
editdistdp.c:507:9: style: Unused variable: db_status [unusedVariable]
editdistdp.c:575:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
editdistdp.c:672:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
editdistdp.c:765:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
editdistdp.c:705:19: style: Unused variable: de [unusedVariable]
editdistdp.c:1492:9: style: Unused variable: temp [unusedVariable]
est_evidence.dy:41:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
est_evidence.dy:64:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
est_evidence.dy:185:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASE_A [valueFlowBailoutIncompleteVar]
est_evidence.dy:33:61: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
est_evidence.dy:154:49: style: Parameter 'seq' can be declared as pointer to const. However it seems that 'Wise2_est_utr5_start' is a callback function, if 'seq' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
est_evidence.dy:147:20: note: You might need to cast the function pointer here
est_evidence.dy:154:49: note: Parameter 'seq' can be declared as pointer to const
est_evidence.dy:156:17: style: Variable 'est' can be declared as pointer to const [constVariablePointer]
est_evidence.dy:167:47: style: Parameter 'seq' can be declared as pointer to const. However it seems that 'Wise2_est_utr3_end' is a callback function, if 'seq' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
est_evidence.dy:146:18: note: You might need to cast the function pointer here
est_evidence.dy:167:47: note: Parameter 'seq' can be declared as pointer to const
est_evidence.dy:169:17: style: Variable 'est' can be declared as pointer to const [constVariablePointer]
est_evidence.dy:214:54: style: Parameter 'seq' can be declared as pointer to const. However it seems that 'Wise2_est_cds_frameshift' is a callback function, if 'seq' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
est_evidence.dy:143:24: note: You might need to cast the function pointer here
est_evidence.dy:214:54: note: Parameter 'seq' can be declared as pointer to const
est_evidence.dy:216:17: style: Variable 'est' can be declared as pointer to const [constVariablePointer]
est_evidence.dy:252:49: style: Parameter 'seq' can be declared as pointer to const. However it seems that 'Wise2_est_intron_pot' is a callback function, if 'seq' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
est_evidence.dy:141:24: note: You might need to cast the function pointer here
est_evidence.dy:252:49: note: Parameter 'seq' can be declared as pointer to const
est_evidence.dy:254:17: style: Variable 'est' can be declared as pointer to const [constVariablePointer]
est_evidence.dy:314:42: style: Parameter 'seq' can be declared as pointer to const. However it seems that 'Wise2_est_3ss' is a callback function, if 'seq' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
est_evidence.dy:136:17: note: You might need to cast the function pointer here
est_evidence.dy:314:42: note: Parameter 'seq' can be declared as pointer to const
est_evidence.dy:317:17: style: Variable 'est' can be declared as pointer to const [constVariablePointer]
est_evidence.dy:341:43: style: Parameter 'seq' can be declared as pointer to const. However it seems that 'Wise2_est_5ss' is a callback function, if 'seq' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
est_evidence.dy:137:17: note: You might need to cast the function pointer here
est_evidence.dy:341:43: note: Parameter 'seq' can be declared as pointer to const
est_evidence.dy:370:46: style: Parameter 'seq' can be declared as pointer to const. However it seems that 'Wise2_est_utr_pot' is a callback function, if 'seq' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
est_evidence.dy:139:17: note: You might need to cast the function pointer here
est_evidence.dy:370:46: note: Parameter 'seq' can be declared as pointer to const
est_evidence.dy:373:17: style: Variable 'est' can be declared as pointer to const [constVariablePointer]
est_evidence.dy:183:7: style: Unused variable: i [unusedVariable]
est_evidence.dy:203:7: style: Unused variable: i [unusedVariable]
estfrag3.c:495:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
estfrag3.c:547:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
estfrag3.c:632:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estfrag3.c:971:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
estfrag3.c:1110:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estfrag3.c:1129:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estfrag3.c:1414:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estfrag3.c:1454:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estfrag3.c:1538:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
estfrag3.c:1569:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estfrag3.c:1609:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estfrag3.c:2437:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estfrag3.c:2654:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estfrag3.c:2703:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estfrag3.c:2818:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estfrag3.c:3532:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estfrag3.c:3840:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estfrag3.c:4051:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estfrag3.c:4143:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estfrag3.c:4562:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estfrag3.c:5767:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estfrag3.c:6076:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estfrag3.c:1196:25: style: The if condition is the same as the previous if condition [duplicateCondition]
estfrag3.c:1192:25: note: First condition
estfrag3.c:1196:25: note: Second condition
estfrag3.c:1346:25: style: The if condition is the same as the previous if condition [duplicateCondition]
estfrag3.c:1340:25: note: First condition
estfrag3.c:1346:25: note: Second condition
estfrag3.c:1409:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
estfrag3.c:2428:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
estfrag3.c:2422:15: note: 'hiddenj' is assigned value 'startj' here.
estfrag3.c:2428:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
estfrag3.c:1475:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
estfrag3.c:1467:15: note: stopstate is assigned
estfrag3.c:1475:15: note: stopstate is overwritten
estfrag3.c:132:11: style: Variable 'SIG_1_3' can be declared as pointer to const [constVariablePointer]
estfrag3.c:133:11: style: Variable 'SIG_1_2' can be declared as pointer to const [constVariablePointer]
estfrag3.c:134:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
estfrag3.c:135:11: style: Variable 'SIG_1_4' can be declared as pointer to const [constVariablePointer]
estfrag3.c:136:11: style: Variable 'SIG_1_5' can be declared as pointer to const [constVariablePointer]
estfrag3.c:137:11: style: Variable 'SIG_0_3' can be declared as pointer to const [constVariablePointer]
estfrag3.c:138:11: style: Variable 'SIG_0_2' can be declared as pointer to const [constVariablePointer]
estfrag3.c:139:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
estfrag3.c:140:11: style: Variable 'SIG_0_4' can be declared as pointer to const [constVariablePointer]
estfrag3.c:141:11: style: Variable 'SIG_0_5' can be declared as pointer to const [constVariablePointer]
estfrag3.c:142:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
estfrag3.c:175:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
estfrag3.c:4129:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
estfrag3.c:5161:44: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
estfrag3.c:6120:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
estfrag3.c:3524:11: 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]
estfrag3.c:3828:11: 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]
estfrag3.c:4132:11: 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]
estfrag3.c:64:46: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
estfrag3.c:4980:46: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
estfrag3.c:541:20: style: Variable 'target_pos' is assigned a value that is never used. [unreadVariable]
estfrag3.c:932:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
estfrag3.c:1025:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
estfrag3.c:965:19: style: Unused variable: de [unusedVariable]
estfrag3.c:2241:9: style: Unused variable: temp [unusedVariable]
estloop3.c:563:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
estloop3.c:837:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
estloop3.c:914:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estloop3.c:1318:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
estloop3.c:1451:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estloop3.c:1470:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estloop3.c:1781:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estloop3.c:1821:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estloop3.c:1924:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
estloop3.c:1955:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estloop3.c:1995:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estloop3.c:2862:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estloop3.c:3079:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estloop3.c:3128:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estloop3.c:3243:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estloop3.c:3957:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estloop3.c:4265:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estloop3.c:4476:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estloop3.c:4568:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estloop3.c:5082:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estloop3.c:6392:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estloop3.c:6764:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estloop3.c:1776:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
estloop3.c:2853:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
estloop3.c:2847:15: note: 'hiddenj' is assigned value 'startj' here.
estloop3.c:2853:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
estloop3.c:133:11: style: Variable 'SIG_1_3' can be declared as pointer to const [constVariablePointer]
estloop3.c:134:11: style: Variable 'SIG_1_2' can be declared as pointer to const [constVariablePointer]
estloop3.c:135:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
estloop3.c:136:11: style: Variable 'SIG_1_4' can be declared as pointer to const [constVariablePointer]
estloop3.c:137:11: style: Variable 'SIG_1_5' can be declared as pointer to const [constVariablePointer]
estloop3.c:138:11: style: Variable 'SIG_0_3' can be declared as pointer to const [constVariablePointer]
estloop3.c:139:11: style: Variable 'SIG_0_2' can be declared as pointer to const [constVariablePointer]
estloop3.c:140:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
estloop3.c:141:11: style: Variable 'SIG_0_4' can be declared as pointer to const [constVariablePointer]
estloop3.c:142:11: style: Variable 'SIG_0_5' can be declared as pointer to const [constVariablePointer]
estloop3.c:143:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
estloop3.c:176:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
estloop3.c:4554:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
estloop3.c:5724:44: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
estloop3.c:6809:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
estloop3.c:3949:11: 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]
estloop3.c:4253:11: 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]
estloop3.c:4557:11: 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]
estloop3.c:65:46: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
estloop3.c:5543:46: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
estloop3.c:831:20: style: Variable 'target_pos' is assigned a value that is never used. [unreadVariable]
estloop3.c:928:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
estloop3.c:1281:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
estloop3.c:1372:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
estloop3.c:1312:19: style: Unused variable: de [unusedVariable]
estloop3.c:1809:19: style: Unused variable: pau [unusedVariable]
estquick3.c:333:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
estquick3.c:607:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
estquick3.c:684:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estquick3.c:866:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
estquick3.c:999:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estquick3.c:1018:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estquick3.c:1183:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estquick3.c:1223:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estquick3.c:1307:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
estquick3.c:1338:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estquick3.c:1378:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estquick3.c:1903:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estquick3.c:2010:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estquick3.c:2059:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estquick3.c:2174:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estquick3.c:2448:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estquick3.c:2602:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estquick3.c:2703:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estquick3.c:2795:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estquick3.c:2970:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estquick3.c:3628:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estquick3.c:3779:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estquick3.c:1178:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
estquick3.c:1894:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
estquick3.c:1888:15: note: 'hiddenj' is assigned value 'startj' here.
estquick3.c:1894:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
estquick3.c:1244:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
estquick3.c:1236:15: note: stopstate is assigned
estquick3.c:1244:15: note: stopstate is overwritten
estquick3.c:132:11: style: Variable 'SIG_1_3' can be declared as pointer to const [constVariablePointer]
estquick3.c:133:11: style: Variable 'SIG_1_2' can be declared as pointer to const [constVariablePointer]
estquick3.c:134:11: style: Variable 'SIG_1_4' can be declared as pointer to const [constVariablePointer]
estquick3.c:135:11: style: Variable 'SIG_0_3' can be declared as pointer to const [constVariablePointer]
estquick3.c:136:11: style: Variable 'SIG_0_2' can be declared as pointer to const [constVariablePointer]
estquick3.c:137:11: style: Variable 'SIG_0_4' can be declared as pointer to const [constVariablePointer]
estquick3.c:138:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
estquick3.c:171:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
estquick3.c:2781:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
estquick3.c:3342:46: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
estquick3.c:3823:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
estquick3.c:2440:11: 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]
estquick3.c:2590:11: 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]
estquick3.c:2784:11: 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]
estquick3.c:64:47: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
estquick3.c:3161:47: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
estquick3.c:601:20: style: Variable 'target_pos' is assigned a value that is never used. [unreadVariable]
estquick3.c:698:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
estquick3.c:829:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
estquick3.c:920:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
estquick3.c:860:19: style: Unused variable: de [unusedVariable]
estquick3.c:1765:9: style: Unused variable: temp [unusedVariable]
estslim3.c:371:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
estslim3.c:645:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
estslim3.c:722:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estslim3.c:942:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
estslim3.c:1075:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estslim3.c:1094:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estslim3.c:1287:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estslim3.c:1327:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estslim3.c:1411:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
estslim3.c:1442:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estslim3.c:1482:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estslim3.c:2057:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estslim3.c:2174:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estslim3.c:2223:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estslim3.c:2338:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estslim3.c:2652:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estslim3.c:2820:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estslim3.c:2931:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estslim3.c:3023:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estslim3.c:3272:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estslim3.c:4052:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estslim3.c:4241:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estslim3.c:1282:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
estslim3.c:2048:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
estslim3.c:2042:15: note: 'hiddenj' is assigned value 'startj' here.
estslim3.c:2048:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
estslim3.c:1348:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
estslim3.c:1340:15: note: stopstate is assigned
estslim3.c:1348:15: note: stopstate is overwritten
estslim3.c:132:11: style: Variable 'SIG_1_3' can be declared as pointer to const [constVariablePointer]
estslim3.c:133:11: style: Variable 'SIG_1_2' can be declared as pointer to const [constVariablePointer]
estslim3.c:134:11: style: Variable 'SIG_1_4' can be declared as pointer to const [constVariablePointer]
estslim3.c:135:11: style: Variable 'SIG_0_3' can be declared as pointer to const [constVariablePointer]
estslim3.c:136:11: style: Variable 'SIG_0_2' can be declared as pointer to const [constVariablePointer]
estslim3.c:137:11: style: Variable 'SIG_0_4' can be declared as pointer to const [constVariablePointer]
estslim3.c:138:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
estslim3.c:171:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
estslim3.c:3009:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
estslim3.c:3694:44: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
estslim3.c:4285:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
estslim3.c:2644:11: 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]
estslim3.c:2808:11: 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]
estslim3.c:3012:11: 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]
estslim3.c:64:46: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
estslim3.c:3513:46: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
estslim3.c:639:20: style: Variable 'target_pos' is assigned a value that is never used. [unreadVariable]
estslim3.c:736:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
estslim3.c:905:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
estslim3.c:996:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
estslim3.c:936:19: style: Unused variable: de [unusedVariable]
estslim3.c:1893:9: style: Unused variable: temp [unusedVariable]
estslimloop.c:460:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
estslimloop.c:734:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
estslimloop.c:811:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estslimloop.c:1120:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
estslimloop.c:1253:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estslimloop.c:1272:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estslimloop.c:1507:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estslimloop.c:1547:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estslimloop.c:1650:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
estslimloop.c:1681:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estslimloop.c:1721:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estslimloop.c:2360:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estslimloop.c:2477:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estslimloop.c:2526:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estslimloop.c:2641:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estslimloop.c:2955:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estslimloop.c:3123:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estslimloop.c:3234:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estslimloop.c:3326:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estslimloop.c:3714:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estslimloop.c:4664:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estslimloop.c:4941:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estslimloop.c:1502:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
estslimloop.c:2351:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
estslimloop.c:2345:15: note: 'hiddenj' is assigned value 'startj' here.
estslimloop.c:2351:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
estslimloop.c:133:11: style: Variable 'SIG_1_3' can be declared as pointer to const [constVariablePointer]
estslimloop.c:134:11: style: Variable 'SIG_1_2' can be declared as pointer to const [constVariablePointer]
estslimloop.c:135:11: style: Variable 'SIG_1_4' can be declared as pointer to const [constVariablePointer]
estslimloop.c:136:11: style: Variable 'SIG_0_3' can be declared as pointer to const [constVariablePointer]
estslimloop.c:137:11: style: Variable 'SIG_0_2' can be declared as pointer to const [constVariablePointer]
estslimloop.c:138:11: style: Variable 'SIG_0_4' can be declared as pointer to const [constVariablePointer]
estslimloop.c:139:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
estslimloop.c:172:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
estslimloop.c:3312:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
estslimloop.c:4205:52: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
estslimloop.c:4986:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
estslimloop.c:2947:11: 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]
estslimloop.c:3111:11: 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]
estslimloop.c:3315:11: 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]
estslimloop.c:65:50: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
estslimloop.c:4024:50: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
estslimloop.c:728:20: style: Variable 'target_pos' is assigned a value that is never used. [unreadVariable]
estslimloop.c:825:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
estslimloop.c:1083:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
estslimloop.c:1174:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
estslimloop.c:1114:19: style: Unused variable: de [unusedVariable]
estslimloop.c:1535:19: style: Unused variable: pau [unusedVariable]
wise-2.4.1/src/models/estwise.c:185:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Score2Bits [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/estwise.c:494:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/estwise.c:695:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
estwise3.c:479:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
estwise3.c:753:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
estwise3.c:830:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estwise3.c:1150:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
estwise3.c:1283:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estwise3.c:1302:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estwise3.c:1575:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estwise3.c:1615:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estwise3.c:1699:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
estwise3.c:1730:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estwise3.c:1770:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estwise3.c:2585:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estwise3.c:2802:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estwise3.c:2851:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
estwise3.c:2966:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estwise3.c:3680:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estwise3.c:3988:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estwise3.c:4199:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estwise3.c:4291:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estwise3.c:4680:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
estwise3.c:5840:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estwise3.c:6129:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
estwise3.c:1570:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
estwise3.c:2576:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
estwise3.c:2570:15: note: 'hiddenj' is assigned value 'startj' here.
estwise3.c:2576:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
estwise3.c:1636:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
estwise3.c:1628:15: note: stopstate is assigned
estwise3.c:1636:15: note: stopstate is overwritten
estwise3.c:132:11: style: Variable 'SIG_1_3' can be declared as pointer to const [constVariablePointer]
estwise3.c:133:11: style: Variable 'SIG_1_2' can be declared as pointer to const [constVariablePointer]
estwise3.c:134:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
estwise3.c:135:11: style: Variable 'SIG_1_4' can be declared as pointer to const [constVariablePointer]
estwise3.c:136:11: style: Variable 'SIG_1_5' can be declared as pointer to const [constVariablePointer]
estwise3.c:137:11: style: Variable 'SIG_0_3' can be declared as pointer to const [constVariablePointer]
estwise3.c:138:11: style: Variable 'SIG_0_2' can be declared as pointer to const [constVariablePointer]
estwise3.c:139:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
estwise3.c:140:11: style: Variable 'SIG_0_4' can be declared as pointer to const [constVariablePointer]
estwise3.c:141:11: style: Variable 'SIG_0_5' can be declared as pointer to const [constVariablePointer]
estwise3.c:142:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
estwise3.c:175:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
estwise3.c:4277:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
estwise3.c:5262:44: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
estwise3.c:6173:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
estwise3.c:3672:11: 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]
estwise3.c:3976:11: 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]
estwise3.c:4280:11: 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]
estwise3.c:64:46: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
estwise3.c:5081:46: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
estwise3.c:747:20: style: Variable 'target_pos' is assigned a value that is never used. [unreadVariable]
estwise3.c:844:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
estwise3.c:1113:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
estwise3.c:1204:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
estwise3.c:1144:19: style: Unused variable: de [unusedVariable]
estwise3.c:2401:9: style: Unused variable: temp [unusedVariable]
wise-2.4.1/src/models/estwisedb.c:227:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/estwisedb.c:727:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/estwisedb.c:1003:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/estwisedb.c:174:14: style: Local variable 'alb' shadows outer variable [shadowVariable]
wise-2.4.1/src/models/estwisedb.c:163:12: note: Shadowed declaration
wise-2.4.1/src/models/estwisedb.c:174:14: note: Shadow variable
wise-2.4.1/src/models/estwisedb.c:175:13: style: Local variable 'pal' shadows outer variable [shadowVariable]
wise-2.4.1/src/models/estwisedb.c:164:12: note: Shadowed declaration
wise-2.4.1/src/models/estwisedb.c:175:13: note: Shadow variable
wise-2.4.1/src/models/estwisedb.c:176:21: style: Local variable 'mss' shadows outer variable [shadowVariable]
wise-2.4.1/src/models/estwisedb.c:166:19: note: Shadowed declaration
wise-2.4.1/src/models/estwisedb.c:176:21: note: Shadow variable
wise-2.4.1/src/models/estwisedb.c:178:10: style: Local variable 'cdna' shadows outer variable [shadowVariable]
wise-2.4.1/src/models/estwisedb.c:46:8: note: Shadowed declaration
wise-2.4.1/src/models/estwisedb.c:178:10: note: Shadow variable
wise-2.4.1/src/models/estwisedb.c:360:9: style: Variable 'alb' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/estwisedb.c:362:9: style: Variable 'mss' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/estwisedb.c:363:10: style: Variable 'cdna' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/estwisedb.c:364:13: style: Variable 'temptsm' is assigned a value that is never used. [unreadVariable]
estwrap.dy:306:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
estwrap.dy:408:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
estwrap.dy:390:12: style: Variable 'ale' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/models/evopairwise.c:201:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NMaskType_BANNED [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/evopairwise.c:309:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/evopairwise.c:115:34: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/evopairwise.c:123:19: style: Variable 'negative_dm' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/models/evopairwise.c:134:16: style: Variable 'pseudo' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/evopairwise.c:135:13: style: Variable 'neg' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/evopairwise.c:145:20: style: Variable 'nonsyn_sites' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/evopairwise.c:182:18: style: Variable 'nonsyn_sites' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/evopairwise.c:187:20: style: Variable 'nonsyn_sites' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/evopairwise.c:202:15: style: Variable 'negative_dm' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/evopairwise.c:273:7: style: Unused variable: i [unusedVariable]
wise-2.4.1/src/models/fivestar.c:85:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/fivestar.c:44:10: style: Unused variable: hmmer_file [unusedVariable]
wise-2.4.1/src/models/fivestar.c:45:10: style: Unused variable: sequence_file [unusedVariable]
wise-2.4.1/src/models/fivestar.c:67:7: style: Unused variable: i [unusedVariable]
wise-2.4.1/src/models/fivestarscan.c:76:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/fivestarscan.c:64:14: style: Variable 'alb' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/models/fivestarscan.c:106:61: error: Uninitialized variable: dpri [uninitvar]
wise-2.4.1/src/models/fivestarscan.c:107:9: style: Variable 'alb' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/fivestarscan.c:50:10: style: Unused variable: bits [unusedVariable]
wise-2.4.1/src/models/fivestarscan.c:51:7: style: Unused variable: i [unusedVariable]
wise-2.4.1/src/models/fivestarscan.c:60:13: style: Unused variable: ha [unusedVariable]
wise-2.4.1/src/models/fivestarsearch.c:62:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
fivestate.c:435:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
fivestate.c:551:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
fivestate.c:605:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
fivestate.c:895:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
fivestate.c:1025:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
fivestate.c:1044:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
fivestate.c:1286:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
fivestate.c:1326:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
fivestate.c:1410:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
fivestate.c:1441:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
fivestate.c:1481:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
fivestate.c:2154:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
fivestate.c:2317:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
fivestate.c:2370:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
fivestate.c:2485:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
fivestate.c:2925:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
fivestate.c:3159:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
fivestate.c:3316:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
fivestate.c:3412:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
fivestate.c:3775:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
fivestate.c:4745:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
fivestate.c:5005:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
fivestate.c:1281:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
fivestate.c:2145:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
fivestate.c:2139:15: note: 'hiddenj' is assigned value 'startj' here.
fivestate.c:2145:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
fivestate.c:1347:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
fivestate.c:1339:15: note: stopstate is assigned
fivestate.c:1347:15: note: stopstate is overwritten
fivestate.c:134:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
fivestate.c:135:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
fivestate.c:136:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
fivestate.c:169:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
fivestate.c:515:44: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
fivestate.c:3398:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
fivestate.c:4274:60: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
fivestate.c:5051:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
fivestate.c:3412:11: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3413:11: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3414:11: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3415:11: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3416:11: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3427:17: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3429:21: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3431:16: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3435:23: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3438:16: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3442:23: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3459:16: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3463:23: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3466:16: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3470:23: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3477:10: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3479:11: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3489:72: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3490:70: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3504:17: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3506:21: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3508:16: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3512:23: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3515:16: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3519:23: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3536:16: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3540:23: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3547:10: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3549:11: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3559:72: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3560:70: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3574:17: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3576:21: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3578:16: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3582:23: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3585:16: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3589:23: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3606:16: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3610:23: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3617:10: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3619:11: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3629:72: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3630:70: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3644:17: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3646:21: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3648:16: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3652:23: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3655:16: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3659:23: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3662:16: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3666:23: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3673:10: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3675:11: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3685:72: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3686:70: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3700:17: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3702:21: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3704:16: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3708:23: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3729:10: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3731:11: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3741:72: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:3742:70: style: Modulo of one is always equal to zero [moduloofone]
fivestate.c:2917:11: 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]
fivestate.c:3147:11: 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]
fivestate.c:3401:11: 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]
fivestate.c:66:54: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
fivestate.c:4093:54: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
fivestate.c:619:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
fivestate.c:859:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
fivestate.c:949:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
fivestate.c:889:19: style: Unused variable: de [unusedVariable]
fivestate.c:1965:9: style: Unused variable: temp [unusedVariable]
fivestatemodel.dy:126:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
fivestatemodel.dy:149:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
fivestatemodel.dy:457:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQUENCE_PROTEIN [valueFlowBailoutIncompleteVar]
fivestatemodel.dy:523:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
fivestatemodel.dy:167:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
fivestatemodel.dy:147:51: style: Parameter 'context' can be declared as pointer to const [constParameterPointer]
fivestatemodel.dy:153:10: style: Variable 'file' can be declared as pointer to const [constVariablePointer]
fivestatemodel.dy:236:5: style: Variable 'f' is assigned a value that is never used. [unreadVariable]
fivestatemodel.dy:201:7: style: Unused variable: max [unusedVariable]
fivestatemodel.dy:205:21: style: Unused variable: tsm [unusedVariable]
genedisplay.dy:159:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
genedisplay.dy:461:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BC_RIGHT [valueFlowBailoutIncompleteVar]
genedisplay.dy:478:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BC_RIGHT [valueFlowBailoutIncompleteVar]
genedisplay.dy:504:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BC_RIGHT [valueFlowBailoutIncompleteVar]
genedisplay.dy:510:5: warning: sprintf format string requires 0 parameters but 1 is given. [wrongPrintfScanfArgNum]
genedisplay.dy:159:17: warning: Either the condition 'alc==NULL' is redundant or there is possible null pointer dereference: alc. [nullPointerRedundantCheck]
genedisplay.dy:166:13: note: Assuming that condition 'alc==NULL' is not redundant
genedisplay.dy:159:17: note: Null pointer dereference
genedisplay.dy:269:15: warning: Either the condition 'alc_temp==NULL' is redundant or there is possible null pointer dereference: alc_temp. [nullPointerRedundantCheck]
genedisplay.dy:278:17: note: Assuming that condition 'alc_temp==NULL' is not redundant
genedisplay.dy:269:15: note: Null pointer dereference
genedisplay.dy:471:101: style: Parameter 'dna' can be declared as pointer to const [constParameterPointer]
genedisplay.dy:471:130: style: Parameter 'alc' can be declared as pointer to const [constParameterPointer]
genedisplay.dy:498:123: style: Parameter 'dna' can be declared as pointer to const [constParameterPointer]
genedisplay.dy:527:75: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
genedisplay.dy:560:75: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
genefrequency.dy:137:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASE_A [valueFlowBailoutIncompleteVar]
genefrequency.dy:240:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASE_N [valueFlowBailoutIncompleteVar]
genefrequency.dy:512:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
genefrequency.dy:694:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
genefrequency.dy:724:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
genefrequency.dy:772:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
genefrequency.dy:901:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
genefrequency.dy:967:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
genefrequency.dy:1028:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
genefrequency.dy:1079:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
genefrequency.dy:694:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
genefrequency.dy:777:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
genefrequency.dy:778:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
genefrequency.dy:794:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
genefrequency.dy:795:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
genefrequency.dy:811:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
genefrequency.dy:812:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
genefrequency.dy:914:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
genefrequency.dy:915:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
genefrequency.dy:980:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
genefrequency.dy:981:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
genefrequency.dy:1038:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
genefrequency.dy:1039:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
genefrequency.dy:1079:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
genefrequency.dy:1080:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
genefrequency.dy:778:10: style: Variable 'runner' is reassigned a value before the old one has been used. [redundantAssignment]
genefrequency.dy:777:10: note: runner is assigned
genefrequency.dy:778:10: note: runner is overwritten
genefrequency.dy:795:14: style: Variable 'runner' is reassigned a value before the old one has been used. [redundantAssignment]
genefrequency.dy:794:14: note: runner is assigned
genefrequency.dy:795:14: note: runner is overwritten
genefrequency.dy:812:14: style: Variable 'runner' is reassigned a value before the old one has been used. [redundantAssignment]
genefrequency.dy:811:14: note: runner is assigned
genefrequency.dy:812:14: note: runner is overwritten
genefrequency.dy:1039:10: style: Variable 'runner' is reassigned a value before the old one has been used. [redundantAssignment]
genefrequency.dy:1038:10: note: runner is assigned
genefrequency.dy:1039:10: note: runner is overwritten
genefrequency.dy:360:35: style: Parameter 'codon' can be declared as pointer to const [constParameterPointer]
genefrequency.dy:407:34: style: Parameter 'base' can be declared as pointer to const [constParameterPointer]
genefrequency.dy:453:43: style: Parameter 'gsc' can be declared as pointer to const [constParameterPointer]
genefrequency.dy:898:10: style: Variable 'number' can be declared as pointer to const [constVariablePointer]
genefrequency.dy:964:10: style: Variable 'number' can be declared as pointer to const [constVariablePointer]
genefrequency.dy:1029:10: style: Variable 'runner' can be declared as pointer to const [constVariablePointer]
genefrequency.c:1554:62: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
genefrequency.c:1598:62: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
genefrequency.c:1642:49: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
genefrequency.c:1689:46: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
genefrequency.c:1733:54: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
genefrequency.c:1777:54: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
geneloop21.c:1054:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
geneloop21.c:1332:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
geneloop21.c:1411:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
geneloop21.c:2286:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
geneloop21.c:2425:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
geneloop21.c:2444:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
geneloop21.c:3065:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
geneloop21.c:3105:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
geneloop21.c:3208:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
geneloop21.c:3239:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
geneloop21.c:3279:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
geneloop21.c:4915:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
geneloop21.c:5492:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
geneloop21.c:5577:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
geneloop21.c:5692:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
geneloop21.c:7336:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
geneloop21.c:8164:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
geneloop21.c:8735:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
geneloop21.c:8863:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
geneloop21.c:10014:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
geneloop21.c:12441:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
geneloop21.c:13278:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
geneloop21.c:2878:39: style: The if condition is the same as the previous if condition [duplicateCondition]
geneloop21.c:2874:39: note: First condition
geneloop21.c:2878:39: note: Second condition
geneloop21.c:3060:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
geneloop21.c:4906:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
geneloop21.c:4900:15: note: 'hiddenj' is assigned value 'startj' here.
geneloop21.c:4906:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
geneloop21.c:155:11: style: Variable 'SIG_1_3' can be declared as pointer to const [constVariablePointer]
geneloop21.c:156:11: style: Variable 'SIG_1_6' can be declared as pointer to const [constVariablePointer]
geneloop21.c:157:11: style: Variable 'SIG_1_5' can be declared as pointer to const [constVariablePointer]
geneloop21.c:158:11: style: Variable 'SIG_1_4' can be declared as pointer to const [constVariablePointer]
geneloop21.c:159:11: style: Variable 'SIG_1_2' can be declared as pointer to const [constVariablePointer]
geneloop21.c:160:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
geneloop21.c:161:11: style: Variable 'SIG_0_3' can be declared as pointer to const [constVariablePointer]
geneloop21.c:162:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
geneloop21.c:163:11: style: Variable 'SIG_0_8' can be declared as pointer to const [constVariablePointer]
geneloop21.c:164:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
geneloop21.c:165:11: style: Variable 'SIG_0_9' can be declared as pointer to const [constVariablePointer]
geneloop21.c:166:11: style: Variable 'SIG_0_10' can be declared as pointer to const [constVariablePointer]
geneloop21.c:199:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
geneloop21.c:8849:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
geneloop21.c:11120:48: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
geneloop21.c:13345:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
geneloop21.c:7328:11: 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]
geneloop21.c:8152:11: 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]
geneloop21.c:8852:11: 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]
geneloop21.c:87:48: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
geneloop21.c:10939:48: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
geneloop21.c:1326:20: style: Variable 'target_pos' is assigned a value that is never used. [unreadVariable]
geneloop21.c:1425:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
geneloop21.c:2247:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
geneloop21.c:2340:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
geneloop21.c:2280:19: style: Unused variable: de [unusedVariable]
geneloop21.c:3093:19: style: Unused variable: pau [unusedVariable]
geneloop6.c:548:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
geneloop6.c:822:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
geneloop6.c:899:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
geneloop6.c:1274:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
geneloop6.c:1407:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
geneloop6.c:1426:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
geneloop6.c:1714:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
geneloop6.c:1754:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
geneloop6.c:1857:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
geneloop6.c:1888:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
geneloop6.c:1928:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
geneloop6.c:2750:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
geneloop6.c:2975:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
geneloop6.c:3030:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
geneloop6.c:3145:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
geneloop6.c:3807:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
geneloop6.c:4129:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
geneloop6.c:4348:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
geneloop6.c:4446:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
geneloop6.c:4899:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
geneloop6.c:6065:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
geneloop6.c:6408:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
geneloop6.c:1709:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
geneloop6.c:2741:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
geneloop6.c:2735:15: note: 'hiddenj' is assigned value 'startj' here.
geneloop6.c:2741:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
geneloop6.c:137:11: style: Variable 'SIG_1_3' can be declared as pointer to const [constVariablePointer]
geneloop6.c:138:11: style: Variable 'SIG_1_6' can be declared as pointer to const [constVariablePointer]
geneloop6.c:139:11: style: Variable 'SIG_1_5' can be declared as pointer to const [constVariablePointer]
geneloop6.c:140:11: style: Variable 'SIG_1_4' can be declared as pointer to const [constVariablePointer]
geneloop6.c:141:11: style: Variable 'SIG_1_2' can be declared as pointer to const [constVariablePointer]
geneloop6.c:142:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
geneloop6.c:143:11: style: Variable 'SIG_0_3' can be declared as pointer to const [constVariablePointer]
geneloop6.c:144:11: style: Variable 'SIG_0_6' can be declared as pointer to const [constVariablePointer]
geneloop6.c:145:11: style: Variable 'SIG_0_5' can be declared as pointer to const [constVariablePointer]
geneloop6.c:146:11: style: Variable 'SIG_0_4' can be declared as pointer to const [constVariablePointer]
geneloop6.c:147:11: style: Variable 'SIG_0_2' can be declared as pointer to const [constVariablePointer]
geneloop6.c:148:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
geneloop6.c:149:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
geneloop6.c:150:11: style: Variable 'SIG_0_8' can be declared as pointer to const [constVariablePointer]
geneloop6.c:151:11: style: Variable 'SIG_0_9' can be declared as pointer to const [constVariablePointer]
geneloop6.c:152:11: style: Variable 'SIG_0_10' can be declared as pointer to const [constVariablePointer]
geneloop6.c:185:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
geneloop6.c:4432:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
geneloop6.c:5482:46: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
geneloop6.c:6456:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
geneloop6.c:3799:11: 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]
geneloop6.c:4117:11: 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]
geneloop6.c:4435:11: 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]
geneloop6.c:69:47: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
geneloop6.c:5301:47: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
geneloop6.c:816:20: style: Variable 'target_pos' is assigned a value that is never used. [unreadVariable]
geneloop6.c:913:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
geneloop6.c:1237:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
geneloop6.c:1328:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
geneloop6.c:1268:19: style: Unused variable: de [unusedVariable]
geneloop6.c:1742:19: style: Unused variable: pau [unusedVariable]
geneoutput.dy:49:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
geneoutput.dy:35:61: style: Parameter 'para' can be declared as pointer to const [constParameterPointer]
geneparameter.dy:232:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQUENCE_GENOMIC [valueFlowBailoutIncompleteVar]
geneparameter.dy:147:25: style: Unused variable: rmds [unusedVariable]
geneparameter.dy:148:25: style: Unused variable: cse [unusedVariable]
geneparser21.dy:181:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASE_A [valueFlowBailoutIncompleteVar]
geneparser21.dy:211:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASE_T [valueFlowBailoutIncompleteVar]
genephase6.c:788:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
genephase6.c:908:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
genephase6.c:964:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genephase6.c:1498:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
genephase6.c:1634:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genephase6.c:1653:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genephase6.c:2024:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genephase6.c:2064:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genephase6.c:2167:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
genephase6.c:2198:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genephase6.c:2238:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genephase6.c:3234:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genephase6.c:3459:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genephase6.c:3514:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genephase6.c:3629:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genephase6.c:4291:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genephase6.c:4613:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genephase6.c:4832:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genephase6.c:4930:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genephase6.c:5604:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genephase6.c:7089:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genephase6.c:7585:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genephase6.c:2019:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
genephase6.c:3225:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
genephase6.c:3219:15: note: 'hiddenj' is assigned value 'startj' here.
genephase6.c:3225:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
genephase6.c:223:11: style: Variable 'SIG_1_3' can be declared as pointer to const [constVariablePointer]
genephase6.c:224:11: style: Variable 'SIG_1_6' can be declared as pointer to const [constVariablePointer]
genephase6.c:225:11: style: Variable 'SIG_1_5' can be declared as pointer to const [constVariablePointer]
genephase6.c:226:11: style: Variable 'SIG_1_4' can be declared as pointer to const [constVariablePointer]
genephase6.c:227:11: style: Variable 'SIG_1_2' can be declared as pointer to const [constVariablePointer]
genephase6.c:228:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
genephase6.c:229:11: style: Variable 'SIG_0_3' can be declared as pointer to const [constVariablePointer]
genephase6.c:230:11: style: Variable 'SIG_0_6' can be declared as pointer to const [constVariablePointer]
genephase6.c:231:11: style: Variable 'SIG_0_5' can be declared as pointer to const [constVariablePointer]
genephase6.c:232:11: style: Variable 'SIG_0_4' can be declared as pointer to const [constVariablePointer]
genephase6.c:233:11: style: Variable 'SIG_0_2' can be declared as pointer to const [constVariablePointer]
genephase6.c:234:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
genephase6.c:235:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
genephase6.c:236:11: style: Variable 'SIG_0_8' can be declared as pointer to const [constVariablePointer]
genephase6.c:237:11: style: Variable 'SIG_0_9' can be declared as pointer to const [constVariablePointer]
genephase6.c:238:11: style: Variable 'SIG_0_10' can be declared as pointer to const [constVariablePointer]
genephase6.c:271:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
genephase6.c:870:38: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
genephase6.c:4916:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
genephase6.c:6320:48: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
genephase6.c:7638:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
genephase6.c:4283:11: 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]
genephase6.c:4601:11: 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]
genephase6.c:4919:11: 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]
genephase6.c:155:48: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
genephase6.c:6139:48: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
genephase6.c:978:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
genephase6.c:1460:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
genephase6.c:1552:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
genephase6.c:1492:19: style: Unused variable: de [unusedVariable]
genephase6.c:2052:19: style: Unused variable: pau [unusedVariable]
genestats.dy:559:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQUENCE_GENOMIC [valueFlowBailoutIncompleteVar]
genestats.dy:587:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genestats.dy:614:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genestats.dy:637:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genestats.dy:664:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genestats.dy:703:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genestats.dy:743:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genestats.dy:783:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
genestats.dy:919:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
genestats.dy:1005:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
genestats.dy:1018:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
genestats.dy:1019:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
genestats.dy:610:52: style: Parameter 'seq' can be declared as pointer to const. However it seems that 'Wise2_scored_ag_eval_func' is a callback function, if 'seq' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
genestats.dy:591:20: note: You might need to cast the function pointer here
genestats.dy:610:52: note: Parameter 'seq' can be declared as pointer to const
genestats.dy:660:52: style: Parameter 'seq' can be declared as pointer to const. However it seems that 'Wise2_scored_gt_eval_func' is a callback function, if 'seq' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
genestats.dy:641:20: note: You might need to cast the function pointer here
genestats.dy:660:52: note: Parameter 'seq' can be declared as pointer to const
genestats.dy:728:73: style: Parameter 'seq' can be declared as pointer to const. However it seems that 'Wise2_pwmDNA_splice_ComplexSequence_eval_func' is a callback function, if 'seq' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
genestats.dy:707:23: note: You might need to cast the function pointer here
genestats.dy:728:73: note: Parameter 'seq' can be declared as pointer to const
genestats.dy:1002:10: style: Variable 'number' can be declared as pointer to const [constVariablePointer]
genestats.dy:915:10: style: Unused variable: d [unusedVariable]
genestretch6.c:582:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
genestretch6.c:858:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
genestretch6.c:936:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genestretch6.c:1345:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
genestretch6.c:1481:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genestretch6.c:1500:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genestretch6.c:1811:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genestretch6.c:1851:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genestretch6.c:1954:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
genestretch6.c:1985:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genestretch6.c:2025:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genestretch6.c:2885:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genestretch6.c:3110:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genestretch6.c:3165:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genestretch6.c:3280:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genestretch6.c:3942:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genestretch6.c:4264:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genestretch6.c:4483:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genestretch6.c:4581:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genestretch6.c:5101:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genestretch6.c:6351:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genestretch6.c:6726:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genestretch6.c:1806:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
genestretch6.c:2876:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
genestretch6.c:2870:15: note: 'hiddenj' is assigned value 'startj' here.
genestretch6.c:2876:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
genestretch6.c:138:11: style: Variable 'SIG_1_3' can be declared as pointer to const [constVariablePointer]
genestretch6.c:139:11: style: Variable 'SIG_1_6' can be declared as pointer to const [constVariablePointer]
genestretch6.c:140:11: style: Variable 'SIG_1_5' can be declared as pointer to const [constVariablePointer]
genestretch6.c:141:11: style: Variable 'SIG_1_4' can be declared as pointer to const [constVariablePointer]
genestretch6.c:142:11: style: Variable 'SIG_1_2' can be declared as pointer to const [constVariablePointer]
genestretch6.c:143:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
genestretch6.c:144:11: style: Variable 'SIG_0_3' can be declared as pointer to const [constVariablePointer]
genestretch6.c:145:11: style: Variable 'SIG_0_6' can be declared as pointer to const [constVariablePointer]
genestretch6.c:146:11: style: Variable 'SIG_0_5' can be declared as pointer to const [constVariablePointer]
genestretch6.c:147:11: style: Variable 'SIG_0_4' can be declared as pointer to const [constVariablePointer]
genestretch6.c:148:11: style: Variable 'SIG_0_2' can be declared as pointer to const [constVariablePointer]
genestretch6.c:149:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
genestretch6.c:150:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
genestretch6.c:151:11: style: Variable 'SIG_0_8' can be declared as pointer to const [constVariablePointer]
genestretch6.c:152:11: style: Variable 'SIG_0_9' can be declared as pointer to const [constVariablePointer]
genestretch6.c:153:11: style: Variable 'SIG_0_10' can be declared as pointer to const [constVariablePointer]
genestretch6.c:186:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
genestretch6.c:4567:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
genestretch6.c:5719:52: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
genestretch6.c:6775:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
genestretch6.c:3934:11: 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]
genestretch6.c:4252:11: 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]
genestretch6.c:4570:11: 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]
genestretch6.c:70:50: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
genestretch6.c:5538:50: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
genestretch6.c:852:20: style: Variable 'target_pos' is assigned a value that is never used. [unreadVariable]
genestretch6.c:950:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
genestretch6.c:1307:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
genestretch6.c:1399:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
genestretch6.c:1339:19: style: Unused variable: de [unusedVariable]
genestretch6.c:1839:19: style: Unused variable: pau [unusedVariable]
geneutil.dy:121:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
geneutil.dy:346:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
geneutil.dy:371:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
geneutil.dy:435:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
geneutil.dy:603:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
geneutil.dy:912:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
geneutil.dy:937:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
geneutil.dy:968:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
geneutil.dy:989:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
geneutil.dy:1028:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
geneutil.dy:825:70: style: Expression is always false because 'else if' condition matches previous condition at line 823. [multiCondition]
geneutil.dy:123:11: style: Condition 'trace' is always true [knownConditionTrueFalse]
geneutil.dy:109:15: note: Assignment 'trace=1', assigned value is 1
geneutil.dy:123:11: note: Condition 'trace' is always true
geneutil.dy:320:11: style: Condition 'trace' is always true [knownConditionTrueFalse]
geneutil.dy:109:15: note: Assignment 'trace=1', assigned value is 1
geneutil.dy:320:11: note: Condition 'trace' is always true
geneutil.dy:1025:13: style: Condition 'alc!=NULL' is always true [knownConditionTrueFalse]
geneutil.dy:860:16: warning: Either the condition 'alc!=NULL' is redundant or there is possible null pointer dereference: alc. [nullPointerRedundantCheck]
geneutil.dy:857:16: note: Assuming that condition 'alc!=NULL' is not redundant
geneutil.dy:860:16: note: Null pointer dereference
geneutil.dy:1035:13: warning: Either the condition 'alc==NULL' is redundant or there is possible null pointer dereference: alc. [nullPointerRedundantCheck]
geneutil.dy:1042:12: note: Assuming that condition 'alc==NULL' is not redundant
geneutil.dy:1035:13: note: Null pointer dereference
geneutil.dy:1037:44: warning: Either the condition 'alc==NULL' is redundant or there is possible null pointer dereference: alc. [nullPointerRedundantCheck]
geneutil.dy:1042:12: note: Assuming that condition 'alc==NULL' is not redundant
geneutil.dy:1037:44: note: Null pointer dereference
geneutil.dy:1143:13: warning: Either the condition 'alc==NULL' is redundant or there is possible null pointer dereference: alc. [nullPointerRedundantCheck]
geneutil.dy:1150:12: note: Assuming that condition 'alc==NULL' is not redundant
geneutil.dy:1143:13: note: Null pointer dereference
geneutil.dy:1145:44: warning: Either the condition 'alc==NULL' is redundant or there is possible null pointer dereference: alc. [nullPointerRedundantCheck]
geneutil.dy:1150:12: note: Assuming that condition 'alc==NULL' is not redundant
geneutil.dy:1145:44: note: Null pointer dereference
geneutil.dy:291:7: style: Redundant assignment of 'temp' to itself. [selfAssignment]
geneutil.dy:509:15: style: Redundant assignment of 'ex->end' to itself. [selfAssignment]
geneutil.dy:57:97: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
geneutil.dy:104:14: style: Variable 'coll' can be declared as pointer to const [constVariablePointer]
geneutil.dy:966:10: style: Variable 'la' can be declared as pointer to const [constVariablePointer]
geneutil.dy:987:49: style: Parameter 'alc' can be declared as pointer to const [constParameterPointer]
geneutil.dy:1006:42: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
geneutil.dy:111:19: style: Variable 'is_reversed' is assigned a value that is never used. [unreadVariable]
geneutil.dy:97:7: style: Variable 'count' is assigned a value that is never used. [unreadVariable]
geneutil.dy:107:15: style: Unused variable: intron_start [unusedVariable]
geneutil.dy:456:15: style: Variable 'exon_start' is assigned a value that is never used. [unreadVariable]
geneutil.dy:595:12: style: Variable 'dosf' is assigned a value that is never used. [unreadVariable]
geneutil.dy:596:13: style: Variable 'phase' is assigned a value that is never used. [unreadVariable]
geneutil.dy:818:13: style: Variable 'phase' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/genewise.c:283:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ispseudo [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/genewise.c:774:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/genewise.c:1069:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/genewise.c:446:10: style: Unused variable: ifp [unusedVariable]
genewise21.c:1218:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
genewise21.c:1496:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
genewise21.c:1575:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise21.c:2612:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
genewise21.c:2751:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genewise21.c:2770:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genewise21.c:3479:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genewise21.c:3519:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genewise21.c:3622:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
genewise21.c:3653:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genewise21.c:3693:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genewise21.c:5538:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise21.c:6115:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise21.c:6200:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genewise21.c:6315:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise21.c:7959:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise21.c:8787:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise21.c:9358:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise21.c:9486:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise21.c:10875:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise21.c:13659:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genewise21.c:14653:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genewise21.c:3217:39: style: The if condition is the same as the previous if condition [duplicateCondition]
genewise21.c:3213:39: note: First condition
genewise21.c:3217:39: note: Second condition
genewise21.c:3474:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
genewise21.c:5529:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
genewise21.c:5523:15: note: 'hiddenj' is assigned value 'startj' here.
genewise21.c:5529:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
genewise21.c:162:11: style: Variable 'SIG_1_3' can be declared as pointer to const [constVariablePointer]
genewise21.c:163:11: style: Variable 'SIG_1_6' can be declared as pointer to const [constVariablePointer]
genewise21.c:164:11: style: Variable 'SIG_1_5' can be declared as pointer to const [constVariablePointer]
genewise21.c:165:11: style: Variable 'SIG_1_4' can be declared as pointer to const [constVariablePointer]
genewise21.c:166:11: style: Variable 'SIG_1_2' can be declared as pointer to const [constVariablePointer]
genewise21.c:167:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
genewise21.c:168:11: style: Variable 'SIG_0_3' can be declared as pointer to const [constVariablePointer]
genewise21.c:169:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
genewise21.c:170:11: style: Variable 'SIG_0_8' can be declared as pointer to const [constVariablePointer]
genewise21.c:171:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
genewise21.c:172:11: style: Variable 'SIG_0_9' can be declared as pointer to const [constVariablePointer]
genewise21.c:173:11: style: Variable 'SIG_0_10' can be declared as pointer to const [constVariablePointer]
genewise21.c:206:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
genewise21.c:9472:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
genewise21.c:12131:48: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
genewise21.c:14725:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
genewise21.c:7951:11: 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]
genewise21.c:8775:11: 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]
genewise21.c:9475:11: 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]
genewise21.c:94:48: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
genewise21.c:11950:48: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
genewise21.c:1490:20: style: Variable 'target_pos' is assigned a value that is never used. [unreadVariable]
genewise21.c:1589:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
genewise21.c:2573:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
genewise21.c:2666:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
genewise21.c:2606:19: style: Unused variable: de [unusedVariable]
genewise21.c:3507:19: style: Unused variable: pau [unusedVariable]
genewise4.c:446:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
genewise4.c:720:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
genewise4.c:797:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise4.c:1074:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
genewise4.c:1207:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genewise4.c:1226:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genewise4.c:1464:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genewise4.c:1504:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genewise4.c:1588:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
genewise4.c:1619:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genewise4.c:1659:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genewise4.c:2394:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise4.c:2585:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise4.c:2636:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genewise4.c:2751:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise4.c:3329:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise4.c:3601:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise4.c:3786:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise4.c:3880:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise4.c:4201:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise4.c:5191:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genewise4.c:5437:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genewise4.c:1459:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
genewise4.c:2385:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
genewise4.c:2379:15: note: 'hiddenj' is assigned value 'startj' here.
genewise4.c:2385:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
genewise4.c:1525:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
genewise4.c:1517:15: note: stopstate is assigned
genewise4.c:1525:15: note: stopstate is overwritten
genewise4.c:134:11: style: Variable 'SIG_1_3' can be declared as pointer to const [constVariablePointer]
genewise4.c:135:11: style: Variable 'SIG_1_6' can be declared as pointer to const [constVariablePointer]
genewise4.c:136:11: style: Variable 'SIG_1_5' can be declared as pointer to const [constVariablePointer]
genewise4.c:137:11: style: Variable 'SIG_1_4' can be declared as pointer to const [constVariablePointer]
genewise4.c:138:11: style: Variable 'SIG_1_2' can be declared as pointer to const [constVariablePointer]
genewise4.c:139:11: style: Variable 'SIG_0_3' can be declared as pointer to const [constVariablePointer]
genewise4.c:140:11: style: Variable 'SIG_0_6' can be declared as pointer to const [constVariablePointer]
genewise4.c:141:11: style: Variable 'SIG_0_5' can be declared as pointer to const [constVariablePointer]
genewise4.c:142:11: style: Variable 'SIG_0_4' can be declared as pointer to const [constVariablePointer]
genewise4.c:143:11: style: Variable 'SIG_0_2' can be declared as pointer to const [constVariablePointer]
genewise4.c:144:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
genewise4.c:145:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
genewise4.c:146:11: style: Variable 'SIG_0_8' can be declared as pointer to const [constVariablePointer]
genewise4.c:147:11: style: Variable 'SIG_0_9' can be declared as pointer to const [constVariablePointer]
genewise4.c:148:11: style: Variable 'SIG_0_10' can be declared as pointer to const [constVariablePointer]
genewise4.c:181:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
genewise4.c:3866:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
genewise4.c:4714:46: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
genewise4.c:5482:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
genewise4.c:3321:11: 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]
genewise4.c:3589:11: 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]
genewise4.c:3869:11: 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]
genewise4.c:66:47: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
genewise4.c:4533:47: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
genewise4.c:714:20: style: Variable 'target_pos' is assigned a value that is never used. [unreadVariable]
genewise4.c:811:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
genewise4.c:1037:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
genewise4.c:1128:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
genewise4.c:1068:19: style: Unused variable: de [unusedVariable]
genewise4.c:2216:9: style: Unused variable: temp [unusedVariable]
genewise6.c:504:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
genewise6.c:778:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
genewise6.c:855:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise6.c:1186:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
genewise6.c:1319:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genewise6.c:1338:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genewise6.c:1614:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genewise6.c:1654:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genewise6.c:1738:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
genewise6.c:1769:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genewise6.c:1809:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genewise6.c:2606:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise6.c:2831:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise6.c:2886:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genewise6.c:3001:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise6.c:3663:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise6.c:3985:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise6.c:4204:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise6.c:4302:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise6.c:4709:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewise6.c:5831:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genewise6.c:6131:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genewise6.c:1609:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
genewise6.c:2597:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
genewise6.c:2591:15: note: 'hiddenj' is assigned value 'startj' here.
genewise6.c:2597:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
genewise6.c:1675:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
genewise6.c:1667:15: note: stopstate is assigned
genewise6.c:1675:15: note: stopstate is overwritten
genewise6.c:136:11: style: Variable 'SIG_1_3' can be declared as pointer to const [constVariablePointer]
genewise6.c:137:11: style: Variable 'SIG_1_6' can be declared as pointer to const [constVariablePointer]
genewise6.c:138:11: style: Variable 'SIG_1_5' can be declared as pointer to const [constVariablePointer]
genewise6.c:139:11: style: Variable 'SIG_1_4' can be declared as pointer to const [constVariablePointer]
genewise6.c:140:11: style: Variable 'SIG_1_2' can be declared as pointer to const [constVariablePointer]
genewise6.c:141:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
genewise6.c:142:11: style: Variable 'SIG_0_3' can be declared as pointer to const [constVariablePointer]
genewise6.c:143:11: style: Variable 'SIG_0_6' can be declared as pointer to const [constVariablePointer]
genewise6.c:144:11: style: Variable 'SIG_0_5' can be declared as pointer to const [constVariablePointer]
genewise6.c:145:11: style: Variable 'SIG_0_4' can be declared as pointer to const [constVariablePointer]
genewise6.c:146:11: style: Variable 'SIG_0_2' can be declared as pointer to const [constVariablePointer]
genewise6.c:147:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
genewise6.c:148:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
genewise6.c:149:11: style: Variable 'SIG_0_8' can be declared as pointer to const [constVariablePointer]
genewise6.c:150:11: style: Variable 'SIG_0_9' can be declared as pointer to const [constVariablePointer]
genewise6.c:151:11: style: Variable 'SIG_0_10' can be declared as pointer to const [constVariablePointer]
genewise6.c:184:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
genewise6.c:4288:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
genewise6.c:5274:46: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
genewise6.c:6178:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
genewise6.c:3655:11: 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]
genewise6.c:3973:11: 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]
genewise6.c:4291:11: 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]
genewise6.c:68:47: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
genewise6.c:5093:47: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
genewise6.c:772:20: style: Variable 'target_pos' is assigned a value that is never used. [unreadVariable]
genewise6.c:869:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
genewise6.c:1149:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
genewise6.c:1240:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
genewise6.c:1180:19: style: Unused variable: de [unusedVariable]
genewise6.c:2416:9: style: Unused variable: temp [unusedVariable]
wise-2.4.1/src/models/genewisedb.c:265:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/genewisedb.c:909:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/genewisedb.c:1233:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/genewisedb.c:213:14: style: Local variable 'alb' shadows outer variable [shadowVariable]
wise-2.4.1/src/models/genewisedb.c:192:12: note: Shadowed declaration
wise-2.4.1/src/models/genewisedb.c:213:14: note: Shadow variable
wise-2.4.1/src/models/genewisedb.c:214:13: style: Local variable 'pal' shadows outer variable [shadowVariable]
wise-2.4.1/src/models/genewisedb.c:193:12: note: Shadowed declaration
wise-2.4.1/src/models/genewisedb.c:214:13: note: Shadow variable
wise-2.4.1/src/models/genewisedb.c:215:19: style: Local variable 'gr' shadows outer variable [shadowVariable]
wise-2.4.1/src/models/genewisedb.c:195:17: note: Shadowed declaration
wise-2.4.1/src/models/genewisedb.c:215:19: note: Shadow variable
wise-2.4.1/src/models/genewisedb.c:217:21: style: Local variable 'mss' shadows outer variable [shadowVariable]
wise-2.4.1/src/models/genewisedb.c:198:19: note: Shadowed declaration
wise-2.4.1/src/models/genewisedb.c:217:21: note: Shadow variable
wise-2.4.1/src/models/genewisedb.c:455:10: style: Variable 'gent' is assigned a value that is never used. [unreadVariable]
genewisehsp.dy:151:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
genewisehsp.dy:363:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable target_start [valueFlowBailoutIncompleteVar]
genewisehsp.dy:112:7: warning: If memory allocation fails, then there is a possible null pointer dereference: temp_seq [nullPointerOutOfMemory]
genewisehsp.dy:110:22: note: Assuming allocation function fails
genewisehsp.dy:110:22: note: Assignment 'temp_seq=calloc(1+dna->len/3,sizeof(char))', assigned value is 0
genewisehsp.dy:112:7: note: Null pointer dereference
genewisehsp.dy:114:5: warning: If memory allocation fails, then there is a possible null pointer dereference: temp_seq [nullPointerOutOfMemory]
genewisehsp.dy:110:22: note: Assuming allocation function fails
genewisehsp.dy:110:22: note: Assignment 'temp_seq=calloc(1+dna->len/3,sizeof(char))', assigned value is 0
genewisehsp.dy:114:5: note: Null pointer dereference
genewisehsp.dy:118:26: warning: If memory allocation fails, then there is a possible null pointer dereference: temp_seq [nullPointerOutOfMemory]
genewisehsp.dy:110:22: note: Assuming allocation function fails
genewisehsp.dy:110:22: note: Assignment 'temp_seq=calloc(1+dna->len/3,sizeof(char))', assigned value is 0
genewisehsp.dy:118:26: note: Null pointer dereference
genewisehsp.dy:68:120: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
genewisehsp.dy:331:45: style: Parameter 'one' can be declared as pointer to const. However it seems that 'Wise2_compare_GeneWiseHSP_start' is a callback function, if 'one' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
genewisehsp.dy:196:33: note: You might need to cast the function pointer here
genewisehsp.dy:331:45: note: Parameter 'one' can be declared as pointer to const
genewisehsp.dy:331:63: style: Parameter 'two' can be declared as pointer to const. However it seems that 'Wise2_compare_GeneWiseHSP_start' is a callback function, if 'two' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
genewisehsp.dy:196:33: note: You might need to cast the function pointer here
genewisehsp.dy:331:63: note: Parameter 'two' can be declared as pointer to const
genewisehsp.dy:348:45: style: Parameter 'one' can be declared as pointer to const. However it seems that 'Wise2_compare_GeneWiseHSP_score' is a callback function, if 'one' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
genewisehsp.dy:147:31: note: You might need to cast the function pointer here
genewisehsp.dy:348:45: note: Parameter 'one' can be declared as pointer to const
genewisehsp.dy:348:63: style: Parameter 'two' can be declared as pointer to const. However it seems that 'Wise2_compare_GeneWiseHSP_score' is a callback function, if 'two' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
genewisehsp.dy:147:31: note: You might need to cast the function pointer here
genewisehsp.dy:348:63: note: Parameter 'two' can be declared as pointer to const
genewisehsp.dy:78:15: style: Variable 'can_use' is assigned a value that is never used. [unreadVariable]
genewisemodel.dy:210:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
genewisemodel.dy:567:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
genewisemodel.dy:675:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
genewisemodel.dy:830:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
genewisemodel.dy:964:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genewisemodel.dy:567:16: warning: Either the condition 'col==NULL' is redundant or there is possible null pointer dereference: col. [nullPointerRedundantCheck]
genewisemodel.dy:573:15: note: Assuming that condition 'col==NULL' is not redundant
genewisemodel.dy:567:16: note: Null pointer dereference
genewisemodel.dy:569:24: warning: Either the condition 'col==NULL' is redundant or there is possible null pointer dereference: col. [nullPointerRedundantCheck]
genewisemodel.dy:573:15: note: Assuming that condition 'col==NULL' is not redundant
genewisemodel.dy:569:24: note: Null pointer dereference
genewisemodel.dy:570:29: warning: Either the condition 'col==NULL' is redundant or there is possible null pointer dereference: col. [nullPointerRedundantCheck]
genewisemodel.dy:573:15: note: Assuming that condition 'col==NULL' is not redundant
genewisemodel.dy:570:29: note: Null pointer dereference
genewisemodel.dy:587:24: warning: Either the condition 'col==NULL' is redundant or there is possible null pointer dereference: col. [nullPointerRedundantCheck]
genewisemodel.dy:592:15: note: Assuming that condition 'col==NULL' is not redundant
genewisemodel.dy:587:24: note: Null pointer dereference
genewisemodel.dy:588:29: warning: Either the condition 'col==NULL' is redundant or there is possible null pointer dereference: col. [nullPointerRedundantCheck]
genewisemodel.dy:592:15: note: Assuming that condition 'col==NULL' is not redundant
genewisemodel.dy:588:29: note: Null pointer dereference
genewisemodel.dy:589:29: warning: Either the condition 'col==NULL' is redundant or there is possible null pointer dereference: col. [nullPointerRedundantCheck]
genewisemodel.dy:592:15: note: Assuming that condition 'col==NULL' is not redundant
genewisemodel.dy:589:29: note: Null pointer dereference
genewisemodel.dy:600:24: warning: Either the condition 'col==NULL' is redundant or there is possible null pointer dereference: col. [nullPointerRedundantCheck]
genewisemodel.dy:604:15: note: Assuming that condition 'col==NULL' is not redundant
genewisemodel.dy:600:24: note: Null pointer dereference
genewisemodel.dy:610:7: style: Statements following 'continue' will never be executed. [unreachableCode]
genewisemodel.dy:110:43: style: Parameter 'gws' can be declared as pointer to const [constParameterPointer]
genewisemodel.dy:201:53: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
genewisemodel.dy:114:10: error: Uninitialized variable: out [uninitvar]
genewisemodel.dy:112:10: style: Variable 'out' is not assigned a value. [unassignedVariable]
genewisemodeldb.dy:54:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
genewisemodeldb.dy:106:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_END [valueFlowBailoutIncompleteVar]
genewisemodeldb.dy:379:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
genewisemodeldb.dy:435:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_END [valueFlowBailoutIncompleteVar]
genome_evidence.dy:60:3: error: Found an exit path from function with non-void return type that has missing return statement [missingReturn]
wise-2.4.1/src/models/genomewise.c:117:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/genomewise.c:186:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/genomewise.c:95:10: style: Variable 'divide_string' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/models/genomewise.c:179:34: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/genomewise.c:81:28: style: Variable 'kbyte' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/genomewise.c:95:24: style: Variable 'divide_string' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/genomewise.c:81:7: style: Variable 'kbyte' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/genomewise.c:95:10: style: Variable 'divide_string' is assigned a value that is never used. [unreadVariable]
genomewise9.c:657:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
genomewise9.c:783:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
genomewise9.c:842:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genomewise9.c:1337:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
genomewise9.c:1482:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genomewise9.c:1501:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genomewise9.c:1867:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genomewise9.c:1907:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genomewise9.c:2010:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
genomewise9.c:2041:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genomewise9.c:2081:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genomewise9.c:2983:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genomewise9.c:3219:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genomewise9.c:3282:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
genomewise9.c:3397:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genomewise9.c:4005:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genomewise9.c:4348:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genomewise9.c:4578:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genomewise9.c:4684:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genomewise9.c:5343:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
genomewise9.c:6704:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genomewise9.c:7158:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
genomewise9.c:1862:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
genomewise9.c:2974:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
genomewise9.c:2968:15: note: 'hiddenj' is assigned value 'startj' here.
genomewise9.c:2974:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
genomewise9.c:145:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
genomewise9.c:146:11: style: Variable 'SIG_0_3' can be declared as pointer to const [constVariablePointer]
genomewise9.c:147:11: style: Variable 'SIG_0_6' can be declared as pointer to const [constVariablePointer]
genomewise9.c:148:11: style: Variable 'SIG_0_5' can be declared as pointer to const [constVariablePointer]
genomewise9.c:149:11: style: Variable 'SIG_0_4' can be declared as pointer to const [constVariablePointer]
genomewise9.c:150:11: style: Variable 'SIG_0_2' can be declared as pointer to const [constVariablePointer]
genomewise9.c:151:11: style: Variable 'SIG_0_8' can be declared as pointer to const [constVariablePointer]
genomewise9.c:152:11: style: Variable 'SIG_0_9' can be declared as pointer to const [constVariablePointer]
genomewise9.c:153:11: style: Variable 'SIG_0_10' can be declared as pointer to const [constVariablePointer]
genomewise9.c:186:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
genomewise9.c:742:39: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
genomewise9.c:4670:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
genomewise9.c:6010:50: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
genomewise9.c:7215:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
genomewise9.c:3997:11: 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]
genomewise9.c:4336:11: 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]
genomewise9.c:4673:11: 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]
genomewise9.c:77:49: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
genomewise9.c:5829:49: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
genomewise9.c:856:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
genomewise9.c:1296:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
genomewise9.c:1391:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
genomewise9.c:1331:19: style: Unused variable: de [unusedVariable]
genomewise9.c:1895:19: style: Unused variable: pau [unusedVariable]
gwlite.c:463:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
gwlite.c:737:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
gwlite.c:814:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
gwlite.c:1123:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
gwlite.c:1256:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
gwlite.c:1275:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
gwlite.c:1535:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
gwlite.c:1575:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
gwlite.c:1659:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
gwlite.c:1690:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
gwlite.c:1730:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
gwlite.c:2479:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
gwlite.c:2682:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
gwlite.c:2737:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
gwlite.c:2852:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
gwlite.c:3432:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
gwlite.c:3724:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
gwlite.c:3921:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
gwlite.c:4019:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
gwlite.c:4398:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
gwlite.c:5444:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
gwlite.c:5722:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
gwlite.c:1530:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
gwlite.c:2470:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
gwlite.c:2464:15: note: 'hiddenj' is assigned value 'startj' here.
gwlite.c:2470:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
gwlite.c:1596:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
gwlite.c:1588:15: note: stopstate is assigned
gwlite.c:1596:15: note: stopstate is overwritten
gwlite.c:135:11: style: Variable 'SIG_1_3' can be declared as pointer to const [constVariablePointer]
gwlite.c:136:11: style: Variable 'SIG_1_2' can be declared as pointer to const [constVariablePointer]
gwlite.c:137:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
gwlite.c:138:11: style: Variable 'SIG_0_3' can be declared as pointer to const [constVariablePointer]
gwlite.c:139:11: style: Variable 'SIG_0_2' can be declared as pointer to const [constVariablePointer]
gwlite.c:140:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
gwlite.c:141:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
gwlite.c:174:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
gwlite.c:4005:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
gwlite.c:4931:54: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
gwlite.c:5769:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
gwlite.c:3424:11: 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]
gwlite.c:3712:11: 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]
gwlite.c:4008:11: 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]
gwlite.c:67:51: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
gwlite.c:4750:51: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
gwlite.c:731:20: style: Variable 'target_pos' is assigned a value that is never used. [unreadVariable]
gwlite.c:828:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
gwlite.c:1086:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
gwlite.c:1177:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
gwlite.c:1117:19: style: Unused variable: de [unusedVariable]
gwlite.c:2293:9: style: Unused variable: temp [unusedVariable]
gwlitemodel.dy:87:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
gwlitemodel.dy:196:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
gwlitemodel.dy:82:41: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
gwquickdb.dy:44:3: error: Found an exit path from function with non-void return type that has missing return statement [missingReturn]
gwquickdb.dy:73:3: error: Found an exit path from function with non-void return type that has missing return statement [missingReturn]
gwrap.dy:559:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
gwrap.dy:269:10: warning: Either the condition 'gpara==NULL' is redundant or there is possible null pointer dereference: gpara. [nullPointerRedundantCheck]
gwrap.dy:279:43: note: Assuming that condition 'gpara==NULL' is not redundant
gwrap.dy:269:10: note: Null pointer dereference
gwrap.dy:562:3: warning: Either the condition 'gwdb==NULL' is redundant or there is possible null pointer dereference: gwdb. [nullPointerRedundantCheck]
gwrap.dy:563:12: note: Assuming that condition 'gwdb==NULL' is not redundant
gwrap.dy:562:3: note: Null pointer dereference
gwrap.dy:256:14: style: Variable 'dna' can be declared as pointer to const [constVariablePointer]
gwrap.dy:496:9: style: Variable 'pal' is assigned a value that is never used. [unreadVariable]
gwrap.dy:498:9: style: Variable 'cps' is assigned a value that is never used. [unreadVariable]
gwrap.dy:500:9: style: Variable 'ids' is assigned a value that is never used. [unreadVariable]
gwrap.dy:502:8: style: Variable 'cs' is assigned a value that is never used. [unreadVariable]
gwrap.dy:504:8: style: Variable 'gw' is assigned a value that is never used. [unreadVariable]
gwrap.dy:506:9: style: Variable 'gws' is assigned a value that is never used. [unreadVariable]
gwrap.dy:510:9: style: Variable 'rcs' is assigned a value that is never used. [unreadVariable]
gwrap.dy:512:10: style: Variable 'gp4s' is assigned a value that is never used. [unreadVariable]
gwrap.dy:514:10: style: Variable 'ggms' is assigned a value that is never used. [unreadVariable]
gwrap.dy:660:9: style: Variable 'ids' is assigned a value that is never used. [unreadVariable]
gwrap.dy:668:9: style: Variable 'rcs' is assigned a value that is never used. [unreadVariable]
gwrap.dy:670:10: style: Variable 'gp4s' is assigned a value that is never used. [unreadVariable]
gwrap.dy:557:25: style: Unused variable: tempcse [unusedVariable]
wise-2.4.1/src/models/hmminfo.c:8:1: portability: Omitted return type of function 'main' defaults to int, this is not supported by ISO C99 and later standards. [returnImplicitInt]
wise-2.4.1/src/models/hmminfo.c:17:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/hmminfo.c:21:16: style: The comparison 'show_all == 1' is always true. [knownConditionTrueFalse]
wise-2.4.1/src/models/hmminfo.c:12:18: note: 'show_all' is assigned value '1' here.
wise-2.4.1/src/models/hmminfo.c:21:16: note: The comparison 'show_all == 1' is always true.
hsp2aln_sw.dy:176:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
hsp2aln_sw.dy:203:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query [valueFlowBailoutIncompleteVar]
hsp2aln_sw.dy:261:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_start [valueFlowBailoutIncompleteVar]
hsp2aln_sw.dy:155:79: style: Parameter 'lm' can be declared as pointer to const [constParameterPointer]
hsp2aln_sw.dy:155:94: style: Parameter 'dpri' can be declared as pointer to const [constParameterPointer]
hsp2aln_sw.dy:155:131: style: Parameter 'para' can be declared as pointer to const [constParameterPointer]
hsp2aln_sw.dy:194:105: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
largeblockdp.c:355:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
largeblockdp.c:421:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
largeblockdp.c:458:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
largeblockdp.c:674:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
largeblockdp.c:825:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
largeblockdp.c:844:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
largeblockdp.c:1034:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
largeblockdp.c:1074:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
largeblockdp.c:1158:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
largeblockdp.c:1189:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
largeblockdp.c:1229:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
largeblockdp.c:1785:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
largeblockdp.c:1905:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
largeblockdp.c:1956:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
largeblockdp.c:2071:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
largeblockdp.c:2368:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
largeblockdp.c:2541:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
largeblockdp.c:2655:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
largeblockdp.c:2749:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
largeblockdp.c:2974:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
largeblockdp.c:3699:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
largeblockdp.c:3878:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
largeblockdp.c:1029:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
largeblockdp.c:1776:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
largeblockdp.c:1770:15: note: 'hiddenj' is assigned value 'startj' here.
largeblockdp.c:1776:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
largeblockdp.c:1095:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
largeblockdp.c:1087:15: note: stopstate is assigned
largeblockdp.c:1095:15: note: stopstate is overwritten
largeblockdp.c:134:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
largeblockdp.c:135:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
largeblockdp.c:136:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
largeblockdp.c:169:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
largeblockdp.c:2735:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
largeblockdp.c:3373:62: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
largeblockdp.c:3923:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
largeblockdp.c:2749:11: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2750:11: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2751:11: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2752:11: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2763:17: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2765:21: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2767:16: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2771:23: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2774:16: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2778:23: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2781:16: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2785:23: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2806:10: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2808:11: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2818:73: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2819:71: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2833:17: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2835:21: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2837:16: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2841:23: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2848:10: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2850:11: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2859:17: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2861:21: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2863:16: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2867:23: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2874:10: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2876:11: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2885:17: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2887:21: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2903:16: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2907:23: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2910:16: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2914:23: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2917:16: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2921:23: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2928:10: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2930:11: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2940:73: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2941:71: style: Modulo of one is always equal to zero [moduloofone]
largeblockdp.c:2360:11: 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]
largeblockdp.c:2529:11: 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]
largeblockdp.c:2738:11: 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]
largeblockdp.c:66:55: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
largeblockdp.c:3192:55: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
largeblockdp.c:400:9: style: Unused variable: db_status [unusedVariable]
largeblockdp.c:472:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
largeblockdp.c:631:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
largeblockdp.c:728:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
largeblockdp.c:668:19: style: Unused variable: de [unusedVariable]
largeblockdp.c:1631:9: style: Unused variable: temp [unusedVariable]
wise-2.4.1/src/models/lba.c:87:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
localcishit.dy:96:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
localcishit.dy:182:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
localcishit.dy:362:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
localcishit.dy:547:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
localcishit.dy:631:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
localcishit.dy:356:5: warning: If memory allocation fails, then there is a possible null pointer dereference: forward_used [nullPointerOutOfMemory]
localcishit.dy:354:24: note: Assuming allocation function fails
localcishit.dy:354:24: note: Assignment 'forward_used=calloc(forward->len,sizeof(int))', assigned value is 0
localcishit.dy:356:5: note: Null pointer dereference
localcishit.dy:362:9: warning: If memory allocation fails, then there is a possible null pointer dereference: forward_used [nullPointerOutOfMemory]
localcishit.dy:354:24: note: Assuming allocation function fails
localcishit.dy:354:24: note: Assignment 'forward_used=calloc(forward->len,sizeof(int))', assigned value is 0
localcishit.dy:362:9: note: Null pointer dereference
localcishit.dy:425:5: warning: If memory allocation fails, then there is a possible null pointer dereference: reverse_used [nullPointerOutOfMemory]
localcishit.dy:423:24: note: Assuming allocation function fails
localcishit.dy:423:24: note: Assignment 'reverse_used=calloc(reverse->len,sizeof(int))', assigned value is 0
localcishit.dy:425:5: note: Null pointer dereference
localcishit.dy:430:9: warning: If memory allocation fails, then there is a possible null pointer dereference: reverse_used [nullPointerOutOfMemory]
localcishit.dy:423:24: note: Assuming allocation function fails
localcishit.dy:423:24: note: Assignment 'reverse_used=calloc(reverse->len,sizeof(int))', assigned value is 0
localcishit.dy:430:9: note: Null pointer dereference
localcishit.dy:221:86: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
localcishit.dy:280:45: style: Parameter 'a' can be declared as pointer to const. However it seems that 'Wise2_compare_LocalCisHit_score' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
localcishit.dy:272:27: note: You might need to cast the function pointer here
localcishit.dy:280:45: note: Parameter 'a' can be declared as pointer to const
localcishit.dy:280:61: style: Parameter 'b' can be declared as pointer to const. However it seems that 'Wise2_compare_LocalCisHit_score' is a callback function, if 'b' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
localcishit.dy:272:27: note: You might need to cast the function pointer here
localcishit.dy:280:61: note: Parameter 'b' can be declared as pointer to const
localcishit.dy:285:45: style: Parameter 'a' can be declared as pointer to const. However it seems that 'Wise2_compare_LocalCisHit_start' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
localcishit.dy:277:27: note: You might need to cast the function pointer here
localcishit.dy:285:45: note: Parameter 'a' can be declared as pointer to const
localcishit.dy:285:61: style: Parameter 'b' can be declared as pointer to const. However it seems that 'Wise2_compare_LocalCisHit_start' is a callback function, if 'b' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
localcishit.dy:277:27: note: You might need to cast the function pointer here
localcishit.dy:285:61: note: Parameter 'b' can be declared as pointer to const
localcishit.dy:290:48: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
localcishit.dy:290:64: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
localcishit.dy:299:49: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
localcishit.dy:299:65: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
localcishit.dy:309:27: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
localcishit.dy:326:150: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
localcishit.dy:109:11: style: Variable 'qstart' is assigned a value that is never used. [unreadVariable]
localcishit.dy:110:11: style: Variable 'tstart' is assigned a value that is never used. [unreadVariable]
localcishit.dy:111:10: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
localcishit.dy:88:7: style: Unused variable: qend [unusedVariable]
localcishit.dy:89:7: style: Unused variable: tend [unusedVariable]
localcishit.dy:90:7: style: Unused variable: score_start [unusedVariable]
localclonewisedp.c:380:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
localclonewisedp.c:516:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
localclonewisedp.c:553:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
localclonewisedp.c:790:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
localclonewisedp.c:941:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
localclonewisedp.c:960:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
localclonewisedp.c:1151:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
localclonewisedp.c:1191:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
localclonewisedp.c:1275:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
localclonewisedp.c:1306:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
localclonewisedp.c:1346:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
localclonewisedp.c:1897:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
localclonewisedp.c:2007:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
localclonewisedp.c:2056:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
localclonewisedp.c:2171:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
localclonewisedp.c:2448:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
localclonewisedp.c:2605:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
localclonewisedp.c:2709:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
localclonewisedp.c:2801:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
localclonewisedp.c:3036:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
localclonewisedp.c:3787:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
localclonewisedp.c:3987:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
localclonewisedp.c:1146:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
localclonewisedp.c:1888:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
localclonewisedp.c:1882:15: note: 'hiddenj' is assigned value 'startj' here.
localclonewisedp.c:1888:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
localclonewisedp.c:1212:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
localclonewisedp.c:1204:15: note: stopstate is assigned
localclonewisedp.c:1212:15: note: stopstate is overwritten
localclonewisedp.c:132:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
localclonewisedp.c:133:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
localclonewisedp.c:134:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
localclonewisedp.c:167:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
localclonewisedp.c:467:42: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
localclonewisedp.c:2787:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
localclonewisedp.c:3442:56: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
localclonewisedp.c:4031:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
localclonewisedp.c:2801:11: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2802:11: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2803:11: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2814:17: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2816:21: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2818:16: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2822:23: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2825:16: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2829:23: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2832:16: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2836:23: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2839:16: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2843:23: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2864:10: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2866:11: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2876:70: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2877:68: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2891:17: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2893:21: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2895:16: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2899:23: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2902:16: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2906:23: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2927:10: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2929:11: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2939:70: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2940:68: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2954:17: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2956:21: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2958:16: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2962:23: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2965:16: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2969:23: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2990:10: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:2992:11: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:3002:70: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:3003:68: style: Modulo of one is always equal to zero [moduloofone]
localclonewisedp.c:789:11: style: int result is assigned to long long variable. If the variable is long long to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
localclonewisedp.c:2440:11: 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]
localclonewisedp.c:2593:11: 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]
localclonewisedp.c:2790:11: 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]
localclonewisedp.c:64:52: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
localclonewisedp.c:3261:52: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
localclonewisedp.c:495:9: style: Unused variable: db_status [unusedVariable]
localclonewisedp.c:567:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
localclonewisedp.c:747:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
localclonewisedp.c:844:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
localclonewisedp.c:784:19: style: Unused variable: de [unusedVariable]
localclonewisedp.c:1735:9: style: Unused variable: temp [unusedVariable]
localdba.c:448:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
localdba.c:508:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
localdba.c:539:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
localdba.c:847:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
localdba.c:980:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
localdba.c:999:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
localdba.c:1257:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
localdba.c:1297:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
localdba.c:1381:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
localdba.c:1412:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
localdba.c:1452:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
localdba.c:2178:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
localdba.c:2366:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
localdba.c:2421:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
localdba.c:2536:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
localdba.c:3056:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
localdba.c:3327:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
localdba.c:3509:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
localdba.c:3607:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
localdba.c:3995:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
localdba.c:5025:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
localdba.c:5302:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
localdba.c:1252:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
localdba.c:2169:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
localdba.c:2163:15: note: 'hiddenj' is assigned value 'startj' here.
localdba.c:2169:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
localdba.c:1318:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
localdba.c:1310:15: note: stopstate is assigned
localdba.c:1318:15: note: stopstate is overwritten
localdba.c:135:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
localdba.c:136:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
localdba.c:137:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
localdba.c:170:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
localdba.c:3593:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
localdba.c:4520:64: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
localdba.c:5349:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
localdba.c:3607:11: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3608:11: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3609:11: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3610:11: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3611:11: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3612:11: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3623:17: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3625:21: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3627:16: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3631:23: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3634:16: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3638:23: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3655:16: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3659:23: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3666:10: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3668:11: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3678:74: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3679:72: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3693:17: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3695:21: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3697:16: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3701:23: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3704:16: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3708:23: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3725:16: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3729:23: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3736:10: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3738:11: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3748:74: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3749:72: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3763:17: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3765:21: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3767:16: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3771:23: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3774:16: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3778:23: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3795:16: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3799:23: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3806:10: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3808:11: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3818:74: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3819:72: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3833:17: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3835:21: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3837:16: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3841:23: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3844:16: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3848:23: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3865:16: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3869:23: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3876:10: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3878:11: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3888:74: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3889:72: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3903:17: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3905:21: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3907:16: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3911:23: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3914:16: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3918:23: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3921:16: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3925:23: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3928:16: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3932:23: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3939:10: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3941:11: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3950:17: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3952:21: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3954:16: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3958:23: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3965:10: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3967:11: style: Modulo of one is always equal to zero [moduloofone]
localdba.c:3048:11: 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]
localdba.c:3315:11: 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]
localdba.c:3596:11: 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]
localdba.c:67:56: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
localdba.c:4339:56: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
localdba.c:487:9: style: Unused variable: db_status [unusedVariable]
localdba.c:553:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
localdba.c:810:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
localdba.c:901:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
localdba.c:841:19: style: Unused variable: de [unusedVariable]
localdba.c:1983:9: style: Unused variable: temp [unusedVariable]
wise-2.4.1/src/models/makepwm.c:12:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/makerandomdb.c:20:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/makeseqerror.c:24:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
mapstruct.dy:379:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
mapstruct.dy:425:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
mapstruct.dy:425:7: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
mapstruct.dy:426:7: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
mapstruct.dy:427:7: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
mapstruct.dy:428:7: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
mapstruct.dy:429:7: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
mapstruct.dy:162:47: style: Parameter 'one' can be declared as pointer to const [constParameterPointer]
mapstruct.dy:162:68: style: Parameter 'two' can be declared as pointer to const [constParameterPointer]
mapstruct.dy:323:66: style: Parameter 'clone_name' can be declared as pointer to const [constParameterPointer]
mapstruct.dy:350:42: style: Parameter 'a' can be declared as pointer to const. However it seems that 'Wise2_start_comp_MappedClone' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
mapstruct.dy:392:27: note: You might need to cast the function pointer here
mapstruct.dy:350:42: note: Parameter 'a' can be declared as pointer to const
mapstruct.dy:350:58: style: Parameter 'b' can be declared as pointer to const. However it seems that 'Wise2_start_comp_MappedClone' is a callback function, if 'b' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
mapstruct.dy:392:27: note: You might need to cast the function pointer here
mapstruct.dy:350:58: note: Parameter 'b' can be declared as pointer to const
mapstruct.dy:414:10: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
mapstruct.dy:415:10: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
mapstruct.dy:120:13: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
mapstruct.dy:119:7: style: Unused variable: i [unusedVariable]
mapstruct.dy:120:7: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
mapstruct.c:1005:9: style: Unused variable: j [unusedVariable]
matchsum.dy:145:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
matchsum.dy:83:69: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
matchsum.dy:211:48: style: Parameter 'ms' can be declared as pointer to const [constParameterPointer]
matchsum.dy:282:47: style: Parameter 'ms' can be declared as pointer to const [constParameterPointer]
matchsum.c:693:49: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
matchsum.c:737:48: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
matchsum.c:781:49: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
matchsum.c:825:49: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
matchsum.c:869:47: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
matchsum.c:913:45: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
matchsum.c:957:47: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
matchsum.c:1001:45: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
matchsum.c:1045:48: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
matchsum.c:1089:52: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
matchsum.c:1133:48: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
matchsum.c:1177:52: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/motifcluster.c:98:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/motifcluster.c:60:18: style: Variable 'end_on_seq' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/motifcluster.c:61:17: style: Variable 'seq_count' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/motifcluster.c:60:7: style: Variable 'end_on_seq' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/motifcluster.c:61:7: style: Variable 'seq_count' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/motifdiff.c:105:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/motifdiff.c:143:12: style: Condition 'sa==NULL' is always false [knownConditionTrueFalse]
wise-2.4.1/src/models/motifdiff.c:251:15: style: Condition 'seen_one==seen_two' is always true [knownConditionTrueFalse]
wise-2.4.1/src/models/motifdiff.c:233:20: note: Assuming that condition 'seen_one!=seen_two' is not redundant
wise-2.4.1/src/models/motifdiff.c:251:15: note: Condition 'seen_one==seen_two' is always true
wise-2.4.1/src/models/motifdiff.c:176:11: warning: Unused variable value 'one_pos' [constStatement]
wise-2.4.1/src/models/motifdiff.c:179:11: warning: Unused variable value 'two_pos' [constStatement]
wise-2.4.1/src/models/motifdiff.c:43:32: style: Unused variable: comp [unusedVariable]
wise-2.4.1/src/models/motifdiff.c:45:28: style: Unused variable: comparap [unusedVariable]
wise-2.4.1/src/models/motifdiff.c:54:11: style: Variable 'show_compara' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/motifdiff.c:57:7: style: Variable 'end_on_seq' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/motifdiff.c:58:7: style: Variable 'seq_count' is assigned a value that is never used. [unreadVariable]
motifmatrix.dy:53:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NMaskType_BANNED [valueFlowBailoutIncompleteVar]
motifmatrix.c:533:9: style: Unused variable: j [unusedVariable]
motifmatrixdp.c:331:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:392:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:424:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:617:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:753:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:772:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:946:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:986:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:1070:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:1101:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:1141:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:1690:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:1807:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:1856:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:1971:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:2285:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:2453:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:2564:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:2656:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:2845:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:3541:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:3702:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
motifmatrixdp.c:941:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
motifmatrixdp.c:1681:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
motifmatrixdp.c:1675:15: note: 'hiddenj' is assigned value 'startj' here.
motifmatrixdp.c:1681:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
motifmatrixdp.c:1007:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
motifmatrixdp.c:999:15: note: stopstate is assigned
motifmatrixdp.c:1007:15: note: stopstate is overwritten
motifmatrixdp.c:133:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
motifmatrixdp.c:134:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
motifmatrixdp.c:135:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
motifmatrixdp.c:168:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
motifmatrixdp.c:2642:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
motifmatrixdp.c:3233:60: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
motifmatrixdp.c:3746:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
motifmatrixdp.c:2656:11: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2657:11: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2658:11: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2669:17: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2671:21: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2673:16: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2677:23: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2680:16: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2684:23: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2687:16: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2691:23: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2694:16: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2698:23: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2719:10: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2721:11: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2731:72: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2732:70: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2746:17: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2748:21: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2750:16: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2754:23: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2757:16: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2761:23: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2764:16: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2768:23: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2775:10: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2777:11: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2786:17: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2788:21: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2790:16: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2794:23: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2797:16: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2801:23: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2804:16: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2808:23: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2815:10: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2817:11: style: Modulo of one is always equal to zero [moduloofone]
motifmatrixdp.c:2277:11: 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]
motifmatrixdp.c:2441:11: 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]
motifmatrixdp.c:2645:11: 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]
motifmatrixdp.c:65:54: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
motifmatrixdp.c:3052:54: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
motifmatrixdp.c:371:9: style: Unused variable: db_status [unusedVariable]
motifmatrixdp.c:438:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
motifmatrixdp.c:579:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
motifmatrixdp.c:671:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
motifmatrixdp.c:611:19: style: Unused variable: de [unusedVariable]
motifmatrixdp.c:1550:9: style: Unused variable: temp [unusedVariable]
wise-2.4.1/src/models/motifwise.c:93:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/motifwise.c:68:7: style: Unused variable: i [unusedVariable]
wise-2.4.1/src/models/mutatedna.c:47:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/mutatedna.c:44:3: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory]
wise-2.4.1/src/models/mutatedna.c:27:15: note: Assuming allocation function fails
wise-2.4.1/src/models/mutatedna.c:27:15: note: Assignment 'seq=calloc(sizeof(char),dna->len*2)', assigned value is 0
wise-2.4.1/src/models/mutatedna.c:44:3: note: Null pointer dereference
wise-2.4.1/src/models/oldpostwise.c:118:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable homolog [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/oldpostwise.c:187:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/oldpostwise.c:326:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/oldpostwise.c:344:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/oldpostwise.c:377:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/oldpostwise.c:407:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/oldpostwise.c:92:37: style: Parameter 'gen' can be declared as pointer to const. However it seems that 'make_ace_gene_name' is a callback function, if 'gen' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise-2.4.1/src/models/oldpostwise.c:191:158: note: You might need to cast the function pointer here
wise-2.4.1/src/models/oldpostwise.c:92:37: note: Parameter 'gen' can be declared as pointer to const
wise-2.4.1/src/models/oldpostwise.c:92:48: style: Parameter 'protein_name' can be declared as pointer to const. However it seems that 'make_ace_gene_name' is a callback function, if 'protein_name' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise-2.4.1/src/models/oldpostwise.c:191:158: note: You might need to cast the function pointer here
wise-2.4.1/src/models/oldpostwise.c:92:48: note: Parameter 'protein_name' can be declared as pointer to const
wise-2.4.1/src/models/oldpostwise.c:95:10: style: Variable 'alpha' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/models/oldpostwise.c:96:15: style: Unused variable: secondno [unusedVariable]
wise-2.4.1/src/models/oldpostwise.c:113:13: style: Unused variable: g [unusedVariable]
wise-2.4.1/src/models/oldpostwise.c:191:9: style: Variable 'count' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/oldpostwise.c:391:10: style: Unused variable: help [unusedVariable]
wise-2.4.1/src/models/oldpostwise.c:393:10: style: Unused variable: efp [unusedVariable]
pairwiseshortdna.dy:55:11: style: Variable 'forward_tree' can be declared as pointer to const [constVariablePointer]
pairwiseshortdna.dy:56:11: style: Variable 'reverse_tree' can be declared as pointer to const [constVariablePointer]
pairwiseshortdna.dy:66:18: style: Variable 'forward_tree' is allocated memory that is never used. [unusedAllocatedMemory]
pairwiseshortdna.dy:67:18: style: Variable 'reverse_tree' is allocated memory that is never used. [unusedAllocatedMemory]
pba.c:357:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
pba.c:641:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
pba.c:723:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
pba.c:935:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
pba.c:1083:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
pba.c:1102:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
pba.c:1287:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
pba.c:1327:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
pba.c:1411:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
pba.c:1442:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
pba.c:1482:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
pba.c:2026:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
pba.c:2148:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
pba.c:2199:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
pba.c:2314:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
pba.c:2613:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
pba.c:2788:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
pba.c:2904:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
pba.c:2998:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
pba.c:3209:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
pba.c:3914:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
pba.c:4090:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
pba.c:1282:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
pba.c:2017:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
pba.c:2011:15: note: 'hiddenj' is assigned value 'startj' here.
pba.c:2017:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
pba.c:1348:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
pba.c:1340:15: note: stopstate is assigned
pba.c:1348:15: note: stopstate is overwritten
pba.c:134:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
pba.c:135:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
pba.c:136:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
pba.c:169:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
pba.c:2984:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
pba.c:3599:66: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
pba.c:4135:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
pba.c:2998:11: style: Modulo of one is always equal to zero [moduloofone]
pba.c:2999:11: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3000:11: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3001:11: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3012:17: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3014:21: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3030:16: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3034:23: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3041:10: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3043:11: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3053:75: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3054:73: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3068:17: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3070:21: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3072:16: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3076:23: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3083:10: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3085:11: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3094:17: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3096:21: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3098:16: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3102:23: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3109:10: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3111:11: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3120:17: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3122:21: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3124:16: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3128:23: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3131:16: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3135:23: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3138:16: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3142:23: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3145:16: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3149:23: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3152:16: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3156:23: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3163:10: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3165:11: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3175:75: style: Modulo of one is always equal to zero [moduloofone]
pba.c:3176:73: style: Modulo of one is always equal to zero [moduloofone]
pba.c:2605:11: 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]
pba.c:2776:11: 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]
pba.c:2987:11: 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]
pba.c:66:57: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
pba.c:3418:57: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
pba.c:635:20: style: Variable 'target_pos' is assigned a value that is never used. [unreadVariable]
pba.c:737:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
pba.c:893:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
pba.c:989:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
pba.c:929:19: style: Unused variable: de [unusedVariable]
pba.c:1883:9: style: Unused variable: temp [unusedVariable]
pfamhmmer1db.dy:97:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_END [valueFlowBailoutIncompleteVar]
pfamhmmer1db.dy:200:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
pfamhmmer1db.dy:200:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
pfamhmmer1db.dy:205:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
pfamhmmer1db.dy:223:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
pfamhmmer1db.dy:53:73: style: Parameter 'phd' can be declared as pointer to const [constParameterPointer]
pfamhmmer1db.dy:126:77: style: Parameter 'dir' can be declared as pointer to const [constParameterPointer]
pfamhmmer1db.c:646:43: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
pfamhmmer1db.c:690:51: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
pfamhmmer1db.c:734:44: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
pfamhmmer1db.c:778:54: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
pfamhmmer1db.c:822:59: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
pfamhmmer1db.c:866:60: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
pfamhmmer1db.c:910:59: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
pfamhmmer1db.c:954:61: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
phasemodel.dy:63:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
phasemodel.dy:135:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
phasemodel.dy:250:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
phasemodel.dy:241:9: error: Buffer is accessed out of bounds: name [bufferAccessOutOfBounds]
phasemodel.dy:275:107: style: Parameter 'rm' can be declared as pointer to const [constParameterPointer]
phasemodel.dy:275:120: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
phasemodel.dy:278:23: style: Variable 'pl' can be declared as pointer to const [constVariablePointer]
phasemodel.dy:64:10: style: Unused variable: run1 [unusedVariable]
phasemodel.dy:65:10: style: Unused variable: run2 [unusedVariable]
phasemodel.dy:231:14: style: Unused variable: input [unusedVariable]
phasemodel.dy:233:7: style: Unused variable: j [unusedVariable]
wise-2.4.1/src/models/promotercluster.c:46:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/promotercluster.c:33:19: style: Unused variable: set [unusedVariable]
wise-2.4.1/src/models/promoterwise.c:102:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NMaskType_BANNED [valueFlowBailoutIncompleteVar]
proteinsw.c:308:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
proteinsw.c:586:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
proteinsw.c:665:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
proteinsw.c:830:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
proteinsw.c:969:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
proteinsw.c:988:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
proteinsw.c:1139:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
proteinsw.c:1179:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
proteinsw.c:1263:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
proteinsw.c:1294:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
proteinsw.c:1334:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
proteinsw.c:1811:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
proteinsw.c:1899:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
proteinsw.c:1948:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
proteinsw.c:2063:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
proteinsw.c:2258:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
proteinsw.c:2385:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
proteinsw.c:2467:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
proteinsw.c:2559:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
proteinsw.c:2706:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
proteinsw.c:3288:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
proteinsw.c:3420:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
proteinsw.c:1134:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
proteinsw.c:1802:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
proteinsw.c:1796:15: note: 'hiddenj' is assigned value 'startj' here.
proteinsw.c:1802:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
proteinsw.c:1200:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
proteinsw.c:1192:15: note: stopstate is assigned
proteinsw.c:1200:15: note: stopstate is overwritten
proteinsw.c:132:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
proteinsw.c:133:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
proteinsw.c:134:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
proteinsw.c:167:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
proteinsw.c:2545:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
proteinsw.c:3046:46: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
proteinsw.c:3464:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
proteinsw.c:2559:11: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2560:11: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2561:11: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2572:17: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2574:21: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2576:16: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2580:23: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2583:16: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2587:23: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2608:10: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2610:11: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2620:65: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2621:63: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2635:17: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2637:21: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2639:16: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2643:23: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2650:10: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2652:11: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2661:17: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2663:21: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2665:16: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2669:23: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2676:10: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2678:11: style: Modulo of one is always equal to zero [moduloofone]
proteinsw.c:2250:11: 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]
proteinsw.c:2373:11: 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]
proteinsw.c:2548:11: 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]
proteinsw.c:64:47: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
proteinsw.c:2865:47: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
proteinsw.c:580:20: style: Variable 'target_pos' is assigned a value that is never used. [unreadVariable]
proteinsw.c:679:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
proteinsw.c:791:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
proteinsw.c:884:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
proteinsw.c:824:19: style: Unused variable: de [unusedVariable]
proteinsw.c:1677:9: style: Unused variable: temp [unusedVariable]
wise-2.4.1/src/models/pseudowise.c:75:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/pseudowise.c:199:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/pseudowise.c:50:56: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/pseudowise.c:50:71: style: Parameter 'pep' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/pseudowise.c:50:86: style: Parameter 'cdna' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/pseudowise.c:50:101: style: Parameter 'gen' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/pseudowise.c:50:115: style: Parameter 'protein' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/pseudowise.c:57:7: style: Unused variable: i [unusedVariable]
wise-2.4.1/src/models/pseudowise.c:57:9: style: Unused variable: j [unusedVariable]
wise-2.4.1/src/models/pseudowise.c:220:10: style: Variable 'offset' is assigned a value that is never used. [unreadVariable]
pseudowise7.c:514:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
pseudowise7.c:790:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
pseudowise7.c:868:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
pseudowise7.c:1213:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
pseudowise7.c:1349:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
pseudowise7.c:1368:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
pseudowise7.c:1654:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
pseudowise7.c:1694:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
pseudowise7.c:1778:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
pseudowise7.c:1809:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
pseudowise7.c:1849:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
pseudowise7.c:2664:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
pseudowise7.c:2901:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
pseudowise7.c:2958:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
pseudowise7.c:3073:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
pseudowise7.c:3757:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
pseudowise7.c:4097:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
pseudowise7.c:4328:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
pseudowise7.c:4428:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
pseudowise7.c:4855:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
pseudowise7.c:6002:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
pseudowise7.c:6315:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
pseudowise7.c:1649:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
pseudowise7.c:2655:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
pseudowise7.c:2649:15: note: 'hiddenj' is assigned value 'startj' here.
pseudowise7.c:2655:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
pseudowise7.c:1715:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
pseudowise7.c:1707:15: note: stopstate is assigned
pseudowise7.c:1715:15: note: stopstate is overwritten
pseudowise7.c:136:11: style: Variable 'SIG_1_3' can be declared as pointer to const [constVariablePointer]
pseudowise7.c:137:11: style: Variable 'SIG_1_6' can be declared as pointer to const [constVariablePointer]
pseudowise7.c:138:11: style: Variable 'SIG_1_5' can be declared as pointer to const [constVariablePointer]
pseudowise7.c:139:11: style: Variable 'SIG_1_4' can be declared as pointer to const [constVariablePointer]
pseudowise7.c:140:11: style: Variable 'SIG_0_3' can be declared as pointer to const [constVariablePointer]
pseudowise7.c:141:11: style: Variable 'SIG_0_6' can be declared as pointer to const [constVariablePointer]
pseudowise7.c:142:11: style: Variable 'SIG_0_5' can be declared as pointer to const [constVariablePointer]
pseudowise7.c:143:11: style: Variable 'SIG_0_4' can be declared as pointer to const [constVariablePointer]
pseudowise7.c:144:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
pseudowise7.c:145:11: style: Variable 'SIG_0_2' can be declared as pointer to const [constVariablePointer]
pseudowise7.c:146:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
pseudowise7.c:147:11: style: Variable 'SIG_0_8' can be declared as pointer to const [constVariablePointer]
pseudowise7.c:148:11: style: Variable 'SIG_0_9' can be declared as pointer to const [constVariablePointer]
pseudowise7.c:149:11: style: Variable 'SIG_0_10' can be declared as pointer to const [constVariablePointer]
pseudowise7.c:182:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
pseudowise7.c:4414:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
pseudowise7.c:5430:50: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
pseudowise7.c:6363:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
pseudowise7.c:3749:11: 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]
pseudowise7.c:4085:11: 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]
pseudowise7.c:4417:11: 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]
pseudowise7.c:68:49: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
pseudowise7.c:5249:49: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
pseudowise7.c:784:20: style: Variable 'target_pos' is assigned a value that is never used. [unreadVariable]
pseudowise7.c:882:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
pseudowise7.c:1175:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
pseudowise7.c:1267:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
pseudowise7.c:1207:19: style: Unused variable: de [unusedVariable]
pseudowise7.c:2470:9: style: Unused variable: temp [unusedVariable]
wise-2.4.1/src/models/psw.c:99:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/psw.c:242:25: warning: Uninitialized variable: qend [uninitvar]
wise-2.4.1/src/models/psw.c:227:30: note: Assuming condition is false
wise-2.4.1/src/models/psw.c:242:25: note: Uninitialized variable: qend
wise-2.4.1/src/models/psw.c:243:27: warning: Uninitialized variable: tend [uninitvar]
wise-2.4.1/src/models/psw.c:227:30: note: Assuming condition is false
wise-2.4.1/src/models/psw.c:243:27: note: Uninitialized variable: tend
wise-2.4.1/src/models/pswdb.c:88:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/pswdb.c:97:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/pswdb.c:163:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/pswdb.c:377:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
pwmdna.dy:173:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pwmdna.dy:293:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
pwmdna.dy:314:31: style: Parameter 'pd' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/revcomp.c:12:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/scanwisep.c:308:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/scanwisep.c:403:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable raw_score [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/scanwisep.c:506:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Explicit [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/scanwisep.c:154:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assuming allocation function fails
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assignment 'out=malloc(sizeof(struct ScanWiseHSPImpl))', assigned value is 0
wise-2.4.1/src/models/scanwisep.c:154:3: note: Null pointer dereference
wise-2.4.1/src/models/scanwisep.c:155:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assuming allocation function fails
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assignment 'out=malloc(sizeof(struct ScanWiseHSPImpl))', assigned value is 0
wise-2.4.1/src/models/scanwisep.c:155:3: note: Null pointer dereference
wise-2.4.1/src/models/scanwisep.c:156:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assuming allocation function fails
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assignment 'out=malloc(sizeof(struct ScanWiseHSPImpl))', assigned value is 0
wise-2.4.1/src/models/scanwisep.c:156:3: note: Null pointer dereference
wise-2.4.1/src/models/scanwisep.c:157:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assuming allocation function fails
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assignment 'out=malloc(sizeof(struct ScanWiseHSPImpl))', assigned value is 0
wise-2.4.1/src/models/scanwisep.c:157:3: note: Null pointer dereference
wise-2.4.1/src/models/scanwisep.c:158:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assuming allocation function fails
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assignment 'out=malloc(sizeof(struct ScanWiseHSPImpl))', assigned value is 0
wise-2.4.1/src/models/scanwisep.c:158:3: note: Null pointer dereference
wise-2.4.1/src/models/scanwisep.c:159:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assuming allocation function fails
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assignment 'out=malloc(sizeof(struct ScanWiseHSPImpl))', assigned value is 0
wise-2.4.1/src/models/scanwisep.c:159:3: note: Null pointer dereference
wise-2.4.1/src/models/scanwisep.c:160:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assuming allocation function fails
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assignment 'out=malloc(sizeof(struct ScanWiseHSPImpl))', assigned value is 0
wise-2.4.1/src/models/scanwisep.c:160:3: note: Null pointer dereference
wise-2.4.1/src/models/scanwisep.c:161:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assuming allocation function fails
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assignment 'out=malloc(sizeof(struct ScanWiseHSPImpl))', assigned value is 0
wise-2.4.1/src/models/scanwisep.c:161:3: note: Null pointer dereference
wise-2.4.1/src/models/scanwisep.c:162:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assuming allocation function fails
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assignment 'out=malloc(sizeof(struct ScanWiseHSPImpl))', assigned value is 0
wise-2.4.1/src/models/scanwisep.c:162:3: note: Null pointer dereference
wise-2.4.1/src/models/scanwisep.c:163:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assuming allocation function fails
wise-2.4.1/src/models/scanwisep.c:153:15: note: Assignment 'out=malloc(sizeof(struct ScanWiseHSPImpl))', assigned value is 0
wise-2.4.1/src/models/scanwisep.c:163:3: note: Null pointer dereference
wise-2.4.1/src/models/scanwisep.c:347:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/models/scanwisep.c:346:15: note: Assuming allocation function fails
wise-2.4.1/src/models/scanwisep.c:346:15: note: Assignment 'out=malloc(sizeof(struct HSP2HitListImpl))', assigned value is 0
wise-2.4.1/src/models/scanwisep.c:347:3: note: Null pointer dereference
wise-2.4.1/src/models/scanwisep.c:355:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
wise-2.4.1/src/models/scanwisep.c:346:15: note: Assuming allocation function fails
wise-2.4.1/src/models/scanwisep.c:346:15: note: Assignment 'out=malloc(sizeof(struct HSP2HitListImpl))', assigned value is 0
wise-2.4.1/src/models/scanwisep.c:355:3: note: Null pointer dereference
wise-2.4.1/src/models/scanwisep.c:506:3: warning: Either the condition 'dpri==NULL' is redundant or there is possible null pointer dereference: dpri. [nullPointerRedundantCheck]
wise-2.4.1/src/models/scanwisep.c:537:12: note: Assuming that condition 'dpri==NULL' is not redundant
wise-2.4.1/src/models/scanwisep.c:506:3: note: Null pointer dereference
wise-2.4.1/src/models/scanwisep.c:273:55: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/scanwisep.c:476:25: style: Variable 'ssl' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/models/scanwisep.c:140:10: error: Uninitialized variable: out [legacyUninitvar]
wise-2.4.1/src/models/scanwisep.c:296:13: style: struct member 'convert_data_fulldp::hl' is never used. [unusedStructMember]
wise-2.4.1/src/models/scanwisep.c:297:15: style: struct member 'convert_data_fulldp::dpri' is never used. [unusedStructMember]
wise-2.4.1/src/models/scanwisep.c:70:14: style: Unused variable: seq [unusedVariable]
wise-2.4.1/src/models/scanwisep.c:72:7: style: Unused variable: ret [unusedVariable]
wise-2.4.1/src/models/scanwisep.c:73:7: style: Unused variable: c [unusedVariable]
wise-2.4.1/src/models/scanwisep.c:305:7: style: Unused variable: i [unusedVariable]
wise-2.4.1/src/models/scanwisep.c:326:30: style: Unused variable: conv [unusedVariable]
wise-2.4.1/src/models/scanwisep.c:557:7: style: Variable 'ssl' is assigned a value that is never used. [unreadVariable]
seqaligndisplay.dy:178:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BC_RIGHT [valueFlowBailoutIncompleteVar]
seqaligndisplay.dy:164:47: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
seqerror.dy:121:41: style: Parameter 'se' can be declared as pointer to const [constParameterPointer]
seqhit.dy:114:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
seqhit.dy:180:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
seqhit.dy:222:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
seqhit.dy:273:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
seqhit.dy:222:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
seqhit.dy:227:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
seqhit.dy:238:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
seqhit.dy:241:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
seqhit.dy:244:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
seqhit.dy:247:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
seqhit.dy:250:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
seqhit.dy:273:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
seqhit.dy:278:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
seqhit.dy:289:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
seqhit.dy:292:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
seqhit.dy:295:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
seqhit.dy:298:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
seqhit.dy:301:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
seqhit.dy:92:35: style: Parameter 'sh' can be declared as pointer to const [constParameterPointer]
seqhit.dy:104:47: style: Parameter 'one' can be declared as pointer to const. However it seems that 'Wise2_compare_SegmentHit_by_qstart' is a callback function, if 'one' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
seqhit.dy:100:27: note: You might need to cast the function pointer here
seqhit.dy:104:47: note: Parameter 'one' can be declared as pointer to const
seqhit.dy:104:64: style: Parameter 'two' can be declared as pointer to const. However it seems that 'Wise2_compare_SegmentHit_by_qstart' is a callback function, if 'two' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
seqhit.dy:100:27: note: You might need to cast the function pointer here
seqhit.dy:104:64: note: Parameter 'two' can be declared as pointer to const
seqhit.c:910:73: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
seqhit.c:954:74: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
seqhit.c:1001:51: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
seqhit.c:1045:44: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
seqhit.c:1089:43: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
seqhit.c:1133:41: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
seqhit.c:1177:43: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
seqhit.c:1221:41: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
seqhit.c:1265:45: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
seqhit.c:1309:54: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/seqlist.c:18:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
slimdba.c:315:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
slimdba.c:380:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
slimdba.c:416:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
slimdba.c:594:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
slimdba.c:742:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
slimdba.c:761:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
slimdba.c:919:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
slimdba.c:959:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
slimdba.c:1043:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
slimdba.c:1074:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
slimdba.c:1114:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
slimdba.c:1603:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
slimdba.c:1695:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
slimdba.c:1744:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
slimdba.c:1859:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
slimdba.c:2073:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
slimdba.c:2206:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
slimdba.c:2292:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
slimdba.c:2384:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
slimdba.c:2538:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
slimdba.c:3142:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
slimdba.c:3284:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
slimdba.c:914:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
slimdba.c:1594:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
slimdba.c:1588:15: note: 'hiddenj' is assigned value 'startj' here.
slimdba.c:1594:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
slimdba.c:980:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
slimdba.c:972:15: note: stopstate is assigned
slimdba.c:980:15: note: stopstate is overwritten
slimdba.c:132:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
slimdba.c:133:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
slimdba.c:134:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
slimdba.c:167:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
slimdba.c:2370:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
slimdba.c:2886:62: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
slimdba.c:3328:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
slimdba.c:2384:11: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2385:11: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2386:11: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2397:17: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2399:21: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2401:16: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2405:23: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2408:16: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2412:23: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2415:16: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2419:23: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2426:10: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2428:11: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2437:17: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2439:21: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2441:16: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2445:23: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2466:10: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2468:11: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2477:17: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2479:21: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2481:16: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2485:23: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2492:10: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2494:11: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2504:73: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2505:71: style: Modulo of one is always equal to zero [moduloofone]
slimdba.c:2065:11: 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]
slimdba.c:2194:11: 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]
slimdba.c:2373:11: 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]
slimdba.c:64:55: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
slimdba.c:2705:55: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
slimdba.c:359:9: style: Unused variable: db_status [unusedVariable]
slimdba.c:430:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
slimdba.c:552:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
slimdba.c:648:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
slimdba.c:588:19: style: Unused variable: de [unusedVariable]
slimdba.c:1468:9: style: Unused variable: temp [unusedVariable]
splicesitemodeler.dy:58:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
splicesitemodeler.dy:105:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
standardout.dy:59:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Score2Bits [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/statwise.c:81:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/statwise.c:55:25: style: Unused variable: splice5 [unusedVariable]
wise-2.4.1/src/models/statwise.c:56:25: style: Unused variable: splice3 [unusedVariable]
statwise10.c:72:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
statwise10.c:184:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
statwise10.c:217:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
statwise10.c:453:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
statwise10.c:561:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
statwise10.c:580:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
statwise10.c:643:102: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stay_score [valueFlowBailoutIncompleteVar]
statwise10.c:764:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
statwise10.c:804:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
statwise10.c:907:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
statwise10.c:938:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
statwise10.c:978:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
statwise10.c:1164:102: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stay_score [valueFlowBailoutIncompleteVar]
statwise10.c:1546:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
statwise10.c:1660:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
statwise10.c:1711:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
statwise10.c:1826:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
statwise10.c:2102:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
statwise10.c:2267:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
statwise10.c:2375:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
statwise10.c:2433:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
statwise10.c:2716:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
statwise10.c:2943:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
statwise10.c:3152:102: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stay_score [valueFlowBailoutIncompleteVar]
statwise10.c:3334:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable exit_score [valueFlowBailoutIncompleteVar]
statwise10.c:3388:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
statwise10.c:3580:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable StatWise10 [valueFlowBailoutIncompleteVar]
statwise10.c:759:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
statwise10.c:1537:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
statwise10.c:1531:15: note: 'hiddenj' is assigned value 'startj' here.
statwise10.c:1537:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
statwise10.c:3060:48: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
statwise10.c:2094:11: 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]
statwise10.c:2255:11: 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]
statwise10.c:2426:11: 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]
statwise10.c:163:9: style: Unused variable: db_status [unusedVariable]
statwise10.c:231:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
statwise10.c:414:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
statwise10.c:489:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
statwise10.c:447:19: style: Unused variable: de [unusedVariable]
statwise10.c:792:19: style: Unused variable: pau [unusedVariable]
sw_wrap.dy:108:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQUENCE_PROTEIN [valueFlowBailoutIncompleteVar]
sw_wrap.dy:192:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQUENCE_PROTEIN [valueFlowBailoutIncompleteVar]
sw_wrap.dy:270:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQUENCE_PROTEIN [valueFlowBailoutIncompleteVar]
sw_wrap.dy:402:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
sw_wrap.dy:460:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
sw_wrap.dy:519:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
sw_wrap.dy:426:8: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
sw_wrap.dy:484:8: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
sw_wrap.dy:543:8: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
syexonmodel.dy:109:37: style: Parameter 'sc' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/sywise.c:53:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/sywise.c:105:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text_label [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/sywise.c:243:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/sywise.c:96:37: style: Parameter 'alb' can be declared as pointer to const [constParameterPointer]
wise-2.4.1/src/models/sywise.c:201:19: style: Variable 'gr2' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/models/sywise.c:204:27: style: Variable 'std_opt' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/models/sywise.c:64:10: style: Unused variable: ifp [unusedVariable]
wise-2.4.1/src/models/sywise.c:101:19: style: Variable 'match_score' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/sywise.c:211:25: style: Variable 'show_trans' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/sywise.c:212:25: style: Variable 'show_gene_raw' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/sywise.c:234:11: style: Variable 'std_opt' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/sywise.c:336:7: style: Variable 'gr2' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/sywise.c:168:7: style: Unused variable: i [unusedVariable]
wise-2.4.1/src/models/sywise.c:183:13: style: Unused variable: score_mat [unusedVariable]
wise-2.4.1/src/models/sywise.c:202:13: style: Unused variable: trans [unusedVariable]
wise-2.4.1/src/models/sywise.c:211:11: style: Variable 'show_trans' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/sywise.c:212:11: style: Variable 'show_gene_raw' is assigned a value that is never used. [unreadVariable]
sywise20.c:674:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
sywise20.c:810:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
sywise20.c:847:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
sywise20.c:1361:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
sywise20.c:1512:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
sywise20.c:1531:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
sywise20.c:1915:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
sywise20.c:1955:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
sywise20.c:2058:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
sywise20.c:2089:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
sywise20.c:2129:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
sywise20.c:3155:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
sywise20.c:3484:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
sywise20.c:3555:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
sywise20.c:3670:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
sywise20.c:4546:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
sywise20.c:5024:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
sywise20.c:5347:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
sywise20.c:5461:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
sywise20.c:6113:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
sywise20.c:7567:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
sywise20.c:8042:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
sywise20.c:1910:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
sywise20.c:3146:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
sywise20.c:3140:15: note: 'hiddenj' is assigned value 'startj' here.
sywise20.c:3146:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
sywise20.c:145:11: style: Variable 'SIG_1_3' can be declared as pointer to const [constVariablePointer]
sywise20.c:146:11: style: Variable 'SIG_0_3' can be declared as pointer to const [constVariablePointer]
sywise20.c:147:11: style: Variable 'SIG_1_2' can be declared as pointer to const [constVariablePointer]
sywise20.c:148:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
sywise20.c:149:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
sywise20.c:150:11: style: Variable 'SIG_0_2' can be declared as pointer to const [constVariablePointer]
sywise20.c:183:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
sywise20.c:761:36: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
sywise20.c:5447:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
sywise20.c:6813:44: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
sywise20.c:8099:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
sywise20.c:4538:11: 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]
sywise20.c:5012:11: 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]
sywise20.c:5450:11: 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]
sywise20.c:77:46: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
sywise20.c:6632:46: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
sywise20.c:789:9: style: Unused variable: db_status [unusedVariable]
sywise20.c:861:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
sywise20.c:1318:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
sywise20.c:1415:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
sywise20.c:1355:19: style: Unused variable: de [unusedVariable]
sywise20.c:1943:19: style: Unused variable: pau [unusedVariable]
wise-2.4.1/src/models/test_aligng.c:16:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NMaskType_VARIABLE [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/test_gwhsp.c:25:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/test_splice.c:27:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NMaskType_VARIABLE [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/test_splice.c:15:17: style: Variable 'rm' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/models/test_splice.c:21:6: style: Variable 'rm' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/models/testdna.c:5:1: portability: Omitted return type of function 'main' defaults to int, this is not supported by ISO C99 and later standards. [returnImplicitInt]
wise-2.4.1/src/models/testdna.c:22:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/models/testgenestat.c:32:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
threestatedb.dy:413:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
threestatedb.dy:462:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_END [valueFlowBailoutIncompleteVar]
threestatedb.dy:567:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
threestatedb.dy:613:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_END [valueFlowBailoutIncompleteVar]
threestatedb.c:754:47: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
threestatedb.c:798:52: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
threestatedp.c:344:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
threestatedp.c:460:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
threestatedp.c:514:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
threestatedp.c:715:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
threestatedp.c:845:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
threestatedp.c:864:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
threestatedp.c:1040:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
threestatedp.c:1080:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
threestatedp.c:1164:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
threestatedp.c:1195:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
threestatedp.c:1235:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
threestatedp.c:1762:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
threestatedp.c:1861:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
threestatedp.c:1910:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
threestatedp.c:2025:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
threestatedp.c:2261:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
threestatedp.c:2403:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
threestatedp.c:2496:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
threestatedp.c:2588:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
threestatedp.c:2809:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
threestatedp.c:3513:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
threestatedp.c:3684:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
threestatedp.c:1035:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
threestatedp.c:1753:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
threestatedp.c:1747:15: note: 'hiddenj' is assigned value 'startj' here.
threestatedp.c:1753:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
threestatedp.c:1101:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
threestatedp.c:1093:15: note: stopstate is assigned
threestatedp.c:1101:15: note: stopstate is overwritten
threestatedp.c:132:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
threestatedp.c:133:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
threestatedp.c:134:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
threestatedp.c:167:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
threestatedp.c:424:45: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
threestatedp.c:2574:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
threestatedp.c:3199:62: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
threestatedp.c:3728:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
threestatedp.c:2588:11: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2589:11: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2590:11: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2601:17: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2603:21: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2605:16: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2609:23: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2612:16: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2616:23: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2637:10: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2639:11: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2649:73: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2650:71: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2664:17: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2666:21: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2668:16: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2672:23: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2675:16: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2679:23: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2700:10: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2702:11: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2712:73: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2713:71: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2727:17: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2729:21: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2731:16: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2735:23: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2738:16: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2742:23: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2763:10: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2765:11: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2775:73: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2776:71: style: Modulo of one is always equal to zero [moduloofone]
threestatedp.c:2253:11: 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]
threestatedp.c:2391:11: 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]
threestatedp.c:2577:11: 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]
threestatedp.c:64:55: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
threestatedp.c:3018:55: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
threestatedp.c:528:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
threestatedp.c:679:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
threestatedp.c:769:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
threestatedp.c:709:19: style: Unused variable: de [unusedVariable]
threestatedp.c:1602:9: style: Unused variable: temp [unusedVariable]
threestateloop.c:387:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
threestateloop.c:503:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_ERROR [valueFlowBailoutIncompleteVar]
threestateloop.c:557:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
threestateloop.c:801:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
threestateloop.c:931:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
threestateloop.c:950:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
threestateloop.c:1142:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
threestateloop.c:1182:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
threestateloop.c:1285:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
threestateloop.c:1316:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
threestateloop.c:1356:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
threestateloop.c:1920:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
threestateloop.c:2019:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
threestateloop.c:2068:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
threestateloop.c:2183:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
threestateloop.c:2419:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
threestateloop.c:2561:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
threestateloop.c:2654:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
threestateloop.c:2746:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
threestateloop.c:3027:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
threestateloop.c:3794:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
threestateloop.c:4007:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
threestateloop.c:1137:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
threestateloop.c:1911:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
threestateloop.c:1905:15: note: 'hiddenj' is assigned value 'startj' here.
threestateloop.c:1911:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
threestateloop.c:133:11: style: Variable 'SIG_1_1' can be declared as pointer to const [constVariablePointer]
threestateloop.c:134:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
threestateloop.c:135:11: style: Variable 'SIG_1_0' can be declared as pointer to const [constVariablePointer]
threestateloop.c:168:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
threestateloop.c:467:42: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
threestateloop.c:2732:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
threestateloop.c:3443:56: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
threestateloop.c:4052:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
threestateloop.c:2746:11: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2747:11: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2748:11: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2759:17: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2761:21: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2763:16: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2767:23: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2770:16: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2774:23: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2795:10: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2797:11: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2807:71: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2808:69: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2822:17: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2824:21: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2826:16: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2830:23: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2833:16: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2837:23: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2858:10: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2860:11: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2870:71: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2871:69: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2885:17: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2887:21: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2889:16: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2893:23: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2896:16: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2900:23: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2921:10: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2923:11: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2933:71: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2934:69: style: Modulo of one is always equal to zero [moduloofone]
threestateloop.c:2411:11: 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]
threestateloop.c:2549:11: 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]
threestateloop.c:2735:11: 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]
threestateloop.c:65:52: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
threestateloop.c:3262:52: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
threestateloop.c:571:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
threestateloop.c:765:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
threestateloop.c:855:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
threestateloop.c:795:19: style: Unused variable: de [unusedVariable]
threestateloop.c:1170:19: style: Unused variable: pau [unusedVariable]
threestatemodel.dy:454:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
threestatemodel.dy:551:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQUENCE_PROTEIN [valueFlowBailoutIncompleteVar]
threestatemodel.dy:952:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
threestatemodel.dy:1049:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
threestatemodel.dy:1275:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
threestatemodel.dy:1402:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
threestatemodel.dy:965:26: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
threestatemodel.dy:989:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
threestatemodel.dy:1049:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
threestatemodel.dy:1309:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
threestatemodel.dy:1339:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
threestatemodel.dy:1430:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
threestatemodel.dy:1444:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
threestatemodel.dy:1457:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
threestatemodel.dy:1472:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
threestatemodel.dy:1501:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
threestatemodel.dy:1515:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
threestatemodel.dy:1528:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
threestatemodel.dy:1558:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
threestatemodel.dy:1572:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
threestatemodel.dy:1585:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
threestatemodel.dy:1600:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
threestatemodel.dy:1039:10: style: Variable 'runner' can be declared as pointer to const [constVariablePointer]
threestatemodel.dy:1117:60: style: Parameter 'tsu' can be declared as pointer to const [constParameterPointer]
threestatemodel.dy:1403:10: style: Variable 'runner' can be declared as pointer to const [constVariablePointer]
threestatemodel.c:2332:54: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
threestatemodel.c:2379:51: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
threestatemodel.c:2423:58: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
threestatemodel.c:2467:59: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
threestatemodel.c:2511:59: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
threestatemodel.c:2555:59: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
threestatemodel.c:2599:58: style: Parameter 'obj' can be declared as pointer to const [constParameterPointer]
transfactor.dy:84:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
transfactor.dy:156:154: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq [valueFlowBailoutIncompleteVar]
transfactor.dy:416:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASE_N [valueFlowBailoutIncompleteVar]
transfactor.dy:534:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
transfactor.dy:615:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
transfactor.dy:729:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
transfactor.dy:800:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
transfactor.dy:834:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
transfactor.dy:656:16: warning: Either the condition 'k==5' is redundant or the array 'iupac_map[17][5]' is accessed at index iupac_map[*][5], which is out of bounds. [arrayIndexOutOfBoundsCond]
transfactor.dy:658:8: note: Assuming that condition 'k==5' is not redundant
transfactor.dy:656:16: note: Array index out of bounds
transfactor.dy:145:53: style: Parameter 'tfms' can be declared as pointer to const [constParameterPointer]
transfactor.dy:206:161: style: Parameter 'para' can be declared as pointer to const [constParameterPointer]
transfactor.dy:896:55: style: Parameter 'a' can be declared as pointer to const. However it seems that 'Wise2_compare_start_TransFactorMatch' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
transfactor.dy:904:30: note: You might need to cast the function pointer here
transfactor.dy:896:55: note: Parameter 'a' can be declared as pointer to const
transfactor.dy:896:76: style: Parameter 'b' can be declared as pointer to const. However it seems that 'Wise2_compare_start_TransFactorMatch' is a callback function, if 'b' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
transfactor.dy:904:30: note: You might need to cast the function pointer here
transfactor.dy:896:76: note: Parameter 'b' can be declared as pointer to const
transfactor.dy:882:7: warning: Uninitialized variable: temp [uninitvar]
transfactor.dy:858:36: note: Assuming condition is false
transfactor.dy:882:7: note: Uninitialized variable: temp
transfactor.dy:496:10: style: Variable 'maxj' is assigned a value that is never used. [unreadVariable]
transfactor.dy:501:7: style: Variable 'maxj' is assigned a value that is never used. [unreadVariable]
transfactor.dy:625:7: style: Variable 'seq_no' is assigned a value that is never used. [unreadVariable]
transregion.dy:149:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
transregion.dy:293:9: warning: Unused variable value 'motif_trial' [constStatement]
transregion.dy:96:31: style: Variable 'tfm' can be declared as pointer to const [constVariablePointer]
transregion.dy:321:27: style: Variable 'motif_trial' is assigned a value that is never used. [unreadVariable]
transregiondp.dy:135:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
transregiondp.c:555:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
transregiondp.c:677:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEARCH_ERROR [valueFlowBailoutIncompleteVar]
transregiondp.c:707:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
transregiondp.c:859:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DPIM_Default [valueFlowBailoutIncompleteVar]
transregiondp.c:989:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
transregiondp.c:1008:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
transregiondp.c:1149:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
transregiondp.c:1189:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
transregiondp.c:1273:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REPORT [valueFlowBailoutIncompleteVar]
transregiondp.c:1304:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
transregiondp.c:1344:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
transregiondp.c:1792:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
transregiondp.c:1857:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
transregiondp.c:1904:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_SHADOW [valueFlowBailoutIncompleteVar]
transregiondp.c:2019:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
transregiondp.c:2151:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
transregiondp.c:2245:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
transregiondp.c:2304:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
transregiondp.c:2394:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
transregiondp.c:2537:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGI [valueFlowBailoutIncompleteVar]
transregiondp.c:3100:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
transregiondp.c:3222:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASEMATRIX_TYPE_EXPLICIT [valueFlowBailoutIncompleteVar]
transregiondp.c:1144:12: style: Condition 'out==NULL' is always false [knownConditionTrueFalse]
transregiondp.c:1783:5: style: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value. [duplicateExpression]
transregiondp.c:1777:15: note: 'hiddenj' is assigned value 'startj' here.
transregiondp.c:1783:5: note: Same expression on both sides of '-' because 'startj' and 'hiddenj' represent the same value.
transregiondp.c:1210:15: style: Variable 'stopstate' is reassigned a value before the old one has been used. [redundantAssignment]
transregiondp.c:1202:15: note: stopstate is assigned
transregiondp.c:1210:15: note: stopstate is overwritten
transregiondp.c:396:11: style: Variable 'SIG_0_1' can be declared as pointer to const [constVariablePointer]
transregiondp.c:429:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
transregiondp.c:635:45: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
transregiondp.c:2380:11: style: Variable 'localsp' can be declared as pointer to const [constVariablePointer]
transregiondp.c:2870:62: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
transregiondp.c:3265:25: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
transregiondp.c:2394:11: style: Modulo of one is always equal to zero [moduloofone]
transregiondp.c:2395:11: style: Modulo of one is always equal to zero [moduloofone]
transregiondp.c:2406:17: style: Modulo of one is always equal to zero [moduloofone]
transregiondp.c:2408:21: style: Modulo of one is always equal to zero [moduloofone]
transregiondp.c:2424:16: style: Modulo of one is always equal to zero [moduloofone]
transregiondp.c:2428:23: style: Modulo of one is always equal to zero [moduloofone]
transregiondp.c:2435:10: style: Modulo of one is always equal to zero [moduloofone]
transregiondp.c:2437:11: style: Modulo of one is always equal to zero [moduloofone]
transregiondp.c:2447:73: style: Modulo of one is always equal to zero [moduloofone]
transregiondp.c:2448:71: style: Modulo of one is always equal to zero [moduloofone]
transregiondp.c:2462:17: style: Modulo of one is always equal to zero [moduloofone]
transregiondp.c:2464:21: style: Modulo of one is always equal to zero [moduloofone]
transregiondp.c:2480:16: style: Modulo of one is always equal to zero [moduloofone]
transregiondp.c:2484:23: style: Modulo of one is always equal to zero [moduloofone]
transregiondp.c:2491:10: style: Modulo of one is always equal to zero [moduloofone]
transregiondp.c:2493:11: style: Modulo of one is always equal to zero [moduloofone]
transregiondp.c:2503:73: style: Modulo of one is always equal to zero [moduloofone]
transregiondp.c:2504:71: style: Modulo of one is always equal to zero [moduloofone]
transregiondp.c:858:11: style: int result is assigned to long long variable. If the variable is long long to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
transregiondp.c:2143:11: 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]
transregiondp.c:2233:11: 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]
transregiondp.c:2383:11: 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]
transregiondp.c:328:55: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
transregiondp.c:2689:55: error: Uninitialized variable: holder.dynamite_hard_link [uninitvar]
transregiondp.dy:85:7: style: Unused variable: seqpos [unusedVariable]
transregiondp.c:656:9: style: Unused variable: db_status [unusedVariable]
transregiondp.c:721:11: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
transregiondp.c:823:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
transregiondp.c:913:9: style: Variable 'mat' is assigned a value that is never used. [unreadVariable]
transregiondp.c:853:19: style: Unused variable: de [unusedVariable]
transregiondp.c:1652:9: style: Unused variable: temp [unusedVariable]
wise2xhmmer2.dy:47:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hmmAMINO [valueFlowBailoutIncompleteVar]
wise2xhmmer2.dy:72:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable squid_errno [valueFlowBailoutIncompleteVar]
wise2xhmmer2.dy:383:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DB_RETURN_END [valueFlowBailoutIncompleteVar]
wise2xhmmer2.dy:475:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable spacestr [valueFlowBailoutIncompleteVar]
wise2xhmmer2.dy:475:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
wise2xhmmer2.dy:392:18: style: Variable '*return_status' is reassigned a value before the old one has been used. [redundantAssignment]
wise2xhmmer2.dy:389:20: note: *return_status is assigned
wise2xhmmer2.dy:392:18: note: *return_status is overwritten
wise2xhmmer2.dy:192:62: style: Parameter 'tdb' can be declared as pointer to const. However it seems that 'Wise2_open_for_indexing_ThreeStateDB_HMMer2' is a callback function, if 'tdb' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise2xhmmer2.dy:173:29: note: You might need to cast the function pointer here
wise2xhmmer2.dy:192:62: note: Parameter 'tdb' can be declared as pointer to const
wise2xhmmer2.dy:209:63: style: Parameter 'tdb' can be declared as pointer to const. However it seems that 'Wise2_close_for_indexing_ThreeStateDB_HMMer2' is a callback function, if 'tdb' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
wise2xhmmer2.dy:174:30: note: You might need to cast the function pointer here
wise2xhmmer2.dy:209:63: note: Parameter 'tdb' can be declared as pointer to const
client_multihspscan.dy:67:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
client_multihspscan.dy:144:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAXLINE [valueFlowBailoutIncompleteVar]
client_multihspscan.dy:146:10: style: Variable 'port' can be declared as pointer to const [constVariablePointer]
net_hspscan.dy:52:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable untyped_HSPScanInterfacePara_free [valueFlowBailoutIncompleteVar]
net_hspscan.dy:94:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable untyped_HSPScanInterfacePara_to_Stream [valueFlowBailoutIncompleteVar]
net_hspscan.dy:109:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable untyped_write_Sequence_to_Stream [valueFlowBailoutIncompleteVar]
net_hspscan.dy:123:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable untyped_LinearHSPmanager_to_Stream [valueFlowBailoutIncompleteVar]
net_hspscan.dy:175:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable obj [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/network/wise_proteinindex_server.c:156:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/network/wise_proteinindex_server.c:92:10: style: Variable 'oc_file' can be declared as pointer to const [constVariablePointer]
wise-2.4.1/src/network/wise_proteinindex_server.c:84:13: style: Variable 'count' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/network/wise_proteinindex_server.c:70:7: style: Unused variable: i [unusedVariable]
wise-2.4.1/src/network/wise_proteinindex_server.c:75:14: style: Unused variable: seq [unusedVariable]
wise-2.4.1/src/network/wise_proteinindex_server.c:76:7: style: Unused variable: ret [unusedVariable]
wise-2.4.1/src/network/wise_proteinindex_server.c:84:7: style: Variable 'count' is assigned a value that is never used. [unreadVariable]
wise-2.4.1/src/network/wise_proteinindex_server.c:91:10: style: Unused variable: ior_file [unusedVariable]
wise-2.4.1/src/network/wise_proteinindex_server.c:93:10: style: Unused variable: temp [unusedVariable]
wise-2.4.1/src/other_programs/test_ortho.c:13:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/snp/test_est.c:28:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
wise-2.4.1/src/snp/test_est.c:6:9: style: Unused variable: j [unusedVariable]
wise-2.4.1/src/snp/test_est.c:20:10: style: Unused variable: central [unusedVariable]
directsocketwrite.dy:56:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Wise2WriteStreamInterface [valueFlowBailoutIncompleteVar]
directsocketwrite.dy:58:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
directsocketwrite.dy:56:15: note: Assuming allocation function fails
directsocketwrite.dy:56:15: note: Assignment 'out=malloc(sizeof(Wise2WriteStreamInterface))', assigned value is 0
directsocketwrite.dy:58:3: note: Null pointer dereference
directsocketwrite.dy:59:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
directsocketwrite.dy:56:15: note: Assuming allocation function fails
directsocketwrite.dy:56:15: note: Assignment 'out=malloc(sizeof(Wise2WriteStreamInterface))', assigned value is 0
directsocketwrite.dy:59:3: note: Null pointer dereference
directsocketwrite.dy:60:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
directsocketwrite.dy:56:15: note: Assuming allocation function fails
directsocketwrite.dy:56:15: note: Assignment 'out=malloc(sizeof(Wise2WriteStreamInterface))', assigned value is 0
directsocketwrite.dy:60:3: note: Null pointer dereference
directsocketwrite.dy:62:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
directsocketwrite.dy:56:15: note: Assuming allocation function fails
directsocketwrite.dy:56:15: note: Assignment 'out=malloc(sizeof(Wise2WriteStreamInterface))', assigned value is 0
directsocketwrite.dy:62:3: note: Null pointer dereference
directsocketwrite.dy:69:53: style: Parameter 'dsw' can be declared as pointer to const [constParameterPointer]
directsocketwrite.dy:69:64: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
directsocketwrite.dy:36:9: error: va_list 'ap' was opened but not closed by va_end(). [va_end_missing]
functionclient.dy:72:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
functionclient.dy:113:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
functionclient.dy:188:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AF_INET [valueFlowBailoutIncompleteVar]
functionclient.dy:189:8: style: Obsolescent function 'gethostbyname' called. It is recommended to use 'getaddrinfo' instead. [prohibitedgethostbynameCalled]
functionclient.dy:190:3: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
functionclient.dy:179:20: style: Variable 'hp' can be declared as pointer to const [constVariablePointer]
functionserver.dy:70:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIG_IGN [valueFlowBailoutIncompleteVar]
functionserver.dy:224:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AF_INET [valueFlowBailoutIncompleteVar]
functionserver.dy:107:5: warning: Either the condition '(bytes_in=read(new_socket,buf,sizeof(buf)))==-1' is redundant or the array 'buf[1024]' is accessed at index -1, which is out of bounds. [negativeIndex]
functionserver.dy:103:52: note: Assuming that condition '(bytes_in=read(new_socket,buf,sizeof(buf)))==-1' is not redundant
functionserver.dy:107:5: note: Negative array index
functionserver.dy:253:10: style: Variable 'one' can be declared as pointer to const [constVariablePointer]
functionserver.dy:254:10: style: Variable 'two' can be declared as pointer to const [constVariablePointer]
functionserver.dy:55:10: style: Unused variable: ofp [unusedVariable]
functionserver.dy:216:21: style: Unused variable: name [unusedVariable]
simplebufferedserver.dy:71:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Wise2WriteStreamInterface [valueFlowBailoutIncompleteVar]
simplebufferedserver.dy:93:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AF_INET [valueFlowBailoutIncompleteVar]
simplebufferedserver.dy:128:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
simplebufferedserver.dy:110:3: error: Found an exit path from function with non-void return type that has missing return statement [missingReturn]
simplebufferedserver.dy:73:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
simplebufferedserver.dy:71:15: note: Assuming allocation function fails
simplebufferedserver.dy:71:15: note: Assignment 'out=malloc(sizeof(Wise2WriteStreamInterface))', assigned value is 0
simplebufferedserver.dy:73:3: note: Null pointer dereference
simplebufferedserver.dy:74:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
simplebufferedserver.dy:71:15: note: Assuming allocation function fails
simplebufferedserver.dy:71:15: note: Assignment 'out=malloc(sizeof(Wise2WriteStreamInterface))', assigned value is 0
simplebufferedserver.dy:74:3: note: Null pointer dereference
simplebufferedserver.dy:75:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
simplebufferedserver.dy:71:15: note: Assuming allocation function fails
simplebufferedserver.dy:71:15: note: Assignment 'out=malloc(sizeof(Wise2WriteStreamInterface))', assigned value is 0
simplebufferedserver.dy:75:3: note: Null pointer dereference
simplebufferedserver.dy:77:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
simplebufferedserver.dy:71:15: note: Assuming allocation function fails
simplebufferedserver.dy:71:15: note: Assignment 'out=malloc(sizeof(Wise2WriteStreamInterface))', assigned value is 0
simplebufferedserver.dy:77:3: note: Null pointer dereference
simplebufferedserver.dy:55:51: style: Parameter 'handle' can be declared as pointer to const. However it seems that 'Wise2_close_and_free_simple_buffered_server' is a callback function, if 'handle' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
simplebufferedserver.dy:75:32: note: You might need to cast the function pointer here
simplebufferedserver.dy:55:51: note: Parameter 'handle' can be declared as pointer to const
simplebufferedserver.dy:113:69: style: Parameter 'sbs' can be declared as pointer to const [constParameterPointer]
simplebufferedserver.dy:85:21: style: Unused variable: name [unusedVariable]
simplebufferedserver.dy:122:7: style: Unused variable: new_socket [unusedVariable]
simplebufferedserver.dy:52:9: error: va_list 'ap' was opened but not closed by va_end(). [va_end_missing]
simplesocketclient.dy:73:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Wise2ReadStreamInterface [valueFlowBailoutIncompleteVar]
simplesocketclient.dy:84:8: style: Obsolescent function 'gethostbyname' called. It is recommended to use 'getaddrinfo' instead. [prohibitedgethostbynameCalled]
simplesocketclient.dy:85:3: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
simplesocketclient.dy:74:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
simplesocketclient.dy:73:15: note: Assuming allocation function fails
simplesocketclient.dy:73:15: note: Assignment 'out=malloc(sizeof(Wise2ReadStreamInterface))', assigned value is 0
simplesocketclient.dy:74:3: note: Null pointer dereference
simplesocketclient.dy:75:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
simplesocketclient.dy:73:15: note: Assuming allocation function fails
simplesocketclient.dy:73:15: note: Assignment 'out=malloc(sizeof(Wise2ReadStreamInterface))', assigned value is 0
simplesocketclient.dy:75:3: note: Null pointer dereference
simplesocketclient.dy:76:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
simplesocketclient.dy:73:15: note: Assuming allocation function fails
simplesocketclient.dy:73:15: note: Assignment 'out=malloc(sizeof(Wise2ReadStreamInterface))', assigned value is 0
simplesocketclient.dy:76:3: note: Null pointer dereference
simplesocketclient.dy:80:3: warning: If memory allocation fails, then there is a possible null pointer dereference: handle [nullPointerOutOfMemory]
simplesocketclient.dy:79:18: note: Assuming allocation function fails
simplesocketclient.dy:79:18: note: Assignment 'handle=malloc(sizeof(struct Wise2_SimpleRead_Socket))', assigned value is 0
simplesocketclient.dy:80:3: note: Null pointer dereference
simplesocketclient.dy:81:3: warning: If memory allocation fails, then there is a possible null pointer dereference: handle [nullPointerOutOfMemory]
simplesocketclient.dy:79:18: note: Assuming allocation function fails
simplesocketclient.dy:79:18: note: Assignment 'handle=malloc(sizeof(struct Wise2_SimpleRead_Socket))', assigned value is 0
simplesocketclient.dy:81:3: note: Null pointer dereference
simplesocketclient.dy:88:11: warning: If memory allocation fails, then there is a possible null pointer dereference: handle [nullPointerOutOfMemory]
simplesocketclient.dy:79:18: note: Assuming allocation function fails
simplesocketclient.dy:79:18: note: Assignment 'handle=malloc(sizeof(struct Wise2_SimpleRead_Socket))', assigned value is 0
simplesocketclient.dy:88:11: note: Null pointer dereference
simplesocketclient.dy:92:9: warning: If memory allocation fails, then there is a possible null pointer dereference: handle [nullPointerOutOfMemory]
simplesocketclient.dy:79:18: note: Assuming allocation function fails
simplesocketclient.dy:79:18: note: Assignment 'handle=malloc(sizeof(struct Wise2_SimpleRead_Socket))', assigned value is 0
simplesocketclient.dy:92:9: note: Null pointer dereference
simplesocketclient.dy:96:3: warning: If memory allocation fails, then there is a possible null pointer dereference: handle [nullPointerOutOfMemory]
simplesocketclient.dy:79:18: note: Assuming allocation function fails
simplesocketclient.dy:79:18: note: Assignment 'handle=malloc(sizeof(struct Wise2_SimpleRead_Socket))', assigned value is 0
simplesocketclient.dy:96:3: note: Null pointer dereference
simplesocketclient.dy:96:31: warning: If memory allocation fails, then there is a possible null pointer dereference: handle [nullPointerOutOfMemory]
simplesocketclient.dy:79:18: note: Assuming allocation function fails
simplesocketclient.dy:79:18: note: Assignment 'handle=malloc(sizeof(struct Wise2_SimpleRead_Socket))', assigned value is 0
simplesocketclient.dy:96:31: note: Null pointer dereference
simplesocketclient.dy:98:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
simplesocketclient.dy:73:15: note: Assuming allocation function fails
simplesocketclient.dy:73:15: note: Assignment 'out=malloc(sizeof(Wise2ReadStreamInterface))', assigned value is 0
simplesocketclient.dy:98:3: note: Null pointer dereference
simplesocketclient.dy:46:29: style: Variable 's' can be declared as pointer to const [constVariablePointer]
simplesocketclient.dy:65:66: style: Parameter 'hostname' can be declared as pointer to const [constParameterPointer]
simplesocketclient.dy:71:20: style: Variable 'hp' can be declared as pointer to const [constVariablePointer]
simplesocketclient.dy:33:7: style: Unused variable: ret [unusedVariable]
simplesocketclient.dy:35:10: style: Unused variable: r [unusedVariable]
transferinterface.dy:58:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
transferinterface.dy:69:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
transferinterface.dy:80:9: error: Array 'buffer[1024]' accessed at index 1024, which is out of bounds. [arrayIndexOutOfBounds]
transferinterface.dy:74:12: note: Assuming that condition 'i<1024' is not redundant
transferinterface.dy:80:9: note: Array index out of bounds
wise-2.4.1/src/HMMer2/hmmio.c:322:12: warning: Null pointer dereference: hmmfp [ctunullpointer]
wise-2.4.1/src/HMMer2/hmmalign.c:118:49: note: Assuming that condition '(hmmfp=HMMFileOpen(hmmfile,"HMMERDB"))==NULL' is not redundant
wise-2.4.1/src/HMMer2/hmmalign.c:120:19: note: Calling function HMMFileRead, 1st argument is null
wise-2.4.1/src/HMMer2/hmmio.c:322:12: note: Dereferencing argument hmmfp that is null
wise-2.4.1/src/HMMer2/hmmio.c:327:7: warning: Null pointer dereference: hmmfp [ctunullpointer]
wise-2.4.1/src/HMMer2/hmmconvert.c:137:11: note: Assuming that condition 'test==NULL' is not redundant
wise-2.4.1/src/HMMer2/hmmconvert.c:140:14: note: Calling function HMMFileClose, 1st argument is null
wise-2.4.1/src/HMMer2/hmmio.c:327:7: note: Dereferencing argument hmmfp that is null
wise-2.4.1/src/HMMer2/plan7.c:521:20: warning: Null pointer dereference: hmm [ctunullpointer]
wise-2.4.1/src/HMMer2/hmmemit.c:126:11: note: Assuming that condition 'hmm==NULL' is not redundant
wise-2.4.1/src/HMMer2/hmmemit.c:133:19: note: Calling function Plan7Renormalize, 1st argument is null
wise-2.4.1/src/HMMer2/plan7.c:521:20: note: Dereferencing argument hmm that is null
wise-2.4.1/src/HMMer2/plan7.c:569:3: warning: Null pointer dereference: hmm [ctunullpointer]
wise-2.4.1/src/HMMer2/hmmemit.c:126:11: note: Assuming that condition 'hmm==NULL' is not redundant
wise-2.4.1/src/HMMer2/hmmemit.c:132:19: note: Calling function Plan7NakedConfig, 1st argument is null
wise-2.4.1/src/HMMer2/plan7.c:569:3: note: Dereferencing argument hmm that is null
genomicregion.dy:902:23: warning: If resource allocation fails, then there is a possible null pointer dereference: ifp [ctunullpointerOutOfResources]
genomicregion.dy:743:14: note: Assuming allocation function fails
genomicregion.dy:743:14: note: Assignment 'ifp=popen(buffer,"r")', assigned value is 0
genomicregion.dy:747:34: note: Calling function Wise2_read_EMBL_FT_into_GenomicRegion, 4th argument is null
genomicregion.dy:902:23: note: Dereferencing argument ifp that is null
sequence.dy:864:28: warning: Null pointer dereference: ifp [ctunullpointer]
genomicregion.dy:753:14: note: Assuming allocation function fails
genomicregion.dy:753:14: note: Assignment 'ifp=popen(buffer,"r")', assigned value is 0
genomicregion.dy:755:36: note: Calling function Wise2_read_fasta_Genomic, 1st argument is null
genomic.dy:186:9: note: Calling function Wise2_read_fasta_Sequence, 1st argument is null
sequence.dy:864:28: note: Dereferencing argument ifp that is null
fivestatemodel.dy:209:13: warning: Null pointer dereference: frame [ctunullpointer]
wise-2.4.1/src/models/fivestar.c:92:15: note: Assuming that condition 'frame==NULL' is not redundant
wise-2.4.1/src/models/fivestar.c:94:50: note: Calling function Wise2_FiveStateModel_from_FiveStateFrameSet, 1st argument is null
fivestatemodel.dy:209:13: note: Dereferencing argument frame that is null
mapstruct.dy:379:31: warning: If resource allocation fails, then there is a possible null pointer dereference: ifp [ctunullpointerOutOfResources]
wise-2.4.1/src/models/clonewise.c:252:13: note: Assuming allocation function fails
wise-2.4.1/src/models/clonewise.c:252:13: note: Assignment 'in=fopen(argv[1],"r")', assigned value is 0
wise-2.4.1/src/models/clonewise.c:256:32: note: Calling function Wise2_read_MappedCloneSet, 1st argument is null
mapstruct.dy:379:31: note: Dereferencing argument ifp that is null
diff:
2.17.0 assembly_sanger_project.dy:33:18: portability: Non reentrant function 'readdir' called. For threadsafe applications it is recommended to use the reentrant replacement function 'readdir_r'. [prohibitedreaddirCalled]
head compmat.dy:461:66: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
head compmat.dy:484:83: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
head compmat.dy:564:66: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
head compmat.dy:588:83: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
head dynadebug.dy:169:5: warning: Redundant code: Found unused function. [constStatement]
head dynafunc.dy:1140:10: style: Variable 'matrix_tag' is assigned a value that is never used. [unreadVariable]
head dynafunc.dy:1141:10: style: Variable 'special_tag' is assigned a value that is never used. [unreadVariable]
head dynashadow.dy:2163:3: warning: Redundant code: Found unused function. [constStatement]
head dynashadow.dy:2261:3: warning: Redundant code: Found unused function. [constStatement]
head hsp2hitscan.dy:280:22: error: Uninitialized variable: base[j] [legacyUninitvar]
head hsplookupthreaded.dy:297:39: warning: If memory allocation fails, then there is a possible null pointer dereference: oph [nullPointerOutOfMemory]
     hsplookupthreaded.dy:234:15: note: Assuming allocation function fails
     hsplookupthreaded.dy:234:15: note: Assignment 'oph=calloc(max_oph,sizeof(struct OrderedPosHolder))', assigned value is 0
     hsplookupthreaded.dy:249:12: note: Assuming condition is false
     hsplookupthreaded.dy:297:39: note: Null pointer dereference
head hsplookupthreaded.dy:297:56: warning: If memory allocation fails, then there is a possible null pointer dereference: oph [nullPointerOutOfMemory]
     hsplookupthreaded.dy:234:15: note: Assuming allocation function fails
     hsplookupthreaded.dy:234:15: note: Assignment 'oph=calloc(max_oph,sizeof(struct OrderedPosHolder))', assigned value is 0
     hsplookupthreaded.dy:249:12: note: Assuming condition is false
     hsplookupthreaded.dy:297:56: note: Null pointer dereference
2.17.0 intallocator.dy:395:23: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     intallocator.dy:390:21: note: Assuming allocation function fails
     intallocator.dy:390:21: note: Assignment 'new_block=calloc(512,step_size)', assigned value is 0
     intallocator.dy:395:23: note: Null pointer addition
head linkindex.dy:507:11: style: Variable 'seen_end' is assigned a value that is never used. [unreadVariable]
head mapstruct.dy:120:7: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
head objectinfo.dy:21:83: debug: Function::addArguments found argument 'fgets_func' with varid 0. [varid0]
head probability.dy:172:64: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
head sequence.dy:853:11: style: Variable 'seen_weight' is assigned a value that is never used. [unreadVariable]
head simplesocketclient.dy:96:31: warning: If memory allocation fails, then there is a possible null pointer dereference: handle [nullPointerOutOfMemory]
     simplesocketclient.dy:79:18: note: Assuming allocation function fails
     simplesocketclient.dy:79:18: note: Assignment 'handle=malloc(sizeof(struct Wise2_SimpleRead_Socket))', assigned value is 0
     simplesocketclient.dy:96:31: note: Null pointer dereference
2.17.0 wise-2.4.1/src/base/wiseconfig.c:260:19: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     wise-2.4.1/src/base/wiseconfig.c:246:26: note: Assuming allocation function fails
     wise-2.4.1/src/base/wiseconfig.c:246:10: note: Assignment 'runner=(char*)malloc(sizeof(char)*(strlen(base)+strlen(string)+1))', assigned value is 0
     wise-2.4.1/src/base/wiseconfig.c:260:19: note: Null pointer addition
head wise-2.4.1/src/base/wiseconfig.c:260:19: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     wise-2.4.1/src/base/wiseconfig.c:246:26: note: Assuming allocation function fails
     wise-2.4.1/src/base/wiseconfig.c:246:10: note: Assignment 'runner=(char*)malloc(sizeof(char)*(strlen(base)+strlen(string)+1))', assigned value is 0
     wise-2.4.1/src/base/wiseconfig.c:260:19: note: Null pointer addition
head wise-2.4.1/src/corba/scanwise_protein_index.c:66:7: style: Variable 'count' is assigned a value that is never used. [unreadVariable]
head wise-2.4.1/src/dyc/compugen.c:1052:15: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
     wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
     wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
     wise-2.4.1/src/dyc/compugen.c:1052:15: note: Null pointer dereference
head wise-2.4.1/src/dyc/compugen.c:1052:27: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
     wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
     wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
     wise-2.4.1/src/dyc/compugen.c:1052:27: note: Null pointer dereference
head wise-2.4.1/src/dyc/compugen.c:1054:15: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
     wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
     wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
     wise-2.4.1/src/dyc/compugen.c:1054:15: note: Null pointer dereference
head wise-2.4.1/src/dyc/compugen.c:1054:27: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
     wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
     wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
     wise-2.4.1/src/dyc/compugen.c:1054:27: note: Null pointer dereference
head wise-2.4.1/src/dyc/compugen.c:1054:45: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
     wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
     wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
     wise-2.4.1/src/dyc/compugen.c:1054:45: note: Null pointer dereference
head wise-2.4.1/src/dyc/compugen.c:1054:61: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
     wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
     wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
     wise-2.4.1/src/dyc/compugen.c:1054:61: note: Null pointer dereference
head wise-2.4.1/src/dyc/compugen.c:1054:73: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
     wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
     wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
     wise-2.4.1/src/dyc/compugen.c:1054:73: note: Null pointer dereference
head wise-2.4.1/src/dyc/compugen.c:1056:20: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
     wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
     wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
     wise-2.4.1/src/dyc/compugen.c:1056:20: note: Null pointer dereference
head wise-2.4.1/src/dyc/compugen.c:1056:37: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
     wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
     wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
     wise-2.4.1/src/dyc/compugen.c:1056:37: note: Null pointer dereference
head wise-2.4.1/src/dyc/compugen.c:1056:50: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
     wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
     wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
     wise-2.4.1/src/dyc/compugen.c:1056:50: note: Null pointer dereference
head wise-2.4.1/src/dyc/compugen.c:1056:62: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
     wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
     wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
     wise-2.4.1/src/dyc/compugen.c:1056:62: note: Null pointer dereference
head wise-2.4.1/src/dyc/compugen.c:1056:73: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
     wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
     wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
     wise-2.4.1/src/dyc/compugen.c:1056:73: note: Null pointer dereference
head wise-2.4.1/src/dyc/compugen.c:1056:84: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
     wise-2.4.1/src/dyc/compugen.c:1050:33: note: Assuming allocation function fails
     wise-2.4.1/src/dyc/compugen.c:1050:9: note: Assignment 'out=(struct OneModelTrans*)malloc(sizeof(struct OneModelTrans))', assigned value is 0
     wise-2.4.1/src/dyc/compugen.c:1056:84: note: Null pointer dereference
head wise-2.4.1/src/dyc/compugen.c:1084:26: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
     wise-2.4.1/src/dyc/compugen.c:1081:28: note: Assuming allocation function fails
     wise-2.4.1/src/dyc/compugen.c:1081:8: note: Assignment 'out=(struct OneModel*)malloc(sizeof(struct OneModel))', assigned value is 0
     wise-2.4.1/src/dyc/compugen.c:1084:26: note: Null pointer dereference
head wise-2.4.1/src/dyc/compugen.c:1084:51: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
     wise-2.4.1/src/dyc/compugen.c:1081:28: note: Assuming allocation function fails
     wise-2.4.1/src/dyc/compugen.c:1081:8: note: Assignment 'out=(struct OneModel*)malloc(sizeof(struct OneModel))', assigned value is 0
     wise-2.4.1/src/dyc/compugen.c:1084:51: note: Null pointer dereference
head wise-2.4.1/src/dyc/compugen.c:1099:21: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
     wise-2.4.1/src/dyc/compugen.c:1081:28: note: Assuming allocation function fails
     wise-2.4.1/src/dyc/compugen.c:1081:8: note: Assignment 'out=(struct OneModel*)malloc(sizeof(struct OneModel))', assigned value is 0
     wise-2.4.1/src/dyc/compugen.c:1099:21: note: Null pointer dereference
head wise-2.4.1/src/dynamite_examples/est2gen.c:71:11: style: Variable 'has_outputted' is assigned a value that is never used. [unreadVariable]
head wise-2.4.1/src/dynamite_examples/psw.c:47:11: style: Variable 'has_outputted' is assigned a value that is never used. [unreadVariable]
2.17.0 wise-2.4.1/src/external/mott/gaplib.c:226:68: error: If memory allocation fail: overflow in pointer arithmetic, NULL pointer is subtracted. [nullPointerArithmeticOutOfMemory]
     wise-2.4.1/src/external/mott/gaplib.c:226:33: note: Assuming allocation function fails
     wise-2.4.1/src/external/mott/gaplib.c:226:68: note: Null pointer subtraction
head wise-2.4.1/src/external/mott/gaplib.c:226:68: error: If memory allocation fails: overflow in pointer arithmetic, NULL pointer is subtracted. [nullPointerArithmeticOutOfMemory]
     wise-2.4.1/src/external/mott/gaplib.c:226:33: note: Assuming allocation function fails
     wise-2.4.1/src/external/mott/gaplib.c:226:68: note: Null pointer subtraction
2.17.0 wise-2.4.1/src/external/mott/gaplib.c:254:56: error: If memory allocation fail: overflow in pointer arithmetic, NULL pointer is subtracted. [nullPointerArithmeticOutOfMemory]
     wise-2.4.1/src/external/mott/gaplib.c:254:30: note: Assuming allocation function fails
     wise-2.4.1/src/external/mott/gaplib.c:254:56: note: Null pointer subtraction
head wise-2.4.1/src/external/mott/gaplib.c:254:56: error: If memory allocation fails: overflow in pointer arithmetic, NULL pointer is subtracted. [nullPointerArithmeticOutOfMemory]
     wise-2.4.1/src/external/mott/gaplib.c:254:30: note: Assuming allocation function fails
     wise-2.4.1/src/external/mott/gaplib.c:254:56: note: Null pointer subtraction
head wise-2.4.1/src/external/mott/gaplib.c:264:15: warning: If memory allocation fails, then there is a possible null pointer dereference: h [nullPointerOutOfMemory]
     wise-2.4.1/src/external/mott/gaplib.c:255:32: note: Assuming allocation function fails
     wise-2.4.1/src/external/mott/gaplib.c:255:16: note: Assignment 'h=(double**)calloc(its,sizeof(double*))', assigned value is 0
     wise-2.4.1/src/external/mott/gaplib.c:264:15: note: Null pointer dereference
2.17.0 wise-2.4.1/src/external/mott/gaplib.c:482:12: error: If memory allocation fail: overflow in pointer arithmetic, NULL pointer is subtracted. [nullPointerArithmeticOutOfMemory]
     wise-2.4.1/src/external/mott/gaplib.c:481:26: note: Assuming allocation function fails
     wise-2.4.1/src/external/mott/gaplib.c:481:11: note: Assignment 't_ptr=(double*)calloc(hmax-hmin+1,sizeof(double))', assigned value is 0
     wise-2.4.1/src/external/mott/gaplib.c:482:12: note: Null pointer subtraction
head wise-2.4.1/src/external/mott/gaplib.c:482:12: error: If memory allocation fails: overflow in pointer arithmetic, NULL pointer is subtracted. [nullPointerArithmeticOutOfMemory]
     wise-2.4.1/src/external/mott/gaplib.c:481:26: note: Assuming allocation function fails
     wise-2.4.1/src/external/mott/gaplib.c:481:11: note: Assignment 't_ptr=(double*)calloc(hmax-hmin+1,sizeof(double))', assigned value is 0
     wise-2.4.1/src/external/mott/gaplib.c:482:12: note: Null pointer subtraction
2.17.0 wise-2.4.1/src/external/mott/gaplib.c:517:15: error: If memory allocation fail: overflow in pointer arithmetic, NULL pointer is subtracted. [nullPointerArithmeticOutOfMemory]
     wise-2.4.1/src/external/mott/gaplib.c:516:28: note: Assuming allocation function fails
     wise-2.4.1/src/external/mott/gaplib.c:516:13: note: Assignment 's_ptr=(double*)calloc(max-min+1,sizeof(double))', assigned value is 0
     wise-2.4.1/src/external/mott/gaplib.c:517:15: note: Null pointer subtraction
head wise-2.4.1/src/external/mott/gaplib.c:517:15: error: If memory allocation fails: overflow in pointer arithmetic, NULL pointer is subtracted. [nullPointerArithmeticOutOfMemory]
     wise-2.4.1/src/external/mott/gaplib.c:516:28: note: Assuming allocation function fails
     wise-2.4.1/src/external/mott/gaplib.c:516:13: note: Assignment 's_ptr=(double*)calloc(max-min+1,sizeof(double))', assigned value is 0
     wise-2.4.1/src/external/mott/gaplib.c:517:15: note: Null pointer subtraction
2.17.0 wise-2.4.1/src/external/mott/mott_api.c:179:52: error: If memory allocation fail: overflow in pointer arithmetic, NULL pointer is subtracted. [nullPointerArithmeticOutOfMemory]
     wise-2.4.1/src/external/mott/mott_api.c:179:22: note: Assuming allocation function fails
     wise-2.4.1/src/external/mott/mott_api.c:179:52: note: Null pointer subtraction
head wise-2.4.1/src/external/mott/mott_api.c:179:52: error: If memory allocation fails: overflow in pointer arithmetic, NULL pointer is subtracted. [nullPointerArithmeticOutOfMemory]
     wise-2.4.1/src/external/mott/mott_api.c:179:22: note: Assuming allocation function fails
     wise-2.4.1/src/external/mott/mott_api.c:179:52: note: Null pointer subtraction
head wise-2.4.1/src/external/mott/mott_api.c:265:24: warning: If memory allocation fails, then there is a possible null pointer dereference: freq [nullPointerOutOfMemory]
     wise-2.4.1/src/external/mott/mott_api.c:230:33: note: Assuming allocation function fails
     wise-2.4.1/src/external/mott/mott_api.c:230:18: note: Assignment 'freq=(double*)calloc(256,sizeof(double))', assigned value is 0
     wise-2.4.1/src/external/mott/mott_api.c:265:24: note: Null pointer dereference
head wise-2.4.1/src/models/alignwise.c:125:11: style: Variable 'show_trans' is assigned a value that is never used. [unreadVariable]
head wise-2.4.1/src/models/alignwise.c:127:11: style: Variable 'show_gene_raw' is assigned a value that is never used. [unreadVariable]
head wise-2.4.1/src/models/cdnawise.c:104:10: style: Variable 'ofp' is assigned a value that is never used. [unreadVariable]
head wise-2.4.1/src/models/genomewise.c:81:7: style: Variable 'kbyte' is assigned a value that is never used. [unreadVariable]
head wise-2.4.1/src/models/genomewise.c:95:10: style: Variable 'divide_string' is assigned a value that is never used. [unreadVariable]
head wise-2.4.1/src/models/motifcluster.c:60:7: style: Variable 'end_on_seq' is assigned a value that is never used. [unreadVariable]
head wise-2.4.1/src/models/motifcluster.c:61:7: style: Variable 'seq_count' is assigned a value that is never used. [unreadVariable]
head wise-2.4.1/src/models/sywise.c:211:11: style: Variable 'show_trans' is assigned a value that is never used. [unreadVariable]
head wise-2.4.1/src/models/sywise.c:212:11: style: Variable 'show_gene_raw' is assigned a value that is never used. [unreadVariable]
head wise-2.4.1/src/network/wise_proteinindex_server.c:84:7: style: Variable 'count' is assigned a value that is never used. [unreadVariable]


DONE