2026-05-01 11:18
ftp://ftp.de.debian.org/debian/pool/main/c/codonw/codonw_1.4.4.orig.tar.gz
cppcheck-options: --library=posix --library=gnu --library=bsd  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j6
platform: Linux-7.0.3+deb14-amd64-x86_64-with-glibc2.42
python: 3.13.12
client-version: 1.4.0
compiler: g++ (Debian 15.2.0-17) 15.2.0
cppcheck: head 2.20.0
head-info: e5c4a734 (2026-05-01 11:10:43 +0200)
count: 227 227
elapsed-time: 0.6 0.5
head-timing-info:

old-timing-info:

head results:
codonW/open_fil.c:102:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/open_fil.c:88:13: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/open_fil.c:133:13: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/open_fil.c:186:21: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/open_fil.c:87:35: warning: Either the condition 'default_filename' is redundant or there is possible null pointer dereference: default_filename. [nullPointerRedundantCheck]
codonW/open_fil.c:96:42: note: Assuming that condition 'default_filename' is not redundant
codonW/open_fil.c:87:35: note: Null pointer dereference
codonW/open_fil.c:68:23: style:inconclusive: Function 'open_file' argument 1 names different: declaration 'info' definition 'file_needed'. [funcArgNamesDifferent]
codonW/codonW.h:543:28: note: Function 'open_file' argument 1 names different: declaration 'info' definition 'file_needed'.
codonW/open_fil.c:68:23: note: Function 'open_file' argument 1 names different: declaration 'info' definition 'file_needed'.
codonW/open_fil.c:68:42: style:inconclusive: Function 'open_file' argument 2 names different: declaration 'default_name' definition 'default_filename'. [funcArgNamesDifferent]
codonW/codonW.h:543:40: note: Function 'open_file' argument 2 names different: declaration 'default_name' definition 'default_filename'.
codonW/open_fil.c:68:42: note: Function 'open_file' argument 2 names different: declaration 'default_name' definition 'default_filename'.
codonW/open_fil.c:69:7: style:inconclusive: Function 'open_file' argument 3 names different: declaration 'mode' definition 'write_perm'. [funcArgNamesDifferent]
codonW/codonW.h:543:60: note: Function 'open_file' argument 3 names different: declaration 'mode' definition 'write_perm'.
codonW/open_fil.c:69:7: note: Function 'open_file' argument 3 names different: declaration 'mode' definition 'write_perm'.
codonW/open_fil.c:68:23: style: Parameter 'file_needed' can be declared as pointer to const [constParameterPointer]
codonW/open_fil.c:68:42: style: Parameter 'default_filename' can be declared as pointer to const [constParameterPointer]
codonW/commline.c:103:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/codons.c:130:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/codons.c:361:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/codons.c:800:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/codons.c:950:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/codons.c:1031:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
codonW/codons.c:1071:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/tester.c:76:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
codonW/tester.c:235:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/tester.c:88:17: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/tester.c:125:17: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/tester.c:170:17: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/tester.c:235:5: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/coresp.c:277:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFSIZ [valueFlowBailoutIncompleteVar]
codonW/coresp.c:1271:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFSIZ [valueFlowBailoutIncompleteVar]
codonW/coresp.c:1619:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFSIZ [valueFlowBailoutIncompleteVar]
codonW/menu.c:69:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/menu.c:122:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/menu.c:249:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/menu.c:321:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/menu.c:568:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/menu.c:756:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/menu.c:860:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/menu.c:911:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/menu.c:1023:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/menu.c:1084:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/codon_us.c:344:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/codon_us.c:673:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
codonW/codon_us.c:1283:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/codon_us.c:1305:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
codonW/codon_us.c:1699:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFSIZ [valueFlowBailoutIncompleteVar]
codonW/commline.c:335:16: portability: Assigning an integer to a pointer is not portable. [AssignmentIntegerToAddress]
codonW/commline.c:103:2: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/commline.c:127:2: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/commline.c:142:9: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/commline.c:346:12: style: Variable 'p' is reassigned a value before the old one has been used. [redundantAssignment]
codonW/commline.c:335:16: note: p is assigned
codonW/commline.c:346:12: note: p is overwritten
codonW/commline.c:38:26: style:inconclusive: Function 'proc_comm_line' argument 1 names different: declaration 'argc' definition 'pargc'. [funcArgNamesDifferent]
codonW/codonW.h:571:27: note: Function 'proc_comm_line' argument 1 names different: declaration 'argc' definition 'pargc'.
codonW/commline.c:38:26: note: Function 'proc_comm_line' argument 1 names different: declaration 'argc' definition 'pargc'.
codonW/commline.c:38:42: style:inconclusive: Function 'proc_comm_line' argument 2 names different: declaration 'arg_list' definition 'pargv'. [funcArgNamesDifferent]
codonW/codonW.h:571:41: note: Function 'proc_comm_line' argument 2 names different: declaration 'arg_list' definition 'pargv'.
codonW/commline.c:38:42: note: Function 'proc_comm_line' argument 2 names different: declaration 'arg_list' definition 'pargv'.
codonW/commline.c:38:26: style: Parameter 'pargc' can be declared as pointer to const [constParameterPointer]
codonW/coresp.c:98:5: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
codonW/codons.c:146:53: portability: Undefined behaviour, pointer arithmetic 'Revision+10' is out of bounds. [pointerOutOfBounds]
codonW/codons.c:402:32: style: Array index 'ii' is used before limits check. [arrayIndexThenCheck]
codonW/codons.c:204:35: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/codons.c:1078:20: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/codons.c:1097:28: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/codons.c:1115:5: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/codons.c:1124:4: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/codons.c:1128:5: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/coresp.c:191:9: warning: Either the condition '(fics=open_file("",nfics,"w",0))==NULL' is redundant or there is possible null pointer dereference: fics. [nullPointerRedundantCheck]
codonW/coresp.c:185:42: note: Assuming that condition '(fics=open_file("",nfics,"w",0))==NULL' is not redundant
codonW/coresp.c:191:9: note: Null pointer dereference
codonW/coresp.c:336:21: portability:inconclusive: Casting from float * to const char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
codonW/coresp.c:455:24: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
codonW/coresp.c:473:18: portability:inconclusive: Casting from double * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
codonW/coresp.c:475:10: portability:inconclusive: Casting from double * * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
codonW/coresp.c:483:10: portability:inconclusive: Casting from double * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
codonW/coresp.c:521:20: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
codonW/coresp.c:547:25: portability:inconclusive: Casting from float * to const char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
codonW/coresp.c:572:21: portability:inconclusive: Casting from float * to const char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
codonW/coresp.c:930:25: portability:inconclusive: Casting from float * to const char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
codonW/coresp.c:951:20: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
codonW/coresp.c:1661:20: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
codonW/coresp.c:1666:20: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
codonW/codons.c:1122:18: style: Condition 'HelpMessage==NULL' is always false [knownConditionTrueFalse]
codonW/codons.c:190:5: warning: %i in format string (no. 1) requires 'int' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
codonW/codons.c:196:5: warning: %i in format string (no. 1) requires 'int' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
codonW/codons.c:200:5: warning: %i in format string (no. 1) requires 'int' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
codonW/codons.c:647:7: warning: %d in format string (no. 1) requires 'int' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
codonW/codons.c:647:7: warning: %i in format string (no. 2) requires 'int' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
codonW/codons.c:652:5: warning: %i in format string (no. 1) requires 'int' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
codonW/codons.c:657:7: warning: %d in format string (no. 1) requires 'int' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
codonW/codons.c:657:7: warning: %i in format string (no. 2) requires 'int' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
codonW/codons.c:226:15: warning: Either the condition '(fsummary=open_file("","summary.coa","w",0))==NULL' is redundant or there is possible null pointer dereference: fsummary. [nullPointerRedundantCheck]
codonW/codons.c:213:65: note: Assuming that condition '(fsummary=open_file("","summary.coa","w",0))==NULL' is not redundant
codonW/codons.c:226:15: note: Null pointer dereference
codonW/coresp.c:69:20: style:inconclusive: Function 'textbin' argument 1 names different: declaration 'filein' definition 'fileread'. [funcArgNamesDifferent]
codonW/codonW.h:633:29: note: Function 'textbin' argument 1 names different: declaration 'filein' definition 'fileread'.
codonW/coresp.c:69:20: note: Function 'textbin' argument 1 names different: declaration 'filein' definition 'fileread'.
codonW/coresp.c:169:53: style:inconclusive: Function 'colmout' argument 3 names different: declaration 'paa' definition 'ppaa'. [funcArgNamesDifferent]
codonW/codonW.h:634:62: note: Function 'colmout' argument 3 names different: declaration 'paa' definition 'ppaa'.
codonW/coresp.c:169:53: note: Function 'colmout' argument 3 names different: declaration 'paa' definition 'ppaa'.
codonW/coresp.c:1202:43: style:inconclusive: Function 'inertialig' argument 2 names different: declaration 'filen' definition 'ncout'. [funcArgNamesDifferent]
codonW/codonW.h:640:48: note: Function 'inertialig' argument 2 names different: declaration 'filen' definition 'ncout'.
codonW/coresp.c:1202:43: note: Function 'inertialig' argument 2 names different: declaration 'filen' definition 'ncout'.
codonW/coresp.c:169:53: style: Parameter 'ppaa' can be declared as pointer to const [constParameterPointer]
codonW/coresp.c:327:23: style: Parameter 'v1' can be declared as pointer to const [constParameterPointer]
codonW/coresp.c:559:22: style: Parameter 'v1' can be declared as pointer to const [constParameterPointer]
codonW/codons.c:894:17: style:inconclusive: Function 'my_exit' argument 1 names different: declaration 'exit_value' definition 'error_num'. [funcArgNamesDifferent]
codonW/codonW.h:572:26: note: Function 'my_exit' argument 1 names different: declaration 'exit_value' definition 'error_num'.
codonW/codons.c:894:17: note: Function 'my_exit' argument 1 names different: declaration 'exit_value' definition 'error_num'.
codonW/codons.c:1047:19: style:inconclusive: Function 'chelp' argument 1 names different: declaration 'help' definition 'help_keyword'. [funcArgNamesDifferent]
codonW/codonW.h:578:19: note: Function 'chelp' argument 1 names different: declaration 'help' definition 'help_keyword'.
codonW/codons.c:1047:19: note: Function 'chelp' argument 1 names different: declaration 'help' definition 'help_keyword'.
codonW/codons.c:541:35: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
codonW/codons.c:674:39: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
codonW/codons.c:894:34: style: Parameter 'message' can be declared as pointer to const [constParameterPointer]
codonW/codons.c:1047:19: style: Parameter 'help_keyword' can be declared as pointer to const [constParameterPointer]
codonW/codons.c:1050:8: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
codonW/codons.c:1138:29: style: Parameter 'input' can be declared as pointer to const [constParameterPointer]
codonW/codons.c:117:23: style: Variable 'num_seq' is assigned a value that is never used. [unreadVariable]
codonW/coresp.c:366:12: style: Variable 'a2' is assigned a value that is never used. [unreadVariable]
codonW/coresp.c:1208:22: style: Variable 'temp1' is assigned a value that is never used. [unreadVariable]
codonW/coresp.c:1208:30: style: Variable 'temp2' is assigned a value that is never used. [unreadVariable]
codonW/menu.c:69:9: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:106:9: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:122:15: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:132:17: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:233:9: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:250:17: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:305:9: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:322:17: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:345:13: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:382:13: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:401:13: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:425:13: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:450:13: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:580:9: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:620:17: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:640:17: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:660:17: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:764:9: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:814:10: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:844:9: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:861:17: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:893:9: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:912:17: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:975:5: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:1007:5: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:1024:11: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:1067:5: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:1085:9: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:1097:5: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:1117:5: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:1130:5: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:1224:4: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/menu.c:331:21: warning: Logical conjunction always evaluates to false: c <= 0 && c > 10. [incorrectLogicOperator]
codonW/menu.c:1135:36: style: Redundant condition: The condition 'pcoa->fop_gene == 0' is redundant since 'pcoa->fop_gene < 50' is sufficient. [redundantCondition]
codonW/menu.c:227:13: style: Condition 'loop' is always true [knownConditionTrueFalse]
codonW/menu.c:223:16: note: Assignment 'loop=1', assigned value is 1
codonW/menu.c:227:13: note: Condition 'loop' is always true
codonW/menu.c:270:12: style: Condition 'loop' is always true [knownConditionTrueFalse]
codonW/menu.c:265:16: note: Assignment 'loop=1', assigned value is 1
codonW/menu.c:270:12: note: Condition 'loop' is always true
codonW/menu.c:513:12: style: Condition 'loop' is always true [knownConditionTrueFalse]
codonW/menu.c:490:20: note: Assignment 'loop=1', assigned value is 1
codonW/menu.c:513:12: note: Condition 'loop' is always true
codonW/menu.c:731:13: style: Condition 'loop' is always true [knownConditionTrueFalse]
codonW/menu.c:724:16: note: Assignment 'loop=1', assigned value is 1
codonW/menu.c:731:13: note: Condition 'loop' is always true
codonW/menu.c:838:13: style: Condition 'loop' is always true [knownConditionTrueFalse]
codonW/menu.c:834:16: note: Assignment 'loop=1', assigned value is 1
codonW/menu.c:838:13: note: Condition 'loop' is always true
codonW/menu.c:887:13: style: Condition 'loop' is always true [knownConditionTrueFalse]
codonW/menu.c:883:16: note: Assignment 'loop=1', assigned value is 1
codonW/menu.c:887:13: note: Condition 'loop' is always true
codonW/menu.c:991:11: style: Condition 'loop' is always true [knownConditionTrueFalse]
codonW/menu.c:943:16: note: Assignment 'loop=1', assigned value is 1
codonW/menu.c:991:11: note: Condition 'loop' is always true
codonW/menu.c:1052:11: style: Condition 'loop' is always true [knownConditionTrueFalse]
codonW/menu.c:1046:16: note: Assignment 'loop=1', assigned value is 1
codonW/menu.c:1052:11: note: Condition 'loop' is always true
codonW/menu.c:36:25: style:inconclusive: Function 'main_menu' argument 1 names different: declaration 'c' definition 'menu'. [funcArgNamesDifferent]
codonW/codonW.h:648:27: note: Function 'main_menu' argument 1 names different: declaration 'c' definition 'menu'.
codonW/menu.c:36:25: note: Function 'main_menu' argument 1 names different: declaration 'c' definition 'menu'.
codonW/menu.c:491:14: style: Variable 'choices' can be declared as const array [constVariable]
codonW/menu.c:717:14: style: Variable 'choices' can be declared as const array [constVariable]
codonW/menu.c:1194:20: error: Uninitialized variable: last_row[x%4] [legacyUninitvar]
codonW/codon_us.c:347:6: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/codon_us.c:652:7: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/codon_us.c:759:7: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/codon_us.c:899:10: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/codon_us.c:957:7: warning: Obsolete function 'gets' called. It is recommended to use 'fgets' or 'gets_s' instead. [prohibitedgetsCalled]
codonW/codon_us.c:373:5: warning: %i in format string (no. 1) requires 'int' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
codonW/codon_us.c:479:4: warning: fprintf format string requires 0 parameters but 1 is given. [wrongPrintfScanfArgNum]
codonW/codon_us.c:831:10: warning: %f in format string (no. 1) requires 'double' but the argument type is 'char'. [invalidPrintfArgType_float]
codonW/codon_us.c:988:6: warning: %f in format string (no. 1) requires 'double' but the argument type is 'char'. [invalidPrintfArgType_float]
codonW/codon_us.c:988:6: warning: 'l' in format string (no. 2) is a length modifier and cannot be used without a conversion specifier. [invalidLengthModifierError]
codonW/codon_us.c:994:3: warning: 'l' in format string (no. 1) is a length modifier and cannot be used without a conversion specifier. [invalidLengthModifierError]
codonW/codon_us.c:994:3: warning: 'l' in format string (no. 2) is a length modifier and cannot be used without a conversion specifier. [invalidLengthModifierError]
codonW/codon_us.c:994:3: warning: 'l' in format string (no. 3) is a length modifier and cannot be used without a conversion specifier. [invalidLengthModifierError]
codonW/codon_us.c:1180:9: warning: fprintf format string requires 20 parameters but 21 are given. [wrongPrintfScanfArgNum]
codonW/codon_us.c:2115:7: warning: fprintf format string requires 0 parameters but 1 is given. [wrongPrintfScanfArgNum]
codonW/codon_us.c:2148:7: warning: fprintf format string requires 0 parameters but 1 is given. [wrongPrintfScanfArgNum]
codonW/codon_us.c:1700:7: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
codonW/codon_us.c:1331:13: style: Redundant assignment of 'amino' to itself. [selfAssignment]
codonW/codon_us.c:92:37: style:inconclusive: Function 'initilize_point' argument 2 names different: declaration 'fop_type' definition 'fop_species'. [funcArgNamesDifferent]
codonW/codonW.h:569:39: note: Function 'initilize_point' argument 2 names different: declaration 'fop_type' definition 'fop_species'.
codonW/codon_us.c:92:37: note: Function 'initilize_point' argument 2 names different: declaration 'fop_type' definition 'fop_species'.
codonW/codon_us.c:92:55: style:inconclusive: Function 'initilize_point' argument 3 names different: declaration 'cai_type' definition 'cai_species'. [funcArgNamesDifferent]
codonW/codonW.h:569:54: note: Function 'initilize_point' argument 3 names different: declaration 'cai_type' definition 'cai_species'.
codonW/codon_us.c:92:55: note: Function 'initilize_point' argument 3 names different: declaration 'cai_type' definition 'cai_species'.
codonW/codon_us.c:259:26: style:inconclusive: Function 'codon_error' argument 1 names different: declaration 'last_aa' definition 'x'. [funcArgNamesDifferent]
codonW/codonW.h:580:27: note: Function 'codon_error' argument 1 names different: declaration 'last_aa' definition 'x'.
codonW/codon_us.c:259:26: note: Function 'codon_error' argument 1 names different: declaration 'last_aa' definition 'x'.
codonW/codon_us.c:259:33: style:inconclusive: Function 'codon_error' argument 2 names different: declaration 'valid_stops' definition 'y'. [funcArgNamesDifferent]
codonW/codonW.h:580:40: note: Function 'codon_error' argument 2 names different: declaration 'valid_stops' definition 'y'.
codonW/codon_us.c:259:33: note: Function 'codon_error' argument 2 names different: declaration 'valid_stops' definition 'y'.
codonW/codon_us.c:259:42: style:inconclusive: Function 'codon_error' argument 3 names different: declaration 'title' definition 'ttitle'. [funcArgNamesDifferent]
codonW/codonW.h:580:59: note: Function 'codon_error' argument 3 names different: declaration 'title' definition 'ttitle'.
codonW/codon_us.c:259:42: note: Function 'codon_error' argument 3 names different: declaration 'title' definition 'ttitle'.
codonW/codon_us.c:356:47: style:inconclusive: Function 'codon_usage_out' argument 2 names different: declaration 'ncod' definition 'nncod'. [funcArgNamesDifferent]
codonW/codonW.h:553:47: note: Function 'codon_usage_out' argument 2 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:356:47: note: Function 'codon_usage_out' argument 2 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:357:25: style:inconclusive: Function 'codon_usage_out' argument 4 names different: declaration 'valid_stops' definition 'vvalid_stops'. [funcArgNamesDifferent]
codonW/codonW.h:554:26: note: Function 'codon_usage_out' argument 4 names different: declaration 'valid_stops' definition 'vvalid_stops'.
codonW/codon_us.c:357:25: note: Function 'codon_usage_out' argument 4 names different: declaration 'valid_stops' definition 'vvalid_stops'.
codonW/codon_us.c:357:45: style:inconclusive: Function 'codon_usage_out' argument 5 names different: declaration 'info' definition 'ttitle'. [funcArgNamesDifferent]
codonW/codonW.h:554:45: note: Function 'codon_usage_out' argument 5 names different: declaration 'info' definition 'ttitle'.
codonW/codon_us.c:357:45: note: Function 'codon_usage_out' argument 5 names different: declaration 'info' definition 'ttitle'.
codonW/codon_us.c:401:42: style:inconclusive: Function 'rscu_usage_out' argument 2 names different: declaration 'ncod' definition 'nncod'. [funcArgNamesDifferent]
codonW/codonW.h:555:47: note: Function 'rscu_usage_out' argument 2 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:401:42: note: Function 'rscu_usage_out' argument 2 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:401:55: style:inconclusive: Function 'rscu_usage_out' argument 3 names different: declaration 'naa' definition 'nnaa'. [funcArgNamesDifferent]
codonW/codonW.h:555:62: note: Function 'rscu_usage_out' argument 3 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:401:55: note: Function 'rscu_usage_out' argument 3 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:428:42: style:inconclusive: Function 'raau_usage_out' argument 2 names different: declaration 'naa' definition 'nnaa'. [funcArgNamesDifferent]
codonW/codonW.h:556:47: note: Function 'raau_usage_out' argument 2 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:428:42: note: Function 'raau_usage_out' argument 2 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:485:40: style:inconclusive: Function 'aa_usage_out' argument 2 names different: declaration 'naa' definition 'nnaa'. [funcArgNamesDifferent]
codonW/codonW.h:557:47: note: Function 'aa_usage_out' argument 2 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:485:40: note: Function 'aa_usage_out' argument 2 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:524:44: style:inconclusive: Function 'base_sil_us_out' argument 2 names different: declaration 'ncod' definition 'nncod'. [funcArgNamesDifferent]
codonW/codonW.h:630:48: note: Function 'base_sil_us_out' argument 2 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:524:44: note: Function 'base_sil_us_out' argument 2 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:524:57: style:inconclusive: Function 'base_sil_us_out' argument 3 names different: declaration 'naa' definition 'nnaa'. [funcArgNamesDifferent]
codonW/codonW.h:630:63: note: Function 'base_sil_us_out' argument 3 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:524:57: note: Function 'base_sil_us_out' argument 3 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:584:24: style:inconclusive: Function 'clean_up' argument 1 names different: declaration 'ncod' definition 'nncod'. [funcArgNamesDifferent]
codonW/codonW.h:568:32: note: Function 'clean_up' argument 1 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:584:24: note: Function 'clean_up' argument 1 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:584:41: style:inconclusive: Function 'clean_up' argument 2 names different: declaration 'naa' definition 'nnaa'. [funcArgNamesDifferent]
codonW/codonW.h:568:47: note: Function 'clean_up' argument 2 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:584:41: note: Function 'clean_up' argument 2 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:622:39: style:inconclusive: Function 'cai_out' argument 2 names different: declaration 'ncod' definition 'nncod'. [funcArgNamesDifferent]
codonW/codonW.h:558:47: note: Function 'cai_out' argument 2 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:622:39: note: Function 'cai_out' argument 2 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:725:39: style:inconclusive: Function 'cbi_out' argument 2 names different: declaration 'ncod' definition 'nncod'. [funcArgNamesDifferent]
codonW/codonW.h:559:48: note: Function 'cbi_out' argument 2 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:725:39: note: Function 'cbi_out' argument 2 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:725:56: style:inconclusive: Function 'cbi_out' argument 3 names different: declaration 'naa' definition 'nnaa'. [funcArgNamesDifferent]
codonW/codonW.h:559:64: note: Function 'cbi_out' argument 3 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:725:56: note: Function 'cbi_out' argument 3 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:865:39: style:inconclusive: Function 'fop_out' argument 2 names different: declaration 'ncod' definition 'nncod'. [funcArgNamesDifferent]
codonW/codonW.h:560:47: note: Function 'fop_out' argument 2 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:865:39: note: Function 'fop_out' argument 2 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:1023:41: style:inconclusive: Function 'enc_out' argument 2 names different: declaration 'ncod' definition 'nncod'. [funcArgNamesDifferent]
codonW/codonW.h:583:48: note: Function 'enc_out' argument 2 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:1023:41: note: Function 'enc_out' argument 2 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:1023:58: style:inconclusive: Function 'enc_out' argument 3 names different: declaration 'naa' definition 'nnaa'. [funcArgNamesDifferent]
codonW/codonW.h:583:64: note: Function 'enc_out' argument 3 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:1023:58: note: Function 'enc_out' argument 3 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:1321:18: style:inconclusive: Function 'get_aa' argument 1 names different: declaration 'one_or_3_letter' definition 'which'. [funcArgNamesDifferent]
codonW/codonW.h:586:27: note: Function 'get_aa' argument 1 names different: declaration 'one_or_3_letter' definition 'which'.
codonW/codon_us.c:1321:18: note: Function 'get_aa' argument 1 names different: declaration 'one_or_3_letter' definition 'which'.
codonW/codon_us.c:1321:31: style:inconclusive: Function 'get_aa' argument 2 names different: declaration 'the_dna_word' definition 'codon'. [funcArgNamesDifferent]
codonW/codonW.h:586:51: note: Function 'get_aa' argument 2 names different: declaration 'the_dna_word' definition 'codon'.
codonW/codon_us.c:1321:31: note: Function 'get_aa' argument 2 names different: declaration 'the_dna_word' definition 'codon'.
codonW/codon_us.c:1341:37: style:inconclusive: Function 'cutab_out' argument 2 names different: declaration 'ncod' definition 'nncod'. [funcArgNamesDifferent]
codonW/codonW.h:565:43: note: Function 'cutab_out' argument 2 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:1341:37: note: Function 'cutab_out' argument 2 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:1341:50: style:inconclusive: Function 'cutab_out' argument 3 names different: declaration 'naa' definition 'nnaa'. [funcArgNamesDifferent]
codonW/codonW.h:565:55: note: Function 'cutab_out' argument 3 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:1341:50: note: Function 'cutab_out' argument 3 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:1403:37: style:inconclusive: Function 'dinuc_count' argument 2 names different: declaration 'tot' definition 'ttot'. [funcArgNamesDifferent]
codonW/codonW.h:575:43: note: Function 'dinuc_count' argument 2 names different: declaration 'tot' definition 'ttot'.
codonW/codon_us.c:1403:37: note: Function 'dinuc_count' argument 2 names different: declaration 'tot' definition 'ttot'.
codonW/codon_us.c:1449:37: style:inconclusive: Function 'dinuc_out' argument 2 names different: declaration 'title' definition 'ttitle'. [funcArgNamesDifferent]
codonW/codonW.h:566:43: note: Function 'dinuc_out' argument 2 names different: declaration 'title' definition 'ttitle'.
codonW/codon_us.c:1449:37: note: Function 'dinuc_out' argument 2 names different: declaration 'title' definition 'ttitle'.
codonW/codon_us.c:1548:40: style:inconclusive: Function 'coa_raw_out' argument 2 names different: declaration 'ncod' definition 'nncod'. [funcArgNamesDifferent]
codonW/codonW.h:588:44: note: Function 'coa_raw_out' argument 2 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:1548:40: note: Function 'coa_raw_out' argument 2 names different: declaration 'ncod' definition 'nncod'.
codonW/codon_us.c:1548:53: style:inconclusive: Function 'coa_raw_out' argument 3 names different: declaration 'naa' definition 'nnaa'. [funcArgNamesDifferent]
codonW/codonW.h:588:56: note: Function 'coa_raw_out' argument 3 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:1548:53: note: Function 'coa_raw_out' argument 3 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:1548:65: style:inconclusive: Function 'coa_raw_out' argument 4 names different: declaration 'title' definition 'ttitle'. [funcArgNamesDifferent]
codonW/codonW.h:588:67: note: Function 'coa_raw_out' argument 4 names different: declaration 'title' definition 'ttitle'.
codonW/codon_us.c:1548:65: note: Function 'coa_raw_out' argument 4 names different: declaration 'title' definition 'ttitle'.
codonW/codon_us.c:1639:63: style:inconclusive: Function 'gen_cusort_fop' argument 4 names different: declaration 'summ' definition 'ssummary'. [funcArgNamesDifferent]
codonW/codonW.h:643:65: note: Function 'gen_cusort_fop' argument 4 names different: declaration 'summ' definition 'ssummary'.
codonW/codon_us.c:1639:63: note: Function 'gen_cusort_fop' argument 4 names different: declaration 'summ' definition 'ssummary'.
codonW/codon_us.c:1750:52: style:inconclusive: Function 'highlow' argument 3 names different: declaration 'summ' definition 'ssummary'. [funcArgNamesDifferent]
codonW/codonW.h:592:61: note: Function 'highlow' argument 3 names different: declaration 'summ' definition 'ssummary'.
codonW/codon_us.c:1750:52: note: Function 'highlow' argument 3 names different: declaration 'summ' definition 'ssummary'.
codonW/codon_us.c:2103:41: style:inconclusive: Function 'hydro_out' argument 2 names different: declaration 'naa' definition 'nnaa'. [funcArgNamesDifferent]
codonW/codonW.h:561:47: note: Function 'hydro_out' argument 2 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:2103:41: note: Function 'hydro_out' argument 2 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:2134:41: style:inconclusive: Function 'aromo_out' argument 2 names different: declaration 'naa' definition 'nnaa'. [funcArgNamesDifferent]
codonW/codonW.h:562:47: note: Function 'aromo_out' argument 2 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:2134:41: note: Function 'aromo_out' argument 2 names different: declaration 'naa' definition 'nnaa'.
codonW/codon_us.c:185:27: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:259:42: style: Parameter 'ttitle' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:356:47: style: Parameter 'nncod' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:357:45: style: Parameter 'ttitle' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:401:42: style: Parameter 'nncod' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:401:55: style: Parameter 'nnaa' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:428:42: style: Parameter 'nnaa' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:485:40: style: Parameter 'nnaa' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:524:44: style: Parameter 'nncod' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:524:57: style: Parameter 'nnaa' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:622:39: style: Parameter 'nncod' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:725:39: style: Parameter 'nncod' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:725:56: style: Parameter 'nnaa' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:865:39: style: Parameter 'nncod' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:1023:41: style: Parameter 'nncod' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:1023:58: style: Parameter 'nnaa' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:1341:50: style: Parameter 'nnaa' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:1403:23: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:1449:37: style: Parameter 'ttitle' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:1452:20: style: Variable 'bases' can be declared as const array [constVariable]
codonW/codon_us.c:1548:40: style: Parameter 'nncod' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:1548:53: style: Parameter 'nnaa' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:1591:30: style: Parameter 'ax1' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:1639:26: style: Parameter 'sortax1' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:1755:54: style: Variable 'left_aa' can be declared as pointer to const [constVariablePointer]
codonW/codon_us.c:1755:64: style: Variable 'right_aa' can be declared as pointer to const [constVariablePointer]
codonW/codon_us.c:2103:41: style: Parameter 'nnaa' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:2134:41: style: Parameter 'nnaa' can be declared as pointer to const [constParameterPointer]
codonW/codon_us.c:158:20: style: Variable 'oldcode' is not assigned a value. [unassignedVariable]
diff:


DONE