2025-07-10 06:34
ftp://ftp.de.debian.org/debian/pool/main/m/mustang/mustang_3.2.4.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-6.1.0-37-amd64-x86_64-with-glibc2.36
python: 3.11.2
client-version: 1.3.67
compiler: g++ (Debian 12.2.0-14+deb12u1) 12.2.0
cppcheck: head 2.17.0
head-info: 8f3d36a (2025-07-08 11:07:56 +0200)
count: 222 219
elapsed-time: 2.1 2.4
head-timing-info:

old-timing-info:

head results:
MUSTANG_v3.2.4/src/distmat.cpp:52:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/distmat.cpp:99:33: style: Parameter 'A' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/distmat.cpp:99:45: style: Parameter 'B' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:157:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:380:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:396:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:431:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:455:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:465:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:514:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:656:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:861:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/main.cpp:71:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/main.cpp:90:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/main.cpp:370:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:313:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/jacobi.cpp:131:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/extended_lib_gen_3.cpp:49:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/extended_lib_gen_3.cpp:335:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/ew_2.cpp:166:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable b [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/ew_2.cpp:1074:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/ew_2.cpp:1303:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/ew_2.cpp:1380:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/ew_2.cpp:1395:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:525:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:530:10: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:570:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:575:10: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:54:10: warning: Member variable 'CmdLine::allocSize' is not initialized in the constructor. [uninitMemberVar]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:192:14: style:inconclusive: Technically the member function 'CmdLine::getNoptions' can be const. [functionConst]
MUSTANG_v3.2.4/src/CmdLineParser.h:75:7: note: Technically the member function 'CmdLine::getNoptions' can be const.
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:192:14: note: Technically the member function 'CmdLine::getNoptions' can be const.
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:174:14: performance:inconclusive: Technically the member function 'CmdLine::isOption' can be static (but you may consider moving to unnamed namespace). [functionStatic]
MUSTANG_v3.2.4/src/CmdLineParser.h:91:7: note: Technically the member function 'CmdLine::isOption' can be static (but you may consider moving to unnamed namespace).
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:174:14: note: Technically the member function 'CmdLine::isOption' can be static (but you may consider moving to unnamed namespace).
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:217:14: style:inconclusive: Technically the member function 'CmdLine::isOptionAvailable' can be const. [functionConst]
MUSTANG_v3.2.4/src/CmdLineParser.h:103:7: note: Technically the member function 'CmdLine::isOptionAvailable' can be const.
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:217:14: note: Technically the member function 'CmdLine::isOptionAvailable' can be const.
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:246:14: style:inconclusive: Technically the member function 'CmdLine::getNArgs' can be const. [functionConst]
MUSTANG_v3.2.4/src/CmdLineParser.h:110:7: note: Technically the member function 'CmdLine::getNArgs' can be const.
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:246:14: note: Technically the member function 'CmdLine::getNArgs' can be const.
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:101:2: warning: Possible leak in public function. The pointer 'option' is not deallocated before it is allocated. [publicAllocationError]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:883:8: style: The scope of the variable 'temp' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:287:36: style:inconclusive: Function 'putArgs' argument 1 names different: declaration 'arg' definition 'argmt'. [funcArgNamesDifferent]
MUSTANG_v3.2.4/src/CmdLineParser.h:124:29: note: Function 'putArgs' argument 1 names different: declaration 'arg' definition 'argmt'.
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:287:36: note: Function 'putArgs' argument 1 names different: declaration 'arg' definition 'argmt'.
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:600:8: style: Local variable 'buffer' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:508:7: note: Shadowed declaration
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:600:8: note: Shadow variable
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:611:8: style: Local variable 'buffer' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:508:7: note: Shadowed declaration
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:611:8: note: Shadow variable
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:675:14: style: Local variable 'i' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:637:11: note: Shadowed declaration
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:675:14: note: Shadow variable
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:720:14: style: Local variable 'i' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:637:11: note: Shadowed declaration
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:720:14: note: Shadow variable
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:723:15: style: Local variable 'i' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:720:14: note: Shadowed declaration
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:723:15: note: Shadow variable
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:767:14: style: Local variable 'i' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:637:11: note: Shadowed declaration
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:767:14: note: Shadow variable
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:788:14: style: Local variable 'i' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:637:11: note: Shadowed declaration
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:788:14: note: Shadow variable
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:391:18: style: Parameter 'o' can be declared as pointer to const [constParameterPointer]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:525:9: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:570:9: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:341:7: style: The scope of the variable 'digit' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:52:31: style: Parameter 'dratios' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:69:35: style: Parameter 'dratiosA' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:69:54: style: Parameter 'dratiosB' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:77:33: style: Parameter 'dratiosA' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:77:52: style: Parameter 'dratiosB' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:95:37: style: Parameter 'dcosines' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:117:27: style: Parameter 'rotation_matrix' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:117:56: style: Parameter 'initial_vector' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:143:29: style: Parameter 'x1' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:143:42: style: Parameter 'x2' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:143:55: style: Parameter 'x3' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:173:36: style: Parameter 'A' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:173:48: style: Parameter 'B' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:173:60: style: Parameter 'C' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:173:72: style: Parameter 'D' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:297:30: style: Parameter 'XA' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:297:48: style: Parameter 'XB' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:314:6: style: Variable 'command' can be declared as const array [constVariable]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:354:26: style: Parameter 'A' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/3D_manip_functions.cpp:354:39: style: Parameter 'B' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/main.cpp:224:19: style: Variable 'region_found' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/neighbour_joining.cpp:227:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/output_algn.cpp:72:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/output_algn.cpp:82:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/output_algn.cpp:138:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/output_algn.cpp:194:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/output_algn.cpp:273:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/output_algn.cpp:583:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/neighbour_joining.cpp:131:45: style: Parameter 'R' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/neighbour_joining.cpp:155:64: style: Parameter 'R' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/neighbour_joining.cpp:225:54: style: Parameter 'current_nodes' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:110:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:289:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/pairwise_global_structalgn.cpp:69:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/pairwise_global_structalgn.cpp:159:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/pairwise_global_structalgn.cpp:351:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/pairwise_global_structalgn.cpp:303:18: style: Parameter 'arr' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/pairwise_global_structalgn.cpp:317:43: style: Parameter 'AA' can be declared as pointer to const [constParameterPointer]
MUSTANG_v3.2.4/src/pairwise_global_structalgn.cpp:317:53: style: Parameter 'BB' can be declared as pointer to const [constParameterPointer]
MUSTANG_v3.2.4/src/jacobi.cpp:51:6: style: The scope of the variable 'k' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/jacobi.cpp:52:8: style: The scope of the variable 'p' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/jacobi.cpp:78:34: style: The scope of the variable 'sm' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/jacobi.cpp:122:13: style: Local variable 'i' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/jacobi.cpp:110:11: note: Shadowed declaration
MUSTANG_v3.2.4/src/jacobi.cpp:122:13: note: Shadow variable
MUSTANG_v3.2.4/src/jacobi.cpp:125:14: style: Local variable 'i' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/jacobi.cpp:110:11: note: Shadowed declaration
MUSTANG_v3.2.4/src/jacobi.cpp:125:14: note: Shadow variable
MUSTANG_v3.2.4/src/jacobi.cpp:133:14: style: Local variable 'i' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/jacobi.cpp:110:11: note: Shadowed declaration
MUSTANG_v3.2.4/src/jacobi.cpp:133:14: note: Shadow variable
MUSTANG_v3.2.4/src/jacobi.cpp:137:15: style: Local variable 'i' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/jacobi.cpp:110:11: note: Shadowed declaration
MUSTANG_v3.2.4/src/jacobi.cpp:137:15: note: Shadow variable
MUSTANG_v3.2.4/src/jacobi.cpp:155:14: style: Local variable 'i' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/jacobi.cpp:110:11: note: Shadowed declaration
MUSTANG_v3.2.4/src/jacobi.cpp:155:14: note: Shadow variable
MUSTANG_v3.2.4/src/jacobi.cpp:159:15: style: Local variable 'i' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/jacobi.cpp:110:11: note: Shadowed declaration
MUSTANG_v3.2.4/src/jacobi.cpp:159:15: note: Shadow variable
MUSTANG_v3.2.4/src/primary_lib_gen.cpp:88:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/pdb_ripper_2.cpp:54:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/pdb_ripper_2.cpp:87:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/pdb_ripper_2.cpp:127:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/pdb_ripper_2.cpp:316:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/output_algn.cpp:228:16: style: Obsolete function 'asctime' called. It is recommended to use 'strftime' instead. [prohibitedasctimeCalled]
MUSTANG_v3.2.4/src/output_algn.cpp:228:24: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
MUSTANG_v3.2.4/src/output_algn.cpp:397:53: style: Obsolete function 'asctime' called. It is recommended to use 'strftime' instead. [prohibitedasctimeCalled]
MUSTANG_v3.2.4/src/output_algn.cpp:397:61: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
MUSTANG_v3.2.4/src/output_algn.cpp:640:39: style: Obsolete function 'asctime' called. It is recommended to use 'strftime' instead. [prohibitedasctimeCalled]
MUSTANG_v3.2.4/src/output_algn.cpp:640:47: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
MUSTANG_v3.2.4/src/output_algn.cpp:697:21: style: Obsolete function 'asctime' called. It is recommended to use 'strftime' instead. [prohibitedasctimeCalled]
MUSTANG_v3.2.4/src/output_algn.cpp:697:29: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
MUSTANG_v3.2.4/src/output_algn.cpp:66:20: style: Parameter 'str' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/output_algn.cpp:282:24: style: Variable 'col_groups' can be declared as const array [constVariable]
MUSTANG_v3.2.4/src/output_algn.cpp:526:8: style: Variable 'buff' can be declared as const array [constVariable]
MUSTANG_v3.2.4/src/output_algn.cpp:593:24: style: Variable 'col_groups' can be declared as const array [constVariable]
MUSTANG_v3.2.4/src/output_algn.cpp:590:8: style: struct member 'residue_color_groups::color' is never used. [unusedStructMember]
MUSTANG_v3.2.4/src/progress_align_3.cpp:57:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/progress_align_3.cpp:277:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/progress_align_3.cpp:362:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/progress_align_3.cpp:384:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/progress_align_3.cpp:767:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/progress_align_3.cpp:785:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/read_structures.cpp:67:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:145:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/progress_align_3.cpp:398:3: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
MUSTANG_v3.2.4/src/progress_align_3.cpp:400:3: note: Found duplicate branches for 'if' and 'else'.
MUSTANG_v3.2.4/src/progress_align_3.cpp:398:3: note: Found duplicate branches for 'if' and 'else'.
MUSTANG_v3.2.4/src/sse_RK.cpp:330:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/progress_align_3.cpp:222:46: style: Parameter 'im' can be declared as pointer to const [constParameterPointer]
MUSTANG_v3.2.4/src/progress_align_3.cpp:259:19: style: Parameter 'arr' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/superpose_2.cpp:106:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/superpose_2.cpp:192:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/superpose_2.cpp:242:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/superpose_2.cpp:122:95: style: Parameter 'CM_A' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/superpose_2.cpp:122:111: style: Parameter 'CM_B' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/superpose_2.cpp:203:28: style: Parameter 'eigen_values' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/superpose_2.cpp:208:44: style: Parameter 'eigen_vectors' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/superpose_2.cpp:89:14: style: Variable 'temp' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/sse_RK.cpp:158:3: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
MUSTANG_v3.2.4/src/sse_RK.cpp:182:6: style: The scope of the variable 'ldcntr' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/sse_RK.cpp:183:6: style: The scope of the variable 'Hterminal_flag' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/sse_RK.cpp:158:8: style: Variable 'IRES' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/sse_RK.cpp:182:13: style: Variable 'ldcntr' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/sse_RK.cpp:183:21: style: Variable 'Hterminal_flag' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/superpose_on_core_2.cpp:121:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/superpose_on_core_2.cpp:203:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/superpose_on_core_2.cpp:452:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/superpose_weightedRMS.cpp:106:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/superpose_weightedRMS.cpp:202:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/superpose_weightedRMS.cpp:252:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/superpose_weightedRMS.cpp:122:100: style: Parameter 'CM_A' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/superpose_weightedRMS.cpp:122:116: style: Parameter 'CM_B' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/superpose_weightedRMS.cpp:141:106: style: Parameter 'weights' can be declared as pointer to const [constParameterPointer]
MUSTANG_v3.2.4/src/superpose_weightedRMS.cpp:213:33: style: Parameter 'eigen_values' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/superpose_weightedRMS.cpp:218:49: style: Parameter 'eigen_vectors' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/superpose_weightedRMS.cpp:89:14: style: Variable 'temp' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/upgma.cpp:193:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
MUSTANG_v3.2.4/src/upgma.cpp:191:60: style: Parameter 'current_nodes' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/superpose_on_core_2.cpp:397:6: style: The scope of the variable 'nres' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/superpose_on_core_2.cpp:495:6: style: The scope of the variable 'Size' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/superpose_on_core_2.cpp:228:15: style: Variable 'temp_ins' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/superpose_on_core_2.cpp:397:11: style: Variable 'nres' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/superpose_on_core_2.cpp:438:14: style: Variable 'temp' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/superpose_on_core_2.cpp:495:11: style: Variable 'Size' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/ew_2.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
MUSTANG_v3.2.4/src/ew_2.cpp:268:22: style: Condition 'NEQUIV==5' is always false [knownConditionTrueFalse]
MUSTANG_v3.2.4/src/ew_2.cpp:266:16: note: Assuming that condition 'NEQUIV<5' is not redundant
MUSTANG_v3.2.4/src/ew_2.cpp:268:22: note: Condition 'NEQUIV==5' is always false
MUSTANG_v3.2.4/src/ew_2.cpp:523:6: style: The scope of the variable 'PRUNING_WINDOW' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/ew_2.cpp:802:6: style: The scope of the variable 'H_adj_flag' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/ew_2.cpp:774:29: style: Parameter 'A' can be declared as pointer to const [constParameterPointer]
MUSTANG_v3.2.4/src/ew_2.cpp:774:40: style: Parameter 'B' can be declared as pointer to const [constParameterPointer]
MUSTANG_v3.2.4/src/ew_2.cpp:1223:24: style: Parameter 'arr' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/ew_2.cpp:1238:53: style: Parameter 'TALGN' can be declared as const array [constParameter]
MUSTANG_v3.2.4/src/ew_2.cpp:64:28: style: struct member 'maxfrag_pointer_linkedlist::mflib_ptr' is never used. [unusedStructMember]
MUSTANG_v3.2.4/src/ew_2.cpp:65:37: style: struct member 'maxfrag_pointer_linkedlist::link' is never used. [unusedStructMember]
MUSTANG_v3.2.4/src/ew_2.cpp:70:37: style: struct member 'superposable_fragment_group::mf_hdr_ll' is never used. [unusedStructMember]
MUSTANG_v3.2.4/src/ew_2.cpp:71:37: style: struct member 'superposable_fragment_group::mf_ll_insert_pos' is never used. [unusedStructMember]
MUSTANG_v3.2.4/src/ew_2.cpp:72:6: style: struct member 'superposable_fragment_group::nfrags' is never used. [unusedStructMember]
MUSTANG_v3.2.4/src/ew_2.cpp:73:38: style: struct member 'superposable_fragment_group::link' is never used. [unusedStructMember]
MUSTANG_v3.2.4/src/ew_2.cpp:117:14: style: Variable 'temp1' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/ew_2.cpp:117:26: style: Variable 'temp2' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/ew_2.cpp:117:38: style: Variable 'temp3' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/ew_2.cpp:117:57: style: Variable 'env_function' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/ew_2.cpp:787:15: style: Variable 'CORESIZE' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/ew_2.cpp:802:17: style: Variable 'H_adj_flag' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/ew_2.cpp:1005:15: style: Variable 'repair_flag' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/ew_2.cpp:1017:15: style: Variable 'repair_flag' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:645:20: style: Condition 'struc_ind=0&&A2I_hash[0][i]<=PROT_SIZES[a]-5' is always false [knownConditionTrueFalse]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:466:10: style: The scope of the variable 'deviation' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:428:14: style: Local variable 'l' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:111:7: note: Shadowed declaration
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:428:14: note: Shadow variable
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:431:14: style: Local variable 'l' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:111:7: note: Shadowed declaration
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:431:14: note: Shadow variable
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:435:14: style: Local variable 'l' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:111:7: note: Shadowed declaration
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:435:14: note: Shadow variable
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:437:14: style: Local variable 'l' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:111:7: note: Shadowed declaration
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:437:14: note: Shadow variable
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:447:14: style: Local variable 'l' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:111:7: note: Shadowed declaration
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:447:14: note: Shadow variable
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:450:14: style: Local variable 'l' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:111:7: note: Shadowed declaration
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:450:14: note: Shadow variable
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:454:14: style: Local variable 'l' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:111:7: note: Shadowed declaration
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:454:14: note: Shadow variable
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:456:14: style: Local variable 'l' shadows outer variable [shadowVariable]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:111:7: note: Shadowed declaration
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:456:14: note: Shadow variable
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:57:29: style: Parameter 'A' can be declared as pointer to const [constParameterPointer]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:57:40: style: Parameter 'B' can be declared as pointer to const [constParameterPointer]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:96:5: style: Consider using std::distance algorithm instead of a raw loop. [useStlAlgorithm]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:101:66: style: Consider using std::distance algorithm instead of a raw loop. [useStlAlgorithm]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:571:16: style: Variable 'some_flag' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:617:12: style: Variable 'struc_ind' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:627:58: style: Variable 'struc_ind' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:628:21: style: Variable 'struc_ind' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:646:20: style: Variable 'struc_ind' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:252:5: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:253:8: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:254:8: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:158:3: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:173:7: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:65:8: style: The scope of the variable 'XBAR' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:65:15: style: The scope of the variable 'YBAR' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:65:22: style: The scope of the variable 'ZBAR' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:366:15: style: The scope of the variable 'SUMEA' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:449:9: style: The scope of the variable 'SS' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:506:9: style: The scope of the variable 'XX' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:506:13: style: The scope of the variable 'YY' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:506:17: style: The scope of the variable 'ZZ' can be reduced. [variableScope]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:252:9: style: Variable 'RXV' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:253:12: style: Variable 'RYV' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:254:12: style: Variable 'RZV' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:366:21: style: Variable 'SUMEA' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/multiple_superposition.cpp:568:7: style: Variable 'RMSD' is assigned a value that is never used. [unreadVariable]
MUSTANG_v3.2.4/src/pdb_ripper_2.cpp:174:4: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
MUSTANG_v3.2.4/src/pdb_ripper_2.cpp:396:3: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
MUSTANG_v3.2.4/src/pdb_ripper_2.cpp:405:3: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
MUSTANG_v3.2.4/src/pdb_ripper_2.cpp:335:4: warning: Either the condition 'index==0' is redundant or there is possible null pointer dereference: pdb_trav. [nullPointerRedundantCheck]
MUSTANG_v3.2.4/src/pdb_ripper_2.cpp:331:13: note: Assuming that condition 'index==0' is not redundant
MUSTANG_v3.2.4/src/pdb_ripper_2.cpp:334:13: note: pdb_trav is assigned 'COMPLETE_PDBs[Sindx][index]' here.
MUSTANG_v3.2.4/src/pdb_ripper_2.cpp:335:4: note: Null pointer dereference
diff:
head MUSTANG_v3.2.4/src/3D_manip_functions.cpp:313:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/3D_manip_functions.cpp:313:1: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/CmdLineParser.h:103:7: style:inconclusive: Technically the member function 'CmdLine::isOptionAvailable' can be const. [functionConst]
     MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:217:14: note: Technically the member function 'CmdLine::isOptionAvailable' can be const.
     MUSTANG_v3.2.4/src/CmdLineParser.h:103:7: note: Technically the member function 'CmdLine::isOptionAvailable' can be const.
2.17.0 MUSTANG_v3.2.4/src/CmdLineParser.h:110:7: style:inconclusive: Technically the member function 'CmdLine::getNArgs' can be const. [functionConst]
     MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:246:14: note: Technically the member function 'CmdLine::getNArgs' can be const.
     MUSTANG_v3.2.4/src/CmdLineParser.h:110:7: note: Technically the member function 'CmdLine::getNArgs' can be const.
2.17.0 MUSTANG_v3.2.4/src/CmdLineParser.h:75:7: style:inconclusive: Technically the member function 'CmdLine::getNoptions' can be const. [functionConst]
     MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:192:14: note: Technically the member function 'CmdLine::getNoptions' can be const.
     MUSTANG_v3.2.4/src/CmdLineParser.h:75:7: note: Technically the member function 'CmdLine::getNoptions' can be const.
2.17.0 MUSTANG_v3.2.4/src/CmdLineParser.h:91:7: performance:inconclusive: Technically the member function 'CmdLine::isOption' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:174:14: note: Technically the member function 'CmdLine::isOption' can be static (but you may consider moving to unnamed namespace).
     MUSTANG_v3.2.4/src/CmdLineParser.h:91:7: note: Technically the member function 'CmdLine::isOption' can be static (but you may consider moving to unnamed namespace).
head MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:157:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:157:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:174:14: performance:inconclusive: Technically the member function 'CmdLine::isOption' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     MUSTANG_v3.2.4/src/CmdLineParser.h:91:7: note: Technically the member function 'CmdLine::isOption' can be static (but you may consider moving to unnamed namespace).
     MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:174:14: note: Technically the member function 'CmdLine::isOption' can be static (but you may consider moving to unnamed namespace).
head MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:192:14: style:inconclusive: Technically the member function 'CmdLine::getNoptions' can be const. [functionConst]
     MUSTANG_v3.2.4/src/CmdLineParser.h:75:7: note: Technically the member function 'CmdLine::getNoptions' can be const.
     MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:192:14: note: Technically the member function 'CmdLine::getNoptions' can be const.
head MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:217:14: style:inconclusive: Technically the member function 'CmdLine::isOptionAvailable' can be const. [functionConst]
     MUSTANG_v3.2.4/src/CmdLineParser.h:103:7: note: Technically the member function 'CmdLine::isOptionAvailable' can be const.
     MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:217:14: note: Technically the member function 'CmdLine::isOptionAvailable' can be const.
head MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:246:14: style:inconclusive: Technically the member function 'CmdLine::getNArgs' can be const. [functionConst]
     MUSTANG_v3.2.4/src/CmdLineParser.h:110:7: note: Technically the member function 'CmdLine::getNArgs' can be const.
     MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:246:14: note: Technically the member function 'CmdLine::getNArgs' can be const.
head MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:380:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:380:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:396:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:396:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:431:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:431:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:455:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:455:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:656:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:656:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:861:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/CmdLineParser_2.cpp:861:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/main.cpp:370:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/main.cpp:370:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/main.cpp:71:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/main.cpp:71:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/main.cpp:90:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/main.cpp:90:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/multiple_superposition.cpp:110:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/multiple_superposition.cpp:110:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/multiple_superposition.cpp:289:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/multiple_superposition.cpp:289:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/output_algn.cpp:138:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/output_algn.cpp:138:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/output_algn.cpp:194:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/output_algn.cpp:194:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/output_algn.cpp:273:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/output_algn.cpp:273:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/output_algn.cpp:583:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/output_algn.cpp:583:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/output_algn.cpp:72:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/output_algn.cpp:82:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/output_algn.cpp:82:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/pairwise_global_structalgn.cpp:159:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/pairwise_global_structalgn.cpp:159:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/pairwise_global_structalgn.cpp:351:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/pairwise_global_structalgn.cpp:351:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/pairwise_global_structalgn.cpp:69:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/pairwise_global_structalgn.cpp:69:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/pdb_ripper_2.cpp:127:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/pdb_ripper_2.cpp:127:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/read_structures.cpp:67:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/read_structures.cpp:67:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:101:66: style: Consider using std::distance algorithm instead of a raw loop. [useStlAlgorithm]
head MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:145:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:145:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/refine_pairalgn_2.cpp:96:5: style: Consider using std::distance algorithm instead of a raw loop. [useStlAlgorithm]
head MUSTANG_v3.2.4/src/sse_RK.cpp:330:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/sse_RK.cpp:330:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/superpose_on_core_2.cpp:121:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/superpose_on_core_2.cpp:121:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/superpose_on_core_2.cpp:203:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/superpose_on_core_2.cpp:203:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head MUSTANG_v3.2.4/src/superpose_on_core_2.cpp:452:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 MUSTANG_v3.2.4/src/superpose_on_core_2.cpp:452:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]


DONE