2026-05-04 08:30
ftp://ftp.de.debian.org/debian/pool/main/p/poa/poa_2.0+20060928.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 -j1
platform: Linux-6.8.0-111-generic-x86_64-with-glibc2.39
python: 3.12.3
client-version: 1.3.70
compiler: g++ (Ubuntu 14.2.0-4ubuntu2~24.04.1) 14.2.0
cppcheck: head 2.20.0
head-info: e5c4a73 (2026-05-01 11:10:43 +0200)
count: 397 392
elapsed-time: 5.4 4.8
head-timing-info:

old-timing-info:

head results:
poaV2/align_lpo.c:36:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/align_lpo.c:108:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/align_lpo.c:178:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/align_lpo.c:36:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo.c:37:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo.c:108:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo.c:178:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo.c:179:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo.c:180:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo.c:181:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo.c:182:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo.c:192:7: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo.c:194:7: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo.c:115:9: warning: Possible null pointer dereference: list [nullPointer]
poaV2/align_lpo.c:105:25: note: Assignment 'list=NULL', assigned value is 0
poaV2/align_lpo.c:108:3: note: Assuming condition is true
poaV2/align_lpo.c:115:9: note: Null pointer dereference
poaV2/align_lpo.c:33:20: style: Variable 'left' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo.c:106:20: style: Variable 'right' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo.c:160:38: style: Variable 'my_matrix' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo.c:163:20: style: Variable 'left' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo.c:172:15: style: Variable 'gap_penalty_x' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo.c:172:31: style: Variable 'gap_penalty_y' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo.c:292:3: warning: Uninitialized variable: best_x [uninitvar]
poaV2/align_lpo.c:185:3: note: Assuming condition is false
poaV2/align_lpo.c:292:3: note: Uninitialized variable: best_x
poaV2/align_lpo.c:292:3: warning: Uninitialized variable: best_y [uninitvar]
poaV2/align_lpo.c:185:3: note: Assuming condition is false
poaV2/align_lpo.c:292:3: note: Uninitialized variable: best_y
poaV2/align_lpo2.c:60:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/align_lpo2.c:96:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/align_lpo2.c:185:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/align_lpo2.c:360:7: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
poaV2/align_lpo2.c:359:19: note: outer condition: x_left[i]!=NULL
poaV2/align_lpo2.c:360:7: note: identical inner condition: x_left[i]
poaV2/align_lpo2.c:60:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo2.c:66:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo2.c:70:7: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo2.c:96:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo2.c:97:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo2.c:185:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo2.c:186:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo2.c:199:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo2.c:201:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo2.c:204:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo2.c:207:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo2.c:209:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo2.c:27:22: style: Variable 'src' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo2.c:40:22: style: Variable 'src' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo2.c:94:20: style: Variable 'left' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo2.c:166:37: style: Variable 'xl' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo2.c:172:15: style: Variable 'gap_penalty_x' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo2.c:172:31: style: Variable 'gap_penalty_y' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo2.c:191:5: warning: Uninitialized variable: next_gap_array [uninitvar]
poaV2/align_lpo2.c:185:3: note: Assuming condition is true
poaV2/align_lpo2.c:191:5: note: Uninitialized variable: next_gap_array
poaV2/align_lpo2.c:195:3: warning: Uninitialized variable: next_perp_gap_array [uninitvar]
poaV2/align_lpo2.c:186:3: note: Assuming condition is true
poaV2/align_lpo2.c:195:3: note: Uninitialized variable: next_perp_gap_array
poaV2/align_lpo2.c:194:3: error: Uninitialized variable: next_gap_array [legacyUninitvar]
poaV2/align_lpo2.c:180:16: style: Variable 'n_edges' is assigned a value that is never used. [unreadVariable]
poaV2/align_lpo2.c:289:15: style: Variable 'n_edges' is assigned a value that is never used. [unreadVariable]
poaV2/align_lpo2.c:162:31: style: Unused variable: next_gap [unusedVariable]
poaV2/align_lpo_po.c:39:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/align_lpo_po.c:116:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/align_lpo_po.c:39:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po.c:40:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po.c:116:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po.c:117:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po.c:118:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po.c:119:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po.c:120:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po.c:121:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po.c:92:9: style:inconclusive: Function 'align_lpo_po' argument 7 names different: declaration '<unnamed>' definition 'use_global_alignment'. [funcArgNamesDifferentUnnamed]
poaV2/align_lpo_po.c:36:20: style: Variable 'left' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo_po.c:103:20: style: Variable 'left' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo_po.c:103:35: style: Variable 'y_left' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo_po.c:110:15: style: Variable 'gap_penalty_x' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo_po.c:110:31: style: Variable 'gap_penalty_y' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo_po.c:237:3: warning: Uninitialized variable: best_x [uninitvar]
poaV2/align_lpo_po.c:124:3: note: Assuming condition is false
poaV2/align_lpo_po.c:237:3: note: Uninitialized variable: best_x
poaV2/align_lpo_po.c:237:3: warning: Uninitialized variable: best_y [uninitvar]
poaV2/align_lpo_po.c:124:3: note: Assuming condition is false
poaV2/align_lpo_po.c:237:3: note: Uninitialized variable: best_y
poaV2/align_lpo_po.c:99:42: style: Variable 'nfree_list' is assigned a value that is never used. [unreadVariable]
poaV2/align_lpo_po.c:99:56: style: Variable 'ilast_right' is assigned a value that is never used. [unreadVariable]
poaV2/align_lpo_po.c:138:13: style: Variable 'j_left' is assigned a value that is never used. [unreadVariable]
poaV2/align_lpo_po.c:100:38: style: Unused variable: my_matrix [unusedVariable]
poaV2/align_lpo_po2.c:41:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/align_lpo_po2.c:120:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/align_lpo_po2.c:227:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/align_lpo_po2.c:41:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po2.c:42:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po2.c:43:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po2.c:44:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po2.c:71:7: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po2.c:120:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po2.c:121:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po2.c:227:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po2.c:228:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po2.c:254:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po2.c:256:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po2.c:259:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po2.c:262:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po2.c:264:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po2.c:312:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po2.c:438:5: warning: %ld in format string (no. 2) requires 'long' but the argument type is 'signed int'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po2.c:438:5: warning: %ld in format string (no. 4) requires 'long' but the argument type is 'signed int'. [invalidPrintfArgType_sint]
poaV2/align_lpo_po2.c:185:9: style:inconclusive: Function 'align_lpo_po' argument 7 names different: declaration '<unnamed>' definition 'use_global_alignment'. [funcArgNamesDifferentUnnamed]
poaV2/align_lpo_po2.c:38:22: style: Variable 'src' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo_po2.c:39:20: style: Variable 'lnk' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo_po2.c:118:20: style: Variable 'left' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo_po2.c:200:54: style: Variable 'xl' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo_po2.c:200:59: style: Variable 'yl' can be declared as pointer to const [constVariablePointer]
poaV2/align_lpo_po2.c:233:5: warning: Uninitialized variable: next_gap_array [uninitvar]
poaV2/align_lpo_po2.c:227:3: note: Assuming condition is true
poaV2/align_lpo_po2.c:233:5: note: Uninitialized variable: next_gap_array
poaV2/align_lpo_po2.c:101:22: error: Uninitialized variable: node_type [legacyUninitvar]
poaV2/align_lpo_po2.c:102:28: error: Uninitialized variable: refs_from_right [legacyUninitvar]
poaV2/align_lpo_po2.c:97:3: error: Uninitialized variable: tmp [legacyUninitvar]
poaV2/align_lpo_po2.c:104:23: error: Uninitialized variable: left_links [legacyUninitvar]
poaV2/align_lpo_po2.c:34:10: style: Unused variable: j [unusedVariable]
poaV2/align_score.c:13:17: style: struct member 'LPOMove_T::x' is never used. [unusedStructMember]
poaV2/align_score.c:14:17: style: struct member 'LPOMove_T::y' is never used. [unusedStructMember]
poaV2/align_score.c:15:17: style: struct member 'LPOMove_T::is_aligned' is never used. [unusedStructMember]
poaV2/black_flag.c:33:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/black_flag.c:97:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIG_DFL [valueFlowBailoutIncompleteVar]
poaV2/black_flag.c:109:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/black_flag.c:109:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/black_flag.c:16:14: style: Parameter 'sourcefile' can be declared as const array [constParameter]
poaV2/black_flag.c:18:14: style: Parameter 'sourcefile_revision' can be declared as const array [constParameter]
poaV2/black_flag.c:21:9: style: Variable 'error_names' can be declared as const array [constVariable]
poaV2/black_flag.c:68:9: style: Variable 'crash_mode' can be declared as pointer to const [constVariablePointer]
poaV2/black_flag.c:104:42: style: Parameter 'arg' can be declared as const array [constParameter]
poaV2/buildup_lpo.c:112:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRAP [valueFlowBailoutIncompleteVar]
poaV2/buildup_lpo.c:146:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/buildup_lpo.c:233:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRAP [valueFlowBailoutIncompleteVar]
poaV2/buildup_lpo.c:327:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/buildup_lpo.c:445:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/buildup_lpo.c:146:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/buildup_lpo.c:327:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/buildup_lpo.c:330:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/buildup_lpo.c:353:2: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/buildup_lpo.c:374:2: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/buildup_lpo.c:394:2: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/buildup_lpo.c:445:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/buildup_lpo.c:446:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/buildup_lpo.c:447:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/buildup_lpo.c:448:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/buildup_lpo.c:538:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/buildup_lpo.c:333:12: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
poaV2/buildup_lpo.c:408:65: style:inconclusive: Function 'buildup_progressive_lpo' argument 2 names different: declaration 'seqs' definition 'all_seqs'. [funcArgNamesDifferent]
poaV2/lpo.h:98:66: note: Function 'buildup_progressive_lpo' argument 2 names different: declaration 'seqs' definition 'all_seqs'.
poaV2/buildup_lpo.c:408:65: note: Function 'buildup_progressive_lpo' argument 2 names different: declaration 'seqs' definition 'all_seqs'.
poaV2/buildup_lpo.c:416:44: style:inconclusive: Function 'buildup_progressive_lpo' argument 8 names different: declaration '<unnamed>' definition 'use_global_alignment'. [funcArgNamesDifferentUnnamed]
poaV2/buildup_lpo.c:417:16: style:inconclusive: Function 'buildup_progressive_lpo' argument 9 names different: declaration '<unnamed>' definition 'preserve_sequence_order'. [funcArgNamesDifferentUnnamed]
poaV2/buildup_lpo.c:568:41: style:inconclusive: Function 'buildup_pairwise_lpo' argument 6 names different: declaration '<unnamed>' definition 'use_global_alignment'. [funcArgNamesDifferentUnnamed]
poaV2/buildup_lpo.c:263:56: style: Parameter 'name' can be declared as const array [constParameter]
poaV2/buildup_lpo.c:412:17: style: Parameter 'score_file' can be declared as const array [constParameter]
poaV2/buildup_lpo.c:542:2: warning: Uninitialized variable: perm [uninitvar]
poaV2/buildup_lpo.c:538:5: note: Assuming condition is true
poaV2/buildup_lpo.c:542:2: note: Uninitialized variable: perm
poaV2/buildup_lpo.c:547:39: error: Uninitialized variable: perm [legacyUninitvar]
poaV2/buildup_lpo.c:144:10: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
poaV2/buildup_lpo.c:144:23: style: Unused variable: new_length [unusedVariable]
poaV2/buildup_lpo.c:244:8: style: Variable 'f' is assigned a value that is never used. [unreadVariable]
poaV2/buildup_lpo.c:419:11: style: Unused variable: k [unusedVariable]
poaV2/buildup_lpo.c:419:37: style: Variable 'min_counts' is assigned a value that is never used. [unreadVariable]
poaV2/buildup_lpo.c:570:18: style: Variable 'min_counts1' is assigned a value that is never used. [unreadVariable]
poaV2/buildup_lpo.c:571:18: style: Variable 'min_counts2' is assigned a value that is never used. [unreadVariable]
poaV2/create_seq.c:12:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQUENCE_NAME_MAX [valueFlowBailoutIncompleteVar]
poaV2/create_seq.c:29:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQUENCE_BUFFER_CHUNK [valueFlowBailoutIncompleteVar]
poaV2/create_seq.c:29:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/create_seq.c:22:38: style:inconclusive: Function 'create_seq' argument 2 names different: declaration 'seq' definition 'p_seq'. [funcArgNamesDifferent]
poaV2/seq_util.h:65:38: note: Function 'create_seq' argument 2 names different: declaration 'seq' definition 'p_seq'.
poaV2/create_seq.c:22:38: note: Function 'create_seq' argument 2 names different: declaration 'seq' definition 'p_seq'.
poaV2/create_seq.c:10:11: style: Parameter 'seq_name' can be declared as const array [constParameter]
poaV2/create_seq.c:10:27: style: Parameter 'seq_title' can be declared as const array [constParameter]
poaV2/fasta_format.c:52:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
poaV2/fasta_format.c:35:11: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
poaV2/fasta_format.c:79:35: style: Parameter 'name' can be declared as const array [constParameter]
poaV2/fasta_format.c:79:47: style: Parameter 'title' can be declared as const array [constParameter]
poaV2/fasta_format.c:79:60: style: Parameter 'seq' can be declared as const array [constParameter]
poaV2/heaviest_bundle.c:27:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/heaviest_bundle.c:90:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/heaviest_bundle.c:128:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/heaviest_bundle.c:168:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/heaviest_bundle.c:27:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/heaviest_bundle.c:28:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/heaviest_bundle.c:29:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/heaviest_bundle.c:67:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/heaviest_bundle.c:90:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/heaviest_bundle.c:22:20: style: Variable 'right' can be declared as pointer to const [constVariablePointer]
poaV2/heaviest_bundle.c:23:22: style: Variable 'source' can be declared as pointer to const [constVariablePointer]
poaV2/heaviest_bundle.c:88:22: style: Variable 'source' can be declared as pointer to const [constVariablePointer]
poaV2/heaviest_bundle.c:121:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
poaV2/heaviest_bundle.c:20:9: style: Unused variable: j [unusedVariable]
poaV2/heaviest_bundle.c:20:22: style: Unused variable: iright [unusedVariable]
poaV2/lpo.c:15:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/lpo.c:157:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/lpo.c:189:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/lpo.c:213:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/lpo.c:238:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/lpo.c:252:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/lpo.c:270:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/lpo.c:427:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/lpo.c:500:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/lpo.c:564:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/lpo.c:618:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/lpo.c:15:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo.c:157:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo.c:158:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo.c:159:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo.c:189:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo.c:213:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo.c:238:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo.c:252:7: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo.c:270:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo.c:271:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo.c:427:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo.c:500:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo.c:501:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo.c:502:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo.c:505:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo.c:564:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo.c:618:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo.c:619:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo.c:622:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo.c:81:22: style: Variable 'source' can be declared as pointer to const [constVariablePointer]
poaV2/lpo.c:151:22: style: Variable 'source' can be declared as pointer to const [constVariablePointer]
poaV2/lpo.c:179:13: style: Parameter 'name' can be declared as const array [constParameter]
poaV2/lpo.c:180:13: style: Parameter 'title' can be declared as const array [constParameter]
poaV2/lpo.c:246:66: style: Parameter 'old_s' can be declared as pointer to const [constParameterPointer]
poaV2/lpo.c:247:12: style: Parameter 'iseq_new' can be declared as const array [constParameter]
poaV2/lpo.c:261:56: style: Parameter 'perm' can be declared as pointer to const [constParameterPointer]
poaV2/lpo.c:312:20: style: Variable 'link' can be declared as pointer to const [constVariablePointer]
poaV2/lpo.c:275:5: warning: Uninitialized variable: map [uninitvar]
poaV2/lpo.c:270:3: note: Assuming condition is true
poaV2/lpo.c:275:5: note: Uninitialized variable: map
poaV2/lpo.c:275:14: warning: Uninitialized variable: invmap [uninitvar]
poaV2/lpo.c:271:3: note: Assuming condition is true
poaV2/lpo.c:275:14: note: Uninitialized variable: invmap
poaV2/lpo.c:303:3: error: Uninitialized variable: map [legacyUninitvar]
poaV2/lpo.c:304:3: error: Uninitialized variable: invmap [legacyUninitvar]
poaV2/lpo.c:377:32: style: Variable 'mismatch_length' is assigned a value that is never used. [unreadVariable]
poaV2/lpo.c:377:49: style: Variable 'identity_count' is assigned a value that is never used. [unreadVariable]
poaV2/lpo.c:377:71: style: Variable 'fission_break_point' is assigned a value that is never used. [unreadVariable]
poaV2/lpo.c:377:7: style: Unused variable: i [unusedVariable]
poaV2/lpo.c:738:7: style: Unused variable: i [unusedVariable]
poaV2/lpo.c:769:20: style: Unused variable: new_seq [unusedVariable]
poaV2/lpo_format.c:60:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/lpo_format.c:159:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/lpo_format.c:353:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/lpo_format.c:60:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo_format.c:71:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo_format.c:72:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo_format.c:73:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo_format.c:159:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo_format.c:170:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo_format.c:171:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo_format.c:172:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo_format.c:196:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo_format.c:197:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo_format.c:198:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo_format.c:229:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo_format.c:230:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo_format.c:231:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo_format.c:353:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo_format.c:354:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo_format.c:374:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/lpo_format.c:61:3: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
poaV2/lpo_format.c:62:3: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
poaV2/lpo_format.c:63:3: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
poaV2/lpo_format.c:82:9: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
poaV2/lpo_format.c:87:9: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
poaV2/lpo_format.c:160:3: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
poaV2/lpo_format.c:161:3: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
poaV2/lpo_format.c:162:3: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
poaV2/lpo_format.c:181:9: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
poaV2/lpo_format.c:186:9: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
poaV2/lpo_format.c:202:12: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
poaV2/lpo_format.c:514:2: style: Label 'done' is not used. [unusedLabel]
poaV2/lpo_format.c:143:50: style:inconclusive: Function 'read_lpo_select' argument 2 names different: declaration 'select_ifile' definition 'select_file'. [funcArgNamesDifferent]
poaV2/lpo.h:122:50: note: Function 'read_lpo_select' argument 2 names different: declaration 'select_ifile' definition 'select_file'.
poaV2/lpo_format.c:143:50: note: Function 'read_lpo_select' argument 2 names different: declaration 'select_ifile' definition 'select_file'.
poaV2/lpo_format.c:11:43: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
poaV2/lpo_format.c:12:31: style: Parameter 'score_matrix' can be declared as pointer to const [constParameterPointer]
poaV2/lpo_format.c:15:20: style: Variable 'link' can be declared as pointer to const [constVariablePointer]
poaV2/lpo_format.c:16:22: style: Variable 'source' can be declared as pointer to const [constVariablePointer]
poaV2/lpo_format.c:152:45: style: Variable 'source' can be declared as pointer to const [constVariablePointer]
poaV2/lpo_format.c:338:24: style: Parameter 'symbol' can be declared as const array [constParameter]
poaV2/lpo_format.c:344:22: style: Variable 'source' can be declared as pointer to const [constVariablePointer]
poaV2/lpo_format.c:342:9: style: Unused variable: j [unusedVariable]
poaV2/lpo_format.c:342:42: style: Unused variable: iprint [unusedVariable]
poaV2/lpo_format.c:464:12: style: Unused variable: ial [unusedVariable]
poaV2/lpo_format.c:464:54: style: Unused variable: ipos_local [unusedVariable]
poaV2/main.c:12:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALL_BUNDLES [valueFlowBailoutIncompleteVar]
poaV2/main.c:355:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USERR [valueFlowBailoutIncompleteVar]
poaV2/main.c:183:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/main.c:221:2: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/main.c:254:2: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/main.c:209:28: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
poaV2/main.c:363:7: error: Resource leak: po_file [resourceLeak]
poaV2/main.c:15:81: style: Variable 'al_name' can be declared as pointer to const [constVariablePointer]
poaV2/main.c:17:42: style: Variable 'frame_seq' can be declared as pointer to const [constVariablePointer]
poaV2/main.c:20:36: style: Variable 'fasta_out' can be declared as pointer to const [constVariablePointer]
poaV2/main.c:20:52: style: Variable 'po_out' can be declared as pointer to const [constVariablePointer]
poaV2/main.c:21:6: style: Variable 'seq_filename' can be declared as pointer to const [constVariablePointer]
poaV2/main.c:21:25: style: Variable 'frame_dna_filename' can be declared as pointer to const [constVariablePointer]
poaV2/main.c:22:6: style: Variable 'po_list_filename' can be declared as pointer to const [constVariablePointer]
poaV2/main.c:22:30: style: Variable 'hbmin' can be declared as pointer to const [constVariablePointer]
poaV2/main.c:22:42: style: Variable 'numeric_data' can be declared as pointer to const [constVariablePointer]
poaV2/main.c:22:61: style: Variable 'numeric_data_name' can be declared as pointer to const [constVariablePointer]
poaV2/main.c:23:6: style: Variable 'dna_to_aa' can be declared as pointer to const [constVariablePointer]
poaV2/main.c:23:44: style: Variable 'aafreq_file' can be declared as pointer to const [constVariablePointer]
poaV2/main.c:23:62: style: Variable 'termval_file' can be declared as pointer to const [constVariablePointer]
poaV2/main.c:24:6: style: Variable 'bold_seq_name' can be declared as pointer to const [constVariablePointer]
poaV2/main.c:32:9: style: Variable 'reference_seq_name' can be declared as pointer to const [constVariablePointer]
poaV2/main.c:32:41: style: Variable 'clustal_out' can be declared as pointer to const [constVariablePointer]
poaV2/main.c:345:54: style: Parameter 'po_filename' can be declared as pointer to const [constParameterPointer]
poaV2/main.c:345:73: style: Parameter 'subset_filename' can be declared as pointer to const [constParameterPointer]
poaV2/main.c:12:31: style: Variable 'nframe_seq' is assigned a value that is never used. [unreadVariable]
poaV2/main.c:12:44: style: Variable 'use_reverse_complement' is assigned a value that is never used. [unreadVariable]
poaV2/main.c:15:8: style: Unused variable: score_file [unusedVariable]
poaV2/main.c:15:24: style: Unused variable: seq_file [unusedVariable]
poaV2/main.c:15:81: style: Variable 'al_name' is assigned a value that is never used. [unreadVariable]
poaV2/main.c:17:42: style: Variable 'frame_seq' is assigned a value that is never used. [unreadVariable]
poaV2/main.c:21:25: style: Variable 'frame_dna_filename' is assigned a value that is never used. [unreadVariable]
poaV2/main.c:22:42: style: Variable 'numeric_data' is assigned a value that is never used. [unreadVariable]
poaV2/main.c:22:61: style: Variable 'numeric_data_name' is assigned a value that is never used. [unreadVariable]
poaV2/main.c:23:6: style: Variable 'dna_to_aa' is assigned a value that is never used. [unreadVariable]
poaV2/main.c:23:44: style: Variable 'aafreq_file' is assigned a value that is never used. [unreadVariable]
poaV2/main.c:23:62: style: Variable 'termval_file' is assigned a value that is never used. [unreadVariable]
poaV2/main.c:24:6: style: Variable 'bold_seq_name' is assigned a value that is never used. [unreadVariable]
poaV2/main.c:27:19: style: Variable 'count_sequence_errors' is assigned a value that is never used. [unreadVariable]
poaV2/main.c:27:43: style: Variable 'please_print_snps' is assigned a value that is never used. [unreadVariable]
poaV2/main.c:28:5: style: Variable 'report_consensus_seqs' is assigned a value that is never used. [unreadVariable]
poaV2/main.c:28:29: style: Variable 'report_major_allele' is assigned a value that is never used. [unreadVariable]
poaV2/main.c:29:7: style: Variable 'show_allele_evidence' is assigned a value that is never used. [unreadVariable]
poaV2/main.c:29:30: style: Variable 'please_collapse_lines' is assigned a value that is never used. [unreadVariable]
poaV2/main.c:30:50: style: Unused variable: please_report_similarity [unusedVariable]
poaV2/main.c:32:9: style: Variable 'reference_seq_name' is assigned a value that is never used. [unreadVariable]
poaV2/msa_format.c:95:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USERR [valueFlowBailoutIncompleteVar]
poaV2/msa_format.c:161:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USERR [valueFlowBailoutIncompleteVar]
poaV2/msa_format.c:241:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USERR [valueFlowBailoutIncompleteVar]
poaV2/msa_format.c:318:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/msa_format.c:485:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/msa_format.c:537:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable title [valueFlowBailoutIncompleteVar]
poaV2/msa_format.c:169:7: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:171:7: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:174:7: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:176:7: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:185:5: portability: %d in format string (no. 4) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:185:5: portability: %d in format string (no. 1) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:185:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:248:7: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:250:7: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:252:7: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:254:7: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:268:7: portability: %d in format string (no. 4) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:268:7: portability: %d in format string (no. 1) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:268:7: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:318:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:319:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:326:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:327:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:334:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:347:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:351:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:369:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:375:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:380:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:398:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:406:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:407:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:485:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/msa_format.c:160:9: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
poaV2/msa_format.c:240:11: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
poaV2/msa_format.c:261:7: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
poaV2/msa_format.c:491:26: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
poaV2/msa_format.c:185:5: style: Checking if unsigned expression 'aln_lengths[curr_seq]+strlen(aln)' is less than zero. [unsignedLessThanZero]
poaV2/msa_format.c:268:7: style: Checking if unsigned expression 'aln_lengths[curr_seq]+strlen(aln)' is less than zero. [unsignedLessThanZero]
poaV2/msa_format.c:122:36: style:inconclusive: Function 'read_clustal' argument 1 names different: declaration 'ifile' definition 'fp'. [funcArgNamesDifferent]
poaV2/msa_format.c:43:43: note: Function 'read_clustal' argument 1 names different: declaration 'ifile' definition 'fp'.
poaV2/msa_format.c:122:36: note: Function 'read_clustal' argument 1 names different: declaration 'ifile' definition 'fp'.
poaV2/msa_format.c:221:32: style:inconclusive: Function 'read_pir' argument 1 names different: declaration 'ifile' definition 'fp'. [funcArgNamesDifferent]
poaV2/msa_format.c:47:39: note: Function 'read_pir' argument 1 names different: declaration 'ifile' definition 'fp'.
poaV2/msa_format.c:221:32: note: Function 'read_pir' argument 1 names different: declaration 'ifile' definition 'fp'.
poaV2/msa_format.c:228:27: style: Variable 'keep_seq' can be declared as pointer to const [constVariablePointer]
poaV2/msa_format.c:304:104: style: Parameter 'aln_lengths' can be declared as pointer to const [constParameterPointer]
poaV2/msa_format.c:448:3: error: Uninitialized variable: column_ids [legacyUninitvar]
poaV2/msa_format.c:449:3: error: Uninitialized variable: res_ids [legacyUninitvar]
poaV2/msa_format.c:450:3: error: Uninitialized variable: consens_row [legacyUninitvar]
poaV2/msa_format.c:520:3: error: Uninitialized variable: keep_seq [legacyUninitvar]
poaV2/msa_format.c:126:10: style: Unused variable: j [unusedVariable]
poaV2/msa_format.c:225:10: style: Unused variable: j [unusedVariable]
poaV2/msa_format.c:228:27: style: Variable 'keep_seq' is assigned a value that is never used. [unreadVariable]
poaV2/msa_format.c:306:13: style: Unused variable: k [unusedVariable]
poaV2/numeric_data.c:27:5: error: There is an unknown macro here somewhere. Configuration is required. If LOOP is a macro then please configure it. [unknownMacro]
poaV2/remove_bundle.c:16:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/remove_bundle.c:59:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/remove_bundle.c:128:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/remove_bundle.c:16:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/remove_bundle.c:59:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/remove_bundle.c:128:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/remove_bundle.c:12:45: style: Parameter 'old_to_new' can be declared as const array [constParameter]
poaV2/seq_util.c:92:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUNCATE_GAP_LENGTH [valueFlowBailoutIncompleteVar]
poaV2/seq_util.c:170:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/seq_util.c:171:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/seq_util.c:10:8: style: Parameter 'seq' can be declared as const array [constParameter]
poaV2/seq_util.c:37:34: style: Parameter 'seq' can be declared as const array [constParameter]
poaV2/seq_util.c:38:22: style: Parameter 'symbols' can be declared as const array [constParameter]
poaV2/seq_util.c:63:8: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
poaV2/seq_util.c:63:25: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
poaV2/seq_util.c:82:28: style: Parameter 'filename' can be declared as const array [constParameter]
poaV2/seq_util.c:222:31: style: Parameter 'ifile' can be declared as pointer to const [constParameterPointer]
poaV2/seq_util.c:222:59: style: Parameter 'm' can be declared as pointer to const [constParameterPointer]
poaV2/seq_util.c:222:66: style: Parameter 'subset' can be declared as const array [constParameter]
poaV2/seq_util.c:253:36: style: Parameter 'symbol' can be declared as const array [constParameter]
poaV2/seq_util.c:85:19: style: Unused variable: dna_codes [unusedVariable]
poaV2/stringptr.c:30:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/stringptr.c:67:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
poaV2/stringptr.c:30:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/stringptr.c:40:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/stringptr.c:67:3: portability: %d in format string (no. 4) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/stringptr.c:67:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/stringptr.c:67:3: portability: %d in format string (no. 1) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
poaV2/stringptr.c:31:10: warning: Possible null pointer dereference: s2_temp [nullPointer]
poaV2/stringptr.c:21:44: note: Assignment 's2_temp=NULL', assigned value is 0
poaV2/stringptr.c:23:10: note: Assuming condition is false
poaV2/stringptr.c:30:3: note: Assuming condition is true
poaV2/stringptr.c:31:10: note: Null pointer dereference
poaV2/stringptr.c:67:3: style: Checking if unsigned expression '((strlen(s2)+1)+1)-((strlen(s2)+1)+1)%4096+4096' is less than zero. [unsignedLessThanZero]
poaV2/stringptr.c:21:9: style: Variable 'stringptr_cat_temp_p' can be declared as pointer to const [constVariablePointer]
diff:
head poaV2/align_lpo_po.c:92:9: style:inconclusive: Function 'align_lpo_po' argument 7 names different: declaration '<unnamed>' definition 'use_global_alignment'. [funcArgNamesDifferentUnnamed]
head poaV2/align_lpo_po2.c:185:9: style:inconclusive: Function 'align_lpo_po' argument 7 names different: declaration '<unnamed>' definition 'use_global_alignment'. [funcArgNamesDifferentUnnamed]
head poaV2/buildup_lpo.c:416:44: style:inconclusive: Function 'buildup_progressive_lpo' argument 8 names different: declaration '<unnamed>' definition 'use_global_alignment'. [funcArgNamesDifferentUnnamed]
head poaV2/buildup_lpo.c:417:16: style:inconclusive: Function 'buildup_progressive_lpo' argument 9 names different: declaration '<unnamed>' definition 'preserve_sequence_order'. [funcArgNamesDifferentUnnamed]
head poaV2/buildup_lpo.c:568:41: style:inconclusive: Function 'buildup_pairwise_lpo' argument 6 names different: declaration '<unnamed>' definition 'use_global_alignment'. [funcArgNamesDifferentUnnamed]


DONE