2024-04-21 00:59
ftp://ftp.de.debian.org/debian/pool/main/p/phast/phast_1.6+dfsg.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=pcre  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning -D__GNUC__ --platform=unix64 -j1
platform: Linux-5.15.0-105-generic-x86_64-with-glibc2.35
python: 3.10.12
client-version: 1.3.56
compiler: g++ (Ubuntu 12.3.0-1ubuntu1~22.04) 12.3.0
cppcheck: head 2.13.0
head-info: fb15ac6 (2024-04-20 19:16:41 +0200)
count: 1143 628
elapsed-time: 83.4 154.7
head-timing-info:

old-timing-info:

head results:
phast-1.6/src/dless/dless.c:40:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/dless/dless.c:43:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/dless/dless.c:226:17: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/dless/dlessP.c:54:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
phast-1.6/src/dless/dlessP.c:195:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nnodes [valueFlowBailoutIncompleteVar]
phast-1.6/src/dless/dlessP.c:319:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/dless/dlessP.c:402:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CONS [valueFlowBailoutIncompleteVar]
phast-1.6/src/dless/dlessP.c:58:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/dless/dlessP.c:315:23: style: Parameter 'htmldir' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/dless/dlessP.c:315:45: style: Parameter 'feat' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/dless/dlessP.c:316:37: style: Parameter 'subtree_root_name' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/dless/dlessP.c:316:64: style: Parameter 'id' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/dless/dlessP.c:320:18: style: Variable 's_cons' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/dless/dlessP.c:390:40: style: Parameter 'feat' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/dless/dlessP.c:391:38: style: Parameter 'subtree_root_name' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/dless/dlessP.c:391:65: style: Parameter 'id' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/dless/dlessP.c:394:18: style: Variable 's_cons' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/dless/phast_bd_phylo_hmm.c:46:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BDPhyloHmm [valueFlowBailoutIncompleteVar]
phast-1.6/src/dless/phast_bd_phylo_hmm.c:181:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tree [valueFlowBailoutIncompleteVar]
phast-1.6/src/dless/phast_bd_phylo_hmm.c:214:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tree [valueFlowBailoutIncompleteVar]
phast-1.6/src/dless/phast_bd_phylo_hmm.c:303:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/dless/phast_bd_phylo_hmm.c:370:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/dless/phast_bd_phylo_hmm.c:181:13: style: Variable 'tree' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/exoniphy/exoniphy.c:49:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
phast-1.6/src/exoniphy/exoniphy.c:465:12: style: Local variable 'tmpstr' shadows outer variable [shadowVariable]
phast-1.6/src/exoniphy/exoniphy.c:106:8: note: Shadowed declaration
phast-1.6/src/exoniphy/exoniphy.c:465:12: note: Shadow variable
phast-1.6/src/exoniphy/exoniphy.c:278:11: style: Variable 'default_hmm' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/base/phast_complex_matrix.c:22:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Zmatrix [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_complex_matrix.c:109:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_complex_matrix.c:118:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_complex_matrix.c:237:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_complex_matrix.c:105:26: style: Parameter 'm' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_complex_vector.c:20:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Zvector [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_complex_vector.c:54:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_complex_vector.c:61:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_complex_vector.c:116:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_complex_vector.c:51:26: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_eigen.c:67:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_eigen.c:204:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_eigen.c:160:11: style: Statements following 'return' will never be executed. [unreachableCode]
phast-1.6/src/lib/base/phast_hashtable.c:27:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Hashtable [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_hashtable.c:43:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Hashtable [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_hashtable.c:42:9: style: Variable 'key' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/base/phast_hashtable.c:74:17: style: Parameter 'key1ptr' can be declared as pointer to const. However it seems that 'equal' is a callback function, if 'key1ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
phast-1.6/src/lib/base/phast_hashtable.c:118:61: note: You might need to cast the function pointer here
phast-1.6/src/lib/base/phast_hashtable.c:74:17: note: Parameter 'key1ptr' can be declared as pointer to const
phast-1.6/src/lib/base/phast_hashtable.c:74:32: style: Parameter 'key2' can be declared as pointer to const. However it seems that 'equal' is a callback function, if 'key2' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
phast-1.6/src/lib/base/phast_hashtable.c:118:61: note: You might need to cast the function pointer here
phast-1.6/src/lib/base/phast_hashtable.c:74:32: note: Parameter 'key2' can be declared as pointer to const
phast-1.6/src/lib/base/phast_list_of_lists.c:9:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ListOfLists [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_list_of_lists.c:52:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LIST_LIST [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_list_of_lists.c:63:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_LIST [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_list_of_lists.c:78:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LIST_LIST [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_list_of_lists.c:92:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LIST_LIST [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_list_of_lists.c:103:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_LIST [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_list_of_lists.c:109:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_LIST [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_list_of_lists.c:116:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CHAR_LIST [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_list_of_lists.c:132:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_LIST [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_list_of_lists.c:147:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CHAR_LIST [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_list_of_lists.c:171:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CHAR_LIST [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_list_of_lists.c:193:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_LOG_LIKELIHOOD [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_list_of_lists.c:281:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_NULL_FRAME [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_list_of_lists.c:335:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_PTR_LIST [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_list_of_lists.c:342:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MSA_PTR_LIST [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_list_of_lists.c:349:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MS_PTR_LIST [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_list_of_lists.c:367:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LIST_LIST [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_list_of_lists.c:417:61: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_lists.c:32:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable List [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_lists.c:279:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ASCENDING [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_lists.c:283:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ASCENDING [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_lists.c:303:31: style: Parameter 'l' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_markov_matrix.c:31:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MarkovMatrix [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_markov_matrix.c:78:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DISCRETE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_markov_matrix.c:142:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_markov_matrix.c:568:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REAL_NUM [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_markov_matrix.c:601:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMPLEX_NUM [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_markov_matrix.c:622:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMPLEX_NUM [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_markov_matrix.c:696:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_markov_matrix.c:717:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMPLEX_NUM [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_markov_matrix.c:730:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DISCRETE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_markov_matrix.c:282:7: style: Condition 'do_balancing' is always false [knownConditionTrueFalse]
phast-1.6/src/lib/base/phast_markov_matrix.c:259:20: note: Assignment 'do_balancing=0', assigned value is 0
phast-1.6/src/lib/base/phast_markov_matrix.c:282:7: note: Condition 'do_balancing' is always false
phast-1.6/src/lib/base/phast_markov_matrix.c:438:12: style: Local variable 'sum' shadows outer variable [shadowVariable]
phast-1.6/src/lib/base/phast_markov_matrix.c:252:27: note: Shadowed declaration
phast-1.6/src/lib/base/phast_markov_matrix.c:438:12: note: Shadow variable
phast-1.6/src/lib/base/phast_markov_matrix.c:248:10: style: Variable 'b' can be declared as const array [constVariable]
phast-1.6/src/lib/base/phast_markov_matrix.c:253:26: style: Variable 'mvals' can be declared as const array [constVariable]
phast-1.6/src/lib/base/phast_markov_matrix.c:584:29: style: Parameter 'labels' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_matrix.c:21:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Matrix [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_matrix.c:122:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_matrix.c:213:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nrows [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_matrix.c:267:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_matrix.c:119:24: style: Parameter 'm' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_matrix.c:121:9: style: Variable 'formatstr' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/base/phast_matrix.c:210:70: style: Parameter 'coef' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_matrix.c:328:23: style: Parameter 'A' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_matrix.c:328:34: style: Parameter 'B' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_matrix.c:345:48: style: Parameter 'arr' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_memory_handler.c:635:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_cat_no [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_memory_handler.c:176:9: style: Variable 'old_mem_list' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/base/phast_memory_handler.c:222:30: style: Parameter 'ptr0' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_memory_handler.c:234:44: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_memory_handler.c:234:56: style: Parameter 'function' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_memory_handler.c:255:39: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_memory_handler.c:343:31: style: Parameter 'F' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_memory_handler.c:361:33: style: Parameter 'F' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_memory_handler.c:16:10: style: struct member 'protected_object_struct::function' is never used. [unusedStructMember]
phast-1.6/src/lib/base/phast_memory_handler.c:633:12: style: Variable 'len' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/base/phast_misc.c:205:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_misc.c:281:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_misc.c:299:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_misc.c:311:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_misc.c:322:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_misc.c:368:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_misc.c:528:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_misc.c:698:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable d [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_misc.c:890:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_misc.c:1063:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_misc.c:1216:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFERSIZE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_misc.c:120:31: style: Parameter 'alphabet' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_misc.c:165:23: style: Parameter 'tuple' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_misc.c:165:35: style: Parameter 'inv_alph' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_misc.c:181:26: style: Parameter 'alphabet' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_misc.c:623:29: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_misc.c:655:24: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_misc.c:679:23: style: Variable 'newname' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/base/phast_misc.c:827:36: style: Parameter 'alpha' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_misc.c:952:17: style: Variable 'a' can be declared as const array [constVariable]
phast-1.6/src/lib/base/phast_misc.c:961:17: style: Variable 'b' can be declared as const array [constVariable]
phast-1.6/src/lib/base/phast_misc.c:969:17: style: Variable 'c' can be declared as const array [constVariable]
phast-1.6/src/lib/base/phast_misc.c:978:17: style: Variable 'd' can be declared as const array [constVariable]
phast-1.6/src/lib/base/phast_misc.c:1088:37: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_misc.c:1088:48: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_misc.c:1099:41: style: Parameter 'start_time' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_misc.c:1108:29: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_misc.c:1151:32: style: Parameter 'inv_states' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_misc.c:1255:28: style: Parameter 'vect' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_misc.c:1260:31: style: Parameter 'vect' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_numerical_opt.c:1137:56: debug: Function::addArguments found argument 'x' with varid 0. [varid0]
phast-1.6/src/lib/base/phast_numerical_opt.c:98:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OPT_LOW_PREC [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_numerical_opt.c:131:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OPT_DERIV_FORWARD [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_numerical_opt.c:189:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OPT_NO_BOUND [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_numerical_opt.c:228:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OPT_NO_BOUND [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_numerical_opt.c:246:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OPT_NO_BOUND [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_numerical_opt.c:403:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OPT_DERIV_FORWARD [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_numerical_opt.c:859:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OPT_HIGH_PREC [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_numerical_opt.c:1145:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_numerical_opt.c:1288:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OPT_HIGH_PREC [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_numerical_opt.c:1323:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_numerical_opt.c:1355:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_numerical_opt.c:774:17: style: Condition 'already_failed' is always false [knownConditionTrueFalse]
phast-1.6/src/lib/base/phast_numerical_opt.c:767:11: note: Assuming that condition 'already_failed' is not redundant
phast-1.6/src/lib/base/phast_numerical_opt.c:774:17: note: Condition 'already_failed' is always false
phast-1.6/src/lib/base/phast_numerical_opt.c:1316:17: style: Variable '*final_lambda' is reassigned a value before the old one has been used. [redundantAssignment]
phast-1.6/src/lib/base/phast_numerical_opt.c:1297:21: note: *final_lambda is assigned
phast-1.6/src/lib/base/phast_numerical_opt.c:1316:17: note: *final_lambda is overwritten
phast-1.6/src/lib/base/phast_numerical_opt.c:1316:17: style: Variable '*final_lambda' is reassigned a value before the old one has been used. [redundantAssignment]
phast-1.6/src/lib/base/phast_numerical_opt.c:1307:21: note: *final_lambda is assigned
phast-1.6/src/lib/base/phast_numerical_opt.c:1316:17: note: *final_lambda is overwritten
phast-1.6/src/lib/base/phast_numerical_opt.c:1226:28: style: Variable 'fx2eps' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/base/phast_prob_matrix.c:218:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_prob_matrix.c:260:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nrows [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_prob_matrix.c:358:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nrows [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_prob_vector.c:93:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UPPER [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_prob_vector.c:112:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UPPER [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_prob_vector.c:229:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_prob_vector.c:262:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_prob_vector.c:388:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LOWER [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_prob_vector.c:107:43: style: Parameter 'x_0' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_prob_vector.c:402:29: style: Parameter 'arr' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_stringsplus.c:22:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable String [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_stringsplus.c:36:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_stringsplus.c:42:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_stringsplus.c:93:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_stringsplus.c:143:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFERSIZE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_stringsplus.c:184:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFERSIZE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_stringsplus.c:239:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFERSIZE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_stringsplus.c:264:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFERSIZE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_stringsplus.c:350:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NCHARS [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_stringsplus.c:397:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NCHARS [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_stringsplus.c:505:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_stringsplus.c:646:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_stringsplus.c:660:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_stringsplus.c:313:31: style: Array index 'j' is used before limits check. [arrayIndexThenCheck]
phast-1.6/src/lib/base/phast_stringsplus.c:63:36: style: Parameter 'suffix' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_stringsplus.c:135:37: style: Parameter 'substr' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_stringsplus.c:136:9: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/base/phast_stringsplus.c:287:25: style: Parameter 's1' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_stringsplus.c:287:37: style: Parameter 's2' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_stringsplus.c:291:33: style: Parameter 's1' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_stringsplus.c:295:32: style: Parameter 's1' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_stringsplus.c:295:44: style: Parameter 's2' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_stringsplus.c:299:40: style: Parameter 's1' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_stringsplus.c:426:24: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_stringsplus.c:434:24: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_stringsplus.c:442:29: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_stringsplus.c:442:40: style: Parameter 'substr' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_stringsplus.c:447:37: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_stringsplus.c:453:27: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_stringsplus.c:453:38: style: Parameter 'substr' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_stringsplus.c:459:35: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_stringsplus.c:144:29: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/base/phast_stringsplus.c:144:44: style: Variable 'buffer_used' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/base/phast_stringsplus.c:185:29: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/base/phast_stringsplus.c:185:44: style: Variable 'buffer_used' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/base/phast_vector.c:17:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Vector [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/base/phast_vector.c:23:36: style: Parameter 'array' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_vector.c:71:24: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_vector.c:78:26: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/base/phast_vector.c:78:44: style: Parameter 'formatstr' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/feature/phast_bed.c:22:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_bed.c:200:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_bed.c:84:21: style: Redundant initialization for 'strand'. The initialized value is overwritten before it is read. [redundantInitialization]
phast-1.6/src/lib/feature/phast_bed.c:47:19: note: strand is initialized
phast-1.6/src/lib/feature/phast_bed.c:84:21: note: strand is overwritten
phast-1.6/src/lib/feature/phast_category_map.c:36:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_category_map.c:305:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start_cat_no [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_category_map.c:354:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable feature_types [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_category_map.c:361:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable feature_types [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_category_map.c:381:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start_cat_no [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_category_map.c:391:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CategoryMap [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_category_map.c:432:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_category_map.c:465:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BACKGD_CAT_NAME [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_category_map.c:478:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_category_map.c:535:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_cat_no [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_category_map.c:556:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CategoryRange [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_category_map.c:619:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PHAST_VERSION [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_category_map.c:710:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_category_map.c:756:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Unspooler [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_category_map.c:808:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UnspoolNode [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_category_map.c:859:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_category_map.c:865:11: style: The if condition is the same as the previous if condition [duplicateCondition]
phast-1.6/src/lib/feature/phast_category_map.c:858:11: note: First condition
phast-1.6/src/lib/feature/phast_category_map.c:865:11: note: Second condition
phast-1.6/src/lib/feature/phast_category_map.c:103:14: style: Condition 'cm==NULL' is always false [knownConditionTrueFalse]
phast-1.6/src/lib/feature/phast_category_map.c:195:20: warning: Possible null pointer dereference: cm [nullPointer]
phast-1.6/src/lib/feature/phast_category_map.c:27:21: note: Assignment 'cm=NULL', assigned value is 0
phast-1.6/src/lib/feature/phast_category_map.c:47:34: note: Assuming condition is false
phast-1.6/src/lib/feature/phast_category_map.c:195:20: note: Null pointer dereference
phast-1.6/src/lib/feature/phast_category_map.c:631:11: style: Local variable 'cat' shadows outer variable [shadowVariable]
phast-1.6/src/lib/feature/phast_category_map.c:618:20: note: Shadowed declaration
phast-1.6/src/lib/feature/phast_category_map.c:631:11: note: Shadow variable
phast-1.6/src/lib/feature/phast_category_map.c:224:15: style: Variable 's' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/feature/phast_category_map.c:612:51: style: Parameter 'path' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/feature/phast_category_map.c:613:46: style: Parameter 'path_to_cat' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/feature/phast_category_map.c:616:35: style: Parameter 'grouptag' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/feature/phast_category_map.c:616:52: style: Parameter 'idpref' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/feature/phast_genepred.c:19:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_LONG_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_genepred.c:170:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_LONG_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:34:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:207:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_Feature [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:236:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_Feature [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:293:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_Set [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:308:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_SET_START_SIZE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:341:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_DEFAULT_VERSION [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:387:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_VERSION_TAG [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:410:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_NULL_FRAME [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:540:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:708:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_FeatureGroup [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:753:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_FeatureGroup [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:791:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_FeatureGroup [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:827:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_FeatureGroup [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:877:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:950:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:1068:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_START_TYPE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:1121:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_NULL_FRAME [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:1151:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_LONG_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:1177:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:1213:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:1276:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_EXON_TYPE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:1308:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:1426:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:1437:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:1518:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_NULL_FRAME [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:1790:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_NULL_FRAME [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:1844:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_NULL_FRAME [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:1959:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_NULL_FRAME [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_gff.c:346:8: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
phast-1.6/src/lib/feature/phast_gff.c:1701:8: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
phast-1.6/src/lib/feature/phast_gff.c:1698:6: note: outer condition: overlappingFragments
phast-1.6/src/lib/feature/phast_gff.c:1701:8: note: identical inner condition: overlappingFragments
phast-1.6/src/lib/feature/phast_gff.c:157:14: style: Variable 'strand' is reassigned a value before the old one has been used. [redundantAssignment]
phast-1.6/src/lib/feature/phast_gff.c:130:14: note: strand is assigned
phast-1.6/src/lib/feature/phast_gff.c:157:14: note: strand is overwritten
phast-1.6/src/lib/feature/phast_gff.c:168:13: style: Variable 'frame' is reassigned a value before the old one has been used. [redundantAssignment]
phast-1.6/src/lib/feature/phast_gff.c:131:13: note: frame is assigned
phast-1.6/src/lib/feature/phast_gff.c:168:13: note: frame is overwritten
phast-1.6/src/lib/feature/phast_gff.c:836:23: style: Local variable 'group' shadows outer variable [shadowVariable]
phast-1.6/src/lib/feature/phast_gff.c:819:21: note: Shadowed declaration
phast-1.6/src/lib/feature/phast_gff.c:836:23: note: Shadow variable
phast-1.6/src/lib/feature/phast_gff.c:404:43: style: Parameter 'feat' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/feature/phast_gff.c:567:18: style: Variable 'feat' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/feature/phast_gff.c:607:16: style: Variable 'feat1' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/feature/phast_gff.c:608:16: style: Variable 'feat2' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/feature/phast_gff.c:897:18: style: Variable 'lastfeat' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/feature/phast_gff.c:957:20: style: Variable 'f' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/feature/phast_gff.c:1062:22: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/feature/phast_gff.c:1062:37: style: Variable 'stop' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/feature/phast_gff.c:1284:20: style: Variable 'exon2' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/feature/phast_gff.c:1401:48: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/feature/phast_gff.c:1813:26: style: Variable 'regionFeat' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/feature/phast_gff.c:1813:39: style: Variable 'currFeat' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/feature/phast_gff.c:1903:39: style: Parameter 'maxlen' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/feature/phast_gff.c:1904:11: style: Parameter 'splitFromRight' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/feature/phast_gff.c:1946:39: style: Parameter 'seqname' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/feature/phast_gff.c:1947:13: style: Parameter 'scores' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/feature/phast_gff.c:1948:29: style: Parameter 'src' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/feature/phast_gff.c:1948:40: style: Parameter 'featureName' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/feature/phast_wig.c:32:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_LONG_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_wig.c:104:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_LONG_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/feature/phast_wig.c:154:16: style: Variable 'feat' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/hmm/phast_em.c:128:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGINFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/hmm/phast_hmm.c:43:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HMM [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/hmm/phast_hmm.c:158:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/hmm/phast_hmm.c:186:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRANSITION_MATRIX_TAG [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/hmm/phast_hmm.c:211:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable END_STATE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/hmm/phast_hmm.c:291:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VITERBI [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/hmm/phast_hmm.c:338:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FORWARD [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/hmm/phast_hmm.c:358:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BACKWARD [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/hmm/phast_hmm.c:392:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/hmm/phast_hmm.c:433:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VITERBI [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/hmm/phast_hmm.c:471:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable END_STATE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/hmm/phast_hmm.c:494:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGINFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/hmm/phast_hmm.c:735:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGINFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/hmm/phast_hmm.c:783:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DISCRETE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/hmm/phast_hmm.c:842:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BEGIN_STATE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/hmm/phast_hmm.c:979:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BEGIN_STATE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/hmm/phast_hmm.c:1156:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable END_STATE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/hmm/phast_hmm.c:1222:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGINFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/hmm/phast_hmm.c:589:18: style: Condition 'beg_pseudocounts==NULL' is always false [knownConditionTrueFalse]
phast-1.6/src/lib/hmm/phast_hmm.c:158:10: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
phast-1.6/src/lib/hmm/phast_hmm.c:51:18: warning: Possible null pointer dereference: mm [nullPointer]
phast-1.6/src/lib/hmm/phast_hmm.c:155:20: note: Assignment 'mm=NULL', assigned value is 0
phast-1.6/src/lib/hmm/phast_hmm.c:158:32: note: Assuming condition is false
phast-1.6/src/lib/hmm/phast_hmm.c:181:18: note: Calling function 'hmm_new', 1st argument 'mm' value is 0
phast-1.6/src/lib/hmm/phast_hmm.c:51:18: note: Null pointer dereference
phast-1.6/src/lib/hmm/phast_hmm.c:59:38: warning: Possible null pointer dereference: mm [nullPointer]
phast-1.6/src/lib/hmm/phast_hmm.c:155:20: note: Assignment 'mm=NULL', assigned value is 0
phast-1.6/src/lib/hmm/phast_hmm.c:158:32: note: Assuming condition is false
phast-1.6/src/lib/hmm/phast_hmm.c:181:18: note: Calling function 'hmm_new', 1st argument 'mm' value is 0
phast-1.6/src/lib/hmm/phast_hmm.c:59:38: note: Null pointer dereference
phast-1.6/src/lib/hmm/phast_hmm.c:60:21: warning: Possible null pointer dereference: mm [nullPointer]
phast-1.6/src/lib/hmm/phast_hmm.c:155:20: note: Assignment 'mm=NULL', assigned value is 0
phast-1.6/src/lib/hmm/phast_hmm.c:158:32: note: Assuming condition is false
phast-1.6/src/lib/hmm/phast_hmm.c:181:18: note: Calling function 'hmm_new', 1st argument 'mm' value is 0
phast-1.6/src/lib/hmm/phast_hmm.c:60:21: note: Null pointer dereference
phast-1.6/src/lib/hmm/phast_hmm.c:721:29: style: Parameter 'hmm' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/hmm/phast_hmm.c:838:33: style: Parameter 'path' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/motif/phast_motif.c:56:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_motif.c:123:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_motif.c:258:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_motif.c:288:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MTF_EPSILON [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_motif.c:584:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGINFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_motif.c:749:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGINFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_motif.c:910:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DESCENDING [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_motif.c:964:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_motif.c:1091:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DESCENDING [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_motif.c:1115:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SeqSet [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_motif.c:1141:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nseqs [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_motif.c:1204:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Motif [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_motif.c:1355:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tree [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_motif.c:1496:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tree [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_motif.c:1676:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_motif.c:1741:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGINFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_motif.c:1772:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable names [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_motif.c:448:32: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
phast-1.6/src/lib/motif/phast_motif.c:450:25: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
phast-1.6/src/lib/motif/phast_motif.c:452:47: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
phast-1.6/src/lib/motif/phast_motif.c:453:9: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
phast-1.6/src/lib/motif/phast_motif.c:790:38: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
phast-1.6/src/lib/motif/phast_motif.c:1079:29: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
phast-1.6/src/lib/motif/phast_motif.c:1081:22: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
phast-1.6/src/lib/motif/phast_motif.c:1083:44: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
phast-1.6/src/lib/motif/phast_motif.c:1084:11: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
phast-1.6/src/lib/motif/phast_motif.c:372:8: style: Variable 'sample_lens' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/motif/phast_motif.c:480:8: style: Variable 'sample_lens' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/motif/phast_motif.c:662:58: style: Parameter 'm' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/motif/phast_motif.c:937:33: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/motif/phast_motif.c:959:38: style: Parameter 'consensus' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/motif/phast_motif.c:960:35: style: Parameter 'inv_alph' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/motif/phast_motif.c:1004:62: style: Parameter 'has_motif' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/motif/phast_motif.c:1014:8: style: Variable 'sample_lens' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/motif/phast_motif.c:1372:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/motif/phast_motif.c:1418:12: style: Variable 'msa' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/motif/phast_motif.c:1460:8: style: Variable 'inv_alphabet' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/motif/phast_motif.c:1520:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/motif/phast_motif.c:1613:12: style: Variable 'msa' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/motif/phast_motif.c:1711:26: style: Parameter 'has_motif' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/motif/phast_motif.c:1715:8: style: Variable 'sample_lens' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/motif/phast_tfbs.c:44:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MS [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_tfbs.c:111:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OUTPUT_LINE_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_tfbs.c:136:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_tfbs.c:211:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_tfbs.c:220:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_tfbs.c:443:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_tfbs.c:472:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/motif/phast_tfbs.c:613:19: error: Invalid log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
phast-1.6/src/lib/motif/phast_tfbs.c:651:27: error: Invalid log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
phast-1.6/src/lib/motif/phast_tfbs.c:652:34: error: Invalid log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
phast-1.6/src/lib/motif/phast_tfbs.c:613:15: warning: Passing value 0 to log() leads to implementation-defined result. [wrongmathcall]
phast-1.6/src/lib/motif/phast_tfbs.c:651:23: warning: Passing value 0 to log() leads to implementation-defined result. [wrongmathcall]
phast-1.6/src/lib/motif/phast_tfbs.c:652:30: warning: Passing value 0 to log() leads to implementation-defined result. [wrongmathcall]
phast-1.6/src/lib/motif/phast_tfbs.c:90:28: style: Parameter 'ms' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/motif/phast_tfbs.c:104:34: style: Parameter 'ms' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/motif/phast_tfbs.c:206:31: style: Parameter 'ms' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/motif/phast_tfbs.c:450:8: style: Variable 'bases' can be declared as const array [constVariable]
phast-1.6/src/lib/motif/phast_tfbs.c:496:21: style: Parameter 'previousBases' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/motif/phast_tfbs.c:584:26: style: Parameter 'seqData' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/motif/phast_tfbs.c:621:192: style: Parameter 'strand' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/motif/phast_tfbs.c:623:25: style: Variable 'PWMprob' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/motif/phast_tfbs.c:623:43: style: Variable 'ReversePWMprob' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/msa/phast_local_alignment.c:37:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LocalPwAlignment [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_local_alignment.c:46:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_local_alignment.c:205:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GaplessAlignment [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_local_alignment.c:218:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AlignmentBlock [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_local_alignment.c:284:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_local_alignment.c:441:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ADJUSTRIGHT [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_local_alignment.c:328:12: warning: Possible null pointer dereference: lga [nullPointer]
phast-1.6/src/lib/msa/phast_local_alignment.c:270:27: note: Assignment 'lga=NULL', assigned value is 0
phast-1.6/src/lib/msa/phast_local_alignment.c:275:17: note: Assuming condition is false
phast-1.6/src/lib/msa/phast_local_alignment.c:328:12: note: Null pointer dereference
phast-1.6/src/lib/msa/phast_local_alignment.c:270:21: style: Variable 'lga' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_local_alignment.c:373:19: style: Variable 'last_ab' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_local_alignment.c:374:21: style: Variable 'last_ga' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_local_alignment.c:494:31: style: Variable 'ga' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_local_alignment.c:521:31: style: Variable 'ga' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_local_alignment.c:433:8: style: Variable 'q1' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/msa/phast_maf.c:74:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_STRIP [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf.c:558:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_STRIP [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf.c:858:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_VERY_LONG_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf.c:989:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_VERY_LONG_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf.c:1114:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_VERY_LONG_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf.c:1219:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_VERY_LONG_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf.c:1390:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf.c:1101:20: style: Variable 'gp1' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_maf.c:1102:20: style: Variable 'gp2' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_maf.c:1223:11: style: Variable 's' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_maf.c:1338:27: style: Variable 'nextgp' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_maf.c:219:52: style: Variable 'gapsum_block' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/msa/phast_maf.c:236:17: style: Variable 'gapsum_block' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/msa/phast_maf.c:243:15: style: Variable 'gapsum_block' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/msa/phast_maf_block.c:19:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MafBlock [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf_block.c:30:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MafSubBlock [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf_block.c:41:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MafSubBlock [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf_block.c:71:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MafBlock [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf_block.c:101:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf_block.c:177:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf_block.c:225:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf_block.c:275:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf_block.c:667:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf_block.c:678:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf_block.c:692:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf_block.c:840:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lineType [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf_block.c:864:81: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_maf_block.c:244:73: warning:inconclusive: Logical conjunction always evaluates to false: sub->quality->chars[i] < '0' && sub->quality->chars[i] > '9'. [incorrectLogicOperator]
phast-1.6/src/lib/msa/phast_maf_block.c:331:16: style: Variable 'sub' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_maf_block.c:468:9: style: Variable 'firstseq' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_maf_block.c:543:50: style: Parameter 'keep' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/msa/phast_maf_block.c:545:22: style: Variable 'testSub' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_maf_block.c:662:55: style: Parameter 'argv' can be declared as const array [constParameter]
phast-1.6/src/lib/msa/phast_maf_block.c:682:16: style: Variable 'sub' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_maf_block.c:782:16: style: Variable 'sub' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_maf_block.c:853:16: style: Variable 'refblock' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_maf_block.c:856:20: style: Variable 'prevf' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_maf_block.c:904:9: style: Variable 'refseq' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_maf_block.c:904:23: style: Variable 'refseqName' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_msa.c:63:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MSA [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:108:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:202:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAF [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:258:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:354:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SS [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:454:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_cat_no [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:593:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STRIP_ANY_GAPS [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:634:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:744:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable msa_coord_map [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:828:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable msa_coord_map [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:863:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BACKGD_CAT_NAME [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:1036:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:1137:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable idx_offset [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:1176:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:1208:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:1490:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STRIP_ALL_GAPS [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:1530:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:1694:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:1736:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:1749:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STRIP_ALL_GAPS [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:1803:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:1867:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:1925:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:2028:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:2211:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:2293:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:2475:83: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:2541:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPM [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:2553:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FASTA [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:2563:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:2581:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:2715:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:2763:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:2798:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:2844:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:2872:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:2988:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_msa.c:2547:12: style: Expression is always false because 'else if' condition matches previous condition at line 2544. [multiCondition]
phast-1.6/src/lib/msa/phast_msa.c:151:16: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
phast-1.6/src/lib/msa/phast_msa.c:61:70: style: Parameter 'alphabet' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/msa/phast_msa.c:930:26: style: Parameter 'msa' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/msa/phast_msa.c:1476:47: style: Parameter 'label' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/msa/phast_msa.c:2292:13: style: Variable 's' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_msa.c:2805:41: style: Parameter 'newalph' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/msa/phast_msa.c:2868:33: style: Parameter 'msa' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/msa/phast_msa.c:2924:37: style: Parameter 'delete_cols' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/msa/phast_msa.c:3007:51: style: Parameter 'frame' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/msa/phast_msa.c:1537:15: style: Variable 'sum' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/msa/phast_multi_msa.c:65:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_multi_msa.c:131:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Multi_MSA [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_sufficient_stats.c:256:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MSA_SS [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_sufficient_stats.c:291:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_sufficient_stats.c:344:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PooledMSA [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_sufficient_stats.c:446:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_sufficient_stats.c:557:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_sufficient_stats.c:615:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_sufficient_stats.c:672:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_sufficient_stats.c:935:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_sufficient_stats.c:1049:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_sufficient_stats.c:1248:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_sufficient_stats.c:1277:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_sufficient_stats.c:1298:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_sufficient_stats.c:1351:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_sufficient_stats.c:1398:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/msa/phast_sufficient_stats.c:609:11: style: Variable 'ss' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/msa/phast_sufficient_stats.c:1151:37: style: Parameter 'new_to_old' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/msa/phast_sufficient_stats.c:1092:9: style: Variable 'midpt' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/phylo/phast_bgc_hmm.c:63:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_bgc_hmm.c:178:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bgchmm_struct [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_bgc_hmm.c:224:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MSA [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_bgc_hmm.c:520:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_bgc_hmm.c:568:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_bgc_hmm.c:612:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_bgc_hmm.c:746:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGINFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_bgc_hmm.c:448:19: style: Condition 'post_probs_f!=NULL' is always true [knownConditionTrueFalse]
phast-1.6/src/lib/phylo/phast_bgc_hmm.c:36:16: style: Parameter 'foregd_branch' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_bgc_hmm.c:503:46: style: Parameter 'bgc_informative' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_bgc_hmm.c:560:30: style: Parameter 'path' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_cons.c:25:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable phastCons_struct [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_cons.c:108:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_cons.c:721:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EmData [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_cons.c:830:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_IMAG_EPS [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_cons.c:879:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_cons.c:929:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable estimate_ratemat [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_cons.c:1022:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scale [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_cons.c:1054:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARAMETERIC [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_cons.c:1071:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARAMETERIC [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_cons.c:1150:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable JC69 [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_cons.c:541:18: style: Local variable 'j' shadows outer variable [shadowVariable]
phast-1.6/src/lib/phylo/phast_cons.c:107:10: note: Shadowed declaration
phast-1.6/src/lib/phylo/phast_cons.c:541:18: note: Shadow variable
phast-1.6/src/lib/phylo/phast_cons.c:600:18: style: Local variable 'j' shadows outer variable [shadowVariable]
phast-1.6/src/lib/phylo/phast_cons.c:107:10: note: Shadowed declaration
phast-1.6/src/lib/phylo/phast_cons.c:600:18: note: Shadow variable
phast-1.6/src/lib/phylo/phast_cons.c:277:12: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_dgamma.c:31:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable 0.453642210148e [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_dgamma.c:142:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable 0.5e [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:146:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dparent [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:224:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dparent [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:293:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REAL_NUM [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:379:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:556:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:676:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBTREE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:690:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBTREE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:708:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALL [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:723:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALL [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:756:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALL [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:837:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBTREE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:975:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NNEUT [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:1065:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:1117:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ColFitData [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:1311:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dparent [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:1343:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:1472:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FimGrid [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:1541:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GRIDSIZE1 [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:1600:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_column.c:457:56: style: Parameter 'gradient' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_fit_column.c:735:15: style: Variable 'd' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_fit_column.c:753:51: style: Variable 'this_scale' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/phylo/phast_fit_em.c:57:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGINFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_em.c:443:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Complex [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_em.c:921:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Complex [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_em.c:169:17: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_fit_em.c:339:60: style: Parameter 'params' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_fit_feature.c:92:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBTREE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_feature.c:106:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBTREE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_feature.c:124:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALL [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_feature.c:152:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALL [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_feature.c:236:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBTREE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_feature.c:386:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NNEUT [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_feature.c:477:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_feature.c:562:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dparent [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_feature.c:582:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FeatFitData [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_feature.c:609:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_feature.c:645:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_feature.c:654:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_fit_feature.c:30:73: style: Parameter 'feat' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_fit_feature.c:598:70: style: Parameter 'feat' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_fit_feature.c:634:56: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_fit_feature.c:652:60: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_fit_feature.c:58:50: error: Uninitialized variable: d2 [uninitvar]
phast-1.6/src/lib/phylo/phast_fit_feature.c:149:51: style: Variable 'this_scale' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/phylo/phast_fit_feature.c:416:15: style: Variable 'fim' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/phylo/phast_indel_history.c:28:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IndelHistory [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_history.c:54:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CompactIndelHistory [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_history.c:87:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEL [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_history.c:127:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEL [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_history.c:205:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_history.c:250:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_history.c:304:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_history.c:384:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_history.c:480:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_history.c:693:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_history.c:430:19: style: Condition '!has_bases' is always true [knownConditionTrueFalse]
phast-1.6/src/lib/phylo/phast_indel_history.c:429:9: note: Assuming that condition '!has_bases' is not redundant
phast-1.6/src/lib/phylo/phast_indel_history.c:430:19: note: Condition '!has_bases' is always true
phast-1.6/src/lib/phylo/phast_indel_history.c:464:22: warning: Either the condition 'n==NULL' is redundant or there is possible null pointer dereference: n. [nullPointerRedundantCheck]
phast-1.6/src/lib/phylo/phast_indel_history.c:462:11: note: Assuming that condition 'n==NULL' is not redundant
phast-1.6/src/lib/phylo/phast_indel_history.c:464:22: note: Null pointer dereference
phast-1.6/src/lib/phylo/phast_indel_history.c:79:13: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_indel_history.c:86:14: style: Variable 'indel' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_indel_history.c:117:13: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_indel_history.c:199:67: style: Parameter 'msa_name' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_indel_history.c:199:83: style: Parameter 'prog_name' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_indel_history.c:201:13: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_indel_history.c:214:14: style: Variable 'indel' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_indel_history.c:378:13: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_indel_mod.c:21:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BranchIndelModel [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_mod.c:33:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IndelModel [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_mod.c:48:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IndelModel [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_mod.c:100:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CHILDINS [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_mod.c:150:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_mod.c:171:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SKIP [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_mod.c:237:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NINDEL_STATES [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_mod.c:252:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SKIP [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_mod.c:292:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IndelSuffStats [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_mod.c:310:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable trans_counts [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_mod.c:354:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable trans_counts [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_mod.c:427:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SKIP [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_mod.c:481:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IndelSuffStats [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_indel_mod.c:37:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_indel_mod.c:52:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_indel_mod.c:128:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_indel_mod.c:134:37: style: Parameter 'alpha' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_indel_mod.c:134:52: style: Parameter 'beta' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_indel_mod.c:134:66: style: Parameter 'tau' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_indel_mod.c:141:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_indel_mod.c:148:37: style: Parameter 'ih' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_indel_mod.c:235:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_indel_mod.c:296:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_indel_mod.c:350:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_indel_mod.c:424:53: style: Parameter 'categories' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_indel_mod.c:485:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_phylo_fit.c:42:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable phyloFit_struct [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_phylo_fit.c:227:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_phylo_fit.c:669:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_phylo_fit.c:1218:33: style: The if condition is the same as the previous if condition [duplicateCondition]
phast-1.6/src/lib/phylo/phast_phylo_fit.c:1215:33: note: First condition
phast-1.6/src/lib/phylo/phast_phylo_fit.c:1218:33: note: Second condition
phast-1.6/src/lib/phylo/phast_phylo_fit.c:1244:6: style: Local variable 'i' shadows outer variable [shadowVariable]
phast-1.6/src/lib/phylo/phast_phylo_fit.c:666:7: note: Shadowed declaration
phast-1.6/src/lib/phylo/phast_phylo_fit.c:1244:6: note: Shadow variable
phast-1.6/src/lib/phylo/phast_phylo_fit.c:1244:9: style: Local variable 'j' shadows outer variable [shadowVariable]
phast-1.6/src/lib/phylo/phast_phylo_fit.c:666:10: note: Shadowed declaration
phast-1.6/src/lib/phylo/phast_phylo_fit.c:1244:9: note: Shadow variable
phast-1.6/src/lib/phylo/phast_phylo_fit.c:135:13: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_phylo_fit.c:176:28: style: Parameter 'msa' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_phylo_fit.c:230:13: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_phylo_fit.c:629:60: style: Parameter 'gc' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_phylo_fit.c:767:15: style: Variable 'rl' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_phylo_fit.c:800:12: style: Variable 'node' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_phylo_fit.c:805:9: style: Variable 'node' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/phylo/phast_phylo_fit.c:1244:17: style: Variable 'total' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/phylo/phast_phylo_p.c:31:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable phyloP_struct [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_phylo_p.c:77:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_SCALE_ONLY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_phylo_p.c:200:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SPH [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_phylo_p.c:273:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:135:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LOWER [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:333:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LOWER [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:445:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable post_mean [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:521:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable post_mean_left [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:597:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:675:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:832:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CHAR_LIST [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:864:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:262:112: warning: Either the condition 'mod_fname!=NULL' is redundant or there is possible null pointer dereference: mod_fname. [nullPointerRedundantCheck]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:263:19: note: Assuming that condition 'mod_fname!=NULL' is not redundant
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:262:112: note: Null pointer dereference
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:45:56: style: Parameter 'mod_fname' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:77:43: style: Parameter 'mod_fname' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:77:60: style: Parameter 'msa_fname' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:117:35: style: Parameter 'mod_fname' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:117:52: style: Parameter 'msa_fname' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:179:14: style: Parameter 'mod_fname' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:229:66: style: Parameter 'mod_fname' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:230:34: style: Parameter 'msa_fname' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:293:58: style: Parameter 'mod_fname' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:294:12: style: Parameter 'msa_fname' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:586:49: style: Parameter 'vals' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:586:61: style: Parameter 'chrom' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:636:28: style: Parameter 'pval' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:651:46: style: Parameter 'header' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:651:60: style: Parameter 'chrom' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_phylo_p_print.c:858:60: style: Parameter 'vals' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_subst_distrib.c:46:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_subst_distrib.c:86:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable JumpProcess [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_subst_distrib.c:244:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_subst_distrib.c:299:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_subst_distrib.c:440:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable col_likelihood_wrapper_1d [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_subst_distrib.c:501:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_subst_distrib.c:679:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_subst_distrib.c:877:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable p_value_stats [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_subst_distrib.c:1040:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable p_value_joint_stats [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_subst_distrib.c:1317:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_subst_distrib.c:133:15: style: Local variable 'n' shadows outer variable [shadowVariable]
phast-1.6/src/lib/phylo/phast_subst_distrib.c:87:13: note: Shadowed declaration
phast-1.6/src/lib/phylo/phast_subst_distrib.c:133:15: note: Shadow variable
phast-1.6/src/lib/phylo/phast_subst_distrib.c:292:12: style: Local variable 'c' shadows outer variable [shadowVariable]
phast-1.6/src/lib/phylo/phast_subst_distrib.c:267:31: note: Shadowed declaration
phast-1.6/src/lib/phylo/phast_subst_distrib.c:292:12: note: Shadow variable
phast-1.6/src/lib/phylo/phast_subst_distrib.c:673:12: style: Local variable 'c' shadows outer variable [shadowVariable]
phast-1.6/src/lib/phylo/phast_subst_distrib.c:647:31: note: Shadowed declaration
phast-1.6/src/lib/phylo/phast_subst_distrib.c:673:12: note: Shadow variable
phast-1.6/src/lib/phylo/phast_subst_distrib.c:133:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_subst_distrib.c:873:16: style: Variable 'f' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_subst_distrib.c:1031:16: style: Variable 'f' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_subst_distrib.c:679:47: error: Uninitialized variable: c [legacyUninitvar]
phast-1.6/src/lib/phylo/phast_subst_mods.c:101:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNDEF_MOD [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_subst_mods.c:261:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNREST [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_subst_mods.c:267:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HKY_CODON [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_subst_mods.c:278:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R2 [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_subst_mods.c:358:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable F81 [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_subst_mods.c:2565:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RATEMAT_STR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_subst_mods.c:2773:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMPLEX_NUM [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_subst_mods.c:2806:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HKY85 [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_subst_mods.c:2816:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HKY85 [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_subst_mods.c:1695:58: style:inconclusive: Function 'tm_init_mat_REV' argument 3 names different: declaration 'nbranches' definition 'parm_idx'. [funcArgNamesDifferent]
phast-1.6/src/lib/phylo/phast_subst_mods.c:43:58: note: Function 'tm_init_mat_REV' argument 3 names different: declaration 'nbranches' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:1695:58: note: Function 'tm_init_mat_REV' argument 3 names different: declaration 'nbranches' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:1714:60: style:inconclusive: Function 'tm_init_mat_SSREV' argument 3 names different: declaration 'nbranches' definition 'parm_idx'. [funcArgNamesDifferent]
phast-1.6/src/lib/phylo/phast_subst_mods.c:45:60: note: Function 'tm_init_mat_SSREV' argument 3 names different: declaration 'nbranches' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:1714:60: note: Function 'tm_init_mat_SSREV' argument 3 names different: declaration 'nbranches' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:1745:61: style:inconclusive: Function 'tm_init_mat_UNREST' argument 3 names different: declaration 'nbranches' definition 'parm_idx'. [funcArgNamesDifferent]
phast-1.6/src/lib/phylo/phast_subst_mods.c:47:61: note: Function 'tm_init_mat_UNREST' argument 3 names different: declaration 'nbranches' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:1745:61: note: Function 'tm_init_mat_UNREST' argument 3 names different: declaration 'nbranches' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:1764:57: style:inconclusive: Function 'tm_init_mat_R2' argument 3 names different: declaration 'start_idx' definition 'parm_idx'. [funcArgNamesDifferent]
phast-1.6/src/lib/phylo/phast_subst_mods.c:50:25: note: Function 'tm_init_mat_R2' argument 3 names different: declaration 'start_idx' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:1764:57: note: Function 'tm_init_mat_R2' argument 3 names different: declaration 'start_idx' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:1789:31: style:inconclusive: Function 'tm_init_mat_R2S' argument 3 names different: declaration 'start_idx' definition 'parm_idx'. [funcArgNamesDifferent]
phast-1.6/src/lib/phylo/phast_subst_mods.c:54:26: note: Function 'tm_init_mat_R2S' argument 3 names different: declaration 'start_idx' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:1789:31: note: Function 'tm_init_mat_R2S' argument 3 names different: declaration 'start_idx' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:1845:30: style:inconclusive: Function 'tm_init_mat_U2' argument 3 names different: declaration 'start_idx' definition 'parm_idx'. [funcArgNamesDifferent]
phast-1.6/src/lib/phylo/phast_subst_mods.c:52:25: note: Function 'tm_init_mat_U2' argument 3 names different: declaration 'start_idx' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:1845:30: note: Function 'tm_init_mat_U2' argument 3 names different: declaration 'start_idx' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:1872:34: style:inconclusive: Function 'tm_init_mat_U2S' argument 3 names different: declaration 'start_idx' definition 'parm_idx'. [funcArgNamesDifferent]
phast-1.6/src/lib/phylo/phast_subst_mods.c:56:26: note: Function 'tm_init_mat_U2S' argument 3 names different: declaration 'start_idx' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:1872:34: note: Function 'tm_init_mat_U2S' argument 3 names different: declaration 'start_idx' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:1931:57: style:inconclusive: Function 'tm_init_mat_R3' argument 3 names different: declaration 'start_idx' definition 'parm_idx'. [funcArgNamesDifferent]
phast-1.6/src/lib/phylo/phast_subst_mods.c:58:25: note: Function 'tm_init_mat_R3' argument 3 names different: declaration 'start_idx' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:1931:57: note: Function 'tm_init_mat_R3' argument 3 names different: declaration 'start_idx' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:1960:58: style:inconclusive: Function 'tm_init_mat_R3S' argument 3 names different: declaration 'start_idx' definition 'parm_idx'. [funcArgNamesDifferent]
phast-1.6/src/lib/phylo/phast_subst_mods.c:60:26: note: Function 'tm_init_mat_R3S' argument 3 names different: declaration 'start_idx' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:1960:58: note: Function 'tm_init_mat_R3S' argument 3 names different: declaration 'start_idx' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:2029:25: style:inconclusive: Function 'tm_init_mat_U3' argument 3 names different: declaration 'start_idx' definition 'parm_idx'. [funcArgNamesDifferent]
phast-1.6/src/lib/phylo/phast_subst_mods.c:62:25: note: Function 'tm_init_mat_U3' argument 3 names different: declaration 'start_idx' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:2029:25: note: Function 'tm_init_mat_U3' argument 3 names different: declaration 'start_idx' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:2062:26: style:inconclusive: Function 'tm_init_mat_U3S' argument 3 names different: declaration 'start_idx' definition 'parm_idx'. [funcArgNamesDifferent]
phast-1.6/src/lib/phylo/phast_subst_mods.c:64:26: note: Function 'tm_init_mat_U3S' argument 3 names different: declaration 'start_idx' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:2062:26: note: Function 'tm_init_mat_U3S' argument 3 names different: declaration 'start_idx' definition 'parm_idx'.
phast-1.6/src/lib/phylo/phast_subst_mods.c:2516:9: style: Variable 'states' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_subst_mods.c:2537:9: style: Variable 'states' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_subst_mods.c:2653:50: style: Parameter 'states' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_subst_mods.c:1716:18: style: Variable 'compi' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/phylo/phast_subst_mods.c:2144:13: style: Variable 'val' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/phylo/phast_subst_mods.c:2146:31: style: Variable 'val' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/phylo/phast_tree_likelihoods.c:126:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_likelihoods.c:560:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGINFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_likelihoods.c:617:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TreePosteriors [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_likelihoods.c:893:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_likelihoods.c:106:116: style: Condition 'col_scores==NULL' is always false [knownConditionTrueFalse]
phast-1.6/src/lib/phylo/phast_tree_likelihoods.c:209:22: style: Variable 'iupac_prob' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_tree_likelihoods.c:842:38: style: Parameter 'alphabet' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_tree_likelihoods.c:886:36: style: Parameter 'tuple' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_tree_likelihoods.c:886:48: style: Parameter 'inv_alph' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_tree_likelihoods.c:886:63: style: Parameter 'is_missing' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_tree_likelihoods.c:604:33: style: Variable 'retval' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/phylo/phast_tree_model.c:63:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TreeModel [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:256:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMPLEX_NUM [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:314:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNDEF_MOD [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:368:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:612:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_LOG_LIKELIHOOD [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:718:98: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:848:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:1003:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_SCALE_ONLY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:1093:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_SCALE_ONLY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:1228:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable JC69 [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:1259:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEFAULT_ALPHABET [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:1304:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable order [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:1435:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:1540:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:1750:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_SCALE_ONLY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:1890:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:1923:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:1996:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_BRANCHLENS_NONE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:2088:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable categories [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:2226:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_BRANCHLENS_CLOCK [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:2685:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_BRANCHLENS_CLOCK [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:2936:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_BRANCHLENS_CLOCK [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:3026:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_SCALE_ONLY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:3242:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_BRANCHLENS_CLOCK [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:3369:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:3384:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_BRANCHLENS_CLOCK [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:3492:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AA_ALPHABET [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:3607:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_BRANCHLENS_CLOCK [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:3654:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:3750:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:3763:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AltSubstMod [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:3945:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:4164:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_SCALE_ONLY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_tree_model.c:382:10: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
phast-1.6/src/lib/phylo/phast_tree_model.c:522:19: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
phast-1.6/src/lib/phylo/phast_tree_model.c:919:24: warning:inconclusive: Possible null pointer dereference: s2 [nullPointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:911:15: note: Assignment 's2=NULL', assigned value is 0
phast-1.6/src/lib/phylo/phast_tree_model.c:912:10: note: Assuming condition is false
phast-1.6/src/lib/phylo/phast_tree_model.c:919:24: note: Null pointer dereference
phast-1.6/src/lib/phylo/phast_tree_model.c:3772:22: style: Variable 'am->separate_model' is reassigned a value before the old one has been used. [redundantAssignment]
phast-1.6/src/lib/phylo/phast_tree_model.c:3767:22: note: am->separate_model is assigned
phast-1.6/src/lib/phylo/phast_tree_model.c:3772:22: note: am->separate_model is overwritten
phast-1.6/src/lib/phylo/phast_tree_model.c:232:11: style: Local variable 'j' shadows outer variable [shadowVariable]
phast-1.6/src/lib/phylo/phast_tree_model.c:194:10: note: Shadowed declaration
phast-1.6/src/lib/phylo/phast_tree_model.c:232:11: note: Shadow variable
phast-1.6/src/lib/phylo/phast_tree_model.c:896:9: style: Local variable 'j' shadows outer variable [shadowVariable]
phast-1.6/src/lib/phylo/phast_tree_model.c:811:10: note: Shadowed declaration
phast-1.6/src/lib/phylo/phast_tree_model.c:896:9: note: Shadow variable
phast-1.6/src/lib/phylo/phast_tree_model.c:976:9: style: Local variable 'j' shadows outer variable [shadowVariable]
phast-1.6/src/lib/phylo/phast_tree_model.c:811:10: note: Shadowed declaration
phast-1.6/src/lib/phylo/phast_tree_model.c:976:9: note: Shadow variable
phast-1.6/src/lib/phylo/phast_tree_model.c:2249:18: style: Local variable 'altmod' shadows outer variable [shadowVariable]
phast-1.6/src/lib/phylo/phast_tree_model.c:2214:16: note: Shadowed declaration
phast-1.6/src/lib/phylo/phast_tree_model.c:2249:18: note: Shadow variable
phast-1.6/src/lib/phylo/phast_tree_model.c:2250:20: style: Local variable 'tempmod' shadows outer variable [shadowVariable]
phast-1.6/src/lib/phylo/phast_tree_model.c:2212:18: note: Shadowed declaration
phast-1.6/src/lib/phylo/phast_tree_model.c:2250:20: note: Shadow variable
phast-1.6/src/lib/phylo/phast_tree_model.c:334:15: style: Variable 'altmod' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:762:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:807:25: style: Variable 'tempmod' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:975:15: style: Variable 'node' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:1038:17: style: Variable 'altmod' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:1367:18: style: Variable 'altmod' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:1391:17: style: Variable 'l' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:1392:17: style: Variable 'r' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:2002:17: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:2347:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:2886:13: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:3558:18: style: Variable 'altmod' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:3599:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:3753:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:3854:52: style: Parameter 'node' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:3914:32: style: Parameter 'backgd_sel_param' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:3915:15: style: Parameter 'foregd_sel_param' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:3915:38: style: Parameter 'have_bgc' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:3916:18: style: Parameter 'init_sel_param' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:3917:15: style: Parameter 'sel_param_opt' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:4072:29: style: Parameter 'initWeights' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo/phast_tree_model.c:1333:27: warning: Expression 'nseqs' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion]
phast-1.6/src/lib/phylo/phast_tree_model.c:1316:12: note: Assignment 'nseqs=-1', assigned value is -1
phast-1.6/src/lib/phylo/phast_tree_model.c:1317:17: note: Assuming condition is false
phast-1.6/src/lib/phylo/phast_tree_model.c:1333:27: note: Negative value is converted to an unsigned value
phast-1.6/src/lib/phylo/phast_tree_model.c:1334:26: warning:inconclusive: Expression 'nseqs' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion]
phast-1.6/src/lib/phylo/phast_tree_model.c:1316:12: note: Assignment 'nseqs=-1', assigned value is -1
phast-1.6/src/lib/phylo/phast_tree_model.c:1317:17: note: Assuming condition is false
phast-1.6/src/lib/phylo/phast_tree_model.c:1334:26: note: Negative value is converted to an unsigned value
phast-1.6/src/lib/phylo/phast_trees.c:42:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_VERY_LONG_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_trees.c:63:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_trees.c:205:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TreeNode [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_trees.c:249:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_trees.c:1010:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_trees.c:1144:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_trees.c:1281:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_trees.c:1314:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_trees.c:1580:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo/phast_trees.c:1004:15: style: Local variable 'n' shadows outer variable [shadowVariable]
phast-1.6/src/lib/phylo/phast_trees.c:982:13: note: Shadowed declaration
phast-1.6/src/lib/phylo/phast_trees.c:1004:15: note: Shadow variable
phast-1.6/src/lib/phylo/phast_trees.c:1528:15: style: Local variable 'root_lchild' shadows outer variable [shadowVariable]
phast-1.6/src/lib/phylo/phast_trees.c:1433:26: note: Shadowed declaration
phast-1.6/src/lib/phylo/phast_trees.c:1528:15: note: Shadow variable
phast-1.6/src/lib/phylo/phast_trees.c:778:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_trees.c:884:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_trees.c:915:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_trees.c:1122:11: style: Variable 'inSub' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_trees.c:1404:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_trees.c:1583:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo/phast_trees.c:788:22: warning: Expression '-3' has a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion]
phast-1.6/src/lib/phylo_hmm/phast_gap_patterns.c:37:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GapPatternMap [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_gap_patterns.c:218:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_gap_patterns.c:380:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_PATTERN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_gap_patterns.c:412:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GP_BASE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_gap_patterns.c:443:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_gap_patterns.c:476:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMPLEX_PATTERN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_gap_patterns.c:418:15: style: Local variable 'n' shadows outer variable [shadowVariable]
phast-1.6/src/lib/phylo_hmm/phast_gap_patterns.c:394:13: note: Shadowed declaration
phast-1.6/src/lib/phylo_hmm/phast_gap_patterns.c:418:15: note: Shadow variable
phast-1.6/src/lib/phylo_hmm/phast_gap_patterns.c:165:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo_hmm/phast_gap_patterns.c:379:45: style: Parameter 'gpm' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo_hmm/phast_gap_patterns.c:394:17: style: Variable 'leaf' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/phylo_hmm/phast_gap_patterns.c:438:42: style: Parameter 'pattern' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:67:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PhyloHmm [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:238:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:322:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MISSING_DATA [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:578:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:837:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1041:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARAMETERIC [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1070:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1087:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable order [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1145:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EmData [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1182:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tree [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1206:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARAMETERIC [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1290:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INSERTION_PATTERN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1322:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INSERTION_PATTERN [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1375:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARAMETERIC [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1404:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IndelEstimData [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1189:17: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/phast_rph_util.c:14:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/phast_rph_util.c:20:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/phast_rph_util.c:60:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INTSXP [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/phast_rph_util.c:126:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_bgc_hmm.c:50:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_gff.c:86:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STRSXP [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_gff.c:213:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_gff.c:244:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_NULL_FRAME [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_gff.c:321:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INTSXP [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_gff.c:340:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INTSXP [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_gff.c:460:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_gff.c:546:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_gff.c:676:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_gff.c:244:44: style: Variable 'frameVec' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_gff.c:245:11: style: Variable 'scoreVec' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_gff.c:312:16: style: Variable 'f' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_gff.c:331:16: style: Variable 'f' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_gff.c:349:16: style: Variable 'f' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_gff.c:365:16: style: Variable 'f' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_gff.c:381:16: style: Variable 'f' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_gff.c:397:16: style: Variable 'f' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_gff.c:457:45: error: Uninitialized variable: lol [uninitvar]
phast-1.6/src/lib/rphast/rph_hmm.c:81:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_hmm.c:101:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_hmm.c:161:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_list_of_lists.c:12:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_list_of_lists.c:12:42: style: Variable 'tempvec' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/rphast/rph_msa.c:70:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_msa.c:171:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_NULL_FRAME [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_msa.c:313:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_msa.c:511:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LGLSXP [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_msa.c:529:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_msa.c:580:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_msa.c:596:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INTSXP [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_msa.c:619:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_msa.c:630:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_msa.c:672:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_msa.c:734:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_msa.c:777:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_msa.c:841:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_msa.c:957:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_msa.c:1041:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_msa.c:1123:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_msa.c:1160:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_Set [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_msa.c:1189:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_msa.c:1256:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_msa.c:823:3: warning: Either the condition 'subMsa==NULL' is redundant or there is possible null pointer dereference: subMsa. [nullPointerRedundantCheck]
phast-1.6/src/lib/rphast/rph_msa.c:824:14: note: Assuming that condition 'subMsa==NULL' is not redundant
phast-1.6/src/lib/rphast/rph_msa.c:823:3: note: Null pointer dereference
phast-1.6/src/lib/rphast/rph_msa.c:120:8: style: Variable 'msa' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_msa.c:604:8: style: Variable 'msa' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_msa.c:650:8: style: Variable 'msa' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_msa.c:665:8: style: Variable 'rows' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_msa.c:665:20: style: Variable 'cols' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_msa.c:725:14: style: Variable 'rows' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_msa.c:725:26: style: Variable 'cols' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_msa.c:1158:25: style: Variable 'spec' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_phastCons.c:67:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable use_conditionals [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_phastCons.c:57:11: style: Variable 'intp' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_phastCons.c:58:11: style: Variable 'doublep' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_phyloFit.c:63:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_phyloP.c:60:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_phylo_hmm.c:106:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MISSING_DATA [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_phylo_hmm.c:86:8: style: Variable 'intp' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_subst_mods.c:43:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNDEF_MOD [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_subst_mods.c:52:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tfbs.c:65:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tfbs.c:159:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tfbs.c:180:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tfbs.c:271:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tfbs.c:388:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tfbs.c:401:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tfbs.c:418:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tfbs.c:491:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tfbs.c:505:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tfbs.c:580:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VECSXP [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tfbs.c:687:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VECSXP [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tfbs.c:827:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tfbs.c:861:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tfbs.c:877:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tfbs.c:631:27: error: Invalid log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
phast-1.6/src/lib/rphast/rph_tfbs.c:632:34: error: Invalid log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
phast-1.6/src/lib/rphast/rph_tfbs.c:631:23: warning: Passing value 0 to log() leads to implementation-defined result. [wrongmathcall]
phast-1.6/src/lib/rphast/rph_tfbs.c:632:30: warning: Passing value 0 to log() leads to implementation-defined result. [wrongmathcall]
phast-1.6/src/lib/rphast/rph_tfbs.c:209:7: style: Variable 'inputMS' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_tfbs.c:266:8: style: Variable 'rows' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_tfbs.c:522:7: style: Variable 'ms' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_tfbs.c:383:21: style: Variable 'nextCutAt' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/rphast/rph_tfbs.c:574:25: style: Variable 'PWMprob' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/rphast/rph_tfbs.c:574:43: style: Variable 'ReversePWMprob' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/rphast/rph_tree_model.c:77:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:99:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:117:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:153:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:174:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:217:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:231:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:284:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_LOG_LIKELIHOOD [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:368:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:384:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:400:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:429:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:536:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:552:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:567:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:581:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:598:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:637:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CONTINUOUS [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:652:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:671:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:701:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:734:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CONTINUOUS [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:758:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CONTINUOUS [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:778:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_tree_model.c:494:16: warning: Either the condition 'n==NULL' is redundant or there is possible null pointer dereference: n. [nullPointerRedundantCheck]
phast-1.6/src/lib/rphast/rph_tree_model.c:492:11: note: Assuming that condition 'n==NULL' is not redundant
phast-1.6/src/lib/rphast/rph_tree_model.c:494:16: note: Null pointer dereference
phast-1.6/src/lib/rphast/rph_tree_model.c:720:12: style: Redundant initialization for 'newfreqs'. The initialized value is overwritten before it is read. [redundantInitialization]
phast-1.6/src/lib/rphast/rph_tree_model.c:715:20: note: newfreqs is initialized
phast-1.6/src/lib/rphast/rph_tree_model.c:720:12: note: newfreqs is overwritten
phast-1.6/src/lib/rphast/rph_tree_model.c:143:16: style: Variable 'altmod' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_tree_model.c:164:16: style: Variable 'altmod' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_tree_model.c:269:14: style: Variable 'tm' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_tree_model.c:281:14: style: Variable 'tm' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_tree_model.c:294:14: style: Variable 'tm' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_tree_model.c:308:14: style: Variable 'tm' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_tree_model.c:324:14: style: Variable 'tm' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_tree_model.c:339:14: style: Variable 'tm' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_tree_model.c:350:14: style: Variable 'tm' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_tree_model.c:395:14: style: Variable 'tm' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_tree_model.c:491:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_trees.c:53:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_trees.c:186:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_trees.c:244:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_trees.c:345:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NA_STRING [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_trees.c:474:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
phast-1.6/src/lib/rphast/rph_trees.c:91:13: style: Variable 'tr' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_trees.c:257:18: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_trees.c:354:40: style: Variable 'node' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/lib/rphast/rph_trees.c:53:11: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phast-1.6/src/lib/rphast/rph_trees.c:44:13: style: Variable 'pos' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/rphast/rph_trees.c:44:40: style: Variable 'numparen' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/lib/rphast/rph_wig.c:43:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/phastCons/phastCons.c:74:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/phastCons/phastCons.c:320:33: error: Using pointer to local variable 'tmp' that is out of scope. [invalidLifetime]
phast-1.6/src/phastCons/phastCons.c:311:20: note: Array decayed to pointer here.
phast-1.6/src/phastCons/phastCons.c:283:10: note: Variable created here.
phast-1.6/src/phastCons/phastCons.c:320:33: note: Using pointer to local variable 'tmp' that is out of scope.
phast-1.6/src/phastCons/phastCons.c:27:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/phastMotif/phastMotif.c:141:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
phast-1.6/src/phastMotif/phastMotif.c:26:18: style: Parameter 'prog' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/phastOdds/phastOdds.c:33:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/phastOdds/phastOdds.c:47:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/phastOdds/phastOdds.c:253:20: style: Variable 'f' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/phyloBoot/phyloBoot.c:27:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/phyloBoot/phyloBoot.c:112:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FASTA [valueFlowBailoutIncompleteVar]
phast-1.6/src/phyloBoot/phyloBoot.c:208:15: style: Local variable 'F' shadows outer variable [shadowVariable]
phast-1.6/src/phyloBoot/phyloBoot.c:123:15: note: Shadowed declaration
phast-1.6/src/phyloBoot/phyloBoot.c:208:15: note: Shadow variable
phast-1.6/src/phyloBoot/phyloBoot.c:51:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/phyloBoot/phyloBoot.c:119:9: style: Variable 'dump_mods_root' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/phyloBoot/phyloBoot.c:119:33: style: Variable 'dump_msas_root' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/phyloBoot/phyloBoot.c:141:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/phyloBoot/phyloBoot.c:401:19: style: Variable 'sum' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/phyloBoot/phyloBoot.c:402:51: style: Variable 'sum' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/phyloFit/phyloFit.c:35:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
phast-1.6/src/phyloP/phyloP.c:19:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
phast-1.6/src/prequel/pbsDecode.c:33:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/prequel/pbsDecode.c:24:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/prequel/pbsEncode.c:26:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/prequel/pbsEncode.c:28:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/prequel/pbsScoreMatrix.c:41:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phast-1.6/src/prequel/pbsScoreMatrix.c:27:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/prequel/pbsTrain.c:25:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/prequel/pbsTrain.c:133:39: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
phast-1.6/src/prequel/pbsTrain.c:40:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/prequel/phast_pbs_code.c:19:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PbsCode [valueFlowBailoutIncompleteVar]
phast-1.6/src/prequel/phast_pbs_code.c:50:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PbsCode [valueFlowBailoutIncompleteVar]
phast-1.6/src/prequel/phast_pbs_code.c:92:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/prequel/phast_pbs_code.c:182:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
phast-1.6/src/prequel/phast_pbs_code.c:201:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/prequel/phast_pbs_code.c:276:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/prequel/phast_pbs_code.c:391:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PbsCodeTrainingData [valueFlowBailoutIncompleteVar]
phast-1.6/src/prequel/phast_pbs_code.c:481:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
phast-1.6/src/prequel/phast_pbs_code.c:551:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAX_NBYTES [valueFlowBailoutIncompleteVar]
phast-1.6/src/prequel/phast_pbs_code.c:570:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAX_NBYTES [valueFlowBailoutIncompleteVar]
phast-1.6/src/prequel/phast_pbs_code.c:189:19: warning: Possible null pointer dereference: c [nullPointer]
phast-1.6/src/prequel/phast_pbs_code.c:95:19: note: Assignment 'code=NULL', assigned value is 0
phast-1.6/src/prequel/phast_pbs_code.c:97:32: note: Assuming condition is false
phast-1.6/src/prequel/phast_pbs_code.c:150:21: note: Calling function 'pbs_assign_points', 1st argument 'code' value is 0
phast-1.6/src/prequel/phast_pbs_code.c:189:19: note: Null pointer dereference
phast-1.6/src/prequel/phast_pbs_code.c:20:27: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
phast-1.6/src/prequel/phast_pbs_code.c:52:27: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
phast-1.6/src/prequel/phast_pbs_code.c:560:32: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
phast-1.6/src/prequel/phast_pbs_code.c:162:25: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/prequel/phast_pbs_code.c:162:43: style: Parameter 'comment' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/prequel/phast_pbs_code.c:531:11: style: Variable 'v' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/prequel/phast_pbs_code.c:550:32: style: Parameter 'code' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/prequel/phast_pbs_code.c:569:30: style: Parameter 'code' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/prequel/phast_pbs_code.c:303:10: warning: Uninitialized variable: err [uninitvar]
phast-1.6/src/prequel/phast_pbs_code.c:278:10: note: Assuming condition is false
phast-1.6/src/prequel/phast_pbs_code.c:303:10: note: Uninitialized variable: err
phast-1.6/src/prequel/phast_pbs_code.c:564:10: warning: Uninitialized variable: bytes [uninitvar]
phast-1.6/src/prequel/phast_pbs_code.c:559:32: note: Assuming condition is false
phast-1.6/src/prequel/phast_pbs_code.c:564:10: note: Uninitialized variable: bytes
phast-1.6/src/prequel/phast_simplex_grid.c:30:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SimplexRegion [valueFlowBailoutIncompleteVar]
phast-1.6/src/prequel/phast_simplex_grid.c:66:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SimplexGrid [valueFlowBailoutIncompleteVar]
phast-1.6/src/prequel/phast_simplex_grid.c:10:18: style: Parameter 'coord' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/prequel/phast_simplex_grid.c:29:56: style: Parameter 'coord' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/prequel/prequel.c:29:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/prequel/prequel.c:332:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/prequel/prequel.c:323:22: warning: Either the condition 'n==NULL' is redundant or there is possible null pointer dereference: n. [nullPointerRedundantCheck]
phast-1.6/src/prequel/prequel.c:321:11: note: Assuming that condition 'n==NULL' is not redundant
phast-1.6/src/prequel/prequel.c:323:22: note: Null pointer dereference
phast-1.6/src/prequel/prequel.c:320:15: style: Local variable 'n' shadows outer variable [shadowVariable]
phast-1.6/src/prequel/prequel.c:307:13: note: Shadowed declaration
phast-1.6/src/prequel/prequel.c:320:15: note: Shadow variable
phast-1.6/src/prequel/prequel.c:26:9: style: Variable 'out_root' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/prequel/prequel.c:31:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/prequel/prequel.c:320:15: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/all_dists.c:49:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/all_dists.c:17:18: style: Parameter 'prog' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/all_dists.c:46:35: style: Variable 'lca' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/all_dists.c:54:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/util/base_evolve.c:25:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FASTA [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/base_evolve.c:39:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/util/chooseLines.c:32:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/chooseLines.c:18:18: style: Parameter 'prog' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/clean_genes.c:283:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/clean_genes.c:327:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/clean_genes.c:404:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/clean_genes.c:481:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/clean_genes.c:530:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable strand [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/clean_genes.c:577:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/clean_genes.c:630:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/clean_genes.c:766:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/clean_genes.c:803:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/clean_genes.c:928:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_STOP_TYPE [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/clean_genes.c:959:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_CDS_TYPE [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/clean_genes.c:977:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/clean_genes.c:860:13: style: Local variable 'signals' shadows outer variable [shadowVariable]
phast-1.6/src/util/clean_genes.c:800:9: note: Shadowed declaration
phast-1.6/src/util/clean_genes.c:860:13: note: Shadow variable
phast-1.6/src/util/clean_genes.c:156:21: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/clean_genes.c:156:58: style: Parameter 'is_missing' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/clean_genes.c:177:37: style: Parameter 'feat' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/clean_genes.c:195:25: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/clean_genes.c:203:36: style: Parameter 'feat' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/clean_genes.c:222:28: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/clean_genes.c:231:39: style: Parameter 'feat' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/clean_genes.c:252:28: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/clean_genes.c:260:39: style: Parameter 'feat' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/clean_genes.c:309:15: style: Variable 'g1' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/clean_genes.c:310:15: style: Variable 'g2' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/clean_genes.c:364:19: style: Variable 'g1' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/clean_genes.c:365:19: style: Variable 'g2' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/clean_genes.c:391:33: style: Parameter 'feat' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/clean_genes.c:478:42: style: Parameter 'feat' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/clean_genes.c:501:16: style: Variable 'feat1' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/clean_genes.c:502:16: style: Variable 'feat2' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/clean_genes.c:508:16: style: Variable 'feat1' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/clean_genes.c:509:16: style: Variable 'feat2' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/clean_genes.c:572:62: style: Parameter 'feat' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/clean_genes.c:610:46: style: Parameter 'group' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/clean_genes.c:629:11: style: Variable 'reason' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/clean_genes.c:763:9: style: Variable 'featName' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/clean_genes.c:918:38: style: Parameter 'group' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/clean_genes.c:934:22: style: Variable 'stop' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/clean_genes.c:1337:31: style: Variable 'problem' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/consEntropy.c:28:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/consEntropy.c:66:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/consEntropy.c:138:36: style: Same expression on both sides of '||'. [duplicateExpression]
phast-1.6/src/util/consEntropy.c:55:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/util/consEntropy.c:42:12: warning: Uninitialized variable: mu2 [uninitvar]
phast-1.6/src/util/consEntropy.c:29:10: note: Assuming condition is false
phast-1.6/src/util/consEntropy.c:42:12: note: Uninitialized variable: mu2
phast-1.6/src/util/convert_coords.c:20:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/convert_coords.c:55:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/display_rate_matrix.c:23:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/display_rate_matrix.c:91:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/display_rate_matrix.c:130:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/display_rate_matrix.c:396:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/display_rate_matrix.c:364:12: style: Local variable 'all_ti' shadows outer variable [shadowVariable]
phast-1.6/src/util/display_rate_matrix.c:207:5: note: Shadowed declaration
phast-1.6/src/util/display_rate_matrix.c:364:12: note: Shadow variable
phast-1.6/src/util/display_rate_matrix.c:366:12: style: Local variable 'all_tv' shadows outer variable [shadowVariable]
phast-1.6/src/util/display_rate_matrix.c:207:13: note: Shadowed declaration
phast-1.6/src/util/display_rate_matrix.c:366:12: note: Shadow variable
phast-1.6/src/util/display_rate_matrix.c:384:9: style: Variable 'rate_format_string' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/draw_tree.c:19:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/draw_tree.c:70:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/draw_tree.c:80:16: style: Variable 'tmp' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/eval_predictions.c:105:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/eval_predictions.c:235:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/eval_predictions.c:99:9: style: Variable 'type' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/eval_predictions.c:167:47: style: Parameter 'real_name' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/eval_predictions.c:167:66: style: Parameter 'pred_name' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/hmm_train.c:113:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SS [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/hmm_tweak.c:99:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/hmm_tweak.c:18:18: style: Parameter 'prog' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/hmm_view.c:57:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/hmm_view.c:52:11: style: Variable 'source' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/hmm_view.c:52:20: style: Variable 'sink' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/indelFit.c:31:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/indelFit.c:169:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASE [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/indelFit.c:43:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/util/indelFit.c:106:15: style: Variable 'n1' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/indelFit.c:107:15: style: Variable 'n2' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/indelFit.c:158:13: style: Variable 'node' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/indelHistory.c:32:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/maf_parse.c:274:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/maf_parse.c:184:70: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/maf_parse.c:184:82: style: Parameter 'out_root' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/makeHKY.c:45:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/makeHKY.c:33:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/util/modFreqs.c:32:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HELP [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/modFreqs.c:24:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/util/msa_diff.c:26:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/msa_diff.c:31:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/util/msa_split.c:241:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SS [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/msa_split.c:259:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/msa_split.c:283:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/msa_split.c:337:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/msa_split.c:399:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/msa_split.c:255:42: style: Parameter 'alphabet' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/msa_split.c:278:44: style: Parameter 'label' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/msa_split.c:278:57: style: Parameter 'alphabet' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/msa_split.c:708:23: style: Variable 'prevg' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/msa_view.c:384:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/msa_view.c:403:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/msa_view.c:793:9: style: Local variable 'i' shadows outer variable [shadowVariable]
phast-1.6/src/util/msa_view.c:407:7: note: Shadowed declaration
phast-1.6/src/util/msa_view.c:793:9: note: Shadow variable
phast-1.6/src/util/msa_view.c:405:26: style: Variable 'clean_seqname' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/msa_view.c:415:9: style: Variable 'out_root' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/msa_view.c:424:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/util/phast.c:15:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PHAST_VERSION [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/phast.c:14:26: style: Parameter 'argv' can be declared as const array [constParameter]
phast-1.6/src/util/phastBias.c:77:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/phastBias.c:52:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/util/refeature.c:119:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/refeature.c:23:18: style: Parameter 'prog' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/refeature.c:124:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/util/stringiphy.c:55:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_LONG_LEN [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/stringiphy.c:83:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/stringiphy.c:34:18: style: Parameter 'prog' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/stringiphy.c:53:41: style: Parameter 'gene_tag' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/stringiphy.c:53:57: style: Parameter 'gene_val' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/stringiphy.c:69:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/util/stringiphy.c:158:12: style: Variable 'g1' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/util/treeGen.c:38:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HELP [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/treeGen.c:30:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/util/treeGen.c:187:32: style: Parameter 'name1' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/treeGen.c:187:45: style: Parameter 'name2' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/treeGen.c:211:58: style: Parameter 'lname' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/treeGen.c:247:45: style: Parameter 'lname' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/tree_doctor.c:156:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
phast-1.6/src/util/tree_doctor.c:17:18: style: Parameter 'prog' can be declared as pointer to const [constParameterPointer]
phast-1.6/src/util/tree_doctor.c:159:27: style: Variable 'merge_mod' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/tree_doctor.c:169:17: style: Variable 'long_opts' can be declared as const array [constVariable]
phast-1.6/src/util/tree_doctor.c:345:11: style: Variable 'newname' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/tree_doctor.c:384:12: style: Variable 'node' can be declared as pointer to const [constVariablePointer]
phast-1.6/src/util/tree_doctor.c:389:9: style: Variable 'node' is assigned a value that is never used. [unreadVariable]
phast-1.6/src/prequel/phast_pbs_code.c:189:19: error: Null pointer dereference: c [ctunullpointer]
phast-1.6/src/prequel/phast_pbs_code.c:95:19: note: Assignment 'code=NULL', assigned value is 0
phast-1.6/src/prequel/phast_pbs_code.c:97:32: note: Assuming condition is false
phast-1.6/src/prequel/phast_pbs_code.c:150:20: note: Calling function pbs_assign_points, 1st argument is null
phast-1.6/src/prequel/phast_pbs_code.c:189:19: note: Dereferencing argument c that is null
diff:
head phast-1.6/src/dless/dlessP.c:195:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nnodes [valueFlowBailoutIncompleteVar]
head phast-1.6/src/dless/dlessP.c:319:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/dless/dlessP.c:402:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CONS [valueFlowBailoutIncompleteVar]
head phast-1.6/src/dless/phast_bd_phylo_hmm.c:181:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tree [valueFlowBailoutIncompleteVar]
head phast-1.6/src/dless/phast_bd_phylo_hmm.c:214:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tree [valueFlowBailoutIncompleteVar]
head phast-1.6/src/dless/phast_bd_phylo_hmm.c:303:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/dless/phast_bd_phylo_hmm.c:370:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_complex_matrix.c:109:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_complex_matrix.c:118:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_complex_matrix.c:237:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_complex_vector.c:116:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_complex_vector.c:54:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_complex_vector.c:61:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_eigen.c:204:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
2.13.0 phast-1.6/src/lib/base/phast_eigen.c:48:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable eval_type [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_eigen.c:67:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_hashtable.c:43:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Hashtable [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_list_of_lists.c:103:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_LIST [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_list_of_lists.c:109:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_LIST [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_list_of_lists.c:116:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CHAR_LIST [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_list_of_lists.c:132:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INT_LIST [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_list_of_lists.c:147:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CHAR_LIST [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_list_of_lists.c:171:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CHAR_LIST [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_list_of_lists.c:193:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_LOG_LIKELIHOOD [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_list_of_lists.c:281:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_NULL_FRAME [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_list_of_lists.c:335:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_PTR_LIST [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_list_of_lists.c:342:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MSA_PTR_LIST [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_list_of_lists.c:349:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MS_PTR_LIST [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_list_of_lists.c:367:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LIST_LIST [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_list_of_lists.c:52:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LIST_LIST [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_list_of_lists.c:63:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_LIST [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_list_of_lists.c:78:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LIST_LIST [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_list_of_lists.c:92:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LIST_LIST [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_lists.c:279:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ASCENDING [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_lists.c:283:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ASCENDING [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_markov_matrix.c:142:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_markov_matrix.c:568:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REAL_NUM [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_markov_matrix.c:601:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMPLEX_NUM [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_markov_matrix.c:622:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMPLEX_NUM [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_markov_matrix.c:696:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_markov_matrix.c:717:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMPLEX_NUM [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_markov_matrix.c:730:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DISCRETE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_markov_matrix.c:78:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DISCRETE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_matrix.c:122:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_matrix.c:213:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nrows [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_matrix.c:267:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_matrix.c:345:48: style: Parameter 'arr' can be declared as pointer to const [constParameterPointer]
head phast-1.6/src/lib/base/phast_memory_handler.c:222:30: style: Parameter 'ptr0' can be declared as pointer to const [constParameterPointer]
head phast-1.6/src/lib/base/phast_memory_handler.c:234:44: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
head phast-1.6/src/lib/base/phast_memory_handler.c:234:56: style: Parameter 'function' can be declared as pointer to const [constParameterPointer]
head phast-1.6/src/lib/base/phast_memory_handler.c:343:31: style: Parameter 'F' can be declared as pointer to const [constParameterPointer]
head phast-1.6/src/lib/base/phast_memory_handler.c:361:33: style: Parameter 'F' can be declared as pointer to const [constParameterPointer]
head phast-1.6/src/lib/base/phast_misc.c:1063:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_misc.c:120:31: style: Parameter 'alphabet' can be declared as pointer to const [constParameterPointer]
head phast-1.6/src/lib/base/phast_misc.c:1216:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFERSIZE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_misc.c:165:23: style: Parameter 'tuple' can be declared as pointer to const [constParameterPointer]
head phast-1.6/src/lib/base/phast_misc.c:281:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_misc.c:299:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_misc.c:311:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_misc.c:322:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_misc.c:368:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_misc.c:528:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_misc.c:698:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable d [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_misc.c:890:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_numerical_opt.c:1145:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_numerical_opt.c:1288:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OPT_HIGH_PREC [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_numerical_opt.c:131:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OPT_DERIV_FORWARD [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_numerical_opt.c:1323:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_numerical_opt.c:1355:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_numerical_opt.c:189:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OPT_NO_BOUND [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_numerical_opt.c:228:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OPT_NO_BOUND [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_numerical_opt.c:246:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OPT_NO_BOUND [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_numerical_opt.c:403:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OPT_DERIV_FORWARD [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_numerical_opt.c:859:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OPT_HIGH_PREC [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_prob_matrix.c:260:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nrows [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_prob_matrix.c:358:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nrows [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_prob_vector.c:112:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UPPER [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_prob_vector.c:229:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_prob_vector.c:262:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_prob_vector.c:388:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LOWER [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_stringsplus.c:143:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFERSIZE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_stringsplus.c:184:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFERSIZE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_stringsplus.c:239:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFERSIZE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_stringsplus.c:264:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFERSIZE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_stringsplus.c:350:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NCHARS [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_stringsplus.c:36:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_stringsplus.c:397:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NCHARS [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_stringsplus.c:42:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_stringsplus.c:505:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_stringsplus.c:646:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_stringsplus.c:660:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/base/phast_stringsplus.c:93:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_bed.c:200:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_category_map.c:305:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start_cat_no [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_category_map.c:354:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable feature_types [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_category_map.c:361:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable feature_types [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_category_map.c:381:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start_cat_no [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_category_map.c:391:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CategoryMap [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_category_map.c:432:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_category_map.c:465:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BACKGD_CAT_NAME [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_category_map.c:478:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_category_map.c:535:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_cat_no [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_category_map.c:556:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CategoryRange [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_category_map.c:619:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PHAST_VERSION [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_category_map.c:710:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_category_map.c:756:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Unspooler [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_category_map.c:808:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UnspoolNode [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_category_map.c:859:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_genepred.c:170:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_LONG_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:1068:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_START_TYPE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:1121:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_NULL_FRAME [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:1151:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_LONG_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:1177:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:1213:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:1276:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_EXON_TYPE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:1308:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:1426:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:1437:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:1518:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_NULL_FRAME [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:1790:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_NULL_FRAME [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:1844:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_NULL_FRAME [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:1959:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_NULL_FRAME [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:207:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_Feature [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:236:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_Feature [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:293:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_Set [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:308:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_SET_START_SIZE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:341:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_DEFAULT_VERSION [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:387:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_VERSION_TAG [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:410:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_NULL_FRAME [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:540:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:708:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_FeatureGroup [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:753:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_FeatureGroup [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:791:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_FeatureGroup [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:827:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_FeatureGroup [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:877:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_gff.c:950:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/feature/phast_wig.c:104:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_LONG_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/hmm/phast_hmm.c:1156:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable END_STATE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/hmm/phast_hmm.c:1222:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGINFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/hmm/phast_hmm.c:158:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/hmm/phast_hmm.c:186:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRANSITION_MATRIX_TAG [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/hmm/phast_hmm.c:211:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable END_STATE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/hmm/phast_hmm.c:291:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VITERBI [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/hmm/phast_hmm.c:338:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FORWARD [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/hmm/phast_hmm.c:358:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BACKWARD [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/hmm/phast_hmm.c:392:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/hmm/phast_hmm.c:433:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VITERBI [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/hmm/phast_hmm.c:471:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable END_STATE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/hmm/phast_hmm.c:494:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGINFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/hmm/phast_hmm.c:735:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGINFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/hmm/phast_hmm.c:783:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DISCRETE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/hmm/phast_hmm.c:842:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BEGIN_STATE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/hmm/phast_hmm.c:979:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BEGIN_STATE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_motif.c:1091:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DESCENDING [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_motif.c:1115:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SeqSet [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_motif.c:1141:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nseqs [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_motif.c:1204:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Motif [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_motif.c:123:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_motif.c:1355:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tree [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_motif.c:1496:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tree [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_motif.c:1676:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_motif.c:1741:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGINFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_motif.c:1772:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable names [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_motif.c:258:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_motif.c:288:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MTF_EPSILON [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_motif.c:584:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGINFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_motif.c:749:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGINFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_motif.c:910:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DESCENDING [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_motif.c:964:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_tfbs.c:111:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OUTPUT_LINE_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_tfbs.c:136:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_tfbs.c:211:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_tfbs.c:220:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_tfbs.c:443:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/motif/phast_tfbs.c:472:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_local_alignment.c:205:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GaplessAlignment [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_local_alignment.c:218:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AlignmentBlock [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_local_alignment.c:284:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_local_alignment.c:441:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ADJUSTRIGHT [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_local_alignment.c:46:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_maf.c:1114:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_VERY_LONG_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_maf.c:1219:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_VERY_LONG_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_maf.c:1390:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_maf.c:558:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_STRIP [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_maf.c:858:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_VERY_LONG_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_maf.c:989:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_VERY_LONG_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_maf_block.c:101:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_maf_block.c:177:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_maf_block.c:225:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_maf_block.c:275:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_maf_block.c:30:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MafSubBlock [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_maf_block.c:41:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MafSubBlock [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_maf_block.c:667:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_maf_block.c:678:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_maf_block.c:692:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_maf_block.c:71:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MafBlock [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_maf_block.c:840:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lineType [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_maf_block.c:864:81: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:1036:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:108:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:1137:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable idx_offset [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:1176:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:1208:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:1490:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STRIP_ALL_GAPS [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:1530:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:1694:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:1736:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:1749:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STRIP_ALL_GAPS [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:1803:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:1867:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:1925:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:2028:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:202:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAF [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:2211:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:2293:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:2475:83: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:2541:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MPM [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:2553:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FASTA [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:2563:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:2581:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:258:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:2715:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:2763:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:2798:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:2844:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:2872:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:2988:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:354:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SS [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:454:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_cat_no [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:593:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STRIP_ANY_GAPS [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:634:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:744:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable msa_coord_map [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:828:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable msa_coord_map [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_msa.c:863:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BACKGD_CAT_NAME [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_multi_msa.c:131:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Multi_MSA [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_sufficient_stats.c:1049:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_sufficient_stats.c:1248:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_sufficient_stats.c:1277:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_sufficient_stats.c:1298:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_sufficient_stats.c:1351:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_sufficient_stats.c:1398:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_sufficient_stats.c:291:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_sufficient_stats.c:344:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PooledMSA [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_sufficient_stats.c:446:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_sufficient_stats.c:557:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_sufficient_stats.c:615:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_sufficient_stats.c:672:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/msa/phast_sufficient_stats.c:935:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_bgc_hmm.c:178:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bgchmm_struct [valueFlowBailoutIncompleteVar]
2.13.0 phast-1.6/src/lib/phylo/phast_bgc_hmm.c:222:24: style: Variable 'results' is assigned a value that is never used. [unreadVariable]
head phast-1.6/src/lib/phylo/phast_bgc_hmm.c:224:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MSA [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_bgc_hmm.c:520:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_bgc_hmm.c:568:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_bgc_hmm.c:612:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_bgc_hmm.c:746:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGINFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_cons.c:1022:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scale [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_cons.c:1054:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARAMETERIC [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_cons.c:1071:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARAMETERIC [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_cons.c:108:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_cons.c:1150:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable JC69 [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_cons.c:721:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EmData [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_cons.c:830:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_IMAG_EPS [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_cons.c:879:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_cons.c:929:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable estimate_ratemat [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_dgamma.c:142:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable 0.5e [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_column.c:1065:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_column.c:1117:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ColFitData [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_column.c:1311:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dparent [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_column.c:1343:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_column.c:1472:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FimGrid [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_column.c:1541:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GRIDSIZE1 [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_column.c:1600:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_column.c:224:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dparent [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_column.c:293:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REAL_NUM [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_column.c:379:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_column.c:457:56: style: Parameter 'gradient' can be declared as pointer to const [constParameterPointer]
head phast-1.6/src/lib/phylo/phast_fit_column.c:556:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_column.c:676:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBTREE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_column.c:690:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBTREE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_column.c:708:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALL [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_column.c:723:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALL [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_column.c:756:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALL [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_column.c:837:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBTREE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_column.c:975:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NNEUT [valueFlowBailoutIncompleteVar]
2.13.0 phast-1.6/src/lib/phylo/phast_fit_em.c:126:25: style: Condition 'proj_mod==NULL' is always true [knownConditionTrueFalse]
     phast-1.6/src/lib/phylo/phast_fit_em.c:59:25: note: Assignment 'proj_mod=NULL', assigned value is 0
     phast-1.6/src/lib/phylo/phast_fit_em.c:84:17: note: Assuming condition is false
     phast-1.6/src/lib/phylo/phast_fit_em.c:126:25: note: Condition 'proj_mod==NULL' is always true
head phast-1.6/src/lib/phylo/phast_fit_em.c:443:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Complex [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_em.c:921:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Complex [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_feature.c:106:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBTREE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_feature.c:124:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALL [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_feature.c:152:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALL [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_feature.c:236:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBTREE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_feature.c:386:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NNEUT [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_feature.c:477:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_feature.c:562:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dparent [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_feature.c:582:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FeatFitData [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_feature.c:609:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_feature.c:645:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_fit_feature.c:654:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_history.c:127:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEL [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_history.c:205:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_history.c:250:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_history.c:304:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_history.c:384:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_history.c:480:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_history.c:54:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CompactIndelHistory [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_history.c:693:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_history.c:87:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEL [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_mod.c:100:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CHILDINS [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_mod.c:150:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_mod.c:171:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SKIP [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_mod.c:237:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NINDEL_STATES [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_mod.c:252:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SKIP [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_mod.c:292:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IndelSuffStats [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_mod.c:310:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable trans_counts [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_mod.c:33:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IndelModel [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_mod.c:354:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable trans_counts [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_mod.c:427:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SKIP [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_mod.c:481:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IndelSuffStats [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_indel_mod.c:48:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IndelModel [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_phylo_fit.c:176:28: style: Parameter 'msa' can be declared as pointer to const [constParameterPointer]
head phast-1.6/src/lib/phylo/phast_phylo_fit.c:227:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_phylo_fit.c:669:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_phylo_p.c:200:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SPH [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_phylo_p.c:77:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_SCALE_ONLY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_phylo_p_print.c:333:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LOWER [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_phylo_p_print.c:445:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable post_mean [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_phylo_p_print.c:521:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable post_mean_left [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_phylo_p_print.c:597:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_phylo_p_print.c:675:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_phylo_p_print.c:832:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CHAR_LIST [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_phylo_p_print.c:864:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_subst_distrib.c:1040:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable p_value_joint_stats [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_subst_distrib.c:1317:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_subst_distrib.c:244:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_subst_distrib.c:299:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_subst_distrib.c:440:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable col_likelihood_wrapper_1d [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_subst_distrib.c:501:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_subst_distrib.c:679:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_subst_distrib.c:86:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable JumpProcess [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_subst_distrib.c:877:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable p_value_stats [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_subst_mods.c:2565:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RATEMAT_STR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_subst_mods.c:261:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNREST [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_subst_mods.c:267:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HKY_CODON [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_subst_mods.c:2773:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMPLEX_NUM [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_subst_mods.c:278:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R2 [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_subst_mods.c:2806:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HKY85 [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_subst_mods.c:2816:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HKY85 [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_subst_mods.c:358:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable F81 [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_likelihoods.c:560:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NEGINFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_likelihoods.c:617:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TreePosteriors [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_likelihoods.c:886:36: style: Parameter 'tuple' can be declared as pointer to const [constParameterPointer]
head phast-1.6/src/lib/phylo/phast_tree_likelihoods.c:893:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:1003:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_SCALE_ONLY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:1093:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_SCALE_ONLY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:1228:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable JC69 [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:1259:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEFAULT_ALPHABET [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:1304:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable order [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:1435:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:1540:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:1750:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_SCALE_ONLY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:1890:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:1923:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:1996:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_BRANCHLENS_NONE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:2088:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable categories [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:2226:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_BRANCHLENS_CLOCK [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:256:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMPLEX_NUM [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:2685:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_BRANCHLENS_CLOCK [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:2936:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_BRANCHLENS_CLOCK [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:3026:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_SCALE_ONLY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:314:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNDEF_MOD [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:3242:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_BRANCHLENS_CLOCK [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:3369:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:3384:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_BRANCHLENS_CLOCK [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:3492:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AA_ALPHABET [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:3607:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_BRANCHLENS_CLOCK [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:3654:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:368:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:3750:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:3763:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AltSubstMod [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:3854:52: style: Parameter 'node' can be declared as pointer to const [constParameterPointer]
head phast-1.6/src/lib/phylo/phast_tree_model.c:3945:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:4164:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TM_SCALE_ONLY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:612:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_LOG_LIKELIHOOD [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:718:98: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_tree_model.c:848:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_trees.c:1010:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_trees.c:1144:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_trees.c:1281:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_trees.c:1314:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_trees.c:1580:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_trees.c:205:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TreeNode [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_trees.c:249:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo/phast_trees.c:63:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo_hmm/phast_gap_patterns.c:218:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_SHORT_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo_hmm/phast_gap_patterns.c:380:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_PATTERN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo_hmm/phast_gap_patterns.c:412:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GP_BASE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo_hmm/phast_gap_patterns.c:443:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo_hmm/phast_gap_patterns.c:476:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMPLEX_PATTERN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1041:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARAMETERIC [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1070:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1087:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable order [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1145:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EmData [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1182:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tree [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1206:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARAMETERIC [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1290:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INSERTION_PATTERN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1322:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INSERTION_PATTERN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1375:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARAMETERIC [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:1404:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IndelEstimData [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:238:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:322:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MISSING_DATA [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:578:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/phylo_hmm/phast_phylo_hmm.c:837:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/phast_rph_util.c:126:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/phast_rph_util.c:20:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/phast_rph_util.c:60:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INTSXP [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_gff.c:213:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_gff.c:244:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_NULL_FRAME [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_gff.c:321:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INTSXP [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_gff.c:340:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INTSXP [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_gff.c:460:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_gff.c:546:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_gff.c:676:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_hmm.c:101:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_hmm.c:161:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_msa.c:1041:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_msa.c:1123:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_msa.c:1160:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_Set [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_msa.c:1189:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_msa.c:1256:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_msa.c:171:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_NULL_FRAME [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_msa.c:313:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_msa.c:511:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LGLSXP [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_msa.c:529:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_msa.c:580:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_msa.c:596:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INTSXP [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_msa.c:619:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_msa.c:630:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_msa.c:672:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_msa.c:734:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_msa.c:777:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_msa.c:841:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_msa.c:957:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_subst_mods.c:52:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tfbs.c:159:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tfbs.c:180:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tfbs.c:271:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tfbs.c:388:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tfbs.c:401:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tfbs.c:418:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tfbs.c:491:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tfbs.c:505:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tfbs.c:580:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VECSXP [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tfbs.c:687:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VECSXP [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tfbs.c:827:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tfbs.c:861:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tfbs.c:877:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:117:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:153:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:174:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:217:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:231:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:284:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NULL_LOG_LIKELIHOOD [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:368:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:384:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:400:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:429:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:536:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:552:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:567:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:581:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:598:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:637:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CONTINUOUS [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:652:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:671:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:701:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:734:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CONTINUOUS [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:758:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CONTINUOUS [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:778:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_tree_model.c:99:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_trees.c:186:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_trees.c:244:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_trees.c:345:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NA_STRING [valueFlowBailoutIncompleteVar]
head phast-1.6/src/lib/rphast/rph_trees.c:474:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NilValue [valueFlowBailoutIncompleteVar]
head phast-1.6/src/phyloBoot/phyloBoot.c:112:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FASTA [valueFlowBailoutIncompleteVar]
2.13.0 phast-1.6/src/prequel/pbsScoreMatrix.c:36:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pbs_mode [valueFlowBailoutIncompleteVar]
head phast-1.6/src/prequel/pbsScoreMatrix.c:41:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phast-1.6/src/prequel/phast_pbs_code.c:182:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head phast-1.6/src/prequel/phast_pbs_code.c:201:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/prequel/phast_pbs_code.c:276:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFTY [valueFlowBailoutIncompleteVar]
head phast-1.6/src/prequel/phast_pbs_code.c:391:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PbsCodeTrainingData [valueFlowBailoutIncompleteVar]
head phast-1.6/src/prequel/phast_pbs_code.c:481:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
head phast-1.6/src/prequel/phast_pbs_code.c:50:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PbsCode [valueFlowBailoutIncompleteVar]
head phast-1.6/src/prequel/phast_pbs_code.c:551:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAX_NBYTES [valueFlowBailoutIncompleteVar]
head phast-1.6/src/prequel/phast_pbs_code.c:570:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAX_NBYTES [valueFlowBailoutIncompleteVar]
head phast-1.6/src/prequel/phast_pbs_code.c:92:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/prequel/phast_simplex_grid.c:29:56: style: Parameter 'coord' can be declared as pointer to const [constParameterPointer]
head phast-1.6/src/prequel/phast_simplex_grid.c:66:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SimplexGrid [valueFlowBailoutIncompleteVar]
head phast-1.6/src/prequel/prequel.c:332:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/clean_genes.c:327:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/clean_genes.c:404:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/clean_genes.c:481:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/clean_genes.c:530:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable strand [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/clean_genes.c:577:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/clean_genes.c:630:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/clean_genes.c:766:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chars [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/clean_genes.c:803:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/clean_genes.c:918:38: style: Parameter 'group' can be declared as pointer to const [constParameterPointer]
head phast-1.6/src/util/clean_genes.c:928:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_STOP_TYPE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/clean_genes.c:959:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_CDS_TYPE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/clean_genes.c:977:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/consEntropy.c:66:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/convert_coords.c:55:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/display_rate_matrix.c:130:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/display_rate_matrix.c:396:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/display_rate_matrix.c:91:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/draw_tree.c:70:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/eval_predictions.c:235:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
2.13.0 phast-1.6/src/util/hmm_train.c:185:11: warning:inconclusive: Possible null pointer dereference: cm [nullPointer]
     phast-1.6/src/util/hmm_train.c:120:21: note: Assignment 'cm=NULL', assigned value is 0
     phast-1.6/src/util/hmm_train.c:126:63: note: Assuming condition is false
     phast-1.6/src/util/hmm_train.c:185:11: note: Null pointer dereference
2.13.0 phast-1.6/src/util/hmm_train.c:186:21: warning:inconclusive: Possible null pointer dereference: cm [nullPointer]
     phast-1.6/src/util/hmm_train.c:120:21: note: Assignment 'cm=NULL', assigned value is 0
     phast-1.6/src/util/hmm_train.c:126:63: note: Assuming condition is false
     phast-1.6/src/util/hmm_train.c:186:21: note: Null pointer dereference
head phast-1.6/src/util/indelFit.c:169:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BASE [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/msa_split.c:259:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/msa_split.c:283:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STR_MED_LEN [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/msa_split.c:337:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAP_CHAR [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/msa_split.c:399:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/msa_view.c:403:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FORMAT [valueFlowBailoutIncompleteVar]
head phast-1.6/src/util/phast.c:14:26: style: Parameter 'argv' can be declared as const array [constParameter]
head phast-1.6/src/util/stringiphy.c:83:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]


DONE