2024-05-02 17:12
ftp://ftp.de.debian.org/debian/pool/main/p/phipack/phipack_0.0.20160614.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j1
platform: Linux-5.15.0-102-generic-x86_64-with-glibc2.35
python: 3.10.12
client-version: 1.3.57
compiler: g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
cppcheck: head 2.14.0
head-info: 265a505 (2024-05-02 15:32:09 +0200)
count: 161 161
elapsed-time: 2.7 2.6
head-timing-info:

old-timing-info:

head results:
phipack-0.0.20160614/src/fasta.c:48:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/fasta.c:147:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/fasta.c:211:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/fasta.c:154:3: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
phipack-0.0.20160614/src/fasta.c:41:5: style: Redundant initialization for 'ch'. The initialized value is overwritten before it is read. [redundantInitialization]
phipack-0.0.20160614/src/fasta.c:39:10: note: ch is initialized
phipack-0.0.20160614/src/fasta.c:41:5: note: ch is overwritten
phipack-0.0.20160614/src/fasta.c:145:9: style: Variable 'ch' is reassigned a value before the old one has been used. [redundantAssignment]
phipack-0.0.20160614/src/fasta.c:143:6: note: ch is assigned
phipack-0.0.20160614/src/fasta.c:145:9: note: ch is overwritten
phipack-0.0.20160614/src/fasta.c:233:9: style: Variable 'ch' is reassigned a value before the old one has been used. [redundantAssignment]
phipack-0.0.20160614/src/fasta.c:230:9: note: ch is assigned
phipack-0.0.20160614/src/fasta.c:233:9: note: ch is overwritten
phipack-0.0.20160614/src/fasta.c:235:9: style: Variable 'ch' is reassigned a value before the old one has been used. [redundantAssignment]
phipack-0.0.20160614/src/fasta.c:233:9: note: ch is assigned
phipack-0.0.20160614/src/fasta.c:235:9: note: ch is overwritten
phipack-0.0.20160614/src/fasta.c:237:9: style: Variable 'ch' is reassigned a value before the old one has been used. [redundantAssignment]
phipack-0.0.20160614/src/fasta.c:235:9: note: ch is assigned
phipack-0.0.20160614/src/fasta.c:237:9: note: ch is overwritten
phipack-0.0.20160614/src/fasta.c:48:26: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phipack-0.0.20160614/src/fasta.c:59:6: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phipack-0.0.20160614/src/fasta.c:106:9: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phipack-0.0.20160614/src/fasta.c:147:6: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phipack-0.0.20160614/src/fasta.c:154:13: style: Variable 'base_limit' is assigned a value that is never used. [unreadVariable]
phipack-0.0.20160614/src/fasta.c:245:10: style: Variable 'new_num' is assigned a value that is never used. [unreadVariable]
phipack-0.0.20160614/src/graphCode.c:397:6: style: The if condition is the same as the previous if condition [duplicateCondition]
phipack-0.0.20160614/src/graphCode.c:351:6: note: First condition
phipack-0.0.20160614/src/graphCode.c:397:6: note: Second condition
phipack-0.0.20160614/src/graphCode.c:93:57: style: Local variable 'error' shadows outer function [shadowFunction]
phipack-0.0.20160614/src/mem.h:31:6: note: Shadowed declaration
phipack-0.0.20160614/src/graphCode.c:93:57: note: Shadow variable
phipack-0.0.20160614/src/graphCode.c:177:66: style: Parameter 'break_values' can be declared as pointer to const [constParameterPointer]
phipack-0.0.20160614/src/graphCode.c:177:85: style: Parameter 'site_desc' can be declared as pointer to const [constParameterPointer]
phipack-0.0.20160614/src/main.c:45:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/main.c:252:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/main.c:331:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/main.c:126:13: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
phipack-0.0.20160614/src/main.c:128:8: note: Found duplicate branches for 'if' and 'else'.
phipack-0.0.20160614/src/main.c:126:13: note: Found duplicate branches for 'if' and 'else'.
phipack-0.0.20160614/src/main.c:74:9: style: Variable 'cur' can be declared as pointer to const [constVariablePointer]
phipack-0.0.20160614/src/maxChi.c:139:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/maxChi.c:168:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/maxChi.c:37:98: style: Parameter 'permutation' can be declared as pointer to const [constParameterPointer]
phipack-0.0.20160614/src/maxChi.c:37:117: style: Parameter 'site_desc' can be declared as pointer to const [constParameterPointer]
phipack-0.0.20160614/src/maxChi.c:48:28: style: Variable 'cur_val' is assigned a value that is never used. [unreadVariable]
phipack-0.0.20160614/src/mem.c:104:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/mem.c:82:20: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
phipack-0.0.20160614/src/mem.c:82:31: style: Parameter 'mod' can be declared as pointer to const [constParameterPointer]
phipack-0.0.20160614/src/mem.c:104:6: warning: Storing fclose() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phipack-0.0.20160614/src/misc.c:23:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/misc.c:52:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/misc.c:67:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/misc.c:82:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/misc.c:96:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/misc.c:52:10: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phipack-0.0.20160614/src/misc.c:55:6: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phipack-0.0.20160614/src/misc.c:67:10: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phipack-0.0.20160614/src/misc.c:70:6: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phipack-0.0.20160614/src/misc.c:82:10: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phipack-0.0.20160614/src/misc.c:85:6: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phipack-0.0.20160614/src/misc.c:96:10: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phipack-0.0.20160614/src/misc.c:99:6: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phipack-0.0.20160614/src/pairScore.c:45:47: style: Parameter 'site_states' can be declared as pointer to const [constParameterPointer]
phipack-0.0.20160614/src/pairScore.c:63:23: style: Variable 'cur_vertex' is assigned a value that is never used. [unreadVariable]
phipack-0.0.20160614/src/phylip.c:34:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/phylip.c:57:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/phylip.c:174:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/phylip.c:227:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/phylip.c:168:9: style: Variable 'ch' is reassigned a value before the old one has been used. [redundantAssignment]
phipack-0.0.20160614/src/phylip.c:166:6: note: ch is assigned
phipack-0.0.20160614/src/phylip.c:168:9: note: ch is overwritten
phipack-0.0.20160614/src/phylip.c:274:5: style: Variable 'ch' is reassigned a value before the old one has been used. [redundantAssignment]
phipack-0.0.20160614/src/phylip.c:266:8: note: ch is assigned
phipack-0.0.20160614/src/phylip.c:274:5: note: ch is overwritten
phipack-0.0.20160614/src/phylip.c:40:6: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phipack-0.0.20160614/src/phylip.c:66:7: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phipack-0.0.20160614/src/phylip.c:70:16: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phipack-0.0.20160614/src/phylip.c:80:6: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phipack-0.0.20160614/src/phylip.c:138:9: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phipack-0.0.20160614/src/phylip.c:174:11: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:160:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:371:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:590:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:870:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:1219:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:1330:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:1538:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:1752:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:1958:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:2053:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:2199:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:2304:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:2481:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:1632:7: error: Memory leak: barray [memleak]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:1632:7: error: Memory leak: garray [memleak]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:1656:5: error: Memory leak: barray [memleak]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:1656:5: error: Memory leak: garray [memleak]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:1656:5: error: Memory leak: rarray [memleak]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:663:8: style: The scope of the variable 'i1' can be reduced. [variableScope]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:664:8: style: The scope of the variable 'i2' can be reduced. [variableScope]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:1727:18: style: The scope of the variable 'aparray' can be reduced. [variableScope]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:1730:18: style: The scope of the variable 'bparray' can be reduced. [variableScope]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:1738:18: style: The scope of the variable 'gparray' can be reduced. [variableScope]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:1745:18: style: The scope of the variable 'rparray' can be reduced. [variableScope]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:2419:7: style: The scope of the variable 'j' can be reduced. [variableScope]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:1979:27: style: Parameter 'file_out_name' can be declared as pointer to const [constParameterPointer]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:2222:27: style: Parameter 'file_out_name' can be declared as pointer to const [constParameterPointer]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:973:17: style: Unused variable: c1 [unusedVariable]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:974:17: style: Unused variable: c2 [unusedVariable]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:1524:22: style: Unused variable: magic [unusedVariable]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:2165:7: style: Unused variable: j2 [unusedVariable]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:2168:7: style: Unused variable: result [unusedVariable]
phipack-0.0.20160614/src/ppma_2_bmp/bmp_io.C:2423:7: style: Unused variable: result [unusedVariable]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_2_bmp.C:58:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_2_bmp.C:179:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_2_bmp.C:371:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_2_bmp.C:367:8: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_2_bmp.C:266:7: style: The scope of the variable 'k1' can be reduced. [variableScope]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_2_bmp.C:267:7: style: The scope of the variable 'k2' can be reduced. [variableScope]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_2_bmp.C:21:28: style: Parameter 'argv' can be declared as const array [constParameter]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_2_bmp.C:369:7: style: Variable 'len' is assigned a value that is never used. [unreadVariable]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:71:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:291:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:447:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:562:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:658:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:875:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:688:8: style: Condition 'error' is always false [knownConditionTrueFalse]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:686:29: note: Calling function 'ppma_write_header' returns 0
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:686:29: note: Assignment 'error=ppma_write_header(file_out,file_out_name,xsize,ysize,maxrgb)', assigned value is 0
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:688:8: note: Condition 'error' is always false
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:700:8: style: Condition 'error' is always false [knownConditionTrueFalse]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:698:27: note: Calling function 'ppma_write_data' returns 0
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:698:27: note: Assignment 'error=ppma_write_data(file_out,xsize,ysize,r,g,b)', assigned value is 0
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:700:8: note: Condition 'error' is always false
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:873:8: style: Condition 'error' is always false [knownConditionTrueFalse]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:871:24: note: Calling function 'ppma_example' returns 0
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:871:24: note: Assignment 'error=ppma_example(xsize,ysize,r,g,b)', assigned value is 0
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:873:8: note: Condition 'error' is always false
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:462:15: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:196:9: style: The scope of the variable 'y' can be reduced. [variableScope]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:17:63: style:inconclusive: Function 'ppma_check_data' argument 4 names different: declaration 'rarray' definition 'r'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.H:1:63: note: Function 'ppma_check_data' argument 4 names different: declaration 'rarray' definition 'r'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:17:63: note: Function 'ppma_check_data' argument 4 names different: declaration 'rarray' definition 'r'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:18:8: style:inconclusive: Function 'ppma_check_data' argument 5 names different: declaration 'garray' definition 'g'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.H:2:13: note: Function 'ppma_check_data' argument 5 names different: declaration 'garray' definition 'g'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:18:8: note: Function 'ppma_check_data' argument 5 names different: declaration 'garray' definition 'g'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:18:16: style:inconclusive: Function 'ppma_check_data' argument 6 names different: declaration 'barray' definition 'b'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.H:2:26: note: Function 'ppma_check_data' argument 6 names different: declaration 'barray' definition 'b'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:18:16: note: Function 'ppma_check_data' argument 6 names different: declaration 'barray' definition 'b'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:160:48: style:inconclusive: Function 'ppma_example' argument 3 names different: declaration 'rarray' definition 'r'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.H:3:48: note: Function 'ppma_example' argument 3 names different: declaration 'rarray' definition 'r'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:160:48: note: Function 'ppma_example' argument 3 names different: declaration 'rarray' definition 'r'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:160:56: style:inconclusive: Function 'ppma_example' argument 4 names different: declaration 'garray' definition 'g'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.H:3:61: note: Function 'ppma_example' argument 4 names different: declaration 'garray' definition 'g'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:160:56: note: Function 'ppma_example' argument 4 names different: declaration 'garray' definition 'g'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:160:64: style:inconclusive: Function 'ppma_example' argument 5 names different: declaration 'barray' definition 'b'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.H:3:74: note: Function 'ppma_example' argument 5 names different: declaration 'barray' definition 'b'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:160:64: note: Function 'ppma_example' argument 5 names different: declaration 'barray' definition 'b'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:251:9: style:inconclusive: Function 'ppma_read' argument 5 names different: declaration 'rarrary' definition 'r'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.H:6:14: note: Function 'ppma_read' argument 5 names different: declaration 'rarrary' definition 'r'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:251:9: note: Function 'ppma_read' argument 5 names different: declaration 'rarrary' definition 'r'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:251:18: style:inconclusive: Function 'ppma_read' argument 6 names different: declaration 'garray' definition 'g'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.H:6:29: note: Function 'ppma_read' argument 6 names different: declaration 'garray' definition 'g'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:251:18: note: Function 'ppma_read' argument 6 names different: declaration 'garray' definition 'g'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:251:27: style:inconclusive: Function 'ppma_read' argument 7 names different: declaration 'barray' definition 'b'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.H:6:43: note: Function 'ppma_read' argument 7 names different: declaration 'barray' definition 'b'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:251:27: note: Function 'ppma_read' argument 7 names different: declaration 'barray' definition 'b'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:337:69: style:inconclusive: Function 'ppma_read_data' argument 4 names different: declaration 'rarray' definition 'r'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.H:7:69: note: Function 'ppma_read_data' argument 4 names different: declaration 'rarray' definition 'r'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:337:69: note: Function 'ppma_read_data' argument 4 names different: declaration 'rarray' definition 'r'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:338:8: style:inconclusive: Function 'ppma_read_data' argument 5 names different: declaration 'garray' definition 'g'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.H:8:13: note: Function 'ppma_read_data' argument 5 names different: declaration 'garray' definition 'g'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:338:8: note: Function 'ppma_read_data' argument 5 names different: declaration 'garray' definition 'g'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:338:16: style:inconclusive: Function 'ppma_read_data' argument 6 names different: declaration 'barray' definition 'b'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.H:8:26: note: Function 'ppma_read_data' argument 6 names different: declaration 'barray' definition 'b'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:338:16: note: Function 'ppma_read_data' argument 6 names different: declaration 'barray' definition 'b'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:601:67: style:inconclusive: Function 'ppma_write' argument 4 names different: declaration 'rarray' definition 'r'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.H:12:67: note: Function 'ppma_write' argument 4 names different: declaration 'rarray' definition 'r'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:601:67: note: Function 'ppma_write' argument 4 names different: declaration 'rarray' definition 'r'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:602:8: style:inconclusive: Function 'ppma_write' argument 5 names different: declaration 'garray' definition 'g'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.H:13:12: note: Function 'ppma_write' argument 5 names different: declaration 'garray' definition 'g'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:602:8: note: Function 'ppma_write' argument 5 names different: declaration 'garray' definition 'g'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:602:16: style:inconclusive: Function 'ppma_write' argument 6 names different: declaration 'barray' definition 'b'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.H:13:25: note: Function 'ppma_write' argument 6 names different: declaration 'barray' definition 'b'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:602:16: note: Function 'ppma_write' argument 6 names different: declaration 'barray' definition 'b'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:716:71: style:inconclusive: Function 'ppma_write_data' argument 4 names different: declaration 'rarray' definition 'r'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.H:14:71: note: Function 'ppma_write_data' argument 4 names different: declaration 'rarray' definition 'r'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:716:71: note: Function 'ppma_write_data' argument 4 names different: declaration 'rarray' definition 'r'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:717:8: style:inconclusive: Function 'ppma_write_data' argument 5 names different: declaration 'garray' definition 'g'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.H:15:13: note: Function 'ppma_write_data' argument 5 names different: declaration 'garray' definition 'g'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:717:8: note: Function 'ppma_write_data' argument 5 names different: declaration 'garray' definition 'g'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:717:16: style:inconclusive: Function 'ppma_write_data' argument 6 names different: declaration 'barray' definition 'b'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.H:15:26: note: Function 'ppma_write_data' argument 6 names different: declaration 'barray' definition 'b'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:717:16: note: Function 'ppma_write_data' argument 6 names different: declaration 'barray' definition 'b'.
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:784:52: style: Parameter 'file_out_name' can be declared as pointer to const [constParameterPointer]
phipack-0.0.20160614/src/ppma_2_bmp/ppma_io.C:855:7: style: Unused variable: maxrgb [unusedVariable]
phipack-0.0.20160614/src/profile.c:43:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/profile.c:222:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/profile.c:308:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/profile.c:117:13: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
phipack-0.0.20160614/src/profile.c:119:8: note: Found duplicate branches for 'if' and 'else'.
phipack-0.0.20160614/src/profile.c:117:13: note: Found duplicate branches for 'if' and 'else'.
phipack-0.0.20160614/src/profile.c:74:9: style: Variable 'cur' can be declared as pointer to const [constVariablePointer]
phipack-0.0.20160614/src/queue.c:82:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/queue.c:60:19: style: Variable 'mapped_index' is assigned a value that is never used. [unreadVariable]
phipack-0.0.20160614/src/seqManip.c:58:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inf [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/seqManip.c:123:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inf [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/seqManip.c:177:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inf [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/seqManip.c:309:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable orig_index [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/seqManip.c:347:21: style: The if condition is the same as the previous if condition [duplicateCondition]
phipack-0.0.20160614/src/seqManip.c:336:22: note: First condition
phipack-0.0.20160614/src/seqManip.c:347:21: note: Second condition
phipack-0.0.20160614/src/seqManip.c:254:75: style:inconclusive: Function 'find_states' argument 3 names different: declaration 'ignoreMissing' definition 'stateMissing'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/seqManip.h:50:75: note: Function 'find_states' argument 3 names different: declaration 'ignoreMissing' definition 'stateMissing'.
phipack-0.0.20160614/src/seqManip.c:254:75: note: Function 'find_states' argument 3 names different: declaration 'ignoreMissing' definition 'stateMissing'.
phipack-0.0.20160614/src/seqManip.c:393:78: style:inconclusive: Function 'reorder_chars' argument 3 names different: declaration 'ignoreMissing' definition 'stateMissing'. [funcArgNamesDifferent]
phipack-0.0.20160614/src/seqManip.h:68:78: note: Function 'reorder_chars' argument 3 names different: declaration 'ignoreMissing' definition 'stateMissing'.
phipack-0.0.20160614/src/seqManip.c:393:78: note: Function 'reorder_chars' argument 3 names different: declaration 'ignoreMissing' definition 'stateMissing'.
phipack-0.0.20160614/src/seqManip.c:28:71: style: Parameter 'site_states' can be declared as pointer to const [constParameterPointer]
phipack-0.0.20160614/src/seqManip.c:93:67: style: Parameter 'site_states' can be declared as pointer to const [constParameterPointer]
phipack-0.0.20160614/src/seqManip.c:147:71: style: Parameter 'site_states' can be declared as pointer to const [constParameterPointer]
phipack-0.0.20160614/src/seqManip.c:216:18: style: Variable 'count' is assigned a value that is never used. [unreadVariable]
phipack-0.0.20160614/src/seqManip.c:216:24: style: Variable 'num' is assigned a value that is never used. [unreadVariable]
phipack-0.0.20160614/src/seqManip.c:258:26: style: Variable 'missing_ambig_count' is assigned a value that is never used. [unreadVariable]
phipack-0.0.20160614/src/stats.c:84:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
phipack-0.0.20160614/src/stats.c:109:39: style: Parameter 'num_states' can be declared as pointer to const [constParameterPointer]
phipack-0.0.20160614/src/stats.c:109:55: style: Parameter 'permutation' can be declared as pointer to const [constParameterPointer]
phipack-0.0.20160614/src/stats.c:139:40: style: Parameter 'permutation' can be declared as pointer to const [constParameterPointer]
phipack-0.0.20160614/src/stats.c:120:15: style: Variable 'states_i' is assigned a value that is never used. [unreadVariable]
phipack-0.0.20160614/src/stats.c:127:16: style: Variable 'states_j' is assigned a value that is never used. [unreadVariable]
phipack-0.0.20160614/src/stats.c:166:17: style: Variable 'fscore' is assigned a value that is never used. [unreadVariable]
phipack-0.0.20160614/src/stats.c:166:28: style: Variable 'gscore' is assigned a value that is never used. [unreadVariable]
phipack-0.0.20160614/src/misc.c:95:12: warning: Null pointer dereference: in_file [ctunullpointer]
phipack-0.0.20160614/src/fasta.c:185:14: note: Assuming that condition 'in_file==NULL' is not redundant
phipack-0.0.20160614/src/fasta.c:209:28: note: Calling function skip_non_newline_space, 1st argument is null
phipack-0.0.20160614/src/misc.c:95:12: note: Dereferencing argument in_file that is null
diff:


DONE