2024-04-21 23:58 ftp://ftp.de.debian.org/debian/pool/main/s/samtools/samtools_1.19.2.orig.tar.gz cppcheck-options: --library=posix --library=gnu --library=bsd --library=zlib --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 -j4 platform: Linux-6.1.0-20-amd64-x86_64-with-glibc2.36 python: 3.11.2 client-version: 1.3.56 compiler: g++ (Debian 12.2.0-14) 12.2.0 cppcheck: head 2.14.0 head-info: ea2e716 (2024-04-21 15:59:20 +0200) count: 114 114 elapsed-time: 1.0 1.0 head-timing-info: old-timing-info: head results: samtools-1.19.2/bam2bcf.c:88:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar] samtools-1.19.2/sam_utils.h:37:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_SET_INIT_INT is a macro then please configure it. [unknownMacro] samtools-1.19.2/bam.c:72:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar] samtools-1.19.2/bam_color.c:54:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar] samtools-1.19.2/bam_color.c:83:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar] samtools-1.19.2/bam_color.c:144:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar] samtools-1.19.2/bam2bcf.c:118:43: style: Variable 'min_dist' is assigned a value that is never used. [unreadVariable] samtools-1.19.2/bam_color.c:43:11: style: Variable 'cs' can be declared as pointer to const [constVariablePointer] samtools-1.19.2/bam_color.c:72:11: style: Variable 'cq' can be declared as pointer to const [constVariablePointer] samtools-1.19.2/bam.c:35:40: style:inconclusive: Function 'bam_get_library' argument 1 names different: declaration 'header' definition 'h'. [funcArgNamesDifferent] samtools-1.19.2/bam.h:32:40: note: Function 'bam_get_library' argument 1 names different: declaration 'header' definition 'h'. samtools-1.19.2/bam.c:35:40: note: Function 'bam_get_library' argument 1 names different: declaration 'header' definition 'h'. samtools-1.19.2/bam_quickcheck.c:82:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hts_verbose [valueFlowBailoutIncompleteVar] samtools-1.19.2/bam_samples.c:37:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_STR is a macro then please configure it. [unknownMacro] samtools-1.19.2/bam_tview.h:42:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_STR is a macro then please configure it. [unknownMacro] samtools-1.19.2/bam_lpileup.c:42:1: style:inconclusive: Function 'splay_flatten_node' argument 1 names different: declaration 'node' definition 'head'. [funcArgNamesDifferent] samtools-1.19.2/bam_lpileup.c:42:1: note: Function 'splay_flatten_node' argument 1 names different: declaration 'node' definition 'head'. samtools-1.19.2/bam_lpileup.c:42:1: note: Function 'splay_flatten_node' argument 1 names different: declaration 'node' definition 'head'. samtools-1.19.2/bam_lpileup.c:42:1: style:inconclusive: Function 'splay_insert_node' argument 1 names different: declaration 'node' definition 'head'. [funcArgNamesDifferent] samtools-1.19.2/bam_lpileup.c:42:1: note: Function 'splay_insert_node' argument 1 names different: declaration 'node' definition 'head'. samtools-1.19.2/bam_lpileup.c:42:1: note: Function 'splay_insert_node' argument 1 names different: declaration 'node' definition 'head'. samtools-1.19.2/bam_lpileup.c:222:52: style:inconclusive: Function 'bam_lplbuf_push' argument 2 names different: declaration 'buf' definition 'tv'. [funcArgNamesDifferent] samtools-1.19.2/bam_lpileup.h:52:56: note: Function 'bam_lplbuf_push' argument 2 names different: declaration 'buf' definition 'tv'. samtools-1.19.2/bam_lpileup.c:222:52: note: Function 'bam_lplbuf_push' argument 2 names different: declaration 'buf' definition 'tv'. samtools-1.19.2/bam_lpileup.c:122:30: style: Local variable 'p' shadows outer variable [shadowVariable] samtools-1.19.2/bam_lpileup.c:106:17: note: Shadowed declaration samtools-1.19.2/bam_lpileup.c:122:30: note: Shadow variable samtools-1.19.2/bam_lpileup.c:125:29: style: Local variable 'p' shadows outer variable [shadowVariable] samtools-1.19.2/bam_lpileup.c:122:30: note: Shadowed declaration samtools-1.19.2/bam_lpileup.c:125:29: note: Shadow variable samtools-1.19.2/bam_lpileup.c:176:30: style: Local variable 'p' shadows outer variable [shadowVariable] samtools-1.19.2/bam_lpileup.c:106:17: note: Shadowed declaration samtools-1.19.2/bam_lpileup.c:176:30: note: Shadow variable samtools-1.19.2/bedidx.c:39:1: error: There is an unknown macro here somewhere. Configuration is required. If KSTREAM_INIT is a macro then please configure it. [unknownMacro] samtools-1.19.2/consensus_pileup.c:86:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CPAD [valueFlowBailoutIncompleteVar] samtools-1.19.2/consensus_pileup.c:346:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] samtools-1.19.2/misc/ace2sam.c:35:1: error: There is an unknown macro here somewhere. Configuration is required. If KSTREAM_INIT is a macro then please configure it. [unknownMacro] samtools-1.19.2/misc/maq2sam.c:97:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] samtools-1.19.2/misc/maq2sam.c:207:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] samtools-1.19.2/misc/maq2sam.c:215:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] samtools-1.19.2/bam_quickcheck.c:157:17: style: Local variable 'ret' shadows outer variable [shadowVariable] samtools-1.19.2/bam_quickcheck.c:119:9: note: Shadowed declaration samtools-1.19.2/bam_quickcheck.c:157:17: note: Shadow variable samtools-1.19.2/misc/md5fa.c:32:1: error: There is an unknown macro here somewhere. Configuration is required. If KSEQ_INIT is a macro then please configure it. [unknownMacro] samtools-1.19.2/misc/md5sum-lite.c:40:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] samtools-1.19.2/misc/wgsim.c:46:1: error: There is an unknown macro here somewhere. Configuration is required. If KSEQ_INIT is a macro then please configure it. [unknownMacro] samtools-1.19.2/misc/maq2sam.c:94:5: warning: Return value of function gzread() is not used. [ignoredReturnValue] samtools-1.19.2/misc/maq2sam.c:120:9: warning: Return value of function gzread() is not used. [ignoredReturnValue] samtools-1.19.2/misc/maq2sam.c:126:9: warning: Return value of function gzread() is not used. [ignoredReturnValue] samtools-1.19.2/misc/maq2sam.c:133:5: warning: Return value of function gzread() is not used. [ignoredReturnValue] samtools-1.19.2/misc/maq2sam.c:174:9: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] samtools-1.19.2/sam_opts.c:71:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] samtools-1.19.2/sam_opts.c:140:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar] samtools-1.19.2/consensus_pileup.c:390:31: style: Condition 'phead' is always true [knownConditionTrueFalse] samtools-1.19.2/sample.c:32:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_STR is a macro then please configure it. [unknownMacro] samtools-1.19.2/sam_opts.c:111:18: style: Variable 'opts' can be declared as pointer to const [constVariablePointer] samtools-1.19.2/stats_isize.h:41:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_INT is a macro then please configure it. [unknownMacro] samtools-1.19.2/test/split/test_filter_header_rg.c:180:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar] samtools-1.19.2/test/test.c:44:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] samtools-1.19.2/test/test.c:51:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_WRONLY [valueFlowBailoutIncompleteVar] samtools-1.19.2/test/test.c:62:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] samtools-1.19.2/test/test.c:75:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar] samtools-1.19.2/test/test.c:43:9: error: Return value of allocation function 'freopen' is not stored. [leakReturnValNotUsed] samtools-1.19.2/test/vcf-miniview.c:36:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] samtools-1.19.2/test/vcf-miniview.c:45:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] samtools-1.19.2/tmp_file.c:51:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] samtools-1.19.2/tmp_file.c:66:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam1_t [valueFlowBailoutIncompleteVar] samtools-1.19.2/tmp_file.c:114:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDWR [valueFlowBailoutIncompleteVar] samtools-1.19.2/tmp_file.c:194:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam1_t [valueFlowBailoutIncompleteVar] samtools-1.19.2/tmp_file.c:252:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam1_t [valueFlowBailoutIncompleteVar] samtools-1.19.2/tmp_file.c:381:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam1_t [valueFlowBailoutIncompleteVar] samtools-1.19.2/tmp_file.c:108:9: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] samtools-1.19.2/tmp_file.c:46:41: style: Parameter 'tmp' can be declared as pointer to const [constParameterPointer] samtools-1.19.2/tmp_file.c:250:45: style: Parameter 'inbam' can be declared as pointer to const [constParameterPointer] samtools-1.19.2/test/vcf-miniview.c:84:15: style: Variable 'fixed' can be declared as pointer to const [constVariablePointer] samtools-1.19.2/test/split/test_filter_header_rg.c:227:9: style: The if condition is the same as the previous if condition [duplicateCondition] samtools-1.19.2/test/split/test_filter_header_rg.c:225:9: note: First condition samtools-1.19.2/test/split/test_filter_header_rg.c:227:9: note: Second condition samtools-1.19.2/test/split/test_filter_header_rg.c:270:9: style: The if condition is the same as the previous if condition [duplicateCondition] samtools-1.19.2/test/split/test_filter_header_rg.c:268:9: note: First condition samtools-1.19.2/test/split/test_filter_header_rg.c:270:9: note: Second condition samtools-1.19.2/lz4/lz4.c:567:29: style:inconclusive: Boolean expression 'ip>anchor' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean] samtools-1.19.2/lz4/lz4.c:1159:65: style:inconclusive: Boolean expression '(endOnInput?(ip