2025-11-23 17:53
ftp://ftp.de.debian.org/debian/pool/main/r/r-bioc-edger/r-bioc-edger_4.4.2+dfsg.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 -j4
platform: Linux-5.4.0-216-generic-x86_64-with-glibc2.29
python: 3.8.10
client-version: 1.3.69
compiler: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
cppcheck: head 2.18.0
head-info: cb76e52 (2025-11-22 14:47:37 +0100)
count: 158 157
elapsed-time: 1.8 2.1
head-timing-info:

old-timing-info:

head results:
edgeR/src/R_exports.c:18:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
edgeR/src/R_exports.c:53:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
edgeR/src/R_exports.c:88:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
edgeR/src/R_exports.c:104:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
edgeR/src/R_exports.c:126:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
edgeR/src/R_exports.c:142:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
edgeR/src/R_exports.c:185:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
edgeR/src/R_exports.c:212:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
edgeR/src/R_exports.c:235:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
edgeR/src/R_exports.c:251:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
edgeR/src/R_exports.c:278:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
edgeR/src/R_exports.c:324:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LGLSXP [valueFlowBailoutIncompleteVar]
edgeR/src/R_exports.c:343:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
edgeR/src/R_exports.c:366:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
edgeR/src/R_exports.c:390:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
edgeR/src/R_exports.c:438:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
edgeR/src/R_exports.c:475:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
edgeR/src/R_exports.c:513:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
edgeR/src/compute_apl.c:37:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dsytrf [valueFlowBailoutIncompleteVar]
edgeR/src/compute_cpm.c:53:77: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NaN [valueFlowBailoutIncompleteVar]
edgeR/src/R_process_hairpin_reads.c:397:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
edgeR/src/compute_cpm.c:155:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NA_REAL [valueFlowBailoutIncompleteVar]
edgeR/src/clowess.c:70:21: style: Parameter 'x' can be declared as pointer to const [constParameterPointer]
edgeR/src/clowess.c:70:32: style: Parameter 'y' can be declared as pointer to const [constParameterPointer]
edgeR/src/clowess.c:70:50: style: Parameter 'xs' can be declared as pointer to const [constParameterPointer]
edgeR/src/clowess.c:70:118: style: Parameter 'rw' can be declared as pointer to const [constParameterPointer]
edgeR/src/compute_cpm.c:18:24: style: Parameter 'y' can be declared as pointer to const [constParameterPointer]
edgeR/src/compute_cpm.c:63:24: style: Parameter 'y' can be declared as pointer to const [constParameterPointer]
edgeR/src/compute_apl.c:103:29: warning: Invalid log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
edgeR/src/compute_apl.c:100:24: note: Assignment 'adj=0', assigned value is 0
edgeR/src/compute_apl.c:102:34: note: Assuming condition is false
edgeR/src/compute_apl.c:103:29: note: Invalid argument
edgeR/src/compute_nbdev.c:18:29: style: Parameter 'y' can be declared as pointer to const [constParameterPointer]
edgeR/src/compute_nbdev.c:18:37: style: Parameter 'mu' can be declared as pointer to const [constParameterPointer]
edgeR/src/compute_nbdev.c:53:30: style: Parameter 'y' can be declared as pointer to const [constParameterPointer]
edgeR/src/compute_nbdev.c:53:38: style: Parameter 'mu' can be declared as pointer to const [constParameterPointer]
edgeR/src/compute_apl.c:183:48: style: Parameter 'X' can be declared as pointer to const [constParameterPointer]
edgeR/src/compute_apl.c:183:59: style: Parameter 'W' can be declared as pointer to const [constParameterPointer]
edgeR/src/exact_test_by_dev.c:20:29: style: Parameter 's1' can be declared as pointer to const [constParameterPointer]
edgeR/src/exact_test_by_dev.c:20:38: style: Parameter 's2' can be declared as pointer to const [constParameterPointer]
edgeR/src/exact_test_by_dev.c:20:76: style: Parameter 'disp' can be declared as pointer to const [constParameterPointer]
edgeR/src/glm.c:52:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NegInf [valueFlowBailoutIncompleteVar]
edgeR/src/glm.c:145:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable R_NegInf [valueFlowBailoutIncompleteVar]
edgeR/src/glm.c:244:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dgeqrf [valueFlowBailoutIncompleteVar]
edgeR/src/glm.c:555:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NA_REAL [valueFlowBailoutIncompleteVar]
edgeR/src/glm.c:762:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dgemv [valueFlowBailoutIncompleteVar]
edgeR/src/fmm_spline.c:59:32: style: Parameter 'x' can be declared as pointer to const [constParameterPointer]
edgeR/src/fmm_spline.c:59:43: style: Parameter 'y' can be declared as pointer to const [constParameterPointer]
edgeR/src/init.c:41:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
edgeR/src/good_turing.c:28:34: style: Parameter 'Freq' can be declared as pointer to const [constParameterPointer]
edgeR/src/interpolator.c:92:26: style: Variable 'maxed' is assigned a value that is never used. [unreadVariable]
edgeR/src/loess_by_col.c:25:41: style: Parameter 'y' can be declared as pointer to const [constParameterPointer]
edgeR/src/object.c:7:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REALSXP [valueFlowBailoutIncompleteVar]
edgeR/src/ql_glm.c:290:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dqrdc2 [valueFlowBailoutIncompleteVar]
edgeR/src/object.c:18:10: style: Variable 'dims' can be declared as pointer to const [constVariablePointer]
edgeR/src/object.c:35:10: style: Variable 'dims' can be declared as pointer to const [constVariablePointer]
edgeR/src/object.c:121:28: style: Parameter 'cmat' can be declared as pointer to const [constParameterPointer]
edgeR/src/object.c:22:12: warning: Uninitialized variables: res.dmat, res.imat [uninitvar]
edgeR/src/object.c:7:19: note: Assuming condition is false
edgeR/src/object.c:22:12: note: Uninitialized variables: res.dmat, res.imat
edgeR/src/object.c:47:12: error: Uninitialized variable: res.imat [uninitvar]
edgeR/src/ql_glm.c:185:35: style: Parameter 'y' can be declared as pointer to const [constParameterPointer]
edgeR/src/ql_glm.c:208:31: style: Parameter 'ag' can be declared as pointer to const [constParameterPointer]
edgeR/src/ql_glm.c:208:43: style: Parameter 's2' can be declared as pointer to const [constParameterPointer]
edgeR/src/ql_glm.c:208:55: style: Parameter 'df' can be declared as pointer to const [constParameterPointer]
edgeR/src/glm.c:18:42: style: Parameter 'counts' can be declared as pointer to const [constParameterPointer]
edgeR/src/glm.c:18:58: style: Parameter 'offset' can be declared as pointer to const [constParameterPointer]
edgeR/src/glm.c:18:74: style: Parameter 'disp' can be declared as pointer to const [constParameterPointer]
edgeR/src/glm.c:18:88: style: Parameter 'weights' can be declared as pointer to const [constParameterPointer]
edgeR/src/glm.c:91:103: style: Parameter 'beta' can be declared as pointer to const [constParameterPointer]
edgeR/src/glm.c:184:52: style: Parameter 'group' can be declared as pointer to const [constParameterPointer]
edgeR/src/glm.c:533:65: style: Parameter 'disp' can be declared as pointer to const [constParameterPointer]
edgeR/src/glm.c:533:79: style: Parameter 'w' can be declared as pointer to const [constParameterPointer]
edgeR/src/glm.c:745:68: style: Parameter 'offset' can be declared as pointer to const [constParameterPointer]
edgeR/src/glm.c:784:27: style: Parameter 'mu' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:444:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
edgeR/src/R_process_hairpin_reads.c:445:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
edgeR/src/R_process_hairpin_reads.c:449:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
edgeR/src/R_process_hairpin_reads.c:450:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
edgeR/src/R_process_hairpin_reads.c:114:3: warning: If memory allocation fails, then there is a possible null pointer dereference: this_node [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:113:45: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:113:26: note: Assignment 'this_node=(struct trie_node*)malloc(sizeof(struct trie_node))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:114:3: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:115:3: warning: If memory allocation fails, then there is a possible null pointer dereference: this_node [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:113:45: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:113:26: note: Assignment 'this_node=(struct trie_node*)malloc(sizeof(struct trie_node))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:115:3: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:116:3: warning: If memory allocation fails, then there is a possible null pointer dereference: this_node [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:113:45: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:113:26: note: Assignment 'this_node=(struct trie_node*)malloc(sizeof(struct trie_node))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:116:3: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:120:5: warning: If memory allocation fails, then there is a possible null pointer dereference: this_node [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:113:45: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:113:26: note: Assignment 'this_node=(struct trie_node*)malloc(sizeof(struct trie_node))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:120:5: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:139:3: warning: If memory allocation fails, then there is a possible null pointer dereference: end [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:137:37: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:137:19: note: Assignment 'end=(struct end_node*)malloc(sizeof(struct end_node))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:139:3: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:140:3: warning: If memory allocation fails, then there is a possible null pointer dereference: end [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:137:37: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:137:19: note: Assignment 'end=(struct end_node*)malloc(sizeof(struct end_node))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:140:3: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:327:5: warning: If memory allocation fails, then there is a possible null pointer dereference: new [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:323:29: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:323:15: note: Assignment 'new=(long*)malloc(sizeof(long)*size)', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:327:5: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:395:14: warning: If resource allocation fails, then there is a possible null pointer dereference: fin [nullPointerOutOfResources]
edgeR/src/R_process_hairpin_reads.c:478:14: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:478:14: note: Assignment 'fin=fopen(filename,"r")', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:481:35: note: Calling function 'Get_Lines_In_File', 1st argument 'fin' value is 0
edgeR/src/R_process_hairpin_reads.c:395:14: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:404:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fin [nullPointerOutOfResources]
edgeR/src/R_process_hairpin_reads.c:478:14: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:478:14: note: Assignment 'fin=fopen(filename,"r")', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:481:35: note: Calling function 'Get_Lines_In_File', 1st argument 'fin' value is 0
edgeR/src/R_process_hairpin_reads.c:404:10: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:435:28: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: line [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:430:24: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:430:10: note: Assignment 'line=(char*)malloc(sizeof(char)*(len+1))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:435:28: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:435:39: warning: If resource allocation fails, then there is a possible null pointer dereference: fin [nullPointerOutOfResources]
edgeR/src/R_process_hairpin_reads.c:424:14: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:424:14: note: Assignment 'fin=fopen(filename,"r")', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:435:39: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:438:5: warning: If memory allocation fails, then there is a possible null pointer dereference: new_barcode [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:437:38: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:437:19: note: Assignment 'new_barcode=(struct a_barcode*)malloc(sizeof(struct a_barcode))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:438:5: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:440:13: warning: If memory allocation fails, then there is a possible null pointer dereference: new_barcode [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:437:38: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:437:19: note: Assignment 'new_barcode=(struct a_barcode*)malloc(sizeof(struct a_barcode))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:440:13: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:440:36: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: line [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:430:24: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:430:10: note: Assignment 'line=(char*)malloc(sizeof(char)*(len+1))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:440:36: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:441:5: warning: If memory allocation fails, then there is a possible null pointer dereference: new_barcode [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:437:38: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:437:19: note: Assignment 'new_barcode=(struct a_barcode*)malloc(sizeof(struct a_barcode))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:441:5: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:459:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fin [nullPointerOutOfResources]
edgeR/src/R_process_hairpin_reads.c:424:14: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:424:14: note: Assignment 'fin=fopen(filename,"r")', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:459:10: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:490:28: warning: If memory allocation fails, then there is a possible null pointer dereference: line [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:486:24: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:486:10: note: Assignment 'line=(char*)malloc(len+1)', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:490:28: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:490:39: warning: If resource allocation fails, then there is a possible null pointer dereference: fin [nullPointerOutOfResources]
edgeR/src/R_process_hairpin_reads.c:478:14: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:478:14: note: Assignment 'fin=fopen(filename,"r")', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:490:39: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:493:5: warning: If memory allocation fails, then there is a possible null pointer dereference: new_hairpin [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:492:38: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:492:19: note: Assignment 'new_hairpin=(struct a_hairpin*)malloc(sizeof(struct a_hairpin))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:493:5: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:494:5: warning: If memory allocation fails, then there is a possible null pointer dereference: new_hairpin [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:492:38: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:492:19: note: Assignment 'new_hairpin=(struct a_hairpin*)malloc(sizeof(struct a_hairpin))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:494:5: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:495:13: warning: If memory allocation fails, then there is a possible null pointer dereference: new_hairpin [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:492:38: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:492:19: note: Assignment 'new_hairpin=(struct a_hairpin*)malloc(sizeof(struct a_hairpin))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:495:13: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:495:36: warning: If memory allocation fails, then there is a possible null pointer dereference: line [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:486:24: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:486:10: note: Assignment 'line=(char*)malloc(len+1)', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:495:36: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:498:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fin [nullPointerOutOfResources]
edgeR/src/R_process_hairpin_reads.c:478:14: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:478:14: note: Assignment 'fin=fopen(filename,"r")', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:498:10: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:862:13: warning: If memory allocation fails, then there is a possible null pointer dereference: barcode1 [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:861:30: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:861:16: note: Assignment 'barcode1=(char*)malloc(barcode_length*sizeof(char))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:862:13: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:864:13: warning: If memory allocation fails, then there is a possible null pointer dereference: barcode2 [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:863:30: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:863:16: note: Assignment 'barcode2=(char*)malloc(barcode_length_rev*sizeof(char))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:864:13: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:943:13: warning: If memory allocation fails, then there is a possible null pointer dereference: barcode1 [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:942:30: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:942:16: note: Assignment 'barcode1=(char*)malloc(barcode_length*sizeof(char))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:943:13: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:945:13: warning: If memory allocation fails, then there is a possible null pointer dereference: barcode2 [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:944:30: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:944:16: note: Assignment 'barcode2=(char*)malloc(barcode2_length*sizeof(char))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:945:13: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:1225:28: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: line [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:1201:24: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:1201:10: note: Assignment 'line=(char*)malloc(sizeof(char)*(len+1))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:1225:28: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:1225:39: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: fin [nullPointerOutOfResources]
edgeR/src/R_process_hairpin_reads.c:1202:14: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:1202:14: note: Assignment 'fin=fopen(filename,"r")', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:1225:39: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:1413:13: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
edgeR/src/R_process_hairpin_reads.c:1411:15: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:1411:15: note: Assignment 'fout=fopen(output,"w")', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:1413:13: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:1415:15: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
edgeR/src/R_process_hairpin_reads.c:1411:15: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:1411:15: note: Assignment 'fout=fopen(output,"w")', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:1415:15: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:1417:13: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
edgeR/src/R_process_hairpin_reads.c:1411:15: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:1411:15: note: Assignment 'fout=fopen(output,"w")', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:1417:13: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:1419:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
edgeR/src/R_process_hairpin_reads.c:1411:15: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:1411:15: note: Assignment 'fout=fopen(output,"w")', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:1419:10: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:1443:11: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
edgeR/src/R_process_hairpin_reads.c:1442:15: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:1442:15: note: Assignment 'fout=fopen(output,"w")', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:1443:11: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:1445:13: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
edgeR/src/R_process_hairpin_reads.c:1442:15: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:1442:15: note: Assignment 'fout=fopen(output,"w")', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:1445:13: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:1447:11: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
edgeR/src/R_process_hairpin_reads.c:1442:15: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:1442:15: note: Assignment 'fout=fopen(output,"w")', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:1447:11: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:1448:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
edgeR/src/R_process_hairpin_reads.c:1442:15: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:1442:15: note: Assignment 'fout=fopen(output,"w")', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:1448:10: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:1530:5: warning: If memory allocation fails, then there is a possible null pointer dereference: summary [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:1528:28: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:1528:13: note: Assignment 'summary=(long**)malloc((num_hairpin+1)*sizeof(long*))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:1530:5: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:1535:7: warning: If memory allocation fails, then there is a possible null pointer dereference: summary [nullPointerOutOfMemory]
edgeR/src/R_process_hairpin_reads.c:1528:28: note: Assuming allocation function fails
edgeR/src/R_process_hairpin_reads.c:1528:13: note: Assignment 'summary=(long**)malloc((num_hairpin+1)*sizeof(long*))', assigned value is 0
edgeR/src/R_process_hairpin_reads.c:1535:7: note: Null pointer dereference
edgeR/src/R_process_hairpin_reads.c:445:13: style: Variable 'token' is reassigned a value before the old one has been used. [redundantAssignment]
edgeR/src/R_process_hairpin_reads.c:444:13: note: token is assigned
edgeR/src/R_process_hairpin_reads.c:445:13: note: token is overwritten
edgeR/src/R_process_hairpin_reads.c:450:13: style: Variable 'token' is reassigned a value before the old one has been used. [redundantAssignment]
edgeR/src/R_process_hairpin_reads.c:449:13: note: token is assigned
edgeR/src/R_process_hairpin_reads.c:450:13: note: token is overwritten
edgeR/src/R_process_hairpin_reads.c:146:25: style: Parameter 'node' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:207:9: style: Variable 'cur_seq' can be declared as pointer to const [constVariablePointer]
edgeR/src/R_process_hairpin_reads.c:257:9: style: Variable 'cur_seq' can be declared as pointer to const [constVariablePointer]
edgeR/src/R_process_hairpin_reads.c:409:24: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:422:9: style: Variable 'readline' can be declared as pointer to const [constVariablePointer]
edgeR/src/R_process_hairpin_reads.c:433:10: style: Variable 'token' can be declared as pointer to const [constVariablePointer]
edgeR/src/R_process_hairpin_reads.c:466:24: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:476:9: style: Variable 'readline' can be declared as pointer to const [constVariablePointer]
edgeR/src/R_process_hairpin_reads.c:523:53: style: Parameter 'read' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:663:19: style: Parameter 'sequence1' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:663:36: style: Parameter 'sequence2' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:693:36: style: Parameter 'a_barcode' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:693:53: style: Parameter 'a_barcode_rev' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:729:39: style: Parameter 'a_barcode' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:729:56: style: Parameter 'a_barcode2' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1033:28: style: Parameter 'barcode1' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1033:49: style: Parameter 'barcode2' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1080:19: style: Parameter 'base' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1196:9: style: Variable 'readline' can be declared as pointer to const [constVariablePointer]
edgeR/src/R_process_hairpin_reads.c:1197:9: style: Variable 'readline2' can be declared as pointer to const [constVariablePointer]
edgeR/src/R_process_hairpin_reads.c:1402:28: style: Parameter 'output' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1424:33: style: Parameter 'output' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1424:47: style: Parameter 'arr' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1541:26: style: Parameter 'isPairedReads' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1541:46: style: Parameter 'isDualIndexingReads' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1542:53: style: Parameter 'filecount' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1544:26: style: Parameter 'barcodeLength' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1544:46: style: Parameter 'barcode2Length' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1544:67: style: Parameter 'barcodeLengthRev' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1545:26: style: Parameter 'hairpinLength' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1546:26: style: Parameter 'allowMismatch' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1546:46: style: Parameter 'barcodemismatch' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1546:68: style: Parameter 'hairpinmismatch' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1547:41: style: Parameter 'verbose' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1547:55: style: Parameter 'barcodesInHeader' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1547:78: style: Parameter 'plot_positions' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:1549:11: style: Parameter 'hairpinBeforeBarcode' can be declared as pointer to const [constParameterPointer]
edgeR/src/R_process_hairpin_reads.c:875:18: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
edgeR/src/R_process_hairpin_reads.c:956:18: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
edgeR/src/ql_weights.c:62:23: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
edgeR/src/ql_weights.c:114:23: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
edgeR/src/ql_weights.c:167:23: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
edgeR/src/ql_weights.c:216:23: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
diff:
head edgeR/src/compute_apl.c:183:48: style: Parameter 'X' can be declared as pointer to const [constParameterPointer]


DONE