Flawfinder version 2.0.10, (C) 2001-2019 David A. Wheeler.
Number of rules (primarily dangerous function names) in C/C++ ruleset: 223
Examining data/r-bioc-biostrings-2.58.0/inst/include/Biostrings_defines.h
Examining data/r-bioc-biostrings-2.58.0/inst/include/Biostrings_interface.h
Examining data/r-bioc-biostrings-2.58.0/inst/include/_Biostrings_stubs.c
Examining data/r-bioc-biostrings-2.58.0/src/BAB_class.c
Examining data/r-bioc-biostrings-2.58.0/src/Biostrings.h
Examining data/r-bioc-biostrings-2.58.0/src/BitMatrix.c
Examining data/r-bioc-biostrings-2.58.0/src/IRanges_stubs.c
Examining data/r-bioc-biostrings-2.58.0/src/MIndex_class.c
Examining data/r-bioc-biostrings-2.58.0/src/PreprocessedTB_class.c
Examining data/r-bioc-biostrings-2.58.0/src/R_init_Biostrings.c
Examining data/r-bioc-biostrings-2.58.0/src/RoSeqs_utils.c
Examining data/r-bioc-biostrings-2.58.0/src/S4Vectors_stubs.c
Examining data/r-bioc-biostrings-2.58.0/src/SparseList_utils.c
Examining data/r-bioc-biostrings-2.58.0/src/XStringSetList_class.c
Examining data/r-bioc-biostrings-2.58.0/src/XStringSet_class.c
Examining data/r-bioc-biostrings-2.58.0/src/XString_class.c
Examining data/r-bioc-biostrings-2.58.0/src/XVector_stubs.c
Examining data/r-bioc-biostrings-2.58.0/src/align_needwunsQS.c
Examining data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c
Examining data/r-bioc-biostrings-2.58.0/src/align_utils.c
Examining data/r-bioc-biostrings-2.58.0/src/find_palindromes.c
Examining data/r-bioc-biostrings-2.58.0/src/gtestsim.c
Examining data/r-bioc-biostrings-2.58.0/src/inject_code.c
Examining data/r-bioc-biostrings-2.58.0/src/letter_frequency.c
Examining data/r-bioc-biostrings-2.58.0/src/lowlevel_matching.c
Examining data/r-bioc-biostrings-2.58.0/src/match_PWM.c
Examining data/r-bioc-biostrings-2.58.0/src/match_pattern.c
Examining data/r-bioc-biostrings-2.58.0/src/match_pattern_boyermoore.c
Examining data/r-bioc-biostrings-2.58.0/src/match_pattern_indels.c
Examining data/r-bioc-biostrings-2.58.0/src/match_pattern_shiftor.c
Examining data/r-bioc-biostrings-2.58.0/src/match_pdict.c
Examining data/r-bioc-biostrings-2.58.0/src/match_pdict_ACtree2.c
Examining data/r-bioc-biostrings-2.58.0/src/match_pdict_Twobit.c
Examining data/r-bioc-biostrings-2.58.0/src/match_pdict_utils.c
Examining data/r-bioc-biostrings-2.58.0/src/match_reporting.c
Examining data/r-bioc-biostrings-2.58.0/src/matchprobes.c
Examining data/r-bioc-biostrings-2.58.0/src/pmatchPattern.c
Examining data/r-bioc-biostrings-2.58.0/src/read_fasta_files.c
Examining data/r-bioc-biostrings-2.58.0/src/read_fastq_files.c
Examining data/r-bioc-biostrings-2.58.0/src/replaceAt.c
Examining data/r-bioc-biostrings-2.58.0/src/replace_letter_at.c
Examining data/r-bioc-biostrings-2.58.0/src/strutils.c
Examining data/r-bioc-biostrings-2.58.0/src/translate.c
Examining data/r-bioc-biostrings-2.58.0/src/unstrsplit_methods.c
Examining data/r-bioc-biostrings-2.58.0/src/utils.c
Examining data/r-bioc-biostrings-2.58.0/src/xscat.c

FINAL RESULTS:

data/r-bioc-biostrings-2.58.0/src/matchprobes.c:87:3:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
  strcpy(scratch, y);
data/r-bioc-biostrings-2.58.0/inst/include/Biostrings_defines.h:52:11:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	unsigned char xy2val[256][256];
data/r-bioc-biostrings-2.58.0/src/SparseList_utils.c:11:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char symbbuf[11];
data/r-bioc-biostrings-2.58.0/src/XStringSet_class.c:80:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char classname[40];  /* longest string should be "DNAStringSet" */
data/r-bioc-biostrings-2.58.0/src/XString_class.c:120:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(dest_ptr, CHAR(src) + i1, dest->length);
data/r-bioc-biostrings-2.58.0/src/align_needwunsQS.c:143:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy((char *) RAW(tag), al1, nal * sizeof(char));
data/r-bioc-biostrings-2.58.0/src/align_needwunsQS.c:149:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy((char *) RAW(tag), al2, nal * sizeof(char));
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:870:6:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
					memcpy(tempIntPtr, mismatchBuffer.pattern, mismatchBuffer.usedSpace * sizeof(int));
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:873:6:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
					memcpy(tempIntPtr, mismatchBuffer.subject, mismatchBuffer.usedSpace * sizeof(int));
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:877:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
				memcpy(&mismatchBuffer.pattern[mismatchBuffer.usedSpace], align1Info.mismatch,
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:880:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
				memcpy(&mismatchBuffer.subject[mismatchBuffer.usedSpace], align2Info.mismatch,
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:895:6:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
					memcpy(tempIntPtr, indel1Buffer.start, indel1Buffer.usedSpace * sizeof(int));
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:898:6:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
					memcpy(tempIntPtr, indel1Buffer.width, indel1Buffer.usedSpace * sizeof(int));
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:901:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
				memcpy(&indel1Buffer.start[indel1Buffer.usedSpace], align1Info.startIndel,
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:903:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
				memcpy(&indel1Buffer.width[indel1Buffer.usedSpace], align1Info.widthIndel,
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:918:6:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
					memcpy(tempIntPtr, indel2Buffer.start, indel2Buffer.usedSpace * sizeof(int));
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:921:6:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
					memcpy(tempIntPtr, indel2Buffer.width, indel2Buffer.usedSpace * sizeof(int));
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:924:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
				memcpy(&indel2Buffer.start[indel2Buffer.usedSpace], align2Info.startIndel,
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:926:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
				memcpy(&indel2Buffer.width[indel2Buffer.usedSpace], align2Info.widthIndel,
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:959:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(INTEGER(alignedPatternMismatchValues), mismatchBuffer.pattern,
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:970:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(INTEGER(alignedPatternIndelRangeStart), indel1Buffer.start,
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:972:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(INTEGER(alignedPatternIndelRangeWidth), indel1Buffer.width,
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:997:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(INTEGER(alignedSubjectMismatchValues), mismatchBuffer.subject,
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:1008:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(INTEGER(alignedSubjectIndelRangeStart), indel2Buffer.start,
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:1010:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(INTEGER(alignedSubjectIndelRangeWidth), indel2Buffer.width,
data/r-bioc-biostrings-2.58.0/src/align_utils.c:128:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			memcpy(&alignedStringPtr[index], origStringPtr, *rangeWidth * sizeof(char));
data/r-bioc-biostrings-2.58.0/src/align_utils.c:137:6:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
					memcpy(&alignedStringPtr[index], origStringPtr, copyElements * sizeof(char));
data/r-bioc-biostrings-2.58.0/src/align_utils.c:148:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			memcpy(&alignedStringPtr[index], origStringPtr, copyElements * sizeof(char));
data/r-bioc-biostrings-2.58.0/src/align_utils.c:280:21:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char *outputPtr = (char *) R_alloc((long) (INTEGER(maxNChar)[0] + 1), sizeof(char));
data/r-bioc-biostrings-2.58.0/src/align_utils.c:290:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(outputPtr, patternPtr, numberOfChars * sizeof(char));
data/r-bioc-biostrings-2.58.0/src/inject_code.c:22:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(RAW(tag), X.ptr, X.length);
data/r-bioc-biostrings-2.58.0/src/letter_frequency.c:372:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char ans_elt_buf[16];
data/r-bioc-biostrings-2.58.0/src/match_pdict.c:417:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			memcpy(ans_col, count_buf->elts,
data/r-bioc-biostrings-2.58.0/src/match_pdict_utils.c:173:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(grouped_keys->elts + 1, INTEGER(dups),
data/r-bioc-biostrings-2.58.0/src/read_fasta_files.c:14:8:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static char errmsg_buf[200];
data/r-bioc-biostrings-2.58.0/src/read_fasta_files.c:54:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy((char *) dest->ptr + dest->length,
data/r-bioc-biostrings-2.58.0/src/read_fasta_files.c:243:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char buf[IOBUF_SIZE];
data/r-bioc-biostrings-2.58.0/src/read_fasta_files.c:630:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char buf[IOBUF_SIZE];
data/r-bioc-biostrings-2.58.0/src/read_fastq_files.c:12:8:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static char errmsg_buf[200];
data/r-bioc-biostrings-2.58.0/src/read_fastq_files.c:52:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy((char *) dest->ptr + dest->length,
data/r-bioc-biostrings-2.58.0/src/read_fastq_files.c:310:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char buf[IOBUF_SIZE];
data/r-bioc-biostrings-2.58.0/src/read_fastq_files.c:655:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char buf[IOBUF_SIZE];
data/r-bioc-biostrings-2.58.0/src/replaceAt.c:100:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			memcpy(dest + dest_offset, x_holder->ptr + x_offset,
data/r-bioc-biostrings-2.58.0/src/replaceAt.c:108:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			memcpy(dest + dest_offset, value_elt_holder.ptr,
data/r-bioc-biostrings-2.58.0/src/replaceAt.c:116:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(dest + dest_offset, x_holder->ptr + x_offset,
data/r-bioc-biostrings-2.58.0/src/replace_letter_at.c:13:8:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static char errmsg_buf[200];
data/r-bioc-biostrings-2.58.0/src/replace_letter_at.c:110:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy((char *) RAW(tag), X.ptr, X.length);
data/r-bioc-biostrings-2.58.0/src/translate.c:10:8:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static char errmsg_buf[200];
data/r-bioc-biostrings-2.58.0/src/unstrsplit_methods.c:34:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			memcpy(dest, sep, sep_len);
data/r-bioc-biostrings-2.58.0/src/unstrsplit_methods.c:38:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(dest, x_elt_holder.ptr, x_elt_holder.length);
data/r-bioc-biostrings-2.58.0/src/unstrsplit_methods.c:57:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char ans_element_type[37];  /* longest string should be "DNAString" */
data/r-bioc-biostrings-2.58.0/src/xscat.c:45:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy((char *) RAW(ans_tag) + tag_offset,
data/r-bioc-biostrings-2.58.0/src/xscat.c:124:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			memcpy((char *) ans_elt_holder.ptr +
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:54:7:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
	int* mismatch;
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:192:20:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
				align1InfoPtr->mismatch[align1InfoPtr->lengthMismatch] = nCharString1 - i;
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:193:20:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
				align2InfoPtr->mismatch[align2InfoPtr->lengthMismatch] = nCharString2 - j;
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:394:25:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
		memset(align1InfoPtr->mismatch,   0, alignmentBufferSize * sizeof(int));
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:395:25:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
		memset(align2InfoPtr->mismatch,   0, alignmentBufferSize * sizeof(int));
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:877:74:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
				memcpy(&mismatchBuffer.pattern[mismatchBuffer.usedSpace], align1Info.mismatch,
data/r-bioc-biostrings-2.58.0/src/align_pairwiseAlignment.c:880:74:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
				memcpy(&mismatchBuffer.subject[mismatchBuffer.usedSpace], align2Info.mismatch,
data/r-bioc-biostrings-2.58.0/src/align_utils.c:289:23:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		int numberOfChars = strlen(patternPtr);
data/r-bioc-biostrings-2.58.0/src/match_pattern_indels.c:15:13:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	P.length = strlen(P.ptr);
data/r-bioc-biostrings-2.58.0/src/match_pattern_indels.c:17:13:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	S.length = strlen(S.ptr);
data/r-bioc-biostrings-2.58.0/src/matchprobes.c:75:16:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    rv->len  = strlen(y);
data/r-bioc-biostrings-2.58.0/src/matchprobes.c:80:9:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  len = strlen(y);
data/r-bioc-biostrings-2.58.0/src/read_fasta_files.c:247:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	FASTA_desc_markup_length = strlen(FASTA_desc_markup);
data/r-bioc-biostrings-2.58.0/src/read_fasta_files.c:265:15:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
			nbyte_in = strlen(buf);
data/r-bioc-biostrings-2.58.0/src/read_fastq_files.c:315:30:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	FASTQ_line1_markup_length = strlen(FASTQ_line1_markup);
data/r-bioc-biostrings-2.58.0/src/read_fastq_files.c:316:30:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	FASTQ_line3_markup_length = strlen(FASTQ_line3_markup);
data/r-bioc-biostrings-2.58.0/src/read_fastq_files.c:334:15:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
			nbyte_in = strlen(buf);
data/r-bioc-biostrings-2.58.0/src/strutils.c:49:6:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  if(strlen(pc)!=1) {
data/r-bioc-biostrings-2.58.0/src/strutils.c:51:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          strlen(pc));
data/r-bioc-biostrings-2.58.0/src/strutils.c:63:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      for(j=0; j<strlen(seq); j++) {

ANALYSIS SUMMARY:

Hits = 73
Lines analyzed = 14415 in approximately 0.36 seconds (39928 lines/second)
Physical Source Lines of Code (SLOC) = 10521
Hits@level = [0]  24 [1]  20 [2]  52 [3]   0 [4]   1 [5]   0
Hits@level+ = [0+]  97 [1+]  73 [2+]  53 [3+]   1 [4+]   1 [5+]   0
Hits/KSLOC@level+ = [0+] 9.21966 [1+] 6.9385 [2+] 5.03754 [3+] 0.095048 [4+] 0.095048 [5+]   0
Dot directories skipped = 1 (--followdotdir overrides)
Minimum risk level = 1
Not every hit is necessarily a security vulnerability.
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://dwheeler.com/secure-programs) for more information.