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-genomicalignments-1.26.0/src/GenomicAlignments.h
Examining data/r-bioc-genomicalignments-1.26.0/src/IRanges_stubs.c
Examining data/r-bioc-genomicalignments-1.26.0/src/R_init_GenomicAlignments.c
Examining data/r-bioc-genomicalignments-1.26.0/src/S4Vectors_stubs.c
Examining data/r-bioc-genomicalignments-1.26.0/src/cigar_utils.c
Examining data/r-bioc-genomicalignments-1.26.0/src/coordinate_mapping_methods.c
Examining data/r-bioc-genomicalignments-1.26.0/src/encodeOverlaps_methods.c

FINAL RESULTS:

data/r-bioc-genomicalignments-1.26.0/src/cigar_utils.c:17:8:  [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-genomicalignments-1.26.0/src/cigar_utils.c:264:2:  [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 string_buf[200];
data/r-bioc-genomicalignments-1.26.0/src/cigar_utils.c:476:2:  [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 OPstrbuf[2];
data/r-bioc-genomicalignments-1.26.0/src/cigar_utils.c:887:17:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
		buf_offset += sprintf(cigar_buf + buf_offset,
data/r-bioc-genomicalignments-1.26.0/src/cigar_utils.c:898:9:  [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 cigar_buf[1024];
data/r-bioc-genomicalignments-1.26.0/src/cigar_utils.c:1071:17:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
		buf_offset += sprintf(cigar_buf + buf_offset,
data/r-bioc-genomicalignments-1.26.0/src/cigar_utils.c:1087:9:  [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 cigar_buf[1024];
data/r-bioc-genomicalignments-1.26.0/src/encodeOverlaps_methods.c:37:9:  [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 buf[12]; /* should be enough for 32-bit ints */
data/r-bioc-genomicalignments-1.26.0/src/cigar_utils.c:479:15:  [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).
	allOPs_len = strlen(allOPs);

ANALYSIS SUMMARY:

Hits = 9
Lines analyzed = 2099 in approximately 0.07 seconds (28307 lines/second)
Physical Source Lines of Code (SLOC) = 1611
Hits@level = [0]  17 [1]   1 [2]   8 [3]   0 [4]   0 [5]   0
Hits@level+ = [0+]  26 [1+]   9 [2+]   8 [3+]   0 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 16.139 [1+] 5.58659 [2+] 4.96586 [3+]   0 [4+]   0 [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.