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-variantannotation-1.36.0/src/Biostrings_stubs.c
Examining data/r-bioc-variantannotation-1.36.0/src/IRanges_stubs.c
Examining data/r-bioc-variantannotation-1.36.0/src/R_init_VariantAnnotation.c
Examining data/r-bioc-variantannotation-1.36.0/src/XVector_stubs.c
Examining data/r-bioc-variantannotation-1.36.0/src/dna_hash.c
Examining data/r-bioc-variantannotation-1.36.0/src/dna_hash.h
Examining data/r-bioc-variantannotation-1.36.0/src/rle.c
Examining data/r-bioc-variantannotation-1.36.0/src/rle.h
Examining data/r-bioc-variantannotation-1.36.0/src/strhash.c
Examining data/r-bioc-variantannotation-1.36.0/src/strhash.h
Examining data/r-bioc-variantannotation-1.36.0/src/utilities.c
Examining data/r-bioc-variantannotation-1.36.0/src/utilities.h
Examining data/r-bioc-variantannotation-1.36.0/src/vcffile.c
Examining data/r-bioc-variantannotation-1.36.0/src/vcffile.h
Examining data/r-bioc-variantannotation-1.36.0/src/vcftype.c
Examining data/r-bioc-variantannotation-1.36.0/src/vcftype.h
Examining data/r-bioc-variantannotation-1.36.0/src/writevcf.c
Examining data/r-bioc-variantannotation-1.36.0/src/writevcf.h
FINAL RESULTS:
data/r-bioc-variantannotation-1.36.0/src/dna_hash.c:54:9: [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(buf, value);
data/r-bioc-variantannotation-1.36.0/src/utilities.h:6:19: [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).
#define Strdup(x) strcpy(Calloc(strlen(x) + 1, char), x)
data/r-bioc-variantannotation-1.36.0/src/vcffile.c:44:12: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
(void) vsnprintf(buf, bufsize, fmt, argp);
data/r-bioc-variantannotation-1.36.0/src/writevcf.c:286:9: [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(dest, CHAR(str));
data/r-bioc-variantannotation-1.36.0/src/vcffile.c:34:5: [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(buf, fmt, strlen(fmt) + 1);
data/r-bioc-variantannotation-1.36.0/src/vcffile.c:100:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int z_n = atoi(n);
data/r-bioc-variantannotation-1.36.0/src/vcffile.c:224:51: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
rowRanges->u.list[POS_IDX]->u.integer[irec] = atoi(pos);
data/r-bioc-variantannotation-1.36.0/src/vcftype.c:217:41: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
('.' == *field) ? R_NaInt : atoi(field);
data/r-bioc-variantannotation-1.36.0/src/dna_hash.c:53:28: [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).
char *buf = Calloc(strlen(value) + 1, char);
data/r-bioc-variantannotation-1.36.0/src/dna_hash.c:83:42: [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).
iwidth[idx] = '.' == *cstr ? 0 : strlen(cstr);
data/r-bioc-variantannotation-1.36.0/src/utilities.h:6:33: [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).
#define Strdup(x) strcpy(Calloc(strlen(x) + 1, char), x)
data/r-bioc-variantannotation-1.36.0/src/vcffile.c:31:24: [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).
char *buf = Calloc(strlen(fmt), char);
data/r-bioc-variantannotation-1.36.0/src/vcffile.c:34:22: [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).
memcpy(buf, fmt, strlen(fmt) + 1);
data/r-bioc-variantannotation-1.36.0/src/vcffile.c:536:18: [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).
int n = strlen(buf);
data/r-bioc-variantannotation-1.36.0/src/vcffile.c:553:20: [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 last = strlen(buf) - 1;
ANALYSIS SUMMARY:
Hits = 15
Lines analyzed = 1616 in approximately 0.07 seconds (24273 lines/second)
Physical Source Lines of Code (SLOC) = 1356
Hits@level = [0] 0 [1] 7 [2] 4 [3] 0 [4] 4 [5] 0
Hits@level+ = [0+] 15 [1+] 15 [2+] 8 [3+] 4 [4+] 4 [5+] 0
Hits/KSLOC@level+ = [0+] 11.0619 [1+] 11.0619 [2+] 5.89971 [3+] 2.94985 [4+] 2.94985 [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.