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.