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/ncbi-seg-0.0.20000620/lnfac.h
Examining data/ncbi-seg-0.0.20000620/hiseg.c
Examining data/ncbi-seg-0.0.20000620/genwin.h
Examining data/ncbi-seg-0.0.20000620/debian/patches/genwin.c
Examining data/ncbi-seg-0.0.20000620/debian/patches/seg.c
Examining data/ncbi-seg-0.0.20000620/seg.c
Examining data/ncbi-seg-0.0.20000620/genwin.c
FINAL RESULTS:
data/ncbi-seg-0.0.20000620/genwin.c:97:7: [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(dbase->filename, blastdir);
data/ncbi-seg-0.0.20000620/genwin.c:98:7: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(dbase->filename, name);
data/ncbi-seg-0.0.20000620/genwin.c:99:7: [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(dbase->indexname, indexdir);
data/ncbi-seg-0.0.20000620/genwin.c:100:7: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(dbase->indexname, name);
data/ncbi-seg-0.0.20000620/genwin.c:106:7: [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(dbase->filename, name);
data/ncbi-seg-0.0.20000620/genwin.c:107:7: [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(dbase->indexname, name);
data/ncbi-seg-0.0.20000620/hiseg.c:709:2: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fprintf(stdout, format, 1);
data/ncbi-seg-0.0.20000620/hiseg.c:715:4: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fprintf(stdout, format, i+1);
data/ncbi-seg-0.0.20000620/seg.c:697:2: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fprintf(stdout, format, 1);
data/ncbi-seg-0.0.20000620/seg.c:703:4: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fprintf(stdout, format, i+1);
data/ncbi-seg-0.0.20000620/hiseg.c:135:14: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c=getopt(nargc, nargv, "m:olhaxpqc:nt:"))!=-1)
data/ncbi-seg-0.0.20000620/seg.c:137:14: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c=getopt(nargc, nargv, "m:olhaxpqc:nt:"))!=-1)
data/ncbi-seg-0.0.20000620/genwin.c:44:10: [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 aaflag[128];
data/ncbi-seg-0.0.20000620/genwin.c:45:1: [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 aachar[20];
data/ncbi-seg-0.0.20000620/genwin.c:49:4: [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[STRSIZE];
data/ncbi-seg-0.0.20000620/genwin.c:114:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
else if ((dbase->fp=fopen(dbase->filename, "r"))==NULL)
data/ncbi-seg-0.0.20000620/genwin.c:240:4: [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(win->seq, (parent->seq)+start, length);
data/ncbi-seg-0.0.20000620/genwin.c:622:4: [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(seq->id, bptr, idend);
data/ncbi-seg-0.0.20000620/genwin.c:640:4: [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(seq->name, bptr, namend);
data/ncbi-seg-0.0.20000620/genwin.c:659:4: [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(seq->organism, bptr, orgend);
data/ncbi-seg-0.0.20000620/hiseg.c:110:19: [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).
window = atoi(argv[2]);
data/ncbi-seg-0.0.20000620/hiseg.c:140:24: [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).
hilenmin = atoi(optarg);
data/ncbi-seg-0.0.20000620/hiseg.c:187:24: [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).
charline = atoi(optarg);
data/ncbi-seg-0.0.20000620/hiseg.c:193:23: [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).
maxtrim = atoi(optarg);
data/ncbi-seg-0.0.20000620/hiseg.c:681:2: [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 format[10];
data/ncbi-seg-0.0.20000620/hiseg.c:687:2: [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.
sprintf(format, "%%%dd ", leftspace);
data/ncbi-seg-0.0.20000620/hiseg.c:737:2: [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 buffer[100], leftfmt[20], rightfmt[20];
data/ncbi-seg-0.0.20000620/hiseg.c:746:2: [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.
sprintf(leftfmt, "%%%ds", cline);
data/ncbi-seg-0.0.20000620/hiseg.c:747:2: [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.
sprintf(rightfmt, "%%-%ds", cline);
data/ncbi-seg-0.0.20000620/hiseg.c:853:4: [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 outbuf[HDRLEN+1];
data/ncbi-seg-0.0.20000620/seg.c:111:19: [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).
window = atoi(argv[2]);
data/ncbi-seg-0.0.20000620/seg.c:142:24: [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).
hilenmin = atoi(optarg);
data/ncbi-seg-0.0.20000620/seg.c:189:24: [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).
charline = atoi(optarg);
data/ncbi-seg-0.0.20000620/seg.c:195:23: [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).
maxtrim = atoi(optarg);
data/ncbi-seg-0.0.20000620/seg.c:669:2: [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 format[10];
data/ncbi-seg-0.0.20000620/seg.c:675:2: [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.
sprintf(format, "%%%dd ", leftspace);
data/ncbi-seg-0.0.20000620/seg.c:725:2: [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 buffer[100], leftfmt[20], rightfmt[20];
data/ncbi-seg-0.0.20000620/seg.c:734:2: [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.
sprintf(leftfmt, "%%%ds", cline);
data/ncbi-seg-0.0.20000620/seg.c:735:2: [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.
sprintf(rightfmt, "%%-%ds", cline);
data/ncbi-seg-0.0.20000620/seg.c:841:4: [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 outbuf[HDRLEN+1];
data/ncbi-seg-0.0.20000620/genwin.c:95:41: [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).
dbase->filename = (char *) malloc(strlen(blastdir)+strlen(name)+1);
data/ncbi-seg-0.0.20000620/genwin.c:95:58: [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).
dbase->filename = (char *) malloc(strlen(blastdir)+strlen(name)+1);
data/ncbi-seg-0.0.20000620/genwin.c:96:42: [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).
dbase->indexname = (char *) malloc(strlen(indexdir)+strlen(name)+1);
data/ncbi-seg-0.0.20000620/genwin.c:96:59: [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).
dbase->indexname = (char *) malloc(strlen(indexdir)+strlen(name)+1);
data/ncbi-seg-0.0.20000620/genwin.c:104:41: [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).
dbase->filename = (char *) malloc(strlen(name)+1);
data/ncbi-seg-0.0.20000620/genwin.c:105:42: [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).
dbase->indexname = (char *) malloc(strlen(name)+1);
data/ncbi-seg-0.0.20000620/genwin.c:516:11: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = getc(dbase->fp);
data/ncbi-seg-0.0.20000620/genwin.c:523:17: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c=getc(dbase->fp)) != EOF && c !='\n')
data/ncbi-seg-0.0.20000620/genwin.c:555:11: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((c=getc(fp)) == EOF)
data/ncbi-seg-0.0.20000620/genwin.c:563:11: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = getc(fp);
data/ncbi-seg-0.0.20000620/genwin.c:575:24: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (i=0,itotal=0,c=getc(fp); c != EOF; c=getc(fp))
data/ncbi-seg-0.0.20000620/genwin.c:575:46: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (i=0,itotal=0,c=getc(fp); c != EOF; c=getc(fp))
data/ncbi-seg-0.0.20000620/genwin.c:665:11: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = getc(fp);
data/ncbi-seg-0.0.20000620/genwin.c:689:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c=getc(fp))!='\n' && c!=EOF)
data/ncbi-seg-0.0.20000620/genwin.c:734:30: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (i = 0, itotal = 0, c = getc(fp); c != EOF; c = getc(fp)) {
data/ncbi-seg-0.0.20000620/genwin.c:734:54: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (i = 0, itotal = 0, c = getc(fp); c != EOF; c = getc(fp)) {
data/ncbi-seg-0.0.20000620/genwin.c:788:16: [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).
seq->length = strlen(seq->seq);
data/ncbi-seg-0.0.20000620/hiseg.c:884:20: [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).
i = MIN(HDRLEN, strlen(header));
data/ncbi-seg-0.0.20000620/seg.c:872:20: [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).
i = MIN(HDRLEN, strlen(header));
ANALYSIS SUMMARY:
Hits = 59
Lines analyzed = 4322 in approximately 0.23 seconds (18488 lines/second)
Physical Source Lines of Code (SLOC) = 3489
Hits@level = [0] 41 [1] 19 [2] 28 [3] 2 [4] 10 [5] 0
Hits@level+ = [0+] 100 [1+] 59 [2+] 40 [3+] 12 [4+] 10 [5+] 0
Hits/KSLOC@level+ = [0+] 28.6615 [1+] 16.9103 [2+] 11.4646 [3+] 3.43938 [4+] 2.86615 [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.