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/ecopcr-1.0.1+dfsg/src/ecopcr.c
Parsing failed to find end of parameter list; semicolon terminated it in (stderr,
static void ExitUsage(stat)
int stat;
{
PP "usage: ecoPCR [-d database] [-l value] [-L value] [-e value] [-r taxid] [-i taxid] [-k] oligo1 oligo2\n");
PP "
Examining data/ecopcr-1.0.1+dfsg/src/libapat/CODES/dft_code.h
Examining data/ecopcr-1.0.1+dfsg/src/libapat/CODES/dna_code.h
Examining data/ecopcr-1.0.1+dfsg/src/libapat/CODES/prot_code.h
Examining data/ecopcr-1.0.1+dfsg/src/libapat/Gmach.h
Examining data/ecopcr-1.0.1+dfsg/src/libapat/Gtypes.h
Examining data/ecopcr-1.0.1+dfsg/src/libapat/apat.h
Examining data/ecopcr-1.0.1+dfsg/src/libapat/apat_parse.c
Examining data/ecopcr-1.0.1+dfsg/src/libapat/apat_search.c
Examining data/ecopcr-1.0.1+dfsg/src/libapat/libstki.c
Examining data/ecopcr-1.0.1+dfsg/src/libapat/libstki.h
Examining data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoError.c
Examining data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoIOUtils.c
Examining data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoMalloc.c
Examining data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoapat.c
Examining data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecodna.c
Examining data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecofilter.c
Examining data/ecopcr-1.0.1+dfsg/src/libecoPCR/econame.c
Examining data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecorank.c
Examining data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoseq.c
Examining data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecotax.c
Examining data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoPCR.h
Examining data/ecopcr-1.0.1+dfsg/src/libthermo/nnparams.c
Examining data/ecopcr-1.0.1+dfsg/src/libthermo/nnparams.h
Examining data/ecopcr-1.0.1+dfsg/src/ecogrep.c
Parsing failed to find end of parameter list; semicolon terminated it in (stderr,
static void ExitUsage(stat)
int stat;
{
PP "usage: ecogrep [-d database] [-p pattern] [-i taxid] [-r taxid] [-v] [-h] <file name>\n");
PP "type \"ecogrep -
Examining data/ecopcr-1.0.1+dfsg/src/ecofind.c
Parsing failed to find end of parameter list; semicolon terminated it in (stderr,
static void ExitUsage(stat)
int stat;
{
PP "usage: ecofind [-d database] [-h] [-l] [-P] [-r taxonomic rank] [-p taxid] [-s taxid] <taxon name pattern> ... \n");
Examining data/ecopcr-1.0.1+dfsg/src/ecoisundertaxon.c
Parsing failed to find end of parameter list; semicolon terminated it in (stderr,
static void ExitUsage(stat)
int stat;
{
PP "usage: ecoisundertaxon [-1 taxid] [-2 taxid] [-v] [-h] datafile\n");
PP "type \"ecoisundertaxon -h\" for help\n
FINAL RESULTS:
data/ecopcr-1.0.1+dfsg/src/ecofind.c:147:12: [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.
#define PP fprintf(stderr,
data/ecopcr-1.0.1+dfsg/src/ecofind.c:163:12: [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.
#define PP fprintf(stdout,
data/ecopcr-1.0.1+dfsg/src/ecofind.c:237:12: [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(rankname,optarg);
data/ecopcr-1.0.1+dfsg/src/ecofind.c:243:12: [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(prefix,optarg);
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:76:12: [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.
#define PP fprintf(stdout,
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:110:12: [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.
#define PP fprintf(stderr,
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:182:13: [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(o1,optarg);
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:188:13: [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(o2,optarg);
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:194:13: [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(database,optarg);
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:229:13: [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(p,optarg);
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:335:6: [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(orig,stream);
data/ecopcr-1.0.1+dfsg/src/ecoisundertaxon.c:17:12: [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.
#define PP fprintf(stdout,
data/ecopcr-1.0.1+dfsg/src/ecoisundertaxon.c:48:12: [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.
#define PP fprintf(stderr,
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:15:12: [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.
#define PP fprintf(stdout,
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:95:12: [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.
#define PP fprintf(stderr,
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:375:12: [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(prefix,optarg);
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:466:3: [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(oligo1,argv[optind]);
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:470:3: [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(oligo2,argv[optind]);
data/ecopcr-1.0.1+dfsg/src/libapat/apat_parse.c:345:13: [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(ppat->cpat, buffer);
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoapat.c:184:2: [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(pattern->cpat,pat->cpat);
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoseq.c:61:4: [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(tmp->AC,AC);
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoseq.c:69:4: [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(tmp->DE,DE);
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoseq.c:77:4: [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(tmp->SQ,SQ);
data/ecopcr-1.0.1+dfsg/src/ecofind.c:229:17: [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 ((carg = getopt(argc, argv, "had:p:s:r:lP")) != -1) {
data/ecopcr-1.0.1+dfsg/src/ecofind.c:277:12: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
prefix = getenv("ECOPCRDB");
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:176:17: [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 ((carg = getopt(argc, argv, "1:2:p:d:i:r:e:vh")) != -1) {
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:287:14: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
database = getenv("ECOPCRDB");
data/ecopcr-1.0.1+dfsg/src/ecoisundertaxon.c:77:17: [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 ((carg = getopt(argc, argv, "1:2:vh")) != -1) {
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:367:20: [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 ((carg = getopt(argc, argv, "hcd:l:L:e:i:r:km:a:tD:")) != -1) {
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:484:12: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
prefix = getenv("ECOPCRDB");
data/ecopcr-1.0.1+dfsg/src/libapat/Gmach.h:92:23: [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.
#define HAS_GETOPT_H <getopt.h>
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:315:16: [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).
if ( (file = fopen(argv[optind], "r")) == NULL)
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:136:2: [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 oligo1[MAX_PAT_LEN+1];
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:137:2: [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 oligo2[MAX_PAT_LEN+1];
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:313:2: [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 head[11];
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:314:2: [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 tail[11];
data/ecopcr-1.0.1+dfsg/src/libapat/apat_parse.c:311:9: [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.
char buffer[BUFSIZ];
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoIOUtils.c:96:6: [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).
f = fopen(filename,"rb");
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoPCR.h:26:2: [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 AC[20];
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoPCR.h:31:2: [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 data[1];
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoPCR.h:55:2: [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 name[1];
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoPCR.h:94:2: [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 names[1];
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoseq.c:161:2: [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 filename_buffer[1024];
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoseq.c:194:9: [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 current_prefix[1024];
data/ecopcr-1.0.1+dfsg/src/libthermo/nnparams.c:533:2: [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 nseq[50];
data/ecopcr-1.0.1+dfsg/src/libthermo/nnparams.c:572:2: [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 nseq1[50];
data/ecopcr-1.0.1+dfsg/src/libthermo/nnparams.c:573:2: [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 nseq2[50];
data/ecopcr-1.0.1+dfsg/src/ecofind.c:236:33: [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).
rankname = ECOMALLOC(strlen(optarg)+1,"allocation rankname");
data/ecopcr-1.0.1+dfsg/src/ecofind.c:242:31: [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).
prefix = ECOMALLOC(strlen(optarg)+1,"allocation prefix");
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:30:30: [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).
oligoseq_1->SQ_length = strlen(buffer);
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:34:30: [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).
oligoseq_2->SQ_length = strlen(buffer);
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:38:23: [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).
seq->SQ_length = strlen(buffer);
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:180:28: [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).
o1 = ECOMALLOC(strlen(optarg)+1,
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:186:28: [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).
o2 = ECOMALLOC(strlen(optarg)+1,
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:192:34: [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).
database = ECOMALLOC(strlen(optarg)+1,
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:227:27: [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 = ECOMALLOC(strlen(optarg)+1,
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:242:7: [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(p) > 32){
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:258:7: [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(o1) > 32){
data/ecopcr-1.0.1+dfsg/src/ecogrep.c:272:7: [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(o2) > 32){
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:217:13: [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).
amplength= strlen(amplifia)-rdelta-ldelta;
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:224:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(oligo1,amplifia + rdelta ,o2->patlen);
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:229:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(oligo2, amplifia + rdelta + amplength - o1->patlen,o1->patlen);
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:244:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(oligo1,amplifia+ldelta,o1->patlen);
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:248:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(oligo2,amplifia + ldelta + amplength - o2->patlen,o2->patlen);
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:373:31: [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).
prefix = ECOMALLOC(strlen(optarg)+1,
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:464:22: [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).
oligo1 = ECOMALLOC(strlen(argv[optind])+1,
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:468:22: [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).
oligo2 = ECOMALLOC(strlen(argv[optind])+1,
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:474:15: [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).
circular = strlen(oligo1);
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:475:8: [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(oligo2)>(size_t)circular)
data/ecopcr-1.0.1+dfsg/src/ecopcr.c:476:16: [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).
circular = strlen(oligo2);
data/ecopcr-1.0.1+dfsg/src/libapat/apat_parse.c:62:25: [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).
ebuf = buffer + strlen(buffer);
data/ecopcr-1.0.1+dfsg/src/libapat/apat_parse.c:200:25: [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).
return (*(pat + strlen(pat) - 1) == '#' ? OBLIBIT : 0x0);
data/ecopcr-1.0.1+dfsg/src/libapat/apat_parse.c:344:38: [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 ((ppat->cpat = NEWN(char, strlen(buffer)+1)))
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoIOUtils.c:36:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int32_t read;
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoIOUtils.c:50:6: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read != sizeof(int32_t))
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoIOUtils.c:71:6: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read != *recordSize)
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoIOUtils.c:94:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int32_t read;
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoIOUtils.c:114:6: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read != sizeof(int32_t))
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoapat.c:147:12: [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).
patlen = strlen(pat);
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoapat.c:152:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(pattern->cpat,pat,patlen);
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoapat.c:181:45: [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).
pattern->cpat = ECOMALLOC(sizeof(char)*(strlen(pat->cpat)+1),
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecodna.c:56:20: [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).
se = str + strlen(str) - 1;
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecodna.c:65:14: [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).
se = str + strlen(str) - 1;
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecodna.c:131:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buffer,nucAcSeq + begin,length);
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecodna.c:136:18: [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).
length = end + strlen(nucAcSeq) - begin;
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecodna.c:149:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buffer,nucAcSeq+begin,length - end);
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecodna.c:150:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buffer+(length-end),nucAcSeq ,end);
data/ecopcr-1.0.1+dfsg/src/libecoPCR/econame.c:50:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name->name,raw->names,raw->namelength);
data/ecopcr-1.0.1+dfsg/src/libecoPCR/econame.c:54:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name->classname,(raw->names+raw->namelength),raw->classlength);
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecorank.c:28:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(index->label[i],buffer,rs);
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoseq.c:58:10: [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).
lstr =strlen(AC);
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoseq.c:66:10: [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).
lstr =strlen(DE);
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoseq.c:74:10: [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).
lstr =strlen(SQ);
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoseq.c:121:28: [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).
seq->AC = ECOMALLOC(strlen(raw->AC) +1,
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoseq.c:123:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(seq->AC,raw->AC,strlen(raw->AC));
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoseq.c:123:29: [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).
strncpy(seq->AC,raw->AC,strlen(raw->AC));
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoseq.c:128:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(seq->DE,raw->data,raw->DE_length);
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecoseq.c:204:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(current_prefix,prefix,1023);
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecotax.c:122:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(taxon->name,raw->name,raw->namelength);
data/ecopcr-1.0.1+dfsg/src/libecoPCR/ecotax.c:138:13: [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).
buffsize = strlen(prefix)+10;
data/ecopcr-1.0.1+dfsg/src/libthermo/nnparams.c:471:13: [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).
int lseq = strlen(seq);
data/ecopcr-1.0.1+dfsg/src/libthermo/nnparams.c:484:15: [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).
int seqlen = strlen (inseq);
data/ecopcr-1.0.1+dfsg/src/libthermo/nnparams.c:615:11: [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).
seqlen = strlen (seq);
ANALYSIS SUMMARY:
Hits = 103
Lines analyzed = 5495 in approximately 0.26 seconds (21008 lines/second)
Physical Source Lines of Code (SLOC) = 3549
Hits@level = [0] 83 [1] 56 [2] 16 [3] 8 [4] 23 [5] 0
Hits@level+ = [0+] 186 [1+] 103 [2+] 47 [3+] 31 [4+] 23 [5+] 0
Hits/KSLOC@level+ = [0+] 52.4091 [1+] 29.0223 [2+] 13.2432 [3+] 8.73485 [4+] 6.4807 [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.