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/rnahybrid-2.1.2/src/energy.h
Examining data/rnahybrid-2.1.2/src/fasta.c
Examining data/rnahybrid-2.1.2/src/globals.h
Examining data/rnahybrid-2.1.2/src/hybrid_core.c
Examining data/rnahybrid-2.1.2/src/input.c
Examining data/rnahybrid-2.1.2/src/input.h
Examining data/rnahybrid-2.1.2/src/minmax.h
Examining data/rnahybrid-2.1.2/src/mt19937-1.c
Examining data/rnahybrid-2.1.2/src/mt19937-1.h
Examining data/rnahybrid-2.1.2/src/numerical.h
Examining data/rnahybrid-2.1.2/src/random.h
Examining data/rnahybrid-2.1.2/src/energy.c
Examining data/rnahybrid-2.1.2/src/fasta.h
Examining data/rnahybrid-2.1.2/src/hybrid_core.h
Examining data/rnahybrid-2.1.2/src/numerical.c
Examining data/rnahybrid-2.1.2/src/plot.c
Examining data/rnahybrid-2.1.2/src/plot.h
Examining data/rnahybrid-2.1.2/src/random.c
Examining data/rnahybrid-2.1.2/src/rnacalibrate.c
Examining data/rnahybrid-2.1.2/src/rnaeffective.c
Examining data/rnahybrid-2.1.2/src/rnahybrid.c
FINAL RESULTS:
data/rnahybrid-2.1.2/src/fasta.c:24:3: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
sscanf(s,">%s",ac);
data/rnahybrid-2.1.2/src/hybrid_core.c:1799:5: [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(filename,target_ac);
data/rnahybrid-2.1.2/src/hybrid_core.c:1801:5: [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(filename,query_ac);
data/rnahybrid-2.1.2/src/hybrid_core.c:1803:5: [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(filename,hitcount_str);
data/rnahybrid-2.1.2/src/hybrid_core.c:1811:5: [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(filename,target_ac);
data/rnahybrid-2.1.2/src/hybrid_core.c:1813:5: [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(filename,query_ac);
data/rnahybrid-2.1.2/src/hybrid_core.c:1815:5: [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(filename,hitcount_str);
data/rnahybrid-2.1.2/src/hybrid_core.c:1823:5: [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(filename,target_ac);
data/rnahybrid-2.1.2/src/hybrid_core.c:1825:5: [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(filename,query_ac);
data/rnahybrid-2.1.2/src/hybrid_core.c:1827:5: [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(filename,hitcount_str);
data/rnahybrid-2.1.2/src/rnacalibrate.c:119:11: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
if( access( freq_filename, F_OK ) == -1 ) {
data/rnahybrid-2.1.2/src/rnacalibrate.c:210:5: [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(query_sq,argv[argc-1]);
data/rnahybrid-2.1.2/src/rnacalibrate.c:223:5: [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(target_sq,argv[argc-1-(!qflag)]);
data/rnahybrid-2.1.2/src/rnacalibrate.c:426:8: [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(x, target_sq);
data/rnahybrid-2.1.2/src/rnacalibrate.c:452:4: [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(output.query_ac,query_ac);
data/rnahybrid-2.1.2/src/rnacalibrate.c:468:6: [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(x, target_sq);
data/rnahybrid-2.1.2/src/rnacalibrate.c:494:4: [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(output.query_ac,query_ac);
data/rnahybrid-2.1.2/src/rnacalibrate.c:510:6: [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(x, target_sq);
data/rnahybrid-2.1.2/src/rnacalibrate.c:537:4: [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(output.query_ac,query_ac);
data/rnahybrid-2.1.2/src/rnacalibrate.c:586:4: [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(x, target_sq);
data/rnahybrid-2.1.2/src/rnacalibrate.c:610:7: [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(output.query_ac,query_ac);
data/rnahybrid-2.1.2/src/rnacalibrate.c:625:2: [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(x, target_sq);
data/rnahybrid-2.1.2/src/rnacalibrate.c:650:7: [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(output.query_ac,query_ac);
data/rnahybrid-2.1.2/src/rnacalibrate.c:663:2: [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(x, target_sq);
data/rnahybrid-2.1.2/src/rnacalibrate.c:688:7: [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(output.query_ac,query_ac);
data/rnahybrid-2.1.2/src/rnaeffective.c:122:11: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
if( access( freq_filename, F_OK ) == -1 ) {
data/rnahybrid-2.1.2/src/rnaeffective.c:227:5: [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(query_sq,argv[argc-1]);
data/rnahybrid-2.1.2/src/rnaeffective.c:242:5: [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(target_sq,argv[argc-1-(!qflag)]);
data/rnahybrid-2.1.2/src/rnaeffective.c:446:6: [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(x, target_sq);
data/rnahybrid-2.1.2/src/rnaeffective.c:575:6: [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(x, target_sq);
data/rnahybrid-2.1.2/src/rnahybrid.c:249:5: [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(query_sq,argv[argc-1]);
data/rnahybrid-2.1.2/src/rnahybrid.c:259:5: [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(target_sq,argv[argc-1]);
data/rnahybrid-2.1.2/src/rnahybrid.c:270:5: [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(target_sq,argv[argc-2]);
data/rnahybrid-2.1.2/src/rnahybrid.c:272:5: [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(query_sq,argv[argc-1]);
data/rnahybrid-2.1.2/src/rnahybrid.c:357:8: [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(x, target_sq);
data/rnahybrid-2.1.2/src/rnahybrid.c:371:4: [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(x, target_sq);
data/rnahybrid-2.1.2/src/rnahybrid.c:423:4: [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(x, target_sq);
data/rnahybrid-2.1.2/src/rnahybrid.c:437:7: [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(x, target_sq);
data/rnahybrid-2.1.2/src/rnacalibrate.c:114:15: [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(argc,argv,"d:f:hk:l:m:n:q:st:u:v:")) != EOF)
data/rnahybrid-2.1.2/src/rnaeffective.c:117:15: [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(argc,argv,"d:f:hk:l:m:n:q:st:u:v:")) != EOF)
data/rnahybrid-2.1.2/src/rnahybrid.c:91:15: [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(argc,argv,"b:cd:e:f:g:hm:n:p:q:s:t:u:v:")) != EOF)
data/rnahybrid-2.1.2/src/energy.h:50:1: [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 canPair[ALPHASIZE][ALPHASIZE];
data/rnahybrid-2.1.2/src/fasta.c:15:3: [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 s [MAXLINE];
data/rnahybrid-2.1.2/src/fasta.c:31:3: [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 s [MAXLINE];
data/rnahybrid-2.1.2/src/fasta.c:70:3: [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 s [MAXLINE];
data/rnahybrid-2.1.2/src/hybrid_core.c:1691:4: [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 hitcount_str[50];
data/rnahybrid-2.1.2/src/hybrid_core.c:1795:3: [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(hitcount_str,"%d",hit_count);
data/rnahybrid-2.1.2/src/hybrid_core.c:1804:5: [2] (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). Risk is low because the
source is a constant string.
strcat(filename,".ps");
data/rnahybrid-2.1.2/src/hybrid_core.c:1816:5: [2] (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). Risk is low because the
source is a constant string.
strcat(filename,".png");
data/rnahybrid-2.1.2/src/hybrid_core.c:1828:5: [2] (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). Risk is low because the
source is a constant string.
strcat(filename,".jpg");
data/rnahybrid-2.1.2/src/plot.c:49:3: [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 energy_str[50];
data/rnahybrid-2.1.2/src/plot.c:59:3: [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 buf[2];
data/rnahybrid-2.1.2/src/plot.c:126:3: [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(energy_str,"mfe: %.1f kcal/mol",energy);
data/rnahybrid-2.1.2/src/random.c:25:3: [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 s [MAXLINE];
data/rnahybrid-2.1.2/src/rnacalibrate.c:31:3: [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 query_ac[MAXLINE];
data/rnahybrid-2.1.2/src/rnacalibrate.c:64:3: [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 target_ac[MAXLINE];
data/rnahybrid-2.1.2/src/rnacalibrate.c:65:3: [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 query_ac[MAXLINE];
data/rnahybrid-2.1.2/src/rnacalibrate.c:208:18: [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.
query_sq = (char *) calloc(strlen(argv[argc-1])+1,sizeof(char));
data/rnahybrid-2.1.2/src/rnacalibrate.c:209:5: [2] (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). Risk is low because the source is a constant string.
strcpy(query_ac,"command_line");
data/rnahybrid-2.1.2/src/rnacalibrate.c:221:18: [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.
target_sq = (char *) calloc(strlen(argv[argc-1-(!qflag)])+1,sizeof(char));
data/rnahybrid-2.1.2/src/rnacalibrate.c:222:5: [2] (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). Risk is low because the source is a constant string.
strcpy(target_ac,"command_line");
data/rnahybrid-2.1.2/src/rnacalibrate.c:236:22: [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).
FILE *target = fopen(target_fn,"r");
data/rnahybrid-2.1.2/src/rnacalibrate.c:331:9: [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(freq_filename,"r");
data/rnahybrid-2.1.2/src/rnacalibrate.c:370:20: [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).
FILE *query = fopen( query_fn,"r");
data/rnahybrid-2.1.2/src/rnacalibrate.c:405:19: [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).
FILE *target = fopen(target_fn,"r");
data/rnahybrid-2.1.2/src/rnacalibrate.c:565:22: [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).
FILE *target = fopen(target_fn,"r");
data/rnahybrid-2.1.2/src/rnaeffective.c:58:3: [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 target_ac[MAXLINE];
data/rnahybrid-2.1.2/src/rnaeffective.c:59:3: [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 query_ac[MAXLINE];
data/rnahybrid-2.1.2/src/rnaeffective.c:225:18: [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.
query_sq = (char *) calloc(strlen(argv[argc-1])+1,sizeof(char));
data/rnahybrid-2.1.2/src/rnaeffective.c:226:5: [2] (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). Risk is low because the source is a constant string.
strcpy(query_ac,"command_line");
data/rnahybrid-2.1.2/src/rnaeffective.c:240:18: [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.
target_sq = (char *) calloc(strlen(argv[argc-1-(!qflag)])+1,sizeof(char));
data/rnahybrid-2.1.2/src/rnaeffective.c:241:5: [2] (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). Risk is low because the source is a constant string.
strcpy(target_ac,"command_line");
data/rnahybrid-2.1.2/src/rnaeffective.c:256:21: [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).
FILE *query = fopen(query_fn,"r");
data/rnahybrid-2.1.2/src/rnaeffective.c:348:9: [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(freq_filename,"r");
data/rnahybrid-2.1.2/src/rnaeffective.c:390:19: [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).
FILE *query = fopen(query_fn,"r");
data/rnahybrid-2.1.2/src/rnaeffective.c:425:17: [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).
FILE *target = fopen(target_fn,"r");
data/rnahybrid-2.1.2/src/rnaeffective.c:554:17: [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).
FILE *target = fopen(target_fn,"r");
data/rnahybrid-2.1.2/src/rnahybrid.c:68:3: [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 target_ac[MAXLINE];
data/rnahybrid-2.1.2/src/rnahybrid.c:69:3: [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 query_ac[MAXLINE];
data/rnahybrid-2.1.2/src/rnahybrid.c:247:18: [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.
query_sq = (char *) calloc(strlen(argv[argc-1])+1,sizeof(char));
data/rnahybrid-2.1.2/src/rnahybrid.c:248:5: [2] (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). Risk is low because the source is a constant string.
strcpy(query_ac,"command_line");
data/rnahybrid-2.1.2/src/rnahybrid.c:256:18: [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.
target_sq = (char *) calloc(strlen(argv[argc-1])+1,sizeof(char));
data/rnahybrid-2.1.2/src/rnahybrid.c:258:5: [2] (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). Risk is low because the source is a constant string.
strcpy(target_ac,"command_line");
data/rnahybrid-2.1.2/src/rnahybrid.c:266:18: [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.
target_sq = (char *) calloc(strlen(argv[argc-2])+1,sizeof(char));
data/rnahybrid-2.1.2/src/rnahybrid.c:267:18: [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.
query_sq = (char *) calloc(strlen(argv[argc-1])+1,sizeof(char));
data/rnahybrid-2.1.2/src/rnahybrid.c:268:5: [2] (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). Risk is low because the source is a constant string.
strcpy(target_ac,"command_line");
data/rnahybrid-2.1.2/src/rnahybrid.c:269:5: [2] (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). Risk is low because the source is a constant string.
strcpy(query_ac,"command_line");
data/rnahybrid-2.1.2/src/rnahybrid.c:295:20: [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).
FILE *query = fopen( query_fn,"r");
data/rnahybrid-2.1.2/src/rnahybrid.c:337:19: [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).
FILE *target = fopen(target_fn,"r");
data/rnahybrid-2.1.2/src/rnahybrid.c:407:22: [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).
FILE *target = fopen(target_fn,"r");
data/rnahybrid-2.1.2/src/hybrid_core.c:1749:16: [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).
ali_length = strlen(t1);
data/rnahybrid-2.1.2/src/hybrid_core.c:1796:30: [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).
filename = (char *) calloc(strlen(target_ac)+strlen(query_ac)+strlen(hitcount_str)+7, sizeof(char));
data/rnahybrid-2.1.2/src/hybrid_core.c:1796:48: [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).
filename = (char *) calloc(strlen(target_ac)+strlen(query_ac)+strlen(hitcount_str)+7, sizeof(char));
data/rnahybrid-2.1.2/src/hybrid_core.c:1796:65: [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).
filename = (char *) calloc(strlen(target_ac)+strlen(query_ac)+strlen(hitcount_str)+7, sizeof(char));
data/rnahybrid-2.1.2/src/hybrid_core.c:1800:5: [1] (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). Risk is low because the
source is a constant character.
strcat(filename,"_");
data/rnahybrid-2.1.2/src/hybrid_core.c:1802:5: [1] (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). Risk is low because the
source is a constant character.
strcat(filename,"_");
data/rnahybrid-2.1.2/src/hybrid_core.c:1812:5: [1] (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). Risk is low because the
source is a constant character.
strcat(filename,"_");
data/rnahybrid-2.1.2/src/hybrid_core.c:1814:5: [1] (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). Risk is low because the
source is a constant character.
strcat(filename,"_");
data/rnahybrid-2.1.2/src/hybrid_core.c:1824:5: [1] (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). Risk is low because the
source is a constant character.
strcat(filename,"_");
data/rnahybrid-2.1.2/src/hybrid_core.c:1826:5: [1] (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). Risk is low because the
source is a constant character.
strcat(filename,"_");
data/rnahybrid-2.1.2/src/hybrid_core.c:1840:16: [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).
t_len = strlen(t1);
data/rnahybrid-2.1.2/src/input.c:44:13: [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 len = strlen(sequence);
data/rnahybrid-2.1.2/src/plot.c:65:24: [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).
X = (float *) calloc(strlen(seq)+1,sizeof(float));
data/rnahybrid-2.1.2/src/plot.c:66:24: [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).
Y = (float *) calloc(strlen(seq)+1,sizeof(float));
data/rnahybrid-2.1.2/src/plot.c:70:9: [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(i!=strlen(str))
data/rnahybrid-2.1.2/src/plot.c:81:13: [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).
for(i=0;i<strlen(str);i++)
data/rnahybrid-2.1.2/src/plot.c:199:15: [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).
for(i=0;i<strlen(str);i++)
data/rnahybrid-2.1.2/src/plot.c:213:11: [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).
if(i<strlen(str)-1)
data/rnahybrid-2.1.2/src/plot.c:235:15: [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).
for(i=0;i<strlen(str);i++)
data/rnahybrid-2.1.2/src/plot.c:266:21: [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 = (short) strlen(structure);
data/rnahybrid-2.1.2/src/rnacalibrate.c:208:33: [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).
query_sq = (char *) calloc(strlen(argv[argc-1])+1,sizeof(char));
data/rnahybrid-2.1.2/src/rnacalibrate.c:212:19: [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).
querylength = strlen(argv[argc-1]);
data/rnahybrid-2.1.2/src/rnacalibrate.c:221:33: [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).
target_sq = (char *) calloc(strlen(argv[argc-1-(!qflag)])+1,sizeof(char));
data/rnahybrid-2.1.2/src/rnacalibrate.c:225:20: [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).
targetlength = strlen(target_sq);
data/rnahybrid-2.1.2/src/rnacalibrate.c:251:11: [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(target_sq);
data/rnahybrid-2.1.2/src/rnacalibrate.c:277:16: [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).
seqlen = strlen(target_sq);
data/rnahybrid-2.1.2/src/rnacalibrate.c:338:15: [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).
for (i=0; i<strlen(alphabet); i++) {
data/rnahybrid-2.1.2/src/rnacalibrate.c:340:17: [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).
for (j=0; j<strlen(alphabet); j++)
data/rnahybrid-2.1.2/src/rnacalibrate.c:343:17: [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).
for (j=0; j<strlen(alphabet); j++)
data/rnahybrid-2.1.2/src/rnacalibrate.c:351:15: [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).
for (i=1; i<strlen(alphabet); i++)
data/rnahybrid-2.1.2/src/rnacalibrate.c:353:7: [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).
fdf[strlen(alphabet)-1]=1.0;
data/rnahybrid-2.1.2/src/rnacalibrate.c:355:15: [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).
for (i=0; i<strlen(alphabet); i++) {
data/rnahybrid-2.1.2/src/rnacalibrate.c:357:17: [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).
for (j=0; j<strlen(alphabet); j++)
data/rnahybrid-2.1.2/src/rnacalibrate.c:360:17: [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).
for (j=1; j<strlen(alphabet); j++)
data/rnahybrid-2.1.2/src/rnacalibrate.c:362:15: [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).
fdf_di[i][strlen(alphabet)-1]=1.0;
data/rnahybrid-2.1.2/src/rnacalibrate.c:383:11: [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).
n = strlen(query_sq);
data/rnahybrid-2.1.2/src/rnacalibrate.c:419:10: [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).
m = strlen(target_sq);
data/rnahybrid-2.1.2/src/rnacalibrate.c:425:8: [1] (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). Risk is low because the source is a constant character.
strcpy(x, " ");
data/rnahybrid-2.1.2/src/rnacalibrate.c:460:8: [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).
m = strlen(target_sq);
data/rnahybrid-2.1.2/src/rnacalibrate.c:467:6: [1] (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). Risk is low because the source is a constant character.
strcpy(x, " ");
data/rnahybrid-2.1.2/src/rnacalibrate.c:507:10: [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).
m = strlen(target_sq);
data/rnahybrid-2.1.2/src/rnacalibrate.c:509:6: [1] (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). Risk is low because the source is a constant character.
strcpy(x, " ");
data/rnahybrid-2.1.2/src/rnacalibrate.c:547:9: [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).
n = strlen(query_sq);
data/rnahybrid-2.1.2/src/rnacalibrate.c:579:6: [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).
m = strlen(target_sq);
data/rnahybrid-2.1.2/src/rnacalibrate.c:585:4: [1] (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). Risk is low because the source is a constant character.
strcpy(x, " ");
data/rnahybrid-2.1.2/src/rnacalibrate.c:617:11: [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).
m = strlen(target_sq);
data/rnahybrid-2.1.2/src/rnacalibrate.c:624:2: [1] (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). Risk is low because the source is a constant character.
strcpy(x, " ");
data/rnahybrid-2.1.2/src/rnacalibrate.c:660:6: [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).
m = strlen(target_sq);
data/rnahybrid-2.1.2/src/rnacalibrate.c:662:2: [1] (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). Risk is low because the source is a constant character.
strcpy(x, " ");
data/rnahybrid-2.1.2/src/rnaeffective.c:225:33: [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).
query_sq = (char *) calloc(strlen(argv[argc-1])+1,sizeof(char));
data/rnahybrid-2.1.2/src/rnaeffective.c:229:19: [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).
querylength = strlen(argv[argc-1]);
data/rnahybrid-2.1.2/src/rnaeffective.c:240:33: [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).
target_sq = (char *) calloc(strlen(argv[argc-1-(!qflag)])+1,sizeof(char));
data/rnahybrid-2.1.2/src/rnaeffective.c:244:20: [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).
targetlength = strlen(target_sq);
data/rnahybrid-2.1.2/src/rnaeffective.c:271:11: [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(query_sq);
data/rnahybrid-2.1.2/src/rnaeffective.c:297:16: [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).
seqlen = strlen(query_sq);
data/rnahybrid-2.1.2/src/rnaeffective.c:355:15: [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).
for (i=0; i<strlen(alphabet); i++) {
data/rnahybrid-2.1.2/src/rnaeffective.c:357:17: [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).
for (j=0; j<strlen(alphabet); j++)
data/rnahybrid-2.1.2/src/rnaeffective.c:360:17: [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).
for (j=0; j<strlen(alphabet); j++)
data/rnahybrid-2.1.2/src/rnaeffective.c:368:15: [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).
for (i=1; i<strlen(alphabet); i++)
data/rnahybrid-2.1.2/src/rnaeffective.c:370:7: [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).
fdf[strlen(alphabet)-1]=1.0;
data/rnahybrid-2.1.2/src/rnaeffective.c:372:15: [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).
for (i=0; i<strlen(alphabet); i++) {
data/rnahybrid-2.1.2/src/rnaeffective.c:374:17: [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).
for (j=0; j<strlen(alphabet); j++)
data/rnahybrid-2.1.2/src/rnaeffective.c:377:17: [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).
for (j=1; j<strlen(alphabet); j++)
data/rnahybrid-2.1.2/src/rnaeffective.c:379:15: [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).
fdf_di[i][strlen(alphabet)-1]=1.0;
data/rnahybrid-2.1.2/src/rnaeffective.c:405:16: [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).
seqlen = strlen(query_sq);
data/rnahybrid-2.1.2/src/rnaeffective.c:407:11: [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).
n = strlen(query_sq);
data/rnahybrid-2.1.2/src/rnaeffective.c:439:8: [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).
m = strlen(target_sq);
data/rnahybrid-2.1.2/src/rnaeffective.c:445:6: [1] (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). Risk is low because the source is a constant character.
strcpy(x, " ");
data/rnahybrid-2.1.2/src/rnaeffective.c:536:11: [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).
n = strlen(query_sq);
data/rnahybrid-2.1.2/src/rnaeffective.c:568:8: [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).
m = strlen(target_sq);
data/rnahybrid-2.1.2/src/rnaeffective.c:574:6: [1] (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). Risk is low because the source is a constant character.
strcpy(x, " ");
data/rnahybrid-2.1.2/src/rnahybrid.c:247:33: [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).
query_sq = (char *) calloc(strlen(argv[argc-1])+1,sizeof(char));
data/rnahybrid-2.1.2/src/rnahybrid.c:252:19: [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).
querylength = strlen(argv[argc-1]);
data/rnahybrid-2.1.2/src/rnahybrid.c:256:33: [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).
target_sq = (char *) calloc(strlen(argv[argc-1])+1,sizeof(char));
data/rnahybrid-2.1.2/src/rnahybrid.c:261:20: [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).
targetlength = strlen(argv[argc-1]);
data/rnahybrid-2.1.2/src/rnahybrid.c:266:33: [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).
target_sq = (char *) calloc(strlen(argv[argc-2])+1,sizeof(char));
data/rnahybrid-2.1.2/src/rnahybrid.c:267:33: [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).
query_sq = (char *) calloc(strlen(argv[argc-1])+1,sizeof(char));
data/rnahybrid-2.1.2/src/rnahybrid.c:274:20: [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).
targetlength = strlen(argv[argc-2]);
data/rnahybrid-2.1.2/src/rnahybrid.c:275:19: [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).
querylength = strlen(argv[argc-1]);
data/rnahybrid-2.1.2/src/rnahybrid.c:308:11: [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).
n = strlen(query_sq);
data/rnahybrid-2.1.2/src/rnahybrid.c:350:10: [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).
m = strlen(target_sq);
data/rnahybrid-2.1.2/src/rnahybrid.c:356:8: [1] (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). Risk is low because the source is a constant character.
strcpy(x, " ");
data/rnahybrid-2.1.2/src/rnahybrid.c:368:8: [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).
m = strlen(target_sq);
data/rnahybrid-2.1.2/src/rnahybrid.c:370:4: [1] (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). Risk is low because the source is a constant character.
strcpy(x, " ");
data/rnahybrid-2.1.2/src/rnahybrid.c:382:9: [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).
n = strlen(query_sq);
data/rnahybrid-2.1.2/src/rnahybrid.c:416:6: [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).
m = strlen(target_sq);
data/rnahybrid-2.1.2/src/rnahybrid.c:422:4: [1] (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). Risk is low because the source is a constant character.
strcpy(x, " ");
data/rnahybrid-2.1.2/src/rnahybrid.c:434:11: [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).
m = strlen(target_sq);
data/rnahybrid-2.1.2/src/rnahybrid.c:436:7: [1] (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). Risk is low because the source is a constant character.
strcpy(x, " ");
data/rnahybrid-2.1.2/src/rnahybrid.c:452:17: [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 seq_len = strlen(seq_arg);
ANALYSIS SUMMARY:
Hits = 180
Lines analyzed = 18086 in approximately 1.06 seconds (17059 lines/second)
Physical Source Lines of Code (SLOC) = 16465
Hits@level = [0] 94 [1] 90 [2] 49 [3] 3 [4] 38 [5] 0
Hits@level+ = [0+] 274 [1+] 180 [2+] 90 [3+] 41 [4+] 38 [5+] 0
Hits/KSLOC@level+ = [0+] 16.6414 [1+] 10.9323 [2+] 5.46614 [3+] 2.49013 [4+] 2.30793 [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.