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/poa-2.0+20060928/align_lpo.c
Examining data/poa-2.0+20060928/align_lpo2.c
Examining data/poa-2.0+20060928/align_lpo_po.c
Examining data/poa-2.0+20060928/align_lpo_po2.c
Examining data/poa-2.0+20060928/align_score.c
Examining data/poa-2.0+20060928/align_score.h
Examining data/poa-2.0+20060928/black_flag.c
Examining data/poa-2.0+20060928/buildup_lpo.c
Examining data/poa-2.0+20060928/create_seq.c
Examining data/poa-2.0+20060928/default.h
Examining data/poa-2.0+20060928/fasta_format.c
Examining data/poa-2.0+20060928/heaviest_bundle.c
Examining data/poa-2.0+20060928/lpo.c
Examining data/poa-2.0+20060928/lpo.h
Examining data/poa-2.0+20060928/lpo_format.c
Examining data/poa-2.0+20060928/main.c
Examining data/poa-2.0+20060928/msa_format.c
Examining data/poa-2.0+20060928/msa_format.h
Examining data/poa-2.0+20060928/numeric_data.c
Examining data/poa-2.0+20060928/poa.h
Examining data/poa-2.0+20060928/project.h
Examining data/poa-2.0+20060928/remove_bundle.c
Examining data/poa-2.0+20060928/seq_util.c
Examining data/poa-2.0+20060928/seq_util.h
Examining data/poa-2.0+20060928/stringptr.c
Examining data/poa-2.0+20060928/black_flag.h
FINAL RESULTS:
data/poa-2.0+20060928/black_flag.c:111:5: [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(Program_name,arg[i]);
data/poa-2.0+20060928/black_flag.h:146:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf MESSAGE ;\
data/poa-2.0+20060928/black_flag.h:166:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf MESSAGE ;\
data/poa-2.0+20060928/black_flag.h:198:8: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
(sprintf MESSAGE,\
data/poa-2.0+20060928/black_flag.h:206:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
(sprintf MESSAGE,\
data/poa-2.0+20060928/black_flag.h:212:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
(sprintf MESSAGE,\
data/poa-2.0+20060928/buildup_lpo.c:333:12: [4] (buffer) fscanf:
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.
while (fscanf(ifile," %s %s %lf",name1,name2,&x)==3) { /* READ SCORE FILE */
data/poa-2.0+20060928/default.h:125:49: [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 PRINT_DEBUG(CODE,MESSAGE) {if (CODE<=2) fprintf MESSAGE ;}
data/poa-2.0+20060928/default.h:127:49: [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 PRINT_DEBUG(CODE,MESSAGE) {if (CODE<=1) fprintf MESSAGE ;}
data/poa-2.0+20060928/fasta_format.c:35:11: [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.
if (sscanf(line+1,"%s %[^\n]", /* SKIP PAST > TO READ SEQ NAME*/
data/poa-2.0+20060928/lpo_format.c:61:3: [4] (buffer) fscanf:
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.
fscanf(ifile,"VERSION=%s",version);
data/poa-2.0+20060928/lpo_format.c:160:3: [4] (buffer) fscanf:
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.
fscanf(ifile,"VERSION=%s",version);
data/poa-2.0+20060928/main.c:209:28: [4] (buffer) fscanf:
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.
while (po_list_file && fscanf (po_list_file, " %s", po_list_entry_filename) == 1) {
data/poa-2.0+20060928/msa_format.c:135:7: [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 (line, first_line);
data/poa-2.0+20060928/msa_format.c:160:9: [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.
if (sscanf (line, "%s %[^\n\r]", name, aln) < 2) {
data/poa-2.0+20060928/msa_format.c:211:5: [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 (lposeq->name, lposeq->source_seq[0].name);
data/poa-2.0+20060928/msa_format.c:234:7: [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 (line, first_line);
data/poa-2.0+20060928/msa_format.c:240:11: [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.
if (sscanf (line, ">%s %[^\n\r]", name, title) < 1) {
data/poa-2.0+20060928/msa_format.c:294:5: [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 (lposeq->name, lposeq->source_seq[0].name);
data/poa-2.0+20060928/msa_format.c:376:5: [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 (curr_seq->name, seq_names[i]);
data/poa-2.0+20060928/numeric_data.c:98:5: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(name,source_name_fmt,set_names[j]); /* GENERATE NAME TO MATCH*/
data/poa-2.0+20060928/numeric_data.c:105:5: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(name,target_name_fmt,set_names[j]); /* GENERATE NEW NAME */
data/poa-2.0+20060928/numeric_data.c:106:5: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(title,title_fmt,data->title);
data/poa-2.0+20060928/numeric_data.c:127:9: [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.
if (sscanf(line,">%s NUMERIC_DATA=%s %s",seq_name,data_name,title)>=2) {
data/poa-2.0+20060928/seq_util.c:127:7: [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(DNA_symbols,dna_codes);/*SYMBOLS COUNTED AS DNA FOR AUTORECOG*/
data/poa-2.0+20060928/stringptr.c:44:5: [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(s1->p,stringptr_cat_temp_p);
data/poa-2.0+20060928/stringptr.c:47:5: [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(s1->p + *pos,s2_temp);
data/poa-2.0+20060928/stringptr.c:51:5: [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(s1->p,s2_temp);
data/poa-2.0+20060928/stringptr.c:68:3: [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(s1->p,s2);
data/poa-2.0+20060928/black_flag.c:75:19: [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.
if ((crash_mode=getenv("HANDLE_CRASH")) && 0==strcmp(crash_mode,"NOCORE"))
data/poa-2.0+20060928/black_flag.c:9:1: [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 ERRTXT[1024]
data/poa-2.0+20060928/black_flag.c:21:3: [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 *error_names[max_black_flag_type]
data/poa-2.0+20060928/buildup_lpo.c:175:3: [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(temp,seq->letter+start,sizeof(LPOLetter_T)*(seq->length));
data/poa-2.0+20060928/buildup_lpo.c:325:3: [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 name1[256],name2[256];
data/poa-2.0+20060928/buildup_lpo.c:459:11: [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).
ifile=fopen(score_file,"r");
data/poa-2.0+20060928/default.h:88:26: [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.
(strncpy(S1,S2,LEN),(((char *)(S1))[(LEN)-1]='\0'))
data/poa-2.0+20060928/fasta_format.c:14:3: [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 seq_name[FASTA_NAME_MAX]="",
data/poa-2.0+20060928/fasta_format.c:37:2: [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(seq_title,"untitled"); /* PROTECT AGAINST MISSING NAME */
data/poa-2.0+20060928/heaviest_bundle.c:125:14: [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).
weight=atoi(p+11);
data/poa-2.0+20060928/heaviest_bundle.c:148:3: [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 name[256],title[1024];
data/poa-2.0+20060928/heaviest_bundle.c:156:5: [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(name,"CONSENS%d",ibundle);
data/poa-2.0+20060928/heaviest_bundle.c:160:5: [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(title,"consensus produced by heaviest_bundle, containing %d seqs",
data/poa-2.0+20060928/lpo_format.c:57:3: [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 c,name[1024]="",title[4096]="",version[256]="";
data/poa-2.0+20060928/lpo_format.c:151:3: [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 c,name[1024]="",title[4096]="",version[256]="";
data/poa-2.0+20060928/lpo_format.c:217:2: [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->source_seq+j,seq->source_seq+i,sizeof(LPOSourceInfo_T));
data/poa-2.0+20060928/main.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 score_file[256],seq_file[256],po_list_entry_filename[256],*comment=NULL,*al_name="test align";
data/poa-2.0+20060928/main.c:208:20: [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).
po_list_file = fopen (po_list_filename, "r");
data/poa-2.0+20060928/main.c:233:17: [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).
seq_ifile = fopen (seq_filename, "r");
data/poa-2.0+20060928/main.c:283:22: [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).
if (lpo_file_out=fopen(po_out, "w")) {
data/poa-2.0+20060928/main.c:296:19: [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).
if (seq_ifile=fopen(fasta_out,"w")) { /* FASTA-PIR ALIGNMENT*/
data/poa-2.0+20060928/main.c:310:19: [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).
if (seq_ifile=fopen(clustal_out,"w")) { /* CLUSTAL ALIGNMENT*/
data/poa-2.0+20060928/main.c:353:13: [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).
po_file = fopen (po_filename, "r");
data/poa-2.0+20060928/main.c:360:19: [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).
subset_file = fopen (subset_filename, "r");
data/poa-2.0+20060928/msa_format.c:63:10: [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.
static char line[512]="";
data/poa-2.0+20060928/msa_format.c:130:3: [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 line[512]="", name[512]="", aln[512]="";
data/poa-2.0+20060928/msa_format.c:229:3: [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 line[512]="", name[512]="", title[512]="", aln[512]="";
data/poa-2.0+20060928/msa_format.c:348:3: [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 (lposeq->name, "consens_row");
data/poa-2.0+20060928/msa_format.c:481:3: [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 name[512]="";
data/poa-2.0+20060928/numeric_data.c:95:3: [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 name[256],title[4096];
data/poa-2.0+20060928/numeric_data.c:122:3: [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 line[4096],seq_name[128],data_name[1024],title[2048];
data/poa-2.0+20060928/poa.h:108:3: [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 name[SEQUENCE_NAME_MAX]; /** */
data/poa-2.0+20060928/poa.h:118:3: [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 name[SEQUENCE_NAME_MAX]; /** */
data/poa-2.0+20060928/poa.h:149:3: [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 name[SEQUENCE_NAME_MAX];/** */
data/poa-2.0+20060928/remove_bundle.c:17:3: [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(link,list,sizeof(LPOLetterLink_T));
data/poa-2.0+20060928/remove_bundle.c:37:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(list,link_head,sizeof(LPOLetterLink_T));
data/poa-2.0+20060928/remove_bundle.c:60:3: [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(source,list,sizeof(LPOLetterSource_T));
data/poa-2.0+20060928/remove_bundle.c:77:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(list,source_head,sizeof(LPOLetterSource_T));
data/poa-2.0+20060928/remove_bundle.c:132:2: [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->letter+j,seq->letter+i,sizeof(LPOLetter_T));
data/poa-2.0+20060928/seq_util.c:77:1: [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 DNA_symbols[1024];
data/poa-2.0+20060928/seq_util.c:85:3: [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 line[1024],dna_codes[256];
data/poa-2.0+20060928/seq_util.c:95:9: [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).
ifile=fopen(filename,"r");
data/poa-2.0+20060928/seq_util.h:35:3: [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 symbol[MATRIX_SYMBOL_MAX];
data/poa-2.0+20060928/seq_util.h:47:3: [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 freq_symbol[MATRIX_SYMBOL_MAX];
data/poa-2.0+20060928/stringptr.c:31:3: [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(s2_temp,s2,s2_len); /* COPY THE STRING */
data/poa-2.0+20060928/black_flag.c:108:10: [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).
len+=strlen(arg[i])+2;
data/poa-2.0+20060928/black_flag.c:112:5: [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(Program_name," ");
data/poa-2.0+20060928/default.h:88:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
(strncpy(S1,S2,LEN),(((char *)(S1))[(LEN)-1]='\0'))
data/poa-2.0+20060928/fasta_format.c:51:7: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c=getc(seq_file); /* ?FIRST CHARACTER IS UNIGENE CLUSTER TERMINATOR? */
data/poa-2.0+20060928/fasta_format.c:84:14: [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).
for (j=0;j<strlen(seq);j+=60)
data/poa-2.0+20060928/lpo_format.c:101:22: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((field_id=getc(ifile))!=EOF && '\n'!=field_id) {/* READ FIELDS*/
data/poa-2.0+20060928/lpo_format.c:240:22: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((field_id=getc(ifile))!=EOF && '\n'!=field_id) {/* READ FIELDS*/
data/poa-2.0+20060928/lpo_format.c:479:11: [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 ((len=strlen(seq->source_seq[iseq].name))>indent-1){ /*MUST WE TRUNCATE NAME? */
data/poa-2.0+20060928/msa_format.c:185:57: [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).
REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char);
data/poa-2.0+20060928/msa_format.c:186:17: [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 (i=0; i<strlen(aln); i++) {
data/poa-2.0+20060928/msa_format.c:268:59: [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).
REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char);
data/poa-2.0+20060928/msa_format.c:269:19: [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).
for (i=0; i<strlen(aln); i++) {
data/poa-2.0+20060928/seq_util.c:126:17: [1] (buffer) sscanf:
It's unclear if the %s limit in the format string is small enough
(CWE-120). Check that the limit is sufficiently small, or use a different
input function.
else if (1==sscanf(line,"DNACODES=%99s",dna_codes)) { /* READ DNACODES*/
data/poa-2.0+20060928/seq_util.c:226:11: [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).
nsubset=strlen(subset);
data/poa-2.0+20060928/seq_util.c:257:7: [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).
len=strlen(seq);
data/poa-2.0+20060928/seq_util.c:289:17: [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 ((i=0),(j=strlen(seq)-1);i<=j;i++,j--) {/* SWAP FROM ENDS TO CENTER*/
data/poa-2.0+20060928/stringptr.c:29:20: [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).
total_len=s2_len=strlen(s2)+1;
data/poa-2.0+20060928/stringptr.c:37:20: [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).
total_len += strlen(s1->p);
data/poa-2.0+20060928/stringptr.c:67:16: [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).
GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char);
ANALYSIS SUMMARY:
Hits = 93
Lines analyzed = 6593 in approximately 0.21 seconds (31769 lines/second)
Physical Source Lines of Code (SLOC) = 4582
Hits@level = [0] 86 [1] 19 [2] 44 [3] 1 [4] 29 [5] 0
Hits@level+ = [0+] 179 [1+] 93 [2+] 74 [3+] 30 [4+] 29 [5+] 0
Hits/KSLOC@level+ = [0+] 39.0659 [1+] 20.2968 [2+] 16.1502 [3+] 6.54736 [4+] 6.32911 [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.