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/proda-1.0/Block.h
Examining data/proda-1.0/Consistency.h
Examining data/proda-1.0/GlobalAlign.h
Examining data/proda-1.0/LinkTable.h
Examining data/proda-1.0/LocalAlign.h
Examining data/proda-1.0/Matrix.h
Examining data/proda-1.0/MultiSequence.h
Examining data/proda-1.0/PairAligner.h
Examining data/proda-1.0/ProbModel.h
Examining data/proda-1.0/Score.h
Examining data/proda-1.0/ScoreMatrix.h
Examining data/proda-1.0/Sequence.h
Examining data/proda-1.0/SparseMatrix.h
Examining data/proda-1.0/Tree.h
Examining data/proda-1.0/Types.h
Examining data/proda-1.0/Utilities.h
Examining data/proda-1.0/Consistency.cc
Examining data/proda-1.0/GlobalAlign.cc
Examining data/proda-1.0/LocalAlign.cc
Examining data/proda-1.0/Matrix.cc
Examining data/proda-1.0/Score.cc
Examining data/proda-1.0/ScoreMatrix.cc
Examining data/proda-1.0/Sequence.cc
Examining data/proda-1.0/SparseMatrix.cc
Examining data/proda-1.0/Tree.cc
Examining data/proda-1.0/Utilities.cc
Examining data/proda-1.0/Assert.cc
Examining data/proda-1.0/Assert.h
Examining data/proda-1.0/MultiSequence.cc
Examining data/proda-1.0/AlignedFragment.cc
Examining data/proda-1.0/AlignedFragment.h
Examining data/proda-1.0/Block.cc
Examining data/proda-1.0/PairAligner.cc
Examining data/proda-1.0/ProbModel.cc
Examining data/proda-1.0/Main.cc
FINAL RESULTS:
data/proda-1.0/Main.cc:211:3: [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(file0,filenames[0]);
data/proda-1.0/MultiSequence.cc:242:13: [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.
res = sscanf (ptr + 5, "%s", temp);
data/proda-1.0/MultiSequence.cc:316:5: [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 (data[foundSequence - numSequences + numRead], text);
data/proda-1.0/AlignedFragment.cc:191:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(s,seq[k]+b[k],sizeof(int)*(end[k]-begin[k]+1-b[k]-e[k]));
data/proda-1.0/GlobalAlign.cc:109:3: [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 (newName, seq.GetName(), strlen(seq.GetName())+1);
data/proda-1.0/Main.cc:210:3: [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 file0[260];
data/proda-1.0/Main.cc:216:4: [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(file0,".fasta");
data/proda-1.0/Main.cc:217:12: [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).
fasta = fopen(file0,"w");
data/proda-1.0/Main.cc:219:3: [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(file0,".test");
data/proda-1.0/Main.cc:220:18: [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 *output = fopen(file0,"w");
data/proda-1.0/Matrix.cc:38:3: [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 (data, m.data, sizeof(float) * (layers * rows * cols));
data/proda-1.0/MultiSequence.cc:116:18: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (sequences) memcpy (temp, sequences, sizeof(SequencePtr) * numSequences);
data/proda-1.0/MultiSequence.cc:134:16: [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).
FILE *file = fopen (filename, "r");
data/proda-1.0/MultiSequence.cc:157:16: [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).
FILE *file = fopen (filename, "r");
data/proda-1.0/MultiSequence.cc:176:7: [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, name+1, sizeof(char) * length);
data/proda-1.0/MultiSequence.cc:199:5: [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 (temp+1, data, sizeof(char) * (length+1));
data/proda-1.0/MultiSequence.cc:222:16: [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).
FILE *file = fopen (filename, "r");
data/proda-1.0/MultiSequence.cc:246:7: [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 (name, temp, sizeof(char) * (strlen(temp)+1));
data/proda-1.0/MultiSequence.cc:389:16: [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 const char *groups[47] = {
data/proda-1.0/ProbModel.cc:1036:6: [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(ij,buf,sizeof(SCORE)*NUM_STATES);
data/proda-1.0/ProbModel.cc:1105:6: [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(ij,buf,sizeof(SCORE)*NUM_STATES);
data/proda-1.0/ProbModel.cc:1167:6: [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(ij,buf,sizeof(SCORE)*NUM_STATES);
data/proda-1.0/ProbModel.cc:1225:6: [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(ij,buf,sizeof(SCORE)*NUM_STATES);
data/proda-1.0/ScoreMatrix.cc:39:3: [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 (data, m.data, sizeof(SCORE) * (layers * rows * cols));
data/proda-1.0/Sequence.cc:38:5: [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 (data, rhs.data, sizeof(char) * (length+2));
data/proda-1.0/Sequence.cc:41:2: [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 (align, rhs.align, sizeof(int) * (length+1));
data/proda-1.0/Sequence.cc:44:2: [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 (position, rhs.position, sizeof(int) * (length+1));
data/proda-1.0/Sequence.cc:50:5: [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 (name, rhs.name, sizeof(char) * (strlen(rhs.name)+1));
data/proda-1.0/Sequence.cc:71:7: [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 (data, rhs.data, sizeof(char) * (length+2));
data/proda-1.0/Sequence.cc:74:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy (align, rhs.align, sizeof(int) * (length+1));
data/proda-1.0/Sequence.cc:77:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy (position, rhs.position, sizeof(int) * (length+1));
data/proda-1.0/Sequence.cc:83:7: [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 (name, rhs.name, sizeof(char) * (strlen(rhs.name)+1));
data/proda-1.0/Sequence.cc:221:2: [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 (tmp+1, data+begin, sizeof(char)*length);
data/proda-1.0/Sequence.cc:243:2: [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 (d+1, data+begin, sizeof(char)*(length+1));
data/proda-1.0/Sequence.cc:248:2: [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 (p+1, position + begin,sizeof(int)*(length));
data/proda-1.0/Sequence.cc:252:2: [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 (a, align + begin,sizeof(int)*(length+1));
data/proda-1.0/Utilities.cc:64:7: [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 (buffer, temp, sizeof(char) * length);
data/proda-1.0/Utilities.cc:77:3: [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 (buffer, temp, sizeof(char) * length);
data/proda-1.0/Utilities.cc:92:3: [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 (ret, s, len+1);
data/proda-1.0/Utilities.cc:105:3: [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 (ret, s + i, j - i);
data/proda-1.0/GlobalAlign.cc:90:13: [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 (alignmentPath);
data/proda-1.0/GlobalAlign.cc:95:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
char *newName = new char[strlen(seq.GetName())+1];
data/proda-1.0/GlobalAlign.cc:109:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy (newName, seq.GetName(), strlen(seq.GetName())+1);
data/proda-1.0/Main.cc:212:11: [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).
for(i = strlen(file0)-1; i > 0 && file0[i]!='.'; i--);
data/proda-1.0/MultiSequence.cc:244:29: [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).
char *name = new char[strlen(temp)+1];
data/proda-1.0/MultiSequence.cc:246:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy (name, temp, sizeof(char) * (strlen(temp)+1));
data/proda-1.0/MultiSequence.cc:278:5: [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 (data[i], "@");
data/proda-1.0/MultiSequence.cc:429:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int nameLength = strlen(sequences[0]->GetName());
data/proda-1.0/MultiSequence.cc:433:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
nameLength = max (nameLength, (int) strlen(sequences[i]->GetName()));
data/proda-1.0/MultiSequence.cc:649:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int nameLength = strlen(sequences[0]->GetName());
data/proda-1.0/MultiSequence.cc:653:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
nameLength = max (nameLength, (int) strlen(sequences[i]->GetName()));
data/proda-1.0/Sequence.cc:37:33: [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).
ASSERT (length + 1 == (int) strlen(rhs.data), "Sequence of incorrect length.");
data/proda-1.0/Sequence.cc:48:21: [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).
name = new char[strlen(rhs.name)+1];
data/proda-1.0/Sequence.cc:50:45: [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).
memcpy (name, rhs.name, sizeof(char) * (strlen(rhs.name)+1));
data/proda-1.0/Sequence.cc:81:23: [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).
name = new char[strlen(rhs.name)+1];
data/proda-1.0/Sequence.cc:83:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy (name, rhs.name, sizeof(char) * (strlen(rhs.name)+1));
data/proda-1.0/Sequence.cc:140:18: [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).
this->length = strlen(data) - 1;
data/proda-1.0/Utilities.cc:48:17: [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 (int i = strlen(terminatingChars) - 1; i >= 0; i--)
data/proda-1.0/Utilities.cc:50:17: [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 (int i = strlen(skipChars) - 1; i >= 0; i--)
data/proda-1.0/Utilities.cc:55:16: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((ch = fgetc (file)) != EOF){
data/proda-1.0/Utilities.cc:89:13: [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(s);
data/proda-1.0/Utilities.cc:101:32: [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).
ASSERT (i >= 0 && i <= (int) strlen(s), "Invalid index.");
data/proda-1.0/Utilities.cc:102:32: [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).
ASSERT (j >= i && j <= (int) strlen(s), "Invalid index.");
ANALYSIS SUMMARY:
Hits = 63
Lines analyzed = 6341 in approximately 0.21 seconds (30649 lines/second)
Physical Source Lines of Code (SLOC) = 4424
Hits@level = [0] 98 [1] 23 [2] 37 [3] 0 [4] 3 [5] 0
Hits@level+ = [0+] 161 [1+] 63 [2+] 40 [3+] 3 [4+] 3 [5+] 0
Hits/KSLOC@level+ = [0+] 36.3924 [1+] 14.2405 [2+] 9.04159 [3+] 0.678119 [4+] 0.678119 [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.