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/r-other-mott-happy-2.4/src/Rhappy.c
Examining data/r-other-mott-happy-2.4/src/cmp.c
Examining data/r-other-mott-happy-2.4/src/cmp.h
Examining data/r-other-mott-happy-2.4/src/happy.h
Examining data/r-other-mott-happy-2.4/src/hbcore.c
Examining data/r-other-mott-happy-2.4/src/hbcore.h
Examining data/r-other-mott-happy-2.4/src/hbrem.c
Examining data/r-other-mott-happy-2.4/src/hbrem.h
Examining data/r-other-mott-happy-2.4/src/readline.c
Examining data/r-other-mott-happy-2.4/src/readline.h
Examining data/r-other-mott-happy-2.4/src/stats.c
Examining data/r-other-mott-happy-2.4/src/stats.h
Examining data/r-other-mott-happy-2.4/src/subrout.c

FINAL RESULTS:

data/r-other-mott-happy-2.4/src/Rhappy.c:901:13:  [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.
      if ( (sscanf( line, "marker %s %d %s %lf", marker_name, &(af->alleles), af->chromosome, &(af->position) ) == 4 ) ||  ( sscanf( line, "marker %s %d %lf", marker_name, &(af->alleles), &(af->position) ) == 3 )) {
data/r-other-mott-happy-2.4/src/Rhappy.c:901:126:  [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, "marker %s %d %s %lf", marker_name, &(af->alleles), af->chromosome, &(af->position) ) == 4 ) ||  ( sscanf( line, "marker %s %d %lf", marker_name, &(af->alleles), &(af->position) ) == 3 )) {
data/r-other-mott-happy-2.4/src/Rhappy.c:915:9:  [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, "allele %s", allele_name ) == 1 ) {
data/r-other-mott-happy-2.4/src/Rhappy.c:49:17:  [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).
  if ( ! (dfp = fopen( dfilename, "r" ) ) )
data/r-other-mott-happy-2.4/src/Rhappy.c:56:17:  [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).
  if ( ! (afp = fopen( afilename, "r" ) ) )
data/r-other-mott-happy-2.4/src/Rhappy.c:61:20:  [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).
    if ( ! (anfp = fopen( anfilename, "r" ) ) )
data/r-other-mott-happy-2.4/src/Rhappy.c:385:17:  [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).
	q->sex[q->N] = atoi(sex);
data/r-other-mott-happy-2.4/src/Rhappy.c:649:5:  [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[256];
data/r-other-mott-happy-2.4/src/Rhappy.c:864:3:  [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[10000];
data/r-other-mott-happy-2.4/src/Rhappy.c:865:3:  [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 marker_name[256];
data/r-other-mott-happy-2.4/src/Rhappy.c:866:3:  [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 allele_name[256];
data/r-other-mott-happy-2.4/src/Rhappy.c:900:7:  [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(af->chromosome,"unknown");
data/r-other-mott-happy-2.4/src/happy.h:28:3:  [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 chromosome[20];         /* the chromosome of the marker */
data/r-other-mott-happy-2.4/src/subrout.c:13:3:  [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 sampoutname[25]="SLXsamp_R.dat";
data/r-other-mott-happy-2.4/src/subrout.c:138:3:  [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 sampoutname[25]="SLsamp_R.dat";
data/r-other-mott-happy-2.4/src/Rhappy.c:80:8:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  if ( strlen( CHAR(STRING_ELT(missing_code,0)) ) > 0 ) {
data/r-other-mott-happy-2.4/src/Rhappy.c:663:48:  [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).
      if ( 0 == strncmp( line, "strain_names", strlen("strain_names") ) ) {
data/r-other-mott-happy-2.4/src/Rhappy.c:882:46:  [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 ( 0 == strncmp( line, "strain_names", strlen("strain_names") ) ) {
data/r-other-mott-happy-2.4/src/cmp.c:61:12:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  int la = strlen(a)-1;
data/r-other-mott-happy-2.4/src/cmp.c:62:12:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  int lb = strlen(b)-1;
data/r-other-mott-happy-2.4/src/readline.c:22:14:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while((c=getc(file)))  {
data/r-other-mott-happy-2.4/src/readline.c:36:14:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while((c=getc(file))) {

ANALYSIS SUMMARY:

Hits = 22
Lines analyzed = 5087 in approximately 0.17 seconds (29675 lines/second)
Physical Source Lines of Code (SLOC) = 3747
Hits@level = [0]   4 [1]   7 [2]  12 [3]   0 [4]   3 [5]   0
Hits@level+ = [0+]  26 [1+]  22 [2+]  15 [3+]   3 [4+]   3 [5+]   0
Hits/KSLOC@level+ = [0+] 6.93888 [1+] 5.87136 [2+] 4.0032 [3+] 0.800641 [4+] 0.800641 [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.