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/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/cdriver.c
Examining data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/binding.c
Examining data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h
Examining data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/funcs.h
Examining data/psortb-3.0.6+dfsg/algorithm-hmm/hmm.h
Examining data/psortb-3.0.6+dfsg/algorithm-hmm/hmm-binding.cpp
Examining data/psortb-3.0.6+dfsg/bio-tools-psort-svmloc/bindings.h

FINAL RESULTS:

data/psortb-3.0.6+dfsg/algorithm-hmm/hmm-binding.cpp:57:19:  [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).
  fp = (append) ? fopen(filename, "a") : fopen(filename, "w");
data/psortb-3.0.6+dfsg/algorithm-hmm/hmm-binding.cpp:57:42:  [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).
  fp = (append) ? fopen(filename, "a") : fopen(filename, "w");
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:140:3:  [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[100];  /* name of the HMM */
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:142:3:  [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 alphabet[1000]; /* the alphabet */
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h: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 name[100];  /* name of the HMM */
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:213:3:  [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 alphabet[1000]; /* the alphabet */
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:214:3:  [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 alphabet_2[1000]; /* the alphabet */
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:215:3:  [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 alphabet_3[1000]; /* the alphabet */
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:216:3:  [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 alphabet_4[1000]; /* the alphabet */
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:327:3:  [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 alphabet[1000];
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:342:3:  [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 alphabet[1000];
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:343:3:  [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 alphabet_2[1000];
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:344:3:  [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 alphabet_3[1000];
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:345:3:  [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 alphabet_4[1000];
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:359:3:  [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[50];
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:364:3:  [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 priorfile_name[200];
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:373:3:  [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[50];
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:378:3:  [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 priorfile_name[200];
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:379:3:  [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 priorfile_name_2[200];
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:380:3:  [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 priorfile_name_3[200];
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:381:3:  [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 priorfile_name_4[200];
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:389:3:  [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[200];
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:467:3:  [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 letter[5];
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:477:3:  [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[MAX_SEQ_NAME_SIZE];
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:488:3:  [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[MAX_SEQ_NAME_SIZE];
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:535:3:  [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_letter[5];
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:642:3:  [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_letter[5];
data/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/modhmm0.92b/structs.h:643:3:  [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 template_letter[5];
data/psortb-3.0.6+dfsg/algorithm-hmm/hmm-binding.cpp:71:6:  [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).
  if(strlen(filename) == 0) return -1;
data/psortb-3.0.6+dfsg/algorithm-hmm/hmm-binding.cpp:108:53:  [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((model == NULL) ||(seq == NULL) || (!(seqlen = strlen(seq)))) return NULL;

ANALYSIS SUMMARY:

Hits = 30
Lines analyzed = 1486 in approximately 0.10 seconds (15357 lines/second)
Physical Source Lines of Code (SLOC) = 1036
Hits@level = [0]   5 [1]   2 [2]  28 [3]   0 [4]   0 [5]   0
Hits@level+ = [0+]  35 [1+]  30 [2+]  28 [3+]   0 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 33.7838 [1+] 28.9575 [2+] 27.027 [3+]   0 [4+]   0 [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.