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/rdp-alignment-1.2.0/jni/edu_msu_cme_rdp_alignment_hmm_jni_HMMER3.c
Examining data/rdp-alignment-1.2.0/jni/edu_msu_cme_rdp_alignment_hmm_jni_HMMER3.h
Examining data/rdp-alignment-1.2.0/jni/hmmer_wrapper.c
Examining data/rdp-alignment-1.2.0/jni/hmmer_wrapper.h

FINAL RESULTS:

data/rdp-alignment-1.2.0/jni/hmmer_wrapper.c:40:3:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  vfprintf(stderr, format, argp);
data/rdp-alignment-1.2.0/jni/hmmer_wrapper.c:76:5:  [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(result->model_name, model_name);
data/rdp-alignment-1.2.0/jni/hmmer_wrapper.c:444:19:  [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* seqfile = fopen(argv[2], "r");
data/rdp-alignment-1.2.0/jni/hmmer_wrapper.c:70:20:  [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 name_len = strlen(model_name);
data/rdp-alignment-1.2.0/jni/hmmer_wrapper.c:461:12:  [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).
      line[strlen(line) - 1] = '\0';

ANALYSIS SUMMARY:

Hits = 5
Lines analyzed = 763 in approximately 0.04 seconds (18330 lines/second)
Physical Source Lines of Code (SLOC) = 528
Hits@level = [0]  12 [1]   2 [2]   1 [3]   0 [4]   2 [5]   0
Hits@level+ = [0+]  17 [1+]   5 [2+]   3 [3+]   2 [4+]   2 [5+]   0
Hits/KSLOC@level+ = [0+] 32.197 [1+] 9.4697 [2+] 5.68182 [3+] 3.78788 [4+] 3.78788 [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.