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/e-mem-1.0.1/e-mem.cpp
Examining data/e-mem-1.0.1/e-mem.h
Examining data/e-mem-1.0.1/file.h
Examining data/e-mem-1.0.1/qlist.h

FINAL RESULTS:

data/e-mem-1.0.1/e-mem.cpp:679:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(commonData::nucmer_path, "%s/%d_tmp", getenv("NUCMER_E_MEM_OUTPUT_DIRPATH")?getenv("NUCMER_E_MEM_OUTPUT_DIRPATH"):".",getpid());
data/e-mem-1.0.1/file.h:252:11:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
          sprintf(buffer, "%s/revComp", commonData::nucmer_path);
data/e-mem-1.0.1/file.h:546:15:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
              sprintf(buffer, "%s/revComp", commonData::nucmer_path);
data/e-mem-1.0.1/file.h:695:9:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
        sprintf(buffer, "%s", commonData::nucmer_path);
data/e-mem-1.0.1/file.h:709:13:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
            sprintf(buffer, "%s/%d", commonData::nucmer_path, i);
data/e-mem-1.0.1/file.h:955:9:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
        sprintf(buffer, "%s/%d", commonData::nucmer_path, n1);
data/e-mem-1.0.1/file.h:957:9:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
        sprintf(buffer, "%s/%d", commonData::nucmer_path, n2);
data/e-mem-1.0.1/file.h:991:9:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
        sprintf(buffer, "%s/%d", commonData::nucmer_path, n1);
data/e-mem-1.0.1/file.h:1011:9:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
        sprintf(buffer, "%s/%d", commonData::nucmer_path, numFiles);
data/e-mem-1.0.1/file.h:1018:9:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
        sprintf(buffer, "%s/%d", commonData::nucmer_path, numFiles+1);
data/e-mem-1.0.1/file.h:1035:13:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
            sprintf(buffer, "%s/%d", commonData::nucmer_path, i);
data/e-mem-1.0.1/file.h:1075:13:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
            sprintf(buffer, "%s/revComp", commonData::nucmer_path);
data/e-mem-1.0.1/file.h:1078:9:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
        sprintf(buffer, "%s", commonData::nucmer_path);
data/e-mem-1.0.1/e-mem.cpp:679:51:  [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.
    sprintf(commonData::nucmer_path, "%s/%d_tmp", getenv("NUCMER_E_MEM_OUTPUT_DIRPATH")?getenv("NUCMER_E_MEM_OUTPUT_DIRPATH"):".",getpid());
data/e-mem-1.0.1/e-mem.cpp:679:89:  [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.
    sprintf(commonData::nucmer_path, "%s/%d_tmp", getenv("NUCMER_E_MEM_OUTPUT_DIRPATH")?getenv("NUCMER_E_MEM_OUTPUT_DIRPATH"):".",getpid());
data/e-mem-1.0.1/file.h:43:12:  [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 nucmer_path[256];
data/e-mem-1.0.1/file.h:230:16:  [2] (misc) open:
  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.open(str, ios::in);
data/e-mem-1.0.1/file.h:242:16:  [2] (misc) open:
  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.open(s, ios::in);
data/e-mem-1.0.1/file.h:250:11:  [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 buffer[256];
data/e-mem-1.0.1/file.h:544:15:  [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 buffer[256];
data/e-mem-1.0.1/file.h:547:23:  [2] (misc) open:
  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).
              revFile.open(buffer, ios::out);
data/e-mem-1.0.1/file.h:692:9:  [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 buffer[256];
data/e-mem-1.0.1/file.h:710:25:  [2] (misc) open:
  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).
            TmpFiles[i].open(buffer, mode);
data/e-mem-1.0.1/file.h:951:9:  [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 buffer[256];
data/e-mem-1.0.1/file.h:956:20:  [2] (misc) open:
  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).
        (*forFile).open(buffer, ios::in);
data/e-mem-1.0.1/file.h:958:20:  [2] (misc) open:
  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).
        (*revFile).open(buffer, ios::in);
data/e-mem-1.0.1/file.h:1000:9:  [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 buffer[256];
data/e-mem-1.0.1/file.h:1013:32:  [2] (misc) open:
  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).
            TmpFiles[numFiles].open(buffer, ios::out|ios::trunc);
data/e-mem-1.0.1/file.h:1020:34:  [2] (misc) open:
  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).
            TmpFiles[numFiles+1].open(buffer, ios::out|ios::trunc);
data/e-mem-1.0.1/e-mem.cpp:129:14:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        if (!mismatch)
data/e-mem-1.0.1/e-mem.cpp:177:17:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            if (mismatch) {
data/e-mem-1.0.1/e-mem.cpp:196:14:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        if (!mismatch)
data/e-mem-1.0.1/e-mem.cpp:250:17:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            if (mismatch) {
data/e-mem-1.0.1/file.h:1046:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            while(!TmpFiles[i].read((char *)&m, sizeof (MemExt)).eof()) {

ANALYSIS SUMMARY:

Hits = 34
Lines analyzed = 2217 in approximately 0.10 seconds (22732 lines/second)
Physical Source Lines of Code (SLOC) = 1767
Hits@level = [0]   0 [1]   5 [2]  14 [3]   2 [4]  13 [5]   0
Hits@level+ = [0+]  34 [1+]  34 [2+]  29 [3+]  15 [4+]  13 [5+]   0
Hits/KSLOC@level+ = [0+] 19.2417 [1+] 19.2417 [2+] 16.412 [3+] 8.48896 [4+] 7.3571 [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.