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-bioc-makecdfenv-1.66.0/src/read_cdffile.c

FINAL RESULTS:

data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:430:3:  [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(search_string,unit);
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:471:3:  [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(search_string,unit);
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:523:3:  [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(search_string, unit);
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:540:7:  [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_string, buffy+size);
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:168:11:  [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).
  nCols = atoi(getProperty("Rows", &affyFile, retour));
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:169:11:  [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).
  nRows = atoi(getProperty("Cols", &affyFile, retour));
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:170:14:  [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).
  numUnits = atoi(getProperty("NumberOfUnits", &affyFile, retour));
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:199:17:  [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).
    numBlocks = atoi(retour);
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:215:18:  [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).
      numCells = atoi(retour);
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:334:24:  [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).
    affyFile->stream = fopen(affyFile->filepath, "r");
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:397:7:  [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).
  x = atoi(retour);
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:400:7:  [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).
  y = atoi(retour);
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:614:12:  [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).
  typeQC = atoi(getProperty("type", &affyFile, retour));
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:615:14:  [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).
  numCells = atoi(getProperty("NumberCells", &affyFile, retour));
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:240:6:  [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(retour) <= 1) {
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:408:12:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  buffer = strncpy(buffer, retour, stringLen);
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:427:28:  [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).
  search_string = R_alloc( strlen(unit)+2, SIZE_CHAR);
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:429:3:  [1] (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 character.
  strcat(search_string,"[");
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:431:3:  [1] (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 character.
  strcat(search_string,"]");
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:432:10:  [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).
  size = strlen(search_string);
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:468:28:  [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).
  search_string = R_alloc( strlen(unit)+1, SIZE_CHAR);
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:470:3:  [1] (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 character.
  strcat(search_string,"[");
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:475:10:  [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).
  size = strlen(search_string);
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:517:28:  [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).
  search_string = R_alloc( strlen(unit)+1, SIZE_CHAR);
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:525:3:  [1] (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 character.
  strcat(search_string, "=");
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:527:10:  [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).
  size = strlen(search_string);
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:553:17:  [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).
  result_string[strlen(result_string)-1] = '\0';
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:643:12:  [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).
    while (strlen(retour) <= 1) {
data/r-bioc-makecdfenv-1.66.0/src/read_cdffile.c:683:15:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
      field = strncpy(field, buffer2, stringLen);

ANALYSIS SUMMARY:

Hits = 29
Lines analyzed = 700 in approximately 0.03 seconds (21456 lines/second)
Physical Source Lines of Code (SLOC) = 416
Hits@level = [0]   6 [1]  15 [2]  10 [3]   0 [4]   4 [5]   0
Hits@level+ = [0+]  35 [1+]  29 [2+]  14 [3+]   4 [4+]   4 [5+]   0
Hits/KSLOC@level+ = [0+] 84.1346 [1+] 69.7115 [2+] 33.6538 [3+] 9.61538 [4+] 9.61538 [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.