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-chemminer-3.42.0+dfsg/src/DisjointSets.cpp
Examining data/r-bioc-chemminer-3.42.0+dfsg/src/DisjointSets.h
Examining data/r-bioc-chemminer-3.42.0+dfsg/src/cluster.cc
Examining data/r-bioc-chemminer-3.42.0+dfsg/src/cstrsplit.cc
Examining data/r-bioc-chemminer-3.42.0+dfsg/src/debug.h
Examining data/r-bioc-chemminer-3.42.0+dfsg/src/desc.cc
Examining data/r-bioc-chemminer-3.42.0+dfsg/src/desc.h
Examining data/r-bioc-chemminer-3.42.0+dfsg/src/fingerprints.cc
Examining data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc
Examining data/r-bioc-chemminer-3.42.0+dfsg/src/molecule.cc
Examining data/r-bioc-chemminer-3.42.0+dfsg/src/molecule.h
Examining data/r-bioc-chemminer-3.42.0+dfsg/src/r_wrap.cc
Examining data/r-bioc-chemminer-3.42.0+dfsg/src/script.cc
Examining data/r-bioc-chemminer-3.42.0+dfsg/src/script.h
Examining data/r-bioc-chemminer-3.42.0+dfsg/src/similarity.cc

FINAL RESULTS:

data/r-bioc-chemminer-3.42.0+dfsg/src/debug.h:5:34:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
#define DEBUG_PRINT(fmt,...) LOC printf(fmt,__VA_ARGS__);
data/r-bioc-chemminer-3.42.0+dfsg/src/r_wrap.cc:681:3:  [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(r,name);
data/r-bioc-chemminer-3.42.0+dfsg/src/r_wrap.cc:1286:15:  [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).
      *cptr = strcpy(*cptr, cstr);
data/r-bioc-chemminer-3.42.0+dfsg/src/cluster.cc:59:2:  [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_buf[LINE_BUF_SIZE];
data/r-bioc-chemminer-3.42.0+dfsg/src/desc.h:39:8:  [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 elements[112][3] = {
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:17:2:  [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 num[4];
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:20:12:  [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).
	n_atoms = atoi(num);
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:24:12:  [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).
	n_bonds = atoi(num);
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:30:2:  [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 ele[4] = {0x0, 0x0, 0x0, 0x0};
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:58:2:  [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 num[4];
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:61:9:  [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).
	left = atoi(num);
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:65:10:  [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).
	right = atoi(num);
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:69:14:  [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).
	bond_type = atoi(num);
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:92:3:  [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 buf[MAX_LINE_LENGTH+2];
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:221:2:  [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[MAX_LINE_LENGTH+2]; line[MAX_LINE_LENGTH+1] = '\0';
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:222:2:  [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 buf_4[5]; buf_4[4] = '\0';
data/r-bioc-chemminer-3.42.0+dfsg/src/r_wrap.cc:632:16:  [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 const char hex[17] = "0123456789abcdef";
data/r-bioc-chemminer-3.42.0+dfsg/src/r_wrap.cc:1056:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(pack, ptr, sz);
data/r-bioc-chemminer-3.42.0+dfsg/src/r_wrap.cc:1074:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(ptr, sobj->pack, size);
data/r-bioc-chemminer-3.42.0+dfsg/src/r_wrap.cc:1279:43:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        *cptr = reinterpret_cast< char* >(memcpy((new char[len + 1]), cstr, sizeof(char)*(len + 1)));
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:18:2:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
	strncpy(num, buf, 3);
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:22:2:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
	strncpy(num, buf + 3, 3);
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:59:2:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
	strncpy(num, buf, 3);
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:63:2:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
	strncpy(num, buf + 3, 3);
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:67:2:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
	strncpy(num, buf + 6, 3);
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:98:22:  [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 (ifs.fail() or strlen(buf) > MAX_LINE_LENGTH) {
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:99:9:  [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(buf) > MAX_LINE_LENGTH) 
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:100:106:  [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).
					std::cerr << "SDF not well-formatted : line exceeds "<<MAX_LINE_LENGTH<<" characters" << " len=" << strlen(buf) << " last=" << buf[strlen(buf) - 1] << std::endl;
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:100:137:  [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).
					std::cerr << "SDF not well-formatted : line exceeds "<<MAX_LINE_LENGTH<<" characters" << " len=" << strlen(buf) << " last=" << buf[strlen(buf) - 1] << std::endl;
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:228:7:  [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(line) > MAX_LINE_LENGTH) {
data/r-bioc-chemminer-3.42.0+dfsg/src/formats.cc:237:3:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
		strncpy(buf_4, line, 4);
data/r-bioc-chemminer-3.42.0+dfsg/src/r_wrap.cc:385:25:  [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).
  const char* te = tb + strlen(tb);
data/r-bioc-chemminer-3.42.0+dfsg/src/r_wrap.cc:404:25:  [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).
  const char* te = tb + strlen(tb);
data/r-bioc-chemminer-3.42.0+dfsg/src/r_wrap.cc:680:7:  [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(name) + 1 > (bsz - (r - buff))) return 0;
data/r-bioc-chemminer-3.42.0+dfsg/src/r_wrap.cc:701:26:  [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_t lname = (name ? strlen(name) : 0);
data/r-bioc-chemminer-3.42.0+dfsg/src/r_wrap.cc:706:5:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
    strncpy(r,name,lname+1);
data/r-bioc-chemminer-3.42.0+dfsg/src/r_wrap.cc:1275:15:  [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 len = strlen(cstr);

ANALYSIS SUMMARY:

Hits = 37
Lines analyzed = 3861 in approximately 0.11 seconds (34323 lines/second)
Physical Source Lines of Code (SLOC) = 2734
Hits@level = [0]  15 [1]  17 [2]  17 [3]   0 [4]   3 [5]   0
Hits@level+ = [0+]  52 [1+]  37 [2+]  20 [3+]   3 [4+]   3 [5+]   0
Hits/KSLOC@level+ = [0+] 19.0198 [1+] 13.5333 [2+] 7.31529 [3+] 1.09729 [4+] 1.09729 [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.