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-fmcsr-1.32.0+dfsg/config.h
Examining data/r-bioc-fmcsr-1.32.0+dfsg/src/MCS.cpp
Examining data/r-bioc-fmcsr-1.32.0+dfsg/src/MCS.h
Examining data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.cpp
Examining data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.h
Examining data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSList.h
Examining data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSMap.cpp
Examining data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSMap.h
Examining data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSRingDetector.cpp
Examining data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSRingDetector.h
Examining data/r-bioc-fmcsr-1.32.0+dfsg/src/fmcs_R_wrap.cpp
Examining data/r-bioc-fmcsr-1.32.0+dfsg/src/util.cpp
Examining data/r-bioc-fmcsr-1.32.0+dfsg/src/util.h

FINAL RESULTS:

data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.cpp:70:13:  [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(atoms, other.atoms, sizeof(Atom) * other.atomCount);
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.cpp:75:13:  [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(bonds, other.bonds, sizeof(Bond) * other.bondCount);
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.cpp:87:17:  [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(atoms, other.atoms, sizeof(Atom) * other.atomCount);
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.cpp:92:17:  [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(bonds, other.bonds, sizeof(Bond) * other.bondCount);
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.cpp:123:13:  [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(atoms, that.atoms, sizeof(Atom) * that.atomCount);
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.cpp:128:13:  [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(bonds, that.bonds, sizeof(Bond) * that.bondCount);
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.cpp:349:25:  [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).
    	int oldAtomCount = atoi(atomCountString.c_str());
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.cpp:350:25:  [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).
    	int oldBondCount = atoi(bondCountString.c_str());
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.cpp:377:31:  [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).
    		int oldFirstAtomIndex = atoi(oldBondBlockLine.substr(0, 3).c_str());
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.cpp:378:32:  [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).
    		int oldSecondAtomIndex = atoi(oldBondBlockLine.substr(3, 3).c_str());
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.cpp:434:18:  [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).
    	atomCount = atoi(atomCountString.c_str());
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.cpp:435:18:  [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).
    	bondCount = atoi(bondCountString.c_str());
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.cpp:456:19:  [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).
    		firstAtom = atoi(bondBlockLine.substr(0, 3).c_str()) - 1;
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.cpp:457:20:  [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).
    		secondAtom = atoi(bondBlockLine.substr(3, 3).c_str()) - 1;
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.cpp:458:18:  [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).
    		bondType = atoi(bondBlockLine.substr(6, 3).c_str());
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.h:53:26:  [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 elements[111][3];
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.h:54:26:  [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 code[111];
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSList.h:75:9:  [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(data, m.data, sizeof(T) * m.length);
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSList.h:93:9:  [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(data, m.data, sizeof(T) * m.length);
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSList.h:115:9:  [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(n, data, sizeof(T) * length);
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.cpp:135:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    void MCSCompound::read(const string& sdfString, ReadType type) {
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.cpp:155:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    void MCSCompound::read(const std::string& sdfString) {
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.h:116:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        void read(const std::string& sdfString, ReadType type);
data/r-bioc-fmcsr-1.32.0+dfsg/src/MCSCompound.h:118:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        void read(const std::string& sdfString);
data/r-bioc-fmcsr-1.32.0+dfsg/src/fmcs_R_wrap.cpp:63:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        compoundOne.read(string(*structureStringOne), MCSCompound::SDF);
data/r-bioc-fmcsr-1.32.0+dfsg/src/fmcs_R_wrap.cpp:64:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        compoundTwo.read(string(*structureStringTwo), MCSCompound::SDF);
data/r-bioc-fmcsr-1.32.0+dfsg/src/fmcs_R_wrap.cpp:66:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        compoundOne.read(string(*structureStringOne));
data/r-bioc-fmcsr-1.32.0+dfsg/src/fmcs_R_wrap.cpp:67:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        compoundTwo.read(string(*structureStringTwo));

ANALYSIS SUMMARY:

Hits = 28
Lines analyzed = 2538 in approximately 0.07 seconds (35055 lines/second)
Physical Source Lines of Code (SLOC) = 1844
Hits@level = [0]   0 [1]   8 [2]  20 [3]   0 [4]   0 [5]   0
Hits@level+ = [0+]  28 [1+]  28 [2+]  20 [3+]   0 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 15.1844 [1+] 15.1844 [2+] 10.846 [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.