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/phat-1.6/addons/alpha_3.cpp
Examining data/phat-1.6/addons/rips.cpp
Examining data/phat-1.6/include/phat/algorithms/chunk_reduction.h
Examining data/phat-1.6/include/phat/algorithms/row_reduction.h
Examining data/phat-1.6/include/phat/algorithms/spectral_sequence_reduction.h
Examining data/phat-1.6/include/phat/algorithms/standard_reduction.h
Examining data/phat-1.6/include/phat/algorithms/twist_reduction.h
Examining data/phat-1.6/include/phat/boundary_matrix.h
Examining data/phat-1.6/include/phat/compute_persistence_pairs.h
Examining data/phat-1.6/include/phat/helpers/dualize.h
Examining data/phat-1.6/include/phat/helpers/misc.h
Examining data/phat-1.6/include/phat/helpers/thread_local_storage.h
Examining data/phat-1.6/include/phat/persistence_pairs.h
Examining data/phat-1.6/include/phat/representations/Container_traits.h
Examining data/phat-1.6/include/phat/representations/Pivot_representation.h
Examining data/phat-1.6/include/phat/representations/Uniform_representation.h
Examining data/phat-1.6/include/phat/representations/Unordered_map_container_traits.h
Examining data/phat-1.6/include/phat/representations/bit_tree_pivot_column.h
Examining data/phat-1.6/include/phat/representations/default_representations.h
Examining data/phat-1.6/include/phat/representations/full_pivot_column.h
Examining data/phat-1.6/include/phat/representations/heap_column_rep.h
Examining data/phat-1.6/include/phat/representations/heap_pivot_column.h
Examining data/phat-1.6/include/phat/representations/list_column_rep.h
Examining data/phat-1.6/include/phat/representations/set_column_rep.h
Examining data/phat-1.6/include/phat/representations/sparse_pivot_column.h
Examining data/phat-1.6/include/phat/representations/vector_column_rep.h
Examining data/phat-1.6/python/_phat.cpp
Examining data/phat-1.6/src/benchmark.cpp
Examining data/phat-1.6/src/convert.cpp
Examining data/phat-1.6/src/info.cpp
Examining data/phat-1.6/src/phat.cpp
Examining data/phat-1.6/src/self_test.cpp
Examining data/phat-1.6/src/simple_example.cpp

FINAL RESULTS:

data/phat-1.6/addons/rips.cpp:34:18:  [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).
        skeleton=atoi(argv[2]);
data/phat-1.6/include/phat/boundary_matrix.h:331:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            input_stream.read( (char*)&nr_columns, sizeof( int64_t ) );
data/phat-1.6/include/phat/boundary_matrix.h:337:30:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                input_stream.read( (char*)&cur_dim, sizeof( int64_t ) );
data/phat-1.6/include/phat/boundary_matrix.h:340:30:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                input_stream.read( (char*)&nr_rows, sizeof( int64_t ) );
data/phat-1.6/include/phat/boundary_matrix.h:344:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    input_stream.read( (char*)&cur_row, sizeof( int64_t ) );
data/phat-1.6/include/phat/persistence_pairs.h:101:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            input_stream.read( (char*)&nr_pairs, sizeof( int64_t ) );
data/phat-1.6/include/phat/persistence_pairs.h:104:30:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                input_stream.read( (char*)&birth, sizeof( int64_t ) );
data/phat-1.6/include/phat/persistence_pairs.h:106:30:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                input_stream.read( (char*)&death, sizeof( int64_t ) );

ANALYSIS SUMMARY:

Hits = 8
Lines analyzed = 4557 in approximately 0.17 seconds (26944 lines/second)
Physical Source Lines of Code (SLOC) = 3012
Hits@level = [0]   0 [1]   7 [2]   1 [3]   0 [4]   0 [5]   0
Hits@level+ = [0+]   8 [1+]   8 [2+]   1 [3+]   0 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 2.65604 [1+] 2.65604 [2+] 0.332005 [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.