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/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_compare.c
Examining data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c
Examining data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c
Examining data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c
Examining data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_pairwise_distance.c
Examining data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c
Examining data/python-cogent-2020.2.7a+dfsg/src/cogent3/maths/_period.c

FINAL RESULTS:

data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_compare.c:781:5:  [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(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:789:5:  [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(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:22586:5:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    vsnprintf(msg, 200, fmt, vargs);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:789:5:  [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(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:21890:5:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    vsnprintf(msg, 200, fmt, vargs);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:789:5:  [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(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:19718:5:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    vsnprintf(msg, 200, fmt, vargs);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_pairwise_distance.c:786:5:  [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(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:789:5:  [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(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:18378:5:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    vsnprintf(msg, 200, fmt, vargs);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/maths/_period.c:786:5:  [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(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:23763:18:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            if (!setstate) PyErr_Clear();
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:23764:18:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) {
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:23764:58:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) {
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:23785:16:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    Py_XDECREF(setstate);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:23067:18:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            if (!setstate) PyErr_Clear();
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:23068:18:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) {
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:23068:58:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) {
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:23089:16:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    Py_XDECREF(setstate);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:20843:18:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            if (!setstate) PyErr_Clear();
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:20844:18:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) {
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:20844:58:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) {
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:20865:16:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    Py_XDECREF(setstate);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:19560:18:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            if (!setstate) PyErr_Clear();
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:19561:18:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) {
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:19561:58:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            if (!setstate || __Pyx_setup_reduce_is_named(setstate, __pyx_n_s_setstate_cython)) {
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:19582:16:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    Py_XDECREF(setstate);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_compare.c:734:9:  [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 ascii_chars[128];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_compare.c:3918:5:  [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 ctversion[4], rtversion[4];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_compare.c:3922:9:  [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 message[200];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:742:9:  [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 ascii_chars[128];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:15855:27:  [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.
    __pyx_v_resultp = ((((char **)__pyx_v_resultp)[0]) + __pyx_v_suboffset);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:17596:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent)));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:17628:16:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:18133:12:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    (void)(memcpy(__pyx_v_result, __pyx_v_src->data, __pyx_v_size));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:18881:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      (void)(memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim)));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:19486:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      (void)(memcpy(__pyx_v_data, __pyx_v_item, __pyx_v_itemsize));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:21780:3:  [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(&(__pyx_memoryview_thread_locks[0]), __pyx_t_2, sizeof(__pyx_memoryview_thread_locks[0]) * (8));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:22580:5:  [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 msg[200];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:25685:5:  [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 ctversion[4], rtversion[4];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:25689:9:  [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 message[200];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:742:9:  [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 ascii_chars[128];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:15194:27:  [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.
    __pyx_v_resultp = ((((char **)__pyx_v_resultp)[0]) + __pyx_v_suboffset);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:16935:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent)));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:16967:16:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:17472:12:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    (void)(memcpy(__pyx_v_result, __pyx_v_src->data, __pyx_v_size));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:18220:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      (void)(memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim)));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:18825:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      (void)(memcpy(__pyx_v_data, __pyx_v_item, __pyx_v_itemsize));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:21106:3:  [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(&(__pyx_memoryview_thread_locks[0]), __pyx_t_2, sizeof(__pyx_memoryview_thread_locks[0]) * (8));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:21884:5:  [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 msg[200];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:24989:5:  [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 ctversion[4], rtversion[4];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:24993:9:  [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 message[200];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:742:9:  [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 ascii_chars[128];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:13048:27:  [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.
    __pyx_v_resultp = ((((char **)__pyx_v_resultp)[0]) + __pyx_v_suboffset);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:14789:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent)));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:14821:16:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:15326:12:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    (void)(memcpy(__pyx_v_result, __pyx_v_src->data, __pyx_v_size));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:16074:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      (void)(memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim)));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:16679:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      (void)(memcpy(__pyx_v_data, __pyx_v_item, __pyx_v_itemsize));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:18907:3:  [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(&(__pyx_memoryview_thread_locks[0]), __pyx_t_2, sizeof(__pyx_memoryview_thread_locks[0]) * (8));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:19712:5:  [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 msg[200];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:22708:5:  [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 ctversion[4], rtversion[4];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:22712:9:  [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 message[200];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_pairwise_distance.c:739:9:  [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 ascii_chars[128];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_pairwise_distance.c:6361:5:  [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 warning[200];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_pairwise_distance.c:7573:5:  [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 ctversion[4], rtversion[4];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_pairwise_distance.c:7577:9:  [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 message[200];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:742:9:  [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 ascii_chars[128];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:11868:27:  [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.
    __pyx_v_resultp = ((((char **)__pyx_v_resultp)[0]) + __pyx_v_suboffset);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:13609:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent)));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:13641:16:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        (void)(memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:14146:12:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    (void)(memcpy(__pyx_v_result, __pyx_v_src->data, __pyx_v_size));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:14894:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      (void)(memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim)));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:15499:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      (void)(memcpy(__pyx_v_data, __pyx_v_item, __pyx_v_itemsize));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:17639:3:  [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(&(__pyx_memoryview_thread_locks[0]), __pyx_t_2, sizeof(__pyx_memoryview_thread_locks[0]) * (8));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:18372:5:  [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 msg[200];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:21390:5:  [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 ctversion[4], rtversion[4];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:21394:9:  [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 message[200];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/maths/_period.c:739:9:  [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 ascii_chars[128];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/maths/_period.c:7820:5:  [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 warning[200];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/maths/_period.c:9239:5:  [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 ctversion[4], rtversion[4];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/maths/_period.c:9243:9:  [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 message[200];
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_compare.c:658:87:  [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).
#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_compare.c:779:52:  [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).
    __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c) + 1);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_compare.c:1543:15:  [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).
  __pyx_t_1 = strlen(__pyx_v_seq1); 
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_compare.c:1553:15:  [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).
  __pyx_t_1 = strlen(__pyx_v_seq2); 
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_compare.c:3966:65:  [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).
    return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:666:87:  [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).
#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:787:52:  [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).
    __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c) + 1);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:8821:56:  [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).
    __pyx_t_4 = __Pyx_decode_c_string(__pyx_v_mode, 0, strlen(__pyx_v_mode), NULL, NULL, PyUnicode_DecodeASCII); if (unlikely(!__pyx_t_4)) __PYX_ERR(2, 249, __pyx_L1_error)
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:8865:56:  [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).
    __pyx_t_3 = __Pyx_decode_c_string(__pyx_v_mode, 0, strlen(__pyx_v_mode), NULL, NULL, PyUnicode_DecodeASCII); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 251, __pyx_L1_error)
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:11400:20:  [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).
      __pyx_t_10 = strlen(__pyx_v_self->view.format); 
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:18304:53:  [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).
  __pyx_t_2 = __Pyx_decode_c_string(__pyx_v_msg, 0, strlen(__pyx_v_msg), NULL, NULL, PyUnicode_DecodeASCII); if (unlikely(!__pyx_t_2)) __PYX_ERR(2, 1258, __pyx_L1_error)
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:18396:55:  [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).
    __pyx_t_3 = __Pyx_decode_c_string(__pyx_v_msg, 0, strlen(__pyx_v_msg), NULL, NULL, PyUnicode_DecodeASCII); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 1263, __pyx_L1_error)
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:23063:23:  [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 slen = strlen(cstring);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_pogs.c:25733:65:  [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).
    return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:666:87:  [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).
#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:787:52:  [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).
    __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c) + 1);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:8160:56:  [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).
    __pyx_t_4 = __Pyx_decode_c_string(__pyx_v_mode, 0, strlen(__pyx_v_mode), NULL, NULL, PyUnicode_DecodeASCII); if (unlikely(!__pyx_t_4)) __PYX_ERR(2, 249, __pyx_L1_error)
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:8204:56:  [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).
    __pyx_t_3 = __Pyx_decode_c_string(__pyx_v_mode, 0, strlen(__pyx_v_mode), NULL, NULL, PyUnicode_DecodeASCII); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 251, __pyx_L1_error)
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:10739:20:  [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).
      __pyx_t_10 = strlen(__pyx_v_self->view.format); 
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:17643:53:  [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).
  __pyx_t_2 = __Pyx_decode_c_string(__pyx_v_msg, 0, strlen(__pyx_v_msg), NULL, NULL, PyUnicode_DecodeASCII); if (unlikely(!__pyx_t_2)) __PYX_ERR(2, 1258, __pyx_L1_error)
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:17735:55:  [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).
    __pyx_t_3 = __Pyx_decode_c_string(__pyx_v_msg, 0, strlen(__pyx_v_msg), NULL, NULL, PyUnicode_DecodeASCII); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 1263, __pyx_L1_error)
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:22367:23:  [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 slen = strlen(cstring);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/align/_pairwise_seqs.c:25037:65:  [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).
    return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:666:87:  [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).
#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:787:52:  [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).
    __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c) + 1);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:6014:56:  [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).
    __pyx_t_4 = __Pyx_decode_c_string(__pyx_v_mode, 0, strlen(__pyx_v_mode), NULL, NULL, PyUnicode_DecodeASCII); if (unlikely(!__pyx_t_4)) __PYX_ERR(2, 249, __pyx_L1_error)
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:6058:56:  [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).
    __pyx_t_3 = __Pyx_decode_c_string(__pyx_v_mode, 0, strlen(__pyx_v_mode), NULL, NULL, PyUnicode_DecodeASCII); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 251, __pyx_L1_error)
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:8593:20:  [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).
      __pyx_t_10 = strlen(__pyx_v_self->view.format); 
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:15497:53:  [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).
  __pyx_t_2 = __Pyx_decode_c_string(__pyx_v_msg, 0, strlen(__pyx_v_msg), NULL, NULL, PyUnicode_DecodeASCII); if (unlikely(!__pyx_t_2)) __PYX_ERR(2, 1258, __pyx_L1_error)
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:15589:55:  [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).
    __pyx_t_3 = __Pyx_decode_c_string(__pyx_v_msg, 0, strlen(__pyx_v_msg), NULL, NULL, PyUnicode_DecodeASCII); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 1263, __pyx_L1_error)
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:20069:23:  [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 slen = strlen(cstring);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_likelihood_tree.c:22756:65:  [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).
    return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_pairwise_distance.c:663:87:  [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).
#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_pairwise_distance.c:784:52:  [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).
    __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c) + 1);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_pairwise_distance.c:7621:65:  [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).
    return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:666:87:  [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).
#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:787:52:  [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).
    __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c) + 1);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:4834:56:  [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).
    __pyx_t_4 = __Pyx_decode_c_string(__pyx_v_mode, 0, strlen(__pyx_v_mode), NULL, NULL, PyUnicode_DecodeASCII); if (unlikely(!__pyx_t_4)) __PYX_ERR(2, 249, __pyx_L1_error)
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:4878:56:  [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).
    __pyx_t_3 = __Pyx_decode_c_string(__pyx_v_mode, 0, strlen(__pyx_v_mode), NULL, NULL, PyUnicode_DecodeASCII); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 251, __pyx_L1_error)
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:7413:20:  [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).
      __pyx_t_10 = strlen(__pyx_v_self->view.format); 
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:14317:53:  [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).
  __pyx_t_2 = __Pyx_decode_c_string(__pyx_v_msg, 0, strlen(__pyx_v_msg), NULL, NULL, PyUnicode_DecodeASCII); if (unlikely(!__pyx_t_2)) __PYX_ERR(2, 1258, __pyx_L1_error)
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:14409:55:  [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).
    __pyx_t_3 = __Pyx_decode_c_string(__pyx_v_msg, 0, strlen(__pyx_v_msg), NULL, NULL, PyUnicode_DecodeASCII); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 1263, __pyx_L1_error)
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:18794:23:  [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 slen = strlen(cstring);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/evolve/_solved_models.c:21438:65:  [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).
    return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str));
data/python-cogent-2020.2.7a+dfsg/src/cogent3/maths/_period.c:663:87:  [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).
#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
data/python-cogent-2020.2.7a+dfsg/src/cogent3/maths/_period.c:784:52:  [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).
    __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c) + 1);
data/python-cogent-2020.2.7a+dfsg/src/cogent3/maths/_period.c:2914:15:  [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).
  __pyx_t_1 = strlen(__pyx_v_seq); 
data/python-cogent-2020.2.7a+dfsg/src/cogent3/maths/_period.c:9287:65:  [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).
    return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str));

ANALYSIS SUMMARY:

Hits = 130
Lines analyzed = 117392 in approximately 3.79 seconds (31007 lines/second)
Physical Source Lines of Code (SLOC) = 70451
Hits@level = [0]   0 [1]  48 [2]  55 [3]  16 [4]  11 [5]   0
Hits@level+ = [0+] 130 [1+] 130 [2+]  82 [3+]  27 [4+]  11 [5+]   0
Hits/KSLOC@level+ = [0+] 1.84525 [1+] 1.84525 [2+] 1.16393 [3+] 0.383245 [4+] 0.156137 [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.