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/phylonium-1.3/libs/seqcmp_avx512.c Examining data/phylonium-1.3/libs/revseqcmp.c Examining data/phylonium-1.3/libs/seqcmp.h Examining data/phylonium-1.3/libs/revseqcmp.h Examining data/phylonium-1.3/libs/seqcmp.c Examining data/phylonium-1.3/libs/reallocarray.c Examining data/phylonium-1.3/libs/pfasta.h Examining data/phylonium-1.3/libs/revseqcmp_ssse3.c Examining data/phylonium-1.3/libs/seqcmp_sse2.c Examining data/phylonium-1.3/libs/seqcmp_avx2.c Examining data/phylonium-1.3/libs/compat-stdlib.h Examining data/phylonium-1.3/libs/revseqcmp_avx2.c Examining data/phylonium-1.3/libs/pfasta.c Examining data/phylonium-1.3/src/process.h Examining data/phylonium-1.3/src/sequence.h Examining data/phylonium-1.3/src/evo_model.cxx Examining data/phylonium-1.3/src/phylonium.cxx Examining data/phylonium-1.3/src/io.h Examining data/phylonium-1.3/src/process.cxx Examining data/phylonium-1.3/src/esa.cxx Examining data/phylonium-1.3/src/evo_model.h Examining data/phylonium-1.3/src/global.h Examining data/phylonium-1.3/src/io.cxx Examining data/phylonium-1.3/src/esa.h Examining data/phylonium-1.3/src/sequence.cxx Examining data/phylonium-1.3/test/simf.cxx Examining data/phylonium-1.3/test/catch.hpp Examining data/phylonium-1.3/test/Tsequence.cxx Examining data/phylonium-1.3/test/Tprocess.cxx Examining data/phylonium-1.3/test/Tmain.cxx FINAL RESULTS: data/phylonium-1.3/libs/pfasta.c:98:9: [4] (format) snprintf: 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. (void)snprintf(errstr_buffer, PF_ERROR_STRING_LENGTH, __VA_ARGS__); \ data/phylonium-1.3/src/phylonium.cxx:119:4: [3] (buffer) getopt_long: Some older implementations do not protect against internal buffer overflows (CWE-120, CWE-20). Check implementation on installation, or limit the size of all string inputs. getopt_long(argc, argv, "2b:hp:r:t:v", long_options, &option_index); data/phylonium-1.3/test/catch.hpp:4498:1: [3] (random) random: 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. random(T a, T b) { data/phylonium-1.3/test/catch.hpp:4507:1: [3] (random) random: 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. random(T a, T b) { data/phylonium-1.3/test/catch.hpp:11724:18: [3] (random) srand: 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. std::srand( config.rngSeed() ); data/phylonium-1.3/test/simf.cxx:35:18: [3] (buffer) getopt: Some older implementations do not protect against internal buffer overflows (CWE-120, CWE-20). Check implementation on installation, or limit the size of all string inputs. while ((check = getopt(argc, argv, "d:hl:L:p:rs:")) != -1) { data/phylonium-1.3/libs/pfasta.c:54:14: [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. thread_local char errstr_buffer[PF_ERROR_STRING_LENGTH]; data/phylonium-1.3/libs/pfasta.c:216:3: [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(&chunk, begin + vec_offset * vec_size, vec_size); data/phylonium-1.3/libs/pfasta.c:542:2: [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(ds->str + ds->count, str, length); data/phylonium-1.3/libs/revseqcmp_avx2.c:32:3: [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(&b, self + vec_offset * vec_size, vec_size); data/phylonium-1.3/libs/revseqcmp_avx2.c:35:3: [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(&o, other + pos, vec_size); data/phylonium-1.3/libs/seqcmp_avx2.c:29:3: [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(&begin_chunk, begin + vec_offset * vec_bytes, vec_bytes); data/phylonium-1.3/libs/seqcmp_avx2.c:30:3: [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(&other_chunk, other + vec_offset * vec_bytes, vec_bytes); data/phylonium-1.3/libs/seqcmp_avx2.c:39:3: [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(&begin_chunk, begin + vec_offset * vec_bytes, vec_bytes); data/phylonium-1.3/libs/seqcmp_avx2.c:40:3: [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(&other_chunk, other + vec_offset * vec_bytes, vec_bytes); data/phylonium-1.3/libs/seqcmp_avx512.c:29:3: [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(&begin_chunk, begin + vec_offset * vec_bytes, vec_bytes); data/phylonium-1.3/libs/seqcmp_avx512.c:30:3: [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(&other_chunk, other + vec_offset * vec_bytes, vec_bytes); data/phylonium-1.3/libs/seqcmp_sse2.c:29:3: [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(&begin_chunk, begin + vec_offset * vec_bytes, vec_bytes); data/phylonium-1.3/libs/seqcmp_sse2.c:30:3: [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(&other_chunk, other + vec_offset * vec_bytes, vec_bytes); data/phylonium-1.3/libs/seqcmp_sse2.c:39:3: [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(&begin_chunk, begin + vec_offset * vec_bytes, vec_bytes); data/phylonium-1.3/libs/seqcmp_sse2.c:40:3: [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(&other_chunk, other + vec_offset * vec_bytes, vec_bytes); data/phylonium-1.3/src/esa.cxx:88:2: [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 str[CACHE_LENGTH + 1]; data/phylonium-1.3/src/io.cxx:61:24: [2] (misc) open: 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). int file_descriptor = open(file_name, O_RDONLY); data/phylonium-1.3/test/catch.hpp:2128:13: [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 timeStamp[timeStampSize]; data/phylonium-1.3/test/catch.hpp:4361:29: [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. alignas(alignof(T)) char storage[sizeof(T)]; data/phylonium-1.3/test/catch.hpp:5763:16: [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 char line[CATCH_CONFIG_CONSOLE_WIDTH] = {0}; data/phylonium-1.3/test/catch.hpp:7282:14: [2] (misc) open: 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). void open(); data/phylonium-1.3/test/catch.hpp:11056:14: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. std::memcpy(&i, &f, sizeof(f)); data/phylonium-1.3/test/catch.hpp:11065:14: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. std::memcpy(&i, &d, sizeof(d)); data/phylonium-1.3/test/catch.hpp:11523:9: [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 m_buffer[L_tmpnam] = { 0 }; data/phylonium-1.3/test/catch.hpp:11610:13: [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 buffer[100]; data/phylonium-1.3/test/catch.hpp:11619:23: [2] (tmpfile) tmpfile: Function tmpfile() has a security flaw on some systems (e.g., older System V systems) (CWE-377). m_file = std::tmpfile(); data/phylonium-1.3/test/catch.hpp:11643:9: [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 buffer[100] = {}; data/phylonium-1.3/test/catch.hpp:12065:30: [2] (misc) open: 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). tracker->open(); data/phylonium-1.3/test/catch.hpp:12845:31: [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 **utf8Argv = new char *[ argc ]; data/phylonium-1.3/test/catch.hpp:13004:13: [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 data[bufferSize]; data/phylonium-1.3/test/catch.hpp:13053:23: [2] (misc) open: 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). m_ofs.open( filename.c_str() ); data/phylonium-1.3/test/catch.hpp:13302:13: [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( m_data, m_start, m_size ); data/phylonium-1.3/test/catch.hpp:13823:23: [2] (misc) open: 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). void TrackerBase::open() { data/phylonium-1.3/test/catch.hpp:13923:13: [2] (misc) open: 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). open(); data/phylonium-1.3/test/catch.hpp:14299:21: [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 asChar[sizeof (int)]; data/phylonium-1.3/test/catch.hpp:14968:9: [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 buffer[maxDoubleSize]; data/phylonium-1.3/test/catch.hpp:14975:14: [2] (buffer) sprintf: Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or vsnprintf. Risk is low because the source has a constant maximum length. std::sprintf(buffer, "%.3f", duration); data/phylonium-1.3/test/catch.hpp:15568:10: [2] (misc) open: 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). void open() { data/phylonium-1.3/test/catch.hpp:15603:12: [2] (misc) open: 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). tp.open(); data/phylonium-1.3/test/catch.hpp:15980:13: [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 timeStamp[timeStampSize]; data/phylonium-1.3/test/simf.cxx:97:2: [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[line_length + 1]; data/phylonium-1.3/libs/pfasta.c:150:18: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ssize_t count = read(pp->file_descriptor, pp->buffer, BUFFER_SIZE); data/phylonium-1.3/libs/seqcmp_avx2.c:48:43: [1] (buffer) equal: Function does not check the second iterator for over-read conditions (CWE-126). This function is often discouraged by most C++ coding standards in favor of its safer alternatives provided since C++14. Consider using a form of this function that checks the second iterator before potentially overflowing it. substitutions = vec_offset * vec_bytes - equal; data/phylonium-1.3/libs/seqcmp_avx512.c:36:43: [1] (buffer) equal: Function does not check the second iterator for over-read conditions (CWE-126). This function is often discouraged by most C++ coding standards in favor of its safer alternatives provided since C++14. Consider using a form of this function that checks the second iterator before potentially overflowing it. substitutions = vec_length * vec_bytes - equal; data/phylonium-1.3/libs/seqcmp_sse2.c:48:43: [1] (buffer) equal: Function does not check the second iterator for over-read conditions (CWE-126). This function is often discouraged by most C++ coding standards in favor of its safer alternatives provided since C++14. Consider using a form of this function that checks the second iterator before potentially overflowing it. substitutions = vec_offset * vec_bytes - equal; data/phylonium-1.3/src/process.cxx:526:20: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). #pragma omp atomic read data/phylonium-1.3/test/catch.hpp:3625:29: [1] (buffer) is_permutation: Function does not check the second iterator for over-read conditions (CWE-126). This function is often discouraged by most C++ coding standards in favor of its safer alternatives provided since C++14. Consider using a form of this function that checks the second iterator before potentially overflowing it. return std::is_permutation(m_target.begin(), m_target.end(), vec.begin()); data/phylonium-1.3/test/catch.hpp:12874:36: [1] (buffer) getchar: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). static_cast<void>(std::getchar()); data/phylonium-1.3/test/catch.hpp:12879:36: [1] (buffer) getchar: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). static_cast<void>(std::getchar()); data/phylonium-1.3/test/catch.hpp:13176:50: [1] (buffer) equal: Function does not check the second iterator for over-read conditions (CWE-126). This function is often discouraged by most C++ coding standards in favor of its safer alternatives provided since C++14. Consider using a form of this function that checks the second iterator before potentially overflowing it. return s.size() >= prefix.size() && std::equal(prefix.begin(), prefix.end(), s.begin()); data/phylonium-1.3/test/catch.hpp:13182:50: [1] (buffer) equal: Function does not check the second iterator for over-read conditions (CWE-126). This function is often discouraged by most C++ coding standards in favor of its safer alternatives provided since C++14. Consider using a form of this function that checks the second iterator before potentially overflowing it. return s.size() >= suffix.size() && std::equal(suffix.rbegin(), suffix.rend(), s.rbegin()); data/phylonium-1.3/test/catch.hpp:13268:67: [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). : StringRef( rawChars, static_cast<StringRef::size_type>(std::strlen(rawChars) ) ) ANALYSIS SUMMARY: Hits = 58 Lines analyzed = 21474 in approximately 0.47 seconds (46066 lines/second) Physical Source Lines of Code (SLOC) = 15841 Hits@level = [0] 7 [1] 11 [2] 41 [3] 5 [4] 1 [5] 0 Hits@level+ = [0+] 65 [1+] 58 [2+] 47 [3+] 6 [4+] 1 [5+] 0 Hits/KSLOC@level+ = [0+] 4.10328 [1+] 3.66139 [2+] 2.96698 [3+] 0.378764 [4+] 0.0631273 [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.