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-edger-3.32.0+dfsg/src/R_add_prior_count.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/R_ave_log_cpm.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/R_calculate_cpm.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/R_check_poisson_bound.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/R_compute_apl.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/R_compute_nbdev.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/R_exact_test_by_deviance.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/R_fit_levenberg.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/R_fit_one_group.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/R_get_one_way_fitted.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/R_initialize_levenberg.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/R_loess_by_col.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/R_maximize_interpolant.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c
Examining data/r-bioc-edger-3.32.0+dfsg/src/R_simple_good_turing.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/add_prior.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/add_prior.h
Examining data/r-bioc-edger-3.32.0+dfsg/src/adj_coxreid.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/fmm_spline.c
Examining data/r-bioc-edger-3.32.0+dfsg/src/glm.h
Examining data/r-bioc-edger-3.32.0+dfsg/src/glm_levenberg.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/glm_one_group.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/init.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/interpolator.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/interpolator.h
Examining data/r-bioc-edger-3.32.0+dfsg/src/nbdev.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/objects.cpp
Examining data/r-bioc-edger-3.32.0+dfsg/src/objects.h
Examining data/r-bioc-edger-3.32.0+dfsg/src/utils.h
FINAL RESULTS:
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:422:9: [2] (misc) fopen:
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).
fin = fopen(filename,"r");
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:476:9: [2] (misc) fopen:
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).
fin = fopen(filename,"r");
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:1200:9: [2] (misc) fopen:
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).
fin = fopen(filename,"r");
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:1202:14: [2] (misc) fopen:
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).
finRev = fopen(filename2, "r");
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:1401:10: [2] (misc) fopen:
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).
fout = fopen(output, "w");
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:1432:10: [2] (misc) fopen:
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).
fout = fopen(output, "w");
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:393:8: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ch=fgetc(fin);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:438:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(new_barcode->sequence, line, barcode_length); // copy the barcode line up to the length of the barcode into the barcode struct
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:445:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(new_barcode->sequenceRev, token, barcode_length_rev);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:450:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(new_barcode->sequence2, token, barcode2_length);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:493:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(new_hairpin->sequence, line, hairpin_length); // copy the data retrieved (stored in line) to our new_hairpin struct
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:521:53: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
locate_sequence_in_trie(trie_node *trie_head, char *read, int *found_position) {
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:530:22: [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).
long read_length = strlen(read);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:530:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
long read_length = strlen(read);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:539:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
base = read[j];
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:568:50: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
mismatch_trie_aux(trie_node *current_node, char *read, int pos, int mismatch_left, bool original_pos) {
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:599:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (Base_In_Node(current_node, read[pos])) {
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:600:32: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
match = Get_Links_Position(read[pos]);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:601:70: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
index = mismatch_trie_aux(current_node->links[Get_Links_Position(read[pos])],
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:602:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read, pos + 1, mismatch_left, original_pos);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:617:57: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
index = mismatch_trie_aux(current_node->links[i], read, pos + 1, mismatch_left - 1, original_pos);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:629:53: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
locate_mismatch_in_trie(trie_node *trie_head, char *read, int sequence_length, int mismatch_count, int *found_position, bool original_pos) {
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:645:13: [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(read);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:645:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int len = strlen(read);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:648:42: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
index = mismatch_trie_aux(trie_head, read, i, mismatch_count, original_pos);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:800:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
locate_barcode(char *read, int *found_position) {
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:809:73: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int barcode_index = locate_sequence_in_trie(barcode_single_trie_head, read, found_position);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:816:71: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
barcode_index = locate_mismatch_in_trie(barcode_single_trie_head, read, barcode_length, barcode_n_mismatch, found_position, true);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:828:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
locate_barcode_paired(char *read, char *read_rev, int *found_position, int *found2_position) {
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:848:70: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
barcode1_index = locate_sequence_in_trie(barcode_single_trie_head, read, &found_for_position);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:860:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(barcode1, read + found_for_position, barcode_length);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:862:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(barcode2, read_rev + found_rev_position, barcode_length_rev);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:874:20: [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).
int read_len = strlen(read);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:874:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int read_len = strlen(read);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:875:21: [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 read2_len = strlen(read_rev);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:913:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
locate_barcode_dualIndexing(char *read, int *found_position, int *found2_position){
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:929:70: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
barcode1_index = locate_sequence_in_trie(barcode_single_trie_head, read, &found_for_position);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:941:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(barcode1, read + found_for_position, barcode_length);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:943:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(barcode2, read + found_dual_position, barcode2_length);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:955:20: [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).
int read_len = strlen(read);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:955:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int read_len = strlen(read);
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:996:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
locate_hairpin(char *read, int *barcode_found_position, int *hairpin_found_position) {
data/r-bioc-edger-3.32.0+dfsg/src/R_process_hairpin_reads.c:1257:24: [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).
this_read_length = strlen(line);
ANALYSIS SUMMARY:
Hits = 43
Lines analyzed = 3867 in approximately 0.14 seconds (27520 lines/second)
Physical Source Lines of Code (SLOC) = 2515
Hits@level = [0] 6 [1] 37 [2] 6 [3] 0 [4] 0 [5] 0
Hits@level+ = [0+] 49 [1+] 43 [2+] 6 [3+] 0 [4+] 0 [5+] 0
Hits/KSLOC@level+ = [0+] 19.4831 [1+] 17.0974 [2+] 2.38569 [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.