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-cran-spp-1.16.0/src/pc.h
Examining data/r-cran-spp-1.16.0/src/maqread.cpp
Examining data/r-cran-spp-1.16.0/src/maqmap.c
Examining data/r-cran-spp-1.16.0/src/peaks.cpp
Examining data/r-cran-spp-1.16.0/src/bed2vector.cpp
Examining data/r-cran-spp-1.16.0/src/api_global.h
Examining data/r-cran-spp-1.16.0/src/wdl.cpp
Examining data/r-cran-spp-1.16.0/src/const.h
Examining data/r-cran-spp-1.16.0/src/cdensum.c
Examining data/r-cran-spp-1.16.0/src/maqmap.h
Examining data/r-cran-spp-1.16.0/src/spp_init.c
FINAL RESULTS:
data/r-cran-spp-1.16.0/src/bed2vector.cpp:151:18: [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).
int fstart=atoi(str_start.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:153:16: [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 fend=atoi(str_end.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:286:5: [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).
nm=atoi((str_nm.c_str()+1));
data/r-cran-spp-1.16.0/src/bed2vector.cpp:292:15: [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 len=atoi(str_len.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:295:16: [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 fpos=atoi(str_pos.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:405:5: [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 cline[1024];
data/r-cran-spp-1.16.0/src/bed2vector.cpp:442:11: [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).
FILE *f=fopen(fname,"rb");
data/r-cran-spp-1.16.0/src/bed2vector.cpp:466:5: [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).
nm=atoi((str_nm.c_str()+1));
data/r-cran-spp-1.16.0/src/bed2vector.cpp:472:15: [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 len=atoi(str_len.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:475:16: [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 fpos=atoi(str_pos.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:635:11: [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).
FILE *f=fopen(fname,"rb");
data/r-cran-spp-1.16.0/src/bed2vector.cpp:659:5: [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).
nm=atoi((str_nm.c_str()+1));
data/r-cran-spp-1.16.0/src/bed2vector.cpp:671:16: [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 fpos=atoi(str_pos.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:686:6: [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).
nm1=atoi(nms.substr(0,nms.size()-1).c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:691:6: [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).
nm2=atoi(nms.substr(0,nms.size()-1).c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:829:11: [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).
FILE *f=fopen(fname,"rb");
data/r-cran-spp-1.16.0/src/bed2vector.cpp:857:5: [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).
nm=atoi((str_nm.c_str()+1));
data/r-cran-spp-1.16.0/src/bed2vector.cpp:864:16: [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 fpos=atoi(str_pos.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1017:11: [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).
FILE *f=fopen(fname,"rb");
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1068:16: [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 fpos=atoi(str_pos.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1231:11: [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).
FILE *f=fopen(fname,"rb");
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1269:15: [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 nm0=atoi(str_nm0.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1278:10: [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 nm1=atoi(str_nm1.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1287:12: [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 nm2=atoi(str_nm2.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1318:5: [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).
if(atoi(&lc)==nm) {
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1343:19: [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).
int pos=strand*atoi(str_pos.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1517:11: [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).
FILE *f=fopen(fname,"rb");
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1556:16: [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 fpos=atoi(str_pos.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1731:11: [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).
FILE *f=fopen(fname,"rb");
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1781:15: [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 len=atoi(str_tend.c_str())-atoi(str_tstart.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1781:38: [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 len=atoi(str_tend.c_str())-atoi(str_tstart.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1791:10: [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).
fpos=-1*atoi(str_endpos.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1793:7: [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).
fpos=atoi(str_startpos.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1797:14: [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 nm=atoi(str_ndel.c_str())+atoi(str_nins.c_str())+atoi(str_nsub.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1797:37: [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 nm=atoi(str_ndel.c_str())+atoi(str_nins.c_str())+atoi(str_nsub.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1797:60: [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 nm=atoi(str_ndel.c_str())+atoi(str_nins.c_str())+atoi(str_nsub.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1957:11: [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).
FILE *f=fopen(fname,"rb");
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1978:16: [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 fpos=atoi(str_pos.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1984:14: [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 nm=atoi(str_nm.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:1985:15: [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 len=atoi(str_len.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:2135:11: [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).
FILE *f=fopen(fname,"rb");
data/r-cran-spp-1.16.0/src/bed2vector.cpp:2162:7: [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).
fpos=atoi(str_spos.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:2164:10: [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).
fpos=-1*atoi(str_epos.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:2166:14: [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 nm=atoi(str_qual.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:2289:11: [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).
FILE *f=fopen(fname,"rb");
data/r-cran-spp-1.16.0/src/bed2vector.cpp:2330:5: [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).
nm=atoi(str_mm.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:2333:16: [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 fpos=atoi(str_spos.c_str());;
data/r-cran-spp-1.16.0/src/bed2vector.cpp:2460:11: [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).
FILE *f=fopen(fname,"rb");
data/r-cran-spp-1.16.0/src/bed2vector.cpp:2506:10: [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).
fpos=-1*atoi(str_endpos.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:2508:7: [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).
fpos=atoi(str_startpos.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:2515:19: [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).
int nblocks=atoi(str_nblocks.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:2523:10: [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 sgs=atoi(str_sgs.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:2525:11: [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 slen=atoi(str_slen.c_str());
data/r-cran-spp-1.16.0/src/bed2vector.cpp:2527:10: [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 snm=atoi(str_snm.c_str());
data/r-cran-spp-1.16.0/src/maqmap.h:46:2: [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 name[MAX_NAMELEN];
data/r-cran-spp-1.16.0/src/bed2vector.cpp:84:8: [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).
cline[strlen(cline)-1]='\0';
data/r-cran-spp-1.16.0/src/bed2vector.cpp:293:43: [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).
string chr=*sit++; chr=chr.substr(3,strlen(chr.c_str()));
data/r-cran-spp-1.16.0/src/bed2vector.cpp:473:43: [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).
string chr=*sit++; chr=chr.substr(3,strlen(chr.c_str()));
data/r-cran-spp-1.16.0/src/maqmap.c:37:9: [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).
len = strlen(mm->ref_name[i]) + 1;
ANALYSIS SUMMARY:
Hits = 59
Lines analyzed = 4948 in approximately 0.12 seconds (40679 lines/second)
Physical Source Lines of Code (SLOC) = 3675
Hits@level = [0] 0 [1] 4 [2] 55 [3] 0 [4] 0 [5] 0
Hits@level+ = [0+] 59 [1+] 59 [2+] 55 [3+] 0 [4+] 0 [5+] 0
Hits/KSLOC@level+ = [0+] 16.0544 [1+] 16.0544 [2+] 14.966 [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.