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/clonalframe-1.2/src/alignment.cpp
Examining data/clonalframe-1.2/src/alignment.h
Examining data/clonalframe-1.2/src/alignment_structure.cpp
Examining data/clonalframe-1.2/src/alignment_structure.h
Examining data/clonalframe-1.2/src/alignment_xmfa.cpp
Examining data/clonalframe-1.2/src/alignment_xmfa.h
Examining data/clonalframe-1.2/src/boot.cpp
Examining data/clonalframe-1.2/src/boot.h
Examining data/clonalframe-1.2/src/burst.cpp
Examining data/clonalframe-1.2/src/burst.h
Examining data/clonalframe-1.2/src/ClonalFrame.cpp
Examining data/clonalframe-1.2/src/consensus.cpp
Examining data/clonalframe-1.2/src/consensus.h
Examining data/clonalframe-1.2/src/genes.cpp
Examining data/clonalframe-1.2/src/genes.h
Examining data/clonalframe-1.2/src/hashcell.cpp
Examining data/clonalframe-1.2/src/hashcell.h
Examining data/clonalframe-1.2/src/move.cpp
Examining data/clonalframe-1.2/src/move.h
Examining data/clonalframe-1.2/src/move_ages.cpp
Examining data/clonalframe-1.2/src/move_ages.h
Examining data/clonalframe-1.2/src/move_delta.cpp
Examining data/clonalframe-1.2/src/move_delta.h
Examining data/clonalframe-1.2/src/move_gap.cpp
Examining data/clonalframe-1.2/src/move_gap.h
Examining data/clonalframe-1.2/src/move_hidden.h
Examining data/clonalframe-1.2/src/move_hidden2.cpp
Examining data/clonalframe-1.2/src/move_hidden2.h
Examining data/clonalframe-1.2/src/move_mu.cpp
Examining data/clonalframe-1.2/src/move_mu.h
Examining data/clonalframe-1.2/src/move_nu.cpp
Examining data/clonalframe-1.2/src/move_nu.h
Examining data/clonalframe-1.2/src/move_rho.cpp
Examining data/clonalframe-1.2/src/move_rho.h
Examining data/clonalframe-1.2/src/move_wb.cpp
Examining data/clonalframe-1.2/src/move_wb.h
Examining data/clonalframe-1.2/src/param.cpp
Examining data/clonalframe-1.2/src/param.h
Examining data/clonalframe-1.2/src/recorder.cpp
Examining data/clonalframe-1.2/src/recorder.h
Examining data/clonalframe-1.2/src/timeval.h
Examining data/clonalframe-1.2/src/tree.cpp
Examining data/clonalframe-1.2/src/tree.h
Examining data/clonalframe-1.2/src/tree_coal.cpp
Examining data/clonalframe-1.2/src/tree_coal.h
Examining data/clonalframe-1.2/src/tree_newick.cpp
Examining data/clonalframe-1.2/src/tree_newick.h
Examining data/clonalframe-1.2/src/tree_simple.cpp
Examining data/clonalframe-1.2/src/tree_simple.h
Examining data/clonalframe-1.2/src/tree_upgma.cpp
Examining data/clonalframe-1.2/src/tree_upgma.h
Examining data/clonalframe-1.2/src/move_hidden.cpp
Examining data/clonalframe-1.2/src/util.cpp
Examining data/clonalframe-1.2/src/util.h
FINAL RESULTS:
data/clonalframe-1.2/src/ClonalFrame.cpp:250:24: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if (argc-optind>0) sprintf(outputname,"%s",argv[optind++]); else sprintf(outputname,"%s.out",inputname);
data/clonalframe-1.2/src/ClonalFrame.cpp:250:70: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if (argc-optind>0) sprintf(outputname,"%s",argv[optind++]); else sprintf(outputname,"%s.out",inputname);
data/clonalframe-1.2/src/alignment_xmfa.cpp:200:9: [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(buf2,buf+i);
data/clonalframe-1.2/src/consensus.cpp:174:26: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
pos+=sprintf(res+pos,"%s:%f,",r,age-tokeep[j]->age/tokeep[j]->nb);
data/clonalframe-1.2/src/recorder.cpp:101:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(filename,"%s",out);
data/clonalframe-1.2/src/tree.cpp:323:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(buf,"(%s,%s):%f",l,r,fage-age);
data/clonalframe-1.2/src/tree.cpp:325:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(buf,"(%s,%s):%f",r,l,fage-age);
data/clonalframe-1.2/src/ClonalFrame.cpp:194:17: [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 ((c = getopt (argc, argv, "E:x:y:z:m:d:n:r:t:w:j:e:S:a:b:f:g:l:sMDNRTAGHhBCcUvFILW")) != -1)
data/clonalframe-1.2/src/ClonalFrame.cpp:92:22: [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).
if ((devrandom = fopen("/dev/urandom","r")) == NULL) {
data/clonalframe-1.2/src/ClonalFrame.cpp:197:24: [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).
case('x'):nbit=atoi(optarg);break;
data/clonalframe-1.2/src/ClonalFrame.cpp:198:24: [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).
case('y'):burn=atoi(optarg);break;
data/clonalframe-1.2/src/ClonalFrame.cpp:199:24: [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).
case('z'):thin=atoi(optarg);break;
data/clonalframe-1.2/src/ClonalFrame.cpp:214:28: [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).
case('t'):treeinit=atoi(optarg);break;
data/clonalframe-1.2/src/ClonalFrame.cpp:222:27: [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).
case('e'):nbswaps=atoi(optarg);break;
data/clonalframe-1.2/src/ClonalFrame.cpp:223:36: [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).
case('S'):seeded=true;seed=atoi(optarg);break;
data/clonalframe-1.2/src/ClonalFrame.cpp:233:35: [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).
case('l'):mindistrefsites=atoi(optarg);break;
data/clonalframe-1.2/src/alignment.cpp:238:18: [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(filename,"w");
data/clonalframe-1.2/src/alignment.cpp:245:44: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (getData(j,k)=='N') memcpy(buf+k-beg,"-",1);else memcpy(buf+k-beg,lets+getData(j,k)-'0',1);
data/clonalframe-1.2/src/alignment.cpp:245:73: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (getData(j,k)=='N') memcpy(buf+k-beg,"-",1);else memcpy(buf+k-beg,lets+getData(j,k)-'0',1);
data/clonalframe-1.2/src/alignment.h:55:9: [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 * names[10000];
data/clonalframe-1.2/src/alignment_structure.cpp:29:18: [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(filename,"r");
data/clonalframe-1.2/src/alignment_structure.cpp:91:82: [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.
for (int i=0;i<numLines-1;i++) {names[i]=(char*)calloc(100,sizeof(char));sprintf(names[i],"%d",i+1);}
data/clonalframe-1.2/src/alignment_structure.cpp:104:17: [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.
sprintf(c,"%d",gsl_matrix_int_get(d,j,i));
data/clonalframe-1.2/src/alignment_structure.cpp:141:18: [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(filename,"r");
data/clonalframe-1.2/src/alignment_xmfa.cpp:27:9: [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 buf[10000];
data/clonalframe-1.2/src/alignment_xmfa.cpp:28:9: [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 buf2[1000];
data/clonalframe-1.2/src/alignment_xmfa.cpp:30:18: [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(filename,"r");
data/clonalframe-1.2/src/alignment_xmfa.cpp:109:19: [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).
in[i]=fopen(filename,"r");
data/clonalframe-1.2/src/consensus.cpp:155:9: [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.
sprintf(res+strlen(res),":0.000000");
data/clonalframe-1.2/src/consensus.cpp:171:26: [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.
pos+=sprintf(res+pos,"%d:%f,",first(tokeep[j]->id)+1,age);
data/clonalframe-1.2/src/consensus.cpp:179:9: [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.
sprintf(res+pos-1,")%d",w+1);
data/clonalframe-1.2/src/genes.cpp:28:21: [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 * mapf=fopen(mapfile,"r");
data/clonalframe-1.2/src/genes.cpp:41:22: [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 * genes=fopen(genesfile,"r");
data/clonalframe-1.2/src/recorder.cpp:94:9: [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 filename[1000];
data/clonalframe-1.2/src/recorder.cpp:102:18: [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(filename,"w");
data/clonalframe-1.2/src/tree.cpp:336:13: [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.
sprintf(buf,"%d:%f",i+1,fage-age);
data/clonalframe-1.2/src/tree_newick.cpp:36:20: [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).
newickFile.open(name);
data/clonalframe-1.2/src/util.cpp:36:18: [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(filename,"w");
data/clonalframe-1.2/src/util.cpp:60:18: [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(filename,"w");
data/clonalframe-1.2/src/alignment.cpp:246:17: [1] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source is a constant character.
sprintf(buf+end-beg,"\0");
data/clonalframe-1.2/src/alignment_structure.cpp:39:16: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ch=fgetc(f);
data/clonalframe-1.2/src/alignment_xmfa.cpp:92:25: [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).
length+=strlen(buf);
data/clonalframe-1.2/src/alignment_xmfa.cpp:129:32: [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).
for (j=0;j<strlen(bufin[i]);j++) {
data/clonalframe-1.2/src/alignment_xmfa.cpp:190:17: [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).
if (buf[strlen(buf)-1]=='\n' || buf[strlen(buf)-1]=='\r')
data/clonalframe-1.2/src/alignment_xmfa.cpp:190:45: [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).
if (buf[strlen(buf)-1]=='\n' || buf[strlen(buf)-1]=='\r')
data/clonalframe-1.2/src/alignment_xmfa.cpp:191:17: [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).
buf[strlen(buf)-1]='\0';
data/clonalframe-1.2/src/consensus.cpp:155:21: [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).
sprintf(res+strlen(res),":0.000000");
data/clonalframe-1.2/src/consensus.cpp:165:14: [1] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source is a constant character.
pos+=sprintf(res+pos,"(");
data/clonalframe-1.2/src/tree.cpp:318:32: [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).
buf=(char *)calloc(strlen(l)+strlen(r)+50,sizeof(char));
data/clonalframe-1.2/src/tree.cpp:318:42: [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).
buf=(char *)calloc(strlen(l)+strlen(r)+50,sizeof(char));
ANALYSIS SUMMARY:
Hits = 50
Lines analyzed = 5815 in approximately 0.25 seconds (22979 lines/second)
Physical Source Lines of Code (SLOC) = 3740
Hits@level = [0] 101 [1] 11 [2] 31 [3] 1 [4] 7 [5] 0
Hits@level+ = [0+] 151 [1+] 50 [2+] 39 [3+] 8 [4+] 7 [5+] 0
Hits/KSLOC@level+ = [0+] 40.3743 [1+] 13.369 [2+] 10.4278 [3+] 2.13904 [4+] 1.87166 [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.