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/proteinortho-6.0.24+dfsg/doxygen/proteinortho_clustering.h
Examining data/proteinortho-6.0.24+dfsg/src/basic-types.h
Examining data/proteinortho-6.0.24+dfsg/src/cleanupblastgraph.cpp
Examining data/proteinortho-6.0.24+dfsg/src/graphMinusRemovegraph.cpp
Examining data/proteinortho-6.0.24+dfsg/src/po_tree.c
Examining data/proteinortho-6.0.24+dfsg/src/proteinortho_clustering.cpp
Examining data/proteinortho-6.0.24+dfsg/src/proteinortho_clustering_nolapack.cpp
FINAL RESULTS:
data/proteinortho-6.0.24+dfsg/src/po_tree.c:195:9: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
baum = strcat(baum,(*pnamen)[max[0]]);
data/proteinortho-6.0.24+dfsg/src/po_tree.c:197:9: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
baum = strcat(baum,length_0);
data/proteinortho-6.0.24+dfsg/src/po_tree.c:199:9: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
baum = strcat(baum,(*pnamen)[max[1]]);
data/proteinortho-6.0.24+dfsg/src/po_tree.c:201:9: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
baum = strcat(baum,length_1);
data/proteinortho-6.0.24+dfsg/src/po_tree.c:276:18: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
(*pnamen)[0] = strcat((*pnamen)[0],anz);
data/proteinortho-6.0.24+dfsg/src/po_tree.c:341:4: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
fscanf (datei, "%s ",(*pnamen)[i]);
data/proteinortho-6.0.24+dfsg/src/po_tree.c:345:4: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
fscanf (datei, "%s \n",(*pnamen)[i]);
data/proteinortho-6.0.24+dfsg/src/proteinortho_clustering.cpp:493:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if(system(("cat "+allRMgraphNames+" >"+param_rmgraph).c_str())!=0 || system(("rm "+allRMgraphNames).c_str())!=0){
data/proteinortho-6.0.24+dfsg/src/proteinortho_clustering.cpp:493:72: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if(system(("cat "+allRMgraphNames+" >"+param_rmgraph).c_str())!=0 || system(("rm "+allRMgraphNames).c_str())!=0){
data/proteinortho-6.0.24+dfsg/src/proteinortho_clustering_nolapack.cpp:334:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if(system(("cat "+allRMgraphNames+" >"+param_rmgraph).c_str())!=0 || system(("rm "+allRMgraphNames).c_str())!=0){
data/proteinortho-6.0.24+dfsg/src/proteinortho_clustering_nolapack.cpp:334:72: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if(system(("cat "+allRMgraphNames+" >"+param_rmgraph).c_str())!=0 || system(("rm "+allRMgraphNames).c_str())!=0){
data/proteinortho-6.0.24+dfsg/src/proteinortho_clustering.cpp:431:3: [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.
srand(rand_seed);
data/proteinortho-6.0.24+dfsg/src/proteinortho_clustering_nolapack.cpp:274:3: [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.
srand(rand_seed);
data/proteinortho-6.0.24+dfsg/src/po_tree.c:328:16: [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* datei = fopen (filename, "r");
data/proteinortho-6.0.24+dfsg/src/po_tree.c:413:2: [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 zahl[ende-start+1];
data/proteinortho-6.0.24+dfsg/src/po_tree.c:421:9: [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).
return atoi(zahl);
data/proteinortho-6.0.24+dfsg/src/po_tree.c:436:2: [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 reverse[64];
data/proteinortho-6.0.24+dfsg/src/proteinortho_clustering.cpp:208:16: [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).
if ( (fd = open( "/proc/self/psinfo", O_RDONLY )) == -1 )
data/proteinortho-6.0.24+dfsg/src/proteinortho_clustering.cpp:259:16: [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 ( (fp = fopen( "/proc/self/statm", "r" )) == NULL )
data/proteinortho-6.0.24+dfsg/src/po_tree.c:187:16: [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 newsize = strlen((*pnamen)[max[0]])+strlen((*pnamen)[max[1]])+strlen(anz)+strlen(length_0)+strlen(length_1)+8;
data/proteinortho-6.0.24+dfsg/src/po_tree.c:187:42: [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).
int newsize = strlen((*pnamen)[max[0]])+strlen((*pnamen)[max[1]])+strlen(anz)+strlen(length_0)+strlen(length_1)+8;
data/proteinortho-6.0.24+dfsg/src/po_tree.c:187:68: [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 newsize = strlen((*pnamen)[max[0]])+strlen((*pnamen)[max[1]])+strlen(anz)+strlen(length_0)+strlen(length_1)+8;
data/proteinortho-6.0.24+dfsg/src/po_tree.c:187:80: [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 newsize = strlen((*pnamen)[max[0]])+strlen((*pnamen)[max[1]])+strlen(anz)+strlen(length_0)+strlen(length_1)+8;
data/proteinortho-6.0.24+dfsg/src/po_tree.c:187:97: [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 newsize = strlen((*pnamen)[max[0]])+strlen((*pnamen)[max[1]])+strlen(anz)+strlen(length_0)+strlen(length_1)+8;
data/proteinortho-6.0.24+dfsg/src/po_tree.c:194:9: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
baum = strcat(baum,"(");
data/proteinortho-6.0.24+dfsg/src/po_tree.c:196:9: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
baum = strcat(baum,":");
data/proteinortho-6.0.24+dfsg/src/po_tree.c:198:9: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
baum = strcat(baum,",");
data/proteinortho-6.0.24+dfsg/src/po_tree.c:200:9: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
baum = strcat(baum,":");
data/proteinortho-6.0.24+dfsg/src/po_tree.c:202:9: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
baum = strcat(baum,")");
data/proteinortho-6.0.24+dfsg/src/po_tree.c:271:17: [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).
int newsize = strlen((*pnamen)[0])+strlen(anz)+2;
data/proteinortho-6.0.24+dfsg/src/po_tree.c:271:38: [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 newsize = strlen((*pnamen)[0])+strlen(anz)+2;
data/proteinortho-6.0.24+dfsg/src/po_tree.c:275:18: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
(*pnamen)[0] = strcat((*pnamen)[0],":");
data/proteinortho-6.0.24+dfsg/src/po_tree.c:348:61: [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).
(*pnamen)[i] = (char*) realloc((*pnamen)[i],sizeof(char)*(strlen((*pnamen)[i])+1));
data/proteinortho-6.0.24+dfsg/src/po_tree.c:405:11: [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 (i = strlen(word); i >= 0; i--) {
data/proteinortho-6.0.24+dfsg/src/proteinortho_clustering.cpp:210:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ( read( fd, &psinfo, sizeof(psinfo) ) != sizeof(psinfo) )
ANALYSIS SUMMARY:
Hits = 35
Lines analyzed = 5816 in approximately 0.21 seconds (28284 lines/second)
Physical Source Lines of Code (SLOC) = 3828
Hits@level = [0] 15 [1] 16 [2] 6 [3] 2 [4] 11 [5] 0
Hits@level+ = [0+] 50 [1+] 35 [2+] 19 [3+] 13 [4+] 11 [5+] 0
Hits/KSLOC@level+ = [0+] 13.0617 [1+] 9.14316 [2+] 4.96343 [3+] 3.39603 [4+] 2.87356 [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.