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.