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/clustalw-2.1+lgpl/src/general/UserParameters.cpp
Examining data/clustalw-2.1+lgpl/src/general/statsObject.h
Examining data/clustalw-2.1+lgpl/src/general/RandomAccessLList.h
Examining data/clustalw-2.1+lgpl/src/general/general.h
Examining data/clustalw-2.1+lgpl/src/general/SequenceNotFoundException.h
Examining data/clustalw-2.1+lgpl/src/general/param.h
Examining data/clustalw-2.1+lgpl/src/general/OutputFile.h
Examining data/clustalw-2.1+lgpl/src/general/Utility.h
Examining data/clustalw-2.1+lgpl/src/general/ClustalWResources.h
Examining data/clustalw-2.1+lgpl/src/general/InvalidCombination.cpp
Examining data/clustalw-2.1+lgpl/src/general/SymMatrix.cpp
Examining data/clustalw-2.1+lgpl/src/general/VectorUtility.h
Examining data/clustalw-2.1+lgpl/src/general/SquareMat.h
Examining data/clustalw-2.1+lgpl/src/general/Utility.cpp
Examining data/clustalw-2.1+lgpl/src/general/DebugLog.cpp
Examining data/clustalw-2.1+lgpl/src/general/Stats.h
Examining data/clustalw-2.1+lgpl/src/general/userparams.h
Examining data/clustalw-2.1+lgpl/src/general/UserParameters.h
Examining data/clustalw-2.1+lgpl/src/general/ClustalWResources.cpp
Examining data/clustalw-2.1+lgpl/src/general/Stats.cpp
Examining data/clustalw-2.1+lgpl/src/general/utils.h
Examining data/clustalw-2.1+lgpl/src/general/DebugLog.h
Examining data/clustalw-2.1+lgpl/src/general/VectorOutOfRange.cpp
Examining data/clustalw-2.1+lgpl/src/general/VectorOutOfRange.h
Examining data/clustalw-2.1+lgpl/src/general/clustalw.h
Examining data/clustalw-2.1+lgpl/src/general/Array2D.h
Examining data/clustalw-2.1+lgpl/src/general/SymMatrix.h
Examining data/clustalw-2.1+lgpl/src/general/OutputFile.cpp
Examining data/clustalw-2.1+lgpl/src/general/debuglogObject.h
Examining data/clustalw-2.1+lgpl/src/Clustal.cpp
Examining data/clustalw-2.1+lgpl/src/multipleAlign/LowScoreSegProfile.h
Examining data/clustalw-2.1+lgpl/src/multipleAlign/ProfileAlignAlgorithm.h
Examining data/clustalw-2.1+lgpl/src/multipleAlign/ProfileWithSub.cpp
Examining data/clustalw-2.1+lgpl/src/multipleAlign/Iteration.h
Examining data/clustalw-2.1+lgpl/src/multipleAlign/ProfileBase.h
Examining data/clustalw-2.1+lgpl/src/multipleAlign/ProfileStandard.h
Examining data/clustalw-2.1+lgpl/src/multipleAlign/LowScoreSegProfile.cpp
Examining data/clustalw-2.1+lgpl/src/multipleAlign/ProfileBase.cpp
Examining data/clustalw-2.1+lgpl/src/multipleAlign/MyersMillerProfileAlign.h
Examining data/clustalw-2.1+lgpl/src/multipleAlign/ProfileWithSub.h
Examining data/clustalw-2.1+lgpl/src/multipleAlign/Iteration.cpp
Examining data/clustalw-2.1+lgpl/src/multipleAlign/MSA.h
Examining data/clustalw-2.1+lgpl/src/multipleAlign/MyersMillerProfileAlign.cpp
Examining data/clustalw-2.1+lgpl/src/multipleAlign/ProfileStandard.cpp
Examining data/clustalw-2.1+lgpl/src/multipleAlign/MSA.cpp
Examining data/clustalw-2.1+lgpl/src/clustalw_version.h
Examining data/clustalw-2.1+lgpl/src/Help.h
Examining data/clustalw-2.1+lgpl/src/Clustal.h
Examining data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.h
Examining data/clustalw-2.1+lgpl/src/fileInput/PearsonFileParser.h
Examining data/clustalw-2.1+lgpl/src/fileInput/MSFFileParser.h
Examining data/clustalw-2.1+lgpl/src/fileInput/PIRFileParser.h
Examining data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.h
Examining data/clustalw-2.1+lgpl/src/fileInput/InFileStream.h
Examining data/clustalw-2.1+lgpl/src/fileInput/FileReader.cpp
Examining data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.h
Examining data/clustalw-2.1+lgpl/src/fileInput/InFileStream.cpp
Examining data/clustalw-2.1+lgpl/src/fileInput/GDEFileParser.h
Examining data/clustalw-2.1+lgpl/src/fileInput/FileReader.h
Examining data/clustalw-2.1+lgpl/src/fileInput/FileParser.h
Examining data/clustalw-2.1+lgpl/src/fileInput/FileParser.cpp
Examining data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp
Examining data/clustalw-2.1+lgpl/src/fileInput/GDEFileParser.cpp
Examining data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp
Examining data/clustalw-2.1+lgpl/src/fileInput/PearsonFileParser.cpp
Examining data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp
Examining data/clustalw-2.1+lgpl/src/fileInput/MSFFileParser.cpp
Examining data/clustalw-2.1+lgpl/src/fileInput/PIRFileParser.cpp
Examining data/clustalw-2.1+lgpl/src/main.cpp
Examining data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp
Examining data/clustalw-2.1+lgpl/src/substitutionMatrix/globalmatrix.h
Examining data/clustalw-2.1+lgpl/src/substitutionMatrix/matrices.h
Examining data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.h
Examining data/clustalw-2.1+lgpl/src/alignment/ObjectiveScore.cpp
Examining data/clustalw-2.1+lgpl/src/alignment/Sequence.h
Examining data/clustalw-2.1+lgpl/src/alignment/ObjectiveScore.h
Examining data/clustalw-2.1+lgpl/src/alignment/AlignmentOutput.h
Examining data/clustalw-2.1+lgpl/src/alignment/Alignment.h
Examining data/clustalw-2.1+lgpl/src/alignment/Alignment.cpp
Examining data/clustalw-2.1+lgpl/src/alignment/AlignmentOutput.cpp
Examining data/clustalw-2.1+lgpl/src/alignment/Sequence.cpp
Examining data/clustalw-2.1+lgpl/src/pairwise/PairwiseAlignBase.h
Examining data/clustalw-2.1+lgpl/src/pairwise/FastPairwiseAlign.h
Examining data/clustalw-2.1+lgpl/src/pairwise/FullPairwiseAlign.h
Examining data/clustalw-2.1+lgpl/src/pairwise/FastPairwiseAlign.cpp
Examining data/clustalw-2.1+lgpl/src/pairwise/FullPairwiseAlign.cpp
Examining data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp
Examining data/clustalw-2.1+lgpl/src/interface/CommandLineParser.cpp
Examining data/clustalw-2.1+lgpl/src/interface/CommandLineParser.h
Examining data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.h
Examining data/clustalw-2.1+lgpl/src/tree/UPGMA/Node.cpp
Examining data/clustalw-2.1+lgpl/src/tree/UPGMA/upgmadata.h
Examining data/clustalw-2.1+lgpl/src/tree/UPGMA/RootedClusterTree.h
Examining data/clustalw-2.1+lgpl/src/tree/UPGMA/Node.h
Examining data/clustalw-2.1+lgpl/src/tree/UPGMA/RootedTreeOutput.cpp
Examining data/clustalw-2.1+lgpl/src/tree/UPGMA/RootedGuideTree.cpp
Examining data/clustalw-2.1+lgpl/src/tree/UPGMA/RootedGuideTree.h
Examining data/clustalw-2.1+lgpl/src/tree/UPGMA/UPGMAAlgorithm.cpp
Examining data/clustalw-2.1+lgpl/src/tree/UPGMA/RootedTreeOutput.h
Examining data/clustalw-2.1+lgpl/src/tree/UPGMA/UPGMAAlgorithm.h
Examining data/clustalw-2.1+lgpl/src/tree/UPGMA/RootedClusterTree.cpp
Examining data/clustalw-2.1+lgpl/src/tree/RandomGenerator.h
Examining data/clustalw-2.1+lgpl/src/tree/ClusterTreeOutput.h
Examining data/clustalw-2.1+lgpl/src/tree/ClusterTree.h
Examining data/clustalw-2.1+lgpl/src/tree/UnRootedClusterTree.h
Examining data/clustalw-2.1+lgpl/src/tree/ClusterTreeAlgorithm.h
Examining data/clustalw-2.1+lgpl/src/tree/Tree.h
Examining data/clustalw-2.1+lgpl/src/tree/NJTree.h
Examining data/clustalw-2.1+lgpl/src/tree/ClusterTreeOutput.cpp
Examining data/clustalw-2.1+lgpl/src/tree/NJTree.cpp
Examining data/clustalw-2.1+lgpl/src/tree/TreeInterface.h
Examining data/clustalw-2.1+lgpl/src/tree/TreeInterface.cpp
Examining data/clustalw-2.1+lgpl/src/tree/AlignmentSteps.h
Examining data/clustalw-2.1+lgpl/src/tree/Tree.cpp
Examining data/clustalw-2.1+lgpl/src/tree/dayhoff.h
Examining data/clustalw-2.1+lgpl/src/tree/AlignmentSteps.cpp
Examining data/clustalw-2.1+lgpl/src/tree/ClusterTree.cpp
Examining data/clustalw-2.1+lgpl/src/tree/UnRootedClusterTree.cpp
Examining data/clustalw-2.1+lgpl/src/tree/RandomGenerator.cpp
Examining data/clustalw-2.1+lgpl/src/Help.cpp
FINAL RESULTS:
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:99:17: [4] (buffer) sscanf:
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.
sscanf(_tempStr.c_str(), "%s%s", sname, tseq);
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:318:17: [4] (buffer) sscanf:
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.
sscanf(line + 4, "%s%s", sname, tseq);
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:333:21: [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).
strcat(title, sname);
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:374:17: [4] (buffer) sscanf:
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.
sscanf(line + 4, "%s%s", sname, tseq);
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:389:21: [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).
strcat(title, sname);
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:516:17: [4] (buffer) sscanf:
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.
sscanf(line + 4, "%s%s", sname, tseq);
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:540:17: [4] (buffer) sscanf:
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.
sscanf(line + 4, "%s%s", sname, tseq);
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:304:21: [4] (buffer) sscanf:
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.
sscanf(_line + 2, "%s", _feature);
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:311:29: [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).
strcat(_title, _sname);
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:349:25: [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).
strcat(_title, _sname);
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:414:13: [4] (buffer) sscanf:
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.
if (sscanf(line, "%s%d%d", feature, &startPos, &endPos) != 3)
data/clustalw-2.1+lgpl/src/fileInput/GDEFileParser.cpp:301:21: [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).
strcat(_title, _sname);
data/clustalw-2.1+lgpl/src/fileInput/GDEFileParser.cpp:383:21: [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).
strcat(_title, _sname);
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:319:25: [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).
strcat(_title, _sname);
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:387:13: [4] (buffer) sscanf:
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.
if (sscanf(line, "%d%d%d%s%s%s", &startPos, &endPos, &tmp, str1, str2,
data/clustalw-2.1+lgpl/src/general/Utility.cpp:413:5: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, msg, ap);
data/clustalw-2.1+lgpl/src/general/Utility.cpp:428:5: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, msg, ap);
data/clustalw-2.1+lgpl/src/general/Utility.cpp:443:5: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, msg, ap);
data/clustalw-2.1+lgpl/src/general/Utility.cpp:458:5: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, msg, ap);
data/clustalw-2.1+lgpl/src/general/Utility.cpp:475:9: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stdout, msg, ap);
data/clustalw-2.1+lgpl/src/general/Utility.cpp:491:9: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stdout, msg, ap);
data/clustalw-2.1+lgpl/src/interface/CommandLineParser.cpp:1832:17: [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(hackTempName, (*paramArg)[setPWMatrix].c_str());
data/clustalw-2.1+lgpl/src/interface/CommandLineParser.cpp:1880:17: [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(hackTempName, (*paramArg)[setMatrix].c_str());
data/clustalw-2.1+lgpl/src/interface/CommandLineParser.cpp:1919:17: [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(hackTempName, (*paramArg)[setPWDNAMatrix].c_str());
data/clustalw-2.1+lgpl/src/interface/CommandLineParser.cpp:1958:17: [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(hackTempName, (*paramArg)[setDNAMatrix].c_str());
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:1190:9: [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.
system(lin1.c_str());
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:866:5: [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(str, line2.c_str());
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:978:5: [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(str, line2.c_str());
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1048:17: [4] (buffer) sscanf:
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.
if (sscanf(inline1 + 6, "%d %d %s", &llimit, &ulimit, mat_fileName)
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1449:5: [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(nameOfFile, name);
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1512:5: [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(nameOfFile, name);
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1815:5: [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(fileName, line2.c_str());
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1853:5: [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(str, line2.c_str());
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1884:5: [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(str, line2.c_str());
data/clustalw-2.1+lgpl/src/general/ClustalWResources.cpp:41:16: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
if ((env = getenv(CLUW_INSTALL_DIR)) != 0)
data/clustalw-2.1+lgpl/src/multipleAlign/Iteration.cpp:231:17: [3] (tmpfile) tmpnam:
Temporary file race condition (CWE-377).
tmpnam (buffer);
data/clustalw-2.1+lgpl/src/Clustal.cpp:794:23: [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).
_treeFile.open(phylipName->c_str());
data/clustalw-2.1+lgpl/src/Clustal.cpp:1566:5: [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 treeName[FILENAMELEN]=".score.ph";
data/clustalw-2.1+lgpl/src/Clustal.cpp:1568:5: [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 treeName[FILENAMELEN]="tmp.ph";
data/clustalw-2.1+lgpl/src/Clustal.cpp:1746:19: [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).
_treeFile.open(treeName.c_str());
data/clustalw-2.1+lgpl/src/alignment/AlignmentOutput.cpp:1593:9: [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 temp[MAXLINE];
data/clustalw-2.1+lgpl/src/alignment/AlignmentOutput.cpp:2240:9: [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 tmpName[FILENAMELEN + 15];
data/clustalw-2.1+lgpl/src/alignment/AlignmentOutput.cpp:2413:5: [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 temp[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/alignment/AlignmentOutput.cpp:2452:13: [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).
_fileIn.open(fileName.c_str(), ios::in);
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:57:5: [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 line[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:59:5: [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 tseq[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:61:5: [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 sname[MAXNAMES + 150];
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:78:18: [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).
_fileIn->open(fileName.c_str()); //nige
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:180:5: [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 line[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:186:18: [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).
_fileIn->open(fileName.c_str()); //nige
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:249:5: [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 title[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:251:5: [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 line[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:253:5: [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 lin2[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:255:5: [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 tseq[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:257:5: [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 sname[MAXNAMES + 1];
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:271:18: [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).
_fileIn->open(fileName.c_str()); //nige
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:332:21: [2] (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). Risk is low because the source is a constant string.
strcpy(title, "Found secondary structure in alignment file: ");
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:388:21: [2] (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). Risk is low because the source is a constant string.
strcpy(title, "Found gap penalty mask in alignment file: ");
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:65:5: [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 _line[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:67:5: [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 _sname[MAXNAMES + 1];
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:84:18: [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).
_fileIn->open(fileName.c_str()); //nige
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:200:5: [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 line[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:211:18: [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).
_fileIn->open(fileName.c_str()); //nige
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:249:5: [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 _title[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:250:5: [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 _line[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:251:5: [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 _lin2[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:252:5: [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 _sname[MAXNAMES + 1];
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:253:5: [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 _feature[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:260:18: [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).
_fileIn->open(fileName.c_str()); //nige
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:309:29: [2] (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). Risk is low because the source is a constant string.
strcpy(_title,
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:348:25: [2] (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). Risk is low because the source is a constant string.
strcpy(_title, "Found gap penalty mask in alignment file: ");
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:409:5: [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 c, s, feature[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/FileParser.cpp:66:8: [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).
in.open(filename.c_str(), ios::in);
data/clustalw-2.1+lgpl/src/fileInput/FileParser.h:45:9: [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 chartab[128];
data/clustalw-2.1+lgpl/src/fileInput/FileReader.cpp:182:13: [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).
fileIn->open(line.c_str()); //nige
data/clustalw-2.1+lgpl/src/fileInput/FileReader.cpp:428:5: [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 _lineIn[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/GDEFileParser.cpp:63:5: [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 _line[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/GDEFileParser.cpp:64:5: [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 _sname[MAXNAMES + 1];
data/clustalw-2.1+lgpl/src/fileInput/GDEFileParser.cpp:79:18: [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).
_fileIn->open(fileName.c_str()); //nige
data/clustalw-2.1+lgpl/src/fileInput/GDEFileParser.cpp:178:5: [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 line[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/GDEFileParser.cpp:184:18: [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).
_fileIn->open(fileName.c_str()); //nige
data/clustalw-2.1+lgpl/src/fileInput/GDEFileParser.cpp:227:5: [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 _title[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/GDEFileParser.cpp:228:5: [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 _line[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/GDEFileParser.cpp:229:5: [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 _lin2[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/GDEFileParser.cpp:230:5: [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 _sname[MAXNAMES + 1];
data/clustalw-2.1+lgpl/src/fileInput/GDEFileParser.cpp:237:18: [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).
_fileIn->open(fileName.c_str()); //nige
data/clustalw-2.1+lgpl/src/fileInput/GDEFileParser.cpp:300:21: [2] (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). Risk is low because the source is a constant string.
strcpy(_title, "Found secondary structure in alignment file: ");
data/clustalw-2.1+lgpl/src/fileInput/GDEFileParser.cpp:382:21: [2] (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). Risk is low because the source is a constant string.
strcpy(_title, "Found gap penalty mask in alignment file: ");
data/clustalw-2.1+lgpl/src/fileInput/InFileStream.cpp:56:20: [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).
void InFileStream::open(const char *filename)
data/clustalw-2.1+lgpl/src/fileInput/InFileStream.cpp:60:15: [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).
ifstream::open(filename, ios::in);
data/clustalw-2.1+lgpl/src/fileInput/InFileStream.cpp:103:8: [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).
in.open(filename.c_str(), ios::in);
data/clustalw-2.1+lgpl/src/fileInput/InFileStream.h:29:10: [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).
void open(const char *filename);
data/clustalw-2.1+lgpl/src/fileInput/MSFFileParser.cpp:60:5: [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 _line[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/MSFFileParser.cpp:61:5: [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 _sname[MAXNAMES + 1];
data/clustalw-2.1+lgpl/src/fileInput/MSFFileParser.cpp:74:18: [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).
_fileIn->open(fileName.c_str()); //nige
data/clustalw-2.1+lgpl/src/fileInput/MSFFileParser.cpp:186:5: [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 _line[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/MSFFileParser.cpp:192:18: [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).
_fileIn->open(fileName.c_str()); //nige
data/clustalw-2.1+lgpl/src/fileInput/PIRFileParser.cpp:61:5: [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 _line[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/PIRFileParser.cpp:62:5: [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 _sname[MAXNAMES + 1];
data/clustalw-2.1+lgpl/src/fileInput/PIRFileParser.cpp:63:5: [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 _title[MAXTITLES + 1];
data/clustalw-2.1+lgpl/src/fileInput/PIRFileParser.cpp:77:18: [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).
_fileIn->open(fileName.c_str()); //nige
data/clustalw-2.1+lgpl/src/fileInput/PIRFileParser.cpp:173:5: [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 line[MAXLINE + 1], c;
data/clustalw-2.1+lgpl/src/fileInput/PIRFileParser.cpp:181:18: [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).
_fileIn->open(fileName.c_str()); //nige
data/clustalw-2.1+lgpl/src/fileInput/PearsonFileParser.cpp:76:16: [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).
_fileIn.open(fileName.c_str(),ios::in);
data/clustalw-2.1+lgpl/src/fileInput/PearsonFileParser.cpp:230:16: [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).
_fileIn.open(fileName.c_str(),ios::in);
data/clustalw-2.1+lgpl/src/fileInput/PearsonFileParser.cpp:401:17: [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).
_fileIn.open(fileName.c_str(),ios::in);
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:56:5: [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 _line[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:57:5: [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 _sname[MAXNAMES + 1];
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:71:18: [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).
_fileIn->open(fileName.c_str()); //nige
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:187:5: [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 _line[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:194:18: [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).
_fileIn->open(fileName.c_str()); //nige
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:249:5: [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 _title[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:250:5: [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 _line[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:251:5: [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 _lin2[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:252:5: [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 _sname[MAXNAMES + 1];
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:261:18: [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).
_fileIn->open(fileName.c_str()); //nige
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:318:25: [2] (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). Risk is low because the source is a constant string.
strcpy(_title, "Found secondary structure in alignment file: ");
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:382:5: [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 str1[MAXLINE + 1], str2[MAXLINE + 1], feature[MAXLINE + 1];
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:436:5: [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 key[MAXLINE];
data/clustalw-2.1+lgpl/src/general/ClustalWResources.cpp:104:5: [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 delim[1];
data/clustalw-2.1+lgpl/src/general/ClustalWResources.cpp:110:9: [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).
ifs.open(fileName.c_str(), ifstream::in);
data/clustalw-2.1+lgpl/src/general/DebugLog.cpp:25:14: [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).
logFile->open(logFileName.c_str(), ios::out);
data/clustalw-2.1+lgpl/src/general/Stats.cpp:221:9: [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(&rethash[i*2], "%.2x", hash[i]);
data/clustalw-2.1+lgpl/src/general/Stats.cpp:236:16: [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 *fp = fopen(logfilename.c_str(), "a");
data/clustalw-2.1+lgpl/src/general/Stats.cpp:274:16: [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 *fp = fopen(logfilename.c_str(), "a");
data/clustalw-2.1+lgpl/src/general/Stats.cpp:336:16: [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 *fp = fopen(logfilename.c_str(), "a");
data/clustalw-2.1+lgpl/src/general/UserParameters.cpp:314:13: [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).
outfile.open(parname.c_str(), ofstream::out);
data/clustalw-2.1+lgpl/src/general/Utility.cpp:177:5: [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 line[MAXLINE];
data/clustalw-2.1+lgpl/src/general/Utility.cpp:215:5: [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 line[MAXLINE];
data/clustalw-2.1+lgpl/src/general/Utility.cpp:503:5: [2] (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). Risk is low because the source is a constant string.
strcpy(myname, "clustalw\0");
data/clustalw-2.1+lgpl/src/general/clustalw.h:267:5: [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 name[64];
data/clustalw-2.1+lgpl/src/general/clustalw.h:272:5: [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 title[30];
data/clustalw-2.1+lgpl/src/general/clustalw.h:273:5: [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 string[30];
data/clustalw-2.1+lgpl/src/interface/CommandLineParser.cpp:1831:17: [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 hackTempName[FILENAMELEN + 1];
data/clustalw-2.1+lgpl/src/interface/CommandLineParser.cpp:1879:17: [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 hackTempName[FILENAMELEN + 1];
data/clustalw-2.1+lgpl/src/interface/CommandLineParser.cpp:1918:17: [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 hackTempName[FILENAMELEN + 1];
data/clustalw-2.1+lgpl/src/interface/CommandLineParser.cpp:1957:17: [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 hackTempName[FILENAMELEN + 1];
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:49:5: [2] (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). Risk is low because the source is a constant string.
strcpy(matrixMenu.opt[AABLOSUM].title, "BLOSUM series");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:50:5: [2] (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). Risk is low because the source is a constant string.
strcpy(matrixMenu.opt[AABLOSUM].string, "blosum");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:51:5: [2] (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). Risk is low because the source is a constant string.
strcpy(matrixMenu.opt[AAPAM].title, "PAM series");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:52:5: [2] (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). Risk is low because the source is a constant string.
strcpy(matrixMenu.opt[AAPAM].string, "pam");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:53:5: [2] (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). Risk is low because the source is a constant string.
strcpy(matrixMenu.opt[AAGONNET].title, "Gonnet series");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:54:5: [2] (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). Risk is low because the source is a constant string.
strcpy(matrixMenu.opt[AAGONNET].string, "gonnet");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:55:5: [2] (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). Risk is low because the source is a constant string.
strcpy(matrixMenu.opt[AAIDENTITY].title, "Identity matrix");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:56:5: [2] (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). Risk is low because the source is a constant string.
strcpy(matrixMenu.opt[AAIDENTITY].string, "id");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:57:5: [2] (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). Risk is low because the source is a constant string.
strcpy(matrixMenu.opt[AAUSERDEFINED].title, "User defined");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:61:5: [2] (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). Risk is low because the source is a constant string.
strcpy(dnaMatrixMenu.opt[DNAIUB].title, "IUB");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:62:5: [2] (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). Risk is low because the source is a constant string.
strcpy(dnaMatrixMenu.opt[DNAIUB].string, "iub");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:63:5: [2] (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). Risk is low because the source is a constant string.
strcpy(dnaMatrixMenu.opt[DNACLUSTALW].title, "CLUSTALW(1.6)");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:64:5: [2] (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). Risk is low because the source is a constant string.
strcpy(dnaMatrixMenu.opt[DNACLUSTALW].string, "clustalw");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:65:5: [2] (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). Risk is low because the source is a constant string.
strcpy(dnaMatrixMenu.opt[DNAUSERDEFINED].title, "User defined");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:69:5: [2] (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). Risk is low because the source is a constant string.
strcpy(pwMatrixMenu.opt[PWAABLOSUM].title, "BLOSUM 30");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:70:5: [2] (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). Risk is low because the source is a constant string.
strcpy(pwMatrixMenu.opt[PWAABLOSUM].string, "blosum");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:71:5: [2] (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). Risk is low because the source is a constant string.
strcpy(pwMatrixMenu.opt[PWAAPAM].title, "PAM 350");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:72:5: [2] (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). Risk is low because the source is a constant string.
strcpy(pwMatrixMenu.opt[PWAAPAM].string, "pam");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:73:5: [2] (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). Risk is low because the source is a constant string.
strcpy(pwMatrixMenu.opt[PWAAGONNET].title, "Gonnet 250");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:74:5: [2] (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). Risk is low because the source is a constant string.
strcpy(pwMatrixMenu.opt[PWAAGONNET].string, "gonnet");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:75:5: [2] (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). Risk is low because the source is a constant string.
strcpy(pwMatrixMenu.opt[PWAAIDENTITY].title, "Identity matrix");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:76:5: [2] (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). Risk is low because the source is a constant string.
strcpy(pwMatrixMenu.opt[PWAAIDENTITY].string, "id");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:77:5: [2] (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). Risk is low because the source is a constant string.
strcpy(pwMatrixMenu.opt[PWAAUSER].title, "User defined");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:1110:12: [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.
static char userFile[FILENAMELEN + 1];
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:1112:5: [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 title[10];
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:1117:9: [2] (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). Risk is low because the source is a constant string.
strcpy(title, "PROTEIN");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:1121:9: [2] (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). Risk is low because the source is a constant string.
strcpy(title, "DNA");
data/clustalw-2.1+lgpl/src/multipleAlign/Iteration.cpp:230:17: [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 buffer[L_tmpnam];
data/clustalw-2.1+lgpl/src/multipleAlign/Iteration.cpp:259:17: [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[1024];
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:860:18: [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).
if((infile = fopen(line2.c_str(), "r")) == NULL)
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:972:18: [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).
if((infile = fopen(line2.c_str(), "r"))==NULL)
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:994:5: [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 mat_fileName[FILENAMELEN];
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:995:5: [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 inline1[1024];
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1005:15: [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 ((fd = fopen(fileName, "r")) == NULL)
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1116:5: [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 codes[NUMRES];
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1117:5: [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 inline1[1024];
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1118:5: [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 *args[NUMRES + 4];
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1130:15: [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 ((fd = fopen(fileName, "r")) == NULL)
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1448:5: [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 nameOfFile[30];
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1450:5: [2] (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 string.
strcat(nameOfFile, ".out");
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1511:5: [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 nameOfFile[30];
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1513:5: [2] (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 string.
strcat(nameOfFile, ".out");
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1615:5: [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 userFile[FILENAMELEN + 1];
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1618:5: [2] (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). Risk is low because the source is a constant string.
strcpy(userFile, "mat1");
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1809:18: [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).
if((infile = fopen(line2.c_str(), "r")) == NULL)
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1847:18: [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).
if((infile = fopen(line2.c_str(), "r")) == NULL)
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1878:18: [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).
if((infile = fopen(line2.c_str(), "r")) == NULL)
data/clustalw-2.1+lgpl/src/tree/Tree.cpp:133:14: [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).
file.open(treeFileName.c_str(), ifstream::in);
data/clustalw-2.1+lgpl/src/tree/UPGMA/UPGMAAlgorithm.cpp:53:33: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
(double *)memcpy(new double[sizeDistMat],
data/clustalw-2.1+lgpl/src/fileInput/ClustalFileParser.cpp:92:39: [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 <= (int)strlen(line); j++)
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:107:31: [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 = 5; i <= (int)strlen(_line); i++)
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:114:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(_sname, _line + i, MAXNAMES); // remember entryname
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:115:31: [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 = 0; i <= (int)strlen(_sname); i++)
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:148:17: [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 (strlen(_line) > 2 && _line[strlen(_line) - 1] == '.' &&
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:148:44: [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 (strlen(_line) > 2 && _line[strlen(_line) - 1] == '.' &&
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:149:27: [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).
_line[strlen(_line) - 2] == '.')
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:279:35: [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 = 5; i <= (int)strlen(_line); i++)
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:286:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(_sname, _line + i, MAXNAMES); // remember entryname
data/clustalw-2.1+lgpl/src/fileInput/EMBLFileParser.cpp:287:35: [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 = 0; i <= (int)strlen(_sname); i++)
data/clustalw-2.1+lgpl/src/fileInput/FileReader.cpp:440:18: [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).
lengthLine = strlen(_lineIn) - 1; // Mark Change 20-6-07
data/clustalw-2.1+lgpl/src/fileInput/FileReader.cpp:491:48: [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).
else if (strstr(_lineIn, "MSF") && _lineIn[strlen(_lineIn) - 1] == '.' &&
data/clustalw-2.1+lgpl/src/fileInput/FileReader.cpp:492:17: [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).
_lineIn[strlen(_lineIn) - 2] == '.') // MSF
data/clustalw-2.1+lgpl/src/fileInput/MSFFileParser.cpp:100:39: [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 <= (int)strlen(_line); j++)
data/clustalw-2.1+lgpl/src/fileInput/MSFFileParser.cpp:107:39: [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 (k = j; k <= (int)strlen(_line); k++)
data/clustalw-2.1+lgpl/src/fileInput/MSFFileParser.cpp:116:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(_sname, _line + j, utilityObject->MIN(MAXNAMES, k - j));
data/clustalw-2.1+lgpl/src/fileInput/PIRFileParser.cpp:101:31: [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 = 4; i <= (int)strlen(_line); i++)
data/clustalw-2.1+lgpl/src/fileInput/PIRFileParser.cpp:109:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(_sname, _line + i, MAXNAMES); // remember entryname
data/clustalw-2.1+lgpl/src/fileInput/PIRFileParser.cpp:116:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(_title, _line, MAXTITLES);
data/clustalw-2.1+lgpl/src/fileInput/PIRFileParser.cpp:118:13: [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).
i = strlen(_title);
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:103:31: [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 = 5; i <= (int)strlen(_line); i++)
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:110:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(_sname, _line + i, MAXNAMES); // remember entryname
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:111:31: [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 = 0; i <= (int)strlen(_sname); i++)
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:207:23: [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 (_line[strlen(_line) - 1] == '.' && _line[strlen(_line) - 2] == '.')
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:207:58: [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 (_line[strlen(_line) - 1] == '.' && _line[strlen(_line) - 2] == '.')
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:267:23: [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 (_line[strlen(_line) - 1] == '.' && _line[strlen(_line) - 2] == '.')
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:267:58: [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 (_line[strlen(_line) - 1] == '.' && _line[strlen(_line) - 2] == '.')
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:291:35: [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 = 5; i <= (int)strlen(_line); i++)
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:298:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(_sname, _line + i, MAXNAMES); // remember entryname
data/clustalw-2.1+lgpl/src/fileInput/RSFFileParser.cpp:299:35: [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 = 0; i <= (int)strlen(_sname); i++)
data/clustalw-2.1+lgpl/src/general/Stats.cpp:159:25: [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).
for (int i=0; i<strlen(hash); i++)
data/clustalw-2.1+lgpl/src/general/Stats.cpp:215:23: [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).
mhash(td, thread, strlen(thread));
data/clustalw-2.1+lgpl/src/general/Utility.cpp:55:9: [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).
p = strlen(str) - 1;
data/clustalw-2.1+lgpl/src/general/Utility.cpp:76:9: [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).
p = strlen(str) - 1;
data/clustalw-2.1+lgpl/src/general/Utility.cpp:252:8: [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).
if (strlen(line)<strlen(code))
data/clustalw-2.1+lgpl/src/general/Utility.cpp:252:21: [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).
if (strlen(line)<strlen(code))
data/clustalw-2.1+lgpl/src/general/Utility.cpp:253:8: [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).
n=strlen(line);
data/clustalw-2.1+lgpl/src/general/Utility.cpp:255:8: [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).
n=strlen(code);
data/clustalw-2.1+lgpl/src/general/Utility.cpp:257:32: [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).
return (strncmp(line, code, strlen(code)) == 0);
data/clustalw-2.1+lgpl/src/general/clustalw.h:287:9: [1] (obsolete) ulimit:
This C routine is considered obsolete (as opposed to the shell command by
the same name, which is NOT obsolete) (CWE-676). Use getrlimit(2),
setrlimit(2), and sysconf(3) instead.
int ulimit;
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:58:5: [1] (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). Risk is low because the source is a constant character.
strcpy(matrixMenu.opt[AAUSERDEFINED].string, "");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:66:5: [1] (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). Risk is low because the source is a constant character.
strcpy(dnaMatrixMenu.opt[DNAUSERDEFINED].string, "");
data/clustalw-2.1+lgpl/src/interface/InteractiveMenu.cpp:78:5: [1] (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). Risk is low because the source is a constant character.
strcpy(pwMatrixMenu.opt[PWAAUSER].string, "");
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:620:38: [1] (obsolete) ulimit:
This C routine is considered obsolete (as opposed to the shell command by
the same name, which is NOT obsolete) (CWE-676). Use getrlimit(2),
setrlimit(2), and sysconf(3) instead.
matSeries.mat[i].ulimit)
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:998:20: [1] (obsolete) ulimit:
This C routine is considered obsolete (as opposed to the shell command by
the same name, which is NOT obsolete) (CWE-676). Use getrlimit(2),
setrlimit(2), and sysconf(3) instead.
int n, llimit, ulimit;
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1048:59: [1] (obsolete) ulimit:
This C routine is considered obsolete (as opposed to the shell command by
the same name, which is NOT obsolete) (CWE-676). Use getrlimit(2),
setrlimit(2), and sysconf(3) instead.
if (sscanf(inline1 + 6, "%d %d %s", &llimit, &ulimit, mat_fileName)
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1055:47: [1] (obsolete) ulimit:
This C routine is considered obsolete (as opposed to the shell command by
the same name, which is NOT obsolete) (CWE-676). Use getrlimit(2),
setrlimit(2), and sysconf(3) instead.
if (llimit < 0 || llimit > 100 || ulimit < 0 || ulimit > 100)
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1055:61: [1] (obsolete) ulimit:
This C routine is considered obsolete (as opposed to the shell command by
the same name, which is NOT obsolete) (CWE-676). Use getrlimit(2),
setrlimit(2), and sysconf(3) instead.
if (llimit < 0 || llimit > 100 || ulimit < 0 || ulimit > 100)
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1061:17: [1] (obsolete) ulimit:
This C routine is considered obsolete (as opposed to the shell command by
the same name, which is NOT obsolete) (CWE-676). Use getrlimit(2),
setrlimit(2), and sysconf(3) instead.
if (ulimit <= llimit)
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1064:39: [1] (obsolete) ulimit:
This C routine is considered obsolete (as opposed to the shell command by
the same name, which is NOT obsolete) (CWE-676). Use getrlimit(2),
setrlimit(2), and sysconf(3) instead.
fileName, llimit, ulimit);
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1082:42: [1] (obsolete) ulimit:
This C routine is considered obsolete (as opposed to the shell command by
the same name, which is NOT obsolete) (CWE-676). Use getrlimit(2),
setrlimit(2), and sysconf(3) instead.
matSeries.mat[nmat].ulimit = ulimit;
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1152:30: [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 < (int)strlen(inline1); j++)
data/clustalw-2.1+lgpl/src/substitutionMatrix/SubMatrix.cpp:1235:30: [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 = 0; i < (int)strlen(args[farg]); i++)
ANALYSIS SUMMARY:
Hits = 239
Lines analyzed = 36645 in approximately 0.87 seconds (42041 lines/second)
Physical Source Lines of Code (SLOC) = 27864
Hits@level = [0] 71 [1] 53 [2] 150 [3] 2 [4] 34 [5] 0
Hits@level+ = [0+] 310 [1+] 239 [2+] 186 [3+] 36 [4+] 34 [5+] 0
Hits/KSLOC@level+ = [0+] 11.1255 [1+] 8.57738 [2+] 6.67528 [3+] 1.29199 [4+] 1.22021 [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.