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/m2m-aligner-1.2/tclap-1.2.1/include/tclap/Arg.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/ArgException.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/ArgTraits.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/CmdLine.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/CmdLineInterface.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/CmdLineOutput.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/Constraint.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/DocBookOutput.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/HelpVisitor.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/IgnoreRestVisitor.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/MultiArg.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/MultiSwitchArg.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/OptionalUnlabeledTracker.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/StandardTraits.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/StdOutput.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/SwitchArg.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/UnlabeledMultiArg.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/UnlabeledValueArg.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/ValueArg.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/ValuesConstraint.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/VersionVisitor.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/Visitor.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/XorHandler.h Examining data/m2m-aligner-1.2/tclap-1.2.1/include/tclap/ZshCompletionOutput.h Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test7.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test13.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test12.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test17-a.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test10.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test4.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test20.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test2.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test3.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test19.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test8.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test16.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test6.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test18.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test1.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test14.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test21.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test17.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test11.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test15.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test5.cpp Examining data/m2m-aligner-1.2/tclap-1.2.1/examples/test9.cpp Examining data/m2m-aligner-1.2/mmEM.h Examining data/m2m-aligner-1.2/util.h Examining data/m2m-aligner-1.2/mmEM.cpp Examining data/m2m-aligner-1.2/param.h Examining data/m2m-aligner-1.2/mmAligner.cpp FINAL RESULTS: data/m2m-aligner-1.2/mmEM.cpp:39:12: [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). INITFILE.open(myParam.initFile.c_str()); data/m2m-aligner-1.2/mmEM.cpp:162:12: [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). INITFILE.open(myParam.initFile.c_str()); data/m2m-aligner-1.2/mmEM.cpp:557:12: [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). INPUTFILE.open(filename.c_str()); data/m2m-aligner-1.2/mmEM.cpp:665:13: [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). ALIGNEROUT.open(myParam.alignerOut.c_str()); data/m2m-aligner-1.2/mmEM.cpp:693:12: [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). ALIGNERIN.open(myParam.alignerIn.c_str()); data/m2m-aligner-1.2/mmEM.cpp:1074:10: [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). ALIGNED.open(myParam.outputFilename.c_str()); data/m2m-aligner-1.2/mmEM.cpp:1075:12: [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). NOALIGNED.open(string(myParam.outputFilename + ".err").c_str()); ANALYSIS SUMMARY: Hits = 7 Lines analyzed = 8696 in approximately 0.38 seconds (22909 lines/second) Physical Source Lines of Code (SLOC) = 4709 Hits@level = [0] 0 [1] 0 [2] 7 [3] 0 [4] 0 [5] 0 Hits@level+ = [0+] 7 [1+] 7 [2+] 7 [3+] 0 [4+] 0 [5+] 0 Hits/KSLOC@level+ = [0+] 1.48652 [1+] 1.48652 [2+] 1.48652 [3+] 0 [4+] 0 [5+] 0 Dot directories skipped = 1 (--followdotdir overrides) Minimum risk level = 1 Not every hit is necessarily a security vulnerability. There may be other security vulnerabilities; review your code! See 'Secure Programming HOWTO' (https://dwheeler.com/secure-programs) for more information.