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/cufflinks-2.2.1+dfsg.1/src/GArgs.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/GArgs.h
Examining data/cufflinks-2.2.1+dfsg.1/src/GBase.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/GBase.h
Examining data/cufflinks-2.2.1+dfsg.1/src/GFaSeqGet.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/GFaSeqGet.h
Examining data/cufflinks-2.2.1+dfsg.1/src/GFastaIndex.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/GFastaIndex.h
Examining data/cufflinks-2.2.1+dfsg.1/src/GStr.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/GStr.h
Examining data/cufflinks-2.2.1+dfsg.1/src/assemble.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/assemble.h
Examining data/cufflinks-2.2.1+dfsg.1/src/biascorrection.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/bundles.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/bundles.h
Examining data/cufflinks-2.2.1+dfsg.1/src/clustering.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/clustering.h
Examining data/cufflinks-2.2.1+dfsg.1/src/codons.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/codons.h
Examining data/cufflinks-2.2.1+dfsg.1/src/common.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/common.h
Examining data/cufflinks-2.2.1+dfsg.1/src/compress_gtf.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/cuffcluster.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/cuffcompare.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/cuffdiff.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/cufflinks.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/cuffnorm.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/cuffquant.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/differential.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/differential.h
Examining data/cufflinks-2.2.1+dfsg.1/src/filters.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/filters.h
Examining data/cufflinks-2.2.1+dfsg.1/src/gdna.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/gdna.h
Examining data/cufflinks-2.2.1+dfsg.1/src/genes.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/genes.h
Examining data/cufflinks-2.2.1+dfsg.1/src/gff.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/gff.h
Examining data/cufflinks-2.2.1+dfsg.1/src/gff_utils.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/gff_utils.h
Examining data/cufflinks-2.2.1+dfsg.1/src/gffread.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/graph_optimize.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/graph_optimize.h
Examining data/cufflinks-2.2.1+dfsg.1/src/gtf_reads.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/gtf_to_sam.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/gtf_tracking.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/gtf_tracking.h
Examining data/cufflinks-2.2.1+dfsg.1/src/hits.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/jensen_shannon.cpp
Examining data/cufflinks-2.2.1+dfsg.1/src/lemon/bfs.h
Examining data/cufflinks-2.2.1+dfsg.1/src/lemon/bin_heap.h
Examining data/cufflinks-2.2.1+dfsg.1/src/lemon/bipartite_matching.h
Examining data/cufflinks-2.2.1+dfsg.1/src/lemon/bits/alteration_notifier.h
Examining data/cufflinks-2.2.1+dfsg.1/src/lemon/bits/array_map.h
Examining data/cufflinks-2.2.1+dfsg.1/src/lemon/bits/base_extender.h
Examining data/cufflinks-2.2.1+dfsg.1/src/lemon/bits/debug_map.h
Examining data/cufflinks-2.2.1+dfsg.1/src/lemon/bits/default_map.h
Examining data/cufflinks-2.2.1+dfsg.1/src/lemon/bits/graph_adaptor_extender.h
Examining data/cufflinks-2.2.1+dfsg.1/src/lemon/bits/graph_extender.h
Examining data/cufflinks-2.2.1+dfsg.1/src/lemon/bits/invalid.h
Examining data/cufflinks-2.2.1+dfsg.1/src/lemon/bits/map_extender.h
Examining data/cufflinks-2.2.1+dfsg.1/src/lemon/bits/path_dump.h
Examining data/cufflinks-2.2.1+dfsg.1/src/lemon/bits/traits.h
Examining data/cufflinks-2.2.1+dfsg.1/src/lemon/bits/utility.h