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/bali-phy-3.5.0.2+dfsg/external/immer/immer/algorithm.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/array.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/array_transient.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/atom.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/box.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/config.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/arrays/no_capacity.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/arrays/node.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/arrays/with_capacity.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/combine_standard_layout.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/hamts/bits.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/hamts/champ.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/hamts/champ_iterator.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/hamts/node.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/iterator_facade.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/rbts/bits.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/rbts/node.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/rbts/operations.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/rbts/position.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/rbts/rbtree.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/rbts/rbtree_iterator.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/rbts/rrbtree.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/rbts/rrbtree_iterator.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/rbts/visitor.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/ref_count_base.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/type_traits.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/util.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/experimental/detail/dvektor_impl.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/experimental/dvektor.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/flex_vector.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/flex_vector_transient.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/heap/cpp_heap.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/heap/debug_size_heap.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/heap/free_list_heap.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/heap/free_list_node.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/heap/gc_heap.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/heap/heap_policy.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/heap/identity_heap.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/heap/malloc_heap.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/heap/split_heap.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/heap/tags.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/heap/thread_local_free_list_heap.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/heap/unsafe_free_list_heap.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/heap/with_data.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/map.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/map_transient.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/memory_policy.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/refcount/enable_intrusive_ptr.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/refcount/no_refcount_policy.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/refcount/refcount_policy.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/refcount/unsafe_refcount_policy.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/set.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/set_transient.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/transience/gc_transience_policy.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/transience/no_transience_policy.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/vector.hpp
Examining data/bali-phy-3.5.0.2+dfsg/external/immer/immer/vector_transient.hpp
Examining data/bali-phy-3.5.0.2+dfsg/src/alignment/alignment-constraint.H
Examining data/bali-phy-3.5.0.2+dfsg/src/alignment/alignment-constraint.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/alignment/alignment-random.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/alignment/alignment-util.H
Examining data/bali-phy-3.5.0.2+dfsg/src/alignment/alignment-util.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/alignment/alignment-util2.H
Examining data/bali-phy-3.5.0.2+dfsg/src/alignment/alignment-util2.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/alignment/alignment.H
Examining data/bali-phy-3.5.0.2+dfsg/src/alignment/alignment.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/alignment/index-matrix.H
Examining data/bali-phy-3.5.0.2+dfsg/src/alignment/index-matrix.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/alignment/load.H
Examining data/bali-phy-3.5.0.2+dfsg/src/alignment/load.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/bali-phy/A-T-model.H
Examining data/bali-phy-3.5.0.2+dfsg/src/bali-phy/A-T-model.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/bali-phy/bali-phy.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/bali-phy/cmd_line.H
Examining data/bali-phy-3.5.0.2+dfsg/src/bali-phy/cmd_line.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/bali-phy/files.H
Examining data/bali-phy-3.5.0.2+dfsg/src/bali-phy/files.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/bali-phy/help.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/bali-phy/io.H
Examining data/bali-phy-3.5.0.2+dfsg/src/bali-phy/link-partitions.H
Examining data/bali-phy-3.5.0.2+dfsg/src/bali-phy/link-partitions.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/bali-phy/loggers.H
Examining data/bali-phy-3.5.0.2+dfsg/src/bali-phy/loggers.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/bali-phy/paths.H
Examining data/bali-phy-3.5.0.2+dfsg/src/bali-phy/paths.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/bali-phy/system.H
Examining data/bali-phy-3.5.0.2+dfsg/src/bali-phy/system.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/Alignment.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/Alphabet.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/Array.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/Bits.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/Data.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/Distribution.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/Environment.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/Foreign.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/MCMC.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/Modifiables.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/Pair.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/PopGen.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/Prelude.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/Range.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/Real.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/SMC.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/SModel.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/Text.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/Vector.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/builtins/iota.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/closure.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/closure.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/context.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/context.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/AST_node.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/AST_node.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/apply.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/apply.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/bool.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/bool.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/case.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/case.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/constructor.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/constructor.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/do_block.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/do_block.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/expression.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/expression.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/expression_ref.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/expression_ref.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/index_var.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/indexify.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/indexify.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/lambda.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/lambda.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/let.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/let.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/list.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/list.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/maybe.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/maybe.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/modifiable.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/modifiable.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/operator.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/operator.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/random_variable.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/random_variable.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/reg_var.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/reg_var.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/resolved_symbol.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/resolved_symbol.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/substitute.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/substitute.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/trim.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/trim.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/tuple.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/tuple.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/var.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/expression/var.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/loader.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/loader.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/machine/args.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/machine/args.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/machine/effect.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/machine/effects.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/machine/effects.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/machine/error_exception.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/machine/evaluate.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/machine/gc.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/machine/kahan.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/machine/mapping.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/machine/pool.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/machine/reroot.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/machine/show_graph.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/machine/sums.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/machine/tokens.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/module.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/module.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/object.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/object.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/operation.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/operations.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/operations.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/optimization/float-out.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/optimization/float-out.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/optimization/free-vars.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/optimization/free-vars.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/optimization/free_vars.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/optimization/inliner.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/optimization/inliner.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/optimization/occurrence.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/optimization/occurrence.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/optimization/set-levels.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/optimization/set-levels.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/optimization/simplifier.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/optimization/simplifier.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/param.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/param.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/parser/desugar-case.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/parser/desugar.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/parser/desugar.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/parser/driver.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/parser/lexer.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/parser/located.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/parser/parser.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/parser/rename.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/parser/rename.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/preprocess.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/program.H
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/program.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/computation/type_constant.H
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/2way.H
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/2way.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/3way.H
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/3way.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/5way.H
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/5way.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/A2_states.H
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/alignment-sums.H
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/alignment-sums.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/bits.H
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/dp-array.H
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/dp-array.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/dp-cube.H
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/dp-cube.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/dp-engine.H
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/dp-engine.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/dp-matrix.H
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/dp-matrix.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/dp_hmm.H
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/dp_hmm.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/hmm.H
Examining data/bali-phy-3.5.0.2+dfsg/src/dp/hmm.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/imodel/imodel.H
Examining data/bali-phy-3.5.0.2+dfsg/src/imodel/imodel.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/math/eigenvalue.H
Examining data/bali-phy-3.5.0.2+dfsg/src/math/eigenvalue.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/math/exponential.H
Examining data/bali-phy-3.5.0.2+dfsg/src/math/exponential.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/math/logprod.H
Examining data/bali-phy-3.5.0.2+dfsg/src/math/pow2.H
Examining data/bali-phy-3.5.0.2+dfsg/src/math/pow2.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/AIS.H
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/AIS.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/logger.H
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/logger.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/mcmc.H
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/mcmc.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/moves.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/prob_ratios.H
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/proposals.H
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/proposals.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/sample-alignment.H
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/sample-alignment.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/sample-branch-lengths.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/sample-cube.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/sample-node.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/sample-topology-NNI.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/sample-topology-SPR.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/sample-tri.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/sample-two-nodes.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/sample.H
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/setup.H
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/setup.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/slice-sampling.H
Examining data/bali-phy-3.5.0.2+dfsg/src/mcmc/slice-sampling.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/models/TreeInterface.H
Examining data/bali-phy-3.5.0.2+dfsg/src/models/TreeInterface.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/models/model.H
Examining data/bali-phy-3.5.0.2+dfsg/src/models/model.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/models/parameters.H
Examining data/bali-phy-3.5.0.2+dfsg/src/models/parameters.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/models/parse.H
Examining data/bali-phy-3.5.0.2+dfsg/src/models/parse.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/models/path.H
Examining data/bali-phy-3.5.0.2+dfsg/src/models/path.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/models/rules.H
Examining data/bali-phy-3.5.0.2+dfsg/src/models/rules.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/models/setup.H
Examining data/bali-phy-3.5.0.2+dfsg/src/models/setup.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/models/site-compression.H
Examining data/bali-phy-3.5.0.2+dfsg/src/models/site-compression.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/models/translate.H
Examining data/bali-phy-3.5.0.2+dfsg/src/models/translate.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/models/unification.H
Examining data/bali-phy-3.5.0.2+dfsg/src/models/unification.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/probability/choose.H
Examining data/bali-phy-3.5.0.2+dfsg/src/probability/choose.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/probability/probability.H
Examining data/bali-phy-3.5.0.2+dfsg/src/probability/probability.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/sequence/alphabet.H
Examining data/bali-phy-3.5.0.2+dfsg/src/sequence/alphabet.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/sequence/sequence-format.H
Examining data/bali-phy-3.5.0.2+dfsg/src/sequence/sequence-format.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/sequence/sequence.H
Examining data/bali-phy-3.5.0.2+dfsg/src/sequence/sequence.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/substitution/cache.H
Examining data/bali-phy-3.5.0.2+dfsg/src/substitution/parsimony.H
Examining data/bali-phy-3.5.0.2+dfsg/src/substitution/parsimony.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/substitution/substitution.H
Examining data/bali-phy-3.5.0.2+dfsg/src/substitution/substitution.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/alignment-cat.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/alignment-chop-internal.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/alignment-compare.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/alignment-consensus.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/alignment-convert.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/alignment-distances.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/alignment-draw.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/alignment-find-conserved.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/alignment-find.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/alignment-gild.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/alignment-identity.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/alignment-indices.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/alignment-info.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/alignment-max.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/alignment-smc.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/alignment-thin.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/alignment-translate.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/alignments-diff.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/analyze-rates.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/bootstrap.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/bootstrap.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/colors.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/colors.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/consensus-tree.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/consensus-tree.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/cut-range.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/distance-methods.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/distance-methods.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/distance-report.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/distance-report.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/dos2unix.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/draw-graph.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/draw-tree.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/extract-ancestors.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/findroot.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/findroot.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/inverse.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/inverse.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/joint-A-T.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/joint-A-T.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/joint-indels.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/joint-parsimony.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/make_gaps.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/mctree-mean-lengths.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/mctree.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/mctree.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/model_P.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/optimize.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/optimize.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/parsimony.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/parsimony.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/parsimony2.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/parsimony2.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/partition.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/partition.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/partitions-supported.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/path-graph.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/pickout.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/read-trees.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/read-trees.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/srq-to-plot.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/srqinvert.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/statistics.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/statistics.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/statreport.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/stats-cat.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/stats-merge.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/stats-select.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/stats-table.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/stats-table.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/subsample.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/summarize-ancestors.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/test.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/tree-dist.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/tree-dist.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/tree-mean-lengths.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/tree-partitions.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/tree-reroot.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/tree-tool.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/trees-bootstrap.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/trees-consensus.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/trees-distances.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/trees-pair-distances.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/trees-to-SRQ.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tools/truckgraph3d.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tree-align/link.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tree-align/link.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tree-align/link2.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tree-align/link2.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tree-align/n_indels.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tree-align/n_indels.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tree-align/n_indels2.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tree-align/n_indels2.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tree/newick-tokenizer.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tree/newick-tokenizer.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tree/randomtree.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tree/sequencetree.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tree/sequencetree.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tree/tree-branchnode.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tree/tree-util.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tree/tree-util.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/tree/tree.H
Examining data/bali-phy-3.5.0.2+dfsg/src/tree/tree.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/util/cmdline.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/util/demangle.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/util/file-paths.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/bounds.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/cmdline.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/cow-ptr.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/demangle.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/file-paths.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/index_value.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/io.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/io/matrix.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/io/optional.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/io/vector.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/log-level.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/map.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/mapping.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/math/log-double.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/math/logsum.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/matrix.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/myexception.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/owned-ptr.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/permute.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/ptree.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/range.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/rng.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/set.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/string/convert.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/string/join.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/string/pred.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/string/sanitize.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/string/split.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/string/strip.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/text.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/time.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/truncate.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/include/util/wrap.H
Examining data/bali-phy-3.5.0.2+dfsg/src/util/io.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/util/log-level.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/util/mapping.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/util/myexception.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/util/permute.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/util/ptree.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/util/range.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/util/rng.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/util/string/pred.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/util/string/sanitize.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/util/string/split.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/util/string/strip.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/util/text.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/util/time.cc
Examining data/bali-phy-3.5.0.2+dfsg/src/version.H
Examining data/bali-phy-3.5.0.2+dfsg/src/version.cc
FINAL RESULTS:
data/bali-phy-3.5.0.2+dfsg/src/bali-phy/bali-phy.cc:122:3: [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(cmd.str().c_str());
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/evaluate.cc:178:14: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
if (regs.access(r).flags.test(3))
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/evaluate.cc:181:14: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
regs.access(r).flags.set(3);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/evaluate.cc:187:17: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
assert(regs.access(r).flags.test(3));
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/evaluate.cc:188:10: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
regs.access(r).flags.flip(3);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/evaluate.cc:218:37: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
reg::type_t reg_type = regs.access(r).type;
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/evaluate.cc:280:18: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
regs.access(r).type = reg::type_t::index_var;
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/evaluate.cc:293:18: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
regs.access(r).type = reg::type_t::constant;
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/evaluate.cc:311:27: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
int sp = regs.access(r).created_by.first;
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/evaluate.cc:346:37: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
assert(regs.access(r2).created_by.first == s);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/evaluate.cc:452:14: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
if (regs.access(R).flags.test(3))
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/evaluate.cc:455:14: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
regs.access(R).flags.set(3);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/evaluate.cc:461:17: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
assert(regs.access(R).flags.test(3));
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/evaluate.cc:462:10: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
regs.access(R).flags.flip(3);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/evaluate.cc:480:37: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
reg::type_t reg_type = regs.access(r).type;
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/evaluate.cc:497:18: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
regs.access(r).type = reg::type_t::index_var;
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/evaluate.cc:512:18: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
regs.access(r).type = reg::type_t::constant;
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/evaluate.cc:546:22: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
regs.access(r).type = reg::type_t::changeable;
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/gc.cc:102:23: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
const auto& R = regs.access(r);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.H:132:68: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
const closure& closure_at(int r) const {assert(r); return regs.access(r).C;}
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.H:134:57: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
const closure& operator[](int r) const {return regs.access(r).C;}
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.H:137:52: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
reg::type_t reg_type(int r) const {return regs.access(r).type;}
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.H:544:17: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
return regs.access(r).type == reg::type_t::constant;
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.H:549:17: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
return regs.access(r).type == reg::type_t::unevaluated;
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.H:554:17: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
return regs.access(r).type == reg::type_t::changeable;
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:279:14: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
regs.access(r).flags.set(0);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:294:14: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
if (regs.access(r).flags.test(1))
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:309:14: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
regs.access(r).flags.set(1);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:466:42: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
if (regs.is_used(r) and regs.access(r).flags.any() and not prog_temp[r].test(pdf_bit))
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:495:25: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
assert(regs.access(pdf_reg).flags.test(0) or regs.access(pdf_reg).flags.test(1));
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:495:63: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
assert(regs.access(pdf_reg).flags.test(0) or regs.access(pdf_reg).flags.test(1));
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:496:22: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
if (regs.access(pdf_reg).flags.test(0))
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:733:14: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
if (regs.access(r).type == reg::type_t::constant)
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:904:10: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
regs.access(R).C = std::move(C);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:923:17: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
assert(regs.access(r).created_by.first == 0);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:924:17: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
assert(regs.access(r).created_by.second == 0);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:925:10: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
regs.access(r).created_by = {s,index};
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:1310:18: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
assert( regs.access(r).type == reg::type_t::changeable or regs.access(r).type == reg::type_t::unevaluated );
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:1310:68: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
assert( regs.access(r).type == reg::type_t::changeable or regs.access(r).type == reg::type_t::unevaluated );
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:1312:10: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
regs.access(r).type = reg::type_t::changeable;
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:1397:25: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
assert(regs.access(r).type != reg::type_t::constant);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:1411:25: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
assert(regs.access(r).type != reg::type_t::constant);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:1504:35: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
auto [step, index] = regs.access(r).created_by;
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:1545:29: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
auto& created_by = regs.access(r).created_by;
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:1559:35: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
auto& forward2 = regs.access(backward[j]);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:1562:25: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
assert(regs.access(backward[j]).created_by.second == j);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/graph_register.cc:1612:14: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
if (regs.access(R).type == reg::type_t::constant) return expression_at(R);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/pool.H:322:14: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
const T& access(int i) const {assert(is_used(i) or is_marked(i));return lookup(i).value;}
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/pool.H:323:8: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
T& access(int i) {assert(is_used(i) or is_marked(i));return lookup(i).value;}
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/pool.H:325:46: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
const T& operator[](int i) const {return access(i);}
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/pool.H:326:40: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
T& operator[](int i) {return access(i);}
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/reroot.cc:110:30: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
if (s1 > 0 and steps.access(s1).has_nonforce_effect())
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/reroot.cc:119:30: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
if (s2 > 0 and steps.access(s2).has_nonforce_effect())
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/reroot.cc:201:37: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
assert(regs.access(r2).type == reg::type_t::changeable);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/reroot.cc:286:29: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
assert(regs.access(r2).type == reg::type_t::changeable);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/reroot.cc:328:33: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
assert(regs.access(r2).type == reg::type_t::changeable);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/reroot.cc:345:29: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
assert(regs.access(r2).type == reg::type_t::changeable);
data/bali-phy-3.5.0.2+dfsg/src/computation/machine/show_graph.cc:83:22: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
const reg& R = regs.access(r);
data/bali-phy-3.5.0.2+dfsg/src/bali-phy/cmd_line.cc:38:9: [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 (getenv("HOME")) {
data/bali-phy-3.5.0.2+dfsg/src/bali-phy/cmd_line.cc:39:20: [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.
string home_dir = getenv("HOME");
data/bali-phy-3.5.0.2+dfsg/src/bali-phy/files.cc:189:18: [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 (auto evar = getenv(var))
data/bali-phy-3.5.0.2+dfsg/src/bali-phy/files.cc:242:9: [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 (getenv("SLURM_JOBID"))
data/bali-phy-3.5.0.2+dfsg/src/bali-phy/files.cc:243:26: [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.
s_out<<"SLURM_JOBID: "<<getenv("SLURM_JOBID")<<endl;
data/bali-phy-3.5.0.2+dfsg/src/bali-phy/files.cc:244:9: [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 (getenv("JOB_ID"))
data/bali-phy-3.5.0.2+dfsg/src/bali-phy/files.cc:245:21: [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.
s_out<<"JOB_ID: "<<getenv("JOB_ID")<<endl;
data/bali-phy-3.5.0.2+dfsg/src/bali-phy/files.cc:246:9: [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 (getenv("LSB_JOBID"))
data/bali-phy-3.5.0.2+dfsg/src/bali-phy/files.cc:247:24: [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.
s_out<<"LSB_JOBID: "<<getenv("LSB_JOBID")<<endl;
data/bali-phy-3.5.0.2+dfsg/src/bali-phy/paths.cc:32:9: [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 (getenv("HOME"))
data/bali-phy-3.5.0.2+dfsg/src/bali-phy/paths.cc:34:18: [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.
user_lib_path = getenv("HOME");
data/bali-phy-3.5.0.2+dfsg/src/tools/read-trees.cc:97:14: [3] (random) setstate:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
fileref.setstate(std::ios::badbit);
data/bali-phy-3.5.0.2+dfsg/src/tools/read-trees.cc:282:11: [3] (random) setstate:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
fileref.setstate(std::ios::badbit);
data/bali-phy-3.5.0.2+dfsg/src/tools/read-trees.cc:302:14: [3] (random) setstate:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
fileref.setstate(std::ios::badbit);
data/bali-phy-3.5.0.2+dfsg/src/tools/read-trees.cc:385:15: [3] (random) setstate:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
fileref.setstate(std::ios::badbit);
data/bali-phy-3.5.0.2+dfsg/src/util/file-paths.cc:67:42: [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.
else if (not argv0.is_absolute() and getenv("PATH"))
data/bali-phy-3.5.0.2+dfsg/src/util/file-paths.cc:69:16: [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.
string PATH = getenv("PATH");
data/bali-phy-3.5.0.2+dfsg/src/util/io.cc:62:14: [3] (random) setstate:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
file.setstate(ios::badbit);
data/bali-phy-3.5.0.2+dfsg/src/util/io.cc:71:14: [3] (random) setstate:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
file.setstate(err);
data/bali-phy-3.5.0.2+dfsg/src/util/rng.cc:36:12: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
boost::random::random_device random;
data/bali-phy-3.5.0.2+dfsg/src/util/rng.cc:36:34: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
boost::random::random_device random;
data/bali-phy-3.5.0.2+dfsg/src/util/rng.cc:38:9: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
if (random.entropy())
data/bali-phy-3.5.0.2+dfsg/src/util/rng.cc:41:19: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
unsigned u = random();
data/bali-phy-3.5.0.2+dfsg/src/bali-phy/files.cc:143:5: [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[MAX_COMPUTERNAME_LENGTH + 1];
data/bali-phy-3.5.0.2+dfsg/src/bali-phy/files.cc:155:5: [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[256];
data/bali-phy-3.5.0.2+dfsg/src/computation/parser/parser.cc:3978:5: [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 const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
data/bali-phy-3.5.0.2+dfsg/src/tools/trees-consensus.cc:997:18: [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).
report_file.open(cout,"-",filename,"report file");
data/bali-phy-3.5.0.2+dfsg/src/util/include/util/io.H:54:22: [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).
checked_filebuf* open ( const std::string& s, std::ios_base::openmode mode );
data/bali-phy-3.5.0.2+dfsg/src/util/include/util/io.H:73:10: [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(std::istream&, const std::string&, const std::string&);
data/bali-phy-3.5.0.2+dfsg/src/util/include/util/io.H:74:10: [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(std::istream&, const std::string&, const std::string&,const std::string&);
data/bali-phy-3.5.0.2+dfsg/src/util/include/util/io.H:94:10: [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(std::ostream&, const std::string&, const std::string&);
data/bali-phy-3.5.0.2+dfsg/src/util/include/util/io.H:95:10: [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(std::ostream&, const std::string&, const std::string&,const std::string&);
data/bali-phy-3.5.0.2+dfsg/src/util/io.cc:185:36: [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).
checked_filebuf * checked_filebuf::open ( const std::string& filename, std::ios_base::openmode mode )
data/bali-phy-3.5.0.2+dfsg/src/util/io.cc:193:29: [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).
buf = std::filebuf::open(filename.c_str(), mode);
data/bali-phy-3.5.0.2+dfsg/src/util/io.cc:216:9: [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).
buf.open(filename, ios_base::in);
data/bali-phy-3.5.0.2+dfsg/src/util/io.cc:224:9: [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).
buf.open(filename, ios_base::in);
data/bali-phy-3.5.0.2+dfsg/src/util/io.cc:227:27: [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 istream_or_ifstream::open(std::istream& is, const std::string& is_name, const std::string& filename, const std::string& description)
data/bali-phy-3.5.0.2+dfsg/src/util/io.cc:238:14: [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).
buf->open(filename, ios_base::in);
data/bali-phy-3.5.0.2+dfsg/src/util/io.cc:251:5: [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).
open(is,is_name,filename,"file");
data/bali-phy-3.5.0.2+dfsg/src/util/io.cc:258:5: [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).
open(is,is_name,filename,description);
data/bali-phy-3.5.0.2+dfsg/src/util/io.cc:270:9: [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).
buf.open(filename, flags);
data/bali-phy-3.5.0.2+dfsg/src/util/io.cc:281:9: [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).
buf.open(filename, flags);
data/bali-phy-3.5.0.2+dfsg/src/util/io.cc:284:27: [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 ostream_or_ofstream::open(std::ostream& os, const std::string& os_name, const std::string& filename, const std::string& description)
data/bali-phy-3.5.0.2+dfsg/src/util/io.cc:295:14: [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).
buf->open(filename, ios_base::out|ios_base::trunc);
data/bali-phy-3.5.0.2+dfsg/src/util/io.cc:306:5: [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).
open(os,os_name,filename,"file");
data/bali-phy-3.5.0.2+dfsg/src/util/io.cc:312:5: [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).
open(os,os_name,filename,description);
data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/arrays/no_capacity.hpp:157:19: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
std::equal(data(), data() + size, other.data()));
data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/arrays/with_capacity.hpp:181:19: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
std::equal(data(), data() + size, other.data()));
data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/hamts/champ_iterator.hpp:140:10: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
bool equal(const champ_iterator& other) const
data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/iterator_facade.hpp:33:27: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
static decltype(auto) equal(T1&& x1, T2&& x2)
data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/iterator_facade.hpp:34:17: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
{ return x1.equal(x2); }
data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/iterator_facade.hpp:112:26: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
return access_t::equal(derived(), rhs);
data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/iterator_facade.hpp:116:27: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
return !access_t::equal(derived(), rhs);
data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/rbts/operations.hpp:420:18: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
std::equal(posl.node()->leaf(),
data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/rbts/operations.hpp:423:18: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
std::equal(posl.node()->leaf() + mp,
data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/rbts/operations.hpp:441:21: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
|| std::equal(node->leaf(), node->leaf() + pos.count(),
data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/rbts/rbtree_iterator.hpp:77:10: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
bool equal(const rbtree_iterator& other) const
data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/rbts/rrbtree.hpp:289:47: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
tail_off > tail_off_other ? std::equal(
data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/rbts/rrbtree.hpp:292:47: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
/* otherwise */ : std::equal(
data/bali-phy-3.5.0.2+dfsg/external/immer/immer/detail/rbts/rrbtree_iterator.hpp:79:10: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
bool equal(const rrbtree_iterator& other) const
data/bali-phy-3.5.0.2+dfsg/external/immer/immer/experimental/detail/dvektor_impl.hpp:492:10: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
bool equal(const iterator& other) const
data/bali-phy-3.5.0.2+dfsg/src/alignment/alignment-util.cc:595:12: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
return mismatch;
data/bali-phy-3.5.0.2+dfsg/src/alignment/alignment-util.cc:628:44: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
assert(homologies_total(M1) == match + mismatch);
data/bali-phy-3.5.0.2+dfsg/src/bali-phy/A-T-model.cc:923:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
RT.read(filename);
data/bali-phy-3.5.0.2+dfsg/src/computation/parser/lexer.cc:1166:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(c = getc( yyin )) != EOF && c != '\n'; ++n ) \
data/bali-phy-3.5.0.2+dfsg/src/computation/parser/lexer.cc:2511:37: [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 yy_scan_bytes( yystr, (int) strlen(yystr) );
data/bali-phy-3.5.0.2+dfsg/src/tools/alignment-cat.cc:489:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
RT.read(*tree);
data/bali-phy-3.5.0.2+dfsg/src/tools/make_gaps.cc:31:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
args.read(argc,argv);
data/bali-phy-3.5.0.2+dfsg/src/tools/make_gaps.cc:43:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
T.read(args["tree"]);
data/bali-phy-3.5.0.2+dfsg/src/tools/truckgraph3d.cc:184:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
args.read(argc,argv);
data/bali-phy-3.5.0.2+dfsg/src/tree/sequencetree.H:68:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
virtual void read(std::istream& file);
data/bali-phy-3.5.0.2+dfsg/src/tree/sequencetree.H:71:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
virtual void read(const std::string& filename);
data/bali-phy-3.5.0.2+dfsg/src/tree/sequencetree.cc:93:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void SequenceTree::read(const string& filename) {
data/bali-phy-3.5.0.2+dfsg/src/tree/sequencetree.cc:95:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(file);
data/bali-phy-3.5.0.2+dfsg/src/tree/sequencetree.cc:98:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void SequenceTree::read(std::istream& file) {
data/bali-phy-3.5.0.2+dfsg/src/tree/sequencetree.cc:335:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(file);
data/bali-phy-3.5.0.2+dfsg/src/util/include/util/mapping.H:130:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::vector<T> read(const std::vector<T>& v,const std::vector<int>& indices)
ANALYSIS SUMMARY:
Hits = 135
Lines analyzed = 131324 in approximately 3.15 seconds (41659 lines/second)
Physical Source Lines of Code (SLOC) = 91690
Hits@level = [0] 15 [1] 31 [2] 23 [3] 23 [4] 58 [5] 0
Hits@level+ = [0+] 150 [1+] 135 [2+] 104 [3+] 81 [4+] 58 [5+] 0
Hits/KSLOC@level+ = [0+] 1.63595 [1+] 1.47235 [2+] 1.13426 [3+] 0.883411 [4+] 0.632566 [5+] 0
Symlinks skipped = 1 (--allowlink overrides but see doc for security issue)
Dot directories skipped = 2 (--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.