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/openstructure-2.2.0/modules/base/pymod/export_generic_property.cc
Examining data/openstructure-2.2.0/modules/base/pymod/export_logger.cc
Examining data/openstructure-2.2.0/modules/base/pymod/export_range.cc
Examining data/openstructure-2.2.0/modules/base/pymod/export_units.cc
Examining data/openstructure-2.2.0/modules/base/pymod/wrap_base.cc
Examining data/openstructure-2.2.0/modules/base/src/boost_filesystem_helper.cc
Examining data/openstructure-2.2.0/modules/base/src/generic_property.cc
Examining data/openstructure-2.2.0/modules/base/src/log.cc
Examining data/openstructure-2.2.0/modules/base/src/log_sink.cc
Examining data/openstructure-2.2.0/modules/base/src/message.cc
Examining data/openstructure-2.2.0/modules/base/src/platform.cc
Examining data/openstructure-2.2.0/modules/base/src/profile.cc
Examining data/openstructure-2.2.0/modules/base/src/stdint.h
Examining data/openstructure-2.2.0/modules/base/src/string_ref.cc
Examining data/openstructure-2.2.0/modules/base/src/test_utils/compare_files.cc
Examining data/openstructure-2.2.0/modules/base/src/units.cc
Examining data/openstructure-2.2.0/modules/base/tests/test_generic_property.cc
Examining data/openstructure-2.2.0/modules/base/tests/test_pod_vector.cc
Examining data/openstructure-2.2.0/modules/base/tests/test_string_ref.cc
Examining data/openstructure-2.2.0/modules/base/tests/tests.cc
Examining data/openstructure-2.2.0/modules/bindings/pymod/export_tmalign.cc
Examining data/openstructure-2.2.0/modules/bindings/pymod/wrap_bindings.cc
Examining data/openstructure-2.2.0/modules/bindings/src/tmalign/BLOSUM.h
Examining data/openstructure-2.2.0/modules/bindings/src/tmalign/HwRMSD.cpp
Examining data/openstructure-2.2.0/modules/bindings/src/tmalign/HwRMSD.h
Examining data/openstructure-2.2.0/modules/bindings/src/tmalign/Kabsch.h
Examining data/openstructure-2.2.0/modules/bindings/src/tmalign/NW.h
Examining data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.cpp
Examining data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.h
Examining data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.cpp
Examining data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.h
Examining data/openstructure-2.2.0/modules/bindings/src/tmalign/basic_fun.h
Examining data/openstructure-2.2.0/modules/bindings/src/tmalign/param_set.h
Examining data/openstructure-2.2.0/modules/bindings/src/tmalign/pdb2fasta.cpp
Examining data/openstructure-2.2.0/modules/bindings/src/tmalign/pdb2ss.cpp
Examining data/openstructure-2.2.0/modules/bindings/src/tmalign/pdb2xyz.cpp
Examining data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h
Examining data/openstructure-2.2.0/modules/bindings/src/tmalign/se.cpp
Examining data/openstructure-2.2.0/modules/bindings/src/tmalign/se.h
Examining data/openstructure-2.2.0/modules/bindings/src/tmalign/xyz_sfetch.cpp
Examining data/openstructure-2.2.0/modules/bindings/src/wrap_tmalign.cc
Examining data/openstructure-2.2.0/modules/conop/pymod/export_amino_acids.cc
Examining data/openstructure-2.2.0/modules/conop/pymod/export_compound.cc
Examining data/openstructure-2.2.0/modules/conop/pymod/export_conop.cc
Examining data/openstructure-2.2.0/modules/conop/pymod/export_diag.cc
Examining data/openstructure-2.2.0/modules/conop/pymod/export_heuristic.cc
Examining data/openstructure-2.2.0/modules/conop/pymod/export_processor.cc
Examining data/openstructure-2.2.0/modules/conop/pymod/export_ring_finder.cc
Examining data/openstructure-2.2.0/modules/conop/pymod/export_rule_based.cc
Examining data/openstructure-2.2.0/modules/conop/pymod/wrap_conop.cc
Examining data/openstructure-2.2.0/modules/conop/src/amino_acids.cc
Examining data/openstructure-2.2.0/modules/conop/src/chemdict_tool.cc
Examining data/openstructure-2.2.0/modules/conop/src/compound.cc
Examining data/openstructure-2.2.0/modules/conop/src/compound_lib.cc
Examining data/openstructure-2.2.0/modules/conop/src/compound_lib_base.cc
Examining data/openstructure-2.2.0/modules/conop/src/conop.cc
Examining data/openstructure-2.2.0/modules/conop/src/diag.cc
Examining data/openstructure-2.2.0/modules/conop/src/heuristic.cc
Examining data/openstructure-2.2.0/modules/conop/src/minimal_compound_lib.cc
Examining data/openstructure-2.2.0/modules/conop/src/model_check.cc
Examining data/openstructure-2.2.0/modules/conop/src/processor.cc
Examining data/openstructure-2.2.0/modules/conop/src/ring_finder.cc
Examining data/openstructure-2.2.0/modules/conop/src/rule_based.cc
Examining data/openstructure-2.2.0/modules/conop/src/standard_compounds.cc
Examining data/openstructure-2.2.0/modules/conop/tests/helper.cc
Examining data/openstructure-2.2.0/modules/conop/tests/test_amino_acids.cc
Examining data/openstructure-2.2.0/modules/conop/tests/test_heuristic_builder.cc
Examining data/openstructure-2.2.0/modules/conop/tests/test_heuristic_conop.cc
Examining data/openstructure-2.2.0/modules/conop/tests/test_rule_based_conop.cc
Examining data/openstructure-2.2.0/modules/conop/tests/tests.cc
Examining data/openstructure-2.2.0/modules/db/pymod/export_linear_db.cc
Examining data/openstructure-2.2.0/modules/db/pymod/wrap_db.cc
Examining data/openstructure-2.2.0/modules/db/src/binary_container.cc
Examining data/openstructure-2.2.0/modules/db/src/extract_data_helper.cc
Examining data/openstructure-2.2.0/modules/db/src/linear_indexer.cc
Examining data/openstructure-2.2.0/modules/db/src/sqlite_wrap.cc
Examining data/openstructure-2.2.0/modules/geom/pymod/export_composite2.cc
Examining data/openstructure-2.2.0/modules/geom/pymod/export_composite2_op.cc
Examining data/openstructure-2.2.0/modules/geom/pymod/export_composite3.cc
Examining data/openstructure-2.2.0/modules/geom/pymod/export_composite3_op.cc
Examining data/openstructure-2.2.0/modules/geom/pymod/export_mat2.cc
Examining data/openstructure-2.2.0/modules/geom/pymod/export_mat3.cc
Examining data/openstructure-2.2.0/modules/geom/pymod/export_mat4.cc
Examining data/openstructure-2.2.0/modules/geom/pymod/export_quat.cc
Examining data/openstructure-2.2.0/modules/geom/pymod/export_transform.cc
Examining data/openstructure-2.2.0/modules/geom/pymod/export_vec2.cc
Examining data/openstructure-2.2.0/modules/geom/pymod/export_vec3.cc
Examining data/openstructure-2.2.0/modules/geom/pymod/export_vec4.cc
Examining data/openstructure-2.2.0/modules/geom/pymod/export_vecmat2_op.cc
Examining data/openstructure-2.2.0/modules/geom/pymod/export_vecmat3_op.cc
Examining data/openstructure-2.2.0/modules/geom/pymod/export_vecmat4_op.cc
Examining data/openstructure-2.2.0/modules/geom/pymod/wrap_geom.cc
Examining data/openstructure-2.2.0/modules/geom/src/aligned_cuboid.cc
Examining data/openstructure-2.2.0/modules/geom/src/composite2.cc
Examining data/openstructure-2.2.0/modules/geom/src/composite2_op.cc
Examining data/openstructure-2.2.0/modules/geom/src/composite3.cc
Examining data/openstructure-2.2.0/modules/geom/src/composite3_op.cc
Examining data/openstructure-2.2.0/modules/geom/src/mat2.cc
Examining data/openstructure-2.2.0/modules/geom/src/mat3.cc
Examining data/openstructure-2.2.0/modules/geom/src/mat4.cc
Examining data/openstructure-2.2.0/modules/geom/src/point_cloud.cc
Examining data/openstructure-2.2.0/modules/geom/src/quat.cc
Examining data/openstructure-2.2.0/modules/geom/src/transform.cc
Examining data/openstructure-2.2.0/modules/geom/src/vec3.cc
Examining data/openstructure-2.2.0/modules/geom/src/vecmat2_op.cc
Examining data/openstructure-2.2.0/modules/geom/src/vecmat3_op.cc
Examining data/openstructure-2.2.0/modules/geom/src/vecmat4_op.cc
Examining data/openstructure-2.2.0/modules/geom/tests/test_composite2.cc
Examining data/openstructure-2.2.0/modules/geom/tests/test_composite3.cc
Examining data/openstructure-2.2.0/modules/geom/tests/test_mat2.cc
Examining data/openstructure-2.2.0/modules/geom/tests/test_mat3.cc
Examining data/openstructure-2.2.0/modules/geom/tests/test_mat4.cc
Examining data/openstructure-2.2.0/modules/geom/tests/test_op2.cc
Examining data/openstructure-2.2.0/modules/geom/tests/test_op3.cc
Examining data/openstructure-2.2.0/modules/geom/tests/test_op4.cc
Examining data/openstructure-2.2.0/modules/geom/tests/test_quat.cc
Examining data/openstructure-2.2.0/modules/geom/tests/test_transform.cc
Examining data/openstructure-2.2.0/modules/geom/tests/test_vec2.cc
Examining data/openstructure-2.2.0/modules/geom/tests/test_vec3.cc
Examining data/openstructure-2.2.0/modules/geom/tests/test_vec4.cc
Examining data/openstructure-2.2.0/modules/geom/tests/tests.cc
Examining data/openstructure-2.2.0/modules/gfx/pymod/export_bitmap.cc
Examining data/openstructure-2.2.0/modules/gfx/pymod/export_color.cc
Examining data/openstructure-2.2.0/modules/gfx/pymod/export_color_ops.cc
Examining data/openstructure-2.2.0/modules/gfx/pymod/export_entity.cc
Examining data/openstructure-2.2.0/modules/gfx/pymod/export_exporter.cc
Examining data/openstructure-2.2.0/modules/gfx/pymod/export_gfx_node.cc
Examining data/openstructure-2.2.0/modules/gfx/pymod/export_gfx_obj.cc
Examining data/openstructure-2.2.0/modules/gfx/pymod/export_glwin_base.cc
Examining data/openstructure-2.2.0/modules/gfx/pymod/export_gradient.cc
Examining data/openstructure-2.2.0/modules/gfx/pymod/export_map.cc
Examining data/openstructure-2.2.0/modules/gfx/pymod/export_primitives.cc
Examining data/openstructure-2.2.0/modules/gfx/pymod/export_render_options.cc
Examining data/openstructure-2.2.0/modules/gfx/pymod/export_scene.cc
Examining data/openstructure-2.2.0/modules/gfx/pymod/export_scene_observer.cc
Examining data/openstructure-2.2.0/modules/gfx/pymod/export_surface.cc
Examining data/openstructure-2.2.0/modules/gfx/pymod/export_symmetry_node.cc
Examining data/openstructure-2.2.0/modules/gfx/pymod/wrap_gfx.cc
Examining data/openstructure-2.2.0/modules/gfx/pymod/export_primlist.cc
Examining data/openstructure-2.2.0/modules/gfx/src/GL/glew.c
Examining data/openstructure-2.2.0/modules/gfx/src/GL/glew.h
Examining data/openstructure-2.2.0/modules/gfx/src/GL/glxew.h
Examining data/openstructure-2.2.0/modules/gfx/src/GL/wglew.h
Examining data/openstructure-2.2.0/modules/gfx/src/bitmap_io.cc
Examining data/openstructure-2.2.0/modules/gfx/src/collada_exporter.cc
Examining data/openstructure-2.2.0/modules/gfx/src/color.cc
Examining data/openstructure-2.2.0/modules/gfx/src/color_ops/basic_gradient_color_op.cc
Examining data/openstructure-2.2.0/modules/gfx/src/color_ops/by_chain_color_op.cc
Examining data/openstructure-2.2.0/modules/gfx/src/color_ops/by_element_color_op.cc
Examining data/openstructure-2.2.0/modules/gfx/src/color_ops/color_op.cc
Examining data/openstructure-2.2.0/modules/gfx/src/color_ops/entity_view_color_op.cc
Examining data/openstructure-2.2.0/modules/gfx/src/color_ops/gradient_color_op.cc
Examining data/openstructure-2.2.0/modules/gfx/src/color_ops/gradient_level_color_op.cc
Examining data/openstructure-2.2.0/modules/gfx/src/color_ops/map_handle_color_op.cc
Examining data/openstructure-2.2.0/modules/gfx/src/color_ops/uniform_color_op.cc
Examining data/openstructure-2.2.0/modules/gfx/src/entity.cc
Examining data/openstructure-2.2.0/modules/gfx/src/exporter.cc
Examining data/openstructure-2.2.0/modules/gfx/src/gfx_node.cc
Examining data/openstructure-2.2.0/modules/gfx/src/gfx_object.cc
Examining data/openstructure-2.2.0/modules/gfx/src/gfx_prim.cc
Examining data/openstructure-2.2.0/modules/gfx/src/gfx_test_object.cc
Examining data/openstructure-2.2.0/modules/gfx/src/gost_exporter.cc
Examining data/openstructure-2.2.0/modules/gfx/src/gradient.cc
Examining data/openstructure-2.2.0/modules/gfx/src/gradient_manager.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/backbone_trace.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/cartoon_renderer.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/cgl_offscreen_buffer.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/connect_renderer_base.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/cpk_renderer.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/custom_renderer.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/debug_renderer.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/entity_detail.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/entity_renderer.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/fast_spheres.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/glx_offscreen_buffer.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/line_trace_renderer.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/map_iso_gen.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/map_iso_gen_o.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/map_iso_gen_s.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/map_octree.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/mapped_property.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/mesa_offscreen_buffer.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/octree_isocont.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/scene_fx.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/simple_renderer.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/sline_renderer.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/tabulated_trig.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/trace_renderer.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/trace_renderer_base.cc
Examining data/openstructure-2.2.0/modules/gfx/src/impl/wgl_offscreen_buffer.cc
Examining data/openstructure-2.2.0/modules/gfx/src/input.cc
Examining data/openstructure-2.2.0/modules/gfx/src/map_iso.cc
Examining data/openstructure-2.2.0/modules/gfx/src/map_slab.cc
Examining data/openstructure-2.2.0/modules/gfx/src/material.cc
Examining data/openstructure-2.2.0/modules/gfx/src/povray.cc
Examining data/openstructure-2.2.0/modules/gfx/src/prim_list.cc
Examining data/openstructure-2.2.0/modules/gfx/src/primitives.cc
Examining data/openstructure-2.2.0/modules/gfx/src/render_options/cartoon_render_options.cc
Examining data/openstructure-2.2.0/modules/gfx/src/render_options/cpk_render_options.cc
Examining data/openstructure-2.2.0/modules/gfx/src/render_options/custom_render_options.cc
Examining data/openstructure-2.2.0/modules/gfx/src/render_options/line_render_options.cc
Examining data/openstructure-2.2.0/modules/gfx/src/render_options/line_trace_render_options.cc
Examining data/openstructure-2.2.0/modules/gfx/src/render_options/render_options.cc
Examining data/openstructure-2.2.0/modules/gfx/src/render_options/simple_render_options.cc
Examining data/openstructure-2.2.0/modules/gfx/src/render_options/sline_render_options.cc
Examining data/openstructure-2.2.0/modules/gfx/src/render_options/trace_render_options.cc
Examining data/openstructure-2.2.0/modules/gfx/src/scene.cc
Examining data/openstructure-2.2.0/modules/gfx/src/selection.cc
Examining data/openstructure-2.2.0/modules/gfx/src/shader.cc
Examining data/openstructure-2.2.0/modules/gfx/src/surface.cc
Examining data/openstructure-2.2.0/modules/gfx/src/symmetry_node.cc
Examining data/openstructure-2.2.0/modules/gfx/src/texture.cc
Examining data/openstructure-2.2.0/modules/gfx/src/vertex_array.cc
Examining data/openstructure-2.2.0/modules/gfx/src/vertex_array_helper.cc
Examining data/openstructure-2.2.0/modules/gfx/tests/test_color.cc
Examining data/openstructure-2.2.0/modules/gfx/tests/test_ent_pov_export.cc
Examining data/openstructure-2.2.0/modules/gfx/tests/test_gfx_node.cc
Examining data/openstructure-2.2.0/modules/gfx/tests/test_map_octree.cc
Examining data/openstructure-2.2.0/modules/gfx/tests/tests.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/data_viewer_proxy.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_alignment_view.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_data_viewer.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_file_loader.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_file_viewer.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_gl_canvas.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_gl_win.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_gosty.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_input.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_main_area.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_menu_bar.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_message_widget.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_overlay.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_overlay_manager.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_panels.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_perspective.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_py_shell.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_scene_selection.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_scene_win.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_sequence_viewer.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_sip_handler.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_tool.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/export_widget.cc
Examining data/openstructure-2.2.0/modules/gui/pymod/wrap_gui.cc
Examining data/openstructure-2.2.0/modules/gui/src/admin.cc
Examining data/openstructure-2.2.0/modules/gui/src/data_viewer/argand.cc
Examining data/openstructure-2.2.0/modules/gui/src/data_viewer/data_viewer.cc
Examining data/openstructure-2.2.0/modules/gui/src/data_viewer/data_viewer_panel.cc
Examining data/openstructure-2.2.0/modules/gui/src/data_viewer/data_viewer_panel_base.cc
Examining data/openstructure-2.2.0/modules/gui/src/data_viewer/draw_overlay.cc
Examining data/openstructure-2.2.0/modules/gui/src/data_viewer/drawing_functions.cc
Examining data/openstructure-2.2.0/modules/gui/src/data_viewer/fft_panel.cc
Examining data/openstructure-2.2.0/modules/gui/src/data_viewer/img2qt.cc
Examining data/openstructure-2.2.0/modules/gui/src/data_viewer/info_panel.cc
Examining data/openstructure-2.2.0/modules/gui/src/data_viewer/mask_overlay.cc
Examining data/openstructure-2.2.0/modules/gui/src/data_viewer/null_overlay.cc
Examining data/openstructure-2.2.0/modules/gui/src/data_viewer/overlay_base.cc
Examining data/openstructure-2.2.0/modules/gui/src/data_viewer/overlay_manager.cc
Examining data/openstructure-2.2.0/modules/gui/src/data_viewer/overlay_manager_gui.cc
Examining data/openstructure-2.2.0/modules/gui/src/data_viewer/pointlist_overlay.cc
Examining data/openstructure-2.2.0/modules/gui/src/data_viewer/pointlist_overlay_base.cc
Examining data/openstructure-2.2.0/modules/gui/src/data_viewer/strategies.cc
Examining data/openstructure-2.2.0/modules/gui/src/data_viewer/viewer_normalizer.cc
Examining data/openstructure-2.2.0/modules/gui/src/dock_widget.cc
Examining data/openstructure-2.2.0/modules/gui/src/file_browser.cc
Examining data/openstructure-2.2.0/modules/gui/src/file_loader.cc
Examining data/openstructure-2.2.0/modules/gui/src/file_type_dialog.cc
Examining data/openstructure-2.2.0/modules/gui/src/file_viewer.cc
Examining data/openstructure-2.2.0/modules/gui/src/gl_canvas.cc
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Examining data/openstructure-2.2.0/modules/io/src/io_utils.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/chemdict_parser.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/entity_io_crd_handler.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/entity_io_mae_handler.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/entity_io_mmcif_handler.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/entity_io_pdb_handler.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/entity_io_pqr_handler.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/entity_io_sdf_handler.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/io_profile.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/load_entity.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/load_surface.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/mmcif_info.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/mmcif_reader.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/pdb_reader.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/pdb_str.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/pdb_writer.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/save_entity.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/sdf_reader.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/sdf_writer.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/star_parser.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/stereochemical_params_reader.cc
Examining data/openstructure-2.2.0/modules/io/src/mol/surface_io_msms_handler.cc
Examining data/openstructure-2.2.0/modules/io/src/seq/clustal_io_handler.cc
Examining data/openstructure-2.2.0/modules/io/src/seq/fasta_io_handler.cc
Examining data/openstructure-2.2.0/modules/io/src/seq/hhm_io_handler.cc
Examining data/openstructure-2.2.0/modules/io/src/seq/load.cc
Examining data/openstructure-2.2.0/modules/io/src/seq/pir_io_handler.cc
Examining data/openstructure-2.2.0/modules/io/src/seq/promod_io_handler.cc
Examining data/openstructure-2.2.0/modules/io/src/seq/pssm_io_handler.cc
Examining data/openstructure-2.2.0/modules/io/src/seq/save.cc
Examining data/openstructure-2.2.0/modules/io/src/zlib.cpp
Examining data/openstructure-2.2.0/modules/io/tests/test_clustal.cc
Examining data/openstructure-2.2.0/modules/io/tests/test_exceptions.cc
Examining data/openstructure-2.2.0/modules/io/tests/test_io_crd.cc
Examining data/openstructure-2.2.0/modules/io/tests/test_io_dcd.cc
Examining data/openstructure-2.2.0/modules/io/tests/test_io_img.cc
Examining data/openstructure-2.2.0/modules/io/tests/test_io_pdb.cc
Examining data/openstructure-2.2.0/modules/io/tests/test_io_sdf.cc
Examining data/openstructure-2.2.0/modules/io/tests/test_io_sequence_profile.cc
Examining data/openstructure-2.2.0/modules/io/tests/test_iomanager.cc
Examining data/openstructure-2.2.0/modules/io/tests/test_mae_standalone.cc
Examining data/openstructure-2.2.0/modules/io/tests/test_mmcif_info.cc
Examining data/openstructure-2.2.0/modules/io/tests/test_mmcif_reader.cc
Examining data/openstructure-2.2.0/modules/io/tests/test_pir.cc
Examining data/openstructure-2.2.0/modules/io/tests/test_star_parser.cc
Examining data/openstructure-2.2.0/modules/io/tests/tests.cc
Examining data/openstructure-2.2.0/modules/mol/alg/pymod/export_accessibility.cc
Examining data/openstructure-2.2.0/modules/mol/alg/pymod/export_clash.cc
Examining data/openstructure-2.2.0/modules/mol/alg/pymod/export_contact_overlap.cc
Examining data/openstructure-2.2.0/modules/mol/alg/pymod/export_entity_to_density.cc
Examining data/openstructure-2.2.0/modules/mol/alg/pymod/export_membrane.cc
Examining data/openstructure-2.2.0/modules/mol/alg/pymod/export_molck.cc
Examining data/openstructure-2.2.0/modules/mol/alg/pymod/export_non_standard.cc
Examining data/openstructure-2.2.0/modules/mol/alg/pymod/export_sec_structure.cc
Examining data/openstructure-2.2.0/modules/mol/alg/pymod/export_structure_analysis.cc
Examining data/openstructure-2.2.0/modules/mol/alg/pymod/export_superpose_frames.cc
Examining data/openstructure-2.2.0/modules/mol/alg/pymod/export_svd_superpose.cc
Examining data/openstructure-2.2.0/modules/mol/alg/pymod/export_trajectory_analysis.cc
Examining data/openstructure-2.2.0/modules/mol/alg/pymod/wrap_mol_alg.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/accessibility.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/adjacency_bitmap.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/clash_score.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/consistency_checks.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/construct_cbeta.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/contact_overlap.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/distance_rmsd_test.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/distance_test_common.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/domain_find.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/entity_to_density.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/filter_clashes.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/find_membrane.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/lddt.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/local_dist_diff_test.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/molck.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/nonstandard.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/pdbize.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/sec_struct.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/sec_structure_segments.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/similarity_matrix.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/structure_analysis.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/superpose_frames.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/svd_superpose.cc
Examining data/openstructure-2.2.0/modules/mol/alg/src/trajectory_analysis.cc
Examining data/openstructure-2.2.0/modules/mol/alg/tests/test_consistency_checks.cc
Examining data/openstructure-2.2.0/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc
Examining data/openstructure-2.2.0/modules/mol/alg/tests/test_superposition.cc
Examining data/openstructure-2.2.0/modules/mol/alg/tests/tests.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_atom.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_atom_view.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_bond.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_bounding_box.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_chain.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_chain_view.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_coord_frame.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_coord_group.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_editors.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_entity.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_entity_property_mapper.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_entity_view.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_property_id.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_query.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_query_view_wrapper.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_residue.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_residue_view.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_surface.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_torsion.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/export_visitor.cc
Examining data/openstructure-2.2.0/modules/mol/base/pymod/wrap_mol.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/atom_base.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/atom_handle.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/atom_view.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/bond_handle.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/bounding_box.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/chain_base.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/chain_handle.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/chain_type.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/chain_view.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/coord_frame.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/coord_group.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/coord_source.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/editor_base.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/entity_base.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/entity_handle.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/entity_observer.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/entity_property_mapper.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/entity_view.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/entity_visitor.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/ics_editor.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/impl/atom_impl.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/impl/atom_prop.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/impl/chain_impl.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/impl/connector_impl.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/impl/dihedral.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/impl/entity_impl.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/impl/fragment_impl.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/impl/query_ast.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/impl/query_impl.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/impl/residue_impl.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/impl/surface_impl.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/impl/torsion_impl.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/in_mem_coord_source.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/not_connected_error.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/property_id.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/query.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/query_error.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/query_state.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/query_view_wrapper.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/residue_base.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/residue_handle.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/residue_view.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/skel_link.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/surface_builder.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/surface_handle.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/torsion_handle.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/transfer_connectivity.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/view_op.cc
Examining data/openstructure-2.2.0/modules/mol/base/src/xcs_editor.cc
Examining data/openstructure-2.2.0/modules/mol/base/tests/test_atom_groups.cc
Examining data/openstructure-2.2.0/modules/mol/base/tests/test_builder.cc
Examining data/openstructure-2.2.0/modules/mol/base/tests/test_chain.cc
Examining data/openstructure-2.2.0/modules/mol/base/tests/test_conn.cc
Examining data/openstructure-2.2.0/modules/mol/base/tests/test_coord_group.cc
Examining data/openstructure-2.2.0/modules/mol/base/tests/test_delete.cc
Examining data/openstructure-2.2.0/modules/mol/base/tests/test_entity.cc
Examining data/openstructure-2.2.0/modules/mol/base/tests/test_ics.cc
Examining data/openstructure-2.2.0/modules/mol/base/tests/test_iterators.cc
Examining data/openstructure-2.2.0/modules/mol/base/tests/test_query.cc
Examining data/openstructure-2.2.0/modules/mol/base/tests/test_query_standalone.cc
Examining data/openstructure-2.2.0/modules/mol/base/tests/test_residue.cc
Examining data/openstructure-2.2.0/modules/mol/base/tests/test_surface.cc
Examining data/openstructure-2.2.0/modules/mol/base/tests/test_transfer_connectivity.cc
Examining data/openstructure-2.2.0/modules/mol/base/tests/test_view.cc
Examining data/openstructure-2.2.0/modules/mol/base/tests/test_view_op.cc
Examining data/openstructure-2.2.0/modules/mol/base/tests/tests.cc
Examining data/openstructure-2.2.0/modules/mol/mm/pymod/export_block_modifiers.cc
Examining data/openstructure-2.2.0/modules/mol/mm/pymod/export_buildingblock.cc
Examining data/openstructure-2.2.0/modules/mol/mm/pymod/export_ff_reader.cc
Examining data/openstructure-2.2.0/modules/mol/mm/pymod/export_forcefield.cc
Examining data/openstructure-2.2.0/modules/mol/mm/pymod/export_index.cc
Examining data/openstructure-2.2.0/modules/mol/mm/pymod/export_interaction.cc
Examining data/openstructure-2.2.0/modules/mol/mm/pymod/export_modeller.cc
Examining data/openstructure-2.2.0/modules/mol/mm/pymod/export_observers.cc
Examining data/openstructure-2.2.0/modules/mol/mm/pymod/export_openmm.cc
Examining data/openstructure-2.2.0/modules/mol/mm/pymod/export_settings.cc
Examining data/openstructure-2.2.0/modules/mol/mm/pymod/export_simulation.cc
Examining data/openstructure-2.2.0/modules/mol/mm/pymod/export_topology.cc
Examining data/openstructure-2.2.0/modules/mol/mm/pymod/wrap_mol_mm.cc
Examining data/openstructure-2.2.0/modules/mol/mm/src/buildingblock.cc
Examining data/openstructure-2.2.0/modules/mol/mm/src/ff_reader.cc
Examining data/openstructure-2.2.0/modules/mol/mm/src/forcefield.cc
Examining data/openstructure-2.2.0/modules/mol/mm/src/gromacs_block_modifiers.cc
Examining data/openstructure-2.2.0/modules/mol/mm/src/heuristic_block_modifiers.cc
Examining data/openstructure-2.2.0/modules/mol/mm/src/interaction.cc
Examining data/openstructure-2.2.0/modules/mol/mm/src/modeller.cc
Examining data/openstructure-2.2.0/modules/mol/mm/src/observer.cc
Examining data/openstructure-2.2.0/modules/mol/mm/src/simulation.cc
Examining data/openstructure-2.2.0/modules/mol/mm/src/state_extractor.cc
Examining data/openstructure-2.2.0/modules/mol/mm/src/steep.cc
Examining data/openstructure-2.2.0/modules/mol/mm/src/system_creator.cc
Examining data/openstructure-2.2.0/modules/mol/mm/src/topology.cc
Examining data/openstructure-2.2.0/modules/mol/mm/src/topology_creator.cc
Examining data/openstructure-2.2.0/modules/mol/mm/tests/test_block.cc
Examining data/openstructure-2.2.0/modules/mol/mm/tests/test_block_modifiers.cc
Examining data/openstructure-2.2.0/modules/mol/mm/tests/test_forcefield.cc
Examining data/openstructure-2.2.0/modules/mol/mm/tests/test_interaction.cc
Examining data/openstructure-2.2.0/modules/mol/mm/tests/test_simulation.cc
Examining data/openstructure-2.2.0/modules/mol/mm/tests/test_topology.cc
Examining data/openstructure-2.2.0/modules/mol/mm/tests/tests.cc
Examining data/openstructure-2.2.0/modules/seq/alg/pymod/wrap_seq_alg.cc
Examining data/openstructure-2.2.0/modules/seq/alg/src/clip_alignment.cc
Examining data/openstructure-2.2.0/modules/seq/alg/src/conservation.cc
Examining data/openstructure-2.2.0/modules/seq/alg/src/contact_prediction_score.cc
Examining data/openstructure-2.2.0/modules/seq/alg/src/contact_weight_matrix.cc
Examining data/openstructure-2.2.0/modules/seq/alg/src/distance_map.cc
Examining data/openstructure-2.2.0/modules/seq/alg/src/entropy.cc
Examining data/openstructure-2.2.0/modules/seq/alg/src/global_align.cc
Examining data/openstructure-2.2.0/modules/seq/alg/src/hmm_pseudo_counts.cc
Examining data/openstructure-2.2.0/modules/seq/alg/src/hmm_score.cc
Examining data/openstructure-2.2.0/modules/seq/alg/src/ins_del.cc
Examining data/openstructure-2.2.0/modules/seq/alg/src/local_align.cc
Examining data/openstructure-2.2.0/modules/seq/alg/src/merge_pairwise_alignments.cc
Examining data/openstructure-2.2.0/modules/seq/alg/src/pair_subst_weight_matrix.cc
Examining data/openstructure-2.2.0/modules/seq/alg/src/semiglobal_align.cc
Examining data/openstructure-2.2.0/modules/seq/alg/src/sequence_identity.cc
Examining data/openstructure-2.2.0/modules/seq/alg/src/sequence_similarity.cc
Examining data/openstructure-2.2.0/modules/seq/alg/src/subst_weight_matrix.cc
Examining data/openstructure-2.2.0/modules/seq/alg/src/variance_map.cc
Examining data/openstructure-2.2.0/modules/seq/alg/tests/test_distance_analysis.cc
Examining data/openstructure-2.2.0/modules/seq/alg/tests/test_merge_pairwise_alignments.cc
Examining data/openstructure-2.2.0/modules/seq/alg/tests/test_sequence_identity.cc
Examining data/openstructure-2.2.0/modules/seq/alg/tests/tests.cc
Examining data/openstructure-2.2.0/modules/seq/base/pymod/export_profile_handle.cc
Examining data/openstructure-2.2.0/modules/seq/base/pymod/export_sequence.cc
Examining data/openstructure-2.2.0/modules/seq/base/pymod/wrap_seq.cc
Examining data/openstructure-2.2.0/modules/seq/base/src/aligned_column.cc
Examining data/openstructure-2.2.0/modules/seq/base/src/aligned_region.cc
Examining data/openstructure-2.2.0/modules/seq/base/src/alignment_handle.cc
Examining data/openstructure-2.2.0/modules/seq/base/src/impl/sequence_impl.cc
Examining data/openstructure-2.2.0/modules/seq/base/src/impl/sequence_list_impl.cc
Examining data/openstructure-2.2.0/modules/seq/base/src/profile_handle.cc
Examining data/openstructure-2.2.0/modules/seq/base/src/sequence_handle.cc
Examining data/openstructure-2.2.0/modules/seq/base/src/sequence_list.cc
Examining data/openstructure-2.2.0/modules/seq/base/src/sequence_op.cc
Examining data/openstructure-2.2.0/modules/seq/base/src/views_from_sequences.cc
Examining data/openstructure-2.2.0/modules/seq/base/tests/test_aligned_column.cc
Examining data/openstructure-2.2.0/modules/seq/base/tests/test_aligned_region.cc
Examining data/openstructure-2.2.0/modules/seq/base/tests/test_alignment.cc
Examining data/openstructure-2.2.0/modules/seq/base/tests/test_profile.cc
Examining data/openstructure-2.2.0/modules/seq/base/tests/test_sequence.cc
Examining data/openstructure-2.2.0/modules/seq/base/tests/tests.cc
Examining data/openstructure-2.2.0/tools/molck/main.cc
FINAL RESULTS:
data/openstructure-2.2.0/modules/mol/alg/src/lddt.cc:129:23: [5] (race) readlink:
This accepts filename arguments; if an attacker can move those files or
change the link content, a race condition results. Also, it does not
terminate with ASCII NUL. (CWE-362, CWE-20). Reconsider approach.
ssize_t count = readlink( "/proc/self/exe", result, 1024 );
data/openstructure-2.2.0/tools/molck/main.cc:111:19: [5] (race) readlink:
This accepts filename arguments; if an attacker can move those files or
change the link content, a race condition results. Also, it does not
terminate with ASCII NUL. (CWE-362, CWE-20). Reconsider approach.
ssize_t count = readlink( "/proc/self/exe", result, 1024 );
data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.cpp:262:32: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (infmt1_opt>=4) strcpy(seqx,PDB_lines1[chain_i][0].c_str());
data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.cpp:300:25: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(seqy,PDB_lines2[chain_j][0].c_str());
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.h:1593:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(dest, "m %18s %14s %14s %14s\n", "t[m]", "u[m][0]", "u[m][1]", "u[m][2]");
data/openstructure-2.2.0/modules/bindings/src/tmalign/pdb2fasta.cpp:112:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(message, "Can not open file: %s\n", xname.c_str());
data/openstructure-2.2.0/modules/bindings/src/tmalign/pdb2ss.cpp:132:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(message, "Can not open file: %s\n", xname.c_str());
data/openstructure-2.2.0/modules/bindings/src/tmalign/pdb2xyz.cpp:108:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(message, "Can not open file: %s\n", xname.c_str());
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:1116:13: [4] (shell) execl:
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.
::execl(shell_path, "sh", "-c", command.c_str(), (char*)NULL);
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:1240:17: [4] (shell) execvp:
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.
::execvp(file.c_str(), arg_v);
data/openstructure-2.2.0/modules/gfx/src/GL/glew.c:101:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(symbolName+1, (const char*)name);
data/openstructure-2.2.0/modules/gfx/src/GL/glew.h:1634:74: [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.
typedef GLvoid* (GLAPIENTRY * PFNGLMAPBUFFERPROC) (GLenum target, GLenum access);
data/openstructure-2.2.0/modules/gfx/src/GL/glew.h:3528:120: [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.
typedef GLvoid * (GLAPIENTRY * PFNGLMAPBUFFERRANGEPROC) (GLenum target, GLintptr offset, GLsizeiptr length, GLbitfield access);
data/openstructure-2.2.0/modules/gfx/src/GL/glew.h:4927:78: [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.
typedef GLvoid * (GLAPIENTRY * PFNGLMAPBUFFERARBPROC) (GLenum target, GLenum access);
data/openstructure-2.2.0/modules/gfx/src/GL/glew.h:6312:83: [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.
typedef GLvoid * (GLAPIENTRY * PFNGLMAPNAMEDBUFFEREXTPROC) (GLuint buffer, GLenum access);
data/openstructure-2.2.0/modules/gfx/src/GL/glew.h:6313:128: [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.
typedef GLvoid * (GLAPIENTRY * PFNGLMAPNAMEDBUFFERRANGEEXTPROC) (GLuint buffer, GLintptr offset, GLsizeiptr length, GLbitfield access);
data/openstructure-2.2.0/modules/gfx/src/GL/glew.h:7655:141: [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.
typedef void (GLAPIENTRY * PFNGLBINDIMAGETEXTUREEXTPROC) (GLuint index, GLuint texture, GLint level, GLboolean layered, GLint layer, GLenum access, GLint format);
data/openstructure-2.2.0/modules/gfx/src/GL/glew.h:10017:82: [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.
typedef void (GLAPIENTRY * PFNGLMAKEBUFFERRESIDENTNVPROC) (GLenum target, GLenum access);
data/openstructure-2.2.0/modules/gfx/src/GL/glew.h:10019:87: [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.
typedef void (GLAPIENTRY * PFNGLMAKENAMEDBUFFERRESIDENTNVPROC) (GLuint buffer, GLenum access);
data/openstructure-2.2.0/modules/io/src/img/tiff_util.cc:39:3: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf(message,1024,fmt,ap);
data/openstructure-2.2.0/modules/mol/mm/src/steep.cc:27:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if(system.getNumConstraints() > 0){
data/openstructure-2.2.0/modules/mol/mm/src/steep.cc:45:22: [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.
for(int i = 0; i < system.getNumParticles(); ++i){
data/openstructure-2.2.0/modules/mol/mm/src/steep.cc:46:8: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if(system.getParticleMass(i) != 0){
data/openstructure-2.2.0/modules/base/src/platform.cc:35:20: [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.
char* ost_root=getenv("OST_ROOT");
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:2102:15: [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.
this->setstate(std::ios_base::failbit);
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:2121:15: [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.
this->setstate(std::ios_base::failbit);
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:2130:15: [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.
this->setstate(std::ios_base::failbit);
data/openstructure-2.2.0/modules/conop/tests/test_rule_based_conop.cc:39:8: [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("OST_ROOT")) {
data/openstructure-2.2.0/modules/conop/tests/test_rule_based_conop.cc:44:17: [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.
SetPrefixPath(getenv("OST_ROOT"));
data/openstructure-2.2.0/modules/gfx/src/impl/glx_offscreen_buffer.cc:36:24: [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.
dpy=XOpenDisplay(getenv("DISPLAY"));
data/openstructure-2.2.0/modules/gfx/src/impl/glx_offscreen_buffer.cc:46:6: [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("DISPLAY")==NULL) {
data/openstructure-2.2.0/modules/gfx/src/impl/mesa_offscreen_buffer.cc:91:6: [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("DISPLAY")==NULL) {
data/openstructure-2.2.0/modules/gfx/src/impl/mesa_offscreen_buffer.cc:97:23: [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.
dpy_ = XOpenDisplay(getenv("DISPLAY"));
data/openstructure-2.2.0/modules/io/tests/test_io_pdb.cc:904:19: [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.
char * ost_root=getenv("OST_ROOT");
data/openstructure-2.2.0/modules/io/tests/test_mmcif_reader.cc:102:21: [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.
char * ost_root = getenv("OST_ROOT");
data/openstructure-2.2.0/modules/bindings/src/tmalign/HwRMSD.cpp:202:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
infmt1_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/HwRMSD.cpp:206:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
infmt2_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/HwRMSD.cpp:210:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
ter_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/HwRMSD.cpp:214:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
split_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/HwRMSD.cpp:242:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
outfmt_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/HwRMSD.cpp:246:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
byresi_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/HwRMSD.cpp:250:20: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
glocal=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/HwRMSD.cpp:254:22: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
iter_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/HwRMSD.h:47:49: [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.
int HwRMSD_main(double **xa, double **ya, const char *seqx, const char *seqy,
data/openstructure-2.2.0/modules/bindings/src/tmalign/HwRMSD.h:47:67: [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.
int HwRMSD_main(double **xa, double **ya, const char *seqx, const char *seqy,
data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.cpp:124:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
infmt1_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.cpp:128:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
infmt2_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.cpp:132:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
ter_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.cpp:136:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
split_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.cpp:164:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
outfmt_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.cpp:168:20: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
glocal=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.cpp:205:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
a_opt=atoi(argv[i + 1]);
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.cpp:241:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
infmt1_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.cpp:245:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
infmt2_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.cpp:249:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
ter_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.cpp:253:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
split_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.cpp:281:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
outfmt_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.cpp:289:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
byresi_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.h:1460:52: [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.
void output_superpose(const string filename, const char *fname_super,
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.h:1469:16: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fin_gz.open("zcat "+filename);
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.h:1475:16: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fin_gz.open("bzcat "+filename);
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.h:1478:14: [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).
else fin.open(filename.c_str());
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.h:1588:10: [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).
fout.open(fname_matrix, ios::out | ios::trunc);
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.h:1592:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char dest[1000];
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.h:1597:13: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(dest, "%d %18.10f %14.10f %14.10f %14.10f\n", k, t[k], u[k][0], u[k][1], u[k][2]);
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.h:1616:11: [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.
const char *chainID1, const char *chainID2,
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.h:1616:33: [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.
const char *chainID1, const char *chainID2,
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.h:1839:11: [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.
const char *seqx, const char *seqy, const int *secx, const int *secy,
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.h:1839:29: [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.
const char *seqx, const char *seqy, const int *secx, const int *secy,
data/openstructure-2.2.0/modules/bindings/src/tmalign/basic_fun.h:162:16: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fin_gz.open("zcat "+filename);
data/openstructure-2.2.0/modules/bindings/src/tmalign/basic_fun.h:168:16: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fin_gz.open("bzcat "+filename);
data/openstructure-2.2.0/modules/bindings/src/tmalign/basic_fun.h:171:14: [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).
else fin.open(filename.c_str());
data/openstructure-2.2.0/modules/bindings/src/tmalign/basic_fun.h:302:15: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
L=atoi(line.c_str());
data/openstructure-2.2.0/modules/bindings/src/tmalign/basic_fun.h:521:16: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fin_gz.open("zcat "+filename);
data/openstructure-2.2.0/modules/bindings/src/tmalign/basic_fun.h:527:16: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fin_gz.open("bzcat "+filename);
data/openstructure-2.2.0/modules/bindings/src/tmalign/basic_fun.h:530:14: [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).
else fin.open(filename.c_str());
data/openstructure-2.2.0/modules/bindings/src/tmalign/basic_fun.h:622:18: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
else if (atoi(resi_vec1[i1].substr(0,4).c_str())<=
data/openstructure-2.2.0/modules/bindings/src/tmalign/basic_fun.h:623:18: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
atoi(resi_vec2[i2].substr(0,4).c_str()))
data/openstructure-2.2.0/modules/bindings/src/tmalign/pdb2fasta.cpp:65:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
ter_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/pdb2fasta.cpp:69:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
split_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/pdb2fasta.cpp:85:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
infmt_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/pdb2fasta.cpp:111:13: [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 message[5000];
data/openstructure-2.2.0/modules/bindings/src/tmalign/pdb2ss.cpp:75:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
ter_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/pdb2ss.cpp:79:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
split_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/pdb2ss.cpp:99:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
infmt_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/pdb2ss.cpp:131:13: [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 message[5000];
data/openstructure-2.2.0/modules/bindings/src/tmalign/pdb2xyz.cpp:63:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
ter_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/pdb2xyz.cpp:67:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
split_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/pdb2xyz.cpp:83:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
infmt_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/pdb2xyz.cpp:107:13: [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 message[5000];
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:119:7: [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(const std::string& cmd, pmode mode);
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:123:7: [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(const std::string& file, const argv_type& argv, pmode mode);
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:156:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fopen(FILE*& in, FILE*& out, FILE*& err);
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:316:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fopen(FILE*& in, FILE*& out, FILE*& err);
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:439:7: [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(const std::string& cmd, pmode mode = pstdout)
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:455:7: [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( const std::string& file,
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:597:7: [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(const std::string& cmd, pmode mode = pstdin)
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:613:7: [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( const std::string& file,
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:737:7: [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(const std::string& cmd, pmode mode = pstdout|pstdin)
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:753:7: [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( const std::string& file,
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:906:7: [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(const std::string& cmd, pmode mode = pstdout|pstdin)
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:922:7: [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( const std::string& file,
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:1033:7: [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(cmd, mode);
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:1058:7: [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(file, argv, mode);
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:1101:28: [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).
basic_pstreambuf<C,T>::open(const std::string& command, pmode mode)
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:1106:20: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
return this->open(shell_path, argv_type(argv, argv+3), mode);
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:1203:28: [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).
basic_pstreambuf<C,T>::open( const std::string& file,
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:2101:17: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (!buf_.open((command_=cmd), mode))
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:2120:17: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (!buf_.open((command_=file), argv, mode))
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:2197:28: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
basic_pstreambuf<C,T>::fopen(FILE*& in, FILE*& out, FILE*& err)
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:2237:26: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
pstream_common<C,T>::fopen(FILE*& fin, FILE*& fout, FILE*& ferr)
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:2239:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
return buf_.fopen(fin, fout, ferr);
data/openstructure-2.2.0/modules/bindings/src/tmalign/se.cpp:163:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
infmt1_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/se.cpp:167:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
infmt2_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/se.cpp:171:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
ter_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/se.cpp:175:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
split_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/se.cpp:203:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
outfmt_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/se.cpp:207:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
byresi_opt=atoi(argv[i + 1]); i++;
data/openstructure-2.2.0/modules/bindings/src/tmalign/xyz_sfetch.cpp:66:15: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
L=atoi(line.c_str());
data/openstructure-2.2.0/modules/bindings/src/tmalign/xyz_sfetch.cpp:101:8: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp.open((filename+".index").c_str());
data/openstructure-2.2.0/modules/gfx/src/GL/glxew.h:1001:3: [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 pipeName[GLX_HYPERPIPE_PIPE_NAME_LENGTH_SGIX];
data/openstructure-2.2.0/modules/gfx/src/GL/glxew.h:1005:3: [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 pipeName[GLX_HYPERPIPE_PIPE_NAME_LENGTH_SGIX];
data/openstructure-2.2.0/modules/gfx/src/GL/glxew.h:1012:3: [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 pipeName[GLX_HYPERPIPE_PIPE_NAME_LENGTH_SGIX];
data/openstructure-2.2.0/modules/gfx/src/GL/glxew.h:1018:3: [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 pipeName[GLX_HYPERPIPE_PIPE_NAME_LENGTH_SGIX];
data/openstructure-2.2.0/modules/gfx/src/bitmap_io.cc:41:10: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if((fp=fopen(filename.c_str(),"wb"))==NULL) {
data/openstructure-2.2.0/modules/gfx/src/bitmap_io.cc:119:10: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if((fp=fopen(filename.c_str(),"rb"))==NULL) {
data/openstructure-2.2.0/modules/gfx/src/gost_exporter.cc:63:9: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file_=fopen(fname.c_str(),"w");
data/openstructure-2.2.0/modules/gfx/src/povray.cc:212:125: [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 PovState::write_cyl(const geom::Vec3& p1, const geom::Vec3& p2, float r, const Color& c, const std::string& name, bool open)
data/openstructure-2.2.0/modules/gfx/src/povray.cc:215:6: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if(open) inc_ << " open";
data/openstructure-2.2.0/modules/gui/src/file_viewer.cc:42:12: [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).
if (file.open(QFile::ReadOnly | QFile::Text))
data/openstructure-2.2.0/modules/gui/src/python_shell/python_interpreter.cc:95:15: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (!script.open(QIODevice::ReadOnly | QIODevice::Text)){
data/openstructure-2.2.0/modules/info/src/info_impl.cc:149:7: [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).
out.open(QIODevice::WriteOnly);
data/openstructure-2.2.0/modules/io/src/img/map_io_dm3_handler.cc:358:9: [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).
uchar open;
data/openstructure-2.2.0/modules/io/src/img/map_io_dm3_handler.cc:359:14: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file_read(&open,sizeof(uchar),1,fp);
data/openstructure-2.2.0/modules/io/src/img/map_io_dm3_handler.cc:362:33: [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).
<< static_cast<int>(open));
data/openstructure-2.2.0/modules/io/src/img/map_io_dm3_handler.cc:418:3: [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 dummy[4];
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:376:3: [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 label[800];
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:437:3: [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 dummy[116];
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:448:3: [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 dummy[116];
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:504:5: [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 machst[4];
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:562:3: [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 dummy[48];
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:596:3: [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 dummy[48];
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:604:3: [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 machst[4]={0x44,0x41,0x00,0x00};// little endian
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:1031:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char header_content[256];
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:1032:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&header_content[0],&header_,256*sizeof(char));
data/openstructure-2.2.0/modules/io/src/img/map_io_spi_handler.cc:160:3: [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 szIDat[12]; // array sized eleven, date of creation (0 if absent)
data/openstructure-2.2.0/modules/io/src/img/map_io_spi_handler.cc:161:3: [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 szITim[8]; // array sized eight, time of creation (0 if absent)
data/openstructure-2.2.0/modules/io/src/img/map_io_spi_handler.cc:162:3: [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 szITit[160]; // array dimensioned 160, title
data/openstructure-2.2.0/modules/io/src/img/tiff_util.cc:35:10: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char message[1024];
data/openstructure-2.2.0/modules/io/src/io_manager.cc:187:14: [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.
unsigned char header[256];
data/openstructure-2.2.0/modules/io/src/io_manager.cc:217:14: [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.
unsigned char header[256];
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:56:3: [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 hdrr[4];
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:75:3: [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 dummy[4];
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:172:3: [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 dummy[4];
data/openstructure-2.2.0/modules/io/src/mol/entity_io_mae_handler.cc:222:17: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
irnum=atoi(p0);
data/openstructure-2.2.0/modules/io/src/mol/entity_io_mae_handler.cc:247:17: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
irnum=atoi(p0);
data/openstructure-2.2.0/modules/io/src/seq/hhm_io_handler.cc:183:3: [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 olcs[20];
data/openstructure-2.2.0/modules/io/src/seq/pssm_io_handler.cc:100:3: [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 olcs[20];
data/openstructure-2.2.0/modules/mol/alg/src/lddt.cc:117:3: [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 result[ 1024 ];
data/openstructure-2.2.0/modules/mol/base/src/impl/query_impl.cc:516:27: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
value=ParamType(atoi(value_string.c_str()));
data/openstructure-2.2.0/modules/mol/base/src/impl/query_impl.cc:688:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
ParamType rnum_val(atoi(query_string_.substr(rnum.GetValueRange().Loc,
data/openstructure-2.2.0/modules/mol/mm/src/ff_reader.cc:298:8: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file.open((file_path.string()).c_str());
data/openstructure-2.2.0/modules/mol/mm/src/observer.cc:62:11: [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).
stream_.open(dcd_filename_.c_str(), std::ios::binary);
data/openstructure-2.2.0/modules/mol/mm/src/topology.cc:1059:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&atom_masses_[old_num_particles],&other->atom_masses_[0],other->GetNumParticles() * sizeof(Real));
data/openstructure-2.2.0/modules/mol/mm/src/topology.cc:1064:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&charges_[old_num_particles],&other->charges_[0],other->GetNumParticles() * sizeof(Real));
data/openstructure-2.2.0/modules/mol/mm/src/topology.cc:1069:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&sigmas_[old_num_particles],&other->sigmas_[0],other->GetNumParticles() * sizeof(Real));
data/openstructure-2.2.0/modules/mol/mm/src/topology.cc:1074:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&epsilons_[old_num_particles],&other->epsilons_[0],other->GetNumParticles() * sizeof(Real));
data/openstructure-2.2.0/modules/mol/mm/src/topology.cc:1079:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&gbsa_radii_[old_num_particles],&other->gbsa_radii_[0],other->GetNumParticles() * sizeof(Real));
data/openstructure-2.2.0/modules/mol/mm/src/topology.cc:1084:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&obc_scaling_[old_num_particles],&other->obc_scaling_[0],other->GetNumParticles() * sizeof(Real));
data/openstructure-2.2.0/modules/seq/alg/src/subst_weight_matrix.cc:134:3: [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 chars[23] = {'A','B','C','D','E','F','G','H','I','K','L','M','N','P','Q',
data/openstructure-2.2.0/tools/molck/main.cc:102:3: [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 result[ 1024 ];
data/openstructure-2.2.0/modules/base/pymod/wrap_base.cc:79:41: [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).
new (storage) ost::StringRef(value, strlen(value));
data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.h:209:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf,seqy+j,gaplen);
data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.h:220:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf,seqx+i,gaplen);
data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.h:231:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf,seqy,j);
data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.h:240:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf,seqx,i);
data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.h:287:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf,seqx+i,xlen-i);
data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.h:291:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf,seqy+j,ylen-j);
data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.h:312:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf,seqy+j,gaplen);
data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.h:323:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf,seqx+i,gaplen);
data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.h:340:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf+j,seqx,i);
data/openstructure-2.2.0/modules/bindings/src/tmalign/NWalign.h:344:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf,seqy,j);
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.h:1696:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(fname_matrix))
data/openstructure-2.2.0/modules/bindings/src/tmalign/TMalign.h:1698:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(fname_super))
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:194:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(char_type* s, std::streamsize n);
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:1268:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
switch (::read(ck_exec[RD], &error_, sizeof(error_)))
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:1903:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
rc = read(rbuf + pbsz, bufsz - pbsz);
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:1915:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
rc = read(rbuf + pbsz, bufsz - pbsz);
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:1963:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
basic_pstreambuf<C,T>::read(char_type* s, std::streamsize n)
data/openstructure-2.2.0/modules/bindings/src/tmalign/pstream.h:1968:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
nread = ::read(rpipe(), s, n * sizeof(char_type));
data/openstructure-2.2.0/modules/bindings/src/tmalign/xyz_sfetch.cpp:118:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
fin.read(buf,end_pos-start_pos);
data/openstructure-2.2.0/modules/conop/src/compound_lib.cc:135:33: [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).
strlen(INSERT_CHEMLIB_INFO_STATEMENT), &stmt, NULL);
data/openstructure-2.2.0/modules/conop/src/compound_lib.cc:145:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(date_str.c_str()), NULL);
data/openstructure-2.2.0/modules/conop/src/compound_lib.cc:148:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(ost_version), NULL);
data/openstructure-2.2.0/modules/conop/src/compound_lib.cc:178:52: [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).
Date date = Date::FromString(StringRef(strr, strlen(strr)));
data/openstructure-2.2.0/modules/conop/src/compound_lib.cc:226:33: [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).
strlen(INSERT_COMPOUND_STATEMENT), &stmt, NULL);
data/openstructure-2.2.0/modules/conop/src/compound_lib.cc:277:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(INSERT_ATOM_STATEMENT), &stmt, NULL);
data/openstructure-2.2.0/modules/conop/src/compound_lib.cc:300:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(INSERT_BOND_STATEMENT), &stmt, NULL);
data/openstructure-2.2.0/modules/conop/src/compound_lib.cc:349:54: [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).
retval=sqlite3_prepare_v2(lib->db_->ptr, *cmd, strlen(*cmd), &stmt, NULL);
data/openstructure-2.2.0/modules/db/src/linear_indexer.cc:29:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(reinterpret_cast<char*>(&num), sizeof(uint16_t));
data/openstructure-2.2.0/modules/db/src/linear_indexer.cc:32:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(reinterpret_cast<char*>(&data_start), sizeof(uint64_t));
data/openstructure-2.2.0/modules/db/src/linear_indexer.cc:36:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(reinterpret_cast<char*>(&size), sizeof(uint16_t));
data/openstructure-2.2.0/modules/db/src/linear_indexer.cc:38:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(&chain_names[i][0], size);
data/openstructure-2.2.0/modules/db/src/linear_indexer.cc:40:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(reinterpret_cast<char*>(&chain_length), sizeof(uint32_t));
data/openstructure-2.2.0/modules/db/src/linear_indexer.cc:69:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(reinterpret_cast<char*>(&loaded_db->current_num_residues_),
data/openstructure-2.2.0/modules/db/src/linear_indexer.cc:73:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(reinterpret_cast<char*>(&num_assemblies), sizeof(uint32_t));
data/openstructure-2.2.0/modules/db/src/linear_indexer.cc:82:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(reinterpret_cast<char*>(&size), sizeof(uint16_t));
data/openstructure-2.2.0/modules/db/src/linear_indexer.cc:84:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(&assembly_name[0], size);
data/openstructure-2.2.0/modules/db/src/linear_indexer.cc:86:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(reinterpret_cast<char*>(&idx), sizeof(uint32_t));
data/openstructure-2.2.0/modules/gfx/src/GL/glew.c:100:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
symbolName = malloc(strlen((const char*)name) + 2);
data/openstructure-2.2.0/modules/gfx/src/GL/glxew.h:296:97: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
typedef Bool ( * PFNGLXMAKECONTEXTCURRENTPROC) (Display *display, GLXDrawable draw, GLXDrawable read, GLXContext ctx);
data/openstructure-2.2.0/modules/gfx/src/GL/glxew.h:1183:93: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
typedef Bool ( * PFNGLXMAKECURRENTREADSGIPROC) (Display* dpy, GLXDrawable draw, GLXDrawable read, GLXContext ctx);
data/openstructure-2.2.0/modules/gui/src/input/spnav_input.cc:47:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120). Risk is low because the source is a
constant string.
strncpy(addr.sun_path, "/var/run/spnav.sock", sizeof(addr.sun_path));
data/openstructure-2.2.0/modules/img/base/src/extent.cc:163:14: [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 Extent::equal(const Extent& b) const
data/openstructure-2.2.0/modules/img/base/src/image_handle.cc:466:10: [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.
return equal(ih);
data/openstructure-2.2.0/modules/img/base/src/image_handle.cc:471:11: [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 !equal(ih);
data/openstructure-2.2.0/modules/img/base/src/image_handle.cc:474:19: [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.
bool ImageHandle::equal(const ImageHandle& ih) const
data/openstructure-2.2.0/modules/img/base/src/image_handle.cc:810:10: [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.
return equal(ih);
data/openstructure-2.2.0/modules/img/base/src/image_handle.cc:815:10: [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.
return equal(ih);
data/openstructure-2.2.0/modules/img/base/src/image_handle.cc:820:11: [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 !equal(ih);
data/openstructure-2.2.0/modules/img/base/src/image_handle.cc:825:11: [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 !equal(ih);
data/openstructure-2.2.0/modules/img/base/src/image_handle.cc:829:24: [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 ConstImageHandle::equal(const ConstImageHandle& h) const
data/openstructure-2.2.0/modules/img/base/src/image_handle.cc:834:24: [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 ConstImageHandle::equal(const ImageHandle& h) const
data/openstructure-2.2.0/modules/img/base/src/image_state/index.cc:35:13: [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 Index::equal(const Index& i) const {
data/openstructure-2.2.0/modules/img/base/src/image_state/index.cc:166:13: [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 i1.equal(i2);
data/openstructure-2.2.0/modules/img/base/src/image_state/index.cc:170:14: [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 !i1.equal(i2);
data/openstructure-2.2.0/modules/img/base/src/physical_units.cc:39:29: [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.
BOOST_STATIC_ASSERT((mpl::equal<Dimensions,D2>::type::value));
data/openstructure-2.2.0/modules/img/base/src/size.cc:124:10: [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.
return equal(s);
data/openstructure-2.2.0/modules/img/base/src/size.cc:129:11: [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 !equal(s);
data/openstructure-2.2.0/modules/img/base/src/size.cc:149:12: [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 Size::equal(const Size& s) const
data/openstructure-2.2.0/modules/io/src/img/map_io_dm3_handler.cc:204:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
stream.read(reinterpret_cast<char*>(ptr),size*count);
data/openstructure-2.2.0/modules/io/src/img/map_io_ipl_handler.cc:170:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
timestr[strlen(timestr)-1] = '\0';
data/openstructure-2.2.0/modules/io/src/img/map_io_ipl_handler.cc:259:6: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&empty[0],fillsize);
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:167:20: [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).
len = std::strlen(ptr);
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:351:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(label,800);
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:450:6: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(dummy,116);
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:461:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(dummy,1);
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:519:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
f.read(machst,4);
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:569:6: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(dummy,48);
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:571:6: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(dummy,8);
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:582:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(dummy,1);
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:637:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
f.read(&buffer[0],header.nr*header.nc);
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:986:6: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(reinterpret_cast<char*>(&header_),256);
data/openstructure-2.2.0/modules/io/src/img/map_io_mrc_handler.cc:1014:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
loc.read(reinterpret_cast<char*>(&header_),256);
data/openstructure-2.2.0/modules/io/src/img/map_io_nanoscope_handler.cc:207:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ff.read(&bdata[0],bdata.size());
data/openstructure-2.2.0/modules/io/src/img/map_io_png_handler.cc:77:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
((std::istream*)a)->read((char*)data, length);
data/openstructure-2.2.0/modules/io/src/img/map_io_spi_handler.cc:297:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
f.read(header.fEmpty1,12);
data/openstructure-2.2.0/modules/io/src/img/map_io_spi_handler.cc:298:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
f.read(header.fRes,27);
data/openstructure-2.2.0/modules/io/src/img/map_io_spi_handler.cc:299:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
f.read(header.fEmpty2,135);
data/openstructure-2.2.0/modules/io/src/img/map_io_spi_handler.cc:300:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
f.read(header.szIDat,12);
data/openstructure-2.2.0/modules/io/src/img/map_io_spi_handler.cc:301:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
f.read(header.szITim,8);
data/openstructure-2.2.0/modules/io/src/img/map_io_spi_handler.cc:302:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
f.read(header.szITit,160);
data/openstructure-2.2.0/modules/io/src/img/tiff_util.cc:48:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
file->read(data,tsize);
data/openstructure-2.2.0/modules/io/src/io_manager.cc:193:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
infile.read(reinterpret_cast<char*>(&header),256);
data/openstructure-2.2.0/modules/io/src/io_manager.cc:218:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
stream.read(reinterpret_cast<char*>(&header),256);
data/openstructure-2.2.0/modules/io/src/io_utils.cc:27:15: [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 std::mismatch( probe.rbegin(), probe.rend(), target.rbegin() ).first == probe.rend();
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:80:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(gap_flag) istream.read(dummy,sizeof(dummy));
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:81:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
istream.read(header.hdrr,sizeof(char)*4);
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:86:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
istream.read(reinterpret_cast<char*>(header.icntrl),sizeof(int)*20);
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:121:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(gap_flag) istream.read(dummy,sizeof(dummy));
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:125:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
istream.read(reinterpret_cast<char*>(&header.ntitle),sizeof(int));
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:130:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(gap_flag) istream.read(dummy,sizeof(dummy));
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:134:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
istream.read(&title[0],sizeof(char)*header.ntitle);
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:138:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(gap_flag) istream.read(dummy,sizeof(dummy));
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:139:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
istream.read(reinterpret_cast<char*>(&header.t_atom_count),sizeof(int));
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:141:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(gap_flag) istream.read(dummy,sizeof(dummy));
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:183:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
istream.read(dummy,sizeof(dummy));
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:185:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
istream.read(reinterpret_cast<char*>(tmp),sizeof(double)*6);
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:193:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
istream.read(dummy,sizeof(dummy));
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:197:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(gap_flag) istream.read(dummy,sizeof(dummy));
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:198:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
istream.read(reinterpret_cast<char*>(&xlist[0]),sizeof(float)*xlist.size());
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:200:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(gap_flag) istream.read(dummy,sizeof(dummy));
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:211:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(gap_flag) istream.read(dummy,sizeof(dummy));
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:212:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
istream.read(reinterpret_cast<char*>(&xlist[0]),sizeof(float)*xlist.size());
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:214:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(gap_flag) istream.read(dummy,sizeof(dummy));
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:225:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(gap_flag) istream.read(dummy,sizeof(dummy));
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:226:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
istream.read(reinterpret_cast<char*>(&xlist[0]),sizeof(float)*xlist.size());
data/openstructure-2.2.0/modules/io/src/mol/dcd_io.cc:228:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(gap_flag) istream.read(dummy,sizeof(dummy));
data/openstructure-2.2.0/modules/io/src/mol/entity_io_mae_handler.cc:112:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(xline.get(),line.c_str(),511);
data/openstructure-2.2.0/modules/io/tests/test_io_sequence_profile.cc:285:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&str[0], str.size());
data/openstructure-2.2.0/modules/io/tests/test_io_sequence_profile.cc:310:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&str[0], str.size());
data/openstructure-2.2.0/modules/io/tests/test_star_parser.cc:250:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
StringRef r1(line1, strlen(line1));
data/openstructure-2.2.0/modules/io/tests/test_star_parser.cc:260:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
StringRef r2(line2, strlen(line2));
data/openstructure-2.2.0/modules/io/tests/test_star_parser.cc:271:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
StringRef r3(line3, strlen(line3));
data/openstructure-2.2.0/modules/mol/alg/src/similarity_matrix.cc:24:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
istream.read(reinterpret_cast<char*>(&the_size), sizeof(size_t));
data/openstructure-2.2.0/modules/mol/alg/src/similarity_matrix.cc:26:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
istream.read(reinterpret_cast<char*>(&sim.Data().front()),
data/openstructure-2.2.0/modules/seq/alg/src/hmm_pseudo_counts.cc:96:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(reinterpret_cast<char*>(&magic_number), sizeof(uint32_t));
data/openstructure-2.2.0/modules/seq/alg/src/hmm_pseudo_counts.cc:106:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(reinterpret_cast<char*>(&version), sizeof(uint8_t));
data/openstructure-2.2.0/modules/seq/alg/src/hmm_pseudo_counts.cc:115:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(reinterpret_cast<char*>(&length), sizeof(uint32_t));
data/openstructure-2.2.0/modules/seq/alg/src/hmm_pseudo_counts.cc:118:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(reinterpret_cast<char*>(&n_profiles),sizeof(uint32_t));
data/openstructure-2.2.0/modules/seq/alg/src/hmm_pseudo_counts.cc:121:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(reinterpret_cast<char*>(&data_size), sizeof(uint32_t));
data/openstructure-2.2.0/modules/seq/alg/src/hmm_pseudo_counts.cc:124:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(reinterpret_cast<char*>(&data[0]), data_size*sizeof(Real));
data/openstructure-2.2.0/modules/seq/base/src/profile_handle.cc:230:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(reinterpret_cast<char*>(&magic_number), sizeof(uint32_t));
data/openstructure-2.2.0/modules/seq/base/src/profile_handle.cc:241:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(reinterpret_cast<char*>(&version), sizeof(uint8_t));
data/openstructure-2.2.0/modules/seq/base/src/profile_handle.cc:251:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(reinterpret_cast<char*>(&total_size),4);
data/openstructure-2.2.0/modules/seq/base/src/profile_handle.cc:256:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(&string_size,1);
data/openstructure-2.2.0/modules/seq/base/src/profile_handle.cc:258:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in_stream.read(&name[0],string_size);
ANALYSIS SUMMARY:
Hits = 297
Lines analyzed = 191254 in approximately 5.12 seconds (37330 lines/second)
Physical Source Lines of Code (SLOC) = 146559
Hits@level = [0] 48 [1] 126 [2] 136 [3] 12 [4] 21 [5] 2
Hits@level+ = [0+] 345 [1+] 297 [2+] 171 [3+] 35 [4+] 23 [5+] 2
Hits/KSLOC@level+ = [0+] 2.354 [1+] 2.02649 [2+] 1.16677 [3+] 0.238812 [4+] 0.156933 [5+] 0.0136464
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.