Package: garlic Version: 1.6-1.1 Usertags: goto-cc During a rebuild of all Debian packages in a clean sid chroot (using cowbuilder and pbuilder) the build failed with the following error. Please note that we use our research compiler tool-chain (using tools from the cbmc package), which permits extended reporting on type inconsistencies at link time.
[...] gcc -o garlic -L/usr/X11R6/lib garlic.o print_usage.o print_help.o print_version.o register.o alloc_gui.o alloc_config.o alloc_mol_complex.o free_memory.o display_init.o disp_color_cap.o color_shifts.o calc_params.o errmsg.o warnmsg.o openfile_r.o read_config.o open_config_file.o extract_int.o ex2ints.o extract_double.o ex2doubles.o extract_phrase.o extract_index.o ex_rot_steps.o ex_trans_steps.o ex_slab_steps.o ex_fading_steps.o extract_args.o parse_options.o parse_color.o load_font.o prepare_cursor.o print_config.o create_windows.o make_pixmap.o make_pixmap2.o rgbs_from_xcolor.o pixel_from_rgbs.o size_hints.o wmhints.o select_events.o hide_control.o load_complex.o read_file.o fileformat.o is_pdb.o read_pdb.o init_header.o pdb_atom.o extract_field.o copypur.o realloc_pdb.o headerline.o geomcenter.o init_slab.o init_fading.o flip_vector.o translate_complex.o extent.o stereo_data.o strong_bonds.o pseudo_bonds.o check_dist.o add_bond.o event_loop.o alloc_nearest.o init_nearest.o main_refresh.o key_press.o rotation_angle.o rotate.o translation_shift.o translate.o slab_shift.o move_back_slab.o move_front_slab.o fading_shift.o move_back_fading.o move_front_fading.o key_release.o refresh_pixmap.o slab.o no_slab.o planar_slab.o sphere_slab.o half_sphere_slab.o cylin_slab.o half_cylin_slab.o project_atoms.o fading.o prepare_color.o no_fading.o planar_fading.o sphere_fading.o half_sphere_fading.o cylin_fading.o half_cylin_fading.o reset_pos_flag.o atoms_style1.o atoms_style2.o atoms_style3.o atoms_style4.o atoms_style5.o atoms_style6.o atoms_style7.o bonds_style1.o bond_style1_quad1.o bond_style1_quad2.o bond_style1_quad3.o bond_style1_quad4.o bonds_style2.o bond_style2_quad1.o bond_style2_quad2.o bond_style2_quad3.o bond_style2_quad4.o bonds_style3.o interpolate_color.o bond_style3_quad1.o bond_style3_quad2.o bond_style3_quad3.o bond_style3_quad4.o bonds_style4.o add_two_colors.o bond_style4_quad1.o bond_style4_quad2.o bond_style4_quad3.o bond_style4_quad4.o bonds_style5.o add_three_colors.o bond_style5_quad1.o bond_style5_quad2.o bond_style5_quad3.o bond_style5_quad4.o draw_system.o motion_notify.o assign_hyphob.o control_refresh.o print_cursor_names.o main_resize.o init_runtime.o add_char.o input_refresh.o eat_left_char.o eat_right_char.o execute_command1.o execute_command2.o truncate_comm.o create_log_file.o load.o catch.o discard.o select.o full_select.o include.o chains.o residue_ranges.o extract_token.o extract_serials.o residue_names.o atom_names.o exclude.o skip_keyword.o apply_selection.o show.o hide.o color_schemes.o init_colors.o color.o special_select.o select_hetero.o select_element.o select_atoms.o quick_select.o replace_command.o atoms.o bonds.o execute_script.o comm_rotate.o comm_translate.o comm_slab.o comm_fading.o log.o prepare_backbone.o background.o text_background.o text_foreground.o change_slab.o change_fading.o full_colors.o is_old.o font.o cpk.o zebra.o chain.o color_hyphob.o mix_colors.o comm_backbone.o hide_no_refresh.o show_no_refresh.o backbone.o hybonds.o generate_hybonds.o hybond_style.o show_backbone.o hide_backbone.o pdb_id.o generate_plane.o stereo.o mono.o position.o copy_doubles.o title.o free_runtime.o draw_titles.o foreground.o prepare_oc.o select_complement.o labels.o draw_labels.o assign_radii.o spacefill.o spacefill_color.o draw_balls.o center.o save.o write_line.o big_spheres.o tag.o draw_tags.o tag_position.o button_press.o control_click.o identify_button.o init_buttons.o write_hints.o extract_sequence.o count_residues.o sequence.o parse_sequence.o sequence_from.o load_sequence.o select_sequence.o compare_sequences.o dihedral_angles.o extract_ncaco.o phi_from_cncac.o psi_from_ncaco.o vector_product.o absolute_value.o scalar_product.o omega_from_cacnca.o select_cis_trans.o ramachandran.o draw_ramachandran.o rama_frame.o rama_mouse.o read_fasta.o save_sequence.o wheel.o wheel_top_view.o wheel_bottom_view.o hydrophobicity.o weight_colors.o angle.o radius.o select_sphere.o disulfide_bonds.o venn.o draw_venn.o spacefill2.o sp2_color.o save_seq_w_numbers.o ssb.o select_alternate.o select_model.o color_model.o window.o plot.o draw_plots.o weighted_hydrophobicity.o average_hydrophobicity.o init_hyphob.o plot_mouse.o project_planes.o draw_planes.o plane_extent.o rotate_plane.o translate_plane.o comm_move.o plane.o select_above.o select_below.o big2.o scale.o pattern.o dock.o align_normal.o align_complexes.o docking_window.o docking_resize.o docking_refresh.o docking_project.o list_exposed_polar.o is_polar.o representative_atoms.o exclude_distant.o draw_bottom.o draw_top.o copy_sequence.o compare.o draw_comparison.o neighborhood.o draw_balls2.o comparison_mouse.o structure.o parse_sec_structure.o copy_sec_structure.o load_sec_structure.o save_sec_structure.o alloc_sec_structure.o sec_structure_from.o create.o open_template_file.o read_template_file.o ex_template_residues.o count_template_res.o create_structure.o required_atoms.o copy_template_atoms.o fix_chain.o reset_phi.o extract_hncac.o phi_from_hncac.o rotate_atom.o parallel_part.o reset_psi.o build_chain.o extract_ncac.o translate_range.o rotate_range.o apply_structure.o generate_phi_psi.o extract_nca.o extract_c.o replace.o extract_n.o refresh_backbone.o edit.o draw_edit_symbol.o draw_squid.o draw_seahorse.o are_atoms_bound.o bond_partners.o edit_phi.o edit_psi.o extract_cac.o small_ramachandran.o edit_omega.o small_omega.o extract_h.o extract_o.o psi_from_ncacn.o is_standard.o extract_four_atoms.o chi1_from_ncacbcg.o chi1_from_ncacbsg.o chi1_from_ncacbcg1.o chi1_from_ncacbog.o chi1_from_ncacbog1.o chi2_from_cacbcgcd.o chi2_from_cacbcgod1.o chi2_from_cacbcgnd1.o chi2_from_cacbcg1cd.o chi2_from_cacbcgcd1.o chi2_from_cacbcgsd.o chi3_from_cbcgcdne.o chi3_from_cbcgcdoe1.o chi3_from_cbcgcdce.o chi3_from_cbcgsdce.o chi4_from_cgcdnecz.o chi4_from_cgcdcenz.o chi5_from_cdnecznh1.o is_part_of_ring.o edit_bond.o edit_chi2.o extract_cacb.o edit_chi1.o extract_cbxg.o resize_complex.o membrane.o inform_user.o alpha_membrane.o extract_ca.o extract_vector.o alpha_membrane_center.o init_membrane.o alpha_normal.o project_membranes.o draw_membranes.o rotate_membrane.o translate_membrane.o select_triplet.o set.o set_phi.o set_psi.o set_omega.o set_chi1.o set_chi2.o set_chi3.o extract_cgxd.o set_chi4.o extract_cdxe.o set_chi5.o extract_necz.o pick_bond.o nice_bonds.o covalent.o covalent2.o half_nice_bond.o probe.o small_atoms.o small_atoms2.o draw_sticks.o half_stick.o command_refresh.o acceptor_dipole.o donor_dipole.o sticks.o balls.o blur.o blur_main_window.o group.o beta_membrane.o extract_cg.o select_tm.o parse_pattern.o select_pattern.o hyphob_function1.o hyphob_function2.o hyphob_function3.o hyphob_function4.o hyphob_function5.o hyphob_function6.o hyphob_function7.o color_size.o command_dump.o is_aromatic.o select_2c3.o select_2cz3.o select_2nz3.o select_3c4.o select_3cz4.o select_3nz4.o select_3c5.o select_3cz5.o select_3nz5.o select_3p5.o select_4c5.o select_4cz5.o select_4nz5.o select_3c6.o select_3cz6.o select_3nz6.o select_4c6.o select_4cz6.o select_4nz6.o select_4p6.o select_5c6.o select_5cz6.o select_5nz6.o select_4c7.o select_4cz7.o select_4nz7.o select_5c7.o select_5cz7.o select_5nz7.o select_5p7.o select_6p7.o select_4c9.o select_4cz9.o select_4nz9.o select_5c9.o select_5cz9.o select_5nz9.o color_weighted.o -lX11 -lm error: conflicting function declarations "BlurMainWindow_" old definition in module main_refresh file main_refresh.c line 174 signed int (RuntimeS *, GUIS *, NearestAtomS *, unsigned long) new definition in module blur_main_window file blur_main_window.c line 47 unsigned long int (RuntimeS *runtimeSP, GUIS *guiSP, NearestAtomS *nearest_atomSP, unsigned long pixelsN) Makefile:159: recipe for target 'garlic' failed make[1]: *** [garlic] Error 64 make[1]: Leaving directory '/srv/jenkins-slave/workspace/sid-goto-cc-garlic/garlic-1.6' debian/rules:11: recipe for target 'build-arch' failed make: *** [build-arch] Error 2 For any platform with sizeof(int)<sizeof(long), the return value will either be truncated to fit into an int, or be missing all the lower bytes (on big endian) even if the value would fit the size of an int. Best, Michael
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