Opened 4 years ago

Closed 3 years ago

#61720 closed defect (fixed)

gwyddion: Undefined symbols for architecture x86_64

Reported by: btywoniuk (Bart) Owned by: rowue (Rolf Würdemann)
Priority: Normal Milestone:
Component: ports Version: 2.6.4
Keywords: bigsur Cc: yeti@…, GTTS2020, nirjharize, ryandesign (Ryan Carsten Schmidt)
Port: gwyddion

Description

When installing gwyddion I'm getting: 

Error: Failed to build gwyddion: command execution failed
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_gwyddion/gwyddion/main.log for details.
Error: Follow https://guide.macports.org/#project.tickets to report a bug.
Error: Processing of port gwyddion failed

When I checked logfile basically, it comes down to "Undefined symbols for architecture x86_64" in libgwyprocess2.la

Logfile details: 

:info:build warning: unknown warning option '-Wno-stringop-truncation'; did you mean '-Wno-string-conversion'? [-Wunknown-warning-option]
:info:build 2 warnings generated.
:info:build 2 warnings generated.
:info:build 2 warnings generated.
:info:build   CCLD     libgwyprocess2.la
:info:build Undefined symbols for architecture x86_64:
:info:build   "_gwy_canonicalize_angle", referenced from:
:info:build       _gwy_data_field_rotate in datafield.o
:info:build       _gwy_data_field_new_rotated in datafield.o
:info:build       _gwy_data_field_grains_get_quantities in grains-values.o
:info:build       _refine_diameter_direction in grains-values.o
:info:build       _step1_estimate in gwyshapefitpreset.o
:info:build       _step2_estimate in gwyshapefitpreset.o
:info:build   "_gwy_expr_compile", referenced from:
:info:build       _gwy_grain_value_resolve_expression in gwygrainvalue.o
:info:build   "_gwy_expr_error_quark", referenced from:
:info:build       _gwy_grain_value_set_expression in gwygrainvalue.o
:info:build   "_gwy_expr_free", referenced from:
:info:build       _gwy_grain_value_resolve_expression in gwygrainvalue.o
:info:build       _gwy_grain_values_calculate in gwygrainvalue.o
:info:build   "_gwy_expr_new", referenced from:
:info:build       _gwy_grain_value_resolve_expression in gwygrainvalue.o
:info:build       _gwy_grain_values_calculate in gwygrainvalue.o
:info:build   "_gwy_expr_resolve_variables", referenced from:
:info:build       _gwy_grain_value_resolve_expression in gwygrainvalue.o
:info:build   "_gwy_expr_vector_execute", referenced from:
:info:build       _gwy_grain_values_calculate in gwygrainvalue.o
:info:build   "_gwy_get_user_dir", referenced from:
:info:build       _gwy_caldata_save_data in gwycaldata.o
:info:build       _gwy_calibration_use in gwycalibration.o
:info:build   "_gwy_guint_sort", referenced from:
:info:build       _gwy_data_field_area_rle_analyse in filters-minmax.o
:info:build       _gwy_triangulation_triangulate_iterative in triangulation.o
:info:build   "_gwy_inventory_find", referenced from:
:info:build       _gwy_grain_values_get_builtin_grain_value in gwygrainvalue.o
:info:build       _ensure_builtin_names in gwygrainvalue.o
:info:build   "_gwy_inventory_forget_order", referenced from:
:info:build       _gwy_cdline_class_intern_init in cdline.o
:info:build       _gwy_shape_fit_preset_class_intern_init in gwyshapefitpreset.o
:info:build   "_gwy_inventory_get_item", referenced from:
:info:build       _gwy_grain_values_get_grain_value in gwygrainvalue.o
:info:build   "_gwy_inventory_get_item_or_default", referenced from:
:info:build       _gwy_calibrations_get_calibration in gwycalibration.o
:info:build   "_gwy_inventory_get_n_items", referenced from:
:info:build       _gwy_grain_values_get_grain_value_by_symbol in gwygrainvalue.o
:info:build   "_gwy_inventory_get_nth_item", referenced from:
:info:build       _gwy_grain_values_get_grain_value_by_symbol in gwygrainvalue.o
:info:build   "_gwy_inventory_insert_item", referenced from:
:info:build       __gwy_cdline_class_setup_presets in cdline.o
:info:build       __gwy_grain_value_class_setup_presets in gwygrainvalue.o
:info:build       __gwy_shape_fit_preset_class_setup_presets in gwyshapefitpreset.o
:info:build   "_gwy_inventory_new", referenced from:
:info:build       _gwy_cdline_class_intern_init in cdline.o
:info:build       _gwy_calibration_class_intern_init in gwycalibration.o
:info:build       _gwy_grain_value_class_intern_init in gwygrainvalue.o
:info:build       _gwy_shape_fit_preset_class_intern_init in gwyshapefitpreset.o
:info:build   "_gwy_inventory_restore_order", referenced from:
:info:build       __gwy_cdline_class_setup_presets in cdline.o
:info:build       __gwy_shape_fit_preset_class_setup_presets in gwyshapefitpreset.o
:info:build   "_gwy_inventory_set_default_item_name", referenced from:
:info:build       __gwy_shape_fit_preset_class_setup_presets in gwyshapefitpreset.o
:info:build   "_gwy_math_choleski_decompose", referenced from:
:info:build       _gwy_data_line_part_fit_polynom in dataline.o
:info:build       _gwy_data_field_grains_get_quantities in grains-values.o
:info:build       _plane_estimate in gwyshapefitpreset.o
:info:build       _sphere_estimate in gwyshapefitpreset.o
:info:build       _gwy_data_field_area_fit_polynom in level.o
:info:build       _gwy_data_field_area_fit_legendre in level.o
:info:build       _gwy_data_field_area_fit_poly_max in level.o
:info:build       ...
:info:build   "_gwy_math_choleski_solve", referenced from:
:info:build       _gwy_data_line_part_fit_polynom in dataline.o
:info:build       _gwy_data_field_grains_get_quantities in grains-values.o
:info:build       _plane_estimate in gwyshapefitpreset.o
:info:build       _sphere_estimate in gwyshapefitpreset.o
:info:build       _gwy_data_field_area_fit_polynom in level.o
:info:build       _gwy_data_field_area_fit_legendre in level.o
:info:build       _gwy_data_field_area_fit_poly_max in level.o
:info:build       ...
:info:build   "_gwy_math_curvature", referenced from:
:info:build       _gwy_data_field_grains_get_quantities in grains-values.o
:info:build   "_gwy_math_find_minimum_1d", referenced from:
:info:build       _gwy_data_field_find_regularization_sigma_for_psf in filters-convdeconv.o
:info:build       _gwy_data_field_find_regularization_sigma_leastsq in filters-convdeconv.o
:info:build       _gwy_data_field_mfm_find_shift_z in mfm.o
:info:build   "_gwy_math_fit_polynom", referenced from:
:info:build       _gwy_data_field_fit_lines in level.o
:info:build   "_gwy_math_histogram", referenced from:
:info:build       _gwy_data_line_distribution in linestats.o
:info:build       _gwy_data_line_dh in linestats.o
:info:build       _compute_autorange in stats.o
:info:build       _gwy_data_field_area_dh in stats.o
:info:build       _gwy_data_field_area_da_mask in stats.o
:info:build   "_gwy_math_kth_rank", referenced from:
:info:build       _gwy_data_field_area_filter_kth_rank in filters-minmax.o
:info:build   "_gwy_math_kth_ranks", referenced from:
:info:build       _gwy_data_field_grains_get_quantities in grains-values.o
:info:build   "_gwy_math_median", referenced from:
:info:build       _trimmed_mean_or_median in correct.o
:info:build       _gwy_data_field_area_filter_median in filters-minmax.o
:info:build       _gwy_data_field_grains_get_quantities in grains-values.o
:info:build       _gwy_data_line_part_get_median in linestats.o
:info:build       _gwy_data_field_area_get_median_mask in stats.o
:info:build       _gwy_data_field_get_median in stats.o
:info:build       _gwy_data_line_get_median_destructive in stats.o
:info:build       ...
:info:build   "_gwy_math_median_uncertainty", referenced from:
:info:build       _gwy_data_field_area_get_median_uncertainty_mask in stats_uncertainty.o
:info:build       _gwy_data_field_get_median_uncertainty in stats_uncertainty.o
:info:build   "_gwy_math_nlfit_derive", referenced from:
:info:build       _cd_circle_down in cdline.o
:info:build       _cd_circle_up in cdline.o
:info:build   "_gwy_math_nlfit_fit_full", referenced from:
:info:build       _cd_circle_down in cdline.o
:info:build       _cd_circle_up in cdline.o
:info:build   "_gwy_math_nlfit_fit_idx_full", referenced from:
:info:build       _gwy_shape_fit_preset_fit in gwyshapefitpreset.o
:info:build       _gwy_shape_fit_preset_quick_fit in gwyshapefitpreset.o
:info:build   "_gwy_math_nlfit_get_sigma", referenced from:
:info:build       _cd_circle_down in cdline.o
:info:build       _cd_circle_up in cdline.o
:info:build   "_gwy_math_nlfit_new", referenced from:
:info:build       _cd_circle_down in cdline.o
:info:build       _cd_circle_up in cdline.o
:info:build   "_gwy_math_nlfit_new_idx", referenced from:
:info:build       _gwy_shape_fit_preset_create_fitter in gwyshapefitpreset.o
:info:build   "_gwy_math_nlfit_set_max_iterations", referenced from:
:info:build       _gwy_shape_fit_preset_quick_fit in gwyshapefitpreset.o
:info:build   "_gwy_math_refine_maximum", referenced from:
:info:build       _gwy_data_field_crosscorrelate_iteration in correlation.o
:info:build   "_gwy_math_refine_maximum_1d", referenced from:
:info:build       _refine_diameter_direction in grains-values.o
:info:build   "_gwy_math_refine_maximum_2d", referenced from:
:info:build       _gwy_data_field_local_maximum in elliptic.o
:info:build   "_gwy_math_sort_with_index", referenced from:
:info:build       _gwy_data_field_area_filter_kth_rank in filters-minmax.o
:info:build       _gwy_data_field_area_filter_trimmed_mean in filters-minmax.o
:info:build   "_gwy_math_trimmed_mean", referenced from:
:info:build       _trimmed_mean_or_median in correct.o
:info:build       _gwy_data_field_new_binned in datafield.o
:info:build       _gwy_data_field_bin in datafield.o
:info:build       _gwy_data_field_area_filter_trimmed_mean in filters-minmax.o
:info:build   "_gwy_md5_get_digest", referenced from:
:info:build       _ensure_checksum in surface.o
:info:build   "_gwy_rand_gen_set_choose_shuffle", referenced from:
:info:build       _gwy_surface_reduce_points in surface.o
:info:build   "_gwy_rand_gen_set_free", referenced from:
:info:build       _gwy_data_field_fractal_correction in fractals.o
:info:build       _gwy_surface_reduce_points in surface.o
:info:build   "_gwy_rand_gen_set_gaussian", referenced from:
:info:build       _gwy_data_field_fractal_correction in fractals.o
:info:build   "_gwy_rand_gen_set_new", referenced from:
:info:build       _gwy_data_field_fractal_correction in fractals.o
:info:build       _gwy_surface_reduce_points in surface.o
:info:build   "_gwy_rand_gen_set_rng", referenced from:
:info:build       _gwy_surface_reduce_points in surface.o
:info:build   "_gwy_resource_class_get_item_type", referenced from:
:info:build       _gwy_cdline_class_intern_init in cdline.o
:info:build       _gwy_calibration_class_intern_init in gwycalibration.o
:info:build       _gwy_grain_value_class_intern_init in gwygrainvalue.o
:info:build       _gwy_shape_fit_preset_class_intern_init in gwyshapefitpreset.o
:info:build   "_gwy_resource_data_changed", referenced from:
:info:build       _gwy_grain_value_set_symbol_markup in gwygrainvalue.o
:info:build       _gwy_grain_value_set_symbol in gwygrainvalue.o
:info:build       _gwy_grain_value_set_power_xy in gwygrainvalue.o
:info:build       _gwy_grain_value_set_power_z in gwygrainvalue.o
:info:build       _gwy_grain_value_set_flags in gwygrainvalue.o
:info:build       _gwy_grain_value_set_expression in gwygrainvalue.o
:info:build   "_gwy_resource_get_is_modifiable", referenced from:
:info:build       _gwy_grain_value_set_symbol_markup in gwygrainvalue.o
:info:build       _gwy_grain_value_set_symbol in gwygrainvalue.o
:info:build       _gwy_grain_value_set_power_xy in gwygrainvalue.o
:info:build       _gwy_grain_value_set_power_z in gwygrainvalue.o
:info:build       _gwy_grain_value_set_flags in gwygrainvalue.o
:info:build       _gwy_grain_value_set_expression in gwygrainvalue.o
:info:build   "_gwy_resource_get_name", referenced from:
:info:build       _gwy_calibration_copy in gwycalibration.o
:info:build       _gwy_grain_value_copy in gwygrainvalue.o
:info:build   "_gwy_resource_get_type", referenced from:
:info:build       _gwy_cdline_get_type_once in cdline.o
:info:build       __gwy_cdline_class_setup_presets in cdline.o
:info:build       _gwy_cdlines in cdline.o
:info:build       _gwy_cdline_class_intern_init in cdline.o
:info:build       _gwy_calibration_get_type_once in gwycalibration.o
:info:build       _gwy_calibration_new in gwycalibration.o
:info:build       _gwy_calibrations in gwycalibration.o
:info:build       ...
:info:build   "_gwy_serializable_clone", referenced from:
:info:build       _gwy_brick_copy_zcalibration in brick.o
:info:build       _gwy_data_field_new_rotated in datafield.o
:info:build   "_gwy_serializable_clone_with_type", referenced from:
:info:build       _gwy_brick_transpose in brick.o
:info:build       _gwy_data_field_bin in datafield.o
:info:build       _gwy_data_field_area_ext_convolve in filters-convdeconv.o
:info:build       __gwy_copy_si_unit in gwyprocess.o
:info:build       _gwy_data_line_func_fft in linestats.o
:info:build       _gwy_data_field_area_dh in stats.o
:info:build       _gwy_data_field_area_minkowski_boundary in stats.o
:info:build       ...
:info:build   "_gwy_serializable_deserialize", referenced from:
:info:build       _gwy_calibration_use in gwycalibration.o
:info:build   "_gwy_serializable_duplicate", referenced from:
:info:build       _gwy_brick_new_alike in brick.o
:info:build       _gwy_brick_copy_zcalibration in brick.o
:info:build       _gwy_brick_transpose in brick.o
:info:build       _gwy_data_field_distort_internal in correct.o
:info:build       _gwy_data_field_affine in correct.o
:info:build       _guess_lattice in correct.o
:info:build       _gwy_data_field_laplace_solve in correct-laplace.o
:info:build       ...
:info:build   "_gwy_serializable_get_type", referenced from:
:info:build       _gwy_brick_get_type_once in brick.o
:info:build       _gwy_data_field_get_type_once in datafield.o
:info:build       _gwy_data_line_get_type_once in dataline.o
:info:build       _gwy_caldata_get_type_once in gwycaldata.o
:info:build       _gwy_spectra_get_type_once in spectra.o
:info:build       _gwy_surface_get_type_once in surface.o
:info:build   "_gwy_serializable_serialize", referenced from:
:info:build       _gwy_caldata_save_data in gwycaldata.o
:info:build   "_gwy_serialize_get_struct_size", referenced from:
:info:build       _gwy_brick_get_size in brick.o
:info:build       _gwy_data_field_get_size in datafield.o
:info:build       _gwy_data_line_get_size in dataline.o
:info:build       _gwy_caldata_get_size in gwycaldata.o
:info:build       _gwy_spectra_get_size in spectra.o
:info:build       _gwy_surface_get_size in surface.o
:info:build   "_gwy_serialize_pack_object_struct", referenced from:
:info:build       _gwy_brick_serialize in brick.o
:info:build       _gwy_data_field_serialize in datafield.o
:info:build       _gwy_data_line_serialize in dataline.o
:info:build       _gwy_caldata_serialize in gwycaldata.o
:info:build       _gwy_spectra_serialize in spectra.o
:info:build       _gwy_surface_serialize in surface.o
:info:build   "_gwy_serialize_unpack_object_struct", referenced from:
:info:build       _gwy_brick_deserialize in brick.o
:info:build       _gwy_data_field_deserialize in datafield.o
:info:build       _gwy_data_line_deserialize in dataline.o
:info:build       _gwy_caldata_deserialize in gwycaldata.o
:info:build       _gwy_spectra_deserialize in spectra.o
:info:build       _gwy_surface_deserialize in surface.o
:info:build   "_gwy_si_unit_divide", referenced from:
:info:build       _set_transfer_function_units in filters-convdeconv.o
:info:build       _gwy_data_field_area_da_mask in stats.o
:info:build       _gwy_data_field_slope_distribution in stats.o
:info:build       _gwy_data_field_get_line_stats_mask in stats.o
:info:build   "_gwy_si_unit_equal", referenced from:
:info:build       _units_are_equal in arithmetic.o
:info:build       _gwy_data_field_correlation_search in correlation.o
:info:build       _gwy_data_field_mfm_perpendicular_medium_force in mfm.o
:info:build       _gwy_data_field_get_line_stats_mask in stats.o
:info:build       _gwy_surface_xy_is_compatible in surface.o
:info:build   "_gwy_si_unit_equal_string", referenced from:
:info:build       _units_are_equal in arithmetic.o
:info:build       _gwy_brick_serialize in brick.o
:info:build       _gwy_brick_get_size in brick.o
:info:build       _gwy_data_field_serialize in datafield.o
:info:build       _gwy_data_field_get_size in datafield.o
:info:build       _gwy_data_line_serialize in dataline.o
:info:build       _gwy_data_line_get_size in dataline.o
:info:build       ...
:info:build   "_gwy_si_unit_get_format", referenced from:
:info:build       _gwy_brick_get_value_format_w in brick.o
:info:build       _gwy_data_line_get_value_format_y in dataline.o
:info:build   "_gwy_si_unit_get_format_with_digits", referenced from:
:info:build       _gwy_data_field_get_value_format_z in datafield.o
:info:build       _gwy_surface_get_value_format_z in surface.o
:info:build   "_gwy_si_unit_get_format_with_resolution", referenced from:
:info:build       _gwy_brick_get_value_format_x in brick.o
:info:build       _gwy_brick_get_value_format_y in brick.o
:info:build       _gwy_brick_get_value_format_z in brick.o
:info:build       _gwy_data_field_get_value_format_xy in datafield.o
:info:build       _gwy_data_line_get_value_format_x in dataline.o
:info:build       _gwy_surface_get_value_format_xy in surface.o
:info:build   "_gwy_si_unit_get_type", referenced from:
:info:build       _gwy_brick_transpose in brick.o
:info:build       _gwy_data_field_area_ext_convolve in filters-convdeconv.o
:info:build       _gwy_grain_quantity_get_units in grains-values.o
:info:build       _gwy_caldata_set_si_unit_x in gwycaldata.o
:info:build       _gwy_caldata_set_si_unit_y in gwycaldata.o
:info:build       _gwy_caldata_set_si_unit_z in gwycaldata.o
:info:build       __gwy_copy_si_unit in gwyprocess.o
:info:build       ...
:info:build   "_gwy_si_unit_multiply", referenced from:
:info:build       _gwy_data_field_correlation_search in correlation.o
:info:build       _gwy_data_field_area_ext_row_convolve in filters-convdeconv.o
:info:build       _gwy_data_field_area_ext_convolve in filters-convdeconv.o
:info:build       _gwy_data_line_psdf in linestats.o
:info:build       _gwy_data_field_mfm_perpendicular_medium_force in mfm.o
:info:build       _gwy_data_field_area_cdh in stats.o
:info:build       _gwy_data_field_area_cda_mask in stats.o
:info:build       ...
:info:build   "_gwy_si_unit_new", referenced from:
:info:build       _gwy_brick_get_si_unit_x in brick.o
:info:build       _gwy_brick_get_si_unit_y in brick.o
:info:build       _gwy_brick_get_si_unit_z in brick.o
:info:build       _gwy_brick_get_si_unit_w in brick.o
:info:build       _gwy_data_field_get_si_unit_xy in datafield.o
:info:build       _gwy_data_field_get_si_unit_z in datafield.o
:info:build       _gwy_data_line_get_si_unit_x in dataline.o
:info:build       ...
:info:build   "_gwy_si_unit_power", referenced from:
:info:build       _gwy_data_field_correlation_search in correlation.o
:info:build       _gwy_grain_quantity_get_units in grains-values.o
:info:build       _gwy_data_field_fft_postprocess in inttrans.o
:info:build       _gwy_data_line_func_fft in linestats.o
:info:build       _gwy_data_line_psdf in linestats.o
:info:build       _gwy_data_line_distribution in linestats.o
:info:build       _gwy_data_field_area_dh in stats.o
:info:build       ...
:info:build   "_gwy_si_unit_power_multiply", referenced from:
:info:build       _gwy_cdline_get_param_units in cdline.o
:info:build       _gwy_data_field_area_ext_convolve in filters-convdeconv.o
:info:build       _set_transfer_function_units in filters-convdeconv.o
:info:build       _gwy_grain_quantity_get_units in grains-values.o
:info:build       _gwy_shape_fit_preset_get_param_units in gwyshapefitpreset.o
:info:build       _gwy_shape_fit_preset_get_secondary_units in gwyshapefitpreset.o
:info:build       _gwy_data_field_area_2dpsdf_mask in stats-acfpsdf.o
:info:build       ...
:info:build   "_gwy_si_unit_set_from_string", referenced from:
:info:build       _gwy_grain_quantity_get_units in grains-values.o
:info:build       _gwy_data_field_waterpour in grains-wshed.o
:info:build       _gwy_data_line_distribution in linestats.o
:info:build       _gwy_data_field_mfm_perpendicular_stray_field in mfm.o
:info:build       _gwy_data_field_mfm_perpendicular_medium_force in mfm.o
:info:build       _gwy_data_field_mfm_parallel_medium in mfm.o
:info:build       _gwy_data_field_mfm_current_line in mfm.o
:info:build       ...
:info:build   "_gwy_sinc", referenced from:
:info:build       _gwy_data_field_mfm_perpendicular_medium_force in mfm.o
:info:build   "_gwy_str_next_line", referenced from:
:info:build       _gwy_calibration_parse in gwycalibration.o
:info:build       _gwy_grain_value_parse in gwygrainvalue.o
:info:build   "_gwy_strisident", referenced from:
:info:build       _gwy_grain_value_set_symbol in gwygrainvalue.o
:info:build       _gwy_grain_value_parse in gwygrainvalue.o
:info:build   "_gwy_type_init", referenced from:
:info:build       _gwy_process_type_init in gwyprocess.o
:info:build   "_gwy_xlnx_int", referenced from:
:info:build       _bin_tree_node_entropies_at_scales in stats-entropy.o
:info:build       _quad_tree_node_entropies_at_scales in stats-entropy.o
:info:build ld: symbol(s) not found for architecture x86_64
:info:build clang: error: linker command failed with exit code 1 (use -v to see invocation)
:info:build make[3]: *** [libgwyprocess2.la] Error 1
:info:build make[3]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_gwyddion/gwyddion/work/gwyddion-2.55/libprocess'
:info:build make[2]: *** [all] Error 2
:info:build make[2]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_gwyddion/gwyddion/work/gwyddion-2.55/libprocess'
:info:build make[1]: *** [all-recursive] Error 1
:info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_gwyddion/gwyddion/work/gwyddion-2.55'
:info:build make: *** [all] Error 2
:info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_gwyddion/gwyddion/work/gwyddion-2.55'
:info:build Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_gwyddion/gwyddion/work/gwyddion-2.55" && /usr/bin/make -j8 -w all 
:info:build Exit code: 2
:error:build Failed to build gwyddion: command execution failed
:debug:build Error code: CHILDSTATUS 12893 2
:debug:build Backtrace: command execution failed
:debug:build     while executing
:debug:build "system {*}$notty {*}$nice $fullcmdstring"
:debug:build     invoked from within
:debug:build "command_exec build"
:debug:build     (procedure "portbuild::build_main" line 8)
:debug:build     invoked from within
:debug:build "$procedure $targetname"
:error:build See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_gwyddion/gwyddion/main.log for details.

Attachments (1)

main.log​ (1.7 MB) - added by nirjharize 4 years ago.
Gwyddion error after After github patch

Download all attachments as: .zip

Change History (16)

comment:1 Changed 4 years ago by ryandesign (Ryan Carsten Schmidt)

Keywords: bigsur added; BigSur MacOSX11.0.sdk x86_64 removed
Owner: set to rowue
Status: new → assigned
Summary: Undefined symbols for architecture x86_64 → gwyddion: Undefined symbols for architecture x86_64

This is probably the well-known macOS 11+ libtool bug.

comment:2 Changed 4 years ago by mf2k (Frank Schima)

Cc: yeti@… added; rowue removed

comment:3 Changed 4 years ago by ryandesign (Ryan Carsten Schmidt)

Cc: GTTS2020 nirjharize added

Has duplicates #61781, #62142. It probably needs the relevant parts of browser:macports-ports/devel/libtool/files/dynamic_lookup-11.patch.

comment:4 Changed 4 years ago by rowue (Rolf Würdemann)

@Ryan: thanks a lot for the hint.

Added the relevant patches from browser:macports-ports/devel/libtool/files/dynamic_lookup-11.patch​ to branch gwyddion-bigsur of ​https://github.com/rowue/macports-ports.git

However: since my machine is to old for macOS 11+, I can't test these patches there (working on 10.x). So it would be nice if one of the reporters test the patches and provide feedback.

How to use git for syncing macports is written on

wiki:howto/SyncingWithGit

where you should use the URL mentioned above instead of the one given in the howto and should switch to the "gwyddion-bigsur" branch. ("git checkout gwyddion-bigsur" after "git clone ...")

Best,

Rolf

Last edited 3 years ago by ryandesign (Ryan Carsten Schmidt) (previous) (diff)

comment:5 Changed 4 years ago by ddrum2000

@Rolf I'm happy to try this out but can help me out a bit on how to test compile this

comment:6 in reply to:  5 ; Changed 4 years ago by rowue (Rolf Würdemann)

Replying to ddrum2000:

@Rolf I'm happy to try this out but can help me out a bit on how to test compile this

How familiar are you with Terminal.app (the shell) and macports?

Are you able to understand and perform the steps written at: wiki:howto/SyncingWithGit ?

Last edited 3 years ago by ryandesign (Ryan Carsten Schmidt) (previous) (diff)

comment:7 Changed 4 years ago by ddrum2000

I can certainly follow the steps in the link you provided. I think the real question is which lines of code from the "SyncingWithGit" page do I need to change to try out your code.

comment:8 in reply to:  6 Changed 4 years ago by ddrum2000

Replying to rowue:

Replying to ddrum2000:

@Rolf I'm happy to try this out but can help me out a bit on how to test compile this

How familiar are you with Terminal.app (the shell) and macports?

Are you able to understand and perform the steps written at: wiki:howto/SyncingWithGit ?

I can certainly follow the steps in the link you provided. I think the real question is which lines of code from the "SyncingWithGit" page do I need to change to try out your code.

Last edited 3 years ago by ryandesign (Ryan Carsten Schmidt) (previous) (diff)

Changed 4 years ago by nirjharize

Attachment: main.log​ added

Gwyddion error after After github patch

comment:9 in reply to:  4 Changed 4 years ago by nirjharize

Replying to rowue:
Okay. I did all the steps you mentioned. I'll list the commands below (I typed on the mac terminal) and it worked for me but now i get new errors on gwyddion installation. Also my username is nirjharize to clarify the chown cmd 

sudo port install git
cd /opt/local/var/macports/sources
sudo mkdir -p github.com/macports/macports-ports/
sudo chown -R nirjharize:admin github.com 
git clone ​https://github.com/rowue/macports-ports.git github.com/macports/macports-ports/
cd github.com/macports/macports-ports
git checkout gwyddion-bigsur

Then I open finder and look for file /opt/local/etc/macports/sources.conf (by pressing command + Shift + G and typing the address). The last line in that file reads: 

#rsync://rsync.macports.org/macports/release/tarballs/ports.tar [default]

Write in the next line after #rsync: 

file:///opt/local/var/macports/sources/github.com/macports/macports-ports/ [default]

Then type in mac terminal: 

sudo port -v sync

Then tried installing gwyddion again by typing this: 

sudo port install gwyddion

Got 1 error and 2 warnings. The main log repeated the fatal error string.h file not found and Error code CHILDSTATUS 28380 2. Attached the main log file and also listing the error that showed on mac terminal: 

Warning: More than one default port source is defined.
Warning: The macOS 11.2 SDK does not appear to be installed. Ports may not build correctly.
Warning: You can install it as part of the Xcode Command Line Tools package by running `xcode-select --install'.
--->  Computing dependencies for gwyddion
--->  Fetching archive for gwyddion
--->  Attempting to fetch gwyddion-2.55_0.darwin_20.arm64.tbz2 from https://ywg.ca.packages.macports.org/mirror/macports/packages/gwyddion
--->  Attempting to fetch gwyddion-2.55_0.darwin_20.arm64.tbz2 from https://kmq.jp.packages.macports.org/gwyddion
--->  Attempting to fetch gwyddion-2.55_0.darwin_20.arm64.tbz2 from https://mse.uk.packages.macports.org/gwyddion
--->  Building gwyddion
Error: Failed to build gwyddion: command execution failed
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_gwyddion/gwyddion/main.log for details.
Error: Follow https://guide.macports.org/#project.tickets to report a bug.
Error: Processing of port gwyddion failed
Last edited 3 years ago by ryandesign (Ryan Carsten Schmidt) (previous) (diff)

comment:10 Changed 4 years ago by rowue (Rolf Würdemann)

Thanks a lot.

At first: it might be better, to have one [default] in "/opt/local/etc/macports/sources.conf", so simply delete the [default] after the path not pointing to my branch (and remove my branch after the test)

Did you check the wiki page (BigSurProblems) about problems with BigSur? There the warning about "macOS 11.2 SDK" is discussed.

Usually I prefer to do a port configure gwyddion and afterwards port -v build gwyddion to get a clear border between dependencies and gwyddion itself.

Best,

Rolf

Last edited 3 years ago by ryandesign (Ryan Carsten Schmidt) (previous) (diff)

comment:11 Changed 4 years ago by nirjharize 

Warning: More than one default port source is defined.
Warning: The macOS 11.2 SDK does not appear to be installed. Ports may not build correctly.
Warning: You can install it as part of the Xcode Command Line Tools package by running `xcode-select --install'.

Regarding the above error, the following mail archive link tells me to ignore it because I tried everything too (from BigSurProblems).

​https://www.mail-archive.com/macports-users@lists.macports.org/msg07213.html

Also can you clarify the following for me? Sorry i am new to bashing mac.

When you say "remove my branch after the test", do you mean that after editing the sources.conf file I write in mac terminal 

sudo port -v sync

Then i open sources.conf and remove the line file:///opt/local/var/macports/sources/github.com/macports/macports-ports/

And then I type back in mac terminal 

port configure gwyddion
port -v build gwyddion
Last edited 3 years ago by ryandesign (Ryan Carsten Schmidt) (previous) (diff)

comment:12 in reply to:  11 Changed 4 years ago by rowue (Rolf Würdemann)

Replying to nirjharize: 

Warning: More than one default port source is defined.
Warning: The macOS 11.2 SDK does not appear to be installed. Ports may not build correctly.
Warning: You can install it as part of the Xcode Command Line Tools package by running `xcode-select --install'.

Regarding the above error, the following mail archive link tells me to ignore it because I tried everything too (from BigSurProblems).

​https://www.mail-archive.com/macports-users@lists.macports.org/msg07213.html

Do you have any version of XCode installed? "string.h" should be installed if XCode (or the SDK) is installed

Also can you clarify the following for me? Sorry i am new to bashing mac.

When you say "remove my branch after the test", do you mean that after editing the sources.conf file I write in mac terminal 

sudo port -v sync

Then i open sources.conf and remove the line file:///opt/local/var/macports/sources/github.com/macports/macports-ports/

And then I type back in mac terminal 

port configure gwyddion
port -v build gwyddion

May branch is the one, you checked out from git (​https://github.com/rowue/macports-ports.git ) and added to "sources.conf" (​file:///opt/local/var/macports/sources/github.com/macports/macports-ports/)

this you should remove from your sources and hard-disk after compiling gwyddion worked.

Best,

Rolf

Last edited 3 years ago by ryandesign (Ryan Carsten Schmidt) (previous) (diff)

comment:13 Changed 4 years ago by nirjharize

Xcode12.5
Build version 12E5234g

When I run `port configure gwyddion1 it gives me the same following error. 

Warning: The macOS 11.2 SDK does not appear to be installed. Ports may not build correctly.
Warning: You can install it as part of the Xcode Command Line Tools package by running `xcode-select --install'

I get the error CLTs are already installed when i run `xcode-select --install'

When I look up the folder /Library/Developer/CommandLineTools/SDKs/ or /Applications/Xcode-beta.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/ I see only MacOSX10.15.sdk and MacOSX11.3.sdk.

When I run port -v build gwyddion, the error warning is still the same. string.h file and time.h file not found.

Last edited 3 years ago by ryandesign (Ryan Carsten Schmidt) (previous) (diff)

comment:14 Changed 3 years ago by ryandesign (Ryan Carsten Schmidt)

Cc: ryandesign added 
clang: warning: no such sysroot directory: '/Library/Developer/CommandLineTools/SDKs/MacOSX11.1.sdk' [-Wmissing-sysroot]

gwyenum.c:23:10: fatal error: 'string.h' file not found

This was because of an SDK path selection bug (#61866) in MacPorts 2.6.4 on macOS 11 and later which was fixed in MacPorts 2.7.0.

The original problem with undefined symbols should be fixed in the way originally indicated. Only one of the configure script or the m4 files should be patched depending on whether or not the port uses autoreconf.

PSA: Everyone please remember to use WikiFormatting and TracLinks when writing in Trac to keep things legible.

comment:15 Changed 3 years ago by ryandesign (Ryan Carsten Schmidt)

Resolution: → fixed
Status: assigned → closed

In 97b8147d14d91e96557c17890d73f4b35061e6ce/macports-ports (master):

gwyddion: Fix macOS 11+ libtool bug

Fix the macOS 11+ libtool bug with undefined symbols by applying the
patch from the libtool port as usual.

Closes: #61720

While we're here, disable silent rules as is customary.

Note: See TracTickets for help on using tickets.