[INFO] fetching crate rsdeseq2 0.2.5...
[INFO] testing rsdeseq2-0.2.5 against 1.99.0-beta.8 for beta-1.100-2
[INFO] extracting crate rsdeseq2 0.2.5 into /workspace/builds/worker-3-tc1/source
[INFO] started tweaking crates.io crate rsdeseq2 0.2.5
[INFO] removed 0 missing examples
[INFO] removed 0 missing tests
[INFO] finished tweaking crates.io crate rsdeseq2 0.2.5
[INFO] tweaked toml for crates.io crate rsdeseq2 0.2.5 written to /workspace/builds/worker-3-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate rsdeseq2 0.2.5 on toolchain 1.99.0-beta.8
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.99.0-beta.8" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate rsdeseq2 0.2.5 already has a lockfile, it will not be regenerated
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.99.0-beta.8" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded rcompat-locfit v0.1.4
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[INFO] [stderr]   Downloaded statrs v0.18.0
[INFO] [stderr]   Downloaded web-sys v0.3.102
[INFO] [stderr]   Downloaded glam v0.33.1
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-m" "1610612736" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:3111399a4047eeb3a02b7a90e478d715f38a8c6669b5c4b49d30a17385265909" "sleep" "infinity", kill_on_drop: false }`
[INFO] [stdout] 8750467c86a9fbc82f0da00b7d2817a8d1e42a329d506dfa2de3e4ba0e1e0748
[INFO] running `Command { std: "docker" "start" "8750467c86a9fbc82f0da00b7d2817a8d1e42a329d506dfa2de3e4ba0e1e0748", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "8750467c86a9fbc82f0da00b7d2817a8d1e42a329d506dfa2de3e4ba0e1e0748", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-w" "/opt/rustwide/workdir" "--user" "0:0" "8750467c86a9fbc82f0da00b7d2817a8d1e42a329d506dfa2de3e4ba0e1e0748" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "8750467c86a9fbc82f0da00b7d2817a8d1e42a329d506dfa2de3e4ba0e1e0748", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-w" "/opt/rustwide/workdir" "--user" "0:0" "8750467c86a9fbc82f0da00b7d2817a8d1e42a329d506dfa2de3e4ba0e1e0748" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stderr]    Compiling libm v0.2.16
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[INFO] [stderr]    Compiling rsdeseq2 v0.2.5 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 23s
[INFO] running `Command { std: "docker" "inspect" "8750467c86a9fbc82f0da00b7d2817a8d1e42a329d506dfa2de3e4ba0e1e0748", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-w" "/opt/rustwide/workdir" "--user" "0:0" "8750467c86a9fbc82f0da00b7d2817a8d1e42a329d506dfa2de3e4ba0e1e0748" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
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[INFO] [stderr]    Compiling rsdeseq2 v0.2.5 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 1m 40s
[INFO] running `Command { std: "docker" "inspect" "8750467c86a9fbc82f0da00b7d2817a8d1e42a329d506dfa2de3e4ba0e1e0748", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-w" "/opt/rustwide/workdir" "--user" "0:0" "8750467c86a9fbc82f0da00b7d2817a8d1e42a329d506dfa2de3e4ba0e1e0748" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.8" "test" "--frozen", kill_on_drop: false }`
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.21s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/rsdeseq2-e5981e5a4607f934)
[INFO] [stdout] 
[INFO] [stdout] running 168 tests
[INFO] [stdout] test all_zero::tests::mask_full_length_values_marks_all_zero_rows ... ok
[INFO] [stdout] test all_zero::tests::expand_values_validates_compact_row_count ... ok
[INFO] [stdout] test core::implementation::tests::all_zero_gene_detection ... ok
[INFO] [stdout] test all_zero::tests::expand_values_restores_full_gene_order ... ok
[INFO] [stdout] test cli::implementation::tests::write_cli_result_sidecars_rejects_missing_refit_diagnostics ... ok
[INFO] [stdout] test all_zero::tests::nonzero_indices_skip_all_zero_rows ... ok
[INFO] [stdout] test all_zero::tests::expand_matrix_restores_full_gene_order_with_nan_rows ... ok
[INFO] [stdout] test cli::implementation::tests::write_cli_result_sidecars_exports_fit_diagnostics ... ok
[INFO] [stdout] test core::implementation::tests::count_matrix_gene_rows_accept_legacy_and_new_ranges ... ok
[INFO] [stdout] test core::implementation::tests::factor_level_low_count_heuristic_requires_exact_two_levels ... ok
[INFO] [stdout] test core::implementation::tests::count_matrix_accepts_u64_when_values_fit ... ok
[INFO] [stdout] test core::implementation::tests::full_deviance_from_log_like_masks_nonfinite_values ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::bounded_log_alpha_proposal_rejects_overflowed_effective_step ... ok
[INFO] [stdout] test core::implementation::tests::count_matrix_gene_rows_reports_range_errors_with_debuggable_match ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::bounded_log_alpha_proposal_keeps_unclamped_step ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::bounded_log_alpha_proposal_rejects_no_movement_at_bound ... ok
[INFO] [stdout] test core::implementation::tests::count_matrix_rejects_bad_length ... ok
[INFO] [stdout] test core::implementation::tests::count_matrix_row_access ... ok
[INFO] [stdout] test core::implementation::tests::factor_level_cooks_filter_uses_low_count_heuristic_only_for_two_levels ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::bounded_log_alpha_proposal_rejects_overflowed_step ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::bounded_log_alpha_proposal_reports_clamped_step ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::checked_div_rejects_nonfinite_dispersion_summaries ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::checked_log_alpha_first_derivative_uses_reduced_product ... ok
[INFO] [stdout] test core::implementation::tests::count_matrix_index_spans_are_copy_and_reusable ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::checked_log_alpha_second_derivative_keeps_cancelling_large_terms ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::cox_reid_weight_terms_keep_overflowed_mu_alpha_product_finite ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::checked_cox_reid_log_alpha_second_derivative_rejects_alpha_square_overflow ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::dispersion_digamma_matches_r_positive_path ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::dispersion_grid_linspace_rejects_nonfinite_arithmetic ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::dispersion_kernel_keeps_small_mu_alpha_terms_stable ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::dispersion_lgamma_matches_r_stirling_thresholds ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::dispersion_prior_log_density_rejects_overflowed_residual_square ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::mu_alpha_terms_keep_overflowed_product_finite ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::cox_reid_weight_terms_reject_overflowed_square ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::dispersion_derivatives_keep_overflowed_mu_alpha_products_finite ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::line_search_armijo_bound_matches_finite_formula ... ok
[INFO] [stdout] test dispersion::gene_est::implementation::tests::line_search_armijo_bound_rejects_nonfinite_arithmetic ... ok
[INFO] [stdout] test dispersion::prior::tests::checked_div_rejects_zero_and_nonfinite_prior_arithmetic ... ok
[INFO] [stdout] test dispersion::prior::tests::kl_divergence_keeps_large_finite_bins_finite ... ok
[INFO] [stdout] test dispersion::prior::tests::low_df_smoother_rejects_overflowed_weighted_accumulation ... ok
[INFO] [stdout] test dispersion::prior::tests::low_df_smoother_rejects_overflowed_response_accumulation ... ok
[INFO] [stdout] test dispersion::prior::tests::tricube_weight_matches_boundary_values ... ok
[INFO] [stdout] test dispersion::prior::tests::kl_divergence_rejects_overflowed_bin_adjustment ... ok
[INFO] [stdout] test dispersion::prior::tests::low_df_linspace_rejects_nonfinite_grid_arithmetic ... ok
[INFO] [stdout] test dispersion::prior::tests::low_df_simulated_residual_rejects_overflowed_scale ... ok
[INFO] [stdout] test dispersion::trend::tests::checked_add_assign_rejects_nonfinite_sum ... ok
[INFO] [stdout] test dispersion::trend::tests::checked_div2_rejects_zero_and_nonfinite_quotients ... ok
[INFO] [stdout] test dispersion::trend::tests::interpolate_parametric_coefficient_avoids_difference_overflow ... ok
[INFO] [stdout] test dispersion::trend::tests::parametric_coefficient_change_rejects_nonfinite_ratio ... ok
[INFO] [stdout] test dispersion::trend::tests::parametric_work_helpers_validate_aligned_rows ... ok
[INFO] [stdout] test dispersion::trend::tests::gamma_deviance_rejects_nonfinite_accumulation ... ok
[INFO] [stdout] test dispersion::trend::tests::parametric_coefficient_change_matches_log_squared_update ... ok
[INFO] [stdout] test dispersion::trend::tests::checked_product_difference_matches_finite_difference ... ok
[INFO] [stdout] test dispersion::trend::tests::checked_product_difference_rejects_nonfinite_product ... ok
[INFO] [stdout] test dispersion::trend::tests::gamma_deviance_keeps_near_perfect_fit_precision ... ok
[INFO] [stdout] test dispersion::trend::tests::weighted_gamma_identity_least_squares_rejects_nonfinite_numerator_product ... ok
[INFO] [stdout] test dispersion::trend::tests::stable_midpoint_handles_opposite_extreme_endpoints ... ok
[INFO] [stdout] test dispersion::trend::tests::weighted_gamma_identity_least_squares_rejects_nonfinite_weights ... ok
[INFO] [stdout] test dispersion::trend::tests::weighted_gamma_identity_least_squares_rejects_nonfinite_coefficients ... ok
[INFO] [stdout] test glm::beta::tests::checked_div2_rejects_zero_and_nonfinite_inputs ... ok
[INFO] [stdout] test glm::beta::tests::checked_scaled_sum_rejects_overflowed_rescale ... ok
[INFO] [stdout] test dispersion::trend::tests::weighted_gamma_identity_least_squares_rejects_nonfinite_determinant_product ... ok
[INFO] [stdout] test glm::beta::tests::stable_interpolate_rejects_overflowed_delta ... ok
[INFO] [stdout] test glm::beta::tests::intercept_working_weights_reject_nonfinite_weight_scaling ... ok
[INFO] [stdout] test glm::beta::tests::mean_dispersion_weight_rejects_nonfinite_arithmetic ... ok
[INFO] [stdout] test glm::beta::tests::weighted_mean_rejects_nonfinite_products ... ok
[INFO] [stdout] test glm::beta::tests::quantile_type7_rejects_overflowed_interpolation ... ok
[INFO] [stdout] test glm::beta::tests::stable_interpolate_preserves_equal_extreme_endpoints ... ok
[INFO] [stdout] test glm::fallback::tests::fallback_rows_follow_deseq2_use_optim_switch ... ok
[INFO] [stdout] test glm::fallback::tests::fallback_rows_validate_dimensions ... ok
[INFO] [stdout] test glm::fallback::tests::force_optim_routes_every_row ... ok
[INFO] [stdout] test glm::irls::tests::bounded_beta_numeric_helpers_reject_nonfinite_accumulation ... ok
[INFO] [stdout] test glm::irls::tests::fitted_mu_rejects_overflowed_linear_predictor ... ok
[INFO] [stdout] test glm::irls::tests::beta_objective_converts_natural_log_ridge_to_log2_penalty ... ok
[INFO] [stdout] test glm::irls::tests::beta_objective_returns_penalty_for_nonfinite_accumulation ... ok
[INFO] [stdout] test glm::irls::tests::beta_numeric_gradient_uses_r_optim_bounded_difference ... ok
[INFO] [stdout] test glm::irls::tests::beta_objective_returns_penalty_for_overflowed_ridge_term ... ok
[INFO] [stdout] test glm::irls::tests::fitted_mu_log2_rejects_overflowed_linear_predictor ... ok
[INFO] [stdout] test glm::irls::tests::fitted_mu_avoids_intermediate_exponential_overflow_with_small_factor ... ok
[INFO] [stdout] test glm::irls::tests::beta_objective_uses_log2_mu_and_nb_kernel_without_gamma_constants ... ok
[INFO] [stdout] test glm::irls::tests::fitted_mu_saturates_final_overflowed_mean_with_small_factor ... ok
[INFO] [stdout] test glm::irls::tests::fitted_mu_saturates_overflowed_exponential_mean ... ok
[INFO] [stdout] test glm::irls::tests::irls_deviance_convergence_stat_rejects_nonfinite_arithmetic ... ok
[INFO] [stdout] test glm::irls::tests::log2_output_scaling_rejects_nonfinite_values ... ok
[INFO] [stdout] test glm::irls::tests::r_optim_candidate_accepts_objective_gap_within_factr_band ... ok
[INFO] [stdout] test glm::irls::tests::r_optim_candidate_disagreement_is_scaled_by_numeric_resolution ... ok
[INFO] [stdout] test glm::irls::tests::r_optim_candidate_rejects_material_objective_gap ... ok
[INFO] [stdout] test glm::irls::tests::weighted_least_squares_helpers_reject_nonfinite_accumulation ... ok
[INFO] [stdout] test glm::irls::tests::working_response_avoids_normalized_mean_overflow ... ok
[INFO] [stdout] test glm::irls::tests::working_response_rejects_nonfinite_arithmetic ... ok
[INFO] [stdout] test glm::irls::tests::optim_start_keeps_finite_beta_on_bounds ... ok
[INFO] [stdout] test glm::irls::tests::optim_start_preserves_backup_qr_natural_log_values ... ok
[INFO] [stdout] test glm::nb::tests::negative_twice_log_likelihood_rejects_nonfinite_scaling ... ok
[INFO] [stdout] test glm::r_arithmetic::tests::frozen_r_4_6_values ... ok
[INFO] [stdout] test glm::wald::tests::checked_shifted_stat_rejects_overflowed_threshold_sum ... ok
[INFO] [stdout] test independent_filtering::tests::independent_filter_numeric_helpers_reject_nonfinite_inputs ... ok
[INFO] [stdout] test io::implementation::tests::align_design_matrix_to_samples_rejects_missing_and_duplicate_samples ... ok
[INFO] [stdout] test glm::irls::tests::optim_fallback_control_matches_r_optim_lbfgsb_defaults ... ok
[INFO] [stdout] test io::implementation::tests::align_gene_numeric_values_to_genes_rejects_missing_and_duplicate_genes ... ok
[INFO] [stdout] test glm::irls::tests::optim_fallback_replays_objective_only_r_optim_hard_real_case_when_available ... ok
[INFO] [stdout] test io::implementation::tests::align_labeled_assay_matrix_to_counts_rejects_missing_and_duplicate_names ... ok
[INFO] [stdout] test io::implementation::tests::align_labeled_assay_matrix_to_counts_uses_gene_and_sample_order ... ok
[INFO] [stdout] test glm::wald::tests::thresholded_wald_returns_missing_for_overflowed_shift ... ok
[INFO] [stdout] test independent_filtering::tests::independent_filter_numeric_helpers_keep_large_finite_values ... ok
[INFO] [stdout] test io::implementation::tests::align_design_matrix_to_samples_uses_count_sample_order ... ok
[INFO] [stdout] test io::implementation::tests::align_sample_levels_to_samples_rejects_missing_and_duplicate_samples ... ok
[INFO] [stdout] test io::implementation::tests::align_gene_numeric_values_to_genes_uses_count_gene_order ... ok
[INFO] [stdout] test io::implementation::tests::align_sample_numeric_values_to_samples_rejects_missing_and_duplicate_samples ... ok
[INFO] [stdout] test io::implementation::tests::read_design_matrix_tsv_reads_numeric_matrix_and_names ... ok
[INFO] [stdout] test io::implementation::tests::align_sample_levels_to_samples_uses_count_sample_order ... ok
[INFO] [stdout] test io::implementation::tests::parse_count_field_rejects_non_integer_numeric_values ... ok
[INFO] [stdout] test io::implementation::tests::align_sample_numeric_values_to_samples_uses_count_sample_order ... ok
[INFO] [stdout] test io::implementation::tests::parse_count_field_accepts_integer_scientific_notation ... ok
[INFO] [stdout] test io::implementation::tests::read_geometric_means_tsv_reads_nonnegative_values ... ok
[INFO] [stdout] test io::implementation::tests::read_design_matrix_tsv_validates_shape_and_values ... ok
[INFO] [stdout] test io::implementation::tests::read_geometric_means_tsv_validates_shape_and_values ... ok
[INFO] [stdout] test io::implementation::tests::read_labeled_design_matrix_tsv_preserves_sample_names ... ok
[INFO] [stdout] test io::implementation::tests::read_labeled_geometric_means_tsv_preserves_gene_names ... ok
[INFO] [stdout] test io::implementation::tests::read_normalization_factors_tsv_validates_shape_and_values ... ok
[INFO] [stdout] test io::implementation::tests::read_observation_weights_tsv_reads_nonnegative_matrix ... ok
[INFO] [stdout] test io::implementation::tests::read_labeled_normalization_factors_tsv_preserves_names ... ok
[INFO] [stdout] test io::implementation::tests::read_labeled_size_factors_tsv_preserves_sample_names ... ok
[INFO] [stdout] test io::implementation::tests::read_observation_weights_tsv_validates_shape_and_values ... ok
[INFO] [stdout] test io::implementation::tests::read_labeled_observation_weights_tsv_preserves_names ... ok
[INFO] [stdout] test io::implementation::tests::read_sample_levels_tsv_reads_labeled_string_levels ... ok
[INFO] [stdout] test io::implementation::tests::read_labeled_wald_t_degrees_of_freedom_tsv_preserves_gene_names ... ok
[INFO] [stdout] test glm::irls::tests::working_weights_reject_nonfinite_arithmetic ... ok
[INFO] [stdout] test io::implementation::tests::read_size_factors_tsv_reads_positive_values ... ok
[INFO] [stdout] test io::implementation::tests::read_normalization_factors_tsv_reads_positive_matrix ... ok
[INFO] [stdout] test io::implementation::tests::read_sample_levels_tsv_validates_shape_and_values ... ok
[INFO] [stdout] test io::implementation::tests::write_base_mean_tsv_validates_names_and_values ... ok
[INFO] [stdout] test io::implementation::tests::read_size_factors_tsv_validates_shape_and_values ... ok
[INFO] [stdout] test io::implementation::tests::read_wald_t_degrees_of_freedom_tsv_reads_finite_values ... ok
[INFO] [stdout] test io::implementation::tests::write_base_metadata_tsv_writes_deseq2_shape_and_validates_lengths ... ok
[INFO] [stdout] test io::implementation::tests::read_wald_t_degrees_of_freedom_tsv_validates_shape_and_values ... ok
[INFO] [stdout] test io::implementation::tests::write_deseq_mcols_diagnostics_tsv_rejects_misaligned_gene_names ... ok
[INFO] [stdout] test io::implementation::tests::write_cooks_diagnostics_tsv_rejects_misaligned_metadata ... ok
[INFO] [stdout] test io::implementation::tests::write_deseq_mcols_diagnostics_tsv_rejects_misaligned_columns ... ok
[INFO] [stdout] test io::implementation::tests::write_cooks_replacement_metadata_tsv_writes_scalar_summary ... ok
[INFO] [stdout] test io::implementation::tests::write_deseq_results_tsv_writes_columns_missing_values_and_logicals ... ok
[INFO] [stdout] test io::implementation::tests::write_count_matrices_tsv_preserves_names_and_fallbacks ... ok
[INFO] [stdout] test io::implementation::tests::write_cooks_diagnostics_tsv_writes_matrix_and_metadata ... ok
[INFO] [stdout] test io::implementation::tests::write_deseq_mcols_diagnostics_tsv_writes_present_columns_and_na_values ... ok
[INFO] [stdout] test io::implementation::tests::write_independent_filter_metadata_tsv_rejects_invalid_shapes ... ok
[INFO] [stdout] test io::implementation::tests::write_independent_filter_metadata_tsv_writes_deseq2_shapes ... ok
[INFO] [stdout] test io::implementation::tests::write_normalization_factors_tsv_writes_deseq2_shape_and_validates_values ... ok
[INFO] [stdout] test io::implementation::tests::write_normalized_counts_tsv_validates_names_and_finite_values ... ok
[INFO] [stdout] test io::implementation::tests::write_size_factors_tsv_validates_names_and_values ... ok
[INFO] [stdout] test io::implementation::tests::write_deseq_results_tsv_rejects_invalid_numeric_rows ... ok
[INFO] [stdout] test math::optim::tests::actual_directional_derivative_uses_clamped_candidate_movement ... ok
[INFO] [stdout] test math::optim::tests::bounded_optimizer_minimizes_quadratic_inside_bounds ... ok
[INFO] [stdout] test math::optim::tests::scalar_helpers_reject_nonfinite_accumulation ... ok
[INFO] [stdout] test math::optim::tests::bounded_optimizer_reports_nonconvergence_for_overflowed_gradient_norm ... ok
[INFO] [stdout] test matrix::tests::matrix_index_spans_are_copy_and_reusable ... ok
[INFO] [stdout] test math::median::tests::median_even_large_values_avoids_midpoint_overflow ... ok
[INFO] [stdout] test math::qr::tests::matrix_rank_rejects_nonfinite_elimination_update ... ok
[INFO] [stdout] test math::median::tests::median_even_length ... ok
[INFO] [stdout] test math::median::tests::median_odd_length ... ok
[INFO] [stdout] test normalization::tests::compensated_sum_rejects_non_finite_values ... ok
[INFO] [stdout] test transform::vst::tests::checked_interpolate_rejects_overflowed_product ... ok
[INFO] [stdout] test matrix::tests::matrix_rows_accept_legacy_and_new_ranges ... ok
[INFO] [stdout] test matrix::tests::matrix_rows_reports_range_errors_with_debuggable_match ... ok
[INFO] [stdout] test transform::vst::tests::checked_local_vst_arithmetic_rejects_nonfinite_subtraction_and_division ... ok
[INFO] [stdout] test transform::vst::tests::quantile_type7_keeps_large_equal_values_finite ... ok
[INFO] [stdout] test transform::vst::tests::quantile_type7_rejects_overflowed_delta ... ok
[INFO] [stdout] test math::median::tests::median_finite_filters_nan ... ok
[INFO] [stdout] test normalization::tests::compensated_sum_preserves_representable_low_order_terms ... ok
[INFO] [stdout] test math::optim::tests::bounded_optimizer_stops_at_active_bound ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 168 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.07s
[INFO] [stdout] 
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/rsdeseq2-d80a2a0ec43dba24)
[INFO] [stdout] 
[INFO] [stdout] running 0 tests
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/base_mean.rs (/opt/rustwide/target/debug/deps/base_mean-309455faa2c5a7fa)
[INFO] [stdout] 
[INFO] [stdout] running 23 tests
[INFO] [stdout] test base_metadata_rejects_nonfinite_accumulation ... ok
[INFO] [stdout] test base_variance_avoids_finite_sum_squares_overflow ... ok
[INFO] [stdout] test base_variance_rejects_overflowed_scaled_deviation ... ok
[INFO] [stdout] test builder_uses_normalization_factors_for_initial_fit_state ... ok
[INFO] [stdout] test builder_preprocesses_observation_weights_when_design_is_supplied ... ok
[INFO] [stdout] test builder_uses_observation_weights_for_initial_base_metadata ... ok
[INFO] [stdout] test builder_with_normalization_factors_does_not_require_estimable_size_factors ... ok
[INFO] [stdout] test normalized_counts_and_base_mean ... ok
[INFO] [stdout] test base_variance_uses_sample_variance_like_row_vars ... ok
[INFO] [stdout] test builder_returns_initial_fit_state ... ok
[INFO] [stdout] test base_variance_is_nan_for_one_sample ... ok
[INFO] [stdout] test normalized_counts_with_gene_sample_factors_and_base_mean ... ok
[INFO] [stdout] test weighted_base_mean_avoids_finite_sum_overflow ... ok
[INFO] [stdout] test weighted_base_metadata_multiplies_normalized_counts_by_weights ... ok
[INFO] [stdout] test fixed_dispersion_wald_pipeline_marks_weight_failed_rows_as_skipped ... ok
[INFO] [stdout] test normalized_counts_reject_overflowed_tiny_size_factor_division ... ok
[INFO] [stdout] test normalized_counts_with_factors_reject_overflowed_tiny_factor_division ... ok
[INFO] [stdout] test weighted_base_variance_avoids_finite_sum_squares_overflow ... ok
[INFO] [stdout] test weighted_base_variance_is_nan_for_one_sample ... ok
[INFO] [stdout] test weighted_base_variance_rejects_overflowed_scaled_deviation ... ok
[INFO] [stdout] test normalization_factors_validate_dimensions_and_positive_values ... ok
[INFO] [stdout] test weighted_base_metadata_rejects_nonfinite_products ... ok
[INFO] [stdout] test weighted_base_metadata_validates_inputs ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 23 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/cli.rs (/opt/rustwide/target/debug/deps/cli-d5c9b127e1124459)
[INFO] [stdout] 
[INFO] [stdout] running 94 tests
[INFO] [stdout] test cli_base_mean_accepts_control_genes ... ok
[INFO] [stdout] test cli_base_mean_accepts_observation_weights ... ok
[INFO] [stdout] test cli_base_mean_accepts_geometric_means ... ok
[INFO] [stdout] test cli_base_mean_accepts_size_factors ... ok
[INFO] [stdout] test cli_base_mean_accepts_normalization_factors ... ok
[INFO] [stdout] test cli_lrt_accepts_control_genes ... ok
[INFO] [stdout] test cli_lrt_accepts_named_contrast ... ok
[INFO] [stdout] test cli_lrt_accepts_coefficient_name ... ok
[INFO] [stdout] test cli_lrt_accepts_list_contrast ... ok
[INFO] [stdout] test cli_lrt_accepts_geometric_means ... ok
[INFO] [stdout] test cli_lrt_rejects_ambiguous_cleaned_factor_level_alias ... ok
[INFO] [stdout] test cli_lrt_rejects_ambiguous_r_cleaned_coefficient_name_alias ... ok
[INFO] [stdout] test cli_lrt_rejects_factor_level_contrast_without_sample_levels ... ok
[INFO] [stdout] test cli_lrt_accepts_factor_level_contrast_with_r_cleaned_level_names ... ok
[INFO] [stdout] test cli_lrt_accepts_factor_level_contrast ... ok
[INFO] [stdout] test cli_lrt_rejects_sample_levels_without_factor_level_contrast ... ok
[INFO] [stdout] test cli_normalized_counts_accepts_control_genes ... ok
[INFO] [stdout] test cli_normalized_counts_accepts_geometric_means ... ok
[INFO] [stdout] test cli_lrt_accepts_factor_level_contrast_with_cleaned_reference_alias ... ok
[INFO] [stdout] test cli_normalized_counts_accepts_normalization_factors ... ok
[INFO] [stdout] test cli_normalized_counts_accepts_size_factors ... ok
[INFO] [stdout] test cli_lrt_writes_result_and_cooks_sidecars ... ok
[INFO] [stdout] test cli_rlog_accepts_control_genes ... ok
[INFO] [stdout] test cli_lrt_accepts_r_cleaned_named_contrast_alias ... ok
[INFO] [stdout] test cli_lrt_accepts_r_cleaned_coefficient_name_alias ... ok
[INFO] [stdout] test cli_lrt_accepts_numeric_contrast ... ok
[INFO] [stdout] test cli_lrt_accepts_result_filter_controls ... ok
[INFO] [stdout] test cli_rlog_frozen_intercepts_require_prior_variance ... ok
[INFO] [stdout] test cli_rlog_prior_variance_requires_frozen_intercepts ... ok
[INFO] [stdout] test cli_rlog_requires_design_when_not_blind ... ok
[INFO] [stdout] test cli_rlog_accepts_frozen_intercepts_in_blind_mode ... ok
[INFO] [stdout] test cli_lrt_writes_deseq_results_table ... ok
[INFO] [stdout] test cli_size_factors_accepts_control_genes ... ok
[INFO] [stdout] test cli_size_factors_accepts_geometric_means ... ok
[INFO] [stdout] test cli_vst_accepts_control_genes ... ok
[INFO] [stdout] test cli_vst_accepts_geometric_means ... ok
[INFO] [stdout] test cli_vst_runs_blind_mean_fit ... ok
[INFO] [stdout] test cli_vst_runs_design_aware_mean_fit ... ok
[INFO] [stdout] test cli_wald_accepts_additive_expanded_beta_prior_coefficient_workflow ... ok
[INFO] [stdout] test cli_rlog_accepts_frozen_intercepts_in_design_aware_mode ... ok
[INFO] [stdout] test cli_wald_accepts_additive_expanded_beta_prior_list_contrast ... ok
[INFO] [stdout] test cli_wald_accepts_additive_expanded_beta_prior_normalization_factors ... ok
[INFO] [stdout] test cli_wald_accepts_additive_expanded_beta_prior_observation_weights ... ok
[INFO] [stdout] test cli_rlog_accepts_normalization_factors ... ok
[INFO] [stdout] test cli_rlog_accepts_geometric_means ... ok
[INFO] [stdout] test cli_wald_accepts_expanded_beta_prior_coefficient_workflow ... ok
[INFO] [stdout] test cli_wald_accepts_expanded_beta_prior_contrast_workflow ... ok
[INFO] [stdout] test cli_wald_accepts_expanded_beta_prior_normalization_factors ... ok
[INFO] [stdout] test cli_wald_accepts_factor_expanded_beta_prior_coefficient_workflow ... ok
[INFO] [stdout] test cli_wald_accepts_factor_expanded_beta_prior_normalization_factors ... ok
[INFO] [stdout] test cli_rlog_accepts_size_factors ... ok
[INFO] [stdout] test cli_wald_accepts_factor_expanded_beta_prior_contrast_workflow ... ok
[INFO] [stdout] test cli_rlog_runs_design_aware_mean_fit ... ok
[INFO] [stdout] test cli_wald_accepts_coefficient_name ... ok
[INFO] [stdout] test cli_rlog_accepts_observation_weights ... ok
[INFO] [stdout] test cli_rlog_runs_blind_mean_fit ... ok
[INFO] [stdout] test cli_wald_accepts_control_genes ... ok
[INFO] [stdout] test cli_wald_accepts_geometric_means ... ok
[INFO] [stdout] test cli_wald_accepts_factor_level_contrast ... ok
[INFO] [stdout] test cli_wald_accepts_lfc_threshold_alternative ... ok
[INFO] [stdout] test cli_wald_accepts_factor_level_contrast_with_r_cleaned_level_names ... ok
[INFO] [stdout] test cli_wald_accepts_list_contrast ... ok
[INFO] [stdout] test cli_wald_accepts_factor_level_contrast_with_cleaned_reference_alias ... ok
[INFO] [stdout] test cli_wald_accepts_named_contrast ... ok
[INFO] [stdout] test cli_wald_additive_beta_prior_writes_cooks_replacement_sidecars ... ok
[INFO] [stdout] test cli_wald_expanded_beta_prior_writes_cooks_replacement_sidecars ... ok
[INFO] [stdout] test cli_wald_factor_beta_prior_writes_cooks_replacement_sidecars ... ok
[INFO] [stdout] test cli_wald_rejects_additive_beta_prior_mismatched_factor_lists ... ok
[INFO] [stdout] test cli_wald_rejects_additive_beta_prior_when_reported_design_disagrees ... ok
[INFO] [stdout] test cli_wald_rejects_ambiguous_cleaned_factor_level_alias ... ok
[INFO] [stdout] test cli_wald_rejects_ambiguous_r_cleaned_coefficient_name_alias ... ok
[INFO] [stdout] test cli_wald_rejects_duplicate_expanded_beta_prior_group_indices ... ok
[INFO] [stdout] test cli_wald_rejects_expanded_beta_prior_group_count_mismatch ... ok
[INFO] [stdout] test cli_wald_rejects_expanded_beta_prior_group_index_outside_expanded_design ... ok
[INFO] [stdout] test cli_wald_rejects_factor_beta_prior_when_reported_design_disagrees ... ok
[INFO] [stdout] test cli_wald_rejects_factor_level_contrast_for_beta_prior_cli ... ok
[INFO] [stdout] test cli_wald_rejects_factor_level_contrast_without_sample_levels ... ok
[INFO] [stdout] test cli_wald_rejects_incomplete_additive_beta_prior_inputs ... ok
[INFO] [stdout] test cli_wald_rejects_incomplete_expanded_beta_prior_inputs ... ok
[INFO] [stdout] test cli_wald_rejects_incomplete_factor_beta_prior_inputs ... ok
[INFO] [stdout] test cli_wald_accepts_numeric_contrast ... ok
[INFO] [stdout] test cli_wald_rejects_mixed_beta_prior_matrix_and_additive_inputs ... ok
[INFO] [stdout] test cli_wald_rejects_mixed_beta_prior_matrix_and_factor_inputs ... ok
[INFO] [stdout] test cli_wald_rejects_mixed_beta_prior_factor_and_additive_inputs ... ok
[INFO] [stdout] test cli_wald_accepts_r_cleaned_coefficient_name_alias ... ok
[INFO] [stdout] test cli_wald_accepts_size_factors ... ok
[INFO] [stdout] test cli_wald_accepts_observation_weights ... ok
[INFO] [stdout] test cli_wald_rejects_replacement_sidecars_without_replacement_refit ... ok
[INFO] [stdout] test cli_wald_accepts_r_cleaned_named_contrast_alias ... ok
[INFO] [stdout] test cli_wald_accepts_result_filter_controls ... ok
[INFO] [stdout] test cli_wald_writes_deseq_results_table ... ok
[INFO] [stdout] test cli_wald_writes_cooks_replacement_sidecars ... ok
[INFO] [stdout] test cli_wald_writes_result_and_cooks_sidecars ... ok
[INFO] [stdout] test cli_wald_accepts_t_pvalue_options ... ok
[INFO] [stdout] 
[INFO] [stderr]      Running tests/contrasts.rs (/opt/rustwide/target/debug/deps/contrasts-008778d7d0f0766f)
[INFO] [stdout] test result: ok. 94 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 21.89s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 51 tests
[INFO] [stdout] test coefficient_name_contrast_resolves_r_cleaned_aliases ... ok
[INFO] [stdout] test coefficient_name_contrast_resolves_component_cleaned_interaction_aliases ... ok
[INFO] [stdout] test coefficient_name_contrast_matches_requested_cleaned_alias_against_stored_names ... ok
[INFO] [stdout] test contrast_all_zero_factor_levels_matches_deseq2_character_shape ... ok
[INFO] [stdout] test coefficient_name_contrast_resolves_to_unit_vector ... ok
[INFO] [stdout] test coefficient_name_contrast_rejects_ambiguous_r_cleaned_aliases ... ok
[INFO] [stdout] test coefficient_name_contrast_rejects_ambiguous_component_cleaned_interaction_aliases ... ok
[INFO] [stdout] test coefficient_name_contrast_resolves_component_cleaned_factor_aliases ... ok
[INFO] [stdout] test coefficient_name_contrast_prefers_exact_name_over_cleaned_alias ... ok
[INFO] [stdout] test contrast_all_zero_numeric_matches_deseq2_expanded_shape ... ok
[INFO] [stdout] test contrast_all_zero_numeric_validates_inputs ... ok
[INFO] [stdout] test coefficient_name_contrast_resolves_cleaned_formula_transform_interaction_aliases ... ok
[INFO] [stdout] test contrast_all_zero_factor_levels_rejects_ambiguous_cleaned_level_aliases ... ok
[INFO] [stdout] test contrast_all_zero_factor_levels_resolves_cleaned_level_aliases ... ok
[INFO] [stdout] test factor_level_contrast_rejects_ambiguous_candidate_name_aliases ... ok
[INFO] [stdout] test contrast_all_zero_factor_levels_validates_inputs ... ok
[INFO] [stdout] test factor_level_contrast_infers_shared_reference_without_factor_level_separator ... ok
[INFO] [stdout] test contrast_all_zero_numeric_rejects_overflowed_design_score ... ok
[INFO] [stdout] test contrast_all_zero_numeric_keeps_large_cancelling_design_score_finite ... ok
[INFO] [stdout] test factor_level_contrast_infers_shared_reference_with_r_like_names ... ok
[INFO] [stdout] test contrast_specs_expose_stable_result_metadata_labels ... ok
[INFO] [stdout] test factor_level_contrast_rejects_ambiguous_formula_factor_transform_aliases ... ok
[INFO] [stdout] test factor_level_contrast_uses_r_like_make_names_for_candidates ... ok
[INFO] [stdout] test factor_level_contrast_rejects_ambiguous_shared_reference_names ... ok
[INFO] [stdout] test factor_level_contrast_uses_r_reserved_word_make_names_for_candidates ... ok
[INFO] [stdout] test factor_level_contrast_resolves_standard_reference_shapes ... ok
[INFO] [stdout] test factor_level_contrast_resolves_no_intercept_formula_factor_labels ... ok
[INFO] [stdout] test list_contrast_resolves_r_cleaned_coefficient_aliases ... ok
[INFO] [stdout] test factor_level_contrast_validates_inputs ... ok
[INFO] [stdout] test factor_level_contrast_resolves_expanded_shapes ... ok
[INFO] [stdout] test list_contrast_requires_deseq2_style_signed_list_values ... ok
[INFO] [stdout] test list_contrast_resolves_component_cleaned_interaction_aliases ... ok
[INFO] [stdout] test model_frame_factor_level_contrast_accepts_r_cleaned_level_aliases ... ok
[INFO] [stdout] test model_frame_factor_level_contrast_infers_and_overrides_reference ... ok
[INFO] [stdout] test model_frame_factor_level_contrast_allows_unused_declared_reference ... ok
[INFO] [stdout] test model_frame_factor_level_contrast_prefers_exact_levels_before_cleaned_aliases ... ok
[INFO] [stdout] test model_frame_factor_level_contrast_rejects_ambiguous_level_aliases ... ok
[INFO] [stdout] test list_contrast_rejects_ambiguous_component_cleaned_interaction_aliases ... ok
[INFO] [stdout] test model_frame_factor_level_contrast_accepts_r_cleaned_factor_name_alias ... ok
[INFO] [stdout] test model_frame_factor_level_contrast_uses_declared_level_reference ... ok
[INFO] [stdout] test numeric_contrast_resolves_after_validation ... ok
[INFO] [stdout] test original_results_condition_factor_contrast_shapes_are_preserved ... ok
[INFO] [stdout] test original_results_invalid_contrast_shapes_are_rejected ... ok
[INFO] [stdout] test model_frame_factor_level_contrast_resolves_cleaned_observed_reference_alias ... ok
[INFO] [stdout] test model_frame_factor_level_contrast_resolves_cleaned_reference_aliases ... ok
[INFO] [stdout] test results_contrast_character_preserves_character_all_zero_semantics ... ok
[INFO] [stdout] test results_contrast_list_and_numeric_use_numeric_all_zero_semantics ... ok
[INFO] [stdout] test list_contrast_resolves_like_deseq2_name_lists ... ok
[INFO] [stdout] test original_zero_zero_d_vs_b_contrast_shape_is_preserved ... ok
[INFO] [stdout] test model_frame_factor_level_contrast_validates_factor_metadata ... ok
[INFO] [stdout] test factor_level_contrast_resolves_formula_factor_transform_names ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 51 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.05s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/cooks.rs (/opt/rustwide/target/debug/deps/cooks-3921116ed6035bb7)
[INFO] [stdout] 
[INFO] [stdout] running 16 tests
[INFO] [stdout] test cooks_distance_validates_dimensions ... ok
[INFO] [stdout] test prepare_cooks_replacement_refit_identifies_refit_rows_and_base_metadata ... ok
[INFO] [stdout] test original_infinite_min_replicates_disables_outlier_replacement ... ok
[INFO] [stdout] test replace_outlier_counts_rejects_nonfinite_scaled_mean ... ok
[INFO] [stdout] test replace_outlier_counts_skips_when_samples_do_not_exceed_coefficients ... ok
[INFO] [stdout] test replace_outlier_counts_respects_replaceable_samples_and_missing_cooks ... ok
[INFO] [stdout] test replace_outlier_counts_validates_options_and_dimensions ... ok
[INFO] [stdout] test robust_dispersion_keeps_large_finite_row_mean ... ok
[INFO] [stdout] test max_cooks_after_replacement_refit_zeros_replaceable_columns ... ok
[INFO] [stdout] test cooks_distance_masks_overflowed_variance ... ok
[INFO] [stdout] test replace_outlier_counts_uses_normalization_factors_when_supplied ... ok
[INFO] [stdout] test robust_dispersion_uses_trimmed_cell_variance_when_replicated_cells_exist ... ok
[INFO] [stdout] test samples_for_cooks_matches_model_matrix_cells ... ok
[INFO] [stdout] test record_max_cooks_returns_missing_without_replicated_cells ... ok
[INFO] [stdout] test replace_outlier_counts_uses_trimmed_mean_and_size_factors ... ok
[INFO] [stdout] test cooks_distance_matches_hand_formula_for_intercept_cell ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 16 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/cooks_reference.rs (/opt/rustwide/target/debug/deps/cooks_reference-123f18b67fb73421)
[INFO] [stdout] 
[INFO] [stdout] running 2 tests
[INFO] [stdout] test cooks_replacement_counts_match_optional_deseq2_reference ... ok
[INFO] [stderr]      Running tests/design.rs (/opt/rustwide/target/debug/deps/design-cf267f44fbc70cd3)
[INFO] [stdout] test cooks_replacement_refit_plan_matches_optional_deseq2_reference ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 2 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 66 tests
[INFO] [stdout] test design_matrix_sample_rows_accept_legacy_and_new_ranges ... ok
[INFO] [stdout] test design_matrix_detects_dependent_columns ... ok
[INFO] [stdout] test expanded_additive_design_includes_numeric_covariates_unchanged ... ok
[INFO] [stdout] test expanded_additive_design_with_interactions_builds_factor_pair_terms ... ok
[INFO] [stdout] test expanded_additive_design_with_interactions_validates_specs ... ok
[INFO] [stdout] test design_matrix_reports_full_rank ... ok
[INFO] [stdout] test design_matrix_reports_zero_columns_in_full_rank_error ... ok
[INFO] [stdout] test design_rank_validates_tolerance ... ok
[INFO] [stdout] test expanded_factor_design_builds_expanded_and_standard_surfaces ... ok
[INFO] [stdout] test expanded_factor_design_validates_inputs ... ok
[INFO] [stdout] test expanded_formula_design_accepts_interactions_without_main_effects ... ok
[INFO] [stdout] test design_matrix_resolves_coefficient_names ... ok
[INFO] [stdout] test expanded_formula_design_expands_star_terms ... ok
[INFO] [stdout] test expanded_formula_design_from_model_frame_handles_offsets_and_validation ... ok
[INFO] [stdout] test expanded_additive_design_with_all_interactions_builds_numeric_interactions ... ok
[INFO] [stdout] test expanded_formula_design_from_model_frame_infers_and_overrides_references ... ok
[INFO] [stdout] test expanded_formula_design_from_model_frame_keeps_unused_declared_reference ... ok
[INFO] [stdout] test expanded_formula_design_from_model_frame_uses_declared_factor_levels ... ok
[INFO] [stdout] test expanded_formula_design_from_model_frame_validates_declared_factor_levels ... ok
[INFO] [stdout] test expanded_formula_design_builds_supported_pairwise_terms ... ok
[INFO] [stdout] test expanded_additive_design_validates_numeric_covariates ... ok
[INFO] [stdout] test expanded_formula_design_rejects_ambiguous_r_cleaned_variable_aliases ... ok
[INFO] [stdout] test expanded_formula_design_from_model_frame_supports_quoted_column_names ... ok
[INFO] [stdout] test expanded_formula_design_resolves_r_cleaned_variable_aliases ... ok
[INFO] [stdout] test expanded_formula_design_supports_droplevels_factor_transform ... ok
[INFO] [stdout] test expanded_formula_design_supports_dot_power_terms ... ok
[INFO] [stdout] test expanded_additive_factor_design_builds_multiple_factor_surfaces ... ok
[INFO] [stdout] test expanded_additive_factor_design_validates_inputs ... ok
[INFO] [stdout] test expanded_formula_design_supports_intercept_only_formula ... ok
[INFO] [stdout] test expanded_formula_design_supports_dot_main_effects ... ok
[INFO] [stdout] test expanded_formula_design_simplifies_duplicate_formula_terms ... ok
[INFO] [stdout] test expanded_formula_design_supports_intercept_removal ... ok
[INFO] [stdout] test expanded_formula_design_supports_leading_unary_plus ... ok
[INFO] [stdout] test expanded_formula_design_supports_numeric_identity_transform ... ok
[INFO] [stdout] test expanded_formula_design_supports_numeric_power_transforms ... ok
[INFO] [stdout] test expanded_formula_design_supports_numeric_scalar_arithmetic_transform ... ok
[INFO] [stdout] test expanded_formula_design_supports_nested_parenthesized_groups ... ok
[INFO] [stdout] test expanded_formula_design_supports_orthogonal_polynomial_transforms ... ok
[INFO] [stdout] test expanded_formula_design_supports_numeric_binary_arithmetic_transform ... ok
[INFO] [stdout] test expanded_formula_design_from_model_frame_supports_dot_main_effects ... ok
[INFO] [stdout] test expanded_formula_design_supports_pairwise_nested_terms ... ok
[INFO] [stdout] test expanded_formula_design_supports_scalar_left_numeric_arithmetic_transform ... ok
[INFO] [stdout] test expanded_formula_design_supports_signed_numeric_identity_transform ... ok
[INFO] [stdout] test expanded_formula_design_supports_term_subtraction ... ok
[INFO] [stdout] test expanded_formula_design_supports_three_way_terms ... ok
[INFO] [stdout] test expanded_formula_design_transform_parser_handles_nested_parentheses_and_quotes ... ok
[INFO] [stdout] test expanded_formula_design_supports_raw_polynomial_transforms ... ok
[INFO] [stdout] test expanded_formula_design_validates_unsupported_terms ... ok
[INFO] [stdout] test expanded_formula_design_with_offsets_extracts_formula_offsets ... ok
[INFO] [stdout] test expanded_formula_design_supports_parenthesized_groups ... ok
[INFO] [stdout] test expanded_formula_design_supports_arbitrary_order_terms ... ok
[INFO] [stdout] test expanded_formula_design_supports_factor_identity_transforms ... ok
[INFO] [stdout] test expanded_formula_design_with_offsets_supports_numeric_transform_offsets ... ok
[INFO] [stdout] test formula_model_frame_factor_reference_aliases_prefer_exact_and_reject_ambiguous ... ok
[INFO] [stdout] test formula_model_frame_numeric_aliases_prefer_exact_and_reject_ambiguous ... ok
[INFO] [stdout] test expanded_formula_design_supports_parenthesized_power_terms ... ok
[INFO] [stdout] test expanded_formula_design_with_offsets_carries_formula_local_model_frame ... ok
[INFO] [stdout] test formula_model_frame_reference_alias_can_resolve_observed_levels_without_declared_levels ... ok
[INFO] [stdout] test formula_model_frame_reference_rejects_ambiguous_cleaned_level_aliases ... ok
[INFO] [stdout] test intercept_only_design_has_named_all_ones_column ... ok
[INFO] [stdout] test formula_model_frame_reference_accepts_cleaned_level_aliases ... ok
[INFO] [stdout] test expanded_formula_design_supports_relevel_factor_transform ... ok
[INFO] [stdout] test formula_model_frame_resolves_r_cleaned_factor_reference_aliases ... ok
[INFO] [stdout] test formula_offset_detection_is_syntax_level ... ok
[INFO] [stdout] test original_design_full_rank_error_reports_unnamed_zero_column_index ... ok
[INFO] [stdout] test expanded_formula_design_supports_numeric_function_transforms ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 66 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.09s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/diagnostics.rs (/opt/rustwide/target/debug/deps/diagnostics-ba9dab780753a3f7)
[INFO] [stdout] 
[INFO] [stdout] running 6 tests
[INFO] [stdout] test deseq2_mcols_diagnostics_are_empty_before_glm_stages ... ok
[INFO] [stdout] test deseq2_mcols_diagnostics_use_wald_beta_conv_shape ... ok
[INFO] [stdout] test deseq2_mcols_diagnostics_include_gene_wise_dispersion_iterations ... ok
[INFO] [stdout] test deseq2_mcols_diagnostics_use_lrt_full_and_reduced_shapes ... ok
[INFO] [stdout] test deseq2_mcols_diagnostics_include_dispersion_fit_type ... ok
[INFO] [stdout] test deseq2_mcols_diagnostics_include_map_dispersion_columns ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 6 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.13s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 48 tests
[INFO] [stderr]      Running tests/dispersion_gene_est.rs (/opt/rustwide/target/debug/deps/dispersion_gene_est-9add4206215f777b)
[INFO] [stdout] test builder_rejects_rank_deficient_linear_mu_design ... ok
[INFO] [stdout] test cox_reid_adjustment_matches_intercept_hand_formula ... ok
[INFO] [stdout] test cox_reid_derivative_matches_finite_difference ... ok
[INFO] [stdout] test builder_attaches_linear_mu_gene_wise_dispersion_state ... ok
[INFO] [stdout] test cox_reid_log_posterior_adds_log_determinant_penalty ... ok
[INFO] [stdout] test dispersion_estimator_validates_residual_degrees_of_freedom ... ok
[INFO] [stdout] test dispersion_line_search_no_cr_matches_grid_scale ... ok
[INFO] [stdout] test dispersion_grid_prefers_minimum_for_perfect_fit ... ok
[INFO] [stdout] test dispersion_prior_kernel_matches_deseq2_formula ... ok
[INFO] [stdout] test dispersion_prior_validates_finite_positive_parameters ... ok
[INFO] [stdout] test builder_attaches_glm_mu_gene_wise_dispersion_state ... ok
[INFO] [stdout] test gene_wise_dispersion_options_reject_zero_niter ... ok
[INFO] [stdout] test dispersion_grid_with_cox_reid_returns_bounded_estimate ... ok
[INFO] [stdout] test cox_reid_second_derivative_matches_finite_difference ... ok
[INFO] [stdout] test initial_dispersion_uses_min_of_rough_and_moments_then_bounds ... ok
[INFO] [stdout] test likelihood_derivative_matches_finite_difference ... ok
[INFO] [stdout] test likelihood_second_derivative_matches_finite_difference ... ok
[INFO] [stdout] test line_search_preserves_high_initial_value_before_final_cap ... ok
[INFO] [stdout] test line_search_with_prior_moves_toward_prior_mean ... ok
[INFO] [stdout] test linear_mu_gene_wise_dispersion_estimator_expands_all_zero_rows ... ok
[INFO] [stdout] test linear_mu_gene_wise_dispersion_estimator_uses_normalization_factor_offsets ... ok
[INFO] [stdout] test moments_dispersion_matches_deseq2_formula ... ok
[INFO] [stdout] test moments_dispersion_rejects_overflowed_inverse_size_factor_sum ... ok
[INFO] [stdout] test moments_dispersion_rejects_overflowed_normalization_factor_column_sum ... ok
[INFO] [stdout] test moments_dispersion_uses_normalization_factor_column_means ... ok
[INFO] [stdout] test posterior_second_derivative_matches_finite_difference_with_prior_and_weights ... ok
[INFO] [stdout] test prior_derivative_matches_finite_difference_with_cox_reid ... ok
[INFO] [stdout] test prior_log_posterior_adds_expected_penalty ... ok
[INFO] [stdout] test rough_dispersion_keeps_large_finite_relative_residuals ... ok
[INFO] [stdout] test rough_dispersion_matches_deseq2_formula ... ok
[INFO] [stdout] test glm_mu_gene_wise_dispersion_estimator_refits_means_and_expands_all_zero_rows ... ok
[INFO] [stdout] test weighted_cox_reid_adjustment_matches_intercept_hand_formula ... ok
[INFO] [stdout] test weighted_cox_reid_adjustment_uses_thresholded_design_subset ... ok
[INFO] [stdout] test weighted_cox_reid_rejects_overflowed_column_subset_sum ... ok
[INFO] [stdout] test dispersion_line_search_improves_objective ... ok
[INFO] [stdout] test weighted_likelihood_derivative_matches_finite_difference ... ok
[INFO] [stdout] test weighted_likelihood_kernel_matches_unweighted_for_unit_weights ... ok
[INFO] [stdout] test dispersion_kernel_differs_from_full_likelihood_by_alpha_constant ... ok
[INFO] [stdout] test log_posterior_derivative_matches_finite_difference_with_cox_reid ... ok
[INFO] [stdout] test weighted_likelihood_second_derivative_matches_finite_difference ... ok
[INFO] [stdout] test weighted_glm_mu_gene_wise_dispersion_matches_deseq2_fitidx_weight_rows ... ok
[INFO] [stdout] test weighted_line_search_and_grid_with_prior_return_finite_estimates ... ok
[INFO] [stdout] test weighted_posterior_derivative_matches_finite_difference ... ok
[INFO] [stdout] test weighted_cox_reid_second_derivative_matches_finite_difference ... ok
[INFO] [stdout] test weighted_likelihood_rejects_overflowed_weighted_term ... ok
[INFO] [stdout] test cox_reid_adjustment_rejects_overflowed_design_product ... ok
[INFO] [stdout] test linear_model_mu_projects_rows_onto_design_cells ... ok
[INFO] [stdout] test weighted_glm_mu_gene_wise_dispersion_matches_deseq2_weighted_cox_reid ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 48 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.14s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/dispersion_map.rs (/opt/rustwide/target/debug/deps/dispersion_map-913e15b5305234c7)
[INFO] [stdout] 
[INFO] [stdout] running 11 tests
[INFO] [stdout] test estimate_map_dispersions_runs_prior_aware_line_search ... ok
[INFO] [stdout] test estimate_map_dispersions_accepts_observation_weights ... ok
[INFO] [stdout] test map_dispersion_outlier_matches_log_residual_rule ... ok
[INFO] [stdout] test map_dispersion_outlier_rejects_overflowed_threshold_arithmetic ... ok
[INFO] [stdout] test estimate_map_dispersions_expands_all_zero_rows_as_missing ... ok
[INFO] [stdout] test estimate_map_dispersions_replaces_outlier_final_dispersion_with_gene_estimate ... ok
[INFO] [stdout] test map_dispersion_outlier_rejects_non_positive_threshold_multiplier ... ok
[INFO] [stdout] test estimate_map_dispersions_validates_dimensions ... ok
[INFO] [stdout] test map_dispersion_initial_value_matches_deseq2_rule ... ok
[INFO] [stdout] test estimate_map_dispersions_unit_weights_match_unweighted ... ok
[INFO] [stdout] test estimate_map_dispersions_uses_grid_fallback_when_line_search_does_not_converge ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 11 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/dispersion_prior.rs (/opt/rustwide/target/debug/deps/dispersion_prior-0dfc323cbfb63bb6)
[INFO] [stdout] 
[INFO] [stdout] running 12 tests
[INFO] [stdout] test prior_variance_errors_when_no_rows_above_min_disp ... ok
[INFO] [stdout] test prior_variance_subtracts_sampling_variance_and_floors_at_quarter ... ok
[INFO] [stdout] test estimate_dispersion_prior_wraps_prior_variance_stage ... ok
[INFO] [stdout] test log_dispersion_residuals_use_above_min_rule_and_skip_missing_rows ... ok
[INFO] [stdout] test prior_variance_uses_quarter_floor_when_sampling_variance_is_large ... ok
[INFO] [stdout] test trigamma_keeps_large_finite_recurrence_and_rejects_overflow ... ok
[INFO] [stdout] test low_df_prior_variance_validates_supported_df_range ... ok
[INFO] [stdout] test mad_squared_matches_r_default_constant ... ok
[INFO] [stdout] test mad_squared_rejects_overflowed_variance ... ok
[INFO] [stdout] test prior_variance_with_saturated_model_does_not_subtract_or_floor ... ok
[INFO] [stdout] test trigamma_matches_known_values ... ok
[INFO] [stdout] test low_df_prior_variance_uses_deterministic_histogram_match ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 12 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 1.20s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/dispersion_reference.rs (/opt/rustwide/target/debug/deps/dispersion_reference-21d822810fcb4e91)
[INFO] [stdout] 
[INFO] [stdout] running 23 tests
[INFO] [stdout] test local_dispersion_trend_floor_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test local_dispersion_trend_matches_optional_deseq2_reference_shape ... ok
[INFO] [stdout] test dispersion_prior_variance_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test local_dispersion_trend_mixed_threshold_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test map_dispersion_matches_optional_deseq2_internal_reference ... ok
[INFO] [stdout] test mean_dispersion_trend_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_dispersion_reference_is_explicit_future_work ... ok
[INFO] [stdout] test local_dispersion_trend_predicts_optional_deseq2_reference_means ... ok
[INFO] [stdout] test native_normalization_factor_dispersion_intermediates_match_optional_deseq2_reference ... ok
[INFO] [stdout] test native_weighted_glm_mu_cox_reid_gene_wise_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_glm_mu_cox_reid_gene_wise_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_glm_mu_mean_map_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_glm_mu_local_cox_reid_map_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test parametric_dispersion_trend_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test parametric_dispersion_trend_predicts_optional_deseq2_reference_means ... ok
[INFO] [stdout] test low_df_dispersion_prior_variance_matches_optional_deseq2_reference_inputs ... ok
[INFO] [stdout] test supplied_fixed_dispersions_from_optional_reference_are_preserved ... ok
[INFO] [stdout] test native_weighted_glm_mu_map_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_weighted_glm_mu_local_map_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_glm_mu_mean_cox_reid_map_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_weighted_glm_mu_local_cox_reid_map_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_glm_mu_local_map_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_weighted_glm_mu_mean_cox_reid_map_matches_optional_deseq2_reference ... ok
[INFO] [stderr]      Running tests/dispersion_trend.rs (/opt/rustwide/target/debug/deps/dispersion_trend-7a26c6d2307651e2)
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 23 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 4.36s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 47 tests
[INFO] [stdout] test dispersion_trends_report_generic_mean_validation_context ... ok
[INFO] [stdout] test fit_dispersion_trends_reject_invalid_min_disp_options ... ok
[INFO] [stdout] test fit_local_dispersion_trend_recovers_log_linear_curve ... ok
[INFO] [stdout] test fit_dispersion_trend_dispatches_default_fit_types ... ok
[INFO] [stdout] test fit_local_dispersion_trend_sorts_fit_rows_once ... ok
[INFO] [stdout] test fit_local_dispersion_trend_returns_nan_for_missing_fitted_rows ... ok
[INFO] [stdout] test fit_local_dispersion_trend_handles_duplicated_means_with_lower_degree_fallback ... ok
[INFO] [stdout] test fit_local_dispersion_trend_uses_constant_fit_for_single_usable_row ... ok
[INFO] [stdout] test fit_local_dispersion_trend_uses_min_disp_floor_when_all_estimates_are_near_minimum ... ok
[INFO] [stdout] test fit_mean_dispersion_trend_keeps_large_even_median_finite ... ok
[INFO] [stdout] test fit_mean_dispersion_trend_keeps_large_finite_averages_finite ... ok
[INFO] [stdout] test fit_mean_dispersion_trend_rejects_invalid_trim_controls ... ok
[INFO] [stdout] test fit_mean_dispersion_trend_returns_nan_for_missing_fitted_rows ... ok
[INFO] [stdout] test fit_mean_dispersion_trend_uses_deseq2_trimmed_mean ... ok
[INFO] [stdout] test fit_parametric_dispersion_trend_errors_when_all_estimates_at_minimum ... ok
[INFO] [stdout] test fit_parametric_dispersion_trend_recovers_exact_curve ... ok
[INFO] [stdout] test fit_parametric_dispersion_trend_rejects_invalid_numeric_controls ... ok
[INFO] [stdout] test fit_parametric_dispersion_trend_rejects_zero_iteration_limits ... ok
[INFO] [stdout] test dispersion_trends_validate_fit_state_before_allow_missing_evaluation ... ok
[INFO] [stdout] test fit_parametric_dispersion_trend_returns_nan_for_missing_fitted_rows ... ok
[INFO] [stdout] test fit_parametric_dispersion_trend_validates_dimensions ... ok
[INFO] [stdout] test local_dispersion_trend_enum_reports_min_disp_floor_usage ... ok
[INFO] [stdout] test fit_dispersion_trend_rejects_glm_gam_poi_until_supported ... ok
[INFO] [stdout] test fit_dispersion_trends_reject_empty_inputs ... ok
[INFO] [stdout] test builder_mean_fit_type_dispatch_populates_constant_disp_fit ... ok
[INFO] [stdout] test fit_local_dispersion_trend_validates_inputs ... ok
[INFO] [stdout] test local_dispersion_trend_keeps_large_weighted_constant_fit_finite ... ok
[INFO] [stdout] test local_dispersion_trend_rejects_invalid_manual_shape_options ... ok
[INFO] [stdout] test local_dispersion_trend_rejects_inconsistent_empty_manual_fit_state ... ok
[INFO] [stdout] test fit_mean_dispersion_trend_keeps_deseq2_viability_gate ... ok
[INFO] [stdout] test builder_local_fit_type_dispatch_populates_local_disp_fit ... ok
[INFO] [stdout] test fit_parametric_dispersion_trend_robustly_ignores_large_residual_outlier ... ok
[INFO] [stdout] test local_dispersion_trend_rejects_manually_unsorted_fit_rows ... ok
[INFO] [stdout] test local_dispersion_trend_uses_weighted_constant_fallback_for_rank_degenerate_window ... ok
[INFO] [stdout] test local_trend_use_for_fit_matches_deseq2_threshold ... ok
[INFO] [stdout] test mean_trend_use_for_mean_matches_deseq2_threshold ... ok
[INFO] [stdout] test parametric_trend_evaluates_deseq2_formula ... ok
[INFO] [stdout] test parametric_trend_rejects_overflowed_tiny_mean_fit ... ok
[INFO] [stdout] test parametric_trend_use_for_fit_matches_min_disp_rule ... ok
[INFO] [stdout] test trend_selection_helpers_reject_invalid_min_disp ... ok
[INFO] [stdout] test trend_selection_helpers_report_helper_specific_dimension_contexts ... ok
[INFO] [stdout] test mean_trend_evaluates_constant_for_positive_means ... ok
[INFO] [stdout] test mean_trend_reports_trend_specific_invalid_fit_context ... ok
[INFO] [stdout] test mean_trend_use_for_fit_matches_deseq2_viability_threshold ... ok
[INFO] [stdout] test local_dispersion_trend_rejects_overflowed_fitted_value ... ok
[INFO] [stdout] test local_dispersion_trend_rejects_overflowing_manual_weights ... ok
[INFO] [stdout] test local_dispersion_trend_rejects_invalid_manual_fit_values_and_weights ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 47 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.02s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/glm_intercept.rs (/opt/rustwide/target/debug/deps/glm_intercept-de4384fc29b5c970)
[INFO] [stdout] 
[INFO] [stdout] running 10 tests
[INFO] [stdout] test intercept_only_fit_keeps_large_finite_normalized_mean ... ok
[INFO] [stdout] test intercept_only_fit_rejects_nonfinite_reconstructed_mu ... ok
[INFO] [stdout] test intercept_only_fit_uses_size_factors_to_reconstruct_mu ... ok
[INFO] [stdout] test intercept_only_fit_rejects_nonfinite_normalized_mean ... ok
[INFO] [stdout] test intercept_only_fit_rejects_nonfinite_output_covariance ... ok
[INFO] [stdout] test intercept_only_weighted_fit_keeps_large_finite_normalized_mean ... ok
[INFO] [stdout] test intercept_only_fit_validates_inputs ... ok
[INFO] [stdout] test intercept_only_unweighted_fit_matches_deseq2_shortcut_formulas ... ok
[INFO] [stdout] test intercept_only_fit_rejects_all_zero_rows ... ok
[INFO] [stdout] test intercept_only_weighted_fit_matches_deseq2_shortcut_formulas ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 10 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/glm_irls.rs (/opt/rustwide/target/debug/deps/glm_irls-4d7f797d96c3cfde)
[INFO] [stdout] 
[INFO] [stdout] running 46 tests
[INFO] [stdout] test beta_prior_estimated_refit_weight_helpers_validate_inputs ... ok
[INFO] [stdout] test beta_prior_refit_matches_manual_ridge_options ... ok
[INFO] [stdout] test beta_prior_quantile_matches_type7_upper_abs_quantile ... ok
[INFO] [stdout] test beta_prior_estimated_refit_runs_mle_then_shrunk_fit ... ok
[INFO] [stdout] test beta_prior_refit_weight_helpers_validate_inputs ... ok
[INFO] [stdout] test beta_prior_variance_filters_large_betas_and_sets_intercept_wide ... ok
[INFO] [stdout] test beta_prior_variance_handles_extreme_mean_dispersion_weights ... ok
[INFO] [stdout] test beta_prior_refit_with_weights_matches_normalization_factor_path ... ok
[INFO] [stdout] test beta_prior_variance_validates_dimensions_and_options ... ok
[INFO] [stdout] test beta_prior_refit_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test beta_prior_estimated_refit_weights_influence_mle_and_prior_fit ... ok
[INFO] [stdout] test beta_prior_weighted_quantile_rejects_overflowed_variance ... ok
[INFO] [stdout] test beta_prior_weighted_quantile_rejects_overflowed_weight_sum ... ok
[INFO] [stdout] test beta_prior_quantile_rejects_overflowed_variance ... ok
[INFO] [stdout] test beta_prior_estimated_refit_accepts_normalization_factors_and_weights ... ok
[INFO] [stdout] test beta_prior_variance_to_ridge_lambda_matches_deseq2_scale ... ok
[INFO] [stdout] test beta_prior_estimated_refit_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test expanded_model_group_contrast_uses_average_weights ... ok
[INFO] [stdout] test beta_prior_variance_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test expanded_model_group_helpers_validate_inputs ... ok
[INFO] [stdout] test expanded_model_fit_collapse_returns_standard_glm_surface ... ok
[INFO] [stdout] test fit_irls_dispatches_general_irls_for_multi_coefficient_design ... ok
[INFO] [stdout] test beta_prior_weighted_quantile_uses_row_weights ... ok
[INFO] [stdout] test estimate_beta_wraps_fixed_dispersion_beta_dispatch ... ok
[INFO] [stdout] test expanded_model_beta_average_collapses_grouped_coefficients ... ok
[INFO] [stdout] test expanded_model_covariance_average_propagates_grouped_uncertainty ... ok
[INFO] [stdout] test irls_optim_fallback_log_likelihood_uses_min_mu_floored_means ... ok
[INFO] [stdout] test irls_default_refits_failed_rows_with_bounded_optimizer ... ok
[INFO] [stdout] test irls_all_one_weights_match_unweighted_fit ... ok
[INFO] [stdout] test irls_optim_fallback_preserves_pre_optim_hat_diagonal ... ok
[INFO] [stdout] test irls_intercept_only_agrees_with_intercept_shortcut_for_equal_size_factors ... ok
[INFO] [stdout] test irls_qr_solver_matches_weighted_normal_equations ... ok
[INFO] [stdout] test irls_qr_solver_matches_normal_equations_with_vector_ridge ... ok
[INFO] [stdout] test irls_optim_fallback_refits_nonconverged_rows_when_enabled ... ok
[INFO] [stdout] test expanded_beta_prior_refit_runs_expanded_fit_and_collapses_standard_surface ... ok
[INFO] [stdout] test irls_rejects_all_zero_rows ... ok
[INFO] [stdout] test irls_qr_solver_handles_default_ridge ... ok
[INFO] [stdout] test irls_two_group_design_recovers_known_log2_fold_change ... ok
[INFO] [stdout] test irls_validates_inputs ... ok
[INFO] [stdout] test irls_vector_ridge_can_penalize_one_coefficient ... ok
[INFO] [stdout] test fit_irls_dispatches_intercept_only_shortcut ... ok
[INFO] [stdout] test fit_with_dispersion_wraps_fixed_dispersion_irls ... ok
[INFO] [stdout] test irls_vector_ridge_matches_scalar_ridge_when_values_match ... ok
[INFO] [stdout] test irls_qr_solver_matches_normal_equations_for_two_group_design ... ok
[INFO] [stdout] test irls_zero_weight_sample_does_not_influence_fit ... ok
[INFO] [stdout] test original_qr_results_match_non_qr_results_on_stable_rows ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 46 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.05s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/independent_filtering.rs (/opt/rustwide/target/debug/deps/independent_filtering-866d40f9a7c1fb1a)
[INFO] [stdout] 
[INFO] [stdout] running 10 tests
[INFO] [stdout] test default_theta_starts_at_fraction_of_zero_filter_values ... ok
[INFO] [stdout] test filtered_p_adjustments_match_filtered_bh_shape ... ok
[INFO] [stdout] test lowess_fit_matches_r_stats_lowess_for_default_filter_grid_fixture ... ok
[INFO] [stdout] test independent_filtering_applies_selected_threshold_and_metadata ... ok
[INFO] [stdout] test independent_filtering_rejects_invalid_options ... ok
[INFO] [stdout] test selected_filter_index_keeps_large_rejection_counts_finite ... ok
[INFO] [stdout] test independent_filtering_disabled_recomputes_regular_bh ... ok
[INFO] [stdout] test selected_filter_index_matches_deseq2_lowess_rule_fixture ... ok
[INFO] [stdout] test lowess_fit_matches_r_stats_lowess_for_dense_custom_theta_fixture ... ok
[INFO] [stderr]      Running tests/lrt.rs (/opt/rustwide/target/debug/deps/lrt-70d9eee7fd60aafa)
[INFO] [stdout] test selected_filter_index_matches_deseq2_dense_custom_theta_fixture ... ok
[INFO] [stderr]      Running tests/lrt_pipeline.rs (/opt/rustwide/target/debug/deps/lrt_pipeline-7634baa858c53491)
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 10 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.10s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 8 tests
[INFO] [stdout] test lrt_test_keeps_large_cancelling_log_likelihood_difference ... ok
[INFO] [stdout] test lrt_test_handles_missing_log_likelihoods ... ok
[INFO] [stdout] test lrt_test_masks_finite_difference_with_overflowed_scale ... ok
[INFO] [stdout] test lrt_test_bounds_extreme_finite_pvalues ... ok
[INFO] [stdout] test lrt_test_matches_chisq_upper_tail ... ok
[INFO] [stdout] test lrt_test_masks_overflowed_deviance_statistic ... ok
[INFO] [stdout] test lrt_test_validates_inputs ... ok
[INFO] [stdout] test original_lrt_uses_model_rank_difference_and_upper_tail_shape ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 8 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 21 tests
[INFO] [stdout] test fixed_dispersion_lrt_factor_level_contrast_applies_low_count_cooks_gate ... ok
[INFO] [stdout] test fixed_dispersion_lrt_coefficient_uses_stored_formula_low_count_cooks_gate ... ok
[INFO] [stdout] test fixed_dispersion_lrt_list_contrast_accepts_cleaned_positive_and_negative_aliases ... ok
[INFO] [stdout] test fixed_dispersion_lrt_contrast_replacement_preserves_metadata ... ok
[INFO] [stdout] test fixed_dispersion_lrt_formula_ordered_contrast_uses_formula_local_metadata ... ok
[INFO] [stdout] test fixed_dispersion_lrt_cooks_replacement_refits_marked_rows ... ok
[INFO] [stdout] test fixed_dispersion_lrt_list_contrast_replacement_accepts_cleaned_positive_and_negative_aliases ... ok
[INFO] [stdout] test fixed_dispersion_lrt_pipeline_expands_all_zero_rows ... ok
[INFO] [stdout] test fixed_dispersion_lrt_named_replacement_uses_stored_formula_low_count_cooks_gate ... ok
[INFO] [stdout] test fixed_dispersion_lrt_model_frame_contrast_uses_unused_declared_reference_with_expanded_design ... ok
[INFO] [stdout] test fixed_dispersion_lrt_pipeline_uses_normalization_factors_for_offsets ... ok
[INFO] [stdout] test fixed_dispersion_lrt_pipeline_fits_full_and_reduced_models ... ok
[INFO] [stdout] test fixed_dispersion_lrt_factor_level_contrast_only_zeroes_lfc ... ok
[INFO] [stdout] test fixed_dispersion_lrt_model_frame_contrast_uses_declared_factor_levels ... ok
[INFO] [stdout] test fixed_dispersion_lrt_pipeline_validates_inputs ... ok
[INFO] [stdout] test fixed_dispersion_lrt_replacement_skips_when_no_rows_are_marked ... ok
[INFO] [stdout] test fixed_dispersion_lrt_reverse_numeric_replacement_uses_stored_formula_low_count_cooks_gate ... ok
[INFO] [stdout] test fixed_dispersion_lrt_factor_level_replacement_preserves_metadata ... ok
[INFO] [stdout] test lrt_replacement_numeric_contrast_validates_stored_model_frame_metadata ... ok
[INFO] [stdout] test fixed_dispersion_lrt_model_frame_contrast_accepts_cleaned_factor_name_alias ... ok
[INFO] [stdout] test fixed_dispersion_lrt_coefficient_uses_cleaned_stored_reference_for_cooks_gate ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 21 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.05s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/lrt_reference.rs (/opt/rustwide/target/debug/deps/lrt_reference-1176836a13f0ca09)
[INFO] [stdout] 
[INFO] [stdout] running 10 tests
[INFO] [stdout] test fixed_dispersion_lrt_matches_optional_deseq2_internal_reference ... ok
[INFO] [stdout] test fixed_dispersion_weighted_lrt_matches_optional_deseq2_internal_reference ... ok
[INFO] [stdout] test native_glm_mu_mean_cox_reid_lrt_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_weighted_glm_mu_local_cox_reid_lrt_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_glm_mu_local_lrt_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_weighted_glm_mu_lrt_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_weighted_glm_mu_mean_cox_reid_lrt_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_weighted_glm_mu_local_lrt_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_glm_mu_mean_lrt_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_glm_mu_local_cox_reid_lrt_matches_optional_deseq2_reference ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 10 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 3.81s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/multiple_testing.rs (/opt/rustwide/target/debug/deps/multiple_testing-2ec9dd8431e56bb5)
[INFO] [stdout] 
[INFO] [stdout] running 4 tests
[INFO] [stdout] test original_bh_adjust_handles_ties_endpoints_and_omitted_values ... ok
[INFO] [stdout] test bh_adjust_known_example ... ok
[INFO] [stdout] test bh_adjust_rejects_invalid_f64_input ... ok
[INFO] [stdout] test bh_adjust_preserves_missing_values ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 4 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]      Running tests/native_lrt_pipeline.rs (/opt/rustwide/target/debug/deps/native_lrt_pipeline-ea85b74c89e2b932)
[INFO] [stdout] running 44 tests
[INFO] [stdout] test fitted_lrt_object_applies_numeric_contrast_all_zero_from_stored_design ... ok
[INFO] [stdout] test native_formula_lrt_default_uses_stored_formula_low_count_cooks_gate ... ok
[INFO] [stdout] test fitted_lrt_object_uses_stored_model_frame_for_character_contrast_results ... ok
[INFO] [stdout] test native_formula_lrt_default_uses_cleaned_stored_reference_for_cooks_gate ... ok
[INFO] [stdout] test native_glm_mu_lrt_contrast_keeps_lrt_pvalues_and_reports_contrast_effect ... ok
[INFO] [stdout] test fixed_lrt_supports_stored_model_frame_dot_power_design ... ok
[INFO] [stdout] test native_glm_mu_lrt_factor_level_contrast_applies_low_count_cooks_gate ... ok
[INFO] [stdout] test native_glm_mu_lrt_cooks_replacement_refit_merges_refit_rows ... ok
[INFO] [stdout] test native_glm_mu_local_lrt_matches_fixed_pipeline_when_reusing_final_dispersions ... ok
[INFO] [stdout] test lrt_results_contrast_request_canonicalizes_cleaned_sample_level_aliases ... ok
[INFO] [stdout] test native_glm_mu_lrt_cooks_replacement_refit_skips_when_no_rows_are_marked ... ok
[INFO] [stdout] test lrt_results_contrast_request_routes_character_list_and_numeric_forms ... ok
[INFO] [stdout] test native_linear_mu_local_lrt_matches_fixed_pipeline_when_reusing_final_dispersions ... ok
[INFO] [stdout] test native_glm_mu_lrt_preserves_diagnostics_and_all_zero_rows ... ok
[INFO] [stdout] test native_glm_mu_lrt_matches_fixed_pipeline_when_reusing_final_dispersions ... ok
[INFO] [stdout] test native_linear_mu_lrt_contrast_matches_fixed_pipeline_when_reusing_final_dispersions ... ok
[INFO] [stdout] test native_glm_mu_lrt_factor_level_contrast_cooks_replacement_preserves_metadata ... ok
[INFO] [stdout] test native_linear_mu_lrt_matches_fixed_pipeline_when_reusing_final_dispersions ... ok
[INFO] [stdout] test native_glm_mu_lrt_contrast_cooks_replacement_refit_merges_refit_rows ... ok
[INFO] [stdout] test native_linear_mu_lrt_contrast_specs_set_metadata_and_factor_levels ... ok
[INFO] [stdout] test top_level_fit_lrt_with_results_accepts_coefficient_name ... ok
[INFO] [stdout] test top_level_fit_lrt_runs_default_glm_mu_lrt_for_last_coefficient ... ok
[INFO] [stdout] test top_level_fit_lrt_with_results_accepts_r_cleaned_coefficient_name_alias ... ok
[INFO] [stdout] test top_level_fit_lrt_with_results_cooks_replacement_validates_reduced_design ... ok
[INFO] [stdout] test top_level_lrt_contrast_spec_resolves_named_full_model_effect ... ok
[INFO] [stdout] test top_level_fit_lrt_with_results_returns_default_lrt_results ... ok
[INFO] [stdout] test native_lrt_parametric_contrast_helpers_ignore_builder_fit_type ... ok
[INFO] [stdout] test top_level_fit_lrt_with_results_cooks_replacement_accepts_coefficient_name ... ok
[INFO] [stdout] test top_level_fit_lrt_with_results_cooks_replacement_runs_default_glm_mu_lrt ... ok
[INFO] [stdout] test top_level_lrt_formula_contrast_helpers_use_model_frame_metadata ... ok
[INFO] [stdout] test top_level_lrt_formula_helpers_build_full_and_reduced_designs ... ok
[INFO] [stdout] test top_level_lrt_formula_list_contrast_accepts_cleaned_positive_and_negative_aliases ... ok
[INFO] [stdout] test top_level_lrt_formula_list_contrast_accepts_r_cleaned_quoted_coefficient_alias ... ok
[INFO] [stdout] test top_level_lrt_formula_list_contrast_cooks_replacement_accepts_cleaned_numeric_transform_alias ... ok
[INFO] [stdout] test top_level_lrt_formula_contrast_request_uses_cleaned_stored_model_frame_factor_name ... ok
[INFO] [stdout] test top_level_lrt_formula_list_contrast_cooks_replacement_accepts_cleaned_positive_and_negative_aliases ... ok
[INFO] [stdout] test top_level_lrt_formula_list_contrast_cooks_replacement_accepts_r_cleaned_quoted_coefficient_alias ... ok
[INFO] [stdout] test top_level_lrt_formula_fit_state_retains_model_frame_metadata ... ok
[INFO] [stdout] test top_level_lrt_formula_numeric_contrast_cooks_replacement_retains_numeric_transform_metadata ... ok
[INFO] [stdout] test top_level_lrt_formula_with_results_accepts_r_cleaned_quoted_coefficient_alias ... ok
[INFO] [stdout] test top_level_lrt_fit_only_helpers_match_result_helpers ... ok
[INFO] [stdout] test native_glm_mu_lrt_contrast_all_zero_only_zeroes_lfc ... ok
[INFO] [stdout] test native_lrt_replacement_numeric_contrasts_do_not_infer_low_count_gate_from_multifactor_frame ... ok
[INFO] [stdout] test native_glm_mu_lrt_factor_level_contrast_uses_character_all_zero_cleanup ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 44 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 3.83s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/native_wald_pipeline.rs (/opt/rustwide/target/debug/deps/native_wald_pipeline-0f84c90c3a39dc47)
[INFO] [stdout] 
[INFO] [stdout] running 97 tests
[INFO] [stdout] test builder_default_fast_vst_uses_deseq2_nsub_default ... ok
[INFO] [stdout] test builder_fast_vst_glm_mu_applies_subset_trend_to_full_counts ... ok
[INFO] [stdout] test builder_fast_vst_glm_mu_preserves_normalization_factors ... ok
[INFO] [stdout] test builder_fits_glm_mu_dispersion_trend_on_fast_vst_subset ... ok
[INFO] [stdout] test builder_fast_vst_subset_trend_preserves_observation_weights ... ok
[INFO] [stdout] test builder_auto_vst_uses_fast_subset_when_observation_weights_are_present ... ok
[INFO] [stdout] test builder_auto_vst_uses_fast_subset_when_enough_rows_are_eligible ... ok
[INFO] [stdout] test builder_blind_auto_vst_uses_intercept_only_design ... ok
[INFO] [stdout] test builder_auto_vst_uses_full_trend_when_default_fast_subset_is_too_large ... ok
[INFO] [stdout] test fitted_frozen_rlog_requires_final_dispersions_and_matching_inputs ... ok
[INFO] [stdout] test fitted_map_state_drives_rlog_transform ... ok
[INFO] [stdout] test builder_blind_frozen_rlog_glm_mu_uses_intercept_only_design ... ok
[INFO] [stdout] test fitted_map_state_drives_frozen_rlog_transform_with_normalization_factors ... ok
[INFO] [stdout] test builder_blind_rlog_glm_mu_uses_intercept_only_design ... ok
[INFO] [stdout] test fitted_rlog_requires_map_dispersions_and_matching_counts ... ok
[INFO] [stdout] test fitted_state_builds_fast_vst_subset_from_base_mean_and_aligned_inputs ... ok
[INFO] [stdout] test fitted_map_state_drives_frozen_rlog_transform ... ok
[INFO] [stdout] test fitted_vst_requires_stored_dispersion_trend_and_matching_counts ... ok
[INFO] [stdout] test fitted_wald_object_applies_numeric_contrast_all_zero_from_stored_design ... ok
[INFO] [stdout] test builder_frozen_rlog_glm_mu_matches_manual_fit_state_reuse ... ok
[INFO] [stdout] test fitted_trend_state_drives_norm_and_vst_transforms ... ok
[INFO] [stdout] test fitted_frozen_rlog_expands_all_zero_rows_with_frozen_intercepts ... ok
[INFO] [stdout] test fixed_lrt_model_frame_contrast_retains_formula_derived_metadata ... ok
[INFO] [stdout] test fitted_state_can_apply_external_subset_trend_to_full_counts ... ok
[INFO] [stdout] test fitted_map_state_drives_rlog_transform_with_normalization_factors ... ok
[INFO] [stdout] test native_formula_wald_default_uses_stored_formula_low_count_cooks_gate ... ok
[INFO] [stdout] test fitted_rlog_expands_all_zero_rows_as_zero_transform_rows ... ok
[INFO] [stdout] test fixed_wald_supports_stored_model_frame_dot_power_design ... ok
[INFO] [stdout] test builder_rlog_glm_mu_matches_manual_fit_state_transform ... ok
[INFO] [stdout] test native_formula_wald_default_uses_cleaned_stored_reference_for_cooks_gate ... ok
[INFO] [stdout] test native_glm_mu_contrast_cooks_replacement_refit_merges_refit_rows ... ok
[INFO] [stdout] test native_glm_mu_cooks_replacement_refit_skips_when_no_rows_are_marked ... ok
[INFO] [stdout] test native_glm_mu_factor_level_contrast_applies_low_count_cooks_gate ... ok
[INFO] [stdout] test native_glm_mu_generic_mean_wald_runs_through_map_and_glm ... ok
[INFO] [stdout] test native_glm_mu_generic_mean_map_runs_through_selected_trend ... ok
[INFO] [stdout] test native_glm_mu_local_wald_matches_fixed_pipeline_when_reusing_final_dispersions ... ok
[INFO] [stdout] test native_glm_mu_contrast_spec_cooks_replacement_preserves_metadata ... ok
[INFO] [stdout] test native_glm_mu_cooks_replacement_refit_merges_refit_rows ... ok
[INFO] [stdout] test native_glm_mu_factor_level_contrast_cooks_replacement_preserves_metadata ... ok
[INFO] [stdout] test native_glm_mu_parametric_map_preserves_dispersion_intermediates ... ok
[INFO] [stdout] test native_linear_mu_generic_mean_wald_matches_fixed_pipeline_when_reusing_final_dispersions ... ok
[INFO] [stdout] test native_linear_mu_generic_pipeline_accepts_local_and_rejects_glm_gam_poi ... ok
[INFO] [stdout] test native_glm_mu_observation_weights_run_through_wald ... ok
[INFO] [stdout] test fitted_wald_object_uses_stored_model_frame_for_character_contrast_results ... ok
[INFO] [stdout] test native_linear_mu_generic_mean_wald_runs_through_map_and_glm ... ok
[INFO] [stdout] test native_glm_mu_wald_contrast_matches_fixed_pipeline_when_reusing_final_dispersions ... ok
[INFO] [stdout] test native_linear_mu_local_wald_matches_fixed_pipeline_when_reusing_final_dispersions ... ok
[INFO] [stdout] test native_glm_mu_parametric_wald_matches_fixed_pipeline_when_reusing_final_dispersions ... ok
[INFO] [stdout] test native_linear_mu_parametric_wald_accepts_normalization_factors ... ok
[INFO] [stdout] test native_linear_mu_parametric_wald_preserves_dispersion_intermediates ... ok
[INFO] [stdout] test native_linear_mu_parametric_wald_matches_fixed_pipeline_when_reusing_final_dispersions ... ok
[INFO] [stdout] test native_linear_mu_parametric_wald_validates_coefficient_index ... ok
[INFO] [stdout] test native_glm_mu_unit_weights_match_unweighted_wald ... ok
[INFO] [stdout] test native_glm_mu_wald_contrast_specs_set_metadata_and_factor_levels ... ok
[INFO] [stdout] test top_level_fit_contrast_specs_return_default_glm_mu_wald_fits ... ok
[INFO] [stdout] test top_level_fit_contrast_returns_default_glm_mu_wald_contrast_fit ... ok
[INFO] [stdout] test top_level_fit_keeps_lrt_explicit_until_reduced_design_is_supplied ... ok
[INFO] [stdout] test native_replacement_named_contrasts_use_stored_formula_low_count_cooks_gate ... ok
[INFO] [stdout] test top_level_fit_runs_default_glm_mu_wald_for_last_coefficient ... ok
[INFO] [stdout] test native_linear_mu_wald_contrast_matches_fixed_pipeline_when_reusing_final_dispersions ... ok
[INFO] [stdout] test top_level_fit_uses_stored_reduced_design_for_lrt ... ok
[INFO] [stdout] test top_level_fit_with_results_accepts_r_cleaned_coefficient_name_alias ... ok
[INFO] [stdout] test top_level_fit_with_results_contrast_keeps_lrt_explicit ... ok
[INFO] [stdout] test native_linear_mu_wald_contrast_specs_set_metadata_and_factor_levels ... ok
[INFO] [stdout] test top_level_fit_with_results_accepts_coefficient_name ... ok
[INFO] [stdout] test top_level_fit_with_results_cooks_replacement_keeps_lrt_explicit ... ok
[INFO] [stdout] test native_wald_parametric_contrast_helpers_ignore_builder_fit_type ... ok
[INFO] [stdout] test top_level_fit_with_results_contrast_specs_set_metadata ... ok
[INFO] [stdout] test top_level_fit_with_results_contrast_runs_default_glm_mu_wald_contrast ... ok
[INFO] [stdout] test top_level_fit_with_results_name_uses_stored_reduced_design_for_lrt ... ok
[INFO] [stdout] test top_level_fit_with_results_returns_default_wald_results ... ok
[INFO] [stdout] test top_level_fit_with_results_contrast_cooks_replacement_runs_default_glm_mu_wald_contrast ... ok
[INFO] [stdout] test top_level_formula_contrast_request_uses_cleaned_stored_model_frame_factor_name ... ok
[INFO] [stdout] test top_level_formula_contrast_request_uses_formula_derived_factor_metadata ... ok
[INFO] [stdout] test top_level_fit_with_results_contrast_spec_cooks_replacement_preserves_metadata ... ok
[INFO] [stdout] test top_level_fit_with_results_cooks_replacement_accepts_coefficient_name ... ok
[INFO] [stdout] test top_level_formula_list_contrast_accepts_r_cleaned_quoted_coefficient_alias ... ok
[INFO] [stdout] test top_level_formula_list_contrast_accepts_cleaned_positive_and_negative_aliases ... ok
[INFO] [stdout] test top_level_formula_model_frame_cleans_factor_result_names ... ok
[INFO] [stdout] test top_level_formula_numeric_contrast_cooks_replacement_retains_numeric_transform_metadata ... ok
[INFO] [stdout] test top_level_formula_contrast_replacement_uses_formula_derived_factor_metadata ... ok
[INFO] [stdout] test top_level_formula_list_contrast_cooks_replacement_accepts_cleaned_numeric_transform_alias ... ok
[INFO] [stdout] test top_level_formula_list_contrast_cooks_replacement_accepts_r_cleaned_quoted_coefficient_alias ... ok
[INFO] [stdout] test top_level_formula_list_contrast_cooks_replacement_accepts_cleaned_positive_and_negative_aliases ... ok
[INFO] [stdout] test top_level_results_character_contrast_request_requires_sample_levels ... ok
[INFO] [stdout] test top_level_formula_with_results_accepts_r_cleaned_quoted_coefficient_alias ... ok
[INFO] [stdout] test top_level_fit_with_results_cooks_replacement_runs_default_glm_mu_wald ... ok
[INFO] [stdout] test top_level_formula_fit_state_retains_model_frame_metadata ... ok
[INFO] [stdout] test top_level_lrt_contrast_methods_use_stored_reduced_design ... ok
[INFO] [stdout] test top_level_lrt_formula_replacement_refit_retains_formula_derived_metadata ... ok
[INFO] [stdout] test top_level_results_contrast_request_canonicalizes_cleaned_sample_level_aliases ... ok
[INFO] [stdout] test top_level_test_output_routes_lrt_cooks_replacement_with_stored_reduced_design ... ok
[INFO] [stdout] test top_level_test_output_routes_wald_cooks_replacement ... ok
[INFO] [stdout] test top_level_lrt_formula_contrast_uses_formula_derived_factor_metadata ... ok
[INFO] [stdout] test top_level_test_output_routes_lrt_cooks_replacement_contrasts ... ok
[INFO] [stdout] test top_level_results_contrast_request_routes_character_list_and_numeric_forms ... ok
[INFO] [stdout] test native_replacement_numeric_contrasts_do_not_infer_low_count_gate_from_multifactor_frame ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 97 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 3.47s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/nb_likelihood.rs (/opt/rustwide/target/debug/deps/nb_likelihood-9aef7e0827a2ed31)
[INFO] [stdout] 
[INFO] [stdout] running 12 tests
[INFO] [stdout] test nb_log_pmf_matches_hand_formula ... ok
[INFO] [stdout] test nb_log_pmf_zero_count_stays_finite_for_tiny_mu_dispersion ... ok
[INFO] [stdout] test nb_log_pmf_stays_finite_when_mu_dispersion_product_overflows ... ok
[INFO] [stdout] test nb_log_pmf_keeps_extreme_zero_count_product_finite ... ok
[INFO] [stdout] test negative_twice_log_likelihood_matches_deseq2_deviance_convention ... ok
[INFO] [stdout] test row_log_likelihood_sums_sample_log_pmfs ... ok
[INFO] [stdout] test weighted_log_likelihood_matches_deseq2_row_sum_shape ... ok
[INFO] [stdout] test math_distribution_helpers_wrap_nb_likelihood_primitives ... ok
[INFO] [stdout] test nb_log_pmf_approaches_poisson_for_small_dispersion ... ok
[INFO] [stdout] test nb_likelihood_validates_inputs ... ok
[INFO] [stdout] test weighted_log_likelihood_rejects_nonfinite_weighted_term ... ok
[INFO] [stdout] test matrix_log_likelihood_is_rowwise ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 12 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.08s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/observation_weights.rs (/opt/rustwide/target/debug/deps/observation_weights-31cc744694b3891d)
[INFO] [stdout] 
[INFO] [stdout] running 7 tests
[INFO] [stdout] test observation_weights_are_normalized_by_gene_row_max ... ok
[INFO] [stdout] test observation_weights_reject_overflowed_cox_reid_column_sum ... ok
[INFO] [stdout] test observation_weights_use_thresholded_subset_for_cox_reid_check ... ok
[INFO] [stdout] test observation_weights_validate_inputs ... ok
[INFO] [stdout] test builder_keeps_weight_threshold_shared_with_dispersion_options ... ok
[INFO] [stdout] test observation_weights_for_non_full_rank_design_use_zero_column_check ... ok
[INFO] [stdout] test observation_weights_flag_rows_that_drop_design_rank ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 7 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/results.rs (/opt/rustwide/target/debug/deps/results-afb62f5d3eeb6d1b)
[INFO] [stdout] 
[INFO] [stdout] running 53 tests
[INFO] [stdout] test apply_cooks_cutoff_masks_outlier_pvalues_and_recomputes_padj ... ok
[INFO] [stdout] test build_lrt_contrast_results_uses_contrast_effect_but_lrt_test_columns ... ok
[INFO] [stdout] test apply_cooks_cutoff_none_leaves_results_unchanged ... ok
[INFO] [stdout] test apply_cooks_cutoff_rejects_nonfinite_max_cooks ... ok
[INFO] [stdout] test build_wald_contrast_results_from_expanded_model_fit_reports_collapsed_contrast ... ok
[INFO] [stdout] test build_wald_contrast_results_rejects_invalid_optional_outputs ... ok
[INFO] [stdout] test build_wald_contrast_results_uses_contrast_columns ... ok
[INFO] [stdout] test apply_cooks_cutoff_low_count_heuristic_masks_when_outlier_count_is_not_low ... ok
[INFO] [stdout] test build_lrt_contrast_results_validates_lrt_and_contrast_outputs ... ok
[INFO] [stdout] test apply_cooks_cutoff_low_count_heuristic_spares_rows_with_three_larger_counts ... ok
[INFO] [stdout] test build_lrt_results_rejects_invalid_optional_outputs ... ok
[INFO] [stdout] test build_lrt_results_uses_full_model_beta_and_lrt_pvalue ... ok
[INFO] [stdout] test build_lrt_results_validates_dimensions ... ok
[INFO] [stdout] test build_wald_contrast_results_validates_dimensions ... ok
[INFO] [stdout] test build_wald_results_from_expanded_beta_prior_fit_uses_collapsed_prior_fit ... ok
[INFO] [stdout] test build_wald_results_from_expanded_model_fit_reports_collapsed_coefficients ... ok
[INFO] [stdout] test build_wald_results_omits_optional_metadata_when_absent ... ok
[INFO] [stdout] test build_wald_results_populates_deseq2_shaped_columns ... ok
[INFO] [stdout] test build_wald_results_preserves_missing_pvalues_and_padj ... ok
[INFO] [stdout] test build_wald_results_validates_dimensions ... ok
[INFO] [stdout] test default_cooks_cutoff_matches_deseq2_f_distribution_shape ... ok
[INFO] [stdout] test apply_cooks_cutoff_low_count_heuristic_validates_inputs ... ok
[INFO] [stdout] test fit_expanded_additive_beta_prior_wald_results_accepts_numeric_interactions ... ok
[INFO] [stdout] test fit_expanded_beta_prior_wald_cooks_replacement_carries_weights_into_refit ... ok
[INFO] [stdout] test fit_expanded_beta_prior_wald_results_accepts_offsets_and_weights ... ok
[INFO] [stdout] test fit_expanded_beta_prior_wald_results_runs_fit_and_result_workflow ... ok
[INFO] [stdout] test fit_expanded_beta_prior_wald_normalization_factor_cooks_replacement_refits_marked_rows ... ok
[INFO] [stdout] test fit_expanded_additive_beta_prior_wald_results_accepts_numeric_covariates ... ok
[INFO] [stdout] test fit_expanded_beta_prior_wald_results_with_cooks_replacement_refits_marked_rows ... ok
[INFO] [stdout] test fit_expanded_beta_prior_wald_results_with_cooks_replacement_skips_unmarked_rows ... ok
[INFO] [stdout] test fit_expanded_additive_beta_prior_wald_results_builds_design_and_matches_direct_workflow ... ok
[INFO] [stdout] test fit_expanded_factor_beta_prior_wald_results_accepts_normalization_factors_and_weights ... ok
[INFO] [stdout] test fit_expanded_additive_beta_prior_wald_results_accepts_normalization_factors_and_weights ... ok
[INFO] [stdout] test fit_expanded_additive_beta_prior_wald_results_accepts_factor_interactions ... ok
[INFO] [stdout] test fit_expanded_factor_beta_prior_wald_results_builds_design_and_matches_direct_workflow ... ok
[INFO] [stdout] test fit_expanded_formula_beta_prior_wald_replacement_matches_additive_workflow ... ok
[INFO] [stdout] test fit_expanded_additive_beta_prior_wald_normalization_factor_replacement_matches_direct_workflow ... ok
[INFO] [stdout] test fit_expanded_factor_beta_prior_wald_replacement_builds_design_and_matches_direct_workflow ... ok
[INFO] [stdout] test fit_expanded_factor_beta_prior_wald_normalization_factor_replacement_matches_direct_workflow ... ok
[INFO] [stdout] test original_result_frame_keeps_optional_diagnostics_ordered_and_typed ... ok
[INFO] [stdout] test fit_expanded_formula_beta_prior_wald_results_matches_additive_workflow ... ok
[INFO] [stdout] test recompute_padj_rejects_invalid_mutated_pvalues ... ok
[INFO] [stdout] test resolve_cooks_cutoff_handles_disabled_threshold_and_invalid_values ... ok
[INFO] [stdout] test result_data_frame_assembles_typed_columns_and_metadata ... ok
[INFO] [stdout] test result_column_schema_matches_current_deseq2_shape ... ok
[INFO] [stdout] test result_table_metadata_exposes_description_label_precedence ... ok
[INFO] [stdout] test result_table_metadata_preserves_resolved_numeric_contrast ... ok
[INFO] [stdout] test fit_expanded_formula_beta_prior_wald_replacement_applies_formula_offsets ... ok
[INFO] [stdout] test fit_expanded_formula_beta_prior_wald_results_applies_formula_offsets ... ok
[INFO] [stdout] test fit_expanded_additive_beta_prior_wald_replacement_builds_design_and_matches_direct_workflow ... ok
[INFO] [stdout] test fit_expanded_formula_beta_prior_wald_results_accepts_normalization_factors_and_weights ... ok
[INFO] [stdout] test fit_expanded_formula_model_frame_beta_prior_wald_matches_formula_workflow ... ok
[INFO] [stdout] test fit_expanded_formula_model_frame_beta_prior_wald_normalized_matches_formula_workflow ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 53 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 1.67s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/results_reference.rs (/opt/rustwide/target/debug/deps/results_reference-5f56748fcb84e62e)
[INFO] [stdout] 
[INFO] [stdout] running 12 tests
[INFO] [stdout] test full_deseq2_results_reference_shape_is_documented ... ok
[INFO] [stdout] test normalization_factors_match_optional_deseq2_reference ... ok
[INFO] [stdout] test normalization_stage_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test normalized_counts_match_optional_deseq2_reference ... ok
[INFO] [stdout] test weighted_base_metadata_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_weighted_glm_mu_mean_cox_reid_results_match_optional_deseq2_references ... ok
[INFO] [stdout] test native_glm_mu_local_cox_reid_results_match_optional_deseq2_references ... ok
[INFO] [stdout] test native_weighted_glm_mu_local_results_match_optional_deseq2_references ... ok
[INFO] [stdout] test native_glm_mu_mean_wald_results_match_optional_deseq2_reference ... ok
[INFO] [stdout] test native_glm_mu_mean_lrt_results_match_optional_deseq2_reference ... ok
[INFO] [stdout] test native_glm_mu_local_results_match_optional_deseq2_references ... ok
[INFO] [stdout] test native_weighted_glm_mu_local_cox_reid_results_match_optional_deseq2_references ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 12 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 4.57s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/se_covariance_reference.rs (/opt/rustwide/target/debug/deps/se_covariance_reference-91768c430563575b)
[INFO] [stdout] 
[INFO] [stdout] running 1 test
[INFO] [stdout] test hard_high_dispersion_fixed_dispersions_match_deseq2_se_covariance ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 1 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.02s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 13 tests
[INFO] [stderr]      Running tests/size_factors.rs (/opt/rustwide/target/debug/deps/size_factors-0c604938bab8059b)
[INFO] [stdout] test poscounts_size_factors_with_zeros ... ok
[INFO] [stdout] test control_gene_indices_are_validated ... ok
[INFO] [stdout] test control_genes_subset_size_factors ... ok
[INFO] [stdout] test original_norm_matrix_path_preempts_size_factors ... ok
[INFO] [stdout] test supplied_geo_means_all_zero_are_rejected ... ok
[INFO] [stdout] test builder_validates_control_gene_mask_length ... ok
[INFO] [stdout] test supplied_geo_means_are_stabilized ... ok
[INFO] [stdout] test supplied_geo_means_length_is_validated ... ok
[INFO] [stdout] test builder_uses_supplied_geometric_means ... ok
[INFO] [stdout] test ratio_size_factors_use_deseq2_log_scale_location ... ok
[INFO] [stdout] test size_factor_geometric_means_keep_large_counts_finite ... ok
[INFO] [stdout] test builder_accepts_control_gene_mask ... ok
[INFO] [stderr]      Running tests/thread_invariance.rs (/opt/rustwide/target/debug/deps/thread_invariance-7ad622382922cc10)
[INFO] [stdout] test ratio_size_factors_hand_computable ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 13 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 1 test
[INFO] [stdout] test strict_builder_is_deterministic_for_initial_stages ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 1 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/transform.rs (/opt/rustwide/target/debug/deps/transform-2865680a68f23f00)
[INFO] [stdout] 
[INFO] [stdout] running 47 tests
[INFO] [stdout] test fast_vst_subset_normalized_counts_validates_base_mean_length ... ok
[INFO] [stdout] test fast_vst_subset_indices_reject_invalid_inputs ... ok
[INFO] [stdout] test fast_vst_subset_matrix_rows_keeps_aligned_factor_rows ... ok
[INFO] [stdout] test fast_vst_subset_normalized_counts_returns_selected_rows_in_deseq2_order ... ok
[INFO] [stdout] test count_matrix_select_rows_preserves_fast_vst_order_and_names ... ok
[INFO] [stdout] test fast_vst_eligible_count_matches_base_mean_threshold ... ok
[INFO] [stdout] test fast_vst_subset_indices_use_r_round_half_to_even_positions ... ok
[INFO] [stdout] test fast_vst_subset_indices_match_deseq2_ordered_base_mean_rule ... ok
[INFO] [stdout] test local_vst_normalization_factor_summary_uses_column_geometric_means ... ok
[INFO] [stdout] test local_vst_size_factor_summary_matches_mean_inverse_size_factor ... ok
[INFO] [stdout] test frozen_rlog_validates_offsets_and_intercepts ... ok
[INFO] [stdout] test norm_transform_applies_log2_count_plus_one ... ok
[INFO] [stdout] test norm_transform_rejects_negative_and_non_finite_counts ... ok
[INFO] [stdout] test fast_vst_subset_returns_aligned_counts_normalized_factors_and_weights ... ok
[INFO] [stdout] test norm_transform_value_keeps_tiny_counts_precise ... ok
[INFO] [stdout] test norm_transform_value_matches_scalar_formula ... ok
[INFO] [stdout] test fast_vst_subset_validates_all_aligned_matrix_shapes ... ok
[INFO] [stdout] test local_vst_size_factor_summaries_keep_large_finite_means ... ok
[INFO] [stdout] test public_vst_aliases_mean_fit_branch ... ok
[INFO] [stdout] test original_fast_vst_single_subset_uses_first_ordered_eligible_row ... ok
[INFO] [stdout] test local_vst_size_factor_summaries_reject_invalid_values ... ok
[INFO] [stdout] test rlog_sample_effect_design_and_prior_match_frozen_shape ... ok
[INFO] [stdout] test rlog_sample_prior_variance_matches_weighted_log_fold_change_rule ... ok
[INFO] [stdout] test rlog_sample_design_and_prior_variance_match_sample_effect_shape ... ok
[INFO] [stdout] test vst_local_applies_numerical_integration_and_log2_scaling ... ok
[INFO] [stdout] test vst_local_rejects_negative_counts_and_bad_size_factor_summary ... ok
[INFO] [stdout] test vst_mean_rejects_negative_and_non_finite_counts ... ok
[INFO] [stdout] test rlog_with_size_factors_returns_finite_sample_effect_transform ... ok
[INFO] [stdout] test vst_local_rejects_overflowed_variance_curve ... ok
[INFO] [stdout] test vst_mean_applies_deseq2_mean_fit_closed_form ... ok
[INFO] [stdout] test vst_mean_value_stays_finite_when_dispersion_count_overflows ... ok
[INFO] [stdout] test rlog_normalization_factor_path_matches_equivalent_size_factors ... ok
[INFO] [stdout] test rlog_estimated_prior_normalization_factor_path_matches_manual_two_step_path ... ok
[INFO] [stdout] test vst_parametric_rejects_invalid_trend_coefficients ... ok
[INFO] [stdout] test vst_parametric_applies_deseq2_parametric_closed_form ... ok
[INFO] [stdout] test vst_parametric_rejects_negative_and_non_finite_counts ... ok
[INFO] [stdout] test frozen_rlog_size_factor_path_matches_equivalent_normalization_factors ... ok
[INFO] [stdout] test vst_parametric_value_stays_finite_for_extreme_counts ... ok
[INFO] [stdout] test rlog_estimated_prior_size_factor_path_matches_manual_two_step_path ... ok
[INFO] [stdout] test vst_mean_rejects_non_positive_and_non_finite_dispersion ... ok
[INFO] [stdout] test vst_mean_value_is_log2_like_for_large_counts ... ok
[INFO] [stdout] test vst_with_dispersion_trend_factor_helpers_reject_bad_factor_inputs ... ok
[INFO] [stdout] test vst_parametric_value_stays_finite_when_dispersion_count_overflows ... ok
[INFO] [stdout] test vst_parametric_value_is_log2_like_for_large_counts ... ok
[INFO] [stdout] test vst_with_dispersion_trend_and_normalization_factors_computes_local_variance_term ... ok
[INFO] [stdout] test vst_with_dispersion_trend_and_size_factors_computes_local_variance_term ... ok
[INFO] [stdout] test vst_with_dispersion_trend_dispatches_parametric_mean_and_local_branches ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 47 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.04s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/wald.rs (/opt/rustwide/target/debug/deps/wald-d6d80134177ceb31)
[INFO] [stdout] 
[INFO] [stdout] running 30 tests
[INFO] [stdout] test original_use_t_vector_degrees_of_freedom_drive_pvalues ... ok
[INFO] [stdout] test two_sided_t_pvalue_matches_r_pt_shape ... ok
[INFO] [stdout] test wald_probability_helpers_bound_or_reject_public_pvalues ... ok
[INFO] [stdout] test original_use_t_threshold_alternatives_use_t_tails ... ok
[INFO] [stdout] test wald_pvalues_compose_with_bh_adjustment ... ok
[INFO] [stdout] test two_sided_t_pvalue_uses_stable_upper_tail ... ok
[INFO] [stdout] test original_use_t_novel_contrast_uses_t_tail ... ok
[INFO] [stdout] test wald_test_coefficient_can_use_less_abs_lfc_threshold ... ok
[INFO] [stdout] test original_greater_abs_upshot_matches_greater_abs_at_zero_threshold ... ok
[INFO] [stdout] test wald_stat_and_pvalue_match_default_deseq2_normal_path ... ok
[INFO] [stdout] test wald_test_coefficient_can_use_greater_abs_lfc_threshold ... ok
[INFO] [stdout] test wald_test_coefficient_can_use_older_greater_abs_lfc_threshold ... ok
[INFO] [stdout] test wald_test_coefficient_can_use_t_lfc_threshold ... ok
[INFO] [stdout] test wald_test_coefficient_can_use_one_sided_thresholds ... ok
[INFO] [stdout] test wald_test_coefficient_can_use_residual_t_degrees_of_freedom ... ok
[INFO] [stdout] test wald_test_coefficient_preserves_statistic_when_t_df_is_missing ... ok
[INFO] [stdout] test wald_test_coefficient_can_use_scalar_t_degrees_of_freedom ... ok
[INFO] [stdout] test wald_test_contrast_masks_nonfinite_estimate_or_variance_accumulation ... ok
[INFO] [stdout] test wald_test_contrast_keeps_large_cancelling_accumulations_finite ... ok
[INFO] [stdout] test wald_test_contrast_orders_variance_products_by_magnitude ... ok
[INFO] [stdout] test wald_test_coefficient_rejects_invalid_threshold_options ... ok
[INFO] [stdout] test wald_test_coefficient_selects_requested_column ... ok
[INFO] [stdout] test wald_test_coefficient_upshot_masks_overflowed_threshold_formula ... ok
[INFO] [stdout] test wald_test_coefficient_upper_tail_keeps_extreme_threshold_pvalue_finite ... ok
[INFO] [stdout] test wald_test_coefficient_validates_per_gene_degrees_of_freedom_length ... ok
[INFO] [stdout] test wald_test_validates_coefficient_index ... ok
[INFO] [stderr]      Running tests/wald_pipeline.rs (/opt/rustwide/target/debug/deps/wald_pipeline-f04641bb8d634def)
[INFO] [stdout] test wald_test_wraps_selected_coefficient_with_options ... ok
[INFO] [stdout] test wald_test_contrast_uses_full_beta_covariance ... ok
[INFO] [stdout] test wald_test_contrast_validates_inputs ... ok
[INFO] [stdout] test wald_test_returns_none_for_missing_or_invalid_se ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 30 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.02s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 52 tests
[INFO] [stdout] test fixed_dispersion_wald_contrast_matches_selected_coefficient_for_two_group_design ... ok
[INFO] [stdout] test fixed_dispersion_wald_contrast_applies_explicit_cooks_cutoff ... ok
[INFO] [stdout] test fixed_dispersion_wald_contrast_marks_weight_failed_rows_as_skipped ... ok
[INFO] [stdout] test fixed_dispersion_wald_coefficient_uses_stored_formula_low_count_cooks_gate ... ok
[INFO] [stdout] test fixed_dispersion_wald_coefficient_uses_cleaned_stored_reference_for_cooks_gate ... ok
[INFO] [stdout] test fixed_dispersion_wald_contrast_spec_infers_shared_reference_factor_levels ... ok
[INFO] [stdout] test builder_try_model_frame_validates_wrapper_metadata ... ok
[INFO] [stdout] test fixed_dispersion_wald_contrast_spec_cooks_replacement_preserves_metadata ... ok
[INFO] [stdout] test fixed_dispersion_wald_contrast_applies_contrast_all_zero_numeric ... ok
[INFO] [stdout] test fixed_dispersion_wald_factor_level_contrast_applies_low_count_cooks_gate ... ok
[INFO] [stdout] test fixed_dispersion_wald_contrast_cooks_replacement_refits_marked_rows ... ok
[INFO] [stdout] test fixed_dispersion_wald_contrast_spec_resolves_factor_level_shape ... ok
[INFO] [stdout] test fixed_dispersion_wald_formula_ordered_contrast_uses_formula_local_metadata ... ok
[INFO] [stdout] test fixed_dispersion_wald_list_contrast_accepts_cleaned_positive_and_negative_aliases ... ok
[INFO] [stdout] test fixed_dispersion_wald_factor_level_contrast_applies_character_contrast_all_zero ... ok
[INFO] [stdout] test fixed_dispersion_wald_list_contrast_replacement_accepts_cleaned_positive_and_negative_aliases ... ok
[INFO] [stdout] test fixed_dispersion_wald_contrast_validates_inputs ... ok
[INFO] [stdout] test fixed_dispersion_wald_contrast_spec_resolves_coefficient_name ... ok
[INFO] [stdout] test fixed_dispersion_wald_model_frame_contrast_uses_unused_declared_reference_with_expanded_design ... ok
[INFO] [stdout] test fixed_dispersion_wald_model_frame_contrast_accepts_cleaned_factor_name_alias ... ok
[INFO] [stdout] test fixed_dispersion_wald_model_frame_contrast_uses_declared_factor_levels ... ok
[INFO] [stdout] test fixed_dispersion_wald_pipeline_applies_explicit_cooks_cutoff ... ok
[INFO] [stdout] test fixed_dispersion_wald_pipeline_can_use_lfc_threshold ... ok
[INFO] [stdout] test fixed_dispersion_wald_pipeline_can_disable_independent_filtering ... ok
[INFO] [stdout] test fixed_dispersion_wald_pipeline_can_disable_cooks_cutoff ... ok
[INFO] [stdout] test fixed_dispersion_wald_pipeline_can_use_t_pvalues ... ok
[INFO] [stdout] test fixed_dispersion_wald_pipeline_can_use_qr_irls_solver ... ok
[INFO] [stdout] test fixed_dispersion_wald_cooks_replacement_refits_marked_rows ... ok
[INFO] [stdout] test fixed_dispersion_wald_pipeline_handles_all_zero_only_with_supplied_size_factors ... ok
[INFO] [stdout] test fixed_dispersion_wald_contrast_spec_resolves_name_lists ... ok
[INFO] [stdout] test fixed_dispersion_wald_pipeline_applies_independent_filtering ... ok
[INFO] [stdout] test fixed_dispersion_wald_pipeline_expands_all_zero_rows ... ok
[INFO] [stdout] test fixed_dispersion_wald_named_replacement_uses_stored_formula_low_count_cooks_gate ... ok
[INFO] [stdout] test fixed_dispersion_wald_pipeline_uses_intercept_shortcut ... ok
[INFO] [stdout] test fixed_dispersion_wald_pipeline_uses_irls_for_two_group_design ... ok
[INFO] [stdout] test fixed_dispersion_wald_pipeline_uses_normalization_factors_for_offsets ... ok
[INFO] [stdout] test fixed_dispersion_wald_results_character_contrast_requires_sample_levels ... ok
[INFO] [stdout] test fixed_dispersion_wald_pipeline_validates_inputs ... ok
[INFO] [stdout] test fixed_dispersion_wald_pipeline_validates_per_gene_t_df_length ... ok
[INFO] [stdout] test model_frame_contrast_routes_validate_metadata_for_numeric_requests ... ok
[INFO] [stdout] test fixed_dispersion_wald_replacement_skips_when_no_rows_are_marked ... ok
[INFO] [stdout] test fixed_dispersion_wald_reverse_numeric_replacement_uses_stored_formula_low_count_cooks_gate ... ok
[INFO] [stdout] test original_zero_intercept_factor_level_contrasts_return_signed_lfcs ... ok
[INFO] [stdout] test original_zero_weighted_sample_matches_removed_sample_fit ... ok
[INFO] [stdout] test fixed_dispersion_wald_factor_level_cooks_replacement_preserves_metadata ... ok
[INFO] [stdout] test fixed_dispersion_wald_results_character_contrast_uses_formula_model_frame ... ok
[INFO] [stdout] test original_weighted_contrast_lfc_se_does_not_depend_on_contrast_type ... ok
[INFO] [stdout] test fixed_dispersion_wald_results_contrast_canonicalizes_cleaned_sample_level_aliases ... ok
[INFO] [stdout] test fixed_dispersion_wald_replacement_uses_stored_formula_low_count_cooks_gate ... ok
[INFO] [stdout] test original_zero_zero_list_contrast_zeroes_lfc_like_numeric_contrast ... ok
[INFO] [stdout] test fixed_dispersion_wald_results_contrast_routes_deseq2_contrast_forms ... ok
[INFO] [stdout] test wald_replacement_numeric_contrast_validates_stored_model_frame_metadata ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 52 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.05s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/wald_reference.rs (/opt/rustwide/target/debug/deps/wald_reference-a00ee9ad4014302f)
[INFO] [stdout] 
[INFO] [stdout] running 13 tests
[INFO] [stdout] test fixed_dispersion_wald_t_matches_optional_deseq2_internal_reference ... ok
[INFO] [stdout] test fixed_dispersion_wald_matches_optional_deseq2_internal_reference ... ok
[INFO] [stdout] test fixed_dispersion_cooks_match_optional_deseq2_internal_reference ... ok
[INFO] [stdout] test fixed_dispersion_weighted_wald_matches_optional_deseq2_internal_reference ... ok
[INFO] [stdout] test fixed_dispersion_force_optim_wald_matches_optional_deseq2_internal_reference ... ok
[INFO] [stdout] test native_glm_mu_local_cox_reid_wald_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_glm_mu_mean_wald_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_glm_mu_local_wald_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_weighted_glm_mu_mean_cox_reid_wald_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_weighted_glm_mu_local_wald_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_glm_mu_mean_cox_reid_wald_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_weighted_glm_mu_local_cox_reid_wald_matches_optional_deseq2_reference ... ok
[INFO] [stdout] test native_weighted_glm_mu_wald_matches_optional_deseq2_reference ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 13 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 3.82s
[INFO] [stdout] 
[INFO] [stderr]    Doc-tests rsdeseq2
[INFO] [stdout] 
[INFO] [stdout] running 0 tests
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "8750467c86a9fbc82f0da00b7d2817a8d1e42a329d506dfa2de3e4ba0e1e0748", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "8750467c86a9fbc82f0da00b7d2817a8d1e42a329d506dfa2de3e4ba0e1e0748", kill_on_drop: false }`
[INFO] [stdout] 8750467c86a9fbc82f0da00b7d2817a8d1e42a329d506dfa2de3e4ba0e1e0748
