[INFO] fetching crate rust_deseq2 0.1.0...
[INFO] testing rust_deseq2-0.1.0 against master#1f7f8ea0721a3b1eb73e6c6d25cccb371434b320 for pr-154065-1
[INFO] extracting crate rust_deseq2 0.1.0 into /workspace/builds/worker-6-tc1/source
[INFO] started tweaking crates.io crate rust_deseq2 0.1.0
[INFO] finished tweaking crates.io crate rust_deseq2 0.1.0
[INFO] tweaked toml for crates.io crate rust_deseq2 0.1.0 written to /workspace/builds/worker-6-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate rust_deseq2 0.1.0 on toolchain 1f7f8ea0721a3b1eb73e6c6d25cccb371434b320
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1f7f8ea0721a3b1eb73e6c6d25cccb371434b320" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate rust_deseq2 0.1.0 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" "+1f7f8ea0721a3b1eb73e6c6d25cccb371434b320" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded noisy_float v0.2.0
[INFO] [stderr]   Downloaded zmij v1.0.9
[INFO] [stderr]   Downloaded jiff-static v0.2.17
[INFO] [stderr]   Downloaded jiff v0.2.17
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/source:/opt/rustwide/workdir:ro,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" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+1f7f8ea0721a3b1eb73e6c6d25cccb371434b320" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] d01a5ecc5431d4caf6cf50bd3451fee08fed2c0c0876f9fae9428d15c4d012fb
[INFO] running `Command { std: "docker" "start" "-a" "d01a5ecc5431d4caf6cf50bd3451fee08fed2c0c0876f9fae9428d15c4d012fb", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "d01a5ecc5431d4caf6cf50bd3451fee08fed2c0c0876f9fae9428d15c4d012fb", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "d01a5ecc5431d4caf6cf50bd3451fee08fed2c0c0876f9fae9428d15c4d012fb", kill_on_drop: false }`
[INFO] [stdout] d01a5ecc5431d4caf6cf50bd3451fee08fed2c0c0876f9fae9428d15c4d012fb
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/source:/opt/rustwide/workdir:ro,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" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+1f7f8ea0721a3b1eb73e6c6d25cccb371434b320" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 491c8af4286f99217500d6b9a376bb2a38c0992b1dcab89b9f2f0e2b1ea16d01
[INFO] running `Command { std: "docker" "start" "-a" "491c8af4286f99217500d6b9a376bb2a38c0992b1dcab89b9f2f0e2b1ea16d01", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.179
[INFO] [stderr]    Compiling zerocopy v0.8.31
[INFO] [stderr]    Compiling matrixmultiply v0.3.10
[INFO] [stderr]    Compiling bytemuck v1.24.0
[INFO] [stderr]    Compiling regex-syntax v0.8.8
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling zmij v1.0.9
[INFO] [stderr]    Compiling syn v2.0.113
[INFO] [stderr]    Compiling anyhow v1.0.100
[INFO] [stderr]    Compiling itertools v0.13.0
[INFO] [stderr]    Compiling clap_builder v4.5.54
[INFO] [stderr]    Compiling csv-core v0.1.13
[INFO] [stderr]    Compiling ryu v1.0.22
[INFO] [stderr]    Compiling jiff v0.2.17
[INFO] [stderr]    Compiling safe_arch v0.7.4
[INFO] [stderr]    Compiling csv v1.4.0
[INFO] [stderr]    Compiling wide v0.7.33
[INFO] [stderr]    Compiling serde_json v1.0.148
[INFO] [stderr]    Compiling regex-automata v0.4.13
[INFO] [stderr]    Compiling num-complex v0.4.6
[INFO] [stderr]    Compiling num-integer v0.1.46
[INFO] [stderr]    Compiling approx v0.5.1
[INFO] [stderr]    Compiling noisy_float v0.2.0
[INFO] [stderr]    Compiling getrandom v0.2.16
[INFO] [stderr]    Compiling num-rational v0.4.2
[INFO] [stderr]    Compiling rand_core v0.6.4
[INFO] [stderr]    Compiling ndarray v0.16.1
[INFO] [stderr]    Compiling ppv-lite86 v0.2.21
[INFO] [stderr]    Compiling simba v0.9.1
[INFO] [stderr]    Compiling rand_chacha v0.3.1
[INFO] [stderr]    Compiling rand v0.8.5
[INFO] [stderr]    Compiling thiserror-impl v2.0.17
[INFO] [stderr]    Compiling clap_derive v4.5.49
[INFO] [stderr]    Compiling serde_derive v1.0.228
[INFO] [stderr]    Compiling rand_distr v0.4.3
[INFO] [stderr]    Compiling regex v1.12.2
[INFO] [stderr]    Compiling env_filter v0.1.4
[INFO] [stderr]    Compiling env_logger v0.11.8
[INFO] [stderr]    Compiling thiserror v2.0.17
[INFO] [stderr]    Compiling clap v4.5.54
[INFO] [stderr]    Compiling serde v1.0.228
[INFO] [stderr]    Compiling ndarray-stats v0.6.0
[INFO] [stderr]    Compiling nalgebra v0.33.2
[INFO] [stderr]    Compiling statrs v0.18.0
[INFO] [stderr]    Compiling rust_deseq2 v0.1.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 38.64s
[INFO] running `Command { std: "docker" "inspect" "491c8af4286f99217500d6b9a376bb2a38c0992b1dcab89b9f2f0e2b1ea16d01", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "491c8af4286f99217500d6b9a376bb2a38c0992b1dcab89b9f2f0e2b1ea16d01", kill_on_drop: false }`
[INFO] [stdout] 491c8af4286f99217500d6b9a376bb2a38c0992b1dcab89b9f2f0e2b1ea16d01
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/source:/opt/rustwide/workdir:ro,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" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+1f7f8ea0721a3b1eb73e6c6d25cccb371434b320" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] e719f4ebd10a340b1f4282751954018b7b25aeba7bcecd49d08aa421207aded3
[INFO] running `Command { std: "docker" "start" "-a" "e719f4ebd10a340b1f4282751954018b7b25aeba7bcecd49d08aa421207aded3", kill_on_drop: false }`
[INFO] [stderr]    Compiling rustix v1.1.3
[INFO] [stderr]    Compiling getrandom v0.3.4
[INFO] [stderr]    Compiling tempfile v3.24.0
[INFO] [stderr]    Compiling rust_deseq2 v0.1.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 9.70s
[INFO] running `Command { std: "docker" "inspect" "e719f4ebd10a340b1f4282751954018b7b25aeba7bcecd49d08aa421207aded3", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "e719f4ebd10a340b1f4282751954018b7b25aeba7bcecd49d08aa421207aded3", kill_on_drop: false }`
[INFO] [stdout] e719f4ebd10a340b1f4282751954018b7b25aeba7bcecd49d08aa421207aded3
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/source:/opt/rustwide/workdir:ro,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" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+1f7f8ea0721a3b1eb73e6c6d25cccb371434b320" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] deaac8bb7e2032a745d461b703ac258f16b1ed059def3e402926ea67da761952
[INFO] running `Command { std: "docker" "start" "-a" "deaac8bb7e2032a745d461b703ac258f16b1ed059def3e402926ea67da761952", kill_on_drop: false }`
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.19s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/rust_deseq2-0e8a446cdc6e0bed)
[INFO] [stdout] 
[INFO] [stdout] running 87 tests
[INFO] [stdout] test data::builder::tests::test_builder_basic ... ok
[INFO] [stdout] test data::count_matrix::tests::test_library_sizes ... ok
[INFO] [stdout] test data::count_matrix::tests::test_count_matrix_creation ... ok
[INFO] [stdout] test data::collapse::tests::test_collapse_replicates_invalid_column ... ok
[INFO] [stdout] test data::dataset::tests::test_dataset_creation ... ok
[INFO] [stdout] test data::count_matrix::tests::test_negative_counts_rejected ... ok
[INFO] [stdout] test data::dataset::tests::test_size_factor_setting ... ok
[INFO] [stdout] test data::metadata::tests::test_sample_metadata ... ok
[INFO] [stdout] test data::builder::tests::test_builder_missing_counts ... ok
[INFO] [stdout] test data::builder::tests::test_builder_with_batch ... ok
[INFO] [stdout] test dispersion::map::tests::test_trigamma ... ok
[INFO] [stdout] test filter::cooks::tests::test_trimmed_mean ... ok
[INFO] [stdout] test data::dataset::tests::test_normalization_factors_setting ... ok
[INFO] [stdout] test dispersion::map::tests::test_prior_variance_estimation ... ok
[INFO] [stdout] test dispersion::map::tests::test_map_shrinkage ... ok
[INFO] [stdout] test filter::cooks::tests::test_default_cutoff ... ok
[INFO] [stdout] test filter::independent::tests::test_independent_filtering ... ok
[INFO] [stdout] test dispersion::gene_wise::tests::test_debug_gene_0317 ... ok
[INFO] [stdout] test data::dataset::tests::test_normalization_factors_override_size_factors ... ok
[INFO] [stdout] test dispersion::gene_wise::tests::test_max_disp_formula ... ok
[INFO] [stdout] test dispersion::gene_wise::tests::test_debug_gene_0201 ... ok
[INFO] [stdout] test dispersion::trend::tests::test_gamma_glm_identity ... ok
[INFO] [stdout] test dispersion::trend::tests::test_local_trend_fallback ... ok
[INFO] [stdout] test dispersion::trend::tests::test_hermite_interpolation ... ok
[INFO] [stdout] test filter::independent::tests::test_lowess_basic_linear ... ok
[INFO] [stdout] test filter::independent::tests::test_lowess_robustness_iterations ... ok
[INFO] [stdout] test filter::independent::tests::test_lowess_two_points ... ok
[INFO] [stdout] test filter::independent::tests::test_lowess_single_point ... ok
[INFO] [stdout] test glm::design::tests::test_check_full_rank_linear_combination ... ok
[INFO] [stdout] test glm::design::tests::test_check_full_rank_single_column ... ok
[INFO] [stdout] test glm::design::tests::test_check_full_rank_identity ... ok
[INFO] [stdout] test data::collapse::tests::test_collapse_replicates ... ok
[INFO] [stdout] test dispersion::gene_wise::tests::test_gene_wise_dispersion ... ok
[INFO] [stdout] test glm::negative_binomial::tests::test_nb_variance ... ok
[INFO] [stdout] test glm::design::tests::test_three_level_design ... ok
[INFO] [stdout] test glm::negative_binomial::tests::test_nb_weight ... ok
[INFO] [stdout] test normalization::counts::tests::test_fpkm ... ok
[INFO] [stdout] test normalization::counts::tests::test_fpm ... ok
[INFO] [stdout] test glm::negative_binomial::tests::test_nb_log_likelihood ... ok
[INFO] [stdout] test normalization::size_factors::tests::test_size_factor_estimation ... ok
[INFO] [stdout] test shrinkage::apeglm::tests::test_lbfgs_quadratic ... ok
[INFO] [stdout] test glm::design::tests::test_check_full_rank_wide_matrix ... ok
[INFO] [stdout] test rng::tests::test_r_rng_rchisq ... ok
[INFO] [stdout] test glm::design::tests::test_check_full_rank_zero_column ... ok
[INFO] [stdout] test rng::tests::test_r_rng_runif ... ok
[INFO] [stdout] test shrinkage::apeglm::tests::test_prior_var_large_se ... ok
[INFO] [stdout] test glm::design::tests::test_design_matrix_creation ... ok
[INFO] [stdout] test shrinkage::apeglm::tests::test_svalue ... ok
[INFO] [stdout] test shrinkage::ashr::tests::test_compute_svalues ... ok
[INFO] [stdout] test glm::negative_binomial::tests::test_nb_mean ... ok
[INFO] [stdout] test shrinkage::apeglm::tests::test_finite_difference_hessian_quadratic ... ok
[INFO] [stdout] test shrinkage::ashr::tests::test_create_sigma_grid ... ok
[INFO] [stdout] test shrinkage::normal::tests::test_lfc_shrinkage_requires_dds ... ok
[INFO] [stdout] test shrinkage::apeglm::tests::test_lbfgs_rosenbrock ... ok
[INFO] [stdout] test shrinkage::apeglm::tests::test_prior_var_basic ... ok
[INFO] [stdout] test shrinkage::ashr::tests::test_update_pi ... ok
[INFO] [stdout] test normalization::size_factors::tests::test_normalized_counts ... ok
[INFO] [stdout] test stats::tests::test_step_interp_right_basic ... ok
[INFO] [stdout] test stats::tests::test_weighted_quantile_upper ... ok
[INFO] [stdout] test testing::fdr::tests::test_bh_basic ... ok
[INFO] [stdout] test testing::fdr::tests::test_bh_with_nan ... ok
[INFO] [stdout] test io::csv::tests::test_read_count_matrix ... ok
[INFO] [stdout] test testing::fdr::tests::test_bh_ordering ... ok
[INFO] [stdout] test stats::tests::test_weighted_quantile_simple ... ok
[INFO] [stdout] test stats::tests::test_weighted_quantile_skewed ... ok
[INFO] [stdout] test testing::pvalue::tests::test_pvalue_range ... ok
[INFO] [stdout] test testing::lrt::tests::test_nb_log_likelihood_basic ... ok
[INFO] [stdout] test testing::pvalue::tests::test_pvalue_symmetric ... ok
[INFO] [stdout] test testing::pvalue::tests::test_pvalue_zero ... ok
[INFO] [stdout] test testing::lrt::tests::test_allzero_gene ... ok
[INFO] [stdout] test glm::design::tests::test_check_full_rank_valid ... ok
[INFO] [stdout] test testing::pvalue::tests::test_pvalue_t_distribution ... ok
[INFO] [stdout] test transform::rlog::tests::test_fit_rlog_gene_zero_counts ... ok
[INFO] [stdout] test transform::vst::tests::test_vst_mean_single ... ok
[INFO] [stdout] test transform::rlog::tests::test_qr_solve_augmented_ridge ... ok
[INFO] [stdout] test transform::vst::tests::test_vst_parametric_single ... ok
[INFO] [stdout] test transform::rlog::tests::test_qr_solve_augmented_simple ... ok
[INFO] [stdout] test testing::wald::tests::test_wald_use_t_parameter ... ok
[INFO] [stdout] test transform::rlog::tests::test_sparse_test ... ok
[INFO] [stdout] test stats::tests::test_match_weighted_upper_quantile_for_variance ... ok
[INFO] [stdout] test transform::vst::tests::test_vst_zero_handling ... ok
[INFO] [stdout] test transform::rlog::tests::test_fit_rlog_gene_simple ... ok
[INFO] [stdout] test testing::wald::tests::test_wald_test ... ok
[INFO] [stdout] test testing::wald::tests::test_wald_numeric_contrast ... ok
[INFO] [stdout] test testing::lrt::tests::test_lrt_with_design_matrices ... ok
[INFO] [stdout] test shrinkage::apeglm::tests::test_prior_var_small_se ... ok
[INFO] [stdout] test tests::test_full_pipeline ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 87 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.04s
[INFO] [stdout] 
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/rust_deseq2-0a406dfc896bf7fb)
[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]    Doc-tests rust_deseq2
[INFO] [stdout] 
[INFO] [stdout] running 4 tests
[INFO] [stdout] test src/data/builder.rs - data::builder::DESeqDataSetBuilder (line 16) ... ignored
[INFO] [stdout] test src/lib.rs - (line 8) ... ignored
[INFO] [stdout] test src/shrinkage/ashr.rs - shrinkage::ashr::shrink_lfc_ashr (line 92) ... ignored
[INFO] [stdout] test src/transform/vst.rs - transform::vst::vst (line 69) ... ignored
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 0 passed; 0 failed; 4 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "deaac8bb7e2032a745d461b703ac258f16b1ed059def3e402926ea67da761952", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "deaac8bb7e2032a745d461b703ac258f16b1ed059def3e402926ea67da761952", kill_on_drop: false }`
[INFO] [stdout] deaac8bb7e2032a745d461b703ac258f16b1ed059def3e402926ea67da761952
