[INFO] cloning repository https://github.com/keithyin/align-hmm [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/keithyin/align-hmm" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkeithyin%2Falign-hmm", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkeithyin%2Falign-hmm'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] a0fa9a7347a7f5964fcaa64b15654e3602cbeab4 [INFO] checking keithyin/align-hmm against master#64b185eddaa1d7ddf5e0c024be23b9cbba6c1722 for pr-143929 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkeithyin%2Falign-hmm" "/workspace/builds/worker-4-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-4-tc1/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/keithyin/align-hmm [INFO] finished tweaking git repo https://github.com/keithyin/align-hmm [INFO] tweaked toml for git repo https://github.com/keithyin/align-hmm written to /workspace/builds/worker-4-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/keithyin/align-hmm on toolchain 64b185eddaa1d7ddf5e0c024be23b9cbba6c1722 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+64b185eddaa1d7ddf5e0c024be23b9cbba6c1722" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/keithyin/align-hmm 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" "+64b185eddaa1d7ddf5e0c024be23b9cbba6c1722" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded buffer-redux v1.0.2 [INFO] [stderr] Downloaded gskits v0.11.0 [INFO] [stderr] Downloaded mm2 v0.16.0 [INFO] [stderr] Downloaded minimap2 v0.1.22+minimap2.2.28 [INFO] [stderr] Downloaded bio v2.0.3 [INFO] [stderr] Downloaded statrs v0.17.1 [INFO] [stderr] Downloaded rust-htslib v0.49.0 [INFO] [stderr] Downloaded needletail v0.6.1 [INFO] [stderr] Downloaded minimap2-sys v0.1.20+minimap2.2.28 [INFO] [stderr] Downloaded nalgebra v0.32.6 [INFO] [stderr] Downloaded hts-sys v2.2.0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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" 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[stdout] warning: unused import: `common::IDX_BASE_MAP` [INFO] [stdout] --> src/em_training/fb.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | common::IDX_BASE_MAP, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `decode_2_bases` [INFO] [stdout] --> src/em_training/fb.rs:8:20 [INFO] [stdout] | [INFO] [stdout] 8 | use super::model::{decode_2_bases, decode_emit_base, encode_2_bases, Template, TemplatePos}; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `common::IDX_BASE_MAP` [INFO] [stdout] --> src/em_training/fb_v2.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | common::IDX_BASE_MAP, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `decode_2_bases` [INFO] [stdout] --> src/em_training/fb_v2.rs:8:20 [INFO] [stdout] | [INFO] [stdout] 8 | use super::model::{decode_2_bases, decode_emit_base, encode_2_bases, Template, TemplatePos}; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `gskits::file_reader::bed_reader::BedRowData` [INFO] [stdout] --> src/em_training/fb_v2.rs:228:9 [INFO] [stdout] | [INFO] [stdout] 228 | use gskits::file_reader::bed_reader::BedRowData; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `fb::veterbi_decode` [INFO] [stdout] --> src/em_training.rs:17:5 [INFO] [stdout] | [INFO] [stdout] 17 | use fb::veterbi_decode; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unnecessary parentheses around method argument [INFO] [stdout] --> src/em_training.rs:273:9 [INFO] [stdout] | [INFO] [stdout] 273 | (alpha_dp[[tot_row - 2, tot_col - 2]] [INFO] [stdout] | ^ [INFO] [stdout] ... [INFO] [stdout] 279 | )), [INFO] [stdout] | ^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_parens)]` on by default [INFO] [stdout] help: remove these parentheses [INFO] [stdout] | [INFO] [stdout] 273 ~ alpha_dp[[tot_row - 2, tot_col - 2]] [INFO] [stdout] 274 | + beta_dp[[tot_row - 1, tot_col - 1]] [INFO] [stdout] ... [INFO] [stdout] 278 | cur_base_enc, [INFO] [stdout] 279 ~ ), [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Array` and `stack` [INFO] [stdout] --> src/hmm_model.rs:2:18 [INFO] [stdout] | [INFO] [stdout] 2 | use ndarray::{s, stack, Array, Array1, Array2, Array3, Axis, Dimension}; [INFO] [stdout] | ^^^^^ ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `boundaries_4_100` and `v1` [INFO] [stdout] --> src/main.rs:16:18 [INFO] [stdout] | [INFO] [stdout] 16 | use hmm_models::{boundaries_4_100, v1}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ ^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `common::IDX_BASE_MAP` [INFO] [stdout] --> src/em_training/fb.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | common::IDX_BASE_MAP, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `decode_2_bases` [INFO] [stdout] --> src/em_training/fb.rs:8:20 [INFO] [stdout] | [INFO] [stdout] 8 | use super::model::{decode_2_bases, decode_emit_base, encode_2_bases, Template, TemplatePos}; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `common::IDX_BASE_MAP` [INFO] [stdout] --> src/em_training/fb_v2.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | common::IDX_BASE_MAP, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `decode_2_bases` [INFO] [stdout] --> src/em_training/fb_v2.rs:8:20 [INFO] [stdout] | [INFO] [stdout] 8 | use super::model::{decode_2_bases, decode_emit_base, encode_2_bases, Template, TemplatePos}; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `fb::veterbi_decode` [INFO] [stdout] --> src/em_training.rs:17:5 [INFO] [stdout] | [INFO] [stdout] 17 | use fb::veterbi_decode; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unnecessary parentheses around method argument [INFO] [stdout] --> src/em_training.rs:273:9 [INFO] [stdout] | [INFO] [stdout] 273 | (alpha_dp[[tot_row - 2, tot_col - 2]] [INFO] [stdout] | ^ [INFO] [stdout] ... [INFO] [stdout] 279 | )), [INFO] [stdout] | ^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_parens)]` on by default [INFO] [stdout] help: remove these parentheses [INFO] [stdout] | [INFO] [stdout] 273 ~ alpha_dp[[tot_row - 2, tot_col - 2]] [INFO] [stdout] 274 | + beta_dp[[tot_row - 1, tot_col - 1]] [INFO] [stdout] ... [INFO] [stdout] 278 | cur_base_enc, [INFO] [stdout] 279 ~ ), [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Array` and `stack` [INFO] [stdout] --> src/hmm_model.rs:2:18 [INFO] [stdout] | [INFO] [stdout] 2 | use ndarray::{s, stack, Array, Array1, Array2, Array3, Axis, Dimension}; [INFO] [stdout] | ^^^^^ ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `boundaries_4_100` and `v1` [INFO] [stdout] --> src/main.rs:16:18 [INFO] [stdout] | [INFO] [stdout] 16 | use hmm_models::{boundaries_4_100, v1}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ ^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Dimension` [INFO] [stdout] --> src/hmm_model.rs:2:62 [INFO] [stdout] | [INFO] [stdout] 2 | use ndarray::{s, stack, Array, Array1, Array2, Array3, Axis, Dimension}; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Dimension` [INFO] [stdout] --> src/hmm_model.rs:2:62 [INFO] [stdout] | [INFO] [stdout] 2 | use ndarray::{s, stack, Array, Array1, Array2, Array3, Axis, Dimension}; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `idx` [INFO] [stdout] --> src/em_training.rs:302:17 [INFO] [stdout] | [INFO] [stdout] 302 | for idx in 0..100 { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_idx` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `ref_base` [INFO] [stdout] --> src/supervised_training.rs:391:25 [INFO] [stdout] | [INFO] [stdout] 391 | let ref_base = ref_base as u8; [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_base` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `cnt` is assigned to, but never used [INFO] [stdout] --> src/dataset.rs:65:13 [INFO] [stdout] | [INFO] [stdout] 65 | let mut cnt = 0; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_cnt` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `ref_base` [INFO] [stdout] --> src/supervised_training.rs:391:25 [INFO] [stdout] | [INFO] [stdout] 391 | let ref_base = ref_base as u8; [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_base` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `cnt` is assigned to, but never used [INFO] [stdout] --> src/dataset.rs:65:13 [INFO] [stdout] | [INFO] [stdout] 65 | let mut cnt = 0; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_cnt` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `encode_emit_base` is never used [INFO] [stdout] --> src/em_training/model.rs:26:8 [INFO] [stdout] | [INFO] [stdout] 26 | pub fn encode_emit_base(dw_bucket: u8, base: u8) -> u8 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `add_to_ctx_move_prob_numerator` and `add_to_move_ctx_emit_prob_numerator` are never used [INFO] [stdout] --> src/hmm_model.rs:317:12 [INFO] [stdout] | [INFO] [stdout] 309 | impl HmmBuilder { [INFO] [stdout] | --------------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 317 | pub fn add_to_ctx_move_prob_numerator(&mut self, ctx: u8, movement: TransState, prob: f64) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 321 | pub fn add_to_move_ctx_emit_prob_numerator( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `get_hmm_model` is never used [INFO] [stdout] --> src/hmm_models/v2.rs:5:8 [INFO] [stdout] | [INFO] [stdout] 5 | pub fn get_hmm_model() -> HmmModel { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `forward` is never used [INFO] [stdout] --> src/em_training/fb.rs:21:8 [INFO] [stdout] | [INFO] [stdout] 21 | pub fn forward(encoded_query: &[u8], template: &Template, hmm_model: &HmmModel) -> Array2 { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `forward_with_log_sum_exp_trick` is never used [INFO] [stdout] --> src/em_training/fb.rs:106:8 [INFO] [stdout] | [INFO] [stdout] 106 | pub fn forward_with_log_sum_exp_trick( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `backward` is never used [INFO] [stdout] --> src/em_training/fb.rs:195:8 [INFO] [stdout] | [INFO] [stdout] 195 | pub fn backward(encoded_query: &[u8], template: &Template, hmm_model: &HmmModel) -> Array2 { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `backward_with_log_sum_exp_trick` is never used [INFO] [stdout] --> src/em_training/fb.rs:289:8 [INFO] [stdout] | [INFO] [stdout] 289 | pub fn backward_with_log_sum_exp_trick( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `encode_emit_base` is never used [INFO] [stdout] --> src/em_training/model.rs:26:8 [INFO] [stdout] | [INFO] [stdout] 26 | pub fn encode_emit_base(dw_bucket: u8, base: u8) -> u8 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `new`, `add_to_ctx_move_prob_numerator`, `add_to_move_ctx_emit_prob_numerator`, and `merge` are never used [INFO] [stdout] --> src/hmm_model.rs:310:12 [INFO] [stdout] | [INFO] [stdout] 309 | impl HmmBuilder { [INFO] [stdout] | --------------- associated items in this implementation [INFO] [stdout] 310 | pub fn new() -> Self { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 317 | pub fn add_to_ctx_move_prob_numerator(&mut self, ctx: u8, movement: TransState, prob: f64) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 321 | pub fn add_to_move_ctx_emit_prob_numerator( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 332 | pub fn merge(&mut self, other: &HmmBuilder) { [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `get_hmm_model` is never used [INFO] [stdout] --> src/hmm_models/v1.rs:6:8 [INFO] [stdout] | [INFO] [stdout] 6 | pub fn get_hmm_model() -> HmmModel { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `get_hmm_model` is never used [INFO] [stdout] --> src/hmm_models/v2.rs:5:8 [INFO] [stdout] | [INFO] [stdout] 5 | pub fn get_hmm_model() -> HmmModel { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `get_hmm_model` is never used [INFO] [stdout] --> src/hmm_models/boundaries_4_100.rs:5:8 [INFO] [stdout] | [INFO] [stdout] 5 | pub fn get_hmm_model() -> HmmModel { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 3m 49s [INFO] running `Command { std: "docker" "inspect" "f6a08cfd8157effd485b1fb7debfae68dde0be413c32cba8064284c1c83aca8a", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f6a08cfd8157effd485b1fb7debfae68dde0be413c32cba8064284c1c83aca8a", kill_on_drop: false }` [INFO] [stdout] f6a08cfd8157effd485b1fb7debfae68dde0be413c32cba8064284c1c83aca8a