[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 }`
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[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] a0fa9a7347a7f5964fcaa64b15654e3602cbeab4
[INFO] checking keithyin/align-hmm against master#df1ae0f7dd168513de2d89beb2cb7a95d4fdc118 for pr-159343
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkeithyin%2Falign-hmm" "/workspace/builds/worker-1-tc1/source", kill_on_drop: false }`
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[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-1-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/keithyin/align-hmm on toolchain df1ae0f7dd168513de2d89beb2cb7a95d4fdc118
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+df1ae0f7dd168513de2d89beb2cb7a95d4fdc118" "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" "+df1ae0f7dd168513de2d89beb2cb7a95d4fdc118" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
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[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)]` (part of `#[warn(unused)]`) 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)]` (part of `#[warn(unused)]`) 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)]` (part of `#[warn(unused)]`) 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)]` (part of `#[warn(unused)]`) 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: `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)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `cnt` is assigned to, but never used
[INFO] [stdout]   --> src/dataset.rs:65:9
[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: value assigned to `cnt` is never read
[INFO] [stdout]   --> src/dataset.rs:68:9
[INFO] [stdout]    |
[INFO] [stdout] 68 |         cnt += 1;
[INFO] [stdout]    |         ^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: maybe it is overwritten before being read?
[INFO] [stdout]    = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[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)]` (part of `#[warn(unused)]`) 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:65:9
[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: value assigned to `cnt` is never read
[INFO] [stdout]   --> src/dataset.rs:68:9
[INFO] [stdout]    |
[INFO] [stdout] 68 |         cnt += 1;
[INFO] [stdout]    |         ^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: maybe it is overwritten before being read?
[INFO] [stdout]    = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[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<f64> {
[INFO] [stdout]    |        ^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) 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<f64> {
[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] [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)]` (part of `#[warn(unused)]`) 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] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 3m 20s
[INFO] running `Command { std: "docker" "inspect" "3a50c7ce57ddb5ecb090466a5aa4e6e8c6e1c5fb644df56be328b07008e72bab", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "3a50c7ce57ddb5ecb090466a5aa4e6e8c6e1c5fb644df56be328b07008e72bab", kill_on_drop: false }`
[INFO] [stdout] 3a50c7ce57ddb5ecb090466a5aa4e6e8c6e1c5fb644df56be328b07008e72bab
