[INFO] fetching crate redeem-properties 0.1.2...
[INFO] checking redeem-properties-0.1.2 against be3da1e8c043bb6f1f335463d3b1335cdf50b03c for pr-162597
[INFO] extracting crate redeem-properties 0.1.2 into /workspace/builds/worker-5-tc2/source
[INFO] started tweaking crates.io crate redeem-properties 0.1.2
[INFO] removed 0 missing examples
[INFO] removed 0 missing tests
[INFO] finished tweaking crates.io crate redeem-properties 0.1.2
[INFO] tweaked toml for crates.io crate redeem-properties 0.1.2 written to /workspace/builds/worker-5-tc2/source/Cargo.toml
[INFO] validating manifest of crates.io crate redeem-properties 0.1.2 on toolchain be3da1e8c043bb6f1f335463d3b1335cdf50b03c
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+be3da1e8c043bb6f1f335463d3b1335cdf50b03c" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate redeem-properties 0.1.2 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" "+be3da1e8c043bb6f1f335463d3b1335cdf50b03c" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/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@sha256:8683fc1fc2eb5c9ac98e0d076ab094b2ffac7f99da555d2b6a2e27f346de2ec7" "sleep" "infinity", kill_on_drop: false }`
[INFO] [stdout] c140bccf68b4794515bc5ab863de2e91124eddc963700252314bb4d0243340e1
[INFO] running `Command { std: "docker" "start" "c140bccf68b4794515bc5ab863de2e91124eddc963700252314bb4d0243340e1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "c140bccf68b4794515bc5ab863de2e91124eddc963700252314bb4d0243340e1", 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" "c140bccf68b4794515bc5ab863de2e91124eddc963700252314bb4d0243340e1" "/opt/rustwide/cargo-home/bin/cargo" "+be3da1e8c043bb6f1f335463d3b1335cdf50b03c" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "c140bccf68b4794515bc5ab863de2e91124eddc963700252314bb4d0243340e1", 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=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-w" "/opt/rustwide/workdir" "--user" "0:0" "c140bccf68b4794515bc5ab863de2e91124eddc963700252314bb4d0243340e1" "/opt/rustwide/cargo-home/bin/cargo" "+be3da1e8c043bb6f1f335463d3b1335cdf50b03c" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
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[INFO] [stdout] warning: unused import: `IndexOp`
[INFO] [stdout]  --> src/building_blocks/bilstm.rs:1:26
[INFO] [stdout]   |
[INFO] [stdout] 1 | use candle_core::{DType, IndexOp, Result, Tensor};
[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: `std::sync::atomic::Ordering`
[INFO] [stdout]  --> src/building_blocks/featurize.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use std::sync::atomic::Ordering;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `aa_indices_tensor`, `get_mod_features_from_parsed`, `get_modification_indices`, `get_modification_string`, `remove_mass_shift`, and `self`
[INFO] [stdout]   --> src/models/model_interface.rs:3:9
[INFO] [stdout]    |
[INFO] [stdout]  3 |         self, aa_indices_tensor, aa_indices_tensor_from_arc, get_mod_features_from_parsed,
[INFO] [stdout]    |         ^^^^  ^^^^^^^^^^^^^^^^^                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 11 |             get_modification_indices, get_modification_string, parse_instrument_index,
[INFO] [stdout]    |             ^^^^^^^^^^^^^^^^^^^^^^^^  ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 12 |             remove_mass_shift,
[INFO] [stdout]    |             ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `AtomicUsize` and `Ordering`
[INFO] [stdout]   --> src/models/model_interface.rs:24:25
[INFO] [stdout]    |
[INFO] [stdout] 24 | use std::sync::atomic::{AtomicUsize, Ordering};
[INFO] [stdout]    |                         ^^^^^^^^^^^  ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `process::Output`
[INFO] [stdout]   --> src/models/model_interface.rs:28:5
[INFO] [stdout]    |
[INFO] [stdout] 28 |     process::Output,
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `AtomicUsize` and `Ordering`
[INFO] [stdout]  --> src/models/ms2_bert_model.rs:6:25
[INFO] [stdout]   |
[INFO] [stdout] 6 | use std::sync::atomic::{AtomicUsize, Ordering};
[INFO] [stdout]   |                         ^^^^^^^^^^^  ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::utils::utils::get_tensor_stats`
[INFO] [stdout]  --> src/models/ms2_bert_model.rs:9:5
[INFO] [stdout]   |
[INFO] [stdout] 9 | use crate::utils::utils::get_tensor_stats;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Tensor`
[INFO] [stdout]  --> src/models/ms2_model.rs:6:27
[INFO] [stdout]   |
[INFO] [stdout] 6 | use candle_core::{Device, Tensor};
[INFO] [stdout]   |                           ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Tensor`
[INFO] [stdout]  --> src/models/rt_model.rs:9:27
[INFO] [stdout]   |
[INFO] [stdout] 9 | use candle_core::{Device, Tensor};
[INFO] [stdout]   |                           ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `candle_nn::VarMap`
[INFO] [stdout]   --> src/models/rt_model.rs:10:5
[INFO] [stdout]    |
[INFO] [stdout] 10 | use candle_nn::VarMap;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::ops::Deref`
[INFO] [stdout]   --> src/models/rt_model.rs:12:5
[INFO] [stdout]    |
[INFO] [stdout] 12 | use std::ops::Deref;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Arc` and `Mutex`
[INFO] [stdout]  --> src/utils/logging.rs:3:23
[INFO] [stdout]   |
[INFO] [stdout] 3 | use std::sync::{mpsc, Arc, Mutex};
[INFO] [stdout]   |                       ^^^  ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::ops::Index`
[INFO] [stdout]   --> src/utils/peptdeep_utils.rs:13:5
[INFO] [stdout]    |
[INFO] [stdout] 13 | use std::ops::Index;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::f64::consts::PI`
[INFO] [stdout]  --> src/utils/utils.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use std::f64::consts::PI;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `IndexOp`
[INFO] [stdout]  --> src/building_blocks/bilstm.rs:1:26
[INFO] [stdout]   |
[INFO] [stdout] 1 | use candle_core::{DType, IndexOp, Result, Tensor};
[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: `std::sync::atomic::Ordering`
[INFO] [stdout]  --> src/building_blocks/featurize.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use std::sync::atomic::Ordering;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::path::PathBuf`
[INFO] [stdout]    --> src/building_blocks/featurize.rs:241:9
[INFO] [stdout]     |
[INFO] [stdout] 241 |     use std::path::PathBuf;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::path::PathBuf`
[INFO] [stdout]    --> src/models/ccs_cnn_tf_model.rs:340:9
[INFO] [stdout]     |
[INFO] [stdout] 340 |     use std::path::PathBuf;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `aa_indices_tensor`, `get_mod_features_from_parsed`, `get_modification_indices`, `get_modification_string`, `remove_mass_shift`, and `self`
[INFO] [stdout]   --> src/models/model_interface.rs:3:9
[INFO] [stdout]    |
[INFO] [stdout]  3 |         self, aa_indices_tensor, aa_indices_tensor_from_arc, get_mod_features_from_parsed,
[INFO] [stdout]    |         ^^^^  ^^^^^^^^^^^^^^^^^                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 11 |             get_modification_indices, get_modification_string, parse_instrument_index,
[INFO] [stdout]    |             ^^^^^^^^^^^^^^^^^^^^^^^^  ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 12 |             remove_mass_shift,
[INFO] [stdout]    |             ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `AtomicUsize` and `Ordering`
[INFO] [stdout]   --> src/models/model_interface.rs:24:25
[INFO] [stdout]    |
[INFO] [stdout] 24 | use std::sync::atomic::{AtomicUsize, Ordering};
[INFO] [stdout]    |                         ^^^^^^^^^^^  ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Deref` and `process::Output`
[INFO] [stdout]   --> src/models/model_interface.rs:27:11
[INFO] [stdout]    |
[INFO] [stdout] 27 |     ops::{Deref, Index},
[INFO] [stdout]    |           ^^^^^
[INFO] [stdout] 28 |     process::Output,
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `AtomicUsize` and `Ordering`
[INFO] [stdout]  --> src/models/ms2_bert_model.rs:6:25
[INFO] [stdout]   |
[INFO] [stdout] 6 | use std::sync::atomic::{AtomicUsize, Ordering};
[INFO] [stdout]   |                         ^^^^^^^^^^^  ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::utils::utils::get_tensor_stats`
[INFO] [stdout]  --> src/models/ms2_bert_model.rs:9:5
[INFO] [stdout]   |
[INFO] [stdout] 9 | use crate::utils::utils::get_tensor_stats;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Tensor`
[INFO] [stdout]  --> src/models/ms2_model.rs:6:27
[INFO] [stdout]   |
[INFO] [stdout] 6 | use candle_core::{Device, Tensor};
[INFO] [stdout]   |                           ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Tensor`
[INFO] [stdout]  --> src/models/rt_model.rs:9:27
[INFO] [stdout]   |
[INFO] [stdout] 9 | use candle_core::{Device, Tensor};
[INFO] [stdout]   |                           ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `candle_nn::VarMap`
[INFO] [stdout]   --> src/models/rt_model.rs:10:5
[INFO] [stdout]    |
[INFO] [stdout] 10 | use candle_nn::VarMap;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::ops::Deref`
[INFO] [stdout]   --> src/models/rt_model.rs:12:5
[INFO] [stdout]    |
[INFO] [stdout] 12 | use std::ops::Deref;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Arc` and `Mutex`
[INFO] [stdout]  --> src/utils/logging.rs:3:23
[INFO] [stdout]   |
[INFO] [stdout] 3 | use std::sync::{mpsc, Arc, Mutex};
[INFO] [stdout]   |                       ^^^  ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Arc` and `Mutex`
[INFO] [stdout]    --> src/utils/logging.rs:221:21
[INFO] [stdout]     |
[INFO] [stdout] 221 |     use std::sync::{Arc, Mutex};
[INFO] [stdout]     |                     ^^^  ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::ops::Index`
[INFO] [stdout]   --> src/utils/peptdeep_utils.rs:13:5
[INFO] [stdout]    |
[INFO] [stdout] 13 | use std::ops::Index;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `regex::Regex`
[INFO] [stdout]    --> src/utils/peptdeep_utils.rs:735:9
[INFO] [stdout]     |
[INFO] [stdout] 735 |     use regex::Regex;
[INFO] [stdout]     |         ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::f64::consts::PI`
[INFO] [stdout]  --> src/utils/utils.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use std::f64::consts::PI;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Device`, `Result`, and `Tensor`
[INFO] [stdout]    --> src/utils/utils.rs:201:23
[INFO] [stdout]     |
[INFO] [stdout] 201 |     use candle_core::{Device, Result, Tensor};
[INFO] [stdout]     |                       ^^^^^^  ^^^^^^  ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Deref`
[INFO] [stdout]   --> src/models/model_interface.rs:27:11
[INFO] [stdout]    |
[INFO] [stdout] 27 |     ops::{Deref, Index},
[INFO] [stdout]    |           ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `layer_idx`
[INFO] [stdout]   --> src/building_blocks/bilstm.rs:83:9
[INFO] [stdout]    |
[INFO] [stdout] 83 |         layer_idx: &i32,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_layer_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: `hn_concat`
[INFO] [stdout]    --> src/building_blocks/bilstm.rs:155:13
[INFO] [stdout]     |
[INFO] [stdout] 155 |         let hn_concat = Tensor::cat(&[last_forward_state, last_backward_state], 1)?; // Shape: [1, 256]
[INFO] [stdout]     |             ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_hn_concat`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `seq_len`
[INFO] [stdout]    --> src/building_blocks/bilstm.rs:174:26
[INFO] [stdout]     |
[INFO] [stdout] 174 |         let (batch_size, seq_len, input_size) = xs.dims3()?;
[INFO] [stdout]     |                          ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_seq_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `input_size`
[INFO] [stdout]    --> src/building_blocks/bilstm.rs:174:35
[INFO] [stdout]     |
[INFO] [stdout] 174 |         let (batch_size, seq_len, input_size) = xs.dims3()?;
[INFO] [stdout]     |                                   ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_input_size`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `mod_feature_size`
[INFO] [stdout]    --> src/building_blocks/building_blocks.rs:623:9
[INFO] [stdout]     |
[INFO] [stdout] 623 |         mod_feature_size: usize,
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mod_feature_size`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `batch_size`
[INFO] [stdout]    --> src/building_blocks/building_blocks.rs:636:14
[INFO] [stdout]     |
[INFO] [stdout] 636 |         let (batch_size, seq_len, _) = mod_x.dims3()?;
[INFO] [stdout]     |              ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_batch_size`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `seq_len`
[INFO] [stdout]    --> src/building_blocks/building_blocks.rs:636:26
[INFO] [stdout]     |
[INFO] [stdout] 636 |         let (batch_size, seq_len, _) = mod_x.dims3()?;
[INFO] [stdout]     |                          ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_seq_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `output_attentions`
[INFO] [stdout]    --> src/building_blocks/building_blocks.rs:879:9
[INFO] [stdout]     |
[INFO] [stdout] 879 |         output_attentions: bool,
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_output_attentions`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `b`
[INFO] [stdout]     --> src/building_blocks/building_blocks.rs:1278:14
[INFO] [stdout]      |
[INFO] [stdout] 1278 |         let (b, s, d) = x.dims3()?;
[INFO] [stdout]      |              ^ help: if this is intentional, prefix it with an underscore: `_b`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `s`
[INFO] [stdout]     --> src/building_blocks/building_blocks.rs:1278:17
[INFO] [stdout]      |
[INFO] [stdout] 1278 |         let (b, s, d) = x.dims3()?;
[INFO] [stdout]      |                 ^ help: if this is intentional, prefix it with an underscore: `_s`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `d`
[INFO] [stdout]     --> src/building_blocks/building_blocks.rs:1278:20
[INFO] [stdout]      |
[INFO] [stdout] 1278 |         let (b, s, d) = x.dims3()?;
[INFO] [stdout]      |                    ^ help: if this is intentional, prefix it with an underscore: `_d`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `b`
[INFO] [stdout]     --> src/building_blocks/building_blocks.rs:1282:14
[INFO] [stdout]      |
[INFO] [stdout] 1282 |         let (b, s, d) = x.dims3()?;
[INFO] [stdout]      |              ^ help: if this is intentional, prefix it with an underscore: `_b`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `s`
[INFO] [stdout]     --> src/building_blocks/building_blocks.rs:1282:17
[INFO] [stdout]      |
[INFO] [stdout] 1282 |         let (b, s, d) = x.dims3()?;
[INFO] [stdout]      |                 ^ help: if this is intentional, prefix it with an underscore: `_s`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `d`
[INFO] [stdout]     --> src/building_blocks/building_blocks.rs:1282:20
[INFO] [stdout]      |
[INFO] [stdout] 1282 |         let (b, s, d) = x.dims3()?;
[INFO] [stdout]      |                    ^ help: if this is intentional, prefix it with an underscore: `_d`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `input_dim`
[INFO] [stdout]   --> src/building_blocks/nn.rs:88:9
[INFO] [stdout]    |
[INFO] [stdout] 88 |         input_dim: usize,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_input_dim`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/models/ccs_cnn_tf_model.rs:48:13
[INFO] [stdout]    |
[INFO] [stdout] 48 |         let mut varmap = VarMap::new();
[INFO] [stdout]    |             ----^^^^^^
[INFO] [stdout]    |             |
[INFO] [stdout]    |             help: remove this `mut`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `layer_idx`
[INFO] [stdout]   --> src/building_blocks/bilstm.rs:83:9
[INFO] [stdout]    |
[INFO] [stdout] 83 |         layer_idx: &i32,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_layer_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: `hn_concat`
[INFO] [stdout]    --> src/building_blocks/bilstm.rs:155:13
[INFO] [stdout]     |
[INFO] [stdout] 155 |         let hn_concat = Tensor::cat(&[last_forward_state, last_backward_state], 1)?; // Shape: [1, 256]
[INFO] [stdout]     |             ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_hn_concat`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `seq_len`
[INFO] [stdout]    --> src/building_blocks/bilstm.rs:174:26
[INFO] [stdout]     |
[INFO] [stdout] 174 |         let (batch_size, seq_len, input_size) = xs.dims3()?;
[INFO] [stdout]     |                          ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_seq_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `input_size`
[INFO] [stdout]    --> src/building_blocks/bilstm.rs:174:35
[INFO] [stdout]     |
[INFO] [stdout] 174 |         let (batch_size, seq_len, input_size) = xs.dims3()?;
[INFO] [stdout]     |                                   ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_input_size`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `h0`
[INFO] [stdout]    --> src/building_blocks/bilstm.rs:269:13
[INFO] [stdout]     |
[INFO] [stdout] 269 |         let h0 = Tensor::zeros(
[INFO] [stdout]     |             ^^ help: if this is intentional, prefix it with an underscore: `_h0`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `c0`
[INFO] [stdout]    --> src/building_blocks/bilstm.rs:274:13
[INFO] [stdout]     |
[INFO] [stdout] 274 |         let c0 = Tensor::zeros(
[INFO] [stdout]     |             ^^ help: if this is intentional, prefix it with an underscore: `_c0`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unreachable pattern
[INFO] [stdout]    --> src/models/model_interface.rs:515:13
[INFO] [stdout]     |
[INFO] [stdout] 515 |             _ => Err(anyhow::anyhow!(
[INFO] [stdout]     |             ^ no value can reach this
[INFO] [stdout]     |
[INFO] [stdout] note: multiple earlier patterns match some of the same values
[INFO] [stdout]    --> src/models/model_interface.rs:515:13
[INFO] [stdout]     |
[INFO] [stdout] 487 |             PropertyType::RT => {
[INFO] [stdout]     |             ---------------- matches some of the same values
[INFO] [stdout] ...
[INFO] [stdout] 497 |             PropertyType::CCS => {
[INFO] [stdout]     |             ----------------- matches some of the same values
[INFO] [stdout] ...
[INFO] [stdout] 507 |             PropertyType::MS2 => {
[INFO] [stdout]     |             ----------------- matches some of the same values
[INFO] [stdout] ...
[INFO] [stdout] 515 |             _ => Err(anyhow::anyhow!(
[INFO] [stdout]     |             ^ collectively making this unreachable
[INFO] [stdout]     = note: `#[warn(unreachable_patterns)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `mod_feature_size`
[INFO] [stdout]    --> src/building_blocks/building_blocks.rs:623:9
[INFO] [stdout]     |
[INFO] [stdout] 623 |         mod_feature_size: usize,
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mod_feature_size`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `batch_size`
[INFO] [stdout]    --> src/building_blocks/building_blocks.rs:636:14
[INFO] [stdout]     |
[INFO] [stdout] 636 |         let (batch_size, seq_len, _) = mod_x.dims3()?;
[INFO] [stdout]     |              ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_batch_size`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `seq_len`
[INFO] [stdout]    --> src/building_blocks/building_blocks.rs:636:26
[INFO] [stdout]     |
[INFO] [stdout] 636 |         let (batch_size, seq_len, _) = mod_x.dims3()?;
[INFO] [stdout]     |                          ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_seq_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `output_attentions`
[INFO] [stdout]    --> src/building_blocks/building_blocks.rs:879:9
[INFO] [stdout]     |
[INFO] [stdout] 879 |         output_attentions: bool,
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_output_attentions`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `b`
[INFO] [stdout]     --> src/building_blocks/building_blocks.rs:1278:14
[INFO] [stdout]      |
[INFO] [stdout] 1278 |         let (b, s, d) = x.dims3()?;
[INFO] [stdout]      |              ^ help: if this is intentional, prefix it with an underscore: `_b`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `s`
[INFO] [stdout]     --> src/building_blocks/building_blocks.rs:1278:17
[INFO] [stdout]      |
[INFO] [stdout] 1278 |         let (b, s, d) = x.dims3()?;
[INFO] [stdout]      |                 ^ help: if this is intentional, prefix it with an underscore: `_s`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `d`
[INFO] [stdout]     --> src/building_blocks/building_blocks.rs:1278:20
[INFO] [stdout]      |
[INFO] [stdout] 1278 |         let (b, s, d) = x.dims3()?;
[INFO] [stdout]      |                    ^ help: if this is intentional, prefix it with an underscore: `_d`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `b`
[INFO] [stdout]     --> src/building_blocks/building_blocks.rs:1282:14
[INFO] [stdout]      |
[INFO] [stdout] 1282 |         let (b, s, d) = x.dims3()?;
[INFO] [stdout]      |              ^ help: if this is intentional, prefix it with an underscore: `_b`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `s`
[INFO] [stdout]     --> src/building_blocks/building_blocks.rs:1282:17
[INFO] [stdout]      |
[INFO] [stdout] 1282 |         let (b, s, d) = x.dims3()?;
[INFO] [stdout]      |                 ^ help: if this is intentional, prefix it with an underscore: `_s`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `d`
[INFO] [stdout]     --> src/building_blocks/building_blocks.rs:1282:20
[INFO] [stdout]      |
[INFO] [stdout] 1282 |         let (b, s, d) = x.dims3()?;
[INFO] [stdout]      |                    ^ help: if this is intentional, prefix it with an underscore: `_d`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/models/model_interface.rs:828:21
[INFO] [stdout]     |
[INFO] [stdout] 828 |                 let mut t = target.clone();
[INFO] [stdout]     |                     ----^
[INFO] [stdout]     |                     |
[INFO] [stdout]     |                     help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `tgt_flat` is never read
[INFO] [stdout]     --> src/models/model_interface.rs:1058:29
[INFO] [stdout]      |
[INFO] [stdout] 1058 | ...                   tgt_flat = Tensor::zeros(
[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: value assigned to `tgt_flat` is never read
[INFO] [stdout]    --> src/models/model_interface.rs:927:25
[INFO] [stdout]     |
[INFO] [stdout] 927 |                         tgt_flat = Tensor::zeros(
[INFO] [stdout]     |                         ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `val_batches`
[INFO] [stdout]     --> src/models/model_interface.rs:1027:21
[INFO] [stdout]      |
[INFO] [stdout] 1027 |                 let val_batches =
[INFO] [stdout]      |                     ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_val_batches`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `modifications`
[INFO] [stdout]     --> src/models/model_interface.rs:1242:9
[INFO] [stdout]      |
[INFO] [stdout] 1242 |         modifications: HashMap<
[INFO] [stdout]      |         ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_modifications`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `seq_len`
[INFO] [stdout]     --> src/models/model_interface.rs:1571:26
[INFO] [stdout]      |
[INFO] [stdout] 1571 |         let (batch_size, seq_len, feature_size) = predicts.shape().dims3()?;
[INFO] [stdout]      |                          ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_seq_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `feature_size`
[INFO] [stdout]     --> src/models/model_interface.rs:1571:35
[INFO] [stdout]      |
[INFO] [stdout] 1571 |         let (batch_size, seq_len, feature_size) = predicts.shape().dims3()?;
[INFO] [stdout]      |                                   ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_feature_size`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `expect_out`
[INFO] [stdout]    --> src/building_blocks/featurize.rs:257:13
[INFO] [stdout]     |
[INFO] [stdout] 257 |         let expect_out = Tensor::from_vec(
[INFO] [stdout]     |             ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_expect_out`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `input_dim`
[INFO] [stdout]   --> src/building_blocks/nn.rs:88:9
[INFO] [stdout]    |
[INFO] [stdout] 88 |         input_dim: usize,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_input_dim`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/models/rt_cnn_transformer_model.rs:45:13
[INFO] [stdout]    |
[INFO] [stdout] 45 |         let mut varmap = VarMap::new();
[INFO] [stdout]    |             ----^^^^^^
[INFO] [stdout]    |             |
[INFO] [stdout]    |             help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/models/ccs_cnn_tf_model.rs:48:13
[INFO] [stdout]    |
[INFO] [stdout] 48 |         let mut varmap = VarMap::new();
[INFO] [stdout]    |             ----^^^^^^
[INFO] [stdout]    |             |
[INFO] [stdout]    |             help: remove this `mut`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unreachable pattern
[INFO] [stdout]    --> src/models/model_interface.rs:515:13
[INFO] [stdout]     |
[INFO] [stdout] 515 |             _ => Err(anyhow::anyhow!(
[INFO] [stdout]     |             ^ no value can reach this
[INFO] [stdout]     |
[INFO] [stdout] note: multiple earlier patterns match some of the same values
[INFO] [stdout]    --> src/models/model_interface.rs:515:13
[INFO] [stdout]     |
[INFO] [stdout] 487 |             PropertyType::RT => {
[INFO] [stdout]     |             ---------------- matches some of the same values
[INFO] [stdout] ...
[INFO] [stdout] 497 |             PropertyType::CCS => {
[INFO] [stdout]     |             ----------------- matches some of the same values
[INFO] [stdout] ...
[INFO] [stdout] 507 |             PropertyType::MS2 => {
[INFO] [stdout]     |             ----------------- matches some of the same values
[INFO] [stdout] ...
[INFO] [stdout] 515 |             _ => Err(anyhow::anyhow!(
[INFO] [stdout]     |             ^ collectively making this unreachable
[INFO] [stdout]     = note: `#[warn(unreachable_patterns)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/utils/peptdeep_utils.rs:307:9
[INFO] [stdout]     |
[INFO] [stdout] 307 |     let mut offset = 0;
[INFO] [stdout]     |         ----^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `offset`
[INFO] [stdout]    --> src/utils/peptdeep_utils.rs:307:9
[INFO] [stdout]     |
[INFO] [stdout] 307 |     let mut offset = 0;
[INFO] [stdout]     |         ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_offset`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `offset` is assigned to, but never used
[INFO] [stdout]    --> src/utils/peptdeep_utils.rs:377:9
[INFO] [stdout]     |
[INFO] [stdout] 377 |     let mut offset = 0;
[INFO] [stdout]     |         ^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_offset` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `offset` is never read
[INFO] [stdout]    --> src/utils/peptdeep_utils.rs:388:17
[INFO] [stdout]     |
[INFO] [stdout] 388 |                 offset += mat.end() - mat.start();
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/models/model_interface.rs:828:21
[INFO] [stdout]     |
[INFO] [stdout] 828 |                 let mut t = target.clone();
[INFO] [stdout]     |                     ----^
[INFO] [stdout]     |                     |
[INFO] [stdout]     |                     help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated function `new` is never used
[INFO] [stdout]    --> src/building_blocks/building_blocks.rs:514:8
[INFO] [stdout]     |
[INFO] [stdout] 513 | impl AAEmbedding {
[INFO] [stdout]     | ---------------- associated function in this implementation
[INFO] [stdout] 514 |     fn new(hidden_size: usize, vb: &nn::VarBuilder) -> Result<Self> {
[INFO] [stdout]     |        ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated function `new` is never used
[INFO] [stdout]    --> src/building_blocks/building_blocks.rs:542:8
[INFO] [stdout]     |
[INFO] [stdout] 541 | impl PositionalEncoding {
[INFO] [stdout]     | ----------------------- associated function in this implementation
[INFO] [stdout] 542 |     fn new(out_features: usize, max_len: usize, device: &Device) -> Result<Self> {
[INFO] [stdout]     |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated function `new` is never used
[INFO] [stdout]    --> src/building_blocks/building_blocks.rs:661:8
[INFO] [stdout]     |
[INFO] [stdout] 660 | impl Input26aaModPositionalEncoding {
[INFO] [stdout]     | ----------------------------------- associated function in this implementation
[INFO] [stdout] 661 |     fn new(_out_features: usize, _max_len: usize, _device: &Device) -> Result<Self> {
[INFO] [stdout]     |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated function `new` is never used
[INFO] [stdout]    --> src/building_blocks/building_blocks.rs:868:8
[INFO] [stdout]     |
[INFO] [stdout] 867 | impl ModLossNN {
[INFO] [stdout]     | -------------- associated function in this implementation
[INFO] [stdout] 868 |     fn new() -> Self {
[INFO] [stdout]     |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `tgt_flat` is never read
[INFO] [stdout]     --> src/models/model_interface.rs:1058:29
[INFO] [stdout]      |
[INFO] [stdout] 1058 | ...                   tgt_flat = Tensor::zeros(
[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: constant `CHARGE_FACTOR` is never used
[INFO] [stdout]   --> src/models/ccs_cnn_lstm_model.rs:21:7
[INFO] [stdout]    |
[INFO] [stdout] 21 | const CHARGE_FACTOR: f64 = 0.1;
[INFO] [stdout]    |       ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `tgt_flat` is never read
[INFO] [stdout]    --> src/models/model_interface.rs:927:25
[INFO] [stdout]     |
[INFO] [stdout] 927 |                         tgt_flat = Tensor::zeros(
[INFO] [stdout]     |                         ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `NCE_FACTOR` is never used
[INFO] [stdout]   --> src/models/ccs_cnn_lstm_model.rs:22:7
[INFO] [stdout]    |
[INFO] [stdout] 22 | const NCE_FACTOR: f64 = 0.01;
[INFO] [stdout]    |       ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `val_batches`
[INFO] [stdout]     --> src/models/model_interface.rs:1027:21
[INFO] [stdout]      |
[INFO] [stdout] 1027 |                 let val_batches =
[INFO] [stdout]      |                     ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_val_batches`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `var_store`, `fixed_sequence_len`, `num_frag_types`, `num_modloss_types`, and `mask_modloss` are never read
[INFO] [stdout]   --> src/models/ccs_cnn_lstm_model.rs:28:5
[INFO] [stdout]    |
[INFO] [stdout] 27 | pub struct CCSCNNLSTMModel {
[INFO] [stdout]    |            --------------- fields in this struct
[INFO] [stdout] 28 |     var_store: VarBuilder<'static>,
[INFO] [stdout]    |     ^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 32 |     fixed_sequence_len: usize,
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 33 |     // Total number of fragment types of a fragmentation position to predict
[INFO] [stdout] 34 |     num_frag_types: usize,
[INFO] [stdout]    |     ^^^^^^^^^^^^^^
[INFO] [stdout] 35 |     // Number of fragment types of a fragmentation position to predict, by default 0
[INFO] [stdout] 36 |     num_modloss_types: usize,
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 37 |     // If True, the modloss layer will be disabled, by default True
[INFO] [stdout] 38 |     mask_modloss: bool,
[INFO] [stdout]    |     ^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `CCSCNNLSTMModel` has a derived impl for the trait `Clone`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `CHARGE_FACTOR` is never used
[INFO] [stdout]   --> src/models/ccs_cnn_tf_model.rs:22:7
[INFO] [stdout]    |
[INFO] [stdout] 22 | const CHARGE_FACTOR: f64 = 0.1;
[INFO] [stdout]    |       ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `NCE_FACTOR` is never used
[INFO] [stdout]   --> src/models/ccs_cnn_tf_model.rs:23:7
[INFO] [stdout]    |
[INFO] [stdout] 23 | const NCE_FACTOR: f64 = 0.01;
[INFO] [stdout]    |       ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `var_store` is never read
[INFO] [stdout]   --> src/models/ccs_cnn_tf_model.rs:30:5
[INFO] [stdout]    |
[INFO] [stdout] 29 | pub struct CCSCNNTFModel {
[INFO] [stdout]    |            ------------- field in this struct
[INFO] [stdout] 30 |     var_store: VarBuilder<'static>,
[INFO] [stdout]    |     ^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `CCSCNNTFModel` has a derived impl for the trait `Clone`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `CHARGE_FACTOR` is never used
[INFO] [stdout]   --> src/models/ms2_bert_model.rs:23:7
[INFO] [stdout]    |
[INFO] [stdout] 23 | const CHARGE_FACTOR: f64 = 0.1;
[INFO] [stdout]    |       ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `NCE_FACTOR` is never used
[INFO] [stdout]   --> src/models/ms2_bert_model.rs:24:7
[INFO] [stdout]    |
[INFO] [stdout] 24 | const NCE_FACTOR: f64 = 0.01;
[INFO] [stdout]    |       ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `var_store`, `fixed_sequence_len`, `num_frag_types`, and `modloss_nn` are never read
[INFO] [stdout]   --> src/models/ms2_bert_model.rs:30:5
[INFO] [stdout]    |
[INFO] [stdout] 29 | pub struct MS2BertModel {
[INFO] [stdout]    |            ------------ fields in this struct
[INFO] [stdout] 30 |     var_store: VarBuilder<'static>,
[INFO] [stdout]    |     ^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 34 |     fixed_sequence_len: usize,
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 35 |     // Total number of fragment types of a fragmentation position to predict
[INFO] [stdout] 36 |     num_frag_types: usize,
[INFO] [stdout]    |     ^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 49 |     modloss_nn: ModLossNN,
[INFO] [stdout]    |     ^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `MS2BertModel` has a derived impl for the trait `Clone`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `var_store` is never read
[INFO] [stdout]   --> src/models/rt_cnn_transformer_model.rs:25:5
[INFO] [stdout]    |
[INFO] [stdout] 24 | pub struct RTCNNTFModel {
[INFO] [stdout]    |            ------------ field in this struct
[INFO] [stdout] 25 |     var_store: VarBuilder<'static>,
[INFO] [stdout]    |     ^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `RTCNNTFModel` has a derived impl for the trait `Clone`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `description` is never read
[INFO] [stdout]   --> src/utils/logging.rs:31:5
[INFO] [stdout]    |
[INFO] [stdout] 26 | pub struct Progress {
[INFO] [stdout]    |            -------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 31 |     description: String,                         // Description for the progress bar
[INFO] [stdout]    |     ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `modifications`
[INFO] [stdout]     --> src/models/model_interface.rs:1242:9
[INFO] [stdout]      |
[INFO] [stdout] 1242 |         modifications: HashMap<
[INFO] [stdout]      |         ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_modifications`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `seq_len`
[INFO] [stdout]     --> src/models/model_interface.rs:1571:26
[INFO] [stdout]      |
[INFO] [stdout] 1571 |         let (batch_size, seq_len, feature_size) = predicts.shape().dims3()?;
[INFO] [stdout]      |                          ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_seq_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `feature_size`
[INFO] [stdout]     --> src/models/model_interface.rs:1571:35
[INFO] [stdout]      |
[INFO] [stdout] 1571 |         let (batch_size, seq_len, feature_size) = predicts.shape().dims3()?;
[INFO] [stdout]      |                                   ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_feature_size`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/models/rt_cnn_lstm_model.rs:459:13
[INFO] [stdout]     |
[INFO] [stdout] 459 |         let mut model =
[INFO] [stdout]     |             ----^^^^^
[INFO] [stdout]     |             |
[INFO] [stdout]     |             help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/models/rt_cnn_transformer_model.rs:45:13
[INFO] [stdout]    |
[INFO] [stdout] 45 |         let mut varmap = VarMap::new();
[INFO] [stdout]    |             ----^^^^^^
[INFO] [stdout]    |             |
[INFO] [stdout]    |             help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Context`
[INFO] [stdout]  --> examples/alphapeptdeep_ms2_bert.rs:1:14
[INFO] [stdout]   |
[INFO] [stdout] 1 | use anyhow::{Context, Result};
[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: `ModificationMap`
[INFO] [stdout]   --> examples/alphapeptdeep_ms2_bert.rs:13:32
[INFO] [stdout]    |
[INFO] [stdout] 13 |             remove_mass_shift, ModificationMap,
[INFO] [stdout]    |                                ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/utils/peptdeep_utils.rs:307:9
[INFO] [stdout]     |
[INFO] [stdout] 307 |     let mut offset = 0;
[INFO] [stdout]     |         ----^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `offset`
[INFO] [stdout]    --> src/utils/peptdeep_utils.rs:307:9
[INFO] [stdout]     |
[INFO] [stdout] 307 |     let mut offset = 0;
[INFO] [stdout]     |         ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_offset`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `offset` is assigned to, but never used
[INFO] [stdout]    --> src/utils/peptdeep_utils.rs:377:9
[INFO] [stdout]     |
[INFO] [stdout] 377 |     let mut offset = 0;
[INFO] [stdout]     |         ^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_offset` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `offset` is never read
[INFO] [stdout]    --> src/utils/peptdeep_utils.rs:388:17
[INFO] [stdout]     |
[INFO] [stdout] 388 |                 offset += mat.end() - mat.start();
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: call to `.clone()` on a reference in this situation does nothing
[INFO] [stdout]    --> examples/alphapeptdeep_ms2_bert.rs:115:30
[INFO] [stdout]     |
[INFO] [stdout] 115 |         charge_map.insert(seq.clone().to_string(), charge);
[INFO] [stdout]     |                              ^^^^^^^^ help: remove this redundant call
[INFO] [stdout]     |
[INFO] [stdout]     = note: the type `str` does not implement `Clone`, so calling `clone` on `&str` copies the reference, which does not do anything and can be removed
[INFO] [stdout]     = note: `#[warn(noop_method_call)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated function `new` is never used
[INFO] [stdout]    --> src/building_blocks/building_blocks.rs:514:8
[INFO] [stdout]     |
[INFO] [stdout] 513 | impl AAEmbedding {
[INFO] [stdout]     | ---------------- associated function in this implementation
[INFO] [stdout] 514 |     fn new(hidden_size: usize, vb: &nn::VarBuilder) -> Result<Self> {
[INFO] [stdout]     |        ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated function `new` is never used
[INFO] [stdout]    --> src/building_blocks/building_blocks.rs:542:8
[INFO] [stdout]     |
[INFO] [stdout] 541 | impl PositionalEncoding {
[INFO] [stdout]     | ----------------------- associated function in this implementation
[INFO] [stdout] 542 |     fn new(out_features: usize, max_len: usize, device: &Device) -> Result<Self> {
[INFO] [stdout]     |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated function `new` is never used
[INFO] [stdout]    --> src/building_blocks/building_blocks.rs:661:8
[INFO] [stdout]     |
[INFO] [stdout] 660 | impl Input26aaModPositionalEncoding {
[INFO] [stdout]     | ----------------------------------- associated function in this implementation
[INFO] [stdout] 661 |     fn new(_out_features: usize, _max_len: usize, _device: &Device) -> Result<Self> {
[INFO] [stdout]     |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated function `new` is never used
[INFO] [stdout]    --> src/building_blocks/building_blocks.rs:868:8
[INFO] [stdout]     |
[INFO] [stdout] 867 | impl ModLossNN {
[INFO] [stdout]     | -------------- associated function in this implementation
[INFO] [stdout] 868 |     fn new() -> Self {
[INFO] [stdout]     |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `CHARGE_FACTOR` is never used
[INFO] [stdout]   --> src/models/ccs_cnn_lstm_model.rs:21:7
[INFO] [stdout]    |
[INFO] [stdout] 21 | const CHARGE_FACTOR: f64 = 0.1;
[INFO] [stdout]    |       ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `NCE_FACTOR` is never used
[INFO] [stdout]   --> src/models/ccs_cnn_lstm_model.rs:22:7
[INFO] [stdout]    |
[INFO] [stdout] 22 | const NCE_FACTOR: f64 = 0.01;
[INFO] [stdout]    |       ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `var_store`, `fixed_sequence_len`, `num_frag_types`, `num_modloss_types`, and `mask_modloss` are never read
[INFO] [stdout]   --> src/models/ccs_cnn_lstm_model.rs:28:5
[INFO] [stdout]    |
[INFO] [stdout] 27 | pub struct CCSCNNLSTMModel {
[INFO] [stdout]    |            --------------- fields in this struct
[INFO] [stdout] 28 |     var_store: VarBuilder<'static>,
[INFO] [stdout]    |     ^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 32 |     fixed_sequence_len: usize,
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 33 |     // Total number of fragment types of a fragmentation position to predict
[INFO] [stdout] 34 |     num_frag_types: usize,
[INFO] [stdout]    |     ^^^^^^^^^^^^^^
[INFO] [stdout] 35 |     // Number of fragment types of a fragmentation position to predict, by default 0
[INFO] [stdout] 36 |     num_modloss_types: usize,
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 37 |     // If True, the modloss layer will be disabled, by default True
[INFO] [stdout] 38 |     mask_modloss: bool,
[INFO] [stdout]    |     ^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `CCSCNNLSTMModel` has a derived impl for the trait `Clone`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `CHARGE_FACTOR` is never used
[INFO] [stdout]   --> src/models/ccs_cnn_tf_model.rs:22:7
[INFO] [stdout]    |
[INFO] [stdout] 22 | const CHARGE_FACTOR: f64 = 0.1;
[INFO] [stdout]    |       ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `NCE_FACTOR` is never used
[INFO] [stdout]   --> src/models/ccs_cnn_tf_model.rs:23:7
[INFO] [stdout]    |
[INFO] [stdout] 23 | const NCE_FACTOR: f64 = 0.01;
[INFO] [stdout]    |       ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `var_store` is never read
[INFO] [stdout]   --> src/models/ccs_cnn_tf_model.rs:30:5
[INFO] [stdout]    |
[INFO] [stdout] 29 | pub struct CCSCNNTFModel {
[INFO] [stdout]    |            ------------- field in this struct
[INFO] [stdout] 30 |     var_store: VarBuilder<'static>,
[INFO] [stdout]    |     ^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `CCSCNNTFModel` has a derived impl for the trait `Clone`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `CHARGE_FACTOR` is never used
[INFO] [stdout]   --> src/models/ms2_bert_model.rs:23:7
[INFO] [stdout]    |
[INFO] [stdout] 23 | const CHARGE_FACTOR: f64 = 0.1;
[INFO] [stdout]    |       ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `NCE_FACTOR` is never used
[INFO] [stdout]   --> src/models/ms2_bert_model.rs:24:7
[INFO] [stdout]    |
[INFO] [stdout] 24 | const NCE_FACTOR: f64 = 0.01;
[INFO] [stdout]    |       ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `var_store`, `fixed_sequence_len`, `num_frag_types`, and `modloss_nn` are never read
[INFO] [stdout]   --> src/models/ms2_bert_model.rs:30:5
[INFO] [stdout]    |
[INFO] [stdout] 29 | pub struct MS2BertModel {
[INFO] [stdout]    |            ------------ fields in this struct
[INFO] [stdout] 30 |     var_store: VarBuilder<'static>,
[INFO] [stdout]    |     ^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 34 |     fixed_sequence_len: usize,
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 35 |     // Total number of fragment types of a fragmentation position to predict
[INFO] [stdout] 36 |     num_frag_types: usize,
[INFO] [stdout]    |     ^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 49 |     modloss_nn: ModLossNN,
[INFO] [stdout]    |     ^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `MS2BertModel` has a derived impl for the trait `Clone`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `var_store` is never read
[INFO] [stdout]   --> src/models/rt_cnn_transformer_model.rs:25:5
[INFO] [stdout]    |
[INFO] [stdout] 24 | pub struct RTCNNTFModel {
[INFO] [stdout]    |            ------------ field in this struct
[INFO] [stdout] 25 |     var_store: VarBuilder<'static>,
[INFO] [stdout]    |     ^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `RTCNNTFModel` has a derived impl for the trait `Clone`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `description` is never read
[INFO] [stdout]   --> src/utils/logging.rs:31:5
[INFO] [stdout]    |
[INFO] [stdout] 26 | pub struct Progress {
[INFO] [stdout]    |            -------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 31 |     description: String,                         // Description for the progress bar
[INFO] [stdout]    |     ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Context`
[INFO] [stdout]  --> examples/alphapeptdeep_ccs_cnn_lstm.rs:1:14
[INFO] [stdout]   |
[INFO] [stdout] 1 | use anyhow::{Context, Result};
[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: `data_handling::PeptideData`
[INFO] [stdout]  --> examples/alphapeptdeep_ccs_cnn_lstm.rs:8:13
[INFO] [stdout]   |
[INFO] [stdout] 8 |     utils::{data_handling::PeptideData, peptdeep_utils::ion_mobility_to_ccs_bruker},
[INFO] [stdout]   |             ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Context`
[INFO] [stdout]  --> examples/redeem_ccs_cnn_tf.rs:1:14
[INFO] [stdout]   |
[INFO] [stdout] 1 | use anyhow::{Context, Result};
[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: `data_handling::PeptideData`
[INFO] [stdout]  --> examples/redeem_ccs_cnn_tf.rs:8:13
[INFO] [stdout]   |
[INFO] [stdout] 8 |     utils::{data_handling::PeptideData, peptdeep_utils::ion_mobility_to_ccs_bruker},
[INFO] [stdout]   |             ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 03s
[INFO] running `Command { std: "docker" "inspect" "c140bccf68b4794515bc5ab863de2e91124eddc963700252314bb4d0243340e1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "c140bccf68b4794515bc5ab863de2e91124eddc963700252314bb4d0243340e1", kill_on_drop: false }`
[INFO] [stdout] c140bccf68b4794515bc5ab863de2e91124eddc963700252314bb4d0243340e1
