[INFO] fetching crate varlociraptor 8.4.10...
[INFO] checking varlociraptor-8.4.10 against master#3139ff09e9d07f7700f8d15ed25a231e29c43627 for pr-121848-3
[INFO] extracting crate varlociraptor 8.4.10 into /workspace/builds/worker-3-tc1/source
[INFO] validating manifest of crates.io crate varlociraptor 8.4.10 on toolchain 3139ff09e9d07f7700f8d15ed25a231e29c43627
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+3139ff09e9d07f7700f8d15ed25a231e29c43627" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking crates.io crate varlociraptor 8.4.10
[INFO] finished tweaking crates.io crate varlociraptor 8.4.10
[INFO] tweaked toml for crates.io crate varlociraptor 8.4.10 written to /workspace/builds/worker-3-tc1/source/Cargo.toml
[INFO] crate crates.io crate varlociraptor 8.4.10 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" "+3139ff09e9d07f7700f8d15ed25a231e29c43627" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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@sha256:923055f121b5182466d55868a8b05e67af8ba4a3a3f6bad814e953ca3cd3ac2a" "/opt/rustwide/cargo-home/bin/cargo" "+3139ff09e9d07f7700f8d15ed25a231e29c43627" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] a57ebe2dbe44b1fa2f604143eb001711992d7846edb59326457d86c9a42c6a8c
[INFO] running `Command { std: "docker" "start" "-a" "a57ebe2dbe44b1fa2f604143eb001711992d7846edb59326457d86c9a42c6a8c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "a57ebe2dbe44b1fa2f604143eb001711992d7846edb59326457d86c9a42c6a8c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "a57ebe2dbe44b1fa2f604143eb001711992d7846edb59326457d86c9a42c6a8c", kill_on_drop: false }`
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[INFO] [stdout] 48ad0745854ec8564a932dbfcdf5e2fdb6048290608d659abe2fb6875a8ef324
[INFO] running `Command { std: "docker" "start" "-a" "48ad0745854ec8564a932dbfcdf5e2fdb6048290608d659abe2fb6875a8ef324", kill_on_drop: false }`
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[INFO] [stderr]     Checking auto_ops v0.3.0
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[INFO] [stderr]     Checking rust-htslib v0.47.0
[INFO] [stderr]     Checking varlociraptor v8.4.10 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `events_to_tags`
[INFO] [stdout]   --> src/filtration/fdr.rs:20:34
[INFO] [stdout]    |
[INFO] [stdout] 20 | use crate::utils::{event_to_tag, events_to_tags, is_phred_scaled};
[INFO] [stdout]    |                                  ^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `events_to_tags`
[INFO] [stdout]   --> src/filtration/fdr.rs:20:34
[INFO] [stdout]    |
[INFO] [stdout] 20 | use crate::utils::{event_to_tag, events_to_tags, is_phred_scaled};
[INFO] [stdout]    |                                  ^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Formatter`
[INFO] [stdout]  --> src/utils/mod.rs:7:32
[INFO] [stdout]   |
[INFO] [stdout] 7 | use std::fmt::{Debug, Display, Formatter};
[INFO] [stdout]   |                                ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Formatter`
[INFO] [stdout]  --> src/utils/mod.rs:7:32
[INFO] [stdout]   |
[INFO] [stdout] 7 | use std::fmt::{Debug, Display, Formatter};
[INFO] [stdout]   |                                ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition name: `has_u128`
[INFO] [stdout]    --> src/variants/evidence/realignment/edit_distance.rs:130:11
[INFO] [stdout]     |
[INFO] [stdout] 130 |     #[cfg(has_u128)]
[INFO] [stdout]     |           ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: expected names are: `clippy`, `debug_assertions`, `doc`, `docsrs`, `doctest`, `feature`, `miri`, `overflow_checks`, `panic`, `proc_macro`, `relocation_model`, `rustfmt`, `sanitize`, `sanitizer_cfi_generalize_pointers`, `sanitizer_cfi_normalize_integers`, `target_abi`, `target_arch`, `target_endian`, `target_env`, `target_family`, `target_feature`, `target_has_atomic`, `target_has_atomic_equal_alignment`, `target_has_atomic_load_store`, `target_os`, `target_pointer_width`, `target_thread_local`, `target_vendor`, `test`, `ub_checks`, `unix`, and `windows`
[INFO] [stdout]     = help: consider using a Cargo feature instead
[INFO] [stdout]     = help: or consider adding in `Cargo.toml` the `check-cfg` lint config for the lint:
[INFO] [stdout]              [lints.rust]
[INFO] [stdout]              unexpected_cfgs = { level = "warn", check-cfg = ['cfg(has_u128)'] }
[INFO] [stdout]     = help: or consider adding `println!("cargo::rustc-check-cfg=cfg(has_u128)");` to the top of the `build.rs`
[INFO] [stdout]     = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout]     = note: `#[warn(unexpected_cfgs)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition name: `has_u128`
[INFO] [stdout]    --> src/variants/evidence/realignment/edit_distance.rs:132:15
[INFO] [stdout]     |
[INFO] [stdout] 132 |     #[cfg(not(has_u128))]
[INFO] [stdout]     |               ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: consider using a Cargo feature instead
[INFO] [stdout]     = help: or consider adding in `Cargo.toml` the `check-cfg` lint config for the lint:
[INFO] [stdout]              [lints.rust]
[INFO] [stdout]              unexpected_cfgs = { level = "warn", check-cfg = ['cfg(has_u128)'] }
[INFO] [stdout]     = help: or consider adding `println!("cargo::rustc-check-cfg=cfg(has_u128)");` to the top of the `build.rs`
[INFO] [stdout]     = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition name: `has_u128`
[INFO] [stdout]    --> src/variants/evidence/realignment/edit_distance.rs:158:15
[INFO] [stdout]     |
[INFO] [stdout] 158 |         #[cfg(has_u128)]
[INFO] [stdout]     |               ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: consider using a Cargo feature instead
[INFO] [stdout]     = help: or consider adding in `Cargo.toml` the `check-cfg` lint config for the lint:
[INFO] [stdout]              [lints.rust]
[INFO] [stdout]              unexpected_cfgs = { level = "warn", check-cfg = ['cfg(has_u128)'] }
[INFO] [stdout]     = help: or consider adding `println!("cargo::rustc-check-cfg=cfg(has_u128)");` to the top of the `build.rs`
[INFO] [stdout]     = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition name: `has_u128`
[INFO] [stdout]    --> src/variants/evidence/realignment/edit_distance.rs:160:19
[INFO] [stdout]     |
[INFO] [stdout] 160 |         #[cfg(not(has_u128))]
[INFO] [stdout]     |                   ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: consider using a Cargo feature instead
[INFO] [stdout]     = help: or consider adding in `Cargo.toml` the `check-cfg` lint config for the lint:
[INFO] [stdout]              [lints.rust]
[INFO] [stdout]              unexpected_cfgs = { level = "warn", check-cfg = ['cfg(has_u128)'] }
[INFO] [stdout]     = help: or consider adding `println!("cargo::rustc-check-cfg=cfg(has_u128)");` to the top of the `build.rs`
[INFO] [stdout]     = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `bio::alignment::AlignmentOperation`
[INFO] [stdout]   --> src/variants/evidence/realignment/pairhmm.rs:12:5
[INFO] [stdout]    |
[INFO] [stdout] 12 | use bio::alignment::AlignmentOperation;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `mem`
[INFO] [stdout]   --> src/variants/model/mod.rs:10:11
[INFO] [stdout]    |
[INFO] [stdout] 10 | use std::{mem, str};
[INFO] [stdout]    |           ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition name: `has_u128`
[INFO] [stdout]    --> src/variants/evidence/realignment/edit_distance.rs:130:11
[INFO] [stdout]     |
[INFO] [stdout] 130 |     #[cfg(has_u128)]
[INFO] [stdout]     |           ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: expected names are: `clippy`, `debug_assertions`, `doc`, `docsrs`, `doctest`, `feature`, `miri`, `overflow_checks`, `panic`, `proc_macro`, `relocation_model`, `rustfmt`, `sanitize`, `sanitizer_cfi_generalize_pointers`, `sanitizer_cfi_normalize_integers`, `target_abi`, `target_arch`, `target_endian`, `target_env`, `target_family`, `target_feature`, `target_has_atomic`, `target_has_atomic_equal_alignment`, `target_has_atomic_load_store`, `target_os`, `target_pointer_width`, `target_thread_local`, `target_vendor`, `test`, `ub_checks`, `unix`, and `windows`
[INFO] [stdout]     = help: consider using a Cargo feature instead
[INFO] [stdout]     = help: or consider adding in `Cargo.toml` the `check-cfg` lint config for the lint:
[INFO] [stdout]              [lints.rust]
[INFO] [stdout]              unexpected_cfgs = { level = "warn", check-cfg = ['cfg(has_u128)'] }
[INFO] [stdout]     = help: or consider adding `println!("cargo::rustc-check-cfg=cfg(has_u128)");` to the top of the `build.rs`
[INFO] [stdout]     = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout]     = note: `#[warn(unexpected_cfgs)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition name: `has_u128`
[INFO] [stdout]    --> src/variants/evidence/realignment/edit_distance.rs:132:15
[INFO] [stdout]     |
[INFO] [stdout] 132 |     #[cfg(not(has_u128))]
[INFO] [stdout]     |               ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: consider using a Cargo feature instead
[INFO] [stdout]     = help: or consider adding in `Cargo.toml` the `check-cfg` lint config for the lint:
[INFO] [stdout]              [lints.rust]
[INFO] [stdout]              unexpected_cfgs = { level = "warn", check-cfg = ['cfg(has_u128)'] }
[INFO] [stdout]     = help: or consider adding `println!("cargo::rustc-check-cfg=cfg(has_u128)");` to the top of the `build.rs`
[INFO] [stdout]     = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition name: `has_u128`
[INFO] [stdout]    --> src/variants/evidence/realignment/edit_distance.rs:158:15
[INFO] [stdout]     |
[INFO] [stdout] 158 |         #[cfg(has_u128)]
[INFO] [stdout]     |               ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: consider using a Cargo feature instead
[INFO] [stdout]     = help: or consider adding in `Cargo.toml` the `check-cfg` lint config for the lint:
[INFO] [stdout]              [lints.rust]
[INFO] [stdout]              unexpected_cfgs = { level = "warn", check-cfg = ['cfg(has_u128)'] }
[INFO] [stdout]     = help: or consider adding `println!("cargo::rustc-check-cfg=cfg(has_u128)");` to the top of the `build.rs`
[INFO] [stdout]     = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition name: `has_u128`
[INFO] [stdout]    --> src/variants/evidence/realignment/edit_distance.rs:160:19
[INFO] [stdout]     |
[INFO] [stdout] 160 |         #[cfg(not(has_u128))]
[INFO] [stdout]     |                   ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: consider using a Cargo feature instead
[INFO] [stdout]     = help: or consider adding in `Cargo.toml` the `check-cfg` lint config for the lint:
[INFO] [stdout]              [lints.rust]
[INFO] [stdout]              unexpected_cfgs = { level = "warn", check-cfg = ['cfg(has_u128)'] }
[INFO] [stdout]     = help: or consider adding `println!("cargo::rustc-check-cfg=cfg(has_u128)");` to the top of the `build.rs`
[INFO] [stdout]     = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `bio::alignment::AlignmentOperation`
[INFO] [stdout]   --> src/variants/evidence/realignment/pairhmm.rs:12:5
[INFO] [stdout]    |
[INFO] [stdout] 12 | use bio::alignment::AlignmentOperation;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `mem`
[INFO] [stdout]   --> src/variants/model/mod.rs:10:11
[INFO] [stdout]    |
[INFO] [stdout] 10 | use std::{mem, str};
[INFO] [stdout]    |           ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `bcf`
[INFO] [stdout]   --> src/variants/types/breakends.rs:20:24
[INFO] [stdout]    |
[INFO] [stdout] 20 | use rust_htslib::{bam, bcf};
[INFO] [stdout]    |                        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::variants::evidence::insert_size::estimate_insert_size`
[INFO] [stdout]   --> src/variants/types/breakends.rs:28:5
[INFO] [stdout]    |
[INFO] [stdout] 28 | use crate::variants::evidence::insert_size::estimate_insert_size;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rust_htslib::bam`
[INFO] [stdout]   --> src/variants/types/deletion.rs:16:5
[INFO] [stdout]    |
[INFO] [stdout] 16 | use rust_htslib::bam;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::variants::evidence::insert_size::estimate_insert_size`
[INFO] [stdout]   --> src/variants/types/deletion.rs:22:5
[INFO] [stdout]    |
[INFO] [stdout] 22 | use crate::variants::evidence::insert_size::estimate_insert_size;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::variants::evidence::observations::read_observation::Strand`
[INFO] [stdout]   --> src/variants/types/deletion.rs:23:5
[INFO] [stdout]    |
[INFO] [stdout] 23 | use crate::variants::evidence::observations::read_observation::Strand;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `AlleleSupportBuilder`
[INFO] [stdout]   --> src/variants/types/deletion.rs:31:20
[INFO] [stdout]    |
[INFO] [stdout] 31 |     AlleleSupport, AlleleSupportBuilder, MultiLocus, PairedEndEvidence, SingleLocus, Variant,
[INFO] [stdout]    |                    ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `itertools::Itertools`
[INFO] [stdout]   --> src/variants/types/mnv.rs:16:5
[INFO] [stdout]    |
[INFO] [stdout] 16 | use itertools::Itertools;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `bcf`
[INFO] [stdout]   --> src/variants/types/breakends.rs:20:24
[INFO] [stdout]    |
[INFO] [stdout] 20 | use rust_htslib::{bam, bcf};
[INFO] [stdout]    |                        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::variants::evidence::insert_size::estimate_insert_size`
[INFO] [stdout]   --> src/variants/types/breakends.rs:28:5
[INFO] [stdout]    |
[INFO] [stdout] 28 | use crate::variants::evidence::insert_size::estimate_insert_size;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rust_htslib::bam`
[INFO] [stdout]   --> src/variants/types/deletion.rs:16:5
[INFO] [stdout]    |
[INFO] [stdout] 16 | use rust_htslib::bam;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::variants::evidence::insert_size::estimate_insert_size`
[INFO] [stdout]   --> src/variants/types/deletion.rs:22:5
[INFO] [stdout]    |
[INFO] [stdout] 22 | use crate::variants::evidence::insert_size::estimate_insert_size;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::variants::evidence::observations::read_observation::Strand`
[INFO] [stdout]   --> src/variants/types/deletion.rs:23:5
[INFO] [stdout]    |
[INFO] [stdout] 23 | use crate::variants::evidence::observations::read_observation::Strand;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `AlleleSupportBuilder`
[INFO] [stdout]   --> src/variants/types/deletion.rs:31:20
[INFO] [stdout]    |
[INFO] [stdout] 31 |     AlleleSupport, AlleleSupportBuilder, MultiLocus, PairedEndEvidence, SingleLocus, Variant,
[INFO] [stdout]    |                    ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `itertools::Itertools`
[INFO] [stdout]   --> src/variants/types/mnv.rs:16:5
[INFO] [stdout]    |
[INFO] [stdout] 16 | use itertools::Itertools;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Evidence`
[INFO] [stdout]   --> src/variants/types/haplotype_block.rs:15:5
[INFO] [stdout]    |
[INFO] [stdout] 15 |     Evidence, Observable, SingleEndEvidence,
[INFO] [stdout]    |     ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::variants::evidence::observations::read_observation::Evidence`
[INFO] [stdout]   --> src/variants/types/replacement.rs:22:5
[INFO] [stdout]    |
[INFO] [stdout] 22 | use crate::variants::evidence::observations::read_observation::Evidence;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::variants::evidence::observations::read_observation::Evidence`
[INFO] [stdout]   --> src/variants/types/replacement.rs:22:5
[INFO] [stdout]    |
[INFO] [stdout] 22 | use crate::variants::evidence::observations::read_observation::Evidence;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Evidence`
[INFO] [stdout]   --> src/variants/types/haplotype_block.rs:15:5
[INFO] [stdout]    |
[INFO] [stdout] 15 |     Evidence, Observable, SingleEndEvidence,
[INFO] [stdout]    |     ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/calling/variants/calling.rs:297:13
[INFO] [stdout]     |
[INFO] [stdout] 297 |         let mut aux_info_collector = self.call_processor.borrow_mut().setup(self)?;
[INFO] [stdout]     |             ----^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |             |
[INFO] [stdout]     |             help: remove this `mut`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_mut)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/calling/variants/calling.rs:297:13
[INFO] [stdout]     |
[INFO] [stdout] 297 |         let mut aux_info_collector = self.call_processor.borrow_mut().setup(self)?;
[INFO] [stdout]     |             ----^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |             |
[INFO] [stdout]     |             help: remove this `mut`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_mut)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `sample_names`
[INFO] [stdout]    --> src/calling/variants/calling.rs:915:9
[INFO] [stdout]     |
[INFO] [stdout] 915 |         sample_names: &grammar::SampleInfo<String>,
[INFO] [stdout]     |         ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_sample_names`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `sample_names`
[INFO] [stdout]    --> src/calling/variants/calling.rs:915:9
[INFO] [stdout]     |
[INFO] [stdout] 915 |         sample_names: &grammar::SampleInfo<String>,
[INFO] [stdout]     |         ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_sample_names`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `work_item`
[INFO] [stdout]    --> src/calling/variants/calling.rs:934:22
[INFO] [stdout]     |
[INFO] [stdout] 934 |     fn filter(&self, work_item: &WorkItem, sample_names: &grammar::SampleInfo<String>) -> bool {
[INFO] [stdout]     |                      ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_work_item`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `work_item`
[INFO] [stdout]    --> src/calling/variants/calling.rs:934:22
[INFO] [stdout]     |
[INFO] [stdout] 934 |     fn filter(&self, work_item: &WorkItem, sample_names: &grammar::SampleInfo<String>) -> bool {
[INFO] [stdout]     |                      ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_work_item`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `sample_names`
[INFO] [stdout]    --> src/calling/variants/calling.rs:934:44
[INFO] [stdout]     |
[INFO] [stdout] 934 |     fn filter(&self, work_item: &WorkItem, sample_names: &grammar::SampleInfo<String>) -> bool {
[INFO] [stdout]     |                                            ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_sample_names`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `sample_names`
[INFO] [stdout]    --> src/calling/variants/calling.rs:934:44
[INFO] [stdout]     |
[INFO] [stdout] 934 |     fn filter(&self, work_item: &WorkItem, sample_names: &grammar::SampleInfo<String>) -> bool {
[INFO] [stdout]     |                                            ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_sample_names`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: irrefutable `if let` pattern
[INFO] [stdout]    --> src/calling/variants/preprocessing/mod.rs:619:28
[INFO] [stdout]     |
[INFO] [stdout] 619 |                         if let HaplotypeIdentifier::Event(event) = haplotype {
[INFO] [stdout]     |                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: this pattern will always match, so the `if let` is useless
[INFO] [stdout]     = help: consider replacing the `if let` with a `let`
[INFO] [stdout]     = note: `#[warn(irrefutable_let_patterns)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: irrefutable `if let` pattern
[INFO] [stdout]    --> src/calling/variants/preprocessing/mod.rs:619:28
[INFO] [stdout]     |
[INFO] [stdout] 619 |                         if let HaplotypeIdentifier::Event(event) = haplotype {
[INFO] [stdout]     |                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: this pattern will always match, so the `if let` is useless
[INFO] [stdout]     = help: consider replacing the `if let` with a `let`
[INFO] [stdout]     = note: `#[warn(irrefutable_let_patterns)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/estimation/contamination.rs:65:13
[INFO] [stdout]    |
[INFO] [stdout] 65 |         let mut vaf_dist = sample_info
[INFO] [stdout]    |             ----^^^^^^^^
[INFO] [stdout]    |             |
[INFO] [stdout]    |             help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `infimum`
[INFO] [stdout]    --> src/estimation/contamination.rs:101:20
[INFO] [stdout]     |
[INFO] [stdout] 101 |             (Some((infimum, count)), None) => {
[INFO] [stdout]     |                    ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_infimum`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `count`
[INFO] [stdout]    --> src/estimation/contamination.rs:101:29
[INFO] [stdout]     |
[INFO] [stdout] 101 |             (Some((infimum, count)), None) => {
[INFO] [stdout]     |                             ^^^^^ help: if this is intentional, prefix it with an underscore: `_count`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/estimation/contamination.rs:65:13
[INFO] [stdout]    |
[INFO] [stdout] 65 |         let mut vaf_dist = sample_info
[INFO] [stdout]    |             ----^^^^^^^^
[INFO] [stdout]    |             |
[INFO] [stdout]    |             help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `infimum`
[INFO] [stdout]    --> src/estimation/contamination.rs:101:20
[INFO] [stdout]     |
[INFO] [stdout] 101 |             (Some((infimum, count)), None) => {
[INFO] [stdout]     |                    ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_infimum`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `count`
[INFO] [stdout]    --> src/estimation/contamination.rs:101:29
[INFO] [stdout]     |
[INFO] [stdout] 101 |             (Some((infimum, count)), None) => {
[INFO] [stdout]     |                             ^^^^^ help: if this is intentional, prefix it with an underscore: `_count`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `payload`
[INFO] [stdout]    --> src/estimation/contamination.rs:166:63
[INFO] [stdout]     |
[INFO] [stdout] 166 |     fn compute(&self, event: &Self::Event, data: &Self::Data, payload: &mut ()) -> LogProb {
[INFO] [stdout]     |                                                               ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_payload`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `payload`
[INFO] [stdout]    --> src/estimation/contamination.rs:166:63
[INFO] [stdout]     |
[INFO] [stdout] 166 |     fn compute(&self, event: &Self::Event, data: &Self::Data, payload: &mut ()) -> LogProb {
[INFO] [stdout]     |                                                               ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_payload`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/estimation/contamination.rs:347:21
[INFO] [stdout]     |
[INFO] [stdout] 347 |                 let mut outfile = File::create(outpath)?;
[INFO] [stdout]     |                     ----^^^^^^^
[INFO] [stdout]     |                     |
[INFO] [stdout]     |                     help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `caller`
[INFO] [stdout]    --> src/estimation/contamination.rs:383:9
[INFO] [stdout]     |
[INFO] [stdout] 383 |         caller: &Caller<Pr, Self, CF>,
[INFO] [stdout]     |         ^^^^^^ help: if this is intentional, prefix it with an underscore: `_caller`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/estimation/contamination.rs:347:21
[INFO] [stdout]     |
[INFO] [stdout] 347 |                 let mut outfile = File::create(outpath)?;
[INFO] [stdout]     |                     ----^^^^^^^
[INFO] [stdout]     |                     |
[INFO] [stdout]     |                     help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `caller`
[INFO] [stdout]    --> src/estimation/contamination.rs:383:9
[INFO] [stdout]     |
[INFO] [stdout] 383 |         caller: &Caller<Pr, Self, CF>,
[INFO] [stdout]     |         ^^^^^^ help: if this is intentional, prefix it with an underscore: `_caller`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/testcase/runner/common/mod.rs:181:13
[INFO] [stdout]     |
[INFO] [stdout] 181 |         let mut path = self.path().join("observations").join(sample_name);
[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/testcase/runner/common/mod.rs:181:13
[INFO] [stdout]     |
[INFO] [stdout] 181 |         let mut path = self.path().join("observations").join(sample_name);
[INFO] [stdout]     |             ----^^^^
[INFO] [stdout]     |             |
[INFO] [stdout]     |             help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `end_reduce` is assigned to, but never used
[INFO] [stdout]    --> src/variants/evidence/realignment/edit_distance.rs:401:21
[INFO] [stdout]     |
[INFO] [stdout] 401 |             let mut end_reduce = 0;
[INFO] [stdout]     |                     ^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_end_reduce` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `opcounts`
[INFO] [stdout]    --> src/variants/evidence/realignment/edit_distance.rs:404:17
[INFO] [stdout]     |
[INFO] [stdout] 404 |             let opcounts = edit_distance_hit.edit_operation_counts().as_ref().unwrap();
[INFO] [stdout]     |                 ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_opcounts`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `end_reduce` is assigned to, but never used
[INFO] [stdout]    --> src/variants/evidence/realignment/edit_distance.rs:401:21
[INFO] [stdout]     |
[INFO] [stdout] 401 |             let mut end_reduce = 0;
[INFO] [stdout]     |                     ^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_end_reduce` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `opcounts`
[INFO] [stdout]    --> src/variants/evidence/realignment/edit_distance.rs:404:17
[INFO] [stdout]     |
[INFO] [stdout] 404 |             let opcounts = edit_distance_hit.edit_operation_counts().as_ref().unwrap();
[INFO] [stdout]     |                 ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_opcounts`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `observation`
[INFO] [stdout]   --> src/variants/model/bias/read_position_bias.rs:50:24
[INFO] [stdout]    |
[INFO] [stdout] 50 |     fn prob_any(&self, observation: &ProcessedReadObservation) -> LogProb {
[INFO] [stdout]    |                        ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_observation`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `observation`
[INFO] [stdout]   --> src/variants/model/bias/read_position_bias.rs:50:24
[INFO] [stdout]    |
[INFO] [stdout] 50 |     fn prob_any(&self, observation: &ProcessedReadObservation) -> LogProb {
[INFO] [stdout]    |                        ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_observation`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]    --> src/variants/types/haplotype_block.rs:192:31
[INFO] [stdout]     |
[INFO] [stdout] 192 |                 .filter_map(|(i, variant)| {
[INFO] [stdout]     |                               ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/variants/types/haplotype_block.rs:289:13
[INFO] [stdout]     |
[INFO] [stdout] 289 |         let mut support = support
[INFO] [stdout]     |             ----^^^^^^^
[INFO] [stdout]     |             |
[INFO] [stdout]     |             help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]    --> src/variants/types/haplotype_block.rs:192:31
[INFO] [stdout]     |
[INFO] [stdout] 192 |                 .filter_map(|(i, variant)| {
[INFO] [stdout]     |                               ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/variants/types/haplotype_block.rs:289:13
[INFO] [stdout]     |
[INFO] [stdout] 289 |         let mut support = support
[INFO] [stdout]     |             ----^^^^^^^
[INFO] [stdout]     |             |
[INFO] [stdout]     |             help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `Iupac` is more private than the item `NodeKind::Variant::refbase`
[INFO] [stdout]   --> src/grammar/vaftree.rs:66:9
[INFO] [stdout]    |
[INFO] [stdout] 66 |         refbase: Iupac,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^ field `NodeKind::Variant::refbase` is reachable at visibility `pub`
[INFO] [stdout]    |
[INFO] [stdout] note: but type `Iupac` is only usable at visibility `pub(crate)`
[INFO] [stdout]   --> src/grammar/formula.rs:21:1
[INFO] [stdout]    |
[INFO] [stdout] 21 | pub(crate) struct Iupac(u8);
[INFO] [stdout]    | ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    = note: `#[warn(private_interfaces)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `Iupac` is more private than the item `NodeKind::Variant::altbase`
[INFO] [stdout]   --> src/grammar/vaftree.rs:67:9
[INFO] [stdout]    |
[INFO] [stdout] 67 |         altbase: Iupac,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^ field `NodeKind::Variant::altbase` is reachable at visibility `pub`
[INFO] [stdout]    |
[INFO] [stdout] note: but type `Iupac` is only usable at visibility `pub(crate)`
[INFO] [stdout]   --> src/grammar/formula.rs:21:1
[INFO] [stdout]    |
[INFO] [stdout] 21 | pub(crate) struct Iupac(u8);
[INFO] [stdout]    | ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `VAFSpectrum` is more private than the item `NodeKind::Sample::vafs`
[INFO] [stdout]     --> src/grammar/vaftree.rs:72:9
[INFO] [stdout]      |
[INFO] [stdout] 72   |         vafs: VAFSpectrum,
[INFO] [stdout]      |         ^^^^^^^^^^^^^^^^^ field `NodeKind::Sample::vafs` is reachable at visibility `pub`
[INFO] [stdout]      |
[INFO] [stdout] note: but type `VAFSpectrum` is only usable at visibility `pub(crate)`
[INFO] [stdout]     --> src/grammar/formula.rs:1029:1
[INFO] [stdout]      |
[INFO] [stdout] 1029 | pub(crate) enum VAFSpectrum {
[INFO] [stdout]      | ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `Log2FoldChangePredicate` is more private than the item `NodeKind::Log2FoldChange::predicate`
[INFO] [stdout]   --> src/grammar/vaftree.rs:77:9
[INFO] [stdout]    |
[INFO] [stdout] 77 |         predicate: Log2FoldChangePredicate,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ field `NodeKind::Log2FoldChange::predicate` is reachable at visibility `pub`
[INFO] [stdout]    |
[INFO] [stdout] note: but type `Log2FoldChangePredicate` is only usable at visibility `pub(crate)`
[INFO] [stdout]   --> src/utils/log2_fold_change.rs:26:1
[INFO] [stdout]    |
[INFO] [stdout] 26 | pub(crate) struct Log2FoldChangePredicate {
[INFO] [stdout]    | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `LikelihoodOperands` is more private than the item `vaftree::Node::contains`
[INFO] [stdout]    --> src/grammar/vaftree.rs:116:5
[INFO] [stdout]     |
[INFO] [stdout] 116 | /     pub fn contains(
[INFO] [stdout] 117 | |         &self,
[INFO] [stdout] 118 | |         operands: &LikelihoodOperands,
[INFO] [stdout] 119 | |         lfcs: &mut Vec<&VafLfc>,
[INFO] [stdout] 120 | |         exclude_sample: Option<usize>,
[INFO] [stdout] 121 | |     ) -> bool {
[INFO] [stdout]     | |_____________^ method `vaftree::Node::contains` is reachable at visibility `pub`
[INFO] [stdout]     |
[INFO] [stdout] note: but type `LikelihoodOperands` is only usable at visibility `pub(crate)`
[INFO] [stdout]    --> src/variants/model/modes/generic.rs:118:1
[INFO] [stdout]     |
[INFO] [stdout] 118 | pub(crate) struct LikelihoodOperands {
[INFO] [stdout]     | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `VafLfc` is more private than the item `vaftree::Node::contains`
[INFO] [stdout]    --> src/grammar/vaftree.rs:116:5
[INFO] [stdout]     |
[INFO] [stdout] 116 | /     pub fn contains(
[INFO] [stdout] 117 | |         &self,
[INFO] [stdout] 118 | |         operands: &LikelihoodOperands,
[INFO] [stdout] 119 | |         lfcs: &mut Vec<&VafLfc>,
[INFO] [stdout] 120 | |         exclude_sample: Option<usize>,
[INFO] [stdout] 121 | |     ) -> bool {
[INFO] [stdout]     | |_____________^ method `vaftree::Node::contains` is reachable at visibility `pub`
[INFO] [stdout]     |
[INFO] [stdout] note: but type `VafLfc` is only usable at visibility `pub(crate)`
[INFO] [stdout]    --> src/variants/model/modes/generic.rs:110:1
[INFO] [stdout]     |
[INFO] [stdout] 110 | pub(crate) struct VafLfc {
[INFO] [stdout]     | ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `variants::model::Variant` is more private than the item `VariantInfo::variant`
[INFO] [stdout]    --> src/utils/collect_variants.rs:33:5
[INFO] [stdout]     |
[INFO] [stdout] 33  |     pub variant: model::Variant,
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^ field `VariantInfo::variant` is reachable at visibility `pub`
[INFO] [stdout]     |
[INFO] [stdout] note: but type `variants::model::Variant` is only usable at visibility `pub(crate)`
[INFO] [stdout]    --> src/variants/model/mod.rs:320:1
[INFO] [stdout]     |
[INFO] [stdout] 320 | pub(crate) enum Variant {
[INFO] [stdout]     | ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `ComplementEvent` is never constructed
[INFO] [stdout]   --> src/lib.rs:68:19
[INFO] [stdout]    |
[INFO] [stdout] 68 | pub(crate) struct ComplementEvent {
[INFO] [stdout]    |                   ^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `BCFGrouper` is never constructed
[INFO] [stdout]    --> src/calling/variants/mod.rs:663:19
[INFO] [stdout]     |
[INFO] [stdout] 663 | pub(crate) struct BCFGrouper<'a>(pub(crate) &'a Variant);
[INFO] [stdout]     |                   ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `epsilon_gap` is never read
[INFO] [stdout]   --> src/estimation/alignment_properties.rs:81:5
[INFO] [stdout]    |
[INFO] [stdout] 60 | pub(crate) struct AlignmentProperties {
[INFO] [stdout]    |                   ------------------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 81 |     epsilon_gap: f64,
[INFO] [stdout]    |     ^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `AlignmentProperties` has derived impls for the traits `Debug` and `Clone`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: methods `max_homopolymer_insertion_len` and `max_homopolymer_deletion_len` are never used
[INFO] [stdout]   --> src/estimation/alignment_properties.rs:85:19
[INFO] [stdout]    |
[INFO] [stdout] 84 | impl AlignmentProperties {
[INFO] [stdout]    | ------------------------ methods in this implementation
[INFO] [stdout] 85 |     pub(crate) fn max_homopolymer_insertion_len(&self) -> u16 {
[INFO] [stdout]    |                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 94 |     pub(crate) fn max_homopolymer_deletion_len(&self) -> u16 {
[INFO] [stdout]    |                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `total` is never read
[INFO] [stdout]    --> src/estimation/contamination.rs:238:5
[INFO] [stdout]     |
[INFO] [stdout] 236 | struct VAFDist {
[INFO] [stdout]     |        ------- field in this struct
[INFO] [stdout] 237 |     histogram: BTreeMap<AlleleFreq, usize>,
[INFO] [stdout] 238 |     total: usize,
[INFO] [stdout]     |     ^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `VAFDist` has derived impls for the traits `Debug` and `Clone`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `MB` is never constructed
[INFO] [stdout]   --> src/estimation/mutational_burden.rs:46:8
[INFO] [stdout]    |
[INFO] [stdout] 46 | struct MB {
[INFO] [stdout]    |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated function `new` is never used
[INFO] [stdout]   --> src/reference.rs:19:19
[INFO] [stdout]    |
[INFO] [stdout] 18 | impl Buffer {
[INFO] [stdout]    | ----------- associated function in this implementation
[INFO] [stdout] 19 |     pub(crate) fn new(fasta: fasta::IndexedReader<fs::File>, capacity: usize) -> Self {
[INFO] [stdout]    |                   ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `base` is never read
[INFO] [stdout]   --> src/utils/homopolymers.rs:17:5
[INFO] [stdout]    |
[INFO] [stdout] 14 | pub(crate) struct HomopolymerIndelOperation {
[INFO] [stdout]    |                   ------------------------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 17 |     base: u8,
[INFO] [stdout]    |     ^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `HomopolymerIndelOperation` has derived impls for the traits `Debug` and `Clone`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `observed_depth` and `expected_ref_depth` are never read
[INFO] [stdout]  --> src/variants/evidence/observations/depth_observation.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | pub struct DepthObservation {
[INFO] [stdout]   |            ---------------- fields in this struct
[INFO] [stdout] 3 |     observed_depth: u64,
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 4 |     expected_ref_depth: f64,
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `DepthObservation` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: methods `start_locus` and `end_locus` are never used
[INFO] [stdout]    --> src/variants/evidence/observations/read_observation.rs:672:8
[INFO] [stdout]     |
[INFO] [stdout] 659 | pub(crate) trait Evidence {
[INFO] [stdout]     |                  -------- methods in this trait
[INFO] [stdout] ...
[INFO] [stdout] 672 |     fn start_locus(&self) -> genome::Locus;
[INFO] [stdout]     |        ^^^^^^^^^^^
[INFO] [stdout] 673 |
[INFO] [stdout] 674 |     fn end_locus(&self) -> genome::Locus;
[INFO] [stdout]     |        ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `maybe_revcomp` is never used
[INFO] [stdout]   --> src/variants/evidence/realignment/mod.rs:61:8
[INFO] [stdout]    |
[INFO] [stdout] 49 | pub(crate) trait Realignable {
[INFO] [stdout]    |                  ----------- method in this trait
[INFO] [stdout] ...
[INFO] [stdout] 61 |     fn maybe_revcomp(&self) -> bool {
[INFO] [stdout]    |        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `certainty_est` is never used
[INFO] [stdout]    --> src/variants/evidence/realignment/pairhmm.rs:489:19
[INFO] [stdout]     |
[INFO] [stdout] 436 | impl<'a> ReadEmission<'a> {
[INFO] [stdout]     | ------------------------- method in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 489 |     pub(crate) fn certainty_est(&self) -> LogProb {
[INFO] [stdout]     |                   ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: trait `AlleleFreqs` is never used
[INFO] [stdout]   --> src/variants/model/mod.rs:68:18
[INFO] [stdout]    |
[INFO] [stdout] 68 | pub(crate) trait AlleleFreqs: Debug {
[INFO] [stdout]    |                  ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `DiscreteAlleleFreqs` is never constructed
[INFO] [stdout]   --> src/variants/model/mod.rs:83:19
[INFO] [stdout]    |
[INFO] [stdout] 83 | pub(crate) struct DiscreteAlleleFreqs {
[INFO] [stdout]    |                   ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `is_singleton` is never used
[INFO] [stdout]    --> src/variants/model/mod.rs:119:19
[INFO] [stdout]     |
[INFO] [stdout] 105 | impl ContinuousAlleleFreqs {
[INFO] [stdout]     | -------------------------- method in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 119 |     pub(crate) fn is_singleton(&self) -> bool {
[INFO] [stdout]     |                   ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: trait `ContaminatedSamplePairView` is never used
[INFO] [stdout]   --> src/variants/model/likelihood.rs:55:18
[INFO] [stdout]    |
[INFO] [stdout] 55 | pub(crate) trait ContaminatedSamplePairView<T> {
[INFO] [stdout]    |                  ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `FlatPrior` is never constructed
[INFO] [stdout]    --> src/variants/model/modes/generic.rs:502:19
[INFO] [stdout]     |
[INFO] [stdout] 502 | pub(crate) struct FlatPrior {
[INFO] [stdout]     |                   ^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `FlatPrior` has a derived impl for the trait `Default`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: trait `TumorNormalPairView` is never used
[INFO] [stdout]   --> src/variants/model/modes/tumor.rs:18:18
[INFO] [stdout]    |
[INFO] [stdout] 18 | pub(crate) trait TumorNormalPairView<T> {
[INFO] [stdout]    |                  ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `protocol_strandedness` is never read
[INFO] [stdout]    --> src/variants/sample.rs:194:5
[INFO] [stdout]     |
[INFO] [stdout] 187 | pub(crate) struct Sample {
[INFO] [stdout]     |                   ------ field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 194 |     protocol_strandedness: ProtocolStrandedness,
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `Sample` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `is_homopolymer_indel` is never used
[INFO] [stdout]    --> src/variants/types/mod.rs:174:8
[INFO] [stdout]     |
[INFO] [stdout] 133 | pub(crate) trait Variant {
[INFO] [stdout]     |                  ------- method in this trait
[INFO] [stdout] ...
[INFO] [stdout] 174 |     fn is_homopolymer_indel(&self) -> bool {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `is_single_contig` is never used
[INFO] [stdout]    --> src/variants/types/mod.rs:448:8
[INFO] [stdout]     |
[INFO] [stdout] 446 | pub(crate) trait Loci {
[INFO] [stdout]     |                  ---- method in this trait
[INFO] [stdout] 447 |     fn contig(&self) -> Option<&str>;
[INFO] [stdout] 448 |     fn is_single_contig(&self) -> bool;
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `deletion_len` is never used
[INFO] [stdout]    --> src/variants/types/breakends.rs:256:8
[INFO] [stdout]     |
[INFO] [stdout] 180 | impl<R: Realigner> BreakendGroup<R> {
[INFO] [stdout]     | ----------------------------------- method in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 256 |     fn deletion_len(&self) -> Option<u64> {
[INFO] [stdout]     |        ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `LocusPlusOne` is never constructed
[INFO] [stdout]     --> src/variants/types/breakends.rs:1225:8
[INFO] [stdout]      |
[INFO] [stdout] 1225 | struct LocusPlusOne<'a>(&'a genome::Locus);
[INFO] [stdout]      |        ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `LocusMinusOne` is never constructed
[INFO] [stdout]     --> src/variants/types/breakends.rs:1237:8
[INFO] [stdout]      |
[INFO] [stdout] 1237 | struct LocusMinusOne<'a>(&'a genome::Locus);
[INFO] [stdout]      |        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: trait `HaplotypeVariant` is never used
[INFO] [stdout]   --> src/variants/types/haplotype_block.rs:81:18
[INFO] [stdout]    |
[INFO] [stdout] 81 | pub(crate) trait HaplotypeVariant: Variant + ToVariantRepresentation {}
[INFO] [stdout]    |                  ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: methods `push_single_locus_paired_end_evidence_variant` and `push_multi_locus_single_end_evidence_variant` are never used
[INFO] [stdout]    --> src/variants/types/haplotype_block.rs:115:19
[INFO] [stdout]     |
[INFO] [stdout] 96  | impl HaplotypeBlock {
[INFO] [stdout]     | ------------------- methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 115 |     pub(crate) fn push_single_locus_paired_end_evidence_variant(
[INFO] [stdout]     |                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 123 |     pub(crate) fn push_multi_locus_single_end_evidence_variant(
[INFO] [stdout]     |                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `Iupac` is more private than the item `NodeKind::Variant::refbase`
[INFO] [stdout]   --> src/grammar/vaftree.rs:66:9
[INFO] [stdout]    |
[INFO] [stdout] 66 |         refbase: Iupac,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^ field `NodeKind::Variant::refbase` is reachable at visibility `pub`
[INFO] [stdout]    |
[INFO] [stdout] note: but type `Iupac` is only usable at visibility `pub(crate)`
[INFO] [stdout]   --> src/grammar/formula.rs:21:1
[INFO] [stdout]    |
[INFO] [stdout] 21 | pub(crate) struct Iupac(u8);
[INFO] [stdout]    | ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    = note: `#[warn(private_interfaces)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `Iupac` is more private than the item `NodeKind::Variant::altbase`
[INFO] [stdout]   --> src/grammar/vaftree.rs:67:9
[INFO] [stdout]    |
[INFO] [stdout] 67 |         altbase: Iupac,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^ field `NodeKind::Variant::altbase` is reachable at visibility `pub`
[INFO] [stdout]    |
[INFO] [stdout] note: but type `Iupac` is only usable at visibility `pub(crate)`
[INFO] [stdout]   --> src/grammar/formula.rs:21:1
[INFO] [stdout]    |
[INFO] [stdout] 21 | pub(crate) struct Iupac(u8);
[INFO] [stdout]    | ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `VAFSpectrum` is more private than the item `NodeKind::Sample::vafs`
[INFO] [stdout]     --> src/grammar/vaftree.rs:72:9
[INFO] [stdout]      |
[INFO] [stdout] 72   |         vafs: VAFSpectrum,
[INFO] [stdout]      |         ^^^^^^^^^^^^^^^^^ field `NodeKind::Sample::vafs` is reachable at visibility `pub`
[INFO] [stdout]      |
[INFO] [stdout] note: but type `VAFSpectrum` is only usable at visibility `pub(crate)`
[INFO] [stdout]     --> src/grammar/formula.rs:1029:1
[INFO] [stdout]      |
[INFO] [stdout] 1029 | pub(crate) enum VAFSpectrum {
[INFO] [stdout]      | ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `Log2FoldChangePredicate` is more private than the item `NodeKind::Log2FoldChange::predicate`
[INFO] [stdout]   --> src/grammar/vaftree.rs:77:9
[INFO] [stdout]    |
[INFO] [stdout] 77 |         predicate: Log2FoldChangePredicate,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ field `NodeKind::Log2FoldChange::predicate` is reachable at visibility `pub`
[INFO] [stdout]    |
[INFO] [stdout] note: but type `Log2FoldChangePredicate` is only usable at visibility `pub(crate)`
[INFO] [stdout]   --> src/utils/log2_fold_change.rs:26:1
[INFO] [stdout]    |
[INFO] [stdout] 26 | pub(crate) struct Log2FoldChangePredicate {
[INFO] [stdout]    | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `LikelihoodOperands` is more private than the item `vaftree::Node::contains`
[INFO] [stdout]    --> src/grammar/vaftree.rs:116:5
[INFO] [stdout]     |
[INFO] [stdout] 116 | /     pub fn contains(
[INFO] [stdout] 117 | |         &self,
[INFO] [stdout] 118 | |         operands: &LikelihoodOperands,
[INFO] [stdout] 119 | |         lfcs: &mut Vec<&VafLfc>,
[INFO] [stdout] 120 | |         exclude_sample: Option<usize>,
[INFO] [stdout] 121 | |     ) -> bool {
[INFO] [stdout]     | |_____________^ method `vaftree::Node::contains` is reachable at visibility `pub`
[INFO] [stdout]     |
[INFO] [stdout] note: but type `LikelihoodOperands` is only usable at visibility `pub(crate)`
[INFO] [stdout]    --> src/variants/model/modes/generic.rs:118:1
[INFO] [stdout]     |
[INFO] [stdout] 118 | pub(crate) struct LikelihoodOperands {
[INFO] [stdout]     | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `VafLfc` is more private than the item `vaftree::Node::contains`
[INFO] [stdout]    --> src/grammar/vaftree.rs:116:5
[INFO] [stdout]     |
[INFO] [stdout] 116 | /     pub fn contains(
[INFO] [stdout] 117 | |         &self,
[INFO] [stdout] 118 | |         operands: &LikelihoodOperands,
[INFO] [stdout] 119 | |         lfcs: &mut Vec<&VafLfc>,
[INFO] [stdout] 120 | |         exclude_sample: Option<usize>,
[INFO] [stdout] 121 | |     ) -> bool {
[INFO] [stdout]     | |_____________^ method `vaftree::Node::contains` is reachable at visibility `pub`
[INFO] [stdout]     |
[INFO] [stdout] note: but type `VafLfc` is only usable at visibility `pub(crate)`
[INFO] [stdout]    --> src/variants/model/modes/generic.rs:110:1
[INFO] [stdout]     |
[INFO] [stdout] 110 | pub(crate) struct VafLfc {
[INFO] [stdout]     | ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `variants::model::Variant` is more private than the item `VariantInfo::variant`
[INFO] [stdout]    --> src/utils/collect_variants.rs:33:5
[INFO] [stdout]     |
[INFO] [stdout] 33  |     pub variant: model::Variant,
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^ field `VariantInfo::variant` is reachable at visibility `pub`
[INFO] [stdout]     |
[INFO] [stdout] note: but type `variants::model::Variant` is only usable at visibility `pub(crate)`
[INFO] [stdout]    --> src/variants/model/mod.rs:320:1
[INFO] [stdout]     |
[INFO] [stdout] 320 | pub(crate) enum Variant {
[INFO] [stdout]     | ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `BCFGrouper` is never constructed
[INFO] [stdout]    --> src/calling/variants/mod.rs:663:19
[INFO] [stdout]     |
[INFO] [stdout] 663 | pub(crate) struct BCFGrouper<'a>(pub(crate) &'a Variant);
[INFO] [stdout]     |                   ^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `epsilon_gap` is never read
[INFO] [stdout]   --> src/estimation/alignment_properties.rs:81:5
[INFO] [stdout]    |
[INFO] [stdout] 60 | pub(crate) struct AlignmentProperties {
[INFO] [stdout]    |                   ------------------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 81 |     epsilon_gap: f64,
[INFO] [stdout]    |     ^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `AlignmentProperties` has derived impls for the traits `Debug` and `Clone`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: methods `max_homopolymer_insertion_len` and `max_homopolymer_deletion_len` are never used
[INFO] [stdout]   --> src/estimation/alignment_properties.rs:85:19
[INFO] [stdout]    |
[INFO] [stdout] 84 | impl AlignmentProperties {
[INFO] [stdout]    | ------------------------ methods in this implementation
[INFO] [stdout] 85 |     pub(crate) fn max_homopolymer_insertion_len(&self) -> u16 {
[INFO] [stdout]    |                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 94 |     pub(crate) fn max_homopolymer_deletion_len(&self) -> u16 {
[INFO] [stdout]    |                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `total` is never read
[INFO] [stdout]    --> src/estimation/contamination.rs:238:5
[INFO] [stdout]     |
[INFO] [stdout] 236 | struct VAFDist {
[INFO] [stdout]     |        ------- field in this struct
[INFO] [stdout] 237 |     histogram: BTreeMap<AlleleFreq, usize>,
[INFO] [stdout] 238 |     total: usize,
[INFO] [stdout]     |     ^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `VAFDist` has derived impls for the traits `Debug` and `Clone`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `MB` is never constructed
[INFO] [stdout]   --> src/estimation/mutational_burden.rs:46:8
[INFO] [stdout]    |
[INFO] [stdout] 46 | struct MB {
[INFO] [stdout]    |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `base` is never read
[INFO] [stdout]   --> src/utils/homopolymers.rs:17:5
[INFO] [stdout]    |
[INFO] [stdout] 14 | pub(crate) struct HomopolymerIndelOperation {
[INFO] [stdout]    |                   ------------------------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 17 |     base: u8,
[INFO] [stdout]    |     ^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `HomopolymerIndelOperation` has derived impls for the traits `Debug` and `Clone`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `observed_depth` and `expected_ref_depth` are never read
[INFO] [stdout]  --> src/variants/evidence/observations/depth_observation.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | pub struct DepthObservation {
[INFO] [stdout]   |            ---------------- fields in this struct
[INFO] [stdout] 3 |     observed_depth: u64,
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 4 |     expected_ref_depth: f64,
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `DepthObservation` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: methods `start_locus` and `end_locus` are never used
[INFO] [stdout]    --> src/variants/evidence/observations/read_observation.rs:672:8
[INFO] [stdout]     |
[INFO] [stdout] 659 | pub(crate) trait Evidence {
[INFO] [stdout]     |                  -------- methods in this trait
[INFO] [stdout] ...
[INFO] [stdout] 672 |     fn start_locus(&self) -> genome::Locus;
[INFO] [stdout]     |        ^^^^^^^^^^^
[INFO] [stdout] 673 |
[INFO] [stdout] 674 |     fn end_locus(&self) -> genome::Locus;
[INFO] [stdout]     |        ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `maybe_revcomp` is never used
[INFO] [stdout]   --> src/variants/evidence/realignment/mod.rs:61:8
[INFO] [stdout]    |
[INFO] [stdout] 49 | pub(crate) trait Realignable {
[INFO] [stdout]    |                  ----------- method in this trait
[INFO] [stdout] ...
[INFO] [stdout] 61 |     fn maybe_revcomp(&self) -> bool {
[INFO] [stdout]    |        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `certainty_est` is never used
[INFO] [stdout]    --> src/variants/evidence/realignment/pairhmm.rs:489:19
[INFO] [stdout]     |
[INFO] [stdout] 436 | impl<'a> ReadEmission<'a> {
[INFO] [stdout]     | ------------------------- method in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 489 |     pub(crate) fn certainty_est(&self) -> LogProb {
[INFO] [stdout]     |                   ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: trait `AlleleFreqs` is never used
[INFO] [stdout]   --> src/variants/model/mod.rs:68:18
[INFO] [stdout]    |
[INFO] [stdout] 68 | pub(crate) trait AlleleFreqs: Debug {
[INFO] [stdout]    |                  ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `DiscreteAlleleFreqs` is never constructed
[INFO] [stdout]   --> src/variants/model/mod.rs:83:19
[INFO] [stdout]    |
[INFO] [stdout] 83 | pub(crate) struct DiscreteAlleleFreqs {
[INFO] [stdout]    |                   ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `is_singleton` is never used
[INFO] [stdout]    --> src/variants/model/mod.rs:119:19
[INFO] [stdout]     |
[INFO] [stdout] 105 | impl ContinuousAlleleFreqs {
[INFO] [stdout]     | -------------------------- method in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 119 |     pub(crate) fn is_singleton(&self) -> bool {
[INFO] [stdout]     |                   ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: trait `ContaminatedSamplePairView` is never used
[INFO] [stdout]   --> src/variants/model/likelihood.rs:55:18
[INFO] [stdout]    |
[INFO] [stdout] 55 | pub(crate) trait ContaminatedSamplePairView<T> {
[INFO] [stdout]    |                  ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `FlatPrior` is never constructed
[INFO] [stdout]    --> src/variants/model/modes/generic.rs:502:19
[INFO] [stdout]     |
[INFO] [stdout] 502 | pub(crate) struct FlatPrior {
[INFO] [stdout]     |                   ^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `FlatPrior` has a derived impl for the trait `Default`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: trait `TumorNormalPairView` is never used
[INFO] [stdout]   --> src/variants/model/modes/tumor.rs:18:18
[INFO] [stdout]    |
[INFO] [stdout] 18 | pub(crate) trait TumorNormalPairView<T> {
[INFO] [stdout]    |                  ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `protocol_strandedness` is never read
[INFO] [stdout]    --> src/variants/sample.rs:194:5
[INFO] [stdout]     |
[INFO] [stdout] 187 | pub(crate) struct Sample {
[INFO] [stdout]     |                   ------ field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 194 |     protocol_strandedness: ProtocolStrandedness,
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `Sample` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `is_homopolymer_indel` is never used
[INFO] [stdout]    --> src/variants/types/mod.rs:174:8
[INFO] [stdout]     |
[INFO] [stdout] 133 | pub(crate) trait Variant {
[INFO] [stdout]     |                  ------- method in this trait
[INFO] [stdout] ...
[INFO] [stdout] 174 |     fn is_homopolymer_indel(&self) -> bool {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `is_single_contig` is never used
[INFO] [stdout]    --> src/variants/types/mod.rs:448:8
[INFO] [stdout]     |
[INFO] [stdout] 446 | pub(crate) trait Loci {
[INFO] [stdout]     |                  ---- method in this trait
[INFO] [stdout] 447 |     fn contig(&self) -> Option<&str>;
[INFO] [stdout] 448 |     fn is_single_contig(&self) -> bool;
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `deletion_len` is never used
[INFO] [stdout]    --> src/variants/types/breakends.rs:256:8
[INFO] [stdout]     |
[INFO] [stdout] 180 | impl<R: Realigner> BreakendGroup<R> {
[INFO] [stdout]     | ----------------------------------- method in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 256 |     fn deletion_len(&self) -> Option<u64> {
[INFO] [stdout]     |        ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `LocusPlusOne` is never constructed
[INFO] [stdout]     --> src/variants/types/breakends.rs:1225:8
[INFO] [stdout]      |
[INFO] [stdout] 1225 | struct LocusPlusOne<'a>(&'a genome::Locus);
[INFO] [stdout]      |        ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `LocusMinusOne` is never constructed
[INFO] [stdout]     --> src/variants/types/breakends.rs:1237:8
[INFO] [stdout]      |
[INFO] [stdout] 1237 | struct LocusMinusOne<'a>(&'a genome::Locus);
[INFO] [stdout]      |        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: trait `HaplotypeVariant` is never used
[INFO] [stdout]   --> src/variants/types/haplotype_block.rs:81:18
[INFO] [stdout]    |
[INFO] [stdout] 81 | pub(crate) trait HaplotypeVariant: Variant + ToVariantRepresentation {}
[INFO] [stdout]    |                  ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: methods `push_single_locus_paired_end_evidence_variant` and `push_multi_locus_single_end_evidence_variant` are never used
[INFO] [stdout]    --> src/variants/types/haplotype_block.rs:115:19
[INFO] [stdout]     |
[INFO] [stdout] 96  | impl HaplotypeBlock {
[INFO] [stdout]     | ------------------- methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 115 |     pub(crate) fn push_single_locus_paired_end_evidence_variant(
[INFO] [stdout]     |                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 123 |     pub(crate) fn push_multi_locus_single_end_evidence_variant(
[INFO] [stdout]     |                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 65 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 67 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 21s
[INFO] running `Command { std: "docker" "inspect" "48ad0745854ec8564a932dbfcdf5e2fdb6048290608d659abe2fb6875a8ef324", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "48ad0745854ec8564a932dbfcdf5e2fdb6048290608d659abe2fb6875a8ef324", kill_on_drop: false }`
[INFO] [stdout] 48ad0745854ec8564a932dbfcdf5e2fdb6048290608d659abe2fb6875a8ef324
[INFO] checking varlociraptor-8.4.10 against try#a2cff3b7a9661c90ec0d581d3f3a69bb97c11138 for pr-121848-3
[INFO] extracting crate varlociraptor 8.4.10 into /workspace/builds/worker-3-tc2/source
[INFO] validating manifest of crates.io crate varlociraptor 8.4.10 on toolchain a2cff3b7a9661c90ec0d581d3f3a69bb97c11138
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+a2cff3b7a9661c90ec0d581d3f3a69bb97c11138" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking crates.io crate varlociraptor 8.4.10
[INFO] finished tweaking crates.io crate varlociraptor 8.4.10
[INFO] tweaked toml for crates.io crate varlociraptor 8.4.10 written to /workspace/builds/worker-3-tc2/source/Cargo.toml
[INFO] crate crates.io crate varlociraptor 8.4.10 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" "+a2cff3b7a9661c90ec0d581d3f3a69bb97c11138" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
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[INFO] [stdout] 375cb68673a3d8b757dc8cad17b63d9f56864a759039afa4300b6154ded8afe5
[INFO] running `Command { std: "docker" "start" "-a" "375cb68673a3d8b757dc8cad17b63d9f56864a759039afa4300b6154ded8afe5", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "375cb68673a3d8b757dc8cad17b63d9f56864a759039afa4300b6154ded8afe5", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "375cb68673a3d8b757dc8cad17b63d9f56864a759039afa4300b6154ded8afe5", kill_on_drop: false }`
[INFO] [stdout] 375cb68673a3d8b757dc8cad17b63d9f56864a759039afa4300b6154ded8afe5
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/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@sha256:923055f121b5182466d55868a8b05e67af8ba4a3a3f6bad814e953ca3cd3ac2a" "/opt/rustwide/cargo-home/bin/cargo" "+a2cff3b7a9661c90ec0d581d3f3a69bb97c11138" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 75f09095ba8d02a6e22296337a2f7db74dee403ecd1e2d544c4a447715360216
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[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]     Checking unicode-normalization v0.1.23
[INFO] [stderr]    Compiling nalgebra-macros v0.1.0
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]    Compiling jemalloc-sys v0.5.4+5.3.0-patched
[INFO] [stderr]    Compiling sysinfo v0.15.9
[INFO] [stderr]     Checking num-rational v0.4.2
[INFO] [stderr]     Checking num-iter v0.1.45
[INFO] [stderr]     Checking atty v0.2.14
[INFO] [stderr]    Compiling GSL-sys v3.0.0
[INFO] [stderr]    Compiling humansize v1.1.1
[INFO] [stderr]     Checking rawpointer v0.1.0
[INFO] [stderr]    Compiling syn v0.15.44
[INFO] [stderr]     Checking futures-task v0.3.30
[INFO] [stderr]    Compiling askama_escape v0.10.3
[INFO] [stderr]    Compiling rustix v0.38.34
[INFO] [stderr]     Checking futures-util v0.3.30
[INFO] [stderr]     Checking idna v0.5.0
[INFO] [stderr]    Compiling hts-sys v2.1.4
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking toml v0.5.11
[INFO] [stderr]     Checking bio-types v1.0.1
[INFO] [stderr]     Checking indexmap v2.2.6
[INFO] [stderr]     Checking num v0.1.42
[INFO] [stderr]     Checking rayon v1.10.0
[INFO] [stderr]    Compiling pest_meta v2.7.11
[INFO] [stderr]     Checking nalgebra v0.29.0
[INFO] [stderr]    Compiling askama_shared v0.12.2
[INFO] [stderr]     Checking futures-channel v0.3.30
[INFO] [stderr]    Compiling derive_builder_core v0.12.0
[INFO] [stderr]    Compiling enum-map-derive v0.17.0
[INFO] [stderr]    Compiling tokio-macros v2.3.0
[INFO] [stderr]    Compiling ring v0.16.20
[INFO] [stderr]     Checking rand v0.4.6
[INFO] [stderr]     Checking csv-core v0.1.11
[INFO] [stderr]     Checking linux-raw-sys v0.4.14
[INFO] [stderr]     Checking fixedbitset v0.4.2
[INFO] [stderr]    Compiling cached_proc_macro_types v0.1.1
[INFO] [stderr]     Checking bitflags v2.6.0
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking futures-io v0.3.30
[INFO] [stderr]     Checking yaml-rust v0.3.5
[INFO] [stderr]     Checking rand v0.3.23
[INFO] [stderr]     Checking futures v0.3.30
[INFO] [stderr]    Compiling cached_proc_macro v0.16.0
[INFO] [stderr]     Checking clap v2.34.0
[INFO] [stderr]    Compiling askama_derive v0.11.2
[INFO] [stderr]     Checking petgraph v0.6.5
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]     Checking csv v1.3.0
[INFO] [stderr]    Compiling derive_builder_macro v0.12.0
[INFO] [stderr]     Checking tokio v1.38.0
[INFO] [stderr]     Checking url v2.5.2
[INFO] [stderr]     Checking enum-map v2.7.3
[INFO] [stderr]    Compiling pest_generator v2.7.11
[INFO] [stderr]     Checking rulinalg v0.3.7
[INFO] [stderr]     Checking indexmap v1.9.3
[INFO] [stderr]     Checking serde_json v1.0.120
[INFO] [stderr]     Checking multimap v0.10.0
[INFO] [stderr]     Checking ndarray v0.15.6
[INFO] [stderr]    Compiling structopt-derive v0.4.18
[INFO] [stderr]    Compiling async-trait v0.1.80
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking ordered-float v4.2.1
[INFO] [stderr]     Checking itertools v0.9.0
[INFO] [stderr]    Compiling itertools v0.8.2
[INFO] [stderr]     Checking instant v0.1.13
[INFO] [stderr]     Checking fastrand v2.1.0
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]     Checking strum v0.25.0
[INFO] [stderr]     Checking async_once v0.2.6
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]     Checking bytecount v0.6.8
[INFO] [stderr]     Checking editdistancek v1.0.2
[INFO] [stderr]     Checking hashbrown v0.13.2
[INFO] [stderr]    Compiling bitflags v1.3.2
[INFO] [stderr]     Checking time v0.3.36
[INFO] [stderr]    Compiling shrinkwraprs v0.3.0
[INFO] [stderr]     Checking cached v0.42.0
[INFO] [stderr]     Checking eval v0.4.3
[INFO] [stderr]     Checking structopt v0.3.26
[INFO] [stderr]     Checking tempfile v3.10.1
[INFO] [stderr]     Checking boolean_expression v0.4.4
[INFO] [stderr]    Compiling derefable v0.1.0
[INFO] [stderr]     Checking GSL v6.0.0
[INFO] [stderr]     Checking rusty-machine v0.5.4
[INFO] [stderr]    Compiling pest_derive v2.7.11
[INFO] [stderr]     Checking serde_yaml v0.8.26
[INFO] [stderr]     Checking progress-logger v0.3.1
[INFO] [stderr]     Checking derive_builder v0.12.0
[INFO] [stderr]     Checking askama v0.11.1
[INFO] [stderr]     Checking half v2.4.1
[INFO] [stderr]     Checking ordered-float v1.1.1
[INFO] [stderr]     Checking bincode v1.3.3
[INFO] [stderr]     Checking fern v0.6.2
[INFO] [stderr]    Compiling getset v0.1.2
[INFO] [stderr]     Checking lru v0.7.8
[INFO] [stderr]    Compiling typed-builder v0.12.0
[INFO] [stderr]     Checking uuid v0.8.2
[INFO] [stderr]     Checking counter v0.5.7
[INFO] [stderr]     Checking itertools v0.10.5
[INFO] [stderr]     Checking auto_ops v0.3.0
[INFO] [stderr]     Checking lru_time_cache v0.11.11
[INFO] [stderr]     Checking env_logger v0.9.3
[INFO] [stderr]     Checking jemallocator v0.5.4
[INFO] [stderr]     Checking rust-htslib v0.47.0
[ERROR] error running command: no output for 300 seconds
[INFO] running `Command { std: "docker" "inspect" "75f09095ba8d02a6e22296337a2f7db74dee403ecd1e2d544c4a447715360216", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "75f09095ba8d02a6e22296337a2f7db74dee403ecd1e2d544c4a447715360216", kill_on_drop: false }`
[INFO] [stdout] 75f09095ba8d02a6e22296337a2f7db74dee403ecd1e2d544c4a447715360216
