[INFO] fetching crate varlociraptor 5.7.0... [INFO] checking varlociraptor-5.7.0 against try#549dafd0516c8b08f912fb001d48e977d0a94c34 for pr-107421 [INFO] extracting crate varlociraptor 5.7.0 into /workspace/builds/worker-3-tc2/source [INFO] validating manifest of crates.io crate varlociraptor 5.7.0 on toolchain 549dafd0516c8b08f912fb001d48e977d0a94c34 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+549dafd0516c8b08f912fb001d48e977d0a94c34" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking crates.io crate varlociraptor 5.7.0 [INFO] finished tweaking crates.io crate varlociraptor 5.7.0 [INFO] tweaked toml for crates.io crate varlociraptor 5.7.0 written to /workspace/builds/worker-3-tc2/source/Cargo.toml [INFO] crate crates.io crate varlociraptor 5.7.0 already has a lockfile, it will not be regenerated [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+549dafd0516c8b08f912fb001d48e977d0a94c34" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [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_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@sha256:3d532c2baa59a8a48e45c3be7eb049f77ac5a58a7a6514a58a8e878df1c3d03d" "/opt/rustwide/cargo-home/bin/cargo" "+549dafd0516c8b08f912fb001d48e977d0a94c34" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] dd6d08f701ef804e1f8ecc1835c46678b63d5de5ebafbbe185c10f16177a6d82 [INFO] running `Command { std: "docker" "start" "-a" "dd6d08f701ef804e1f8ecc1835c46678b63d5de5ebafbbe185c10f16177a6d82", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "dd6d08f701ef804e1f8ecc1835c46678b63d5de5ebafbbe185c10f16177a6d82", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "dd6d08f701ef804e1f8ecc1835c46678b63d5de5ebafbbe185c10f16177a6d82", kill_on_drop: false }` [INFO] [stdout] dd6d08f701ef804e1f8ecc1835c46678b63d5de5ebafbbe185c10f16177a6d82 [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@sha256:3d532c2baa59a8a48e45c3be7eb049f77ac5a58a7a6514a58a8e878df1c3d03d" "/opt/rustwide/cargo-home/bin/cargo" "+549dafd0516c8b08f912fb001d48e977d0a94c34" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 8c7da94592b3dcda430842e6cd5f915fe2285c43321ba6bc0b30db4ceca8ffc5 [INFO] running `Command { std: "docker" "start" "-a" "8c7da94592b3dcda430842e6cd5f915fe2285c43321ba6bc0b30db4ceca8ffc5", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.47 [INFO] [stderr] Compiling libc v0.2.138 [INFO] [stderr] Compiling quote v1.0.21 [INFO] [stderr] Compiling unicode-ident v1.0.5 [INFO] [stderr] Compiling syn v1.0.105 [INFO] [stderr] Compiling libm v0.2.6 [INFO] [stderr] Compiling serde_derive v1.0.148 [INFO] [stderr] Compiling serde v1.0.148 [INFO] [stderr] Compiling pkg-config v0.3.26 [INFO] [stderr] Compiling memchr v2.5.0 [INFO] [stderr] Compiling thiserror v1.0.37 [INFO] [stderr] Compiling fnv v1.0.7 [INFO] [stderr] Checking once_cell v1.16.0 [INFO] [stderr] Compiling num-traits v0.2.15 [INFO] [stderr] Compiling num-integer v0.1.45 [INFO] [stderr] Compiling unicase v2.6.0 [INFO] [stderr] Compiling ident_case v1.0.1 [INFO] [stderr] Compiling strsim v0.10.0 [INFO] [stderr] Compiling ahash v0.7.6 [INFO] [stderr] Compiling rustversion v1.0.9 [INFO] [stderr] Checking either v1.8.0 [INFO] [stderr] 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v0.41.0 [INFO] [stderr] Compiling pest_generator v2.5.1 [INFO] [stderr] Checking derive_builder v0.11.2 [INFO] [stderr] Compiling pest_derive v2.5.1 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking bio-types v0.13.0 [INFO] [stderr] Checking toml v0.5.9 [INFO] [stderr] Checking bstr v0.2.15 [INFO] [stderr] Checking clap v2.34.0 [INFO] [stderr] Checking multimap v0.8.3 [INFO] [stderr] Checking csv v1.1.6 [INFO] [stderr] Checking half v1.8.2 [INFO] [stderr] Checking bincode v1.3.3 [INFO] [stderr] Checking ordered-float v1.1.1 [INFO] [stderr] Checking serde_yaml v0.8.26 [INFO] [stderr] Checking askama_shared v0.12.2 [INFO] [stderr] Checking statrs v0.16.0 [INFO] [stderr] Checking eval v0.4.3 [INFO] [stderr] Checking bio v1.1.0 [INFO] [stderr] Checking structopt v0.3.26 [INFO] [stderr] Compiling askama_derive v0.11.2 [INFO] [stderr] Checking askama v0.11.1 [INFO] [stderr] Checking rust-htslib v0.40.2 [INFO] [stderr] Checking jemallocator v0.3.2 [INFO] [stderr] Checking varlociraptor v5.7.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `ordered_float::NotNan` [INFO] [stdout] --> src/calling/variants/calling.rs:16:5 [INFO] [stdout] | [INFO] [stdout] 16 | use ordered_float::NotNan; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::utils::signif` [INFO] [stdout] --> src/calling/variants/mod.rs:27:5 [INFO] [stdout] | [INFO] [stdout] 27 | use crate::utils::signif; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::calling::variants::calling::CallerBuilder` [INFO] [stdout] --> src/calling/variants/mod.rs:40:16 [INFO] [stdout] | [INFO] [stdout] 40 | pub(crate) use crate::calling::variants::calling::CallerBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::cell::RefCell` [INFO] [stdout] --> src/cli.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use std::cell::RefCell; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Inheritance` [INFO] [stdout] --> src/cli.rs:40:37 [INFO] [stdout] | [INFO] [stdout] 40 | use crate::variants::model::prior::{Inheritance, Prior}; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Contamination` [INFO] [stdout] --> src/cli.rs:41:42 [INFO] [stdout] | [INFO] [stdout] 41 | use crate::variants::model::{AlleleFreq, Contamination, VariantType}; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ordered_float::NotNan` [INFO] [stdout] --> src/estimation/contamination.rs:14:5 [INFO] [stdout] | [INFO] [stdout] 14 | use ordered_float::NotNan; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `statrs::distribution::Empirical` [INFO] [stdout] --> src/estimation/contamination.rs:18:5 [INFO] [stdout] | [INFO] [stdout] 18 | use statrs::distribution::Empirical; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `NUMERICAL_EPSILON` [INFO] [stdout] --> src/estimation/contamination.rs:27:41 [INFO] [stdout] | [INFO] [stdout] 27 | utils::{aux_info::AuxInfoCollector, NUMERICAL_EPSILON}, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Log2FoldChange` [INFO] [stdout] --> src/grammar/vaftree.rs:8:38 [INFO] [stdout] | [INFO] [stdout] 8 | use crate::utils::log2_fold_change::{Log2FoldChange, Log2FoldChangePredicate}; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `serde_yaml::Value` [INFO] [stdout] --> src/testcase/runner/common/version1.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use serde_yaml::Value; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `mem` [INFO] [stdout] --> src/variants/model/mod.rs:9:11 [INFO] [stdout] | [INFO] [stdout] 9 | use std::{mem, str}; [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ordered_float::NotNan` [INFO] [stdout] --> src/calling/variants/calling.rs:16:5 [INFO] [stdout] | [INFO] [stdout] 16 | use ordered_float::NotNan; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::utils::signif` [INFO] [stdout] --> src/calling/variants/mod.rs:27:5 [INFO] [stdout] | [INFO] [stdout] 27 | use crate::utils::signif; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::calling::variants::calling::CallerBuilder` [INFO] [stdout] --> src/calling/variants/mod.rs:40:16 [INFO] [stdout] | [INFO] [stdout] 40 | pub(crate) use crate::calling::variants::calling::CallerBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::cell::RefCell` [INFO] [stdout] --> src/cli.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use std::cell::RefCell; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Inheritance` [INFO] [stdout] --> src/cli.rs:40:37 [INFO] [stdout] | [INFO] [stdout] 40 | use crate::variants::model::prior::{Inheritance, Prior}; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Contamination` [INFO] [stdout] --> src/cli.rs:41:42 [INFO] [stdout] | [INFO] [stdout] 41 | use crate::variants::model::{AlleleFreq, Contamination, VariantType}; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ordered_float::NotNan` [INFO] [stdout] --> src/estimation/contamination.rs:14:5 [INFO] [stdout] | [INFO] [stdout] 14 | use ordered_float::NotNan; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `statrs::distribution::Empirical` [INFO] [stdout] --> src/estimation/contamination.rs:18:5 [INFO] [stdout] | [INFO] [stdout] 18 | use statrs::distribution::Empirical; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `NUMERICAL_EPSILON` [INFO] [stdout] --> src/estimation/contamination.rs:27:41 [INFO] [stdout] | [INFO] [stdout] 27 | utils::{aux_info::AuxInfoCollector, NUMERICAL_EPSILON}, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Log2FoldChange` [INFO] [stdout] --> src/grammar/vaftree.rs:8:38 [INFO] [stdout] | [INFO] [stdout] 8 | use crate::utils::log2_fold_change::{Log2FoldChange, Log2FoldChangePredicate}; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `serde_yaml::Value` [INFO] [stdout] --> src/testcase/runner/common/version1.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use serde_yaml::Value; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `mem` [INFO] [stdout] --> src/variants/model/mod.rs:9:11 [INFO] [stdout] | [INFO] [stdout] 9 | use std::{mem, str}; [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: irrefutable `if let` pattern [INFO] [stdout] --> src/calling/variants/preprocessing/mod.rs:580:28 [INFO] [stdout] | [INFO] [stdout] 580 | 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: 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: irrefutable `if let` pattern [INFO] [stdout] --> src/calling/variants/preprocessing/mod.rs:580:28 [INFO] [stdout] | [INFO] [stdout] 580 | 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: unused variable: `sample_names` [INFO] [stdout] --> src/calling/variants/calling.rs:893:9 [INFO] [stdout] | [INFO] [stdout] 893 | sample_names: &grammar::SampleInfo, [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:912:22 [INFO] [stdout] | [INFO] [stdout] 912 | fn filter(&self, work_item: &WorkItem, sample_names: &grammar::SampleInfo) -> 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:912:44 [INFO] [stdout] | [INFO] [stdout] 912 | fn filter(&self, work_item: &WorkItem, sample_names: &grammar::SampleInfo) -> bool { [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_sample_names` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `infimum` [INFO] [stdout] --> src/estimation/contamination.rs:99:20 [INFO] [stdout] | [INFO] [stdout] 99 | (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:99:29 [INFO] [stdout] | [INFO] [stdout] 99 | (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:164:63 [INFO] [stdout] | [INFO] [stdout] 164 | 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: `caller` [INFO] [stdout] --> src/estimation/contamination.rs:379:9 [INFO] [stdout] | [INFO] [stdout] 379 | caller: &Caller, [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_caller` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `sample_names` [INFO] [stdout] --> src/calling/variants/calling.rs:893:9 [INFO] [stdout] | [INFO] [stdout] 893 | sample_names: &grammar::SampleInfo, [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:912:22 [INFO] [stdout] | [INFO] [stdout] 912 | fn filter(&self, work_item: &WorkItem, sample_names: &grammar::SampleInfo) -> 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:912:44 [INFO] [stdout] | [INFO] [stdout] 912 | fn filter(&self, work_item: &WorkItem, sample_names: &grammar::SampleInfo) -> bool { [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_sample_names` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `i` [INFO] [stdout] --> src/variants/types/haplotype_block.rs:187:31 [INFO] [stdout] | [INFO] [stdout] 187 | .filter_map(|(i, variant)| { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_i` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `infimum` [INFO] [stdout] --> src/estimation/contamination.rs:99:20 [INFO] [stdout] | [INFO] [stdout] 99 | (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:99:29 [INFO] [stdout] | [INFO] [stdout] 99 | (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:164:63 [INFO] [stdout] | [INFO] [stdout] 164 | 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: `caller` [INFO] [stdout] --> src/estimation/contamination.rs:379:9 [INFO] [stdout] | [INFO] [stdout] 379 | caller: &Caller, [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_caller` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `i` [INFO] [stdout] --> src/variants/types/haplotype_block.rs:187:31 [INFO] [stdout] | [INFO] [stdout] 187 | .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/calling/variants/calling.rs:280:13 [INFO] [stdout] | [INFO] [stdout] 280 | 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:280:13 [INFO] [stdout] | [INFO] [stdout] 280 | 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/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: variable does not need to be mutable [INFO] [stdout] --> src/estimation/contamination.rs:356:21 [INFO] [stdout] | [INFO] [stdout] 356 | let mut outfile = File::create(outpath)?; [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/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: variable does not need to be mutable [INFO] [stdout] --> src/estimation/contamination.rs:356:21 [INFO] [stdout] | [INFO] [stdout] 356 | let mut outfile = File::create(outpath)?; [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/variants/types/haplotype_block.rs:284:13 [INFO] [stdout] | [INFO] [stdout] 284 | let mut support = support [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/variants/types/haplotype_block.rs:284:13 [INFO] [stdout] | [INFO] [stdout] 284 | let mut support = support [INFO] [stdout] | ----^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `total` is never read [INFO] [stdout] --> src/estimation/contamination.rs:236:5 [INFO] [stdout] | [INFO] [stdout] 234 | struct VAFDist { [INFO] [stdout] | ------- field in this struct [INFO] [stdout] 235 | histogram: BTreeMap, [INFO] [stdout] 236 | 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] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `signif` is never used [INFO] [stdout] --> src/utils/mod.rs:602:15 [INFO] [stdout] | [INFO] [stdout] 602 | pub(crate) fn signif(float: f64, precision: usize) -> String { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `base` is never read [INFO] [stdout] --> src/utils/homopolymers.rs:15:5 [INFO] [stdout] | [INFO] [stdout] 12 | pub(crate) struct HomopolymerIndelOperation { [INFO] [stdout] | ------------------------- field in this struct [INFO] [stdout] ... [INFO] [stdout] 15 | 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: associated function `certainty_est` is never used [INFO] [stdout] --> src/variants/evidence/realignment/pairhmm.rs:406:19 [INFO] [stdout] | [INFO] [stdout] 406 | pub(crate) fn certainty_est(&self) -> LogProb { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `protocol_strandedness` is never read [INFO] [stdout] --> src/variants/sample.rs:195:5 [INFO] [stdout] | [INFO] [stdout] 188 | pub(crate) struct Sample { [INFO] [stdout] | ------ field in this struct [INFO] [stdout] ... [INFO] [stdout] 195 | 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: associated function `push_single_locus_paired_end_evidence_variant` is never used [INFO] [stdout] --> src/variants/types/haplotype_block.rs:114:19 [INFO] [stdout] | [INFO] [stdout] 114 | pub(crate) fn push_single_locus_paired_end_evidence_variant( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function `push_multi_locus_single_end_evidence_variant` is never used [INFO] [stdout] --> src/variants/types/haplotype_block.rs:122:19 [INFO] [stdout] | [INFO] [stdout] 122 | pub(crate) fn push_multi_locus_single_end_evidence_variant( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `total` is never read [INFO] [stdout] --> src/estimation/contamination.rs:236:5 [INFO] [stdout] | [INFO] [stdout] 234 | struct VAFDist { [INFO] [stdout] | ------- field in this struct [INFO] [stdout] 235 | histogram: BTreeMap, [INFO] [stdout] 236 | 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] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `signif` is never used [INFO] [stdout] --> src/utils/mod.rs:602:15 [INFO] [stdout] | [INFO] [stdout] 602 | pub(crate) fn signif(float: f64, precision: usize) -> String { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `base` is never read [INFO] [stdout] --> src/utils/homopolymers.rs:15:5 [INFO] [stdout] | [INFO] [stdout] 12 | pub(crate) struct HomopolymerIndelOperation { [INFO] [stdout] | ------------------------- field in this struct [INFO] [stdout] ... [INFO] [stdout] 15 | 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: associated function `certainty_est` is never used [INFO] [stdout] --> src/variants/evidence/realignment/pairhmm.rs:406:19 [INFO] [stdout] | [INFO] [stdout] 406 | pub(crate) fn certainty_est(&self) -> LogProb { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `protocol_strandedness` is never read [INFO] [stdout] --> src/variants/sample.rs:195:5 [INFO] [stdout] | [INFO] [stdout] 188 | pub(crate) struct Sample { [INFO] [stdout] | ------ field in this struct [INFO] [stdout] ... [INFO] [stdout] 195 | 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: associated function `push_single_locus_paired_end_evidence_variant` is never used [INFO] [stdout] --> src/variants/types/haplotype_block.rs:114:19 [INFO] [stdout] | [INFO] [stdout] 114 | pub(crate) fn push_single_locus_paired_end_evidence_variant( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function `push_multi_locus_single_end_evidence_variant` is never used [INFO] [stdout] --> src/variants/types/haplotype_block.rs:122:19 [INFO] [stdout] | [INFO] [stdout] 122 | pub(crate) fn push_multi_locus_single_end_evidence_variant( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 34 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 34 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 1m 02s [INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: fs_extra v1.2.0 [INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1` [INFO] running `Command { std: "docker" "inspect" "8c7da94592b3dcda430842e6cd5f915fe2285c43321ba6bc0b30db4ceca8ffc5", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "8c7da94592b3dcda430842e6cd5f915fe2285c43321ba6bc0b30db4ceca8ffc5", kill_on_drop: false }` [INFO] [stdout] 8c7da94592b3dcda430842e6cd5f915fe2285c43321ba6bc0b30db4ceca8ffc5