[INFO] fetching crate varlociraptor 5.3.3... [INFO] checking varlociraptor-5.3.3 against master#77e7b74ad5c0c449fa378faf5edf33dd2e6fed87 for pr-93275 [INFO] extracting crate varlociraptor 5.3.3 into /workspace/builds/worker-6/source [INFO] validating manifest of crates.io crate varlociraptor 5.3.3 on toolchain 77e7b74ad5c0c449fa378faf5edf33dd2e6fed87 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+77e7b74ad5c0c449fa378faf5edf33dd2e6fed87" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking crates.io crate varlociraptor 5.3.3 [INFO] finished tweaking crates.io crate varlociraptor 5.3.3 [INFO] tweaked toml for crates.io crate varlociraptor 5.3.3 written to /workspace/builds/worker-6/source/Cargo.toml [INFO] crate crates.io crate varlociraptor 5.3.3 already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+77e7b74ad5c0c449fa378faf5edf33dd2e6fed87" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded progress-logger v0.3.1 [INFO] [stderr] Downloaded cached_proc_macro_types v0.1.0 [INFO] [stderr] Downloaded lru_time_cache v0.11.11 [INFO] [stderr] Downloaded rust-htslib v0.40.2 [INFO] [stderr] Downloaded askama_derive v0.10.5 [INFO] [stderr] Downloaded triple_accel v0.4.0 [INFO] [stderr] Downloaded askama v0.10.5 [INFO] [stderr] Downloaded askama_shared v0.11.2 [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded GSL v6.0.0 [INFO] [stderr] Downloaded cached v0.26.2 [INFO] [stderr] Downloaded cached_proc_macro v0.7.1 [INFO] [stderr] Downloaded GSL-sys v3.0.0 [INFO] [stderr] Downloaded bio v0.40.0 [INFO] [stderr] Downloaded boolean_expression v0.4.4 [INFO] [stderr] Downloaded eval v0.4.3 [INFO] [stderr] Downloaded itertools-num v0.1.3 [INFO] [stderr] Downloaded bio-types v0.13.0 [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded hts-sys v2.0.3 [INFO] [stderr] Downloaded rulinalg v0.3.7 [INFO] [stderr] Downloaded rusty-machine v0.5.4 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/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@sha256:83125433e4fff17b1ac56874832f668d9df75ee638575aca552b68e127bedee9" "/opt/rustwide/cargo-home/bin/cargo" "+77e7b74ad5c0c449fa378faf5edf33dd2e6fed87" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] ee5d7d72ef2c8c6fa2c66bf5b4554b083822e3d0c8062051e5d0f3dc707536ea [INFO] running `Command { std: "docker" "start" "-a" "ee5d7d72ef2c8c6fa2c66bf5b4554b083822e3d0c8062051e5d0f3dc707536ea", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "ee5d7d72ef2c8c6fa2c66bf5b4554b083822e3d0c8062051e5d0f3dc707536ea", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "ee5d7d72ef2c8c6fa2c66bf5b4554b083822e3d0c8062051e5d0f3dc707536ea", kill_on_drop: false }` [INFO] [stdout] ee5d7d72ef2c8c6fa2c66bf5b4554b083822e3d0c8062051e5d0f3dc707536ea [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/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@sha256:83125433e4fff17b1ac56874832f668d9df75ee638575aca552b68e127bedee9" "/opt/rustwide/cargo-home/bin/cargo" "+77e7b74ad5c0c449fa378faf5edf33dd2e6fed87" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] a19530da9aca82f2e921f466185898b4b6de2a2bdcdfbfafb321f3b34357d3ca [INFO] running `Command { std: "docker" "start" "-a" "a19530da9aca82f2e921f466185898b4b6de2a2bdcdfbfafb321f3b34357d3ca", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Compiling proc-macro2 v1.0.46 [INFO] [stderr] Compiling quote 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[stderr] Checking derive_builder v0.10.2 [INFO] [stderr] Checking futures-executor v0.3.24 [INFO] [stderr] Checking futures v0.3.24 [INFO] [stderr] Compiling pest_generator v2.4.0 [INFO] [stderr] Checking cached v0.26.2 [INFO] [stderr] Compiling pest_derive v2.4.0 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking toml v0.5.9 [INFO] [stderr] Checking bstr v0.2.15 [INFO] [stderr] Checking bio-types v0.13.0 [INFO] [stderr] Checking clap v2.34.0 [INFO] [stderr] Checking ordered-float v1.1.1 [INFO] [stderr] Checking multimap v0.8.3 [INFO] [stderr] Checking csv v1.1.6 [INFO] [stderr] Checking askama_shared v0.11.2 [INFO] [stderr] Checking half v1.8.2 [INFO] [stderr] Checking bincode v1.3.3 [INFO] [stderr] Checking serde_yaml v0.8.26 [INFO] [stderr] Checking eval v0.4.3 [INFO] [stderr] Checking statrs v0.15.0 [INFO] [stderr] Checking structopt v0.3.26 [INFO] [stderr] Checking bio v0.40.0 [INFO] [stderr] Compiling askama_derive v0.10.5 [INFO] [stderr] Checking askama v0.10.5 [INFO] [stderr] Checking rust-htslib v0.40.2 [INFO] [stderr] Checking jemallocator v0.3.2 [INFO] [stderr] Checking varlociraptor v5.3.3 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `iter` [INFO] [stdout] --> src/variants/types/insertion.rs:10:16 [INFO] [stdout] | [INFO] [stdout] 10 | use std::{cmp, iter}; [INFO] [stdout] | ^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `iter` [INFO] [stdout] --> src/variants/types/insertion.rs:10:16 [INFO] [stdout] | [INFO] [stdout] 10 | use std::{cmp, iter}; [INFO] [stdout] | ^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` 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:565:28 [INFO] [stdout] | [INFO] [stdout] 565 | 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:565:28 [INFO] [stdout] | [INFO] [stdout] 565 | 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: `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] = note: `#[warn(unused_variables)]` on by default [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] = note: `#[warn(unused_variables)]` on by default [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] = note: `#[warn(unused_mut)]` on by default [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] = note: `#[warn(unused_mut)]` on by default [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] = note: `#[warn(dead_code)]` on by default [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: 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 `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] = note: `#[warn(dead_code)]` on by default [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: 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: 10 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 10 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 1m 01s [INFO] running `Command { std: "docker" "inspect" "a19530da9aca82f2e921f466185898b4b6de2a2bdcdfbfafb321f3b34357d3ca", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "a19530da9aca82f2e921f466185898b4b6de2a2bdcdfbfafb321f3b34357d3ca", kill_on_drop: false }` [INFO] [stdout] a19530da9aca82f2e921f466185898b4b6de2a2bdcdfbfafb321f3b34357d3ca