[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 ... [INFO] [stderr] Downloaded rusty-machine v0.5.4 [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded rulinalg v0.3.7 [INFO] [stderr] Downloaded derefable v0.1.0 [INFO] [stderr] Downloaded askama_derive v0.11.2 [INFO] [stderr] Downloaded bio-types v1.0.1 [INFO] [stderr] Downloaded askama v0.11.1 [INFO] [stderr] Downloaded typed-builder v0.12.0 [INFO] [stderr] Downloaded editdistancek v1.0.2 [INFO] [stderr] Downloaded askama_shared v0.12.2 [INFO] [stderr] Downloaded triple_accel v0.4.0 [INFO] [stderr] Downloaded GSL-sys v3.0.0 [INFO] [stderr] Downloaded sysinfo v0.15.9 [INFO] [stderr] Downloaded boolean_expression v0.4.4 [INFO] [stderr] Downloaded rust-htslib v0.47.0 [INFO] [stderr] Downloaded eval v0.4.3 [INFO] [stderr] Downloaded progress-logger v0.3.1 [INFO] [stderr] Downloaded GSL v6.0.0 [INFO] [stderr] Downloaded bio v2.0.0 [INFO] [stderr] Downloaded curl-sys v0.4.73+curl-8.8.0 [INFO] [stderr] Downloaded hts-sys v2.1.4 [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 }` [INFO] [stdout] a57ebe2dbe44b1fa2f604143eb001711992d7846edb59326457d86c9a42c6a8c [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_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" "+3139ff09e9d07f7700f8d15ed25a231e29c43627" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 48ad0745854ec8564a932dbfcdf5e2fdb6048290608d659abe2fb6875a8ef324 [INFO] running `Command { std: "docker" "start" "-a" "48ad0745854ec8564a932dbfcdf5e2fdb6048290608d659abe2fb6875a8ef324", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.86 [INFO] [stderr] Compiling libc v0.2.155 [INFO] [stderr] Compiling libm v0.2.8 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling serde v1.0.203 [INFO] [stderr] Compiling memchr v2.7.4 [INFO] [stderr] Compiling thiserror v1.0.61 [INFO] [stderr] Compiling unicase v2.7.0 [INFO] [stderr] Compiling minimal-lexical v0.2.1 [INFO] [stderr] Compiling glob v0.3.1 [INFO] [stderr] Compiling rustversion v1.0.17 [INFO] [stderr] Compiling mime_guess v2.0.5 [INFO] [stderr] Compiling quote v1.0.36 [INFO] [stderr] Compiling nom v7.1.3 [INFO] [stderr] Compiling syn v2.0.68 [INFO] [stderr] Compiling clang-sys v1.8.1 [INFO] [stderr] Compiling aho-corasick v1.1.3 [INFO] [stderr] Compiling libloading v0.8.4 [INFO] [stderr] Compiling ahash v0.7.8 [INFO] [stderr] Checking num-integer v0.1.46 [INFO] [stderr] Compiling matrixmultiply v0.3.8 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling jobserver v0.1.31 [INFO] [stderr] Checking getrandom v0.2.15 [INFO] [stderr] Checking bytemuck v1.16.1 [INFO] [stderr] Checking rand_core v0.6.4 [INFO] [stderr] Compiling bindgen v0.69.4 [INFO] [stderr] Compiling cc v1.0.104 [INFO] [stderr] Checking rand_chacha v0.3.1 [INFO] [stderr] Checking safe_arch v0.7.2 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling regex-automata v0.4.7 [INFO] [stderr] Compiling cexpr v0.6.0 [INFO] [stderr] Checking num-complex v0.4.6 [INFO] [stderr] Compiling cmake v0.1.50 [INFO] [stderr] Compiling openssl-src v300.3.1+3.3.1 [INFO] [stderr] Compiling itertools v0.12.1 [INFO] [stderr] Compiling rustc-hash v1.1.0 [INFO] [stderr] Compiling lazy_static v1.5.0 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling lazycell v1.3.0 [INFO] [stderr] Compiling libz-sys v1.1.18 [INFO] [stderr] Compiling openssl-sys v0.9.102 [INFO] [stderr] Compiling curl-sys v0.4.73+curl-8.8.0 [INFO] [stderr] Compiling darling_core v0.14.4 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling regex v1.10.5 [INFO] [stderr] Compiling bzip2-sys v0.1.11+1.0.8 [INFO] [stderr] Compiling darling_macro v0.14.4 [INFO] [stderr] Compiling darling v0.14.4 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Checking tinyvec v1.6.1 [INFO] [stderr] Compiling serde_derive v1.0.203 [INFO] [stderr] Compiling thiserror-impl v1.0.61 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Checking wide v0.7.25 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Checking rand v0.8.5 [INFO] [stderr] Checking approx v0.5.1 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling doc-comment v0.3.3 [INFO] [stderr] Compiling ucd-trie v0.1.6 [INFO] [stderr] Checking futures-core v0.3.30 [INFO] [stderr] Compiling matrixmultiply v0.1.15 [INFO] [stderr] Checking futures-sink v0.3.30 [INFO] [stderr] Compiling mime v0.3.17 [INFO] [stderr] Compiling strum_macros v0.25.3 [INFO] [stderr] Checking simba v0.6.0 [INFO] [stderr] Compiling pest v2.7.11 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Checking rand_distr v0.4.3 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Checking hashbrown v0.12.3 [INFO] [stderr] Checking unicode-normalization v0.1.23 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling nalgebra-macros v0.1.0 [INFO] [stderr] Compiling hts-sys v2.1.4 [INFO] [stderr] Compiling jemalloc-sys v0.5.4+5.3.0-patched [INFO] [stderr] Compiling sysinfo v0.15.9 [INFO] [stderr] Checking num-iter v0.1.45 [INFO] [stderr] Checking num-rational v0.4.2 [INFO] [stderr] Checking atty v0.2.14 [INFO] [stderr] Compiling GSL-sys v3.0.0 [INFO] [stderr] Checking futures-task v0.3.30 [INFO] [stderr] Checking rawpointer v0.1.0 [INFO] [stderr] Compiling humansize v1.1.1 [INFO] [stderr] Compiling askama_escape v0.10.3 [INFO] [stderr] Compiling syn v0.15.44 [INFO] [stderr] Compiling rustix v0.38.34 [INFO] [stderr] Checking indexmap v2.2.6 [INFO] [stderr] Checking futures-util v0.3.30 [INFO] [stderr] Checking idna v0.5.0 [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 num v0.1.42 [INFO] [stderr] Checking rayon v1.10.0 [INFO] [stderr] Checking nalgebra v0.29.0 [INFO] [stderr] Compiling askama_shared v0.12.2 [INFO] [stderr] Compiling pest_meta v2.7.11 [INFO] [stderr] Checking futures-channel v0.3.30 [INFO] [stderr] Compiling tokio-macros v2.3.0 [INFO] [stderr] Compiling enum-map-derive v0.17.0 [INFO] [stderr] Compiling derive_builder_core v0.12.0 [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 futures-io v0.3.30 [INFO] [stderr] Checking yaml-rust v0.3.5 [INFO] [stderr] Checking fixedbitset v0.4.2 [INFO] [stderr] Checking bitflags v2.6.0 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Compiling cached_proc_macro_types v0.1.1 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling cached_proc_macro v0.16.0 [INFO] [stderr] Compiling askama_derive v0.11.2 [INFO] [stderr] Checking clap v2.34.0 [INFO] [stderr] Compiling derive_builder_macro v0.12.0 [INFO] [stderr] Checking petgraph v0.6.5 [INFO] [stderr] Checking futures v0.3.30 [INFO] [stderr] Checking csv v1.3.0 [INFO] [stderr] Checking rand v0.3.23 [INFO] [stderr] Checking url v2.5.2 [INFO] [stderr] Checking tokio v1.38.0 [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 multimap v0.10.0 [INFO] [stderr] Checking serde_json v1.0.120 [INFO] [stderr] Checking ndarray v0.15.6 [INFO] [stderr] Compiling structopt-derive v0.4.18 [INFO] [stderr] Checking statrs v0.16.1 [INFO] [stderr] Compiling async-trait v0.1.80 [INFO] [stderr] Checking ordered-float v4.2.1 [INFO] [stderr] Checking itertools-num v0.1.3 [INFO] [stderr] Checking itertools v0.9.0 [INFO] [stderr] Compiling itertools v0.8.2 [INFO] [stderr] Checking instant v0.1.13 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Checking async_once v0.2.6 [INFO] [stderr] Compiling bitflags v1.3.2 [INFO] [stderr] Checking bytecount v0.6.8 [INFO] [stderr] Checking hashbrown v0.13.2 [INFO] [stderr] Checking strum v0.25.0 [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Checking triple_accel v0.4.0 [INFO] [stderr] Checking editdistancek v1.0.2 [INFO] [stderr] Checking fastrand v2.1.0 [INFO] [stderr] Checking tempfile v3.10.1 [INFO] [stderr] Compiling shrinkwraprs v0.3.0 [INFO] [stderr] Checking cached v0.42.0 [INFO] [stderr] Checking eval v0.4.3 [INFO] [stderr] Checking boolean_expression v0.4.4 [INFO] [stderr] Checking time v0.3.36 [INFO] [stderr] Checking structopt v0.3.26 [INFO] [stderr] Compiling derefable v0.1.0 [INFO] [stderr] Checking GSL v6.0.0 [INFO] [stderr] Checking rusty-machine v0.5.4 [INFO] [stderr] Checking serde_yaml v0.8.26 [INFO] [stderr] Compiling pest_derive v2.7.11 [INFO] [stderr] Checking bio v2.0.0 [INFO] [stderr] Checking progress-logger v0.3.1 [INFO] [stderr] Checking askama v0.11.1 [INFO] [stderr] Checking derive_builder v0.12.0 [INFO] [stderr] Checking half v2.4.1 [INFO] [stderr] Checking bincode v1.3.3 [INFO] [stderr] Checking ordered-float v1.1.1 [INFO] [stderr] Checking fern v0.6.2 [INFO] [stderr] Checking lru v0.7.8 [INFO] [stderr] Compiling getset v0.1.2 [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 lru_time_cache v0.11.11 [INFO] [stderr] Checking auto_ops v0.3.0 [INFO] [stderr] Checking env_logger v0.9.3 [INFO] [stderr] Checking jemallocator v0.5.4 [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 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 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 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 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 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 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 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 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, [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, [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) -> 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) -> 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) -> 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) -> 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, [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, [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, [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, [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, [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, 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 { [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 { [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 BreakendGroup { [INFO] [stdout] | ----------------------------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 256 | fn deletion_len(&self) -> Option { [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, [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, [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, [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 { [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 { [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 BreakendGroup { [INFO] [stdout] | ----------------------------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 256 | fn deletion_len(&self) -> Option { [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 }` [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@sha256:923055f121b5182466d55868a8b05e67af8ba4a3a3f6bad814e953ca3cd3ac2a" "/opt/rustwide/cargo-home/bin/cargo" "+a2cff3b7a9661c90ec0d581d3f3a69bb97c11138" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [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 [INFO] running `Command { std: "docker" "start" "-a" "75f09095ba8d02a6e22296337a2f7db74dee403ecd1e2d544c4a447715360216", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.86 [INFO] [stderr] Compiling libc v0.2.155 [INFO] [stderr] Compiling libm v0.2.8 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling serde v1.0.203 [INFO] [stderr] Compiling memchr v2.7.4 [INFO] [stderr] Compiling thiserror v1.0.61 [INFO] [stderr] Compiling unicase v2.7.0 [INFO] [stderr] Compiling minimal-lexical v0.2.1 [INFO] [stderr] Compiling glob v0.3.1 [INFO] [stderr] Compiling rustversion v1.0.17 [INFO] [stderr] Compiling quote v1.0.36 [INFO] [stderr] Compiling nom v7.1.3 [INFO] [stderr] Compiling clang-sys v1.8.1 [INFO] [stderr] Compiling syn v2.0.68 [INFO] [stderr] Compiling aho-corasick v1.1.3 [INFO] [stderr] Compiling mime_guess v2.0.5 [INFO] [stderr] Checking num-integer v0.1.46 [INFO] [stderr] Compiling libloading v0.8.4 [INFO] [stderr] Checking getrandom v0.2.15 [INFO] [stderr] Compiling matrixmultiply v0.3.8 [INFO] [stderr] Compiling jobserver v0.1.31 [INFO] [stderr] Checking rand_core v0.6.4 [INFO] [stderr] Compiling ahash v0.7.8 [INFO] [stderr] Checking bytemuck v1.16.1 [INFO] [stderr] Compiling bindgen v0.69.4 [INFO] [stderr] Compiling cc v1.0.104 [INFO] [stderr] Compiling regex-automata v0.4.7 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Checking rand_chacha v0.3.1 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling cexpr v0.6.0 [INFO] [stderr] Checking safe_arch v0.7.2 [INFO] [stderr] Compiling cmake v0.1.50 [INFO] [stderr] Compiling openssl-src v300.3.1+3.3.1 [INFO] [stderr] Checking num-complex v0.4.6 [INFO] [stderr] Compiling itertools v0.12.1 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling lazy_static v1.5.0 [INFO] [stderr] Compiling libz-sys v1.1.18 [INFO] [stderr] Compiling openssl-sys v0.9.102 [INFO] [stderr] Compiling curl-sys v0.4.73+curl-8.8.0 [INFO] [stderr] Compiling darling_core v0.14.4 [INFO] [stderr] Compiling regex v1.10.5 [INFO] [stderr] Compiling bzip2-sys v0.1.11+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling lazycell v1.3.0 [INFO] [stderr] Compiling rustc-hash v1.1.0 [INFO] [stderr] Checking tinyvec v1.6.1 [INFO] [stderr] Compiling darling_macro v0.14.4 [INFO] [stderr] Compiling serde_derive v1.0.203 [INFO] [stderr] Compiling thiserror-impl v1.0.61 [INFO] [stderr] Compiling darling v0.14.4 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Checking wide v0.7.25 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Checking rand v0.8.5 [INFO] [stderr] Checking approx v0.5.1 [INFO] [stderr] Checking futures-sink v0.3.30 [INFO] [stderr] Compiling mime v0.3.17 [INFO] [stderr] Compiling doc-comment v0.3.3 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling ucd-trie v0.1.6 [INFO] [stderr] Checking futures-core v0.3.30 [INFO] [stderr] Compiling matrixmultiply v0.1.15 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Compiling pest v2.7.11 [INFO] [stderr] Compiling strum_macros v0.25.3 [INFO] [stderr] Checking rand_distr v0.4.3 [INFO] [stderr] Checking simba v0.6.0 [INFO] [stderr] Checking hashbrown v0.12.3 [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