[INFO] cloning repository https://github.com/genomicepidemiology/probmap [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/genomicepidemiology/probmap" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fgenomicepidemiology%2Fprobmap", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fgenomicepidemiology%2Fprobmap'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] b44a413a6673a4ee1422b57d3be70aa38e8bdd00 [INFO] testing genomicepidemiology/probmap/b44a413a6673a4ee1422b57d3be70aa38e8bdd00 against beta-2024-09-05 for beta-1.82-1 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fgenomicepidemiology%2Fprobmap" "/workspace/builds/worker-6-tc2/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-6-tc2/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/genomicepidemiology/probmap on toolchain beta-2024-09-05 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+beta-2024-09-05" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/genomicepidemiology/probmap [INFO] finished tweaking git repo https://github.com/genomicepidemiology/probmap [INFO] tweaked toml for git repo https://github.com/genomicepidemiology/probmap written to /workspace/builds/worker-6-tc2/source/Cargo.toml [INFO] crate git repo https://github.com/genomicepidemiology/probmap 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" "+beta-2024-09-05" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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@sha256:96c0aa5895ecf336b730ef27bcdde6e21027415df19888aad3cf1448e5d65d90" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2024-09-05" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] e46cb4035874e881b0caa56a49d3d363872aca21600421f14c50dbf3b69a9562 [INFO] running `Command { std: "docker" "start" "-a" "e46cb4035874e881b0caa56a49d3d363872aca21600421f14c50dbf3b69a9562", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "e46cb4035874e881b0caa56a49d3d363872aca21600421f14c50dbf3b69a9562", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "e46cb4035874e881b0caa56a49d3d363872aca21600421f14c50dbf3b69a9562", kill_on_drop: false }` [INFO] [stdout] e46cb4035874e881b0caa56a49d3d363872aca21600421f14c50dbf3b69a9562 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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@sha256:96c0aa5895ecf336b730ef27bcdde6e21027415df19888aad3cf1448e5d65d90" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2024-09-05" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 53c2cbeb3f2201c3480ca935e52ae9f405d35718af866a26c3a94c2505e186ff [INFO] running `Command { std: "docker" "start" "-a" "53c2cbeb3f2201c3480ca935e52ae9f405d35718af866a26c3a94c2505e186ff", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.66 [INFO] [stderr] Compiling unicode-ident v1.0.11 [INFO] [stderr] Compiling libm v0.2.7 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Compiling version_check v0.9.4 [INFO] [stderr] Compiling libc v0.2.147 [INFO] [stderr] Compiling serde v1.0.186 [INFO] [stderr] Compiling rustix v0.38.8 [INFO] [stderr] Compiling rustversion v1.0.14 [INFO] [stderr] Compiling bytemuck v1.13.1 [INFO] [stderr] Compiling bitflags v2.4.0 [INFO] [stderr] Compiling linux-raw-sys v0.4.5 [INFO] [stderr] Compiling ppv-lite86 v0.2.17 [INFO] [stderr] Compiling num-traits v0.2.16 [INFO] [stderr] Compiling num-integer v0.1.45 [INFO] [stderr] Compiling matrixmultiply v0.3.7 [INFO] [stderr] Compiling paste v1.0.14 [INFO] [stderr] Compiling heck v0.4.1 [INFO] [stderr] Compiling safe_arch v0.7.1 [INFO] [stderr] Compiling num-rational v0.4.1 [INFO] [stderr] Compiling rawpointer v0.2.1 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Compiling typenum v1.16.0 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Compiling aho-corasick v1.0.4 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling wide v0.7.11 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling thiserror v1.0.47 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Compiling anstyle-parse v0.2.1 [INFO] [stderr] Compiling equivalent v1.0.1 [INFO] [stderr] Compiling anstyle-query v1.0.0 [INFO] [stderr] Compiling anstyle v1.0.2 [INFO] [stderr] Compiling either v1.9.0 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling quote v1.0.33 [INFO] [stderr] Compiling hashbrown v0.14.0 [INFO] [stderr] Compiling crc32fast v1.3.2 [INFO] [stderr] Compiling alloc-no-stdlib v2.0.4 [INFO] [stderr] Compiling colorchoice v1.0.0 [INFO] [stderr] Compiling anyhow v1.0.75 [INFO] [stderr] Compiling getrandom v0.2.10 [INFO] [stderr] Compiling syn v2.0.29 [INFO] [stderr] Compiling alloc-stdlib v0.2.2 [INFO] [stderr] Compiling ahash v0.8.3 [INFO] [stderr] Compiling rand_core v0.6.4 [INFO] [stderr] Compiling adler v1.0.2 [INFO] [stderr] Compiling fixedbitset v0.4.2 [INFO] [stderr] Compiling clap_lex v0.5.0 [INFO] [stderr] Compiling is-terminal v0.4.9 [INFO] [stderr] Compiling rand_chacha v0.3.1 [INFO] [stderr] Compiling anstream v0.3.2 [INFO] [stderr] Compiling once_cell v1.18.0 [INFO] [stderr] Compiling bit-vec v0.6.3 [INFO] [stderr] Compiling strsim v0.10.0 [INFO] [stderr] Compiling itoa v1.0.9 [INFO] [stderr] Compiling regex-automata v0.3.6 [INFO] [stderr] Compiling indexmap v2.0.0 [INFO] [stderr] Compiling rand v0.8.5 [INFO] [stderr] Compiling ryu v1.0.15 [INFO] [stderr] Compiling byteorder v1.4.3 [INFO] [stderr] Compiling num-complex v0.4.4 [INFO] [stderr] Compiling approx v0.5.1 [INFO] [stderr] Compiling ordered-float v3.9.1 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling clap_builder v4.3.24 [INFO] [stderr] Compiling bit-set v0.5.3 [INFO] [stderr] Compiling fxhash v0.2.1 [INFO] [stderr] Compiling miniz_oxide v0.7.1 [INFO] [stderr] Compiling brotli-decompressor v2.3.4 [INFO] [stderr] Compiling simba v0.6.0 [INFO] [stderr] Compiling petgraph v0.6.4 [INFO] [stderr] Compiling ndarray v0.15.6 [INFO] [stderr] Compiling itertools v0.11.0 [INFO] [stderr] Compiling editdistancek v1.0.2 [INFO] [stderr] Compiling strum v0.25.0 [INFO] [stderr] Compiling rand_distr v0.4.3 [INFO] [stderr] Compiling triple_accel v0.4.0 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling bytecount v0.6.3 [INFO] [stderr] Compiling flate2 v1.0.27 [INFO] [stderr] Compiling colored v2.0.4 [INFO] [stderr] Compiling itertools v0.10.5 [INFO] [stderr] Compiling rustc-hash v1.1.0 [INFO] [stderr] Compiling nohash-hasher v0.2.0 [INFO] [stderr] Compiling brotli v3.3.4 [INFO] [stderr] Compiling regex v1.9.3 [INFO] [stderr] Compiling serde_derive v1.0.186 [INFO] [stderr] Compiling thiserror-impl v1.0.47 [INFO] [stderr] Compiling strum_macros v0.25.2 [INFO] [stderr] Compiling clap_derive v4.3.12 [INFO] [stderr] Compiling nalgebra-macros v0.1.0 [INFO] [stderr] Compiling enum-map-derive v0.6.0 [INFO] [stderr] Compiling strum_macros v0.24.3 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling getset v0.1.2 [INFO] [stderr] Compiling enum-map v1.1.1 [INFO] [stderr] Compiling bio-types v1.0.0 [INFO] [stderr] Compiling clap v4.3.24 [INFO] [stderr] Compiling nalgebra v0.29.0 [INFO] [stderr] Compiling multimap v0.8.3 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling csv v1.2.2 [INFO] [stderr] Compiling bincode v1.3.3 [INFO] [stderr] Compiling statrs v0.16.0 [INFO] [stderr] Compiling bio v1.3.1 [INFO] [stderr] Compiling probmap v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `Record` [INFO] [stdout] --> src/main.rs:7:19 [INFO] [stdout] | [INFO] [stdout] 7 | fastq::{self, Record, Records}, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Path`, `collections::HashMap`, `hash::BuildHasherDefault`, and `hash::Hash` [INFO] [stdout] --> src/main.rs:10:5 [INFO] [stdout] | [INFO] [stdout] 10 | collections::HashMap, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] 11 | fs, [INFO] [stdout] 12 | hash::BuildHasherDefault, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] 13 | hash::Hash, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] 14 | io::BufReader, [INFO] [stdout] 15 | path::{Path, PathBuf}, [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `CompressorReader` and `CompressorWriter` [INFO] [stdout] --> src/main.rs:18:14 [INFO] [stdout] | [INFO] [stdout] 18 | use brotli::{CompressorReader, CompressorWriter}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `builder::OsStr` [INFO] [stdout] --> src/main.rs:19:12 [INFO] [stdout] | [INFO] [stdout] 19 | use clap::{builder::OsStr, Parser, Subcommand}; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `flate2::write::ZlibEncoder` [INFO] [stdout] --> src/main.rs:22:5 [INFO] [stdout] | [INFO] [stdout] 22 | use flate2::write::ZlibEncoder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `flate2::Compression` [INFO] [stdout] --> src/main.rs:23:5 [INFO] [stdout] | [INFO] [stdout] 23 | use flate2::Compression; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `nohash_hasher::NoHashHasher` [INFO] [stdout] --> src/main.rs:25:5 [INFO] [stdout] | [INFO] [stdout] 25 | use nohash_hasher::NoHashHasher; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `BuildNoHashHasher` and `IntMap` [INFO] [stdout] --> src/main.rs:26:21 [INFO] [stdout] | [INFO] [stdout] 26 | use nohash_hasher::{BuildNoHashHasher, IntMap}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rustc_hash::FxHashMap` [INFO] [stdout] --> src/main.rs:27:5 [INFO] [stdout] | [INFO] [stdout] 27 | use rustc_hash::FxHashMap; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io` [INFO] [stdout] --> src/main.rs:31:5 [INFO] [stdout] | [INFO] [stdout] 31 | use std::io; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `HashMapExt` [INFO] [stdout] --> src/main.rs:4:33 [INFO] [stdout] | [INFO] [stdout] 4 | use ahash::{AHashMap, AHashSet, HashMapExt}; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Deserialize` [INFO] [stdout] --> src/main.rs:28:13 [INFO] [stdout] | [INFO] [stdout] 28 | use serde::{Deserialize, Serialize}; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `output` [INFO] [stdout] --> src/main.rs:132:13 [INFO] [stdout] | [INFO] [stdout] 132 | output, [INFO] [stdout] | ^^^^^^ help: try ignoring the field: `output: _` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `ncbi_taxid` is never read [INFO] [stdout] --> src/main.rs:823:5 [INFO] [stdout] | [INFO] [stdout] 820 | struct MetaEntry { [INFO] [stdout] | --------- field in this struct [INFO] [stdout] ... [INFO] [stdout] 823 | ncbi_taxid: u32, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `MetaEntry` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/main.rs:153:13 [INFO] [stdout] | [INFO] [stdout] 153 | calc_prob_from_input(&kmersize, &db, &input, &tax_groups); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] = note: `#[warn(unused_must_use)]` on by default [INFO] [stdout] help: use `let _ = ...` to ignore the resulting value [INFO] [stdout] | [INFO] [stdout] 153 | let _ = calc_prob_from_input(&kmersize, &db, &input, &tax_groups); [INFO] [stdout] | +++++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/main.rs:667:5 [INFO] [stdout] | [INFO] [stdout] 667 | bincode::serialize_into(&mut comp, object); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] help: use `let _ = ...` to ignore the resulting value [INFO] [stdout] | [INFO] [stdout] 667 | let _ = bincode::serialize_into(&mut comp, object); [INFO] [stdout] | +++++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 16 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 19.90s [INFO] running `Command { std: "docker" "inspect" "53c2cbeb3f2201c3480ca935e52ae9f405d35718af866a26c3a94c2505e186ff", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "53c2cbeb3f2201c3480ca935e52ae9f405d35718af866a26c3a94c2505e186ff", kill_on_drop: false }` [INFO] [stdout] 53c2cbeb3f2201c3480ca935e52ae9f405d35718af866a26c3a94c2505e186ff [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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@sha256:96c0aa5895ecf336b730ef27bcdde6e21027415df19888aad3cf1448e5d65d90" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2024-09-05" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] af6b2817095b9d284d04f91ef2e3417a221569bc96ca4cfb0fd2537f2a42675c [INFO] running `Command { std: "docker" "start" "-a" "af6b2817095b9d284d04f91ef2e3417a221569bc96ca4cfb0fd2537f2a42675c", kill_on_drop: false }` [INFO] [stderr] Compiling probmap v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `Record` [INFO] [stdout] --> src/main.rs:7:19 [INFO] [stdout] | [INFO] [stdout] 7 | fastq::{self, Record, Records}, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Path`, `collections::HashMap`, `hash::BuildHasherDefault`, and `hash::Hash` [INFO] [stdout] --> src/main.rs:10:5 [INFO] [stdout] | [INFO] [stdout] 10 | collections::HashMap, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] 11 | fs, [INFO] [stdout] 12 | hash::BuildHasherDefault, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] 13 | hash::Hash, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] 14 | io::BufReader, [INFO] [stdout] 15 | path::{Path, PathBuf}, [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `CompressorReader` and `CompressorWriter` [INFO] [stdout] --> src/main.rs:18:14 [INFO] [stdout] | [INFO] [stdout] 18 | use brotli::{CompressorReader, CompressorWriter}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `builder::OsStr` [INFO] [stdout] --> src/main.rs:19:12 [INFO] [stdout] | [INFO] [stdout] 19 | use clap::{builder::OsStr, Parser, Subcommand}; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `flate2::write::ZlibEncoder` [INFO] [stdout] --> src/main.rs:22:5 [INFO] [stdout] | [INFO] [stdout] 22 | use flate2::write::ZlibEncoder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `flate2::Compression` [INFO] [stdout] --> src/main.rs:23:5 [INFO] [stdout] | [INFO] [stdout] 23 | use flate2::Compression; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `nohash_hasher::NoHashHasher` [INFO] [stdout] --> src/main.rs:25:5 [INFO] [stdout] | [INFO] [stdout] 25 | use nohash_hasher::NoHashHasher; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `BuildNoHashHasher` and `IntMap` [INFO] [stdout] --> src/main.rs:26:21 [INFO] [stdout] | [INFO] [stdout] 26 | use nohash_hasher::{BuildNoHashHasher, IntMap}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rustc_hash::FxHashMap` [INFO] [stdout] --> src/main.rs:27:5 [INFO] [stdout] | [INFO] [stdout] 27 | use rustc_hash::FxHashMap; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io` [INFO] [stdout] --> src/main.rs:31:5 [INFO] [stdout] | [INFO] [stdout] 31 | use std::io; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `HashMapExt` [INFO] [stdout] --> src/main.rs:4:33 [INFO] [stdout] | [INFO] [stdout] 4 | use ahash::{AHashMap, AHashSet, HashMapExt}; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Deserialize` [INFO] [stdout] --> src/main.rs:28:13 [INFO] [stdout] | [INFO] [stdout] 28 | use serde::{Deserialize, Serialize}; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `output` [INFO] [stdout] --> src/main.rs:132:13 [INFO] [stdout] | [INFO] [stdout] 132 | output, [INFO] [stdout] | ^^^^^^ help: try ignoring the field: `output: _` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `ncbi_taxid` is never read [INFO] [stdout] --> src/main.rs:823:5 [INFO] [stdout] | [INFO] [stdout] 820 | struct MetaEntry { [INFO] [stdout] | --------- field in this struct [INFO] [stdout] ... [INFO] [stdout] 823 | ncbi_taxid: u32, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `MetaEntry` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/main.rs:153:13 [INFO] [stdout] | [INFO] [stdout] 153 | calc_prob_from_input(&kmersize, &db, &input, &tax_groups); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] = note: `#[warn(unused_must_use)]` on by default [INFO] [stdout] help: use `let _ = ...` to ignore the resulting value [INFO] [stdout] | [INFO] [stdout] 153 | let _ = calc_prob_from_input(&kmersize, &db, &input, &tax_groups); [INFO] [stdout] | +++++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/main.rs:667:5 [INFO] [stdout] | [INFO] [stdout] 667 | bincode::serialize_into(&mut comp, object); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] help: use `let _ = ...` to ignore the resulting value [INFO] [stdout] | [INFO] [stdout] 667 | let _ = bincode::serialize_into(&mut comp, object); [INFO] [stdout] | +++++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 16 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 1.29s [INFO] running `Command { std: "docker" "inspect" "af6b2817095b9d284d04f91ef2e3417a221569bc96ca4cfb0fd2537f2a42675c", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "af6b2817095b9d284d04f91ef2e3417a221569bc96ca4cfb0fd2537f2a42675c", kill_on_drop: false }` [INFO] [stdout] af6b2817095b9d284d04f91ef2e3417a221569bc96ca4cfb0fd2537f2a42675c [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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@sha256:96c0aa5895ecf336b730ef27bcdde6e21027415df19888aad3cf1448e5d65d90" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2024-09-05" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] 58ecbf31539306af792dcef8e45b72d4cca0181875a893d51b8f9b93432473e9 [INFO] running `Command { std: "docker" "start" "-a" "58ecbf31539306af792dcef8e45b72d4cca0181875a893d51b8f9b93432473e9", kill_on_drop: false }` [INFO] [stderr] warning: unused import: `Record` [INFO] [stderr] --> src/main.rs:7:19 [INFO] [stderr] | [INFO] [stderr] 7 | fastq::{self, Record, Records}, [INFO] [stderr] | ^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_imports)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused imports: `Path`, `collections::HashMap`, `hash::BuildHasherDefault`, and `hash::Hash` [INFO] [stderr] --> src/main.rs:10:5 [INFO] [stderr] | [INFO] [stderr] 10 | collections::HashMap, [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] 11 | fs, [INFO] [stderr] 12 | hash::BuildHasherDefault, [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] 13 | hash::Hash, [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] 14 | io::BufReader, [INFO] [stderr] 15 | path::{Path, PathBuf}, [INFO] [stderr] | ^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused imports: `CompressorReader` and `CompressorWriter` [INFO] [stderr] --> src/main.rs:18:14 [INFO] [stderr] | [INFO] [stderr] 18 | use brotli::{CompressorReader, CompressorWriter}; [INFO] [stderr] | ^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `builder::OsStr` [INFO] [stderr] --> src/main.rs:19:12 [INFO] [stderr] | [INFO] [stderr] 19 | use clap::{builder::OsStr, Parser, Subcommand}; [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `flate2::write::ZlibEncoder` [INFO] [stderr] --> src/main.rs:22:5 [INFO] [stderr] | [INFO] [stderr] 22 | use flate2::write::ZlibEncoder; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `flate2::Compression` [INFO] [stderr] --> src/main.rs:23:5 [INFO] [stderr] | [INFO] [stderr] 23 | use flate2::Compression; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `nohash_hasher::NoHashHasher` [INFO] [stderr] --> src/main.rs:25:5 [INFO] [stderr] | [INFO] [stderr] 25 | use nohash_hasher::NoHashHasher; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused imports: `BuildNoHashHasher` and `IntMap` [INFO] [stderr] --> src/main.rs:26:21 [INFO] [stderr] | [INFO] [stderr] 26 | use nohash_hasher::{BuildNoHashHasher, IntMap}; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^ ^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `rustc_hash::FxHashMap` [INFO] [stderr] --> src/main.rs:27:5 [INFO] [stderr] | [INFO] [stderr] 27 | use rustc_hash::FxHashMap; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `std::io` [INFO] [stderr] --> src/main.rs:31:5 [INFO] [stderr] | [INFO] [stderr] 31 | use std::io; [INFO] [stderr] | ^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `HashMapExt` [INFO] [stderr] --> src/main.rs:4:33 [INFO] [stderr] | [INFO] [stderr] 4 | use ahash::{AHashMap, AHashSet, HashMapExt}; [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `Deserialize` [INFO] [stderr] --> src/main.rs:28:13 [INFO] [stderr] | [INFO] [stderr] 28 | use serde::{Deserialize, Serialize}; [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused variable: `output` [INFO] [stderr] --> src/main.rs:132:13 [INFO] [stderr] | [INFO] [stderr] 132 | output, [INFO] [stderr] | ^^^^^^ help: try ignoring the field: `output: _` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_variables)]` on by default [INFO] [stderr] [INFO] [stderr] warning: field `ncbi_taxid` is never read [INFO] [stderr] --> src/main.rs:823:5 [INFO] [stderr] | [INFO] [stderr] 820 | struct MetaEntry { [INFO] [stderr] | --------- field in this struct [INFO] [stderr] ... [INFO] [stderr] 823 | ncbi_taxid: u32, [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `MetaEntry` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stderr] = note: `#[warn(dead_code)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused `Result` that must be used [INFO] [stderr] --> src/main.rs:153:13 [INFO] [stderr] | [INFO] [stderr] 153 | calc_prob_from_input(&kmersize, &db, &input, &tax_groups); [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stderr] = note: `#[warn(unused_must_use)]` on by default [INFO] [stderr] help: use `let _ = ...` to ignore the resulting value [INFO] [stderr] | [INFO] [stderr] 153 | let _ = calc_prob_from_input(&kmersize, &db, &input, &tax_groups); [INFO] [stderr] | +++++++ [INFO] [stderr] [INFO] [stderr] warning: unused `Result` that must be used [INFO] [stderr] --> src/main.rs:667:5 [INFO] [stderr] | [INFO] [stderr] 667 | bincode::serialize_into(&mut comp, object); [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stderr] help: use `let _ = ...` to ignore the resulting value [INFO] [stderr] | [INFO] [stderr] 667 | let _ = bincode::serialize_into(&mut comp, object); [INFO] [stderr] | +++++++ [INFO] [stderr] [INFO] [stderr] warning: `probmap` (bin "probmap" test) generated 16 warnings (run `cargo fix --bin "probmap" --tests` to apply 10 suggestions) [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.07s [INFO] [stderr] Running unittests src/main.rs (/opt/rustwide/target/debug/deps/probmap-3d313f2a775f4593) [INFO] [stdout] [INFO] [stdout] running 14 tests [INFO] [stdout] test test::test_calc_probs ... ok [INFO] [stdout] test test::test_annotate_kmers ... ok [INFO] [stdout] test test::test_copy_values_between_vectors ... ok [INFO] [stdout] test test::test_extract_tax_from_list ... ok [INFO] [stdout] test test::test_insert_index_into_tax_vec ... ok [INFO] [stdout] test test::test_insert_or_push_to_vec ... ok [INFO] [stdout] test test::test_insert_zeroes_in_tax_vec ... ok [INFO] [stdout] test test::test_max_bits ... ok [INFO] [stdout] test test::test_new_tax_vec ... ok [INFO] [stdout] test test::test_nuc2int ... ok [INFO] [stdout] test test::test_push_tax_from_bit_vec_to_tax_vec ... ok [INFO] [stdout] test test::test_rev_comp ... ok [INFO] [stdout] test test::test_rev_kmer ... ok [INFO] [stdout] test test::test_get_unique_kmers ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 14 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] running `Command { std: "docker" "inspect" "58ecbf31539306af792dcef8e45b72d4cca0181875a893d51b8f9b93432473e9", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "58ecbf31539306af792dcef8e45b72d4cca0181875a893d51b8f9b93432473e9", kill_on_drop: false }` [INFO] [stdout] 58ecbf31539306af792dcef8e45b72d4cca0181875a893d51b8f9b93432473e9