[INFO] cloning repository https://github.com/genomicsoup/simmr [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/genomicsoup/simmr" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fgenomicsoup%2Fsimmr", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fgenomicsoup%2Fsimmr'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 555a88cf1a642670448f6c3a99fbfd4c9c951683 [INFO] testing genomicsoup/simmr against try#8de4c7234dd9b97c9d76b58671343fdbbc9a433e+target=x86_64-unknown-linux-musl for musl_upgrade_1_2_5_with_libc_patch_0 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fgenomicsoup%2Fsimmr" "/workspace/builds/worker-5-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-5-tc1/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/genomicsoup/simmr [INFO] finished tweaking git repo https://github.com/genomicsoup/simmr [INFO] tweaked toml for git repo https://github.com/genomicsoup/simmr written to /workspace/builds/worker-5-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/genomicsoup/simmr on toolchain 8de4c7234dd9b97c9d76b58671343fdbbc9a433e [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/genomicsoup/simmr 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" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] warning: virtual workspace defaulting to `resolver = "1"` despite one or more workspace members being on edition 2021 which implies `resolver = "2"` [INFO] [stderr] note: to keep the current resolver, specify `workspace.resolver = "1"` in the workspace root's manifest [INFO] [stderr] note: to use the edition 2021 resolver, specify `workspace.resolver = "2"` in the workspace root's manifest [INFO] [stderr] note: for more details see https://doc.rust-lang.org/cargo/reference/resolver.html#resolver-versions [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded noodles v0.40.0 [INFO] [stderr] Downloaded noodles-core v0.11.0 [INFO] [stderr] Downloaded lexical-core v0.8.5 [INFO] [stderr] Downloaded bytecount v0.6.3 [INFO] [stderr] Downloaded needletail v0.4.1 [INFO] [stderr] Downloaded uuid v1.1.2 [INFO] [stderr] Downloaded lexical-util v0.8.5 [INFO] [stderr] Downloaded lexical-write-float v0.8.5 [INFO] [stderr] Downloaded libm v0.2.2 [INFO] [stderr] Downloaded tracing-subscriber v0.3.11 [INFO] [stderr] Downloaded lexical-write-integer v0.8.5 [INFO] [stderr] Downloaded noodles-sam v0.31.0 [INFO] [stderr] Downloaded lexical-parse-float v0.8.5 [INFO] [stderr] Downloaded tracing-core v0.1.27 [INFO] [stderr] Downloaded clap v3.2.11 [INFO] [stderr] Downloaded textwrap v0.15.0 [INFO] [stderr] Downloaded noodles-bam v0.34.0 [INFO] [stderr] Downloaded bitflags v2.3.1 [INFO] [stderr] Downloaded indexmap v1.8.2 [INFO] [stderr] Downloaded noodles-csi v0.19.0 [INFO] [stderr] Downloaded noodles-bgzf v0.22.0 [INFO] [stderr] Downloaded os_str_bytes v6.1.0 [INFO] [stderr] Downloaded lexical-parse-integer v0.8.6 [INFO] [stderr] Downloaded tracing-attributes v0.1.21 [INFO] [stderr] Downloaded tracing v0.1.35 [INFO] [stderr] Downloaded streaming-stats v0.2.3 [INFO] [stderr] Downloaded clap_derive v3.2.7 [INFO] [stderr] Downloaded clap_lex v0.2.2 [INFO] [stderr] Downloaded noodles-fasta v0.23.0 [INFO] [stderr] Downloaded either v1.7.0 [INFO] [stderr] Downloaded tracing-log v0.1.3 [INFO] [stderr] Downloaded lzma-sys v0.1.19 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 2273cbc1396e8f3d95fde0d50497a161671708856b072604e0ccfdedbe7ed93c [INFO] running `Command { std: "docker" "start" "-a" "2273cbc1396e8f3d95fde0d50497a161671708856b072604e0ccfdedbe7ed93c", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "2273cbc1396e8f3d95fde0d50497a161671708856b072604e0ccfdedbe7ed93c", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "2273cbc1396e8f3d95fde0d50497a161671708856b072604e0ccfdedbe7ed93c", kill_on_drop: false }` [INFO] [stdout] 2273cbc1396e8f3d95fde0d50497a161671708856b072604e0ccfdedbe7ed93c [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "build" "--frozen" "--message-format=json" "--target" "x86_64-unknown-linux-musl", kill_on_drop: false }` [INFO] [stdout] 6a634f686403188ce3062d4b782e103b2258b62c1daa267d7a4325e143a82dc0 [INFO] running `Command { std: "docker" "start" "-a" "6a634f686403188ce3062d4b782e103b2258b62c1daa267d7a4325e143a82dc0", kill_on_drop: false }` [INFO] [stderr] warning: virtual workspace defaulting to `resolver = "1"` despite one or more workspace members being on edition 2021 which implies `resolver = "2"` [INFO] [stderr] note: to keep the current resolver, specify `workspace.resolver = "1"` in the workspace root's manifest [INFO] [stderr] note: to use the edition 2021 resolver, specify `workspace.resolver = "2"` in the workspace root's manifest [INFO] [stderr] note: for more details see https://doc.rust-lang.org/cargo/reference/resolver.html#resolver-versions [INFO] [stderr] Compiling libc v0.2.126 [INFO] [stderr] Compiling proc-macro2 v1.0.39 [INFO] [stderr] Compiling unicode-ident v1.0.1 [INFO] [stderr] Compiling syn v1.0.96 [INFO] [stderr] Compiling static_assertions v1.1.0 [INFO] [stderr] Compiling cc v1.0.73 [INFO] [stderr] Compiling pkg-config v0.3.25 [INFO] [stderr] Compiling serde_derive v1.0.137 [INFO] [stderr] Compiling once_cell v1.12.0 [INFO] [stderr] Compiling serde v1.0.137 [INFO] [stderr] Compiling miniz_oxide v0.5.3 [INFO] [stderr] Compiling indexmap v1.8.2 [INFO] [stderr] Compiling libm v0.2.2 [INFO] [stderr] Compiling crossbeam-channel v0.5.8 [INFO] [stderr] Compiling hashbrown v0.11.2 [INFO] [stderr] Compiling num-traits v0.2.15 [INFO] [stderr] Compiling lexical-util v0.8.5 [INFO] [stderr] Compiling memoffset v0.8.0 [INFO] [stderr] Compiling bytes v1.1.0 [INFO] [stderr] Compiling crossbeam-epoch v0.9.14 [INFO] [stderr] Compiling noodles-core v0.11.0 [INFO] [stderr] Compiling log v0.4.17 [INFO] [stderr] Compiling tracing-core v0.1.27 [INFO] [stderr] Compiling bit-vec v0.6.3 [INFO] [stderr] Compiling lexical-write-integer v0.8.5 [INFO] [stderr] Compiling lexical-parse-integer v0.8.6 [INFO] [stderr] Compiling lexical-parse-float v0.8.5 [INFO] [stderr] Compiling rayon-core v1.11.0 [INFO] [stderr] Compiling lexical-write-float v0.8.5 [INFO] [stderr] Compiling flate2 v1.0.24 [INFO] [stderr] Compiling getrandom v0.2.7 [INFO] [stderr] Compiling os_str_bytes v6.1.0 [INFO] [stderr] Compiling bitflags v2.3.1 [INFO] [stderr] Compiling tracing-log v0.1.3 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling quote v1.0.18 [INFO] [stderr] Compiling num_cpus v1.15.0 [INFO] [stderr] Compiling rand_core v0.6.3 [INFO] [stderr] Compiling lexical-core v0.8.5 [INFO] [stderr] Compiling clap_lex v0.2.2 [INFO] [stderr] Compiling crossbeam-deque v0.8.3 [INFO] [stderr] Compiling sharded-slab v0.1.4 [INFO] [stderr] Compiling rand_chacha v0.3.1 [INFO] [stderr] Compiling thread_local v1.1.4 [INFO] [stderr] Compiling regex-automata v0.1.10 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Compiling ansi_term v0.12.1 [INFO] [stderr] Compiling textwrap v0.15.0 [INFO] [stderr] Compiling pin-project-lite v0.2.9 [INFO] [stderr] Compiling noodles-bgzf v0.22.0 [INFO] [stderr] Compiling safemem v0.3.3 [INFO] [stderr] Compiling either v1.7.0 [INFO] [stderr] Compiling rand v0.8.5 [INFO] [stderr] Compiling buf_redux v0.8.4 [INFO] [stderr] Compiling csv-core v0.1.10 [INFO] [stderr] Compiling bytecount v0.6.3 [INFO] [stderr] Compiling bzip2-sys v0.1.11+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.19 [INFO] [stderr] Compiling itoa v0.4.8 [INFO] [stderr] Compiling ryu v1.0.10 [INFO] [stderr] Compiling streaming-stats v0.2.3 [INFO] [stderr] Compiling itertools v0.10.3 [INFO] [stderr] Compiling noodles-fasta v0.23.0 [INFO] [stderr] Compiling noodles-csi v0.19.0 [INFO] [stderr] Compiling tracing-subscriber v0.3.11 [INFO] [stderr] Compiling rayon v1.7.0 [INFO] [stderr] Compiling noodles-sam v0.31.0 [INFO] [stderr] Compiling rand_distr v0.4.3 [INFO] [stderr] Compiling uuid v1.1.2 [INFO] [stderr] Compiling bzip2 v0.4.3 [INFO] [stderr] Compiling noodles-bam v0.34.0 [INFO] [stderr] Compiling noodles v0.40.0 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Compiling clap_derive v3.2.7 [INFO] [stderr] Compiling tracing-attributes v0.1.21 [INFO] [stderr] Compiling tracing v0.1.35 [INFO] [stderr] Compiling xz2 v0.1.7 [INFO] [stderr] Compiling needletail v0.4.1 [INFO] [stderr] Compiling clap v3.2.11 [INFO] [stderr] Compiling bincode v1.3.3 [INFO] [stderr] Compiling bstr v0.2.17 [INFO] [stderr] Compiling shared v0.1.0 (/opt/rustwide/workdir/shared) [INFO] [stdout] warning: unused macro definition: `create_mask` [INFO] [stdout] --> shared/src/encoding.rs:15:14 [INFO] [stdout] | [INFO] [stdout] 15 | macro_rules! create_mask { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_macros)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused macro definition: `set_bits` [INFO] [stdout] --> shared/src/encoding.rs:37:14 [INFO] [stdout] | [INFO] [stdout] 37 | macro_rules! set_bits { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused macro definition: `extract_bits` [INFO] [stdout] --> shared/src/encoding.rs:53:14 [INFO] [stdout] | [INFO] [stdout] 53 | macro_rules! extract_bits { [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Compiling csv v1.1.6 [INFO] [stderr] Compiling simmrd v0.1.0 (/opt/rustwide/workdir/simmrd) [INFO] [stdout] warning: unused imports: `Gamma`, `Normal`, and `Uniform` [INFO] [stdout] --> simmrd/src/main.rs:24:32 [INFO] [stdout] | [INFO] [stdout] 24 | use rand_distr::{Distribution, Gamma, Normal, Uniform, WeightedAliasIndex}; [INFO] [stdout] | ^^^^^ ^^^^^^ ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Compiling simmr v0.1.0 (/opt/rustwide/workdir/simmr) [INFO] [stdout] warning: unused variable: `cigar_ndx` [INFO] [stdout] --> simmrd/src/alignment.rs:205:14 [INFO] [stdout] | [INFO] [stdout] 205 | let (cigar_ndx, cigar_char) = cigar_iter.peek().unwrap(); [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_cigar_ndx` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `invalid_ref_kmers` [INFO] [stdout] --> simmrd/src/alignment.rs:285:13 [INFO] [stdout] | [INFO] [stdout] 285 | let mut invalid_ref_kmers: u32 = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_invalid_ref_kmers` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `invalid_query_kmers` [INFO] [stdout] --> simmrd/src/alignment.rs:286:13 [INFO] [stdout] | [INFO] [stdout] 286 | let mut invalid_query_kmers: u32 = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_invalid_query_kmers` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `e` [INFO] [stdout] --> simmrd/src/alignment.rs:326:17 [INFO] [stdout] | [INFO] [stdout] 326 | Err(e) => { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_e` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `e` [INFO] [stdout] --> simmrd/src/alignment.rs:339:17 [INFO] [stdout] | [INFO] [stdout] 339 | Err(e) => { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_e` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> simmrd/src/alignment.rs:285:9 [INFO] [stdout] | [INFO] [stdout] 285 | let mut invalid_ref_kmers: u32 = 0; [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] --> simmrd/src/alignment.rs:286:9 [INFO] [stdout] | [INFO] [stdout] 286 | let mut invalid_query_kmers: u32 = 0; [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] --> simmrd/src/alignment.rs:346:13 [INFO] [stdout] | [INFO] [stdout] 346 | let mut kmer_counts = kmer_map.entry(ref_kmer_encoded).or_default(); [INFO] [stdout] | ----^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `i` [INFO] [stdout] --> simmrd/src/probability.rs:29:10 [INFO] [stdout] | [INFO] [stdout] 29 | for (i, (refs, alts)) in kmer_map.into_iter().enumerate() { [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] --> simmrd/src/main.rs:33:9 [INFO] [stdout] | [INFO] [stdout] 33 | let mut kmer_map: Arc> = [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `abundance_profiles::base::coverage` [INFO] [stdout] --> simmr/src/abundance_profiles/uniform.rs:7:13 [INFO] [stdout] | [INFO] [stdout] 7 | use crate::{abundance_profiles::base::coverage, genome}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::util` [INFO] [stdout] --> simmr/src/error_profiles/custom_long.rs:20:5 [INFO] [stdout] | [INFO] [stdout] 20 | use crate::util; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rand::prelude::SliceRandom` [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use rand::prelude::SliceRandom; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Gamma` [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:12:32 [INFO] [stdout] | [INFO] [stdout] 12 | use rand_distr::{Distribution, Gamma, Normal, Uniform, WeightedAliasIndex}; [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `stats::stddev` [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:13:5 [INFO] [stdout] | [INFO] [stdout] 13 | use stats::stddev; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::util` [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:20:5 [INFO] [stdout] | [INFO] [stdout] 20 | use crate::util; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `self::custom_long::CustomLongErrorProfile` [INFO] [stdout] --> simmr/src/error_profiles/mod.rs:14:9 [INFO] [stdout] | [INFO] [stdout] 14 | pub use self::custom_long::CustomLongErrorProfile; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rand::rngs::StdRng` [INFO] [stdout] --> simmr/src/genome.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | use rand::rngs::StdRng; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rand::Rng` [INFO] [stdout] --> simmr/src/genome.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use rand::Rng; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rand::SeedableRng` [INFO] [stdout] --> simmr/src/genome.rs:9:5 [INFO] [stdout] | [INFO] [stdout] 9 | use rand::SeedableRng; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs::OpenOptions` [INFO] [stdout] --> simmr/src/simulate.rs:11:5 [INFO] [stdout] | [INFO] [stdout] 11 | use std::fs::OpenOptions; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unreachable pattern [INFO] [stdout] --> simmrd/src/main.rs:497:9 [INFO] [stdout] | [INFO] [stdout] 497 | _ => { [INFO] [stdout] | ^ no value can reach this [INFO] [stdout] | [INFO] [stdout] note: multiple earlier patterns match some of the same values [INFO] [stdout] --> simmrd/src/main.rs:497:9 [INFO] [stdout] | [INFO] [stdout] 495 | cli::Command::Generate(c) => generate_simulation_distributions(&c), [INFO] [stdout] | ------------------------- matches some of the same values [INFO] [stdout] 496 | cli::Command::Simulate(c) => simulate_data(&c), [INFO] [stdout] | ------------------------- matches some of the same values [INFO] [stdout] 497 | _ => { [INFO] [stdout] | ^ collectively making this unreachable [INFO] [stdout] = note: `#[warn(unreachable_patterns)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `serialize_alignments_to_path` is never used [INFO] [stdout] --> simmrd/src/alignment.rs:364:8 [INFO] [stdout] | [INFO] [stdout] 364 | pub fn serialize_alignments_to_path( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `deserialize_alignments_from_path` is never used [INFO] [stdout] --> simmrd/src/alignment.rs:391:8 [INFO] [stdout] | [INFO] [stdout] 391 | pub fn deserialize_alignments_from_path(filepath: &Path) -> Result, String> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `scotts_rule` is never used [INFO] [stdout] --> simmrd/src/probability.rs:70:8 [INFO] [stdout] | [INFO] [stdout] 70 | pub fn scotts_rule(data: &[u8]) -> usize { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unreachable expression [INFO] [stdout] --> simmr/src/error_profiles/custom_long.rs:169:13 [INFO] [stdout] | [INFO] [stdout] 165 | continue; [INFO] [stdout] | -------- any code following this expression is unreachable [INFO] [stdout] ... [INFO] [stdout] 169 | / loop { [INFO] [stdout] 170 | | let qs = rng.gen_range(0..70) as u8; [INFO] [stdout] 171 | | [INFO] [stdout] 172 | | if rng.gen::() <= gaussian(qs as f64, ¢ers, bandwidth) { [INFO] [stdout] ... | [INFO] [stdout] 176 | | } [INFO] [stdout] | |_____________^ unreachable expression [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unreachable_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unreachable expression [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:444:9 [INFO] [stdout] | [INFO] [stdout] 352 | return scores; [INFO] [stdout] | ------------- any code following this expression is unreachable [INFO] [stdout] ... [INFO] [stdout] 444 | scores [INFO] [stdout] | ^^^^^^ unreachable expression [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io::prelude` [INFO] [stdout] --> simmr/src/simulate.rs:12:5 [INFO] [stdout] | [INFO] [stdout] 12 | use std::io::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `num_genomes` [INFO] [stdout] --> simmr/src/abundance_profiles/custom.rs:23:9 [INFO] [stdout] | [INFO] [stdout] 23 | num_genomes: usize, [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_num_genomes` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `total_coverage` [INFO] [stdout] --> simmr/src/abundance_profiles/custom.rs:55:13 [INFO] [stdout] | [INFO] [stdout] 55 | let total_coverage = base::total_coverage( [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_total_coverage` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `nreads` [INFO] [stdout] --> simmr/src/abundance_profiles/custom.rs:89:24 [INFO] [stdout] | [INFO] [stdout] 89 | .map(|(g, (nreads, abund))| { [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_nreads` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `total_coverage` [INFO] [stdout] --> simmr/src/abundance_profiles/uniform.rs:54:13 [INFO] [stdout] | [INFO] [stdout] 54 | let total_coverage = base::total_coverage( [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_total_coverage` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `nreads` [INFO] [stdout] --> simmr/src/abundance_profiles/uniform.rs:88:24 [INFO] [stdout] | [INFO] [stdout] 88 | .map(|(g, (nreads, abund))| { [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_nreads` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unreachable pattern [INFO] [stdout] --> simmr/src/cli.rs:299:9 [INFO] [stdout] | [INFO] [stdout] 299 | _ => todo!(), [INFO] [stdout] | ^ no value can reach this [INFO] [stdout] | [INFO] [stdout] note: multiple earlier patterns match some of the same values [INFO] [stdout] --> simmr/src/cli.rs:299:9 [INFO] [stdout] | [INFO] [stdout] 231 | ErrorProfile::PerfectShort => Box::new(error_profiles::PerfectShortErrorProfile { [INFO] [stdout] | -------------------------- matches some of the same values [INFO] [stdout] ... [INFO] [stdout] 235 | ErrorProfile::MinimalShort => Box::new(error_profiles::MinimalShortErrorProfile { [INFO] [stdout] | -------------------------- matches some of the same values [INFO] [stdout] ... [INFO] [stdout] 254 | ErrorProfile::CustomShort => { [INFO] [stdout] | ------------------------- matches some of the same values [INFO] [stdout] ... [INFO] [stdout] 284 | ErrorProfile::PerfectLong => Box::new(error_profiles::PerfectLongErrorProfile {}), [INFO] [stdout] | ------------------------- matches some of the same values [INFO] [stdout] ... [INFO] [stdout] 299 | _ => todo!(), [INFO] [stdout] | ^ ...and 1 other patterns collectively make this unreachable [INFO] [stdout] = note: `#[warn(unreachable_patterns)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/custom_long.rs:51:31 [INFO] [stdout] | [INFO] [stdout] 51 | fn get_insert_size(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/custom_long.rs:55:38 [INFO] [stdout] | [INFO] [stdout] 55 | fn get_random_insert_size(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `rng` [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:156:17 [INFO] [stdout] | [INFO] [stdout] 156 | let mut rng = match seed { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_rng` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:156:13 [INFO] [stdout] | [INFO] [stdout] 156 | let mut rng = match seed { [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: `rng` [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:329:17 [INFO] [stdout] | [INFO] [stdout] 329 | let mut rng = match seed { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_rng` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:329:13 [INFO] [stdout] | [INFO] [stdout] 329 | let mut rng = match seed { [INFO] [stdout] | ----^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/minimal_long.rs:29:31 [INFO] [stdout] | [INFO] [stdout] 29 | fn get_insert_size(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/minimal_long.rs:33:38 [INFO] [stdout] | [INFO] [stdout] 33 | fn get_random_insert_size(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/minimal_long.rs:146:48 [INFO] [stdout] | [INFO] [stdout] 146 | fn simulate_errors(&self, sequence: &[u8], seed: Option) -> Vec { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `sequence` [INFO] [stdout] --> simmr/src/error_profiles/minimal_short.rs:29:31 [INFO] [stdout] | [INFO] [stdout] 29 | fn simulate_errors(&self, sequence: &[u8], seed: Option) -> Vec { [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_sequence` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/minimal_short.rs:29:48 [INFO] [stdout] | [INFO] [stdout] 29 | fn simulate_errors(&self, sequence: &[u8], seed: Option) -> Vec { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/perfect_long.rs:24:31 [INFO] [stdout] | [INFO] [stdout] 24 | fn get_insert_size(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/perfect_long.rs:28:38 [INFO] [stdout] | [INFO] [stdout] 28 | fn get_random_insert_size(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/perfect_long.rs:32:31 [INFO] [stdout] | [INFO] [stdout] 32 | fn get_read_length(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/perfect_long.rs:125:48 [INFO] [stdout] | [INFO] [stdout] 125 | fn simulate_errors(&self, sequence: &[u8], seed: Option) -> Vec { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/perfect_short.rs:22:31 [INFO] [stdout] | [INFO] [stdout] 22 | fn get_read_length(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/perfect_short.rs:26:38 [INFO] [stdout] | [INFO] [stdout] 26 | fn get_random_read_length(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/perfect_short.rs:30:31 [INFO] [stdout] | [INFO] [stdout] 30 | fn get_insert_size(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/perfect_short.rs:38:38 [INFO] [stdout] | [INFO] [stdout] 38 | fn get_random_insert_size(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `e` [INFO] [stdout] --> simmr/src/simulate.rs:383:25 [INFO] [stdout] | [INFO] [stdout] 383 | Err(e) => continue, [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_e` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> simmr/src/simulate.rs:358:17 [INFO] [stdout] | [INFO] [stdout] 358 | let mut read_length = error_profile.get_random_read_length(seed); [INFO] [stdout] | ----^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `get_random_insert_size` is never used [INFO] [stdout] --> simmr/src/error_profiles/base.rs:14:8 [INFO] [stdout] | [INFO] [stdout] 6 | pub trait ErrorProfile { [INFO] [stdout] | ------------ method in this trait [INFO] [stdout] ... [INFO] [stdout] 14 | fn get_random_insert_size(&self, seed: Option) -> u16; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `CustomLongErrorProfile` is never constructed [INFO] [stdout] --> simmr/src/error_profiles/custom_long.rs:22:12 [INFO] [stdout] | [INFO] [stdout] 22 | pub struct CustomLongErrorProfile { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `gaussian` is never used [INFO] [stdout] --> simmr/src/error_profiles/custom_long.rs:36:4 [INFO] [stdout] | [INFO] [stdout] 36 | fn gaussian(x: f64, xs: &[f64], bandwidth: f64) -> f64 { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `QualityScoreDistribution` is never constructed [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:22:12 [INFO] [stdout] | [INFO] [stdout] 22 | pub struct QualityScoreDistribution { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `gaussian` is never used [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:60:4 [INFO] [stdout] | [INFO] [stdout] 60 | fn gaussian(x: f64, xs: &[f64], bandwidth: f64) -> f64 { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `read_length` and `read_length_std` are never read [INFO] [stdout] --> simmr/src/error_profiles/minimal_long.rs:19:9 [INFO] [stdout] | [INFO] [stdout] 17 | pub struct MinimalLongErrorProfile { [INFO] [stdout] | ----------------------- fields in this struct [INFO] [stdout] 18 | pub mean_phred_score: u8, [INFO] [stdout] 19 | pub read_length: u16, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] 20 | pub read_length_std: f64, [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `uuid` is never read [INFO] [stdout] --> simmr/src/genome.rs:20:9 [INFO] [stdout] | [INFO] [stdout] 18 | pub struct Seq { [INFO] [stdout] | --- field in this struct [INFO] [stdout] 19 | pub id: Vec, [INFO] [stdout] 20 | pub uuid: u64, [INFO] [stdout] | ^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Seq` 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: field `contiguous` is never read [INFO] [stdout] --> simmr/src/genome.rs:40:9 [INFO] [stdout] | [INFO] [stdout] 26 | pub struct Genome { [INFO] [stdout] | ------ field in this struct [INFO] [stdout] ... [INFO] [stdout] 40 | pub contiguous: bool, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Genome` 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 `PERead` is never constructed [INFO] [stdout] --> simmr/src/simulate.rs:36:12 [INFO] [stdout] | [INFO] [stdout] 36 | pub struct PERead { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `PERead` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `LongRead` is never constructed [INFO] [stdout] --> simmr/src/simulate.rs:46:12 [INFO] [stdout] | [INFO] [stdout] 46 | pub struct LongRead { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `LongRead` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 28.49s [INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: buf_redux v0.8.4 [INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1` [INFO] running `Command { std: "docker" "inspect" "6a634f686403188ce3062d4b782e103b2258b62c1daa267d7a4325e143a82dc0", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "6a634f686403188ce3062d4b782e103b2258b62c1daa267d7a4325e143a82dc0", kill_on_drop: false }` [INFO] [stdout] 6a634f686403188ce3062d4b782e103b2258b62c1daa267d7a4325e143a82dc0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "test" "--frozen" "--no-run" "--message-format=json" "--target" "x86_64-unknown-linux-musl", kill_on_drop: false }` [INFO] [stdout] 70289239959d212f78f1ee738d6cdc8c360ab597d5648486fb8bfd4b257312d8 [INFO] running `Command { std: "docker" "start" "-a" "70289239959d212f78f1ee738d6cdc8c360ab597d5648486fb8bfd4b257312d8", kill_on_drop: false }` [INFO] [stderr] warning: virtual workspace defaulting to `resolver = "1"` despite one or more workspace members being on edition 2021 which implies `resolver = "2"` [INFO] [stderr] note: to keep the current resolver, specify `workspace.resolver = "1"` in the workspace root's manifest [INFO] [stderr] note: to use the edition 2021 resolver, specify `workspace.resolver = "2"` in the workspace root's manifest [INFO] [stderr] note: for more details see https://doc.rust-lang.org/cargo/reference/resolver.html#resolver-versions [INFO] [stdout] warning: unused macro definition: `create_mask` [INFO] [stdout] --> shared/src/encoding.rs:15:14 [INFO] [stdout] | [INFO] [stdout] 15 | macro_rules! create_mask { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_macros)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused macro definition: `set_bits` [INFO] [stdout] --> shared/src/encoding.rs:37:14 [INFO] [stdout] | [INFO] [stdout] 37 | macro_rules! set_bits { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused macro definition: `extract_bits` [INFO] [stdout] --> shared/src/encoding.rs:53:14 [INFO] [stdout] | [INFO] [stdout] 53 | macro_rules! extract_bits { [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Compiling shared v0.1.0 (/opt/rustwide/workdir/shared) [INFO] [stderr] Compiling simmrd v0.1.0 (/opt/rustwide/workdir/simmrd) [INFO] [stderr] Compiling simmr v0.1.0 (/opt/rustwide/workdir/simmr) [INFO] [stdout] warning: unused macro definition: `create_mask` [INFO] [stdout] --> shared/src/encoding.rs:15:14 [INFO] [stdout] | [INFO] [stdout] 15 | macro_rules! create_mask { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_macros)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused macro definition: `set_bits` [INFO] [stdout] --> shared/src/encoding.rs:37:14 [INFO] [stdout] | [INFO] [stdout] 37 | macro_rules! set_bits { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused macro definition: `extract_bits` [INFO] [stdout] --> shared/src/encoding.rs:53:14 [INFO] [stdout] | [INFO] [stdout] 53 | macro_rules! extract_bits { [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Gamma`, `Normal`, and `Uniform` [INFO] [stdout] --> simmrd/src/main.rs:24:32 [INFO] [stdout] | [INFO] [stdout] 24 | use rand_distr::{Distribution, Gamma, Normal, Uniform, WeightedAliasIndex}; [INFO] [stdout] | ^^^^^ ^^^^^^ ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `abundance_profiles::base::coverage` [INFO] [stdout] --> simmr/src/abundance_profiles/uniform.rs:7:13 [INFO] [stdout] | [INFO] [stdout] 7 | use crate::{abundance_profiles::base::coverage, genome}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::util` [INFO] [stdout] --> simmr/src/error_profiles/custom_long.rs:20:5 [INFO] [stdout] | [INFO] [stdout] 20 | use crate::util; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rand::prelude::SliceRandom` [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use rand::prelude::SliceRandom; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Gamma` [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:12:32 [INFO] [stdout] | [INFO] [stdout] 12 | use rand_distr::{Distribution, Gamma, Normal, Uniform, WeightedAliasIndex}; [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `stats::stddev` [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:13:5 [INFO] [stdout] | [INFO] [stdout] 13 | use stats::stddev; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::util` [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:20:5 [INFO] [stdout] | [INFO] [stdout] 20 | use crate::util; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `base::ErrorProfile` [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:548:9 [INFO] [stdout] | [INFO] [stdout] 548 | use base::ErrorProfile; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `self::custom_long::CustomLongErrorProfile` [INFO] [stdout] --> simmr/src/error_profiles/mod.rs:14:9 [INFO] [stdout] | [INFO] [stdout] 14 | pub use self::custom_long::CustomLongErrorProfile; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `MinimalShortErrorProfile` [INFO] [stdout] --> simmr/src/error_profiles/../tests/error_profile_tests.rs:5:43 [INFO] [stdout] | [INFO] [stdout] 5 | use crate::error_profiles::{ErrorProfile, MinimalShortErrorProfile, PerfectShortErrorProfile}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rand::rngs::StdRng` [INFO] [stdout] --> simmr/src/genome.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | use rand::rngs::StdRng; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rand::Rng` [INFO] [stdout] --> simmr/src/genome.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use rand::Rng; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rand::SeedableRng` [INFO] [stdout] --> simmr/src/genome.rs:9:5 [INFO] [stdout] | [INFO] [stdout] 9 | use rand::SeedableRng; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs::OpenOptions` [INFO] [stdout] --> simmr/src/simulate.rs:11:5 [INFO] [stdout] | [INFO] [stdout] 11 | use std::fs::OpenOptions; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unreachable expression [INFO] [stdout] --> simmr/src/error_profiles/custom_long.rs:169:13 [INFO] [stdout] | [INFO] [stdout] 165 | continue; [INFO] [stdout] | -------- any code following this expression is unreachable [INFO] [stdout] ... [INFO] [stdout] 169 | / loop { [INFO] [stdout] 170 | | let qs = rng.gen_range(0..70) as u8; [INFO] [stdout] 171 | | [INFO] [stdout] 172 | | if rng.gen::() <= gaussian(qs as f64, ¢ers, bandwidth) { [INFO] [stdout] ... | [INFO] [stdout] 176 | | } [INFO] [stdout] | |_____________^ unreachable expression [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unreachable_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unreachable expression [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:444:9 [INFO] [stdout] | [INFO] [stdout] 352 | return scores; [INFO] [stdout] | ------------- any code following this expression is unreachable [INFO] [stdout] ... [INFO] [stdout] 444 | scores [INFO] [stdout] | ^^^^^^ unreachable expression [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `cigar_ndx` [INFO] [stdout] --> simmrd/src/alignment.rs:205:14 [INFO] [stdout] | [INFO] [stdout] 205 | let (cigar_ndx, cigar_char) = cigar_iter.peek().unwrap(); [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_cigar_ndx` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `invalid_ref_kmers` [INFO] [stdout] --> simmrd/src/alignment.rs:285:13 [INFO] [stdout] | [INFO] [stdout] 285 | let mut invalid_ref_kmers: u32 = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_invalid_ref_kmers` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `invalid_query_kmers` [INFO] [stdout] --> simmrd/src/alignment.rs:286:13 [INFO] [stdout] | [INFO] [stdout] 286 | let mut invalid_query_kmers: u32 = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_invalid_query_kmers` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `e` [INFO] [stdout] --> simmrd/src/alignment.rs:326:17 [INFO] [stdout] | [INFO] [stdout] 326 | Err(e) => { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_e` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `e` [INFO] [stdout] --> simmrd/src/alignment.rs:339:17 [INFO] [stdout] | [INFO] [stdout] 339 | Err(e) => { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_e` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> simmrd/src/alignment.rs:285:9 [INFO] [stdout] | [INFO] [stdout] 285 | let mut invalid_ref_kmers: u32 = 0; [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] --> simmrd/src/alignment.rs:286:9 [INFO] [stdout] | [INFO] [stdout] 286 | let mut invalid_query_kmers: u32 = 0; [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] --> simmrd/src/alignment.rs:346:13 [INFO] [stdout] | [INFO] [stdout] 346 | let mut kmer_counts = kmer_map.entry(ref_kmer_encoded).or_default(); [INFO] [stdout] | ----^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io::prelude` [INFO] [stdout] --> simmr/src/simulate.rs:12:5 [INFO] [stdout] | [INFO] [stdout] 12 | use std::io::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `num_genomes` [INFO] [stdout] --> simmr/src/abundance_profiles/custom.rs:23:9 [INFO] [stdout] | [INFO] [stdout] 23 | num_genomes: usize, [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_num_genomes` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `total_coverage` [INFO] [stdout] --> simmr/src/abundance_profiles/custom.rs:55:13 [INFO] [stdout] | [INFO] [stdout] 55 | let total_coverage = base::total_coverage( [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_total_coverage` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `nreads` [INFO] [stdout] --> simmr/src/abundance_profiles/custom.rs:89:24 [INFO] [stdout] | [INFO] [stdout] 89 | .map(|(g, (nreads, abund))| { [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_nreads` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `total_coverage` [INFO] [stdout] --> simmr/src/abundance_profiles/uniform.rs:54:13 [INFO] [stdout] | [INFO] [stdout] 54 | let total_coverage = base::total_coverage( [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_total_coverage` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `nreads` [INFO] [stdout] --> simmr/src/abundance_profiles/uniform.rs:88:24 [INFO] [stdout] | [INFO] [stdout] 88 | .map(|(g, (nreads, abund))| { [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_nreads` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `i` [INFO] [stdout] --> simmrd/src/probability.rs:29:10 [INFO] [stdout] | [INFO] [stdout] 29 | for (i, (refs, alts)) in kmer_map.into_iter().enumerate() { [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] --> simmrd/src/main.rs:33:9 [INFO] [stdout] | [INFO] [stdout] 33 | let mut kmer_map: Arc> = [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unreachable pattern [INFO] [stdout] --> simmr/src/cli.rs:299:9 [INFO] [stdout] | [INFO] [stdout] 299 | _ => todo!(), [INFO] [stdout] | ^ no value can reach this [INFO] [stdout] | [INFO] [stdout] note: multiple earlier patterns match some of the same values [INFO] [stdout] --> simmr/src/cli.rs:299:9 [INFO] [stdout] | [INFO] [stdout] 231 | ErrorProfile::PerfectShort => Box::new(error_profiles::PerfectShortErrorProfile { [INFO] [stdout] | -------------------------- matches some of the same values [INFO] [stdout] ... [INFO] [stdout] 235 | ErrorProfile::MinimalShort => Box::new(error_profiles::MinimalShortErrorProfile { [INFO] [stdout] | -------------------------- matches some of the same values [INFO] [stdout] ... [INFO] [stdout] 254 | ErrorProfile::CustomShort => { [INFO] [stdout] | ------------------------- matches some of the same values [INFO] [stdout] ... [INFO] [stdout] 284 | ErrorProfile::PerfectLong => Box::new(error_profiles::PerfectLongErrorProfile {}), [INFO] [stdout] | ------------------------- matches some of the same values [INFO] [stdout] ... [INFO] [stdout] 299 | _ => todo!(), [INFO] [stdout] | ^ ...and 1 other patterns collectively make this unreachable [INFO] [stdout] = note: `#[warn(unreachable_patterns)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/custom_long.rs:51:31 [INFO] [stdout] | [INFO] [stdout] 51 | fn get_insert_size(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/custom_long.rs:55:38 [INFO] [stdout] | [INFO] [stdout] 55 | fn get_random_insert_size(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `rng` [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:156:17 [INFO] [stdout] | [INFO] [stdout] 156 | let mut rng = match seed { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_rng` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:156:13 [INFO] [stdout] | [INFO] [stdout] 156 | let mut rng = match seed { [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: `rng` [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:329:17 [INFO] [stdout] | [INFO] [stdout] 329 | let mut rng = match seed { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_rng` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:329:13 [INFO] [stdout] | [INFO] [stdout] 329 | let mut rng = match seed { [INFO] [stdout] | ----^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/minimal_long.rs:29:31 [INFO] [stdout] | [INFO] [stdout] 29 | fn get_insert_size(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/minimal_long.rs:33:38 [INFO] [stdout] | [INFO] [stdout] 33 | fn get_random_insert_size(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/minimal_long.rs:146:48 [INFO] [stdout] | [INFO] [stdout] 146 | fn simulate_errors(&self, sequence: &[u8], seed: Option) -> Vec { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `sequence` [INFO] [stdout] --> simmr/src/error_profiles/minimal_short.rs:29:31 [INFO] [stdout] | [INFO] [stdout] 29 | fn simulate_errors(&self, sequence: &[u8], seed: Option) -> Vec { [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_sequence` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/minimal_short.rs:29:48 [INFO] [stdout] | [INFO] [stdout] 29 | fn simulate_errors(&self, sequence: &[u8], seed: Option) -> Vec { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/perfect_long.rs:24:31 [INFO] [stdout] | [INFO] [stdout] 24 | fn get_insert_size(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/perfect_long.rs:28:38 [INFO] [stdout] | [INFO] [stdout] 28 | fn get_random_insert_size(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/perfect_long.rs:32:31 [INFO] [stdout] | [INFO] [stdout] 32 | fn get_read_length(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/perfect_long.rs:125:48 [INFO] [stdout] | [INFO] [stdout] 125 | fn simulate_errors(&self, sequence: &[u8], seed: Option) -> Vec { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/perfect_short.rs:22:31 [INFO] [stdout] | [INFO] [stdout] 22 | fn get_read_length(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/perfect_short.rs:26:38 [INFO] [stdout] | [INFO] [stdout] 26 | fn get_random_read_length(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/perfect_short.rs:30:31 [INFO] [stdout] | [INFO] [stdout] 30 | fn get_insert_size(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seed` [INFO] [stdout] --> simmr/src/error_profiles/perfect_short.rs:38:38 [INFO] [stdout] | [INFO] [stdout] 38 | fn get_random_insert_size(&self, seed: Option) -> u16 { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unreachable pattern [INFO] [stdout] --> simmrd/src/main.rs:497:9 [INFO] [stdout] | [INFO] [stdout] 497 | _ => { [INFO] [stdout] | ^ no value can reach this [INFO] [stdout] | [INFO] [stdout] note: multiple earlier patterns match some of the same values [INFO] [stdout] --> simmrd/src/main.rs:497:9 [INFO] [stdout] | [INFO] [stdout] 495 | cli::Command::Generate(c) => generate_simulation_distributions(&c), [INFO] [stdout] | ------------------------- matches some of the same values [INFO] [stdout] 496 | cli::Command::Simulate(c) => simulate_data(&c), [INFO] [stdout] | ------------------------- matches some of the same values [INFO] [stdout] 497 | _ => { [INFO] [stdout] | ^ collectively making this unreachable [INFO] [stdout] = note: `#[warn(unreachable_patterns)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `serialize_alignments_to_path` is never used [INFO] [stdout] --> simmrd/src/alignment.rs:364:8 [INFO] [stdout] | [INFO] [stdout] 364 | pub fn serialize_alignments_to_path( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `deserialize_alignments_from_path` is never used [INFO] [stdout] --> simmrd/src/alignment.rs:391:8 [INFO] [stdout] | [INFO] [stdout] 391 | pub fn deserialize_alignments_from_path(filepath: &Path) -> Result, String> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `scotts_rule` is never used [INFO] [stdout] --> simmrd/src/probability.rs:70:8 [INFO] [stdout] | [INFO] [stdout] 70 | pub fn scotts_rule(data: &[u8]) -> usize { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `e` [INFO] [stdout] --> simmr/src/simulate.rs:383:25 [INFO] [stdout] | [INFO] [stdout] 383 | Err(e) => continue, [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_e` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> simmr/src/simulate.rs:358:17 [INFO] [stdout] | [INFO] [stdout] 358 | let mut read_length = error_profile.get_random_read_length(seed); [INFO] [stdout] | ----^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `get_random_insert_size` is never used [INFO] [stdout] --> simmr/src/error_profiles/base.rs:14:8 [INFO] [stdout] | [INFO] [stdout] 6 | pub trait ErrorProfile { [INFO] [stdout] | ------------ method in this trait [INFO] [stdout] ... [INFO] [stdout] 14 | fn get_random_insert_size(&self, seed: Option) -> u16; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `quality_bins2` is never read [INFO] [stdout] --> simmr/src/error_profiles/custom_long.rs:28:9 [INFO] [stdout] | [INFO] [stdout] 22 | pub struct CustomLongErrorProfile { [INFO] [stdout] | ---------------------- field in this struct [INFO] [stdout] ... [INFO] [stdout] 28 | pub quality_bins2: Vec>, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `QualityScoreDistribution` is never constructed [INFO] [stdout] --> simmr/src/error_profiles/custom_short.rs:22:12 [INFO] [stdout] | [INFO] [stdout] 22 | pub struct QualityScoreDistribution { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `read_length` and `read_length_std` are never read [INFO] [stdout] --> simmr/src/error_profiles/minimal_long.rs:19:9 [INFO] [stdout] | [INFO] [stdout] 17 | pub struct MinimalLongErrorProfile { [INFO] [stdout] | ----------------------- fields in this struct [INFO] [stdout] 18 | pub mean_phred_score: u8, [INFO] [stdout] 19 | pub read_length: u16, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] 20 | pub read_length_std: f64, [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `uuid` is never read [INFO] [stdout] --> simmr/src/genome.rs:20:9 [INFO] [stdout] | [INFO] [stdout] 18 | pub struct Seq { [INFO] [stdout] | --- field in this struct [INFO] [stdout] 19 | pub id: Vec, [INFO] [stdout] 20 | pub uuid: u64, [INFO] [stdout] | ^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Seq` 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: field `contiguous` is never read [INFO] [stdout] --> simmr/src/genome.rs:40:9 [INFO] [stdout] | [INFO] [stdout] 26 | pub struct Genome { [INFO] [stdout] | ------ field in this struct [INFO] [stdout] ... [INFO] [stdout] 40 | pub contiguous: bool, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Genome` 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 `PERead` is never constructed [INFO] [stdout] --> simmr/src/simulate.rs:36:12 [INFO] [stdout] | [INFO] [stdout] 36 | pub struct PERead { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `PERead` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `LongRead` is never constructed [INFO] [stdout] --> simmr/src/simulate.rs:46:12 [INFO] [stdout] | [INFO] [stdout] 46 | pub struct LongRead { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `LongRead` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 2.72s [INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: buf_redux v0.8.4 [INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1` [INFO] running `Command { std: "docker" "inspect" "70289239959d212f78f1ee738d6cdc8c360ab597d5648486fb8bfd4b257312d8", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "70289239959d212f78f1ee738d6cdc8c360ab597d5648486fb8bfd4b257312d8", kill_on_drop: false }` [INFO] [stdout] 70289239959d212f78f1ee738d6cdc8c360ab597d5648486fb8bfd4b257312d8 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "test" "--frozen" "--target" "x86_64-unknown-linux-musl", kill_on_drop: false }` [INFO] [stdout] 06f956612fe09425e6a50e2dc2c73d673e56e4fe8c9f983607a6a70f19d19a18 [INFO] running `Command { std: "docker" "start" "-a" "06f956612fe09425e6a50e2dc2c73d673e56e4fe8c9f983607a6a70f19d19a18", kill_on_drop: false }` [INFO] [stderr] warning: virtual workspace defaulting to `resolver = "1"` despite one or more workspace members being on edition 2021 which implies `resolver = "2"` [INFO] [stderr] note: to keep the current resolver, specify `workspace.resolver = "1"` in the workspace root's manifest [INFO] [stderr] note: to use the edition 2021 resolver, specify `workspace.resolver = "2"` in the workspace root's manifest [INFO] [stderr] note: for more details see https://doc.rust-lang.org/cargo/reference/resolver.html#resolver-versions [INFO] [stderr] warning: unused macro definition: `create_mask` [INFO] [stderr] --> shared/src/encoding.rs:15:14 [INFO] [stderr] | [INFO] [stderr] 15 | macro_rules! create_mask { [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_macros)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused macro definition: `set_bits` [INFO] [stderr] --> shared/src/encoding.rs:37:14 [INFO] [stderr] | [INFO] [stderr] 37 | macro_rules! set_bits { [INFO] [stderr] | ^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused macro definition: `extract_bits` [INFO] [stderr] --> shared/src/encoding.rs:53:14 [INFO] [stderr] | [INFO] [stderr] 53 | macro_rules! extract_bits { [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: `shared` (lib) generated 3 warnings [INFO] [stderr] warning: `shared` (lib test) generated 3 warnings (3 duplicates) [INFO] [stderr] warning: unused imports: `Gamma`, `Normal`, and `Uniform` [INFO] [stderr] --> simmrd/src/main.rs:24:32 [INFO] [stderr] | [INFO] [stderr] 24 | use rand_distr::{Distribution, Gamma, Normal, Uniform, WeightedAliasIndex}; [INFO] [stderr] | ^^^^^ ^^^^^^ ^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_imports)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused variable: `cigar_ndx` [INFO] [stderr] --> simmrd/src/alignment.rs:205:14 [INFO] [stderr] | [INFO] [stderr] 205 | let (cigar_ndx, cigar_char) = cigar_iter.peek().unwrap(); [INFO] [stderr] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_cigar_ndx` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_variables)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused variable: `invalid_ref_kmers` [INFO] [stderr] --> simmrd/src/alignment.rs:285:13 [INFO] [stderr] | [INFO] [stderr] 285 | let mut invalid_ref_kmers: u32 = 0; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_invalid_ref_kmers` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `invalid_query_kmers` [INFO] [stderr] --> simmrd/src/alignment.rs:286:13 [INFO] [stderr] | [INFO] [stderr] 286 | let mut invalid_query_kmers: u32 = 0; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_invalid_query_kmers` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `e` [INFO] [stderr] --> simmrd/src/alignment.rs:326:17 [INFO] [stderr] | [INFO] [stderr] 326 | Err(e) => { [INFO] [stderr] | ^ help: if this is intentional, prefix it with an underscore: `_e` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `e` [INFO] [stderr] --> simmrd/src/alignment.rs:339:17 [INFO] [stderr] | [INFO] [stderr] 339 | Err(e) => { [INFO] [stderr] | ^ help: if this is intentional, prefix it with an underscore: `_e` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> simmrd/src/alignment.rs:285:9 [INFO] [stderr] | [INFO] [stderr] 285 | let mut invalid_ref_kmers: u32 = 0; [INFO] [stderr] | ----^^^^^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_mut)]` on by default [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> simmrd/src/alignment.rs:286:9 [INFO] [stderr] | [INFO] [stderr] 286 | let mut invalid_query_kmers: u32 = 0; [INFO] [stderr] | ----^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> simmrd/src/alignment.rs:346:13 [INFO] [stderr] | [INFO] [stderr] 346 | let mut kmer_counts = kmer_map.entry(ref_kmer_encoded).or_default(); [INFO] [stderr] | ----^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `i` [INFO] [stderr] --> simmrd/src/probability.rs:29:10 [INFO] [stderr] | [INFO] [stderr] 29 | for (i, (refs, alts)) in kmer_map.into_iter().enumerate() { [INFO] [stderr] | ^ help: if this is intentional, prefix it with an underscore: `_i` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> simmrd/src/main.rs:33:9 [INFO] [stderr] | [INFO] [stderr] 33 | let mut kmer_map: Arc> = [INFO] [stderr] | ----^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: unreachable pattern [INFO] [stderr] --> simmrd/src/main.rs:497:9 [INFO] [stderr] | [INFO] [stderr] 497 | _ => { [INFO] [stderr] | ^ no value can reach this [INFO] [stderr] | [INFO] [stderr] note: multiple earlier patterns match some of the same values [INFO] [stderr] --> simmrd/src/main.rs:497:9 [INFO] [stderr] | [INFO] [stderr] 495 | cli::Command::Generate(c) => generate_simulation_distributions(&c), [INFO] [stderr] | ------------------------- matches some of the same values [INFO] [stderr] 496 | cli::Command::Simulate(c) => simulate_data(&c), [INFO] [stderr] | ------------------------- matches some of the same values [INFO] [stderr] 497 | _ => { [INFO] [stderr] | ^ collectively making this unreachable [INFO] [stderr] = note: `#[warn(unreachable_patterns)]` on by default [INFO] [stderr] [INFO] [stderr] warning: function `serialize_alignments_to_path` is never used [INFO] [stderr] --> simmrd/src/alignment.rs:364:8 [INFO] [stderr] | [INFO] [stderr] 364 | pub fn serialize_alignments_to_path( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` on by default [INFO] [stderr] [INFO] [stderr] warning: function `deserialize_alignments_from_path` is never used [INFO] [stderr] --> simmrd/src/alignment.rs:391:8 [INFO] [stderr] | [INFO] [stderr] 391 | pub fn deserialize_alignments_from_path(filepath: &Path) -> Result, String> { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `scotts_rule` is never used [INFO] [stderr] --> simmrd/src/probability.rs:70:8 [INFO] [stderr] | [INFO] [stderr] 70 | pub fn scotts_rule(data: &[u8]) -> usize { [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `abundance_profiles::base::coverage` [INFO] [stderr] --> simmr/src/abundance_profiles/uniform.rs:7:13 [INFO] [stderr] | [INFO] [stderr] 7 | use crate::{abundance_profiles::base::coverage, genome}; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_imports)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused import: `crate::util` [INFO] [stderr] --> simmr/src/error_profiles/custom_long.rs:20:5 [INFO] [stderr] | [INFO] [stderr] 20 | use crate::util; [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `rand::prelude::SliceRandom` [INFO] [stderr] --> simmr/src/error_profiles/custom_short.rs:8:5 [INFO] [stderr] | [INFO] [stderr] 8 | use rand::prelude::SliceRandom; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `Gamma` [INFO] [stderr] --> simmr/src/error_profiles/custom_short.rs:12:32 [INFO] [stderr] | [INFO] [stderr] 12 | use rand_distr::{Distribution, Gamma, Normal, Uniform, WeightedAliasIndex}; [INFO] [stderr] | ^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `stats::stddev` [INFO] [stderr] --> simmr/src/error_profiles/custom_short.rs:13:5 [INFO] [stderr] | [INFO] [stderr] 13 | use stats::stddev; [INFO] [stderr] | ^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `crate::util` [INFO] [stderr] --> simmr/src/error_profiles/custom_short.rs:20:5 [INFO] [stderr] | [INFO] [stderr] 20 | use crate::util; [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `base::ErrorProfile` [INFO] [stderr] --> simmr/src/error_profiles/custom_short.rs:548:9 [INFO] [stderr] | [INFO] [stderr] 548 | use base::ErrorProfile; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `self::custom_long::CustomLongErrorProfile` [INFO] [stderr] --> simmr/src/error_profiles/mod.rs:14:9 [INFO] [stderr] | [INFO] [stderr] 14 | pub use self::custom_long::CustomLongErrorProfile; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `MinimalShortErrorProfile` [INFO] [stderr] --> simmr/src/error_profiles/../tests/error_profile_tests.rs:5:43 [INFO] [stderr] | [INFO] [stderr] 5 | use crate::error_profiles::{ErrorProfile, MinimalShortErrorProfile, PerfectShortErrorProfile}; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `rand::rngs::StdRng` [INFO] [stderr] --> simmr/src/genome.rs:7:5 [INFO] [stderr] | [INFO] [stderr] 7 | use rand::rngs::StdRng; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `rand::Rng` [INFO] [stderr] --> simmr/src/genome.rs:8:5 [INFO] [stderr] | [INFO] [stderr] 8 | use rand::Rng; [INFO] [stderr] | ^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `rand::SeedableRng` [INFO] [stderr] --> simmr/src/genome.rs:9:5 [INFO] [stderr] | [INFO] [stderr] 9 | use rand::SeedableRng; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `std::fs::OpenOptions` [INFO] [stderr] --> simmr/src/simulate.rs:11:5 [INFO] [stderr] | [INFO] [stderr] 11 | use std::fs::OpenOptions; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unreachable expression [INFO] [stderr] --> simmr/src/error_profiles/custom_long.rs:169:13 [INFO] [stderr] | [INFO] [stderr] 165 | continue; [INFO] [stderr] | -------- any code following this expression is unreachable [INFO] [stderr] ... [INFO] [stderr] 169 | / loop { [INFO] [stderr] 170 | | let qs = rng.gen_range(0..70) as u8; [INFO] [stderr] 171 | | [INFO] [stderr] 172 | | if rng.gen::() <= gaussian(qs as f64, ¢ers, bandwidth) { [INFO] [stderr] ... | [INFO] [stderr] 176 | | } [INFO] [stderr] | |_____________^ unreachable expression [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unreachable_code)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unreachable expression [INFO] [stderr] --> simmr/src/error_profiles/custom_short.rs:444:9 [INFO] [stderr] | [INFO] [stderr] 352 | return scores; [INFO] [stderr] | ------------- any code following this expression is unreachable [INFO] [stderr] ... [INFO] [stderr] 444 | scores [INFO] [stderr] | ^^^^^^ unreachable expression [INFO] [stderr] [INFO] [stderr] warning: unused import: `std::io::prelude` [INFO] [stderr] --> simmr/src/simulate.rs:12:5 [INFO] [stderr] | [INFO] [stderr] 12 | use std::io::prelude::*; [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused variable: `num_genomes` [INFO] [stderr] --> simmr/src/abundance_profiles/custom.rs:23:9 [INFO] [stderr] | [INFO] [stderr] 23 | num_genomes: usize, [INFO] [stderr] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_num_genomes` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_variables)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused variable: `total_coverage` [INFO] [stderr] --> simmr/src/abundance_profiles/custom.rs:55:13 [INFO] [stderr] | [INFO] [stderr] 55 | let total_coverage = base::total_coverage( [INFO] [stderr] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_total_coverage` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `nreads` [INFO] [stderr] --> simmr/src/abundance_profiles/custom.rs:89:24 [INFO] [stderr] | [INFO] [stderr] 89 | .map(|(g, (nreads, abund))| { [INFO] [stderr] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_nreads` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `total_coverage` [INFO] [stderr] --> simmr/src/abundance_profiles/uniform.rs:54:13 [INFO] [stderr] | [INFO] [stderr] 54 | let total_coverage = base::total_coverage( [INFO] [stderr] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_total_coverage` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `nreads` [INFO] [stderr] --> simmr/src/abundance_profiles/uniform.rs:88:24 [INFO] [stderr] | [INFO] [stderr] 88 | .map(|(g, (nreads, abund))| { [INFO] [stderr] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_nreads` [INFO] [stderr] [INFO] [stderr] warning: unreachable pattern [INFO] [stderr] --> simmr/src/cli.rs:299:9 [INFO] [stderr] | [INFO] [stderr] 299 | _ => todo!(), [INFO] [stderr] | ^ no value can reach this [INFO] [stderr] | [INFO] [stderr] note: multiple earlier patterns match some of the same values [INFO] [stderr] --> simmr/src/cli.rs:299:9 [INFO] [stderr] | [INFO] [stderr] 231 | ErrorProfile::PerfectShort => Box::new(error_profiles::PerfectShortErrorProfile { [INFO] [stderr] | -------------------------- matches some of the same values [INFO] [stderr] ... [INFO] [stderr] 235 | ErrorProfile::MinimalShort => Box::new(error_profiles::MinimalShortErrorProfile { [INFO] [stderr] | -------------------------- matches some of the same values [INFO] [stderr] ... [INFO] [stderr] 254 | ErrorProfile::CustomShort => { [INFO] [stderr] | ------------------------- matches some of the same values [INFO] [stderr] ... [INFO] [stderr] 284 | ErrorProfile::PerfectLong => Box::new(error_profiles::PerfectLongErrorProfile {}), [INFO] [stderr] | ------------------------- matches some of the same values [INFO] [stderr] ... [INFO] [stderr] 299 | _ => todo!(), [INFO] [stderr] | ^ ...and 1 other patterns collectively make this unreachable [INFO] [stderr] = note: `#[warn(unreachable_patterns)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused variable: `seed` [INFO] [stderr] --> simmr/src/error_profiles/custom_long.rs:51:31 [INFO] [stderr] | [INFO] [stderr] 51 | fn get_insert_size(&self, seed: Option) -> u16 { [INFO] [stderr] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `seed` [INFO] [stderr] --> simmr/src/error_profiles/custom_long.rs:55:38 [INFO] [stderr] | [INFO] [stderr] 55 | fn get_random_insert_size(&self, seed: Option) -> u16 { [INFO] [stderr] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `rng` [INFO] [stderr] --> simmr/src/error_profiles/custom_short.rs:156:17 [INFO] [stderr] | [INFO] [stderr] 156 | let mut rng = match seed { [INFO] [stderr] | ^^^ help: if this is intentional, prefix it with an underscore: `_rng` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> simmr/src/error_profiles/custom_short.rs:156:13 [INFO] [stderr] | [INFO] [stderr] 156 | let mut rng = match seed { [INFO] [stderr] | ----^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_mut)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused variable: `rng` [INFO] [stderr] --> simmr/src/error_profiles/custom_short.rs:329:17 [INFO] [stderr] | [INFO] [stderr] 329 | let mut rng = match seed { [INFO] [stderr] | ^^^ help: if this is intentional, prefix it with an underscore: `_rng` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> simmr/src/error_profiles/custom_short.rs:329:13 [INFO] [stderr] | [INFO] [stderr] 329 | let mut rng = match seed { [INFO] [stderr] | ----^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `seed` [INFO] [stderr] --> simmr/src/error_profiles/minimal_long.rs:29:31 [INFO] [stderr] | [INFO] [stderr] 29 | fn get_insert_size(&self, seed: Option) -> u16 { [INFO] [stderr] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `seed` [INFO] [stderr] --> simmr/src/error_profiles/minimal_long.rs:33:38 [INFO] [stderr] | [INFO] [stderr] 33 | fn get_random_insert_size(&self, seed: Option) -> u16 { [INFO] [stderr] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `seed` [INFO] [stderr] --> simmr/src/error_profiles/minimal_long.rs:146:48 [INFO] [stderr] | [INFO] [stderr] 146 | fn simulate_errors(&self, sequence: &[u8], seed: Option) -> Vec { [INFO] [stderr] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `sequence` [INFO] [stderr] --> simmr/src/error_profiles/minimal_short.rs:29:31 [INFO] [stderr] | [INFO] [stderr] 29 | fn simulate_errors(&self, sequence: &[u8], seed: Option) -> Vec { [INFO] [stderr] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_sequence` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `seed` [INFO] [stderr] --> simmr/src/error_profiles/minimal_short.rs:29:48 [INFO] [stderr] | [INFO] [stderr] 29 | fn simulate_errors(&self, sequence: &[u8], seed: Option) -> Vec { [INFO] [stderr] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `seed` [INFO] [stderr] --> simmr/src/error_profiles/perfect_long.rs:24:31 [INFO] [stderr] | [INFO] [stderr] 24 | fn get_insert_size(&self, seed: Option) -> u16 { [INFO] [stderr] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `seed` [INFO] [stderr] --> simmr/src/error_profiles/perfect_long.rs:28:38 [INFO] [stderr] | [INFO] [stderr] 28 | fn get_random_insert_size(&self, seed: Option) -> u16 { [INFO] [stderr] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `seed` [INFO] [stderr] --> simmr/src/error_profiles/perfect_long.rs:32:31 [INFO] [stderr] | [INFO] [stderr] 32 | fn get_read_length(&self, seed: Option) -> u16 { [INFO] [stderr] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `seed` [INFO] [stderr] --> simmr/src/error_profiles/perfect_long.rs:125:48 [INFO] [stderr] | [INFO] [stderr] 125 | fn simulate_errors(&self, sequence: &[u8], seed: Option) -> Vec { [INFO] [stderr] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `seed` [INFO] [stderr] --> simmr/src/error_profiles/perfect_short.rs:22:31 [INFO] [stderr] | [INFO] [stderr] 22 | fn get_read_length(&self, seed: Option) -> u16 { [INFO] [stderr] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `seed` [INFO] [stderr] --> simmr/src/error_profiles/perfect_short.rs:26:38 [INFO] [stderr] | [INFO] [stderr] 26 | fn get_random_read_length(&self, seed: Option) -> u16 { [INFO] [stderr] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `seed` [INFO] [stderr] --> simmr/src/error_profiles/perfect_short.rs:30:31 [INFO] [stderr] | [INFO] [stderr] 30 | fn get_insert_size(&self, seed: Option) -> u16 { [INFO] [stderr] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `seed` [INFO] [stderr] --> simmr/src/error_profiles/perfect_short.rs:38:38 [INFO] [stderr] | [INFO] [stderr] 38 | fn get_random_insert_size(&self, seed: Option) -> u16 { [INFO] [stderr] | ^^^^ help: if this is intentional, prefix it with an underscore: `_seed` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `e` [INFO] [stderr] --> simmr/src/simulate.rs:383:25 [INFO] [stderr] | [INFO] [stderr] 383 | Err(e) => continue, [INFO] [stderr] | ^ help: if this is intentional, prefix it with an underscore: `_e` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> simmr/src/simulate.rs:358:17 [INFO] [stderr] | [INFO] [stderr] 358 | let mut read_length = error_profile.get_random_read_length(seed); [INFO] [stderr] | ----^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: method `get_random_insert_size` is never used [INFO] [stderr] --> simmr/src/error_profiles/base.rs:14:8 [INFO] [stderr] | [INFO] [stderr] 6 | pub trait ErrorProfile { [INFO] [stderr] | ------------ method in this trait [INFO] [stderr] ... [INFO] [stderr] 14 | fn get_random_insert_size(&self, seed: Option) -> u16; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` on by default [INFO] [stderr] [INFO] [stderr] warning: field `quality_bins2` is never read [INFO] [stderr] --> simmr/src/error_profiles/custom_long.rs:28:9 [INFO] [stderr] | [INFO] [stderr] 22 | pub struct CustomLongErrorProfile { [INFO] [stderr] | ---------------------- field in this struct [INFO] [stderr] ... [INFO] [stderr] 28 | pub quality_bins2: Vec>, [INFO] [stderr] | ^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: struct `QualityScoreDistribution` is never constructed [INFO] [stderr] --> simmr/src/error_profiles/custom_short.rs:22:12 [INFO] [stderr] | [INFO] [stderr] 22 | pub struct QualityScoreDistribution { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: fields `read_length` and `read_length_std` are never read [INFO] [stderr] --> simmr/src/error_profiles/minimal_long.rs:19:9 [INFO] [stderr] | [INFO] [stderr] 17 | pub struct MinimalLongErrorProfile { [INFO] [stderr] | ----------------------- fields in this struct [INFO] [stderr] 18 | pub mean_phred_score: u8, [INFO] [stderr] 19 | pub read_length: u16, [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] 20 | pub read_length_std: f64, [INFO] [stderr] | ^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: field `uuid` is never read [INFO] [stderr] --> simmr/src/genome.rs:20:9 [INFO] [stderr] | [INFO] [stderr] 18 | pub struct Seq { [INFO] [stderr] | --- field in this struct [INFO] [stderr] 19 | pub id: Vec, [INFO] [stderr] 20 | pub uuid: u64, [INFO] [stderr] | ^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `Seq` has derived impls for the traits `Debug` and `Clone`, but these are intentionally ignored during dead code analysis [INFO] [stderr] [INFO] [stderr] warning: field `contiguous` is never read [INFO] [stderr] --> simmr/src/genome.rs:40:9 [INFO] [stderr] | [INFO] [stderr] 26 | pub struct Genome { [INFO] [stderr] | ------ field in this struct [INFO] [stderr] ... [INFO] [stderr] 40 | pub contiguous: bool, [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `Genome` has derived impls for the traits `Debug` and `Clone`, but these are intentionally ignored during dead code analysis [INFO] [stderr] [INFO] [stderr] warning: struct `PERead` is never constructed [INFO] [stderr] --> simmr/src/simulate.rs:36:12 [INFO] [stderr] | [INFO] [stderr] 36 | pub struct PERead { [INFO] [stderr] | ^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `PERead` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stderr] [INFO] [stderr] warning: struct `LongRead` is never constructed [INFO] [stderr] --> simmr/src/simulate.rs:46:12 [INFO] [stderr] | [INFO] [stderr] 46 | pub struct LongRead { [INFO] [stderr] | ^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `LongRead` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stderr] [INFO] [stderr] warning: `simmrd` (bin "simmrd" test) generated 15 warnings (run `cargo fix --bin "simmrd" --tests` to apply 5 suggestions) [INFO] [stderr] warning: `simmr` (bin "simmr" test) generated 51 warnings (run `cargo fix --bin "simmr" --tests` to apply 16 suggestions) [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.10s [INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: buf_redux v0.8.4 [INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1` [INFO] [stderr] Running unittests src/lib.rs (/opt/rustwide/target/x86_64-unknown-linux-musl/debug/deps/shared-8c77953bfde2dc7b) [INFO] [stdout] [INFO] [stdout] running 8 tests [INFO] [stdout] test encoding::tests::test_2bit_decoding ... ok [INFO] [stdout] test util::tests::test_complement_0 ... ok [INFO] [stdout] test util::tests::test_bytes_to_string ... ok [INFO] [stdout] test encoding::tests::test_2bit_encoding ... ok [INFO] [stdout] test util::tests::test_complement_1 ... ok [INFO] [stdout] test util::tests::test_complement_2 ... ok [INFO] [stderr] Running unittests src/main.rs (/opt/rustwide/target/x86_64-unknown-linux-musl/debug/deps/simmr-385e38a1c79f7050) [INFO] [stdout] test util::tests::test_mean_1 ... ok [INFO] [stdout] test util::tests::test_std_dev_1 ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 8 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] running 18 tests [INFO] [stdout] test abundance_profiles::abundance_profile_tests::test_uniform_profile ... ok [INFO] [stdout] test error_profiles::custom_long::tests::test_gaussian_function ... ok [INFO] [stdout] test error_profiles::custom_short::tests::test_gaussian_function ... ok [INFO] [stdout] test error_profiles::custom_long::tests::test_simulate_errors ... ok [INFO] [stdout] test simulate::simulate_tests::test_simulate_pe_read_using_zero_error_profile ... ignored, updated the RNG and have to redo ground truth [INFO] [stdout] test simulate::simulate_tests::test_simulate_reads_using_zero_error_profile ... ignored, updated the RNG and have to redo ground truth [INFO] [stdout] test error_profiles::error_profile_tests::test_zero_profile ... ok [INFO] [stdout] test util::util_tests::test_accuracy_to_phred_conversion ... ok [INFO] [stdout] test util::util_tests::test_complement_0 ... ok [INFO] [stdout] test genome::genome_tests::test_genome_from_fasta ... ok [INFO] [stdout] test util::util_tests::test_complement_1 ... ok [INFO] [stdout] test util::util_tests::test_complement_2 ... ok [INFO] [stdout] test util::util_tests::test_encode_quality_score ... ok [INFO] [stdout] test util::util_tests::test_encode_quality_scores ... ok [INFO] [stdout] test util::util_tests::test_phred_to_accuracy_conversion ... ok [INFO] [stdout] test util::util_tests::test_generate_id_using_seed ... ok [INFO] [stdout] test util::util_tests::test_phred_to_probability_conversions ... ok [INFO] [stdout] test util::util_tests::test_probability_to_phred_conversions ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 16 passed; 0 failed; 2 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] [stderr] Running unittests src/main.rs (/opt/rustwide/target/x86_64-unknown-linux-musl/debug/deps/simmrd-e51f50146aa51a60) [INFO] [stdout] [INFO] [stdout] running 3 tests [INFO] [stdout] test alignment::tests::test_expand_cigar ... ok [INFO] [stdout] test alignment::tests::test_reconstruct_alignment ... ok [INFO] [stdout] test alignment::tests::test_expand_md_tag ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 3 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] running `Command { std: "docker" "inspect" "06f956612fe09425e6a50e2dc2c73d673e56e4fe8c9f983607a6a70f19d19a18", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "06f956612fe09425e6a50e2dc2c73d673e56e4fe8c9f983607a6a70f19d19a18", kill_on_drop: false }` [INFO] [stdout] 06f956612fe09425e6a50e2dc2c73d673e56e4fe8c9f983607a6a70f19d19a18