[INFO] cloning repository https://github.com/HopedWall/rs-vgaligner [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/HopedWall/rs-vgaligner" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FHopedWall%2Frs-vgaligner", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FHopedWall%2Frs-vgaligner'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 3f51e57057f6a3df4d3d0b3be268de75401f8da9 [INFO] checking HopedWall/rs-vgaligner against master#dfd7b8d03fb93d0e03147d28b3be6d93260fa94d for pr-87050 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FHopedWall%2Frs-vgaligner" "/workspace/builds/worker-6/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-6/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/HopedWall/rs-vgaligner on toolchain dfd7b8d03fb93d0e03147d28b3be6d93260fa94d [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+dfd7b8d03fb93d0e03147d28b3be6d93260fa94d" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/HopedWall/rs-vgaligner [INFO] finished tweaking git repo https://github.com/HopedWall/rs-vgaligner [INFO] tweaked toml for git repo https://github.com/HopedWall/rs-vgaligner written to /workspace/builds/worker-6/source/Cargo.toml [INFO] crate git repo https://github.com/HopedWall/rs-vgaligner already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+dfd7b8d03fb93d0e03147d28b3be6d93260fa94d" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded serde_with v1.8.1 [INFO] [stderr] Downloaded boomphf v0.5.9 [INFO] [stderr] Downloaded bio-types v0.10.0 [INFO] [stderr] Downloaded wyhash v0.5.0 [INFO] [stderr] Downloaded substring v1.4.5 [INFO] [stderr] Downloaded bio v0.32.0 [INFO] [stderr] Downloaded handlegraph v0.5.0 [INFO] [stderr] Downloaded serde_with_macros v1.4.1 [INFO] [stderr] Downloaded newtype_derive v0.1.4 [INFO] [stderr] Downloaded gfa v0.8.0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+dfd7b8d03fb93d0e03147d28b3be6d93260fa94d" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 36b1eae901e2254447fdbbfc963c0ba3304a376cdac5706db3cbadad854b4a0d [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] running `Command { std: "docker" "start" "-a" "36b1eae901e2254447fdbbfc963c0ba3304a376cdac5706db3cbadad854b4a0d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "36b1eae901e2254447fdbbfc963c0ba3304a376cdac5706db3cbadad854b4a0d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "36b1eae901e2254447fdbbfc963c0ba3304a376cdac5706db3cbadad854b4a0d", kill_on_drop: false }` [INFO] [stdout] 36b1eae901e2254447fdbbfc963c0ba3304a376cdac5706db3cbadad854b4a0d [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "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@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+dfd7b8d03fb93d0e03147d28b3be6d93260fa94d" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 9f2118b294f13bdbecb0aad4cdf0652ac986e7e85ec9dd9c5d2f0f69f338acca [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] running `Command { std: "docker" "start" "-a" "9f2118b294f13bdbecb0aad4cdf0652ac986e7e85ec9dd9c5d2f0f69f338acca", kill_on_drop: false }` [INFO] [stderr] Compiling autocfg v1.0.1 [INFO] [stderr] Compiling unicode-xid v0.2.1 [INFO] [stderr] Compiling syn v1.0.60 [INFO] [stderr] Checking cfg-if v1.0.0 [INFO] [stderr] Compiling serde_derive v1.0.125 [INFO] [stderr] Compiling serde v1.0.125 [INFO] [stderr] Compiling memchr v2.3.4 [INFO] [stderr] Compiling ryu v1.0.5 [INFO] [stderr] Compiling getrandom v0.1.16 [INFO] [stderr] Compiling version_check v0.9.2 [INFO] [stderr] Checking once_cell v1.7.0 [INFO] [stderr] Compiling bitflags v1.2.1 [INFO] [stderr] Checking either v1.6.1 [INFO] [stderr] Compiling unicode-segmentation v1.7.1 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Checking ppv-lite86 v0.2.10 [INFO] [stderr] Compiling doc-comment v0.3.3 [INFO] [stderr] Compiling fnv v1.0.7 [INFO] [stderr] Compiling rayon-core v1.9.0 [INFO] [stderr] Checking scopeguard v1.1.0 [INFO] [stderr] Checking itoa v0.4.7 [INFO] [stderr] Checking hashbrown v0.9.1 [INFO] [stderr] Compiling serde_json v1.0.64 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Compiling ndarray v0.13.1 [INFO] [stderr] Checking arrayvec v0.5.2 [INFO] [stderr] Compiling log v0.4.14 [INFO] [stderr] Checking fixedbitset v0.2.0 [INFO] [stderr] Checking quick-error v1.2.3 [INFO] [stderr] Compiling bio v0.32.0 [INFO] [stderr] Checking array-macro v1.0.5 [INFO] [stderr] Checking bit-vec v0.6.3 [INFO] [stderr] Checking newtype_derive v0.1.4 [INFO] [stderr] Checking triple_accel v0.3.4 [INFO] [stderr] Checking strum v0.18.0 [INFO] [stderr] Checking rand_core v0.6.2 [INFO] [stderr] Checking unicode-width v0.1.8 [INFO] [stderr] Checking strsim v0.8.0 [INFO] [stderr] Checking yaml-rust v0.3.5 [INFO] [stderr] Checking regex-automata v0.1.9 [INFO] [stderr] Checking fxhash v0.2.1 [INFO] [stderr] Checking itertools v0.9.0 [INFO] [stderr] Checking itertools v0.10.1 [INFO] [stderr] Checking thread_local v1.1.3 [INFO] [stderr] Compiling heck v0.3.2 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Checking matrixmultiply v0.2.4 [INFO] [stderr] Compiling nom v5.1.2 [INFO] [stderr] Compiling ahash v0.7.2 [INFO] [stderr] Compiling proc-macro2 v1.0.24 [INFO] [stderr] Compiling num-traits v0.2.14 [INFO] [stderr] Compiling crossbeam-utils v0.8.3 [INFO] [stderr] Compiling memoffset v0.6.1 [INFO] [stderr] Compiling indexmap v1.6.1 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling num-integer v0.1.44 [INFO] [stderr] Compiling rayon v1.5.0 [INFO] [stderr] Compiling substring v1.4.5 [INFO] [stderr] Checking textwrap v0.11.0 [INFO] [stderr] Checking wyhash v0.5.0 [INFO] [stderr] Checking bit-set v0.5.2 [INFO] [stderr] Checking atty v0.2.14 [INFO] [stderr] Checking getrandom v0.2.2 [INFO] [stderr] Compiling quote v1.0.9 [INFO] [stderr] Checking lexical-core v0.7.5 [INFO] [stderr] Checking rand_core v0.5.1 [INFO] [stderr] Checking aho-corasick v0.7.15 [INFO] [stderr] Checking csv-core v0.1.10 [INFO] [stderr] Checking rand_chacha v0.2.2 [INFO] [stderr] Checking petgraph v0.5.1 [INFO] [stderr] Checking regex v1.4.3 [INFO] [stderr] Checking crossbeam-epoch v0.9.3 [INFO] [stderr] Checking crossbeam-channel v0.5.0 [INFO] [stderr] Checking rand v0.7.3 [INFO] [stderr] Checking crossbeam-deque v0.8.0 [INFO] [stderr] Checking itertools-num v0.1.3 [INFO] [stderr] Checking ordered-float v1.1.1 [INFO] [stderr] Checking approx v0.3.2 [INFO] [stderr] Checking statrs v0.12.0 [INFO] [stderr] Compiling darling_core v0.12.4 [INFO] [stderr] Compiling snafu-derive v0.6.10 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling strum_macros v0.20.1 [INFO] [stderr] Compiling enum-map-derive v0.4.6 [INFO] [stderr] Compiling bytemuck_derive v1.0.1 [INFO] [stderr] Compiling getset v0.0.9 [INFO] [stderr] Compiling strum_macros v0.18.0 [INFO] [stderr] Compiling darling_macro v0.12.4 [INFO] [stderr] Checking enum-map v0.6.4 [INFO] [stderr] Checking bytemuck v1.5.1 [INFO] [stderr] Compiling darling v0.12.4 [INFO] [stderr] Compiling serde_with_macros v1.4.1 [INFO] [stderr] Checking snafu v0.6.10 [INFO] [stderr] Checking bio-types v0.10.0 [INFO] [stderr] Checking bstr v0.2.15 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking multimap v0.8.2 [INFO] [stderr] Checking boomphf v0.5.9 [INFO] [stderr] Checking serde_with v1.8.1 [INFO] [stderr] Checking bincode v1.3.3 [INFO] [stderr] Checking clap v2.33.3 [INFO] [stderr] Checking csv v1.1.5 [INFO] [stderr] Checking gfa v0.8.0 [INFO] [stderr] Checking handlegraph v0.5.0 [INFO] [stderr] Checking vgaligner v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `handlegraph::handlegraph::HandleGraph` [INFO] [stdout] --> src/subcommands/index_main.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use handlegraph::handlegraph::HandleGraph; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ahash::RandomState` [INFO] [stdout] --> src/index.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use ahash::RandomState; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `generate_pos_on_ref` [INFO] [stdout] --> src/index.rs:10:5 [INFO] [stdout] | [INFO] [stdout] 10 | generate_pos_on_ref, generate_pos_on_ref_2, Kmer, KmerPos, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::cmp::Ordering` [INFO] [stdout] --> src/index.rs:16:5 [INFO] [stdout] | [INFO] [stdout] 16 | use std::cmp::Ordering; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bstr::io::BufReadExt` [INFO] [stdout] --> src/io.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use bstr::io::BufReadExt; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `itertools::Itertools` [INFO] [stdout] --> src/io.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use itertools::Itertools; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io` [INFO] [stdout] --> src/io.rs:10:5 [INFO] [stdout] | [INFO] [stdout] 10 | use std::io; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Deref`, `Index` [INFO] [stdout] --> src/kmer.rs:17:16 [INFO] [stdout] | [INFO] [stdout] 17 | use std::ops::{Index, Deref}; [INFO] [stdout] | ^^^^^ ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Read` [INFO] [stdout] --> src/serialization.rs:2:22 [INFO] [stdout] | [INFO] [stdout] 2 | use std::io::{Write, Read, BufReader}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `handlegraph::handlegraph::HandleGraph` [INFO] [stdout] --> src/subcommands/index_main.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use handlegraph::handlegraph::HandleGraph; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ahash::RandomState` [INFO] [stdout] --> src/index.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use ahash::RandomState; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::cmp::Ordering` [INFO] [stdout] --> src/index.rs:16:5 [INFO] [stdout] | [INFO] [stdout] 16 | use std::cmp::Ordering; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `handlegraph::handle::Handle` [INFO] [stdout] --> src/index.rs:259:9 [INFO] [stdout] | [INFO] [stdout] 259 | use handlegraph::handle::Handle; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bstr::io::BufReadExt` [INFO] [stdout] --> src/io.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use bstr::io::BufReadExt; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `itertools::Itertools` [INFO] [stdout] --> src/io.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use itertools::Itertools; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io` [INFO] [stdout] --> src/io.rs:10:5 [INFO] [stdout] | [INFO] [stdout] 10 | use std::io; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Deref`, `Index` [INFO] [stdout] --> src/kmer.rs:17:16 [INFO] [stdout] | [INFO] [stdout] 17 | use std::ops::{Index, Deref}; [INFO] [stdout] | ^^^^^ ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Read` [INFO] [stdout] --> src/serialization.rs:2:22 [INFO] [stdout] | [INFO] [stdout] 2 | use std::io::{Write, Read, BufReader}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rayon::prelude` [INFO] [stdout] --> src/io.rs:9:5 [INFO] [stdout] | [INFO] [stdout] 9 | use rayon::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `in_path_file` [INFO] [stdout] --> src/subcommands/map_main.rs:10:9 [INFO] [stdout] | [INFO] [stdout] 10 | let in_path_file = matches.value_of("input-file").unwrap(); [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_in_path_file` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `max_gap_length` [INFO] [stdout] --> src/subcommands/map_main.rs:12:9 [INFO] [stdout] | [INFO] [stdout] 12 | let max_gap_length = matches [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_max_gap_length` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `max_mismatch_rate` [INFO] [stdout] --> src/subcommands/map_main.rs:18:9 [INFO] [stdout] | [INFO] [stdout] 18 | let max_mismatch_rate = matches [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_max_mismatch_rate` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `chain_overlap_max` [INFO] [stdout] --> src/subcommands/map_main.rs:24:9 [INFO] [stdout] | [INFO] [stdout] 24 | let chain_overlap_max = matches [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_chain_overlap_max` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `chain_min_anchors` [INFO] [stdout] --> src/subcommands/map_main.rs:30:9 [INFO] [stdout] | [INFO] [stdout] 30 | let chain_min_anchors = matches [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_chain_min_anchors` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `align_best_n` [INFO] [stdout] --> src/subcommands/map_main.rs:37:9 [INFO] [stdout] | [INFO] [stdout] 37 | let align_best_n = matches [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_align_best_n` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `write_chains` [INFO] [stdout] --> src/subcommands/map_main.rs:43:9 [INFO] [stdout] | [INFO] [stdout] 43 | let write_chains = matches [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_write_chains` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `write_superchains` [INFO] [stdout] --> src/subcommands/map_main.rs:46:9 [INFO] [stdout] | [INFO] [stdout] 46 | let write_superchains = matches [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_write_superchains` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `dont_align` [INFO] [stdout] --> src/subcommands/map_main.rs:49:9 [INFO] [stdout] | [INFO] [stdout] 49 | let dont_align = matches [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_dont_align` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/index.rs:119:13 [INFO] [stdout] | [INFO] [stdout] 119 | let mut kmers_on_graph: Vec = match graph.paths.is_empty() { [INFO] [stdout] | ----^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/index.rs:151:13 [INFO] [stdout] | [INFO] [stdout] 151 | let mut kmers_pos_on_ref : Vec = [INFO] [stdout] | ----^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/io.rs:27:9 [INFO] [stdout] | [INFO] [stdout] 27 | let mut file = File::open(filename)?; [INFO] [stdout] | ----^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/kmer.rs:262:9 [INFO] [stdout] | [INFO] [stdout] 262 | let mut forward_kmers = generate_kmers_linearly_forward(graph, k, edge_max, degree_max); [INFO] [stdout] | ----^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/kmer.rs:263:9 [INFO] [stdout] | [INFO] [stdout] 263 | let mut reverse_kmers = generate_kmers_linearly_reverse(graph, k, edge_max, degree_max); [INFO] [stdout] | ----^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `name` [INFO] [stdout] --> src/io.rs:19:5 [INFO] [stdout] | [INFO] [stdout] 19 | name : String, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `seq` [INFO] [stdout] --> src/io.rs:20:5 [INFO] [stdout] | [INFO] [stdout] 20 | seq : String [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rayon::prelude` [INFO] [stdout] --> src/io.rs:9:5 [INFO] [stdout] | [INFO] [stdout] 9 | use rayon::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `in_path_file` [INFO] [stdout] --> src/subcommands/map_main.rs:10:9 [INFO] [stdout] | [INFO] [stdout] 10 | let in_path_file = matches.value_of("input-file").unwrap(); [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_in_path_file` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `max_gap_length` [INFO] [stdout] --> src/subcommands/map_main.rs:12:9 [INFO] [stdout] | [INFO] [stdout] 12 | let max_gap_length = matches [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_max_gap_length` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `max_mismatch_rate` [INFO] [stdout] --> src/subcommands/map_main.rs:18:9 [INFO] [stdout] | [INFO] [stdout] 18 | let max_mismatch_rate = matches [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_max_mismatch_rate` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `chain_overlap_max` [INFO] [stdout] --> src/subcommands/map_main.rs:24:9 [INFO] [stdout] | [INFO] [stdout] 24 | let chain_overlap_max = matches [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_chain_overlap_max` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `chain_min_anchors` [INFO] [stdout] --> src/subcommands/map_main.rs:30:9 [INFO] [stdout] | [INFO] [stdout] 30 | let chain_min_anchors = matches [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_chain_min_anchors` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `align_best_n` [INFO] [stdout] --> src/subcommands/map_main.rs:37:9 [INFO] [stdout] | [INFO] [stdout] 37 | let align_best_n = matches [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_align_best_n` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `write_chains` [INFO] [stdout] --> src/subcommands/map_main.rs:43:9 [INFO] [stdout] | [INFO] [stdout] 43 | let write_chains = matches [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_write_chains` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `write_superchains` [INFO] [stdout] --> src/subcommands/map_main.rs:46:9 [INFO] [stdout] | [INFO] [stdout] 46 | let write_superchains = matches [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_write_superchains` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `dont_align` [INFO] [stdout] --> src/subcommands/map_main.rs:49:9 [INFO] [stdout] | [INFO] [stdout] 49 | let dont_align = matches [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_dont_align` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `kmers_positions_on_ref` [INFO] [stdout] --> src/index.rs:655:13 [INFO] [stdout] | [INFO] [stdout] 655 | let kmers_positions_on_ref: Vec = [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_kmers_positions_on_ref` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 26 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/index.rs:119:13 [INFO] [stdout] | [INFO] [stdout] 119 | let mut kmers_on_graph: Vec = match graph.paths.is_empty() { [INFO] [stdout] | ----^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/index.rs:151:13 [INFO] [stdout] | [INFO] [stdout] 151 | let mut kmers_pos_on_ref : Vec = [INFO] [stdout] | ----^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/index.rs:425:13 [INFO] [stdout] | [INFO] [stdout] 425 | let mut kmers_on_graph = generate_kmers(&graph, 3, Some(100), Some(100)); [INFO] [stdout] | ----^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/io.rs:27:9 [INFO] [stdout] | [INFO] [stdout] 27 | let mut file = File::open(filename)?; [INFO] [stdout] | ----^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/kmer.rs:262:9 [INFO] [stdout] | [INFO] [stdout] 262 | let mut forward_kmers = generate_kmers_linearly_forward(graph, k, edge_max, degree_max); [INFO] [stdout] | ----^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/kmer.rs:263:9 [INFO] [stdout] | [INFO] [stdout] 263 | let mut reverse_kmers = generate_kmers_linearly_reverse(graph, k, edge_max, degree_max); [INFO] [stdout] | ----^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `name` [INFO] [stdout] --> src/io.rs:19:5 [INFO] [stdout] | [INFO] [stdout] 19 | name : String, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `seq` [INFO] [stdout] --> src/io.rs:20:5 [INFO] [stdout] | [INFO] [stdout] 20 | seq : String [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 28 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 1m 17s [INFO] running `Command { std: "docker" "inspect" "9f2118b294f13bdbecb0aad4cdf0652ac986e7e85ec9dd9c5d2f0f69f338acca", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "9f2118b294f13bdbecb0aad4cdf0652ac986e7e85ec9dd9c5d2f0f69f338acca", kill_on_drop: false }` [INFO] [stdout] 9f2118b294f13bdbecb0aad4cdf0652ac986e7e85ec9dd9c5d2f0f69f338acca