[INFO] cloning repository https://github.com/bluenote-1577/chrom_mini_graph
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/bluenote-1577/chrom_mini_graph" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Fchrom_mini_graph", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Fchrom_mini_graph'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 9177a017c51091fe0da11f40e3da2d23a44d8df4
[INFO] testing bluenote-1577/chrom_mini_graph against master#0d162b25edd5bf0dba9a22e83b614f1113e90474 for pr-150681
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Fchrom_mini_graph" "/workspace/builds/worker-0-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc1/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/bluenote-1577/chrom_mini_graph
[INFO] finished tweaking git repo https://github.com/bluenote-1577/chrom_mini_graph
[INFO] tweaked toml for git repo https://github.com/bluenote-1577/chrom_mini_graph written to /workspace/builds/worker-0-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/bluenote-1577/chrom_mini_graph on toolchain 0d162b25edd5bf0dba9a22e83b614f1113e90474
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+0d162b25edd5bf0dba9a22e83b614f1113e90474" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/bluenote-1577/chrom_mini_graph 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" "+0d162b25edd5bf0dba9a22e83b614f1113e90474" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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@sha256:845e597a41426bbf2703be69acdb67d10b6de511142d05cba7bbe119c898b2c7" "/opt/rustwide/cargo-home/bin/cargo" "+0d162b25edd5bf0dba9a22e83b614f1113e90474" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "start" "-a" "0bf26da5b15e5fdc265ec1ccbf4a23d49d2e34cf28366c992cbaedb3dce11030", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "rm" "-f" "0bf26da5b15e5fdc265ec1ccbf4a23d49d2e34cf28366c992cbaedb3dce11030", kill_on_drop: false }`
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[INFO] [stdout] 810a91c44b8b30acbc8ef842e198f6de16b07499d66af0f2e1db2909124de88e
[INFO] running `Command { std: "docker" "start" "-a" "810a91c44b8b30acbc8ef842e198f6de16b07499d66af0f2e1db2909124de88e", kill_on_drop: false }`
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[INFO] [stderr]    Compiling vec_map v0.8.2
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[INFO] [stderr]    Compiling debruijn v0.3.4
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[INFO] [stderr]    Compiling rust-htslib v0.38.2
[INFO] [stderr]    Compiling chrom_mini_graph v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `debruijn::kmer::Kmer10`
[INFO] [stdout]  --> src/seeding_methods_bit.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use debruijn::kmer::Kmer10;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debruijn::kmer::Kmer12`
[INFO] [stdout]  --> src/seeding_methods_bit.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use debruijn::kmer::Kmer12;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debruijn::kmer::Kmer8`
[INFO] [stdout]  --> src/seeding_methods_bit.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use debruijn::kmer::Kmer8;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `simple_logger::SimpleLogger`
[INFO] [stdout]  --> src/chain.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | use simple_logger::SimpleLogger;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debruijn::Kmer`
[INFO] [stdout]  --> src/chain.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use debruijn::Kmer;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unnecessary parentheses around `if` condition
[INFO] [stdout]     --> src/chain.rs:1335:12
[INFO] [stdout]      |
[INFO] [stdout] 1335 |         if (i > 0 && !chain_reads) {
[INFO] [stdout]      |            ^                     ^
[INFO] [stdout]      |
[INFO] [stdout]      = note: `#[warn(unused_parens)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] help: remove these parentheses
[INFO] [stdout]      |
[INFO] [stdout] 1335 -         if (i > 0 && !chain_reads) {
[INFO] [stdout] 1335 +         if i > 0 && !chain_reads  {
[INFO] [stdout]      |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debruijn::dna_string::*`
[INFO] [stdout]  --> src/align.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use debruijn::dna_string::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `simple_logger::SimpleLogger`
[INFO] [stdout]   --> src/align.rs:15:5
[INFO] [stdout]    |
[INFO] [stdout] 15 | use simple_logger::SimpleLogger;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::avl_tree::SearchTree`
[INFO] [stdout]  --> src/coord_chain.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | use crate::avl_tree::SearchTree;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debruijn::Kmer`
[INFO] [stdout]  --> src/coord_chain.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use debruijn::Kmer;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `smallvec::SmallVec`
[INFO] [stdout]   --> src/coord_chain.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use smallvec::SmallVec;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unreachable statement
[INFO] [stdout]    --> src/align.rs:753:21
[INFO] [stdout]     |
[INFO] [stdout] 752 |                     panic!("{}\n{}", prev_char, cg_str);
[INFO] [stdout]     |                     ----------------------------------- any code following this expression is unreachable
[INFO] [stdout] 753 |                     op = Operation::Sentinel;
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^^ unreachable statement
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unreachable_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unreachable statement
[INFO] [stdout]    --> src/coord_chain.rs:318:9
[INFO] [stdout]     |
[INFO] [stdout] 317 |           return best_superchain_ret;
[INFO] [stdout]     |           -------------------------- any code following this expression is unreachable
[INFO] [stdout] 318 | /         return best_superchain
[INFO] [stdout] 319 | |             .iter_mut()
[INFO] [stdout] 320 | |             .map(|x| (mem::take(&mut x.0), x.3, forward_strand))
[INFO] [stdout] 321 | |             .collect();
[INFO] [stdout]     | |_______________________^ unreachable statement
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/graph_utils.rs:257:5
[INFO] [stdout]     |
[INFO] [stdout] 257 |     mut anchors: Vec<(u32, u32)>,
[INFO] [stdout]     |     ----^^^^^^^
[INFO] [stdout]     |     |
[INFO] [stdout]     |     help: remove this `mut`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `circular`
[INFO] [stdout]    --> src/graph_utils.rs:260:5
[INFO] [stdout]     |
[INFO] [stdout] 260 |     circular: bool,
[INFO] [stdout]     |     ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_circular`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `num_contains_dist_not` is assigned to, but never used
[INFO] [stdout]    --> src/graph_utils.rs:285:9
[INFO] [stdout]     |
[INFO] [stdout] 285 |     let mut num_contains_dist_not = 0;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_num_contains_dist_not` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `num_contains_dist_not` is never read
[INFO] [stdout]    --> src/graph_utils.rs:383:17
[INFO] [stdout]     |
[INFO] [stdout] 383 |                 num_contains_dist_not += 1;
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout]     = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `num_samp_coord` is assigned to, but never used
[INFO] [stdout]   --> src/seeding_methods_bit.rs:82:9
[INFO] [stdout]    |
[INFO] [stdout] 82 |     let mut num_samp_coord = 0;
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: consider using `_num_samp_coord` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `num_samp_coord` is never read
[INFO] [stdout]    --> src/seeding_methods_bit.rs:163:17
[INFO] [stdout]     |
[INFO] [stdout] 163 |                 num_samp_coord += 1;
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `frequent_kmers`
[INFO] [stdout]    --> src/seeding_methods_bit.rs:247:5
[INFO] [stdout]     |
[INFO] [stdout] 247 |     frequent_kmers: &FxHashMap<Kmer16, usize>,
[INFO] [stdout]     |     ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_frequent_kmers`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/chain.rs:64:9
[INFO] [stdout]    |
[INFO] [stdout] 64 |     let mut gap_cost = (ref_order_dist - query_order_dist).abs();
[INFO] [stdout]    |         ----^^^^^^^^
[INFO] [stdout]    |         |
[INFO] [stdout]    |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `count` is assigned to, but never used
[INFO] [stdout]    --> src/chain.rs:241:17
[INFO] [stdout]     |
[INFO] [stdout] 241 |             let mut count = 0;
[INFO] [stdout]     |                 ^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_count` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `count` is never read
[INFO] [stdout]    --> src/chain.rs:260:21
[INFO] [stdout]     |
[INFO] [stdout] 260 |                     count += 1
[INFO] [stdout]     |                     ^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `q_len`
[INFO] [stdout]    --> src/chain.rs:290:9
[INFO] [stdout]     |
[INFO] [stdout] 290 |     let q_len = seeds_q.len();
[INFO] [stdout]     |         ^^^^^ help: if this is intentional, prefix it with an underscore: `_q_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `now`
[INFO] [stdout]    --> src/chain.rs:291:9
[INFO] [stdout]     |
[INFO] [stdout] 291 |     let now = Instant::now();
[INFO] [stdout]     |         ^^^ help: if this is intentional, prefix it with an underscore: `_now`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/chain.rs:480:25
[INFO] [stdout]     |
[INFO] [stdout] 480 |                     let mut tup = colour_paths.get_mut(&colour).unwrap();
[INFO] [stdout]     |                         ----^^^
[INFO] [stdout]     |                         |
[INFO] [stdout]     |                         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `read_length`
[INFO] [stdout]    --> src/chain.rs:454:5
[INFO] [stdout]     |
[INFO] [stdout] 454 |     read_length: usize,
[INFO] [stdout]     |     ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_length`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `read_length`
[INFO] [stdout]    --> src/chain.rs:603:5
[INFO] [stdout]     |
[INFO] [stdout] 603 |     read_length: usize,
[INFO] [stdout]     |     ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_length`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `best_node` is assigned to, but never used
[INFO] [stdout]    --> src/chain.rs:618:9
[INFO] [stdout]     |
[INFO] [stdout] 618 |     let mut best_node = first_node;
[INFO] [stdout]     |         ^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_best_node` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `best_node` is never read
[INFO] [stdout]    --> src/chain.rs:747:21
[INFO] [stdout]     |
[INFO] [stdout] 747 |                     best_node = intermediate_node;
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `mandatory_color`
[INFO] [stdout]     --> src/chain.rs:1170:9
[INFO] [stdout]      |
[INFO] [stdout] 1170 |     let mandatory_color = Color::MAX;
[INFO] [stdout]      |         ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mandatory_color`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/align.rs:494:9
[INFO] [stdout]     |
[INFO] [stdout] 494 |     let mut break_mm = 3;
[INFO] [stdout]     |         ----^^^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `r_node`
[INFO] [stdout]    --> src/align.rs:421:13
[INFO] [stdout]     |
[INFO] [stdout] 421 |         let r_node = &ref_graph[anchors[i].0 as usize];
[INFO] [stdout]     |             ^^^^^^ help: if this is intentional, prefix it with an underscore: `_r_node`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `r_cpy`
[INFO] [stdout]    --> src/align.rs:632:13
[INFO] [stdout]     |
[INFO] [stdout] 632 |         let r_cpy = ref_map_string.clone();
[INFO] [stdout]     |             ^^^^^ help: if this is intentional, prefix it with an underscore: `_r_cpy`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `q_cpy`
[INFO] [stdout]    --> src/align.rs:633:13
[INFO] [stdout]     |
[INFO] [stdout] 633 |         let q_cpy = read_map_string.clone();
[INFO] [stdout]     |             ^^^^^ help: if this is intentional, prefix it with an underscore: `_q_cpy`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `prev_char` is never read
[INFO] [stdout]    --> src/align.rs:761:17
[INFO] [stdout]     |
[INFO] [stdout] 761 |                 prev_char = c;
[INFO] [stdout]     |                 ^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/coord_chain.rs:206:9
[INFO] [stdout]     |
[INFO] [stdout] 206 |     let mut best_superchain =
[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/coord_chain.rs:601:9
[INFO] [stdout]     |
[INFO] [stdout] 601 |     let mut gap_cost = (ref_order_dist - query_order_dist).abs();
[INFO] [stdout]     |         ----^^^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `State` is never constructed
[INFO] [stdout]    --> src/graph_utils.rs:110:8
[INFO] [stdout]     |
[INFO] [stdout] 110 | struct State {
[INFO] [stdout]     |        ^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `block_aligner::scan_block::*`
[INFO] [stdout]  --> src/bin/chrom_mini_graph.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use block_aligner::scan_block::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::mem`
[INFO] [stdout]   --> src/bin/chrom_mini_graph.rs:25:5
[INFO] [stdout]    |
[INFO] [stdout] 25 | use std::mem;
[INFO] [stdout]    |     ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `block_aligner::scores`
[INFO] [stdout]  --> src/bin/chrom_mini_graph.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use block_aligner::scores::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debruijn::Mer`
[INFO] [stdout]   --> src/bin/chrom_mini_graph.rs:19:5
[INFO] [stdout]    |
[INFO] [stdout] 19 | use debruijn::Mer;
[INFO] [stdout]    |     ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/bin/chrom_mini_graph.rs:628:29
[INFO] [stdout]     |
[INFO] [stdout] 628 |                         let mut anc_score_strand_vec = chain::chain_seeds(
[INFO] [stdout]     |                             ----^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |                             |
[INFO] [stdout]     |                             help: remove this `mut`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/bin/chrom_mini_graph.rs:687:41
[INFO] [stdout]     |
[INFO] [stdout] 687 | ...                   let mut base_anc_score_strand_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/bin/chrom_mini_graph.rs:556:13
[INFO] [stdout]     |
[INFO] [stdout] 556 |         let mut anchor_file = BufWriter::new(File::create("read_anchor_hits.txt").unwrap());
[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/bin/chrom_mini_graph.rs:566:13
[INFO] [stdout]     |
[INFO] [stdout] 566 |         let mut num_mapped_reads = Mutex::new(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]    --> src/bin/chrom_mini_graph.rs:569:13
[INFO] [stdout]     |
[INFO] [stdout] 569 |         let mut best_hit_for_read: Mutex<FxHashMap<_, _>> = Mutex::new(FxHashMap::default());
[INFO] [stdout]     |             ----^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |             |
[INFO] [stdout]     |             help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `now`
[INFO] [stdout]    --> src/bin/chrom_mini_graph.rs:752:37
[INFO] [stdout]     |
[INFO] [stdout] 752 | ...                   let now = Instant::now();
[INFO] [stdout]     |                           ^^^ help: if this is intentional, prefix it with an underscore: `_now`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `order_val_last`
[INFO] [stdout]    --> src/bin/chrom_mini_graph.rs:403:17
[INFO] [stdout]     |
[INFO] [stdout] 403 |             let order_val_last = seeds2[qlen - 1].order_val;
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_order_val_last`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `short_reads`
[INFO] [stdout]    --> src/bin/chrom_mini_graph.rs:537:13
[INFO] [stdout]     |
[INFO] [stdout] 537 |         let short_reads = matches_subc.is_present("short_reads");
[INFO] [stdout]     |             ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_short_reads`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `dont_use_kmers`
[INFO] [stdout]    --> src/bin/chrom_mini_graph.rs:544:50
[INFO] [stdout]     |
[INFO] [stdout] 544 |         let (mut ref_graph, chroms, chrom_names, dont_use_kmers): (
[INFO] [stdout]     |                                                  ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_dont_use_kmers`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `anchor_file`
[INFO] [stdout]    --> src/bin/chrom_mini_graph.rs:556:13
[INFO] [stdout]     |
[INFO] [stdout] 556 |         let mut anchor_file = BufWriter::new(File::create("read_anchor_hits.txt").unwrap());
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_anchor_file`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [optimized + debuginfo] target(s) in 4m 24s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nalgebra v0.27.1, nom v5.1.2
[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" "810a91c44b8b30acbc8ef842e198f6de16b07499d66af0f2e1db2909124de88e", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "810a91c44b8b30acbc8ef842e198f6de16b07499d66af0f2e1db2909124de88e", kill_on_drop: false }`
[INFO] [stdout] 810a91c44b8b30acbc8ef842e198f6de16b07499d66af0f2e1db2909124de88e
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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@sha256:845e597a41426bbf2703be69acdb67d10b6de511142d05cba7bbe119c898b2c7" "/opt/rustwide/cargo-home/bin/cargo" "+0d162b25edd5bf0dba9a22e83b614f1113e90474" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 50ab44abd1718197576bc5b47af0245e984cdb55397a10783dfa6e50ebec38be
[INFO] running `Command { std: "docker" "start" "-a" "50ab44abd1718197576bc5b47af0245e984cdb55397a10783dfa6e50ebec38be", kill_on_drop: false }`
[INFO] [stdout] warning: unused import: `debruijn::kmer::Kmer10`
[INFO] [stdout]  --> src/seeding_methods_bit.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use debruijn::kmer::Kmer10;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debruijn::kmer::Kmer12`
[INFO] [stdout]  --> src/seeding_methods_bit.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use debruijn::kmer::Kmer12;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debruijn::kmer::Kmer8`
[INFO] [stdout]  --> src/seeding_methods_bit.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use debruijn::kmer::Kmer8;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `simple_logger::SimpleLogger`
[INFO] [stdout]  --> src/chain.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | use simple_logger::SimpleLogger;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debruijn::Kmer`
[INFO] [stdout]  --> src/chain.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use debruijn::Kmer;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unnecessary parentheses around `if` condition
[INFO] [stdout]     --> src/chain.rs:1335:12
[INFO] [stdout]      |
[INFO] [stdout] 1335 |         if (i > 0 && !chain_reads) {
[INFO] [stdout]      |            ^                     ^
[INFO] [stdout]      |
[INFO] [stdout]      = note: `#[warn(unused_parens)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] help: remove these parentheses
[INFO] [stdout]      |
[INFO] [stdout] 1335 -         if (i > 0 && !chain_reads) {
[INFO] [stdout] 1335 +         if i > 0 && !chain_reads  {
[INFO] [stdout]      |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debruijn::dna_string::*`
[INFO] [stdout]  --> src/align.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use debruijn::dna_string::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `simple_logger::SimpleLogger`
[INFO] [stdout]   --> src/align.rs:15:5
[INFO] [stdout]    |
[INFO] [stdout] 15 | use simple_logger::SimpleLogger;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::avl_tree::SearchTree`
[INFO] [stdout]  --> src/coord_chain.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | use crate::avl_tree::SearchTree;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debruijn::Kmer`
[INFO] [stdout]  --> src/coord_chain.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use debruijn::Kmer;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `smallvec::SmallVec`
[INFO] [stdout]   --> src/coord_chain.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use smallvec::SmallVec;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unreachable statement
[INFO] [stdout]    --> src/align.rs:753:21
[INFO] [stdout]     |
[INFO] [stdout] 752 |                     panic!("{}\n{}", prev_char, cg_str);
[INFO] [stdout]     |                     ----------------------------------- any code following this expression is unreachable
[INFO] [stdout] 753 |                     op = Operation::Sentinel;
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^^ unreachable statement
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unreachable_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unreachable statement
[INFO] [stdout]    --> src/coord_chain.rs:318:9
[INFO] [stdout]     |
[INFO] [stdout] 317 |           return best_superchain_ret;
[INFO] [stdout]     |           -------------------------- any code following this expression is unreachable
[INFO] [stdout] 318 | /         return best_superchain
[INFO] [stdout] 319 | |             .iter_mut()
[INFO] [stdout] 320 | |             .map(|x| (mem::take(&mut x.0), x.3, forward_strand))
[INFO] [stdout] 321 | |             .collect();
[INFO] [stdout]     | |_______________________^ unreachable statement
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/graph_utils.rs:257:5
[INFO] [stdout]     |
[INFO] [stdout] 257 |     mut anchors: Vec<(u32, u32)>,
[INFO] [stdout]     |     ----^^^^^^^
[INFO] [stdout]     |     |
[INFO] [stdout]     |     help: remove this `mut`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `circular`
[INFO] [stdout]    --> src/graph_utils.rs:260:5
[INFO] [stdout]     |
[INFO] [stdout] 260 |     circular: bool,
[INFO] [stdout]     |     ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_circular`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `num_contains_dist_not` is assigned to, but never used
[INFO] [stdout]    --> src/graph_utils.rs:285:9
[INFO] [stdout]     |
[INFO] [stdout] 285 |     let mut num_contains_dist_not = 0;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_num_contains_dist_not` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `num_contains_dist_not` is never read
[INFO] [stdout]    --> src/graph_utils.rs:383:17
[INFO] [stdout]     |
[INFO] [stdout] 383 |                 num_contains_dist_not += 1;
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout]     = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]    Compiling chrom_mini_graph v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: variable `num_samp_coord` is assigned to, but never used
[INFO] [stdout]   --> src/seeding_methods_bit.rs:82:9
[INFO] [stdout]    |
[INFO] [stdout] 82 |     let mut num_samp_coord = 0;
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: consider using `_num_samp_coord` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `num_samp_coord` is never read
[INFO] [stdout]    --> src/seeding_methods_bit.rs:163:17
[INFO] [stdout]     |
[INFO] [stdout] 163 |                 num_samp_coord += 1;
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `frequent_kmers`
[INFO] [stdout]    --> src/seeding_methods_bit.rs:247:5
[INFO] [stdout]     |
[INFO] [stdout] 247 |     frequent_kmers: &FxHashMap<Kmer16, usize>,
[INFO] [stdout]     |     ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_frequent_kmers`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/chain.rs:64:9
[INFO] [stdout]    |
[INFO] [stdout] 64 |     let mut gap_cost = (ref_order_dist - query_order_dist).abs();
[INFO] [stdout]    |         ----^^^^^^^^
[INFO] [stdout]    |         |
[INFO] [stdout]    |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `count` is assigned to, but never used
[INFO] [stdout]    --> src/chain.rs:241:17
[INFO] [stdout]     |
[INFO] [stdout] 241 |             let mut count = 0;
[INFO] [stdout]     |                 ^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_count` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `count` is never read
[INFO] [stdout]    --> src/chain.rs:260:21
[INFO] [stdout]     |
[INFO] [stdout] 260 |                     count += 1
[INFO] [stdout]     |                     ^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `q_len`
[INFO] [stdout]    --> src/chain.rs:290:9
[INFO] [stdout]     |
[INFO] [stdout] 290 |     let q_len = seeds_q.len();
[INFO] [stdout]     |         ^^^^^ help: if this is intentional, prefix it with an underscore: `_q_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `now`
[INFO] [stdout]    --> src/chain.rs:291:9
[INFO] [stdout]     |
[INFO] [stdout] 291 |     let now = Instant::now();
[INFO] [stdout]     |         ^^^ help: if this is intentional, prefix it with an underscore: `_now`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/chain.rs:480:25
[INFO] [stdout]     |
[INFO] [stdout] 480 |                     let mut tup = colour_paths.get_mut(&colour).unwrap();
[INFO] [stdout]     |                         ----^^^
[INFO] [stdout]     |                         |
[INFO] [stdout]     |                         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `read_length`
[INFO] [stdout]    --> src/chain.rs:454:5
[INFO] [stdout]     |
[INFO] [stdout] 454 |     read_length: usize,
[INFO] [stdout]     |     ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_length`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `read_length`
[INFO] [stdout]    --> src/chain.rs:603:5
[INFO] [stdout]     |
[INFO] [stdout] 603 |     read_length: usize,
[INFO] [stdout]     |     ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_length`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `best_node` is assigned to, but never used
[INFO] [stdout]    --> src/chain.rs:618:9
[INFO] [stdout]     |
[INFO] [stdout] 618 |     let mut best_node = first_node;
[INFO] [stdout]     |         ^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_best_node` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `best_node` is never read
[INFO] [stdout]    --> src/chain.rs:747:21
[INFO] [stdout]     |
[INFO] [stdout] 747 |                     best_node = intermediate_node;
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `mandatory_color`
[INFO] [stdout]     --> src/chain.rs:1170:9
[INFO] [stdout]      |
[INFO] [stdout] 1170 |     let mandatory_color = Color::MAX;
[INFO] [stdout]      |         ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mandatory_color`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/align.rs:494:9
[INFO] [stdout]     |
[INFO] [stdout] 494 |     let mut break_mm = 3;
[INFO] [stdout]     |         ----^^^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `r_node`
[INFO] [stdout]    --> src/align.rs:421:13
[INFO] [stdout]     |
[INFO] [stdout] 421 |         let r_node = &ref_graph[anchors[i].0 as usize];
[INFO] [stdout]     |             ^^^^^^ help: if this is intentional, prefix it with an underscore: `_r_node`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `r_cpy`
[INFO] [stdout]    --> src/align.rs:632:13
[INFO] [stdout]     |
[INFO] [stdout] 632 |         let r_cpy = ref_map_string.clone();
[INFO] [stdout]     |             ^^^^^ help: if this is intentional, prefix it with an underscore: `_r_cpy`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `q_cpy`
[INFO] [stdout]    --> src/align.rs:633:13
[INFO] [stdout]     |
[INFO] [stdout] 633 |         let q_cpy = read_map_string.clone();
[INFO] [stdout]     |             ^^^^^ help: if this is intentional, prefix it with an underscore: `_q_cpy`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `prev_char` is never read
[INFO] [stdout]    --> src/align.rs:761:17
[INFO] [stdout]     |
[INFO] [stdout] 761 |                 prev_char = c;
[INFO] [stdout]     |                 ^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/coord_chain.rs:206:9
[INFO] [stdout]     |
[INFO] [stdout] 206 |     let mut best_superchain =
[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/coord_chain.rs:601:9
[INFO] [stdout]     |
[INFO] [stdout] 601 |     let mut gap_cost = (ref_order_dist - query_order_dist).abs();
[INFO] [stdout]     |         ----^^^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `State` is never constructed
[INFO] [stdout]    --> src/graph_utils.rs:110:8
[INFO] [stdout]     |
[INFO] [stdout] 110 | struct State {
[INFO] [stdout]     |        ^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `block_aligner::scan_block::*`
[INFO] [stdout]  --> src/bin/chrom_mini_graph.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use block_aligner::scan_block::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::mem`
[INFO] [stdout]   --> src/bin/chrom_mini_graph.rs:25:5
[INFO] [stdout]    |
[INFO] [stdout] 25 | use std::mem;
[INFO] [stdout]    |     ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debruijn::kmer::Kmer10`
[INFO] [stdout]  --> src/seeding_methods_bit.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use debruijn::kmer::Kmer10;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debruijn::kmer::Kmer12`
[INFO] [stdout]  --> src/seeding_methods_bit.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use debruijn::kmer::Kmer12;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debruijn::kmer::Kmer8`
[INFO] [stdout]  --> src/seeding_methods_bit.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use debruijn::kmer::Kmer8;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `simple_logger::SimpleLogger`
[INFO] [stdout]  --> src/chain.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | use simple_logger::SimpleLogger;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debruijn::Kmer`
[INFO] [stdout]  --> src/chain.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use debruijn::Kmer;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unnecessary parentheses around `if` condition
[INFO] [stdout]     --> src/chain.rs:1335:12
[INFO] [stdout]      |
[INFO] [stdout] 1335 |         if (i > 0 && !chain_reads) {
[INFO] [stdout]      |            ^                     ^
[INFO] [stdout]      |
[INFO] [stdout]      = note: `#[warn(unused_parens)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] help: remove these parentheses
[INFO] [stdout]      |
[INFO] [stdout] 1335 -         if (i > 0 && !chain_reads) {
[INFO] [stdout] 1335 +         if i > 0 && !chain_reads  {
[INFO] [stdout]      |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debruijn::dna_string::*`
[INFO] [stdout]  --> src/align.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use debruijn::dna_string::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `simple_logger::SimpleLogger`
[INFO] [stdout]   --> src/align.rs:15:5
[INFO] [stdout]    |
[INFO] [stdout] 15 | use simple_logger::SimpleLogger;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::avl_tree::SearchTree`
[INFO] [stdout]  --> src/coord_chain.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | use crate::avl_tree::SearchTree;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debruijn::Kmer`
[INFO] [stdout]  --> src/coord_chain.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use debruijn::Kmer;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `smallvec::SmallVec`
[INFO] [stdout]   --> src/coord_chain.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use smallvec::SmallVec;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `block_aligner::scores`
[INFO] [stdout]  --> src/bin/chrom_mini_graph.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use block_aligner::scores::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debruijn::Mer`
[INFO] [stdout]   --> src/bin/chrom_mini_graph.rs:19:5
[INFO] [stdout]    |
[INFO] [stdout] 19 | use debruijn::Mer;
[INFO] [stdout]    |     ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/bin/chrom_mini_graph.rs:628:29
[INFO] [stdout]     |
[INFO] [stdout] 628 |                         let mut anc_score_strand_vec = chain::chain_seeds(
[INFO] [stdout]     |                             ----^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |                             |
[INFO] [stdout]     |                             help: remove this `mut`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/bin/chrom_mini_graph.rs:687:41
[INFO] [stdout]     |
[INFO] [stdout] 687 | ...                   let mut base_anc_score_strand_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/bin/chrom_mini_graph.rs:556:13
[INFO] [stdout]     |
[INFO] [stdout] 556 |         let mut anchor_file = BufWriter::new(File::create("read_anchor_hits.txt").unwrap());
[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/bin/chrom_mini_graph.rs:566:13
[INFO] [stdout]     |
[INFO] [stdout] 566 |         let mut num_mapped_reads = Mutex::new(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]    --> src/bin/chrom_mini_graph.rs:569:13
[INFO] [stdout]     |
[INFO] [stdout] 569 |         let mut best_hit_for_read: Mutex<FxHashMap<_, _>> = Mutex::new(FxHashMap::default());
[INFO] [stdout]     |             ----^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |             |
[INFO] [stdout]     |             help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `now`
[INFO] [stdout]    --> src/bin/chrom_mini_graph.rs:752:37
[INFO] [stdout]     |
[INFO] [stdout] 752 | ...                   let now = Instant::now();
[INFO] [stdout]     |                           ^^^ help: if this is intentional, prefix it with an underscore: `_now`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `order_val_last`
[INFO] [stdout]    --> src/bin/chrom_mini_graph.rs:403:17
[INFO] [stdout]     |
[INFO] [stdout] 403 |             let order_val_last = seeds2[qlen - 1].order_val;
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_order_val_last`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `short_reads`
[INFO] [stdout]    --> src/bin/chrom_mini_graph.rs:537:13
[INFO] [stdout]     |
[INFO] [stdout] 537 |         let short_reads = matches_subc.is_present("short_reads");
[INFO] [stdout]     |             ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_short_reads`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `dont_use_kmers`
[INFO] [stdout]    --> src/bin/chrom_mini_graph.rs:544:50
[INFO] [stdout]     |
[INFO] [stdout] 544 |         let (mut ref_graph, chroms, chrom_names, dont_use_kmers): (
[INFO] [stdout]     |                                                  ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_dont_use_kmers`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `anchor_file`
[INFO] [stdout]    --> src/bin/chrom_mini_graph.rs:556:13
[INFO] [stdout]     |
[INFO] [stdout] 556 |         let mut anchor_file = BufWriter::new(File::create("read_anchor_hits.txt").unwrap());
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_anchor_file`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unreachable statement
[INFO] [stdout]    --> src/align.rs:753:21
[INFO] [stdout]     |
[INFO] [stdout] 752 |                     panic!("{}\n{}", prev_char, cg_str);
[INFO] [stdout]     |                     ----------------------------------- any code following this expression is unreachable
[INFO] [stdout] 753 |                     op = Operation::Sentinel;
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^^ unreachable statement
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unreachable_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unreachable statement
[INFO] [stdout]    --> src/coord_chain.rs:318:9
[INFO] [stdout]     |
[INFO] [stdout] 317 |           return best_superchain_ret;
[INFO] [stdout]     |           -------------------------- any code following this expression is unreachable
[INFO] [stdout] 318 | /         return best_superchain
[INFO] [stdout] 319 | |             .iter_mut()
[INFO] [stdout] 320 | |             .map(|x| (mem::take(&mut x.0), x.3, forward_strand))
[INFO] [stdout] 321 | |             .collect();
[INFO] [stdout]     | |_______________________^ unreachable statement
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/graph_utils.rs:257:5
[INFO] [stdout]     |
[INFO] [stdout] 257 |     mut anchors: Vec<(u32, u32)>,
[INFO] [stdout]     |     ----^^^^^^^
[INFO] [stdout]     |     |
[INFO] [stdout]     |     help: remove this `mut`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `circular`
[INFO] [stdout]    --> src/graph_utils.rs:260:5
[INFO] [stdout]     |
[INFO] [stdout] 260 |     circular: bool,
[INFO] [stdout]     |     ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_circular`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `num_contains_dist_not` is assigned to, but never used
[INFO] [stdout]    --> src/graph_utils.rs:285:9
[INFO] [stdout]     |
[INFO] [stdout] 285 |     let mut num_contains_dist_not = 0;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_num_contains_dist_not` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `num_contains_dist_not` is never read
[INFO] [stdout]    --> src/graph_utils.rs:383:17
[INFO] [stdout]     |
[INFO] [stdout] 383 |                 num_contains_dist_not += 1;
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout]     = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `num_samp_coord` is assigned to, but never used
[INFO] [stdout]   --> src/seeding_methods_bit.rs:82:9
[INFO] [stdout]    |
[INFO] [stdout] 82 |     let mut num_samp_coord = 0;
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: consider using `_num_samp_coord` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `num_samp_coord` is never read
[INFO] [stdout]    --> src/seeding_methods_bit.rs:163:17
[INFO] [stdout]     |
[INFO] [stdout] 163 |                 num_samp_coord += 1;
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `frequent_kmers`
[INFO] [stdout]    --> src/seeding_methods_bit.rs:247:5
[INFO] [stdout]     |
[INFO] [stdout] 247 |     frequent_kmers: &FxHashMap<Kmer16, usize>,
[INFO] [stdout]     |     ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_frequent_kmers`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/chain.rs:64:9
[INFO] [stdout]    |
[INFO] [stdout] 64 |     let mut gap_cost = (ref_order_dist - query_order_dist).abs();
[INFO] [stdout]    |         ----^^^^^^^^
[INFO] [stdout]    |         |
[INFO] [stdout]    |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `count` is assigned to, but never used
[INFO] [stdout]    --> src/chain.rs:241:17
[INFO] [stdout]     |
[INFO] [stdout] 241 |             let mut count = 0;
[INFO] [stdout]     |                 ^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_count` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `count` is never read
[INFO] [stdout]    --> src/chain.rs:260:21
[INFO] [stdout]     |
[INFO] [stdout] 260 |                     count += 1
[INFO] [stdout]     |                     ^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `q_len`
[INFO] [stdout]    --> src/chain.rs:290:9
[INFO] [stdout]     |
[INFO] [stdout] 290 |     let q_len = seeds_q.len();
[INFO] [stdout]     |         ^^^^^ help: if this is intentional, prefix it with an underscore: `_q_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `now`
[INFO] [stdout]    --> src/chain.rs:291:9
[INFO] [stdout]     |
[INFO] [stdout] 291 |     let now = Instant::now();
[INFO] [stdout]     |         ^^^ help: if this is intentional, prefix it with an underscore: `_now`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/chain.rs:480:25
[INFO] [stdout]     |
[INFO] [stdout] 480 |                     let mut tup = colour_paths.get_mut(&colour).unwrap();
[INFO] [stdout]     |                         ----^^^
[INFO] [stdout]     |                         |
[INFO] [stdout]     |                         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `read_length`
[INFO] [stdout]    --> src/chain.rs:454:5
[INFO] [stdout]     |
[INFO] [stdout] 454 |     read_length: usize,
[INFO] [stdout]     |     ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_length`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `read_length`
[INFO] [stdout]    --> src/chain.rs:603:5
[INFO] [stdout]     |
[INFO] [stdout] 603 |     read_length: usize,
[INFO] [stdout]     |     ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_length`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `best_node` is assigned to, but never used
[INFO] [stdout]    --> src/chain.rs:618:9
[INFO] [stdout]     |
[INFO] [stdout] 618 |     let mut best_node = first_node;
[INFO] [stdout]     |         ^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_best_node` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `best_node` is never read
[INFO] [stdout]    --> src/chain.rs:747:21
[INFO] [stdout]     |
[INFO] [stdout] 747 |                     best_node = intermediate_node;
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `mandatory_color`
[INFO] [stdout]     --> src/chain.rs:1170:9
[INFO] [stdout]      |
[INFO] [stdout] 1170 |     let mandatory_color = Color::MAX;
[INFO] [stdout]      |         ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mandatory_color`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/align.rs:494:9
[INFO] [stdout]     |
[INFO] [stdout] 494 |     let mut break_mm = 3;
[INFO] [stdout]     |         ----^^^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `r_node`
[INFO] [stdout]    --> src/align.rs:421:13
[INFO] [stdout]     |
[INFO] [stdout] 421 |         let r_node = &ref_graph[anchors[i].0 as usize];
[INFO] [stdout]     |             ^^^^^^ help: if this is intentional, prefix it with an underscore: `_r_node`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `r_cpy`
[INFO] [stdout]    --> src/align.rs:632:13
[INFO] [stdout]     |
[INFO] [stdout] 632 |         let r_cpy = ref_map_string.clone();
[INFO] [stdout]     |             ^^^^^ help: if this is intentional, prefix it with an underscore: `_r_cpy`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `q_cpy`
[INFO] [stdout]    --> src/align.rs:633:13
[INFO] [stdout]     |
[INFO] [stdout] 633 |         let q_cpy = read_map_string.clone();
[INFO] [stdout]     |             ^^^^^ help: if this is intentional, prefix it with an underscore: `_q_cpy`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `prev_char` is never read
[INFO] [stdout]    --> src/align.rs:761:17
[INFO] [stdout]     |
[INFO] [stdout] 761 |                 prev_char = c;
[INFO] [stdout]     |                 ^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/coord_chain.rs:206:9
[INFO] [stdout]     |
[INFO] [stdout] 206 |     let mut best_superchain =
[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/coord_chain.rs:601:9
[INFO] [stdout]     |
[INFO] [stdout] 601 |     let mut gap_cost = (ref_order_dist - query_order_dist).abs();
[INFO] [stdout]     |         ----^^^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `State` is never constructed
[INFO] [stdout]    --> src/graph_utils.rs:110:8
[INFO] [stdout]     |
[INFO] [stdout] 110 | struct State {
[INFO] [stdout]     |        ^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `test` profile [optimized + debuginfo] target(s) in 2.97s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nalgebra v0.27.1, nom v5.1.2
[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" "50ab44abd1718197576bc5b47af0245e984cdb55397a10783dfa6e50ebec38be", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "50ab44abd1718197576bc5b47af0245e984cdb55397a10783dfa6e50ebec38be", kill_on_drop: false }`
[INFO] [stdout] 50ab44abd1718197576bc5b47af0245e984cdb55397a10783dfa6e50ebec38be
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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@sha256:845e597a41426bbf2703be69acdb67d10b6de511142d05cba7bbe119c898b2c7" "/opt/rustwide/cargo-home/bin/cargo" "+0d162b25edd5bf0dba9a22e83b614f1113e90474" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] af34aa0f0be64448bac92a157e5203f9044fcf5616b7500e71ae2596efaeacae
[INFO] running `Command { std: "docker" "start" "-a" "af34aa0f0be64448bac92a157e5203f9044fcf5616b7500e71ae2596efaeacae", kill_on_drop: false }`
[INFO] [stderr] warning: unused import: `debruijn::kmer::Kmer10`
[INFO] [stderr]  --> src/seeding_methods_bit.rs:3:5
[INFO] [stderr]   |
[INFO] [stderr] 3 | use debruijn::kmer::Kmer10;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `debruijn::kmer::Kmer12`
[INFO] [stderr]  --> src/seeding_methods_bit.rs:4:5
[INFO] [stderr]   |
[INFO] [stderr] 4 | use debruijn::kmer::Kmer12;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `debruijn::kmer::Kmer8`
[INFO] [stderr]  --> src/seeding_methods_bit.rs:6:5
[INFO] [stderr]   |
[INFO] [stderr] 6 | use debruijn::kmer::Kmer8;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `simple_logger::SimpleLogger`
[INFO] [stderr]  --> src/chain.rs:2:5
[INFO] [stderr]   |
[INFO] [stderr] 2 | use simple_logger::SimpleLogger;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `debruijn::Kmer`
[INFO] [stderr]  --> src/chain.rs:8:5
[INFO] [stderr]   |
[INFO] [stderr] 8 | use debruijn::Kmer;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unnecessary parentheses around `if` condition
[INFO] [stderr]     --> src/chain.rs:1335:12
[INFO] [stderr]      |
[INFO] [stderr] 1335 |         if (i > 0 && !chain_reads) {
[INFO] [stderr]      |            ^                     ^
[INFO] [stderr]      |
[INFO] [stderr]      = note: `#[warn(unused_parens)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] help: remove these parentheses
[INFO] [stderr]      |
[INFO] [stderr] 1335 -         if (i > 0 && !chain_reads) {
[INFO] [stderr] 1335 +         if i > 0 && !chain_reads  {
[INFO] [stderr]      |
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `debruijn::dna_string::*`
[INFO] [stderr]  --> src/align.rs:8:5
[INFO] [stderr]   |
[INFO] [stderr] 8 | use debruijn::dna_string::*;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `simple_logger::SimpleLogger`
[INFO] [stderr]   --> src/align.rs:15:5
[INFO] [stderr]    |
[INFO] [stderr] 15 | use simple_logger::SimpleLogger;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `crate::avl_tree::SearchTree`
[INFO] [stderr]  --> src/coord_chain.rs:2:5
[INFO] [stderr]   |
[INFO] [stderr] 2 | use crate::avl_tree::SearchTree;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `debruijn::Kmer`
[INFO] [stderr]  --> src/coord_chain.rs:8:5
[INFO] [stderr]   |
[INFO] [stderr] 8 | use debruijn::Kmer;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `smallvec::SmallVec`
[INFO] [stderr]   --> src/coord_chain.rs:11:5
[INFO] [stderr]    |
[INFO] [stderr] 11 | use smallvec::SmallVec;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unreachable statement
[INFO] [stderr]    --> src/align.rs:753:21
[INFO] [stderr]     |
[INFO] [stderr] 752 |                     panic!("{}\n{}", prev_char, cg_str);
[INFO] [stderr]     |                     ----------------------------------- any code following this expression is unreachable
[INFO] [stderr] 753 |                     op = Operation::Sentinel;
[INFO] [stderr]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^^ unreachable statement
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(unreachable_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unreachable statement
[INFO] [stderr]    --> src/coord_chain.rs:318:9
[INFO] [stderr]     |
[INFO] [stderr] 317 |           return best_superchain_ret;
[INFO] [stderr]     |           -------------------------- any code following this expression is unreachable
[INFO] [stderr] 318 | /         return best_superchain
[INFO] [stderr] 319 | |             .iter_mut()
[INFO] [stderr] 320 | |             .map(|x| (mem::take(&mut x.0), x.3, forward_strand))
[INFO] [stderr] 321 | |             .collect();
[INFO] [stderr]     | |_______________________^ unreachable statement
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/graph_utils.rs:257:5
[INFO] [stderr]     |
[INFO] [stderr] 257 |     mut anchors: Vec<(u32, u32)>,
[INFO] [stderr]     |     ----^^^^^^^
[INFO] [stderr]     |     |
[INFO] [stderr]     |     help: remove this `mut`
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `circular`
[INFO] [stderr]    --> src/graph_utils.rs:260:5
[INFO] [stderr]     |
[INFO] [stderr] 260 |     circular: bool,
[INFO] [stderr]     |     ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_circular`
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: variable `num_contains_dist_not` is assigned to, but never used
[INFO] [stderr]    --> src/graph_utils.rs:285:9
[INFO] [stderr]     |
[INFO] [stderr] 285 |     let mut num_contains_dist_not = 0;
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: consider using `_num_contains_dist_not` instead
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `num_contains_dist_not` is never read
[INFO] [stderr]    --> src/graph_utils.rs:383:17
[INFO] [stderr]     |
[INFO] [stderr] 383 |                 num_contains_dist_not += 1;
[INFO] [stderr]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr]     = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: variable `num_samp_coord` is assigned to, but never used
[INFO] [stderr]   --> src/seeding_methods_bit.rs:82:9
[INFO] [stderr]    |
[INFO] [stderr] 82 |     let mut num_samp_coord = 0;
[INFO] [stderr]    |         ^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: consider using `_num_samp_coord` instead
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `num_samp_coord` is never read
[INFO] [stderr]    --> src/seeding_methods_bit.rs:163:17
[INFO] [stderr]     |
[INFO] [stderr] 163 |                 num_samp_coord += 1;
[INFO] [stderr]     |                 ^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `frequent_kmers`
[INFO] [stderr]    --> src/seeding_methods_bit.rs:247:5
[INFO] [stderr]     |
[INFO] [stderr] 247 |     frequent_kmers: &FxHashMap<Kmer16, usize>,
[INFO] [stderr]     |     ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_frequent_kmers`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]   --> src/chain.rs:64:9
[INFO] [stderr]    |
[INFO] [stderr] 64 |     let mut gap_cost = (ref_order_dist - query_order_dist).abs();
[INFO] [stderr]    |         ----^^^^^^^^
[INFO] [stderr]    |         |
[INFO] [stderr]    |         help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: variable `count` is assigned to, but never used
[INFO] [stderr]    --> src/chain.rs:241:17
[INFO] [stderr]     |
[INFO] [stderr] 241 |             let mut count = 0;
[INFO] [stderr]     |                 ^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: consider using `_count` instead
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `count` is never read
[INFO] [stderr]    --> src/chain.rs:260:21
[INFO] [stderr]     |
[INFO] [stderr] 260 |                     count += 1
[INFO] [stderr]     |                     ^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `q_len`
[INFO] [stderr]    --> src/chain.rs:290:9
[INFO] [stderr]     |
[INFO] [stderr] 290 |     let q_len = seeds_q.len();
[INFO] [stderr]     |         ^^^^^ help: if this is intentional, prefix it with an underscore: `_q_len`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `now`
[INFO] [stderr]    --> src/chain.rs:291:9
[INFO] [stderr]     |
[INFO] [stderr] 291 |     let now = Instant::now();
[INFO] [stderr]     |         ^^^ help: if this is intentional, prefix it with an underscore: `_now`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/chain.rs:480:25
[INFO] [stderr]     |
[INFO] [stderr] 480 |                     let mut tup = colour_paths.get_mut(&colour).unwrap();
[INFO] [stderr]     |                         ----^^^
[INFO] [stderr]     |                         |
[INFO] [stderr]     |                         help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `read_length`
[INFO] [stderr]    --> src/chain.rs:454:5
[INFO] [stderr]     |
[INFO] [stderr] 454 |     read_length: usize,
[INFO] [stderr]     |     ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_length`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `read_length`
[INFO] [stderr]    --> src/chain.rs:603:5
[INFO] [stderr]     |
[INFO] [stderr] 603 |     read_length: usize,
[INFO] [stderr]     |     ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_length`
[INFO] [stderr] 
[INFO] [stderr] warning: variable `best_node` is assigned to, but never used
[INFO] [stderr]    --> src/chain.rs:618:9
[INFO] [stderr]     |
[INFO] [stderr] 618 |     let mut best_node = first_node;
[INFO] [stderr]     |         ^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: consider using `_best_node` instead
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `best_node` is never read
[INFO] [stderr]    --> src/chain.rs:747:21
[INFO] [stderr]     |
[INFO] [stderr] 747 |                     best_node = intermediate_node;
[INFO] [stderr]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `mandatory_color`
[INFO] [stderr]     --> src/chain.rs:1170:9
[INFO] [stderr]      |
[INFO] [stderr] 1170 |     let mandatory_color = Color::MAX;
[INFO] [stderr]      |         ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mandatory_color`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/align.rs:494:9
[INFO] [stderr]     |
[INFO] [stderr] 494 |     let mut break_mm = 3;
[INFO] [stderr]     |         ----^^^^^^^^
[INFO] [stderr]     |         |
[INFO] [stderr]     |         help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `r_node`
[INFO] [stderr]    --> src/align.rs:421:13
[INFO] [stderr]     |
[INFO] [stderr] 421 |         let r_node = &ref_graph[anchors[i].0 as usize];
[INFO] [stderr]     |             ^^^^^^ help: if this is intentional, prefix it with an underscore: `_r_node`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `r_cpy`
[INFO] [stderr]    --> src/align.rs:632:13
[INFO] [stderr]     |
[INFO] [stderr] 632 |         let r_cpy = ref_map_string.clone();
[INFO] [stderr]     |             ^^^^^ help: if this is intentional, prefix it with an underscore: `_r_cpy`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `q_cpy`
[INFO] [stderr]    --> src/align.rs:633:13
[INFO] [stderr]     |
[INFO] [stderr] 633 |         let q_cpy = read_map_string.clone();
[INFO] [stderr]     |             ^^^^^ help: if this is intentional, prefix it with an underscore: `_q_cpy`
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `prev_char` is never read
[INFO] [stderr]    --> src/align.rs:761:17
[INFO] [stderr]     |
[INFO] [stderr] 761 |                 prev_char = c;
[INFO] [stderr]     |                 ^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/coord_chain.rs:206:9
[INFO] [stderr]     |
[INFO] [stderr] 206 |     let mut best_superchain =
[INFO] [stderr]     |         ----^^^^^^^^^^^^^^^
[INFO] [stderr]     |         |
[INFO] [stderr]     |         help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/coord_chain.rs:601:9
[INFO] [stderr]     |
[INFO] [stderr] 601 |     let mut gap_cost = (ref_order_dist - query_order_dist).abs();
[INFO] [stderr]     |         ----^^^^^^^^
[INFO] [stderr]     |         |
[INFO] [stderr]     |         help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: struct `State` is never constructed
[INFO] [stderr]    --> src/graph_utils.rs:110:8
[INFO] [stderr]     |
[INFO] [stderr] 110 | struct State {
[INFO] [stderr]     |        ^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: `chrom_mini_graph` (lib) generated 39 warnings (run `cargo fix --lib -p chrom_mini_graph` to apply 27 suggestions)
[INFO] [stderr] warning: `chrom_mini_graph` (lib test) generated 39 warnings (39 duplicates)
[INFO] [stderr] warning: unused import: `block_aligner::scan_block::*`
[INFO] [stderr]  --> src/bin/chrom_mini_graph.rs:5:5
[INFO] [stderr]   |
[INFO] [stderr] 5 | use block_aligner::scan_block::*;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::mem`
[INFO] [stderr]   --> src/bin/chrom_mini_graph.rs:25:5
[INFO] [stderr]    |
[INFO] [stderr] 25 | use std::mem;
[INFO] [stderr]    |     ^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `block_aligner::scores`
[INFO] [stderr]  --> src/bin/chrom_mini_graph.rs:6:5
[INFO] [stderr]   |
[INFO] [stderr] 6 | use block_aligner::scores::*;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `debruijn::Mer`
[INFO] [stderr]   --> src/bin/chrom_mini_graph.rs:19:5
[INFO] [stderr]    |
[INFO] [stderr] 19 | use debruijn::Mer;
[INFO] [stderr]    |     ^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/bin/chrom_mini_graph.rs:628:29
[INFO] [stderr]     |
[INFO] [stderr] 628 |                         let mut anc_score_strand_vec = chain::chain_seeds(
[INFO] [stderr]     |                             ----^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |                             |
[INFO] [stderr]     |                             help: remove this `mut`
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/bin/chrom_mini_graph.rs:687:41
[INFO] [stderr]     |
[INFO] [stderr] 687 | ...                   let mut base_anc_score_strand_vec =
[INFO] [stderr]     |                           ----^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |                           |
[INFO] [stderr]     |                           help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/bin/chrom_mini_graph.rs:556:13
[INFO] [stderr]     |
[INFO] [stderr] 556 |         let mut anchor_file = BufWriter::new(File::create("read_anchor_hits.txt").unwrap());
[INFO] [stderr]     |             ----^^^^^^^^^^^
[INFO] [stderr]     |             |
[INFO] [stderr]     |             help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/bin/chrom_mini_graph.rs:566:13
[INFO] [stderr]     |
[INFO] [stderr] 566 |         let mut num_mapped_reads = Mutex::new(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]    --> src/bin/chrom_mini_graph.rs:569:13
[INFO] [stderr]     |
[INFO] [stderr] 569 |         let mut best_hit_for_read: Mutex<FxHashMap<_, _>> = Mutex::new(FxHashMap::default());
[INFO] [stderr]     |             ----^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |             |
[INFO] [stderr]     |             help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `now`
[INFO] [stderr]    --> src/bin/chrom_mini_graph.rs:752:37
[INFO] [stderr]     |
[INFO] [stderr] 752 | ...                   let now = Instant::now();
[INFO] [stderr]     |                           ^^^ help: if this is intentional, prefix it with an underscore: `_now`
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `order_val_last`
[INFO] [stderr]    --> src/bin/chrom_mini_graph.rs:403:17
[INFO] [stderr]     |
[INFO] [stderr] 403 |             let order_val_last = seeds2[qlen - 1].order_val;
[INFO] [stderr]     |                 ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_order_val_last`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `short_reads`
[INFO] [stderr]    --> src/bin/chrom_mini_graph.rs:537:13
[INFO] [stderr]     |
[INFO] [stderr] 537 |         let short_reads = matches_subc.is_present("short_reads");
[INFO] [stderr]     |             ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_short_reads`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `dont_use_kmers`
[INFO] [stderr]    --> src/bin/chrom_mini_graph.rs:544:50
[INFO] [stderr]     |
[INFO] [stderr] 544 |         let (mut ref_graph, chroms, chrom_names, dont_use_kmers): (
[INFO] [stderr]     |                                                  ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_dont_use_kmers`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `anchor_file`
[INFO] [stderr]    --> src/bin/chrom_mini_graph.rs:556:13
[INFO] [stderr]     |
[INFO] [stderr] 556 |         let mut anchor_file = BufWriter::new(File::create("read_anchor_hits.txt").unwrap());
[INFO] [stderr]     |             ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_anchor_file`
[INFO] [stderr] 
[INFO] [stderr] warning: `chrom_mini_graph` (bin "chrom_mini_graph" test) generated 14 warnings (run `cargo fix --bin "chrom_mini_graph" -p chrom_mini_graph --tests` to apply 12 suggestions)
[INFO] [stderr]     Finished `test` profile [optimized + debuginfo] target(s) in 0.31s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nalgebra v0.27.1, nom v5.1.2
[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/debug/deps/chrom_mini_graph-f860c3778826cd9f)
[INFO] [stdout] 
[INFO] [stdout] running 7 tests
[INFO] [stdout] test avl_tree::tests::insert_left_rot ... ok
[INFO] [stdout] test avl_tree::tests::left_right_rot ... ok
[INFO] [stdout] test avl_tree::tests::right_left_rot ... ok
[INFO] [stdout] test avl_tree::tests::insert_node ... ok
[INFO] [stdout] test avl_tree::tests::empty_tree ... ok
[INFO] [stdout] test avl_tree::tests::insert_right_rot ... ok
[INFO] [stdout] test avl_tree::tests::random_values ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 7 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.34s
[INFO] [stdout] 
[INFO] [stderr]      Running unittests src/bin/chrom_mini_graph.rs (/opt/rustwide/target/debug/deps/chrom_mini_graph-6186e5c5c691bd80)
[INFO] [stdout] 
[INFO] [stdout] running 0 tests
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stderr]    Doc-tests chrom_mini_graph
[INFO] [stderr] warning: unnecessary parentheses around `if` condition
[INFO] [stderr]     --> src/chain.rs:1335:12
[INFO] [stderr]      |
[INFO] [stderr] 1335 |         if (i > 0 && !chain_reads) {
[INFO] [stderr]      |            ^                     ^
[INFO] [stderr]      |
[INFO] [stderr]      = note: `#[warn(unused_parens)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] help: remove these parentheses
[INFO] [stderr]      |
[INFO] [stderr] 1335 -         if (i > 0 && !chain_reads) {
[INFO] [stderr] 1335 +         if i > 0 && !chain_reads  {
[INFO] [stderr]      |
[INFO] [stderr] 
[INFO] [stderr] warning: 1 warning emitted
[INFO] [stderr] 
[INFO] [stdout] 
[INFO] [stdout] running 5 tests
[INFO] [stdout] test src/avl_tree.rs - avl_tree::SearchTree<T>::contains (line 62) ... FAILED
[INFO] [stdout] test src/avl_tree.rs - avl_tree::SearchTree<T>::insert (line 80) ... FAILED
[INFO] [stdout] test src/avl_tree.rs - avl_tree::SearchTree<T>::is_empty (line 48) ... FAILED
[INFO] [stdout] test src/avl_tree.rs - avl_tree::SearchTree<T>::iter (line 328) ... FAILED
[INFO] [stdout] test src/avl_tree.rs - avl_tree::SearchTree<T>::new (line 33) ... FAILED
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout] 
[INFO] [stdout] ---- src/avl_tree.rs - avl_tree::SearchTree<T>::contains (line 62) stdout ----
[INFO] [stdout] error[E0432]: unresolved import `avltree`
[INFO] [stdout]   --> src/avl_tree.rs:63:5
[INFO] [stdout]    |
[INFO] [stdout] 63 | use avltree::SearchTree;
[INFO] [stdout]    |     ^^^^^^^ use of unresolved module or unlinked crate `avltree`
[INFO] [stdout]    |
[INFO] [stdout]    = help: if you wanted to use a crate named `avltree`, use `cargo add avltree` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/avl_tree.rs - avl_tree::SearchTree<T>::insert (line 80) stdout ----
[INFO] [stdout] error[E0432]: unresolved import `avltree`
[INFO] [stdout]   --> src/avl_tree.rs:81:5
[INFO] [stdout]    |
[INFO] [stdout] 81 | use avltree::SearchTree;
[INFO] [stdout]    |     ^^^^^^^ use of unresolved module or unlinked crate `avltree`
[INFO] [stdout]    |
[INFO] [stdout]    = help: if you wanted to use a crate named `avltree`, use `cargo add avltree` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/avl_tree.rs - avl_tree::SearchTree<T>::is_empty (line 48) stdout ----
[INFO] [stdout] error[E0432]: unresolved import `avltree`
[INFO] [stdout]   --> src/avl_tree.rs:49:5
[INFO] [stdout]    |
[INFO] [stdout] 49 | use avltree::SearchTree;
[INFO] [stdout]    |     ^^^^^^^ use of unresolved module or unlinked crate `avltree`
[INFO] [stdout]    |
[INFO] [stdout]    = help: if you wanted to use a crate named `avltree`, use `cargo add avltree` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/avl_tree.rs - avl_tree::SearchTree<T>::iter (line 328) stdout ----
[INFO] [stdout] error[E0432]: unresolved import `avltree`
[INFO] [stdout]    --> src/avl_tree.rs:329:5
[INFO] [stdout]     |
[INFO] [stdout] 329 | use avltree::SearchTree;
[INFO] [stdout]     |     ^^^^^^^ use of unresolved module or unlinked crate `avltree`
[INFO] [stdout]     |
[INFO] [stdout]     = help: if you wanted to use a crate named `avltree`, use `cargo add avltree` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] ---- src/avl_tree.rs - avl_tree::SearchTree<T>::new (line 33) stdout ----
[INFO] [stdout] error[E0432]: unresolved import `avltree`
[INFO] [stdout]   --> src/avl_tree.rs:34:5
[INFO] [stdout]    |
[INFO] [stdout] 34 | use avltree::SearchTree;
[INFO] [stdout]    |     ^^^^^^^ use of unresolved module or unlinked crate `avltree`
[INFO] [stdout]    |
[INFO] [stdout]    = help: if you wanted to use a crate named `avltree`, use `cargo add avltree` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0432`.
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout]     src/avl_tree.rs - avl_tree::SearchTree<T>::contains (line 62)
[INFO] [stdout]     src/avl_tree.rs - avl_tree::SearchTree<T>::insert (line 80)
[INFO] [stdout]     src/avl_tree.rs - avl_tree::SearchTree<T>::is_empty (line 48)
[INFO] [stdout]     src/avl_tree.rs - avl_tree::SearchTree<T>::iter (line 328)
[INFO] [stdout]     src/avl_tree.rs - avl_tree::SearchTree<T>::new (line 33)
[INFO] [stdout] 
[INFO] [stdout] test result: FAILED. 0 passed; 5 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.19s
[INFO] [stdout] 
[INFO] [stderr] error: doctest failed, to rerun pass `--doc`
[INFO] running `Command { std: "docker" "inspect" "af34aa0f0be64448bac92a157e5203f9044fcf5616b7500e71ae2596efaeacae", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "af34aa0f0be64448bac92a157e5203f9044fcf5616b7500e71ae2596efaeacae", kill_on_drop: false }`
[INFO] [stdout] af34aa0f0be64448bac92a157e5203f9044fcf5616b7500e71ae2596efaeacae
