[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] 5efe0d4b56b7ca94fa70baf8cb6e167a49323f67 [INFO] checking HopedWall/rs-vgaligner against master#f82664191d0e8764b7435b9d72eb0e366b8b1464 for pr-83354 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FHopedWall%2Frs-vgaligner" "/workspace/builds/worker-14/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-14/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/HopedWall/rs-vgaligner on toolchain f82664191d0e8764b7435b9d72eb0e366b8b1464 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+f82664191d0e8764b7435b9d72eb0e366b8b1464" "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-14/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" "+f82664191d0e8764b7435b9d72eb0e366b8b1464" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-14/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-14/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" "rustops/crates-build-env@sha256:f2f6bcd4b43ebee4e173f653a26493129bdb64017c85f916b780ca7fbdbaa79d" "/opt/rustwide/cargo-home/bin/cargo" "+f82664191d0e8764b7435b9d72eb0e366b8b1464" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 7ca43908c70866668368c02da8eac09cceedc7164c50646d33246201c99c6738 [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" "7ca43908c70866668368c02da8eac09cceedc7164c50646d33246201c99c6738", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "7ca43908c70866668368c02da8eac09cceedc7164c50646d33246201c99c6738", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "7ca43908c70866668368c02da8eac09cceedc7164c50646d33246201c99c6738", kill_on_drop: false }` [INFO] [stdout] 7ca43908c70866668368c02da8eac09cceedc7164c50646d33246201c99c6738 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-14/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-14/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" "rustops/crates-build-env@sha256:f2f6bcd4b43ebee4e173f653a26493129bdb64017c85f916b780ca7fbdbaa79d" "/opt/rustwide/cargo-home/bin/cargo" "+f82664191d0e8764b7435b9d72eb0e366b8b1464" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 2f708f78f8cd7aeba8dc86862db33374831a15fa2b24a377c4e98c9ec5eac45c [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" "2f708f78f8cd7aeba8dc86862db33374831a15fa2b24a377c4e98c9ec5eac45c", kill_on_drop: false }` [INFO] [stderr] Compiling autocfg v1.0.1 [INFO] [stderr] Compiling proc-macro2 v1.0.24 [INFO] [stderr] Compiling unicode-xid v0.2.1 [INFO] [stderr] Checking lazy_static v1.4.0 [INFO] [stderr] Compiling version_check v0.9.2 [INFO] [stderr] Compiling bitflags v1.2.1 [INFO] [stderr] Checking once_cell v1.7.0 [INFO] [stderr] Compiling lexical-core v0.7.5 [INFO] [stderr] Compiling feature-probe v0.1.1 [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 fnv v1.0.7 [INFO] [stderr] Compiling bio v0.32.0 [INFO] [stderr] Compiling getrandom v0.2.2 [INFO] [stderr] Checking bit-vec v0.6.3 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking newtype_derive v0.1.4 [INFO] [stderr] Checking triple_accel v0.3.4 [INFO] [stderr] Checking regex-automata v0.1.9 [INFO] [stderr] Checking fxhash v0.2.1 [INFO] [stderr] Checking matrixmultiply v0.2.4 [INFO] [stderr] Checking wyhash v0.5.0 [INFO] [stderr] Checking thread_local v1.1.3 [INFO] [stderr] Checking doc-comment v0.3.3 [INFO] [stderr] Checking atty v0.2.14 [INFO] [stderr] Checking aho-corasick v0.7.15 [INFO] [stderr] Checking csv-core v0.1.10 [INFO] [stderr] Checking bit-set v0.5.2 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Checking statrs v0.12.0 [INFO] [stderr] Compiling nom v5.1.2 [INFO] [stderr] Compiling ahash v0.7.2 [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 num-complex v0.2.4 [INFO] [stderr] Compiling indexmap v1.6.1 [INFO] [stderr] Compiling num-integer v0.1.44 [INFO] [stderr] Compiling rayon v1.5.0 [INFO] [stderr] Compiling substring v1.4.5 [INFO] [stderr] Compiling quote v1.0.9 [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] Compiling syn v1.0.60 [INFO] [stderr] Checking crossbeam-deque v0.8.0 [INFO] [stderr] Checking approx v0.3.2 [INFO] [stderr] Checking ordered-float v1.1.1 [INFO] [stderr] Checking itertools-num v0.1.3 [INFO] [stderr] Checking rayon-core v1.9.0 [INFO] [stderr] Checking ndarray v0.13.1 [INFO] [stderr] Checking boomphf v0.5.9 [INFO] [stderr] Compiling serde_derive v1.0.123 [INFO] [stderr] Compiling enum-map-derive v0.4.6 [INFO] [stderr] Compiling strum_macros v0.20.1 [INFO] [stderr] Compiling snafu-derive v0.6.10 [INFO] [stderr] Compiling bytemuck_derive v1.0.1 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling strum_macros v0.18.0 [INFO] [stderr] Compiling getset v0.0.9 [INFO] [stderr] Checking enum-map v0.6.4 [INFO] [stderr] Checking bytemuck v1.5.1 [INFO] [stderr] Checking bio-types v0.10.0 [INFO] [stderr] Checking snafu v0.6.10 [INFO] [stderr] Checking serde v1.0.123 [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 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/main.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | 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 imports: `Direction`, `NodeId` [INFO] [stdout] --> src/index.rs:2:39 [INFO] [stdout] | [INFO] [stdout] 2 | use handlegraph::handle::{Handle,Edge,Direction,NodeId}; [INFO] [stdout] | ^^^^^^^^^ ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ByteSlice` [INFO] [stdout] --> src/index.rs:5:12 [INFO] [stdout] | [INFO] [stdout] 5 | use bstr::{ByteSlice, ByteVec}; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs::File` [INFO] [stdout] --> src/index.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use std::fs::File; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Read`, `Write` [INFO] [stdout] --> src/index.rs:7:15 [INFO] [stdout] | [INFO] [stdout] 7 | use std::io::{Write, Read}; [INFO] [stdout] | ^^^^^ ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `find_sequence`, `get_bv_rank` [INFO] [stdout] --> src/index.rs:8:20 [INFO] [stdout] | [INFO] [stdout] 8 | use crate::utils::{get_bv_rank, find_sequence, NodeRef, find_sequence_po, find_graph_seq_length}; [INFO] [stdout] | ^^^^^^^^^^^ ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `gfa::gfa::Orientation` [INFO] [stdout] --> src/index.rs:10:5 [INFO] [stdout] | [INFO] [stdout] 10 | use gfa::gfa::Orientation; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `generate_kmers_hash` [INFO] [stdout] --> src/index.rs:11:35 [INFO] [stdout] | [INFO] [stdout] 11 | use crate::kmer::{generate_kmers, generate_kmers_hash, Kmer, KmerPos, generate_pos_on_forward, generate_hash, generate_mphf}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `verify_kmers` [INFO] [stdout] --> src/index.rs:12:71 [INFO] [stdout] | [INFO] [stdout] 12 | use crate::io::{print_bitvec, print_seq_to_file, print_kmers_to_file, verify_kmers, verify_kmers_2}; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `handlegraph::mutablehandlegraph::MutableHandleGraph` [INFO] [stdout] --> src/index.rs:15:5 [INFO] [stdout] | [INFO] [stdout] 15 | use handlegraph::mutablehandlegraph::MutableHandleGraph; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `Node_ref` should have an upper camel case name [INFO] [stdout] --> src/index.rs:56:12 [INFO] [stdout] | [INFO] [stdout] 56 | pub struct Node_ref { [INFO] [stdout] | ^^^^^^^^ help: convert the identifier to upper camel case: `NodeRef` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_camel_case_types)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `handlegraph::mutablehandlegraph::MutableHandleGraph` [INFO] [stdout] --> src/utils.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | use handlegraph::mutablehandlegraph::MutableHandleGraph; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bstr::ByteSlice` [INFO] [stdout] --> src/utils.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use bstr::ByteSlice; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unnecessary parentheses around assigned value [INFO] [stdout] --> src/utils.rs:53:19 [INFO] [stdout] | [INFO] [stdout] 53 | bv_pos += (curr_node.sequence.to_string().len() as u64); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_parens)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unnecessary parentheses around assigned value [INFO] [stdout] --> src/utils.rs:121:19 [INFO] [stdout] | [INFO] [stdout] 121 | bv_pos += (curr_node.sequence.to_string().len() as u64); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `NodeId` [INFO] [stdout] --> src/kmer.rs:3:46 [INFO] [stdout] | [INFO] [stdout] 3 | use handlegraph::handle::{Handle, Direction, NodeId}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::hash::BuildHasher` [INFO] [stdout] --> src/kmer.rs:11:5 [INFO] [stdout] | [INFO] [stdout] 11 | use std::hash::BuildHasher; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::ptr::null` [INFO] [stdout] --> src/io.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use std::ptr::null; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unnecessary parentheses around method argument [INFO] [stdout] --> src/io.rs:63:39 [INFO] [stdout] | [INFO] [stdout] 63 | curr_string.replace_range((i..i+3), curr_kmer.seq.as_str()); [INFO] [stdout] | ^^^^^^^^ help: remove these parentheses [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unnecessary parentheses around method argument [INFO] [stdout] --> src/io.rs:93:35 [INFO] [stdout] | [INFO] [stdout] 93 | curr_string.replace_range((curr_pos.start as usize..curr_pos.end as usize), curr_kmer.seq.as_str()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `handlegraph::handlegraph::HandleGraph` [INFO] [stdout] --> src/main.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | 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 imports: `Direction`, `NodeId` [INFO] [stdout] --> src/index.rs:2:39 [INFO] [stdout] | [INFO] [stdout] 2 | use handlegraph::handle::{Handle,Edge,Direction,NodeId}; [INFO] [stdout] | ^^^^^^^^^ ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs::File` [INFO] [stdout] --> src/index.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use std::fs::File; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Read`, `Write` [INFO] [stdout] --> src/index.rs:7:15 [INFO] [stdout] | [INFO] [stdout] 7 | use std::io::{Write, Read}; [INFO] [stdout] | ^^^^^ ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `find_sequence`, `get_bv_rank` [INFO] [stdout] --> src/index.rs:8:20 [INFO] [stdout] | [INFO] [stdout] 8 | use crate::utils::{get_bv_rank, find_sequence, NodeRef, find_sequence_po, find_graph_seq_length}; [INFO] [stdout] | ^^^^^^^^^^^ ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `gfa::gfa::Orientation` [INFO] [stdout] --> src/index.rs:10:5 [INFO] [stdout] | [INFO] [stdout] 10 | use gfa::gfa::Orientation; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `generate_kmers_hash` [INFO] [stdout] --> src/index.rs:11:35 [INFO] [stdout] | [INFO] [stdout] 11 | use crate::kmer::{generate_kmers, generate_kmers_hash, Kmer, KmerPos, generate_pos_on_forward, generate_hash, generate_mphf}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `verify_kmers` [INFO] [stdout] --> src/index.rs:12:71 [INFO] [stdout] | [INFO] [stdout] 12 | use crate::io::{print_bitvec, print_seq_to_file, print_kmers_to_file, verify_kmers, verify_kmers_2}; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `handlegraph::mutablehandlegraph::MutableHandleGraph` [INFO] [stdout] --> src/index.rs:15:5 [INFO] [stdout] | [INFO] [stdout] 15 | use handlegraph::mutablehandlegraph::MutableHandleGraph; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `Node_ref` should have an upper camel case name [INFO] [stdout] --> src/index.rs:56:12 [INFO] [stdout] | [INFO] [stdout] 56 | pub struct Node_ref { [INFO] [stdout] | ^^^^^^^^ help: convert the identifier to upper camel case: `NodeRef` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_camel_case_types)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `handlegraph::hashgraph::Node` [INFO] [stdout] --> src/index.rs:145:9 [INFO] [stdout] | [INFO] [stdout] 145 | use handlegraph::hashgraph::Node; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `handlegraph::mutablehandlegraph::MutableHandleGraph` [INFO] [stdout] --> src/utils.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | use handlegraph::mutablehandlegraph::MutableHandleGraph; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bstr::ByteSlice` [INFO] [stdout] --> src/utils.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use bstr::ByteSlice; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unnecessary parentheses around assigned value [INFO] [stdout] --> src/utils.rs:53:19 [INFO] [stdout] | [INFO] [stdout] 53 | bv_pos += (curr_node.sequence.to_string().len() as u64); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_parens)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unnecessary parentheses around assigned value [INFO] [stdout] --> src/utils.rs:121:19 [INFO] [stdout] | [INFO] [stdout] 121 | bv_pos += (curr_node.sequence.to_string().len() as u64); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `NodeId` [INFO] [stdout] --> src/kmer.rs:3:46 [INFO] [stdout] | [INFO] [stdout] 3 | use handlegraph::handle::{Handle, Direction, NodeId}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::hash::BuildHasher` [INFO] [stdout] --> src/kmer.rs:11:5 [INFO] [stdout] | [INFO] [stdout] 11 | use std::hash::BuildHasher; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::ptr::null` [INFO] [stdout] --> src/io.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use std::ptr::null; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unnecessary parentheses around method argument [INFO] [stdout] --> src/io.rs:63:39 [INFO] [stdout] | [INFO] [stdout] 63 | curr_string.replace_range((i..i+3), curr_kmer.seq.as_str()); [INFO] [stdout] | ^^^^^^^^ help: remove these parentheses [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unnecessary parentheses around method argument [INFO] [stdout] --> src/io.rs:93:35 [INFO] [stdout] | [INFO] [stdout] 93 | curr_string.replace_range((curr_pos.start as usize..curr_pos.end as usize), curr_kmer.seq.as_str()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `graph_index` [INFO] [stdout] --> src/main.rs:115:9 [INFO] [stdout] | [INFO] [stdout] 115 | let graph_index = Index::build(&graph, kmer_length, max_furcations, max_degree, sampling_rate, out_prefix); [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_graph_index` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `number_nodes` [INFO] [stdout] --> src/index.rs:77:13 [INFO] [stdout] | [INFO] [stdout] 77 | let number_nodes = graph.graph.len(); [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_number_nodes` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `reverse` [INFO] [stdout] --> src/index.rs:88:13 [INFO] [stdout] | [INFO] [stdout] 88 | let reverse = reverse_complement(&forward.as_str()); [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_reverse` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `handle_seq` [INFO] [stdout] --> src/index.rs:124:17 [INFO] [stdout] | [INFO] [stdout] 124 | let handle_seq = node.sequence.to_string(); [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_handle_seq` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `handle_seq_rev` [INFO] [stdout] --> src/index.rs:132:17 [INFO] [stdout] | [INFO] [stdout] 132 | let handle_seq_rev = node_rev.sequence.to_string(); [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_handle_seq_rev` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `sampling_rate` [INFO] [stdout] --> src/index.rs:71:18 [INFO] [stdout] | [INFO] [stdout] 71 | sampling_rate : f32, out_prefix : &str) -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_sampling_rate` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `neighbour` [INFO] [stdout] --> src/kmer.rs:117:77 [INFO] [stdout] | [INFO] [stdout] 117 | graph.handle_edges_iter(handle, Direction::Right).for_each(|neighbour|{ [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_neighbour` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `edge_max` [INFO] [stdout] --> src/kmer.rs:45:52 [INFO] [stdout] | [INFO] [stdout] 45 | pub fn generate_kmers(graph : &HashGraph, k : u64, edge_max : Option, degree_max : Option) -> Vec { [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_edge_max` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `forward` [INFO] [stdout] --> src/kmer.rs:167:61 [INFO] [stdout] | [INFO] [stdout] 167 | pub fn generate_pos_on_forward(kmers_on_graph : &Vec, forward : &String, [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_forward` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seq_bw` [INFO] [stdout] --> src/kmer.rs:168:32 [INFO] [stdout] | [INFO] [stdout] 168 | ... seq_bw : &BitVec, node_ref : &Vec) -> Vec { [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_seq_bw` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seq` [INFO] [stdout] --> src/kmer.rs:204:13 [INFO] [stdout] | [INFO] [stdout] 204 | let seq = kmer_graph_ref.seq.clone(); [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_seq` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `pos_on_fwd` [INFO] [stdout] --> src/kmer.rs:206:13 [INFO] [stdout] | [INFO] [stdout] 206 | let pos_on_fwd = kmers_on_fwd.get(i).unwrap(); [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_pos_on_fwd` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/index.rs:74:13 [INFO] [stdout] | [INFO] [stdout] 74 | let mut index = Index::new(); [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/kmer.rs:128:21 [INFO] [stdout] | [INFO] [stdout] 128 | let mut kmer = Kmer { [INFO] [stdout] | ----^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ByteSlice` [INFO] [stdout] --> src/index.rs:5:12 [INFO] [stdout] | [INFO] [stdout] 5 | use bstr::{ByteSlice, ByteVec}; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `graph_index` [INFO] [stdout] --> src/main.rs:115:9 [INFO] [stdout] | [INFO] [stdout] 115 | let graph_index = Index::build(&graph, kmer_length, max_furcations, max_degree, sampling_rate, out_prefix); [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_graph_index` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `number_nodes` [INFO] [stdout] --> src/index.rs:77:13 [INFO] [stdout] | [INFO] [stdout] 77 | let number_nodes = graph.graph.len(); [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_number_nodes` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `reverse` [INFO] [stdout] --> src/index.rs:88:13 [INFO] [stdout] | [INFO] [stdout] 88 | let reverse = reverse_complement(&forward.as_str()); [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_reverse` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/kmer.rs:197:9 [INFO] [stdout] | [INFO] [stdout] 197 | let mut kmers_hashed: AHashMap = AHashMap::new(); [INFO] [stdout] | ----^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `handle_seq` [INFO] [stdout] --> src/index.rs:124:17 [INFO] [stdout] | [INFO] [stdout] 124 | let handle_seq = node.sequence.to_string(); [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_handle_seq` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `handle_seq_rev` [INFO] [stdout] --> src/index.rs:132:17 [INFO] [stdout] | [INFO] [stdout] 132 | let handle_seq_rev = node_rev.sequence.to_string(); [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_handle_seq_rev` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `sampling_rate` [INFO] [stdout] --> src/index.rs:71:18 [INFO] [stdout] | [INFO] [stdout] 71 | sampling_rate : f32, out_prefix : &str) -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_sampling_rate` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `kmers_on_seq_fwd` [INFO] [stdout] --> src/index.rs:280:13 [INFO] [stdout] | [INFO] [stdout] 280 | let kmers_on_seq_fwd : Vec = generate_pos_on_forward(&kmers_on_graph, &forward, &seq_bv, &node_ref); [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_kmers_on_seq_fwd` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `neighbour` [INFO] [stdout] --> src/kmer.rs:117:77 [INFO] [stdout] | [INFO] [stdout] 117 | graph.handle_edges_iter(handle, Direction::Right).for_each(|neighbour|{ [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_neighbour` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `edge_max` [INFO] [stdout] --> src/kmer.rs:45:52 [INFO] [stdout] | [INFO] [stdout] 45 | pub fn generate_kmers(graph : &HashGraph, k : u64, edge_max : Option, degree_max : Option) -> Vec { [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_edge_max` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `forward` [INFO] [stdout] --> src/kmer.rs:167:61 [INFO] [stdout] | [INFO] [stdout] 167 | pub fn generate_pos_on_forward(kmers_on_graph : &Vec, forward : &String, [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_forward` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seq_bw` [INFO] [stdout] --> src/kmer.rs:168:32 [INFO] [stdout] | [INFO] [stdout] 168 | ... seq_bw : &BitVec, node_ref : &Vec) -> Vec { [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_seq_bw` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seq` [INFO] [stdout] --> src/kmer.rs:204:13 [INFO] [stdout] | [INFO] [stdout] 204 | let seq = kmer_graph_ref.seq.clone(); [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_seq` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `pos_on_fwd` [INFO] [stdout] --> src/kmer.rs:206:13 [INFO] [stdout] | [INFO] [stdout] 206 | let pos_on_fwd = kmers_on_fwd.get(i).unwrap(); [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_pos_on_fwd` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/io.rs:51:9 [INFO] [stdout] | [INFO] [stdout] 51 | let mut null_string = (0..seq.len()).map(|_| "-").collect::(); [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:82:9 [INFO] [stdout] | [INFO] [stdout] 82 | let mut null_string = (0..seq.len()).map(|_| "-").collect::(); [INFO] [stdout] | ----^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `kmer_length` [INFO] [stdout] --> src/index.rs:20:5 [INFO] [stdout] | [INFO] [stdout] 20 | kmer_length : u64, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `sampling_length` [INFO] [stdout] --> src/index.rs:22:5 [INFO] [stdout] | [INFO] [stdout] 22 | sampling_length : u64, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `seq_length` [INFO] [stdout] --> src/index.rs:24:5 [INFO] [stdout] | [INFO] [stdout] 24 | seq_length : u64, [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `seq_fwd` [INFO] [stdout] --> src/index.rs:26:5 [INFO] [stdout] | [INFO] [stdout] 26 | seq_fwd : Vec, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `seq_rev` [INFO] [stdout] --> src/index.rs:28:5 [INFO] [stdout] | [INFO] [stdout] 28 | seq_rev : Vec, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `seq_bv` [INFO] [stdout] --> src/index.rs:30:5 [INFO] [stdout] | [INFO] [stdout] 30 | seq_bv : BitVec, [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `seq_by_rank` [INFO] [stdout] --> src/index.rs:32:5 [INFO] [stdout] | [INFO] [stdout] 32 | seq_by_rank : BitVec, //TODO: check this [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `n_edges` [INFO] [stdout] --> src/index.rs:34:5 [INFO] [stdout] | [INFO] [stdout] 34 | n_edges : u64, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `edges` [INFO] [stdout] --> src/index.rs:36:5 [INFO] [stdout] | [INFO] [stdout] 36 | edges : Vec, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `n_nodes` [INFO] [stdout] --> src/index.rs:38:5 [INFO] [stdout] | [INFO] [stdout] 38 | n_nodes : u64, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `nodes` [INFO] [stdout] --> src/index.rs:40:5 [INFO] [stdout] | [INFO] [stdout] 40 | nodes : Vec, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `n_kmers` [INFO] [stdout] --> src/index.rs:42:5 [INFO] [stdout] | [INFO] [stdout] 42 | n_kmers : u64, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `n_kmer_pos` [INFO] [stdout] --> src/index.rs:44:5 [INFO] [stdout] | [INFO] [stdout] 44 | n_kmer_pos : u64, [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `kmer_pos_ref` [INFO] [stdout] --> src/index.rs:48:5 [INFO] [stdout] | [INFO] [stdout] 48 | kmer_pos_ref : Vec, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `kmer_pos_table` [INFO] [stdout] --> src/index.rs:50:5 [INFO] [stdout] | [INFO] [stdout] 50 | kmer_pos_table : Vec, //TODO: check this [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `loaded` [INFO] [stdout] --> src/index.rs:52:5 [INFO] [stdout] | [INFO] [stdout] 52 | loaded : bool [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `seq_idx` [INFO] [stdout] --> src/index.rs:57:5 [INFO] [stdout] | [INFO] [stdout] 57 | seq_idx : u64, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `edge_idx` [INFO] [stdout] --> src/index.rs:58:5 [INFO] [stdout] | [INFO] [stdout] 58 | edge_idx : u64, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `count_prev` [INFO] [stdout] --> src/index.rs:59:5 [INFO] [stdout] | [INFO] [stdout] 59 | count_prev : u64, [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `kmer_nodeId` should have a snake case name [INFO] [stdout] --> src/kmer.rs:177:13 [INFO] [stdout] | [INFO] [stdout] 177 | let kmer_nodeId = kmer_handle.unpack_number()-1; [INFO] [stdout] | ^^^^^^^^^^^ help: convert the identifier to snake case: `kmer_node_id` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_snake_case)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/index.rs:74:13 [INFO] [stdout] | [INFO] [stdout] 74 | let mut index = Index::new(); [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/kmer.rs:128:21 [INFO] [stdout] | [INFO] [stdout] 128 | let mut kmer = Kmer { [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:197:9 [INFO] [stdout] | [INFO] [stdout] 197 | let mut kmers_hashed: AHashMap = AHashMap::new(); [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:51:9 [INFO] [stdout] | [INFO] [stdout] 51 | let mut null_string = (0..seq.len()).map(|_| "-").collect::(); [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:82:9 [INFO] [stdout] | [INFO] [stdout] 82 | let mut null_string = (0..seq.len()).map(|_| "-").collect::(); [INFO] [stdout] | ----^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `kmer_length` [INFO] [stdout] --> src/index.rs:20:5 [INFO] [stdout] | [INFO] [stdout] 20 | kmer_length : u64, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `sampling_length` [INFO] [stdout] --> src/index.rs:22:5 [INFO] [stdout] | [INFO] [stdout] 22 | sampling_length : u64, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `seq_length` [INFO] [stdout] --> src/index.rs:24:5 [INFO] [stdout] | [INFO] [stdout] 24 | seq_length : u64, [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `seq_fwd` [INFO] [stdout] --> src/index.rs:26:5 [INFO] [stdout] | [INFO] [stdout] 26 | seq_fwd : Vec, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `seq_rev` [INFO] [stdout] --> src/index.rs:28:5 [INFO] [stdout] | [INFO] [stdout] 28 | seq_rev : Vec, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `seq_bv` [INFO] [stdout] --> src/index.rs:30:5 [INFO] [stdout] | [INFO] [stdout] 30 | seq_bv : BitVec, [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `seq_by_rank` [INFO] [stdout] --> src/index.rs:32:5 [INFO] [stdout] | [INFO] [stdout] 32 | seq_by_rank : BitVec, //TODO: check this [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `n_edges` [INFO] [stdout] --> src/index.rs:34:5 [INFO] [stdout] | [INFO] [stdout] 34 | n_edges : u64, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `edges` [INFO] [stdout] --> src/index.rs:36:5 [INFO] [stdout] | [INFO] [stdout] 36 | edges : Vec, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `n_nodes` [INFO] [stdout] --> src/index.rs:38:5 [INFO] [stdout] | [INFO] [stdout] 38 | n_nodes : u64, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `nodes` [INFO] [stdout] --> src/index.rs:40:5 [INFO] [stdout] | [INFO] [stdout] 40 | nodes : Vec, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `n_kmers` [INFO] [stdout] --> src/index.rs:42:5 [INFO] [stdout] | [INFO] [stdout] 42 | n_kmers : u64, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `n_kmer_pos` [INFO] [stdout] --> src/index.rs:44:5 [INFO] [stdout] | [INFO] [stdout] 44 | n_kmer_pos : u64, [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `kmer_pos_ref` [INFO] [stdout] --> src/index.rs:48:5 [INFO] [stdout] | [INFO] [stdout] 48 | kmer_pos_ref : Vec, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `kmer_pos_table` [INFO] [stdout] --> src/index.rs:50:5 [INFO] [stdout] | [INFO] [stdout] 50 | kmer_pos_table : Vec, //TODO: check this [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `loaded` [INFO] [stdout] --> src/index.rs:52:5 [INFO] [stdout] | [INFO] [stdout] 52 | loaded : bool [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `seq_idx` [INFO] [stdout] --> src/index.rs:57:5 [INFO] [stdout] | [INFO] [stdout] 57 | seq_idx : u64, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `edge_idx` [INFO] [stdout] --> src/index.rs:58:5 [INFO] [stdout] | [INFO] [stdout] 58 | edge_idx : u64, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `count_prev` [INFO] [stdout] --> src/index.rs:59:5 [INFO] [stdout] | [INFO] [stdout] 59 | count_prev : u64, [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `kmer_nodeId` should have a snake case name [INFO] [stdout] --> src/kmer.rs:177:13 [INFO] [stdout] | [INFO] [stdout] 177 | let kmer_nodeId = kmer_handle.unpack_number()-1; [INFO] [stdout] | ^^^^^^^^^^^ help: convert the identifier to snake case: `kmer_node_id` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_snake_case)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/io.rs:32:5 [INFO] [stdout] | [INFO] [stdout] 32 | file.write_all(">ref\n".as_bytes()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_must_use)]` on by default [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/io.rs:33:5 [INFO] [stdout] | [INFO] [stdout] 33 | file.write_all(seq.as_bytes()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/io.rs:42:9 [INFO] [stdout] | [INFO] [stdout] 42 | file.write_all(index_str.as_bytes()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/io.rs:43:9 [INFO] [stdout] | [INFO] [stdout] 43 | file.write_all(kmers_str.as_bytes()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/io.rs:55:5 [INFO] [stdout] | [INFO] [stdout] 55 | file.write_all(reference.as_bytes()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/io.rs:66:13 [INFO] [stdout] | [INFO] [stdout] 66 | file.write_all(kmer_string.as_bytes()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/io.rs:86:5 [INFO] [stdout] | [INFO] [stdout] 86 | file.write_all(reference.as_bytes()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/io.rs:95:9 [INFO] [stdout] | [INFO] [stdout] 95 | file.write_all(kmer_string.as_bytes()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/io.rs:32:5 [INFO] [stdout] | [INFO] [stdout] 32 | file.write_all(">ref\n".as_bytes()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_must_use)]` on by default [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/io.rs:33:5 [INFO] [stdout] | [INFO] [stdout] 33 | file.write_all(seq.as_bytes()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/io.rs:42:9 [INFO] [stdout] | [INFO] [stdout] 42 | file.write_all(index_str.as_bytes()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/io.rs:43:9 [INFO] [stdout] | [INFO] [stdout] 43 | file.write_all(kmers_str.as_bytes()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/io.rs:55:5 [INFO] [stdout] | [INFO] [stdout] 55 | file.write_all(reference.as_bytes()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/io.rs:66:13 [INFO] [stdout] | [INFO] [stdout] 66 | file.write_all(kmer_string.as_bytes()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/io.rs:86:5 [INFO] [stdout] | [INFO] [stdout] 86 | file.write_all(reference.as_bytes()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/io.rs:95:9 [INFO] [stdout] | [INFO] [stdout] 95 | file.write_all(kmer_string.as_bytes()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 65 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 67 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 1m 32s [INFO] running `Command { std: "docker" "inspect" "2f708f78f8cd7aeba8dc86862db33374831a15fa2b24a377c4e98c9ec5eac45c", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "2f708f78f8cd7aeba8dc86862db33374831a15fa2b24a377c4e98c9ec5eac45c", kill_on_drop: false }` [INFO] [stdout] 2f708f78f8cd7aeba8dc86862db33374831a15fa2b24a377c4e98c9ec5eac45c