[INFO] fetching crate isONclust3 0.3.0... [INFO] checking isONclust3-0.3.0 against master#350d0ef0ec0493e6d21cfb265cb8211a0e74d766 for pr-145342-1 [INFO] extracting crate isONclust3 0.3.0 into /workspace/builds/worker-2-tc1/source [INFO] started tweaking crates.io crate isONclust3 0.3.0 [INFO] finished tweaking crates.io crate isONclust3 0.3.0 [INFO] tweaked toml for crates.io crate isONclust3 0.3.0 written to /workspace/builds/worker-2-tc1/source/Cargo.toml [INFO] validating manifest of crates.io crate isONclust3 0.3.0 on toolchain 350d0ef0ec0493e6d21cfb265cb8211a0e74d766 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+350d0ef0ec0493e6d21cfb265cb8211a0e74d766" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate crates.io crate isONclust3 0.3.0 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" "+350d0ef0ec0493e6d21cfb265cb8211a0e74d766" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded minimizer-iter v1.2.1 [INFO] [stderr] Downloaded wyhash2 v0.2.1 [INFO] [stderr] Downloaded minimizer-queue v1.2.3 [INFO] [stderr] Downloaded clap-cargo v0.12.0 [INFO] [stderr] Downloaded bio-seq v0.10.0 [INFO] [stderr] Downloaded bio-seq-derive v1.6.4 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+350d0ef0ec0493e6d21cfb265cb8211a0e74d766" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] b5037c2f8e002ee760c8feca4a535239a20c6ffbf01bac50da48e805987a3345 [INFO] running `Command { std: "docker" "start" "-a" "b5037c2f8e002ee760c8feca4a535239a20c6ffbf01bac50da48e805987a3345", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "b5037c2f8e002ee760c8feca4a535239a20c6ffbf01bac50da48e805987a3345", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "b5037c2f8e002ee760c8feca4a535239a20c6ffbf01bac50da48e805987a3345", kill_on_drop: false }` [INFO] [stdout] b5037c2f8e002ee760c8feca4a535239a20c6ffbf01bac50da48e805987a3345 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+350d0ef0ec0493e6d21cfb265cb8211a0e74d766" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] e8c467e10319c54b8a347ea2e68fa33bbd2e9c5c690555698466890a559e83b4 [INFO] running `Command { std: "docker" "start" "-a" "e8c467e10319c54b8a347ea2e68fa33bbd2e9c5c690555698466890a559e83b4", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.92 [INFO] [stderr] Compiling unicode-ident v1.0.14 [INFO] [stderr] Compiling autocfg v1.4.0 [INFO] [stderr] Compiling libm v0.2.11 [INFO] [stderr] Compiling libc v0.2.165 [INFO] [stderr] Checking byteorder v1.5.0 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Checking cfg-if v1.0.0 [INFO] [stderr] Compiling serde v1.0.215 [INFO] [stderr] Checking memchr v2.7.4 [INFO] [stderr] Compiling paste v1.0.15 [INFO] [stderr] Checking bytemuck v1.20.0 [INFO] [stderr] Compiling rustversion v1.0.18 [INFO] [stderr] Compiling heck v0.5.0 [INFO] [stderr] Compiling crossbeam-utils v0.8.20 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Checking safe_arch v0.7.2 [INFO] [stderr] Compiling typenum v1.17.0 [INFO] [stderr] Checking utf8parse v0.2.2 [INFO] [stderr] 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[INFO] [stderr] Compiling syn v2.0.89 [INFO] [stderr] Compiling anyhow v1.0.93 [INFO] [stderr] Checking tap v1.0.1 [INFO] [stderr] Checking equivalent v1.0.1 [INFO] [stderr] Checking hashbrown v0.15.2 [INFO] [stderr] Checking no-std-compat v0.4.1 [INFO] [stderr] Checking strsim v0.11.1 [INFO] [stderr] Checking wyhash2 v0.2.1 [INFO] [stderr] Checking wyz v0.5.1 [INFO] [stderr] Checking crossbeam-deque v0.8.5 [INFO] [stderr] Checking clap_builder v4.5.21 [INFO] [stderr] Checking csv-core v0.1.11 [INFO] [stderr] Checking indexmap v2.6.0 [INFO] [stderr] Checking ryu v1.0.18 [INFO] [stderr] Checking bit-vec v0.6.3 [INFO] [stderr] Checking funty v2.0.0 [INFO] [stderr] Compiling heck v0.4.1 [INFO] [stderr] Checking strength_reduce v0.2.4 [INFO] [stderr] Checking itoa v1.0.14 [INFO] [stderr] Checking fixedbitset v0.4.2 [INFO] [stderr] Checking minimizer-queue v1.2.3 [INFO] [stderr] Checking bit-set v0.5.3 [INFO] [stderr] Checking itertools v0.11.0 [INFO] [stderr] Checking petgraph v0.6.5 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[stderr] Compiling nalgebra-macros v0.1.0 [INFO] [stderr] Compiling bio-seq-derive v1.6.4 [INFO] [stderr] Checking regex v1.11.1 [INFO] [stderr] Checking bio-seq v0.10.0 [INFO] [stderr] Compiling zerocopy-derive v0.7.35 [INFO] [stderr] Compiling serde_derive v1.0.215 [INFO] [stderr] Compiling thiserror-impl v1.0.69 [INFO] [stderr] Compiling derive-new v0.6.0 [INFO] [stderr] Compiling clap_derive v4.5.18 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling enum-map-derive v0.17.0 [INFO] [stderr] Compiling strum_macros v0.25.3 [INFO] [stderr] Checking enum-map v2.7.3 [INFO] [stderr] Checking zerocopy v0.7.35 [INFO] [stderr] Checking bio-types v1.0.4 [INFO] [stderr] Checking ppv-lite86 v0.2.20 [INFO] [stderr] Checking clap v4.5.21 [INFO] [stderr] Checking clap-cargo v0.12.0 [INFO] [stderr] Checking rand_chacha v0.3.1 [INFO] [stderr] Checking rand v0.8.5 [INFO] [stderr] Checking rand_distr v0.4.3 [INFO] [stderr] Checking nalgebra v0.29.0 [INFO] [stderr] Checking csv v1.3.1 [INFO] [stderr] Checking multimap v0.9.1 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking statrs v0.16.1 [INFO] [stderr] Checking bio v1.6.0 [INFO] [stderr] Checking isONclust3 v0.3.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `super::*` [INFO] [stdout] --> src/seeding_and_filtering_seeds.rs:432:9 [INFO] [stdout] | [INFO] [stdout] 432 | use super::*; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashSet` [INFO] [stdout] --> src/generate_sorted_fastq_for_cluster.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use std::collections::HashSet; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `read_ids` should have an upper camel case name [INFO] [stdout] --> src/structs.rs:5:5 [INFO] [stdout] | [INFO] [stdout] 5 | read_ids(HashSet), [INFO] [stdout] | ^^^^^^^^ help: convert the identifier to upper camel case: `ReadIds` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_camel_case_types)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `mini_seqs` should have an upper camel case name [INFO] [stdout] --> src/structs.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | mini_seqs(HashSet), [INFO] [stdout] | ^^^^^^^^^ help: convert the identifier to upper camel case: `MiniSeqs` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `Minimizer_hashed` should have an upper camel case name [INFO] [stdout] --> src/structs.rs:20:12 [INFO] [stdout] | [INFO] [stdout] 20 | pub struct Minimizer_hashed { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: convert the identifier to upper camel case: `MinimizerHashed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `Coord_obj` should have an upper camel case name [INFO] [stdout] --> src/structs.rs:48:19 [INFO] [stdout] | [INFO] [stdout] 48 | pub(crate) struct Coord_obj{ [INFO] [stdout] | ^^^^^^^^^ help: convert the identifier to upper camel case: `CoordObj` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `FastqRecord_isoncl_init` should have an upper camel case name [INFO] [stdout] --> src/structs.rs:103:19 [INFO] [stdout] | [INFO] [stdout] 103 | pub(crate) struct FastqRecord_isoncl_init { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ help: convert the identifier to upper camel case: `FastqRecordIsonclInit` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `internal_gff` should have an upper camel case name [INFO] [stdout] --> src/structs.rs:111:19 [INFO] [stdout] | [INFO] [stdout] 111 | pub(crate) struct internal_gff { [INFO] [stdout] | ^^^^^^^^^^^^ help: convert the identifier to upper camel case: `InternalGff` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io::Read` [INFO] [stdout] --> src/main.rs:32:5 [INFO] [stdout] | [INFO] [stdout] 32 | use std::io::Read; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `Seed_Map` should have an upper camel case name [INFO] [stdout] --> src/main.rs:43:6 [INFO] [stdout] | [INFO] [stdout] 43 | type Seed_Map = FxHashMap>; // Change here to any other hash table implementation, e.g., HashMap, nohash_has... [INFO] [stdout] | ^^^^^^^^ help: convert the identifier to upper camel case: `SeedMap` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `Cluster_ID_Map` should have an upper camel case name [INFO] [stdout] --> src/main.rs:44:6 [INFO] [stdout] | [INFO] [stdout] 44 | type Cluster_ID_Map = FxHashMap>; // Change here to any other hash table implementation, e.g., HashMap,nohas... [INFO] [stdout] | ^^^^^^^^^^^^^^ help: convert the identifier to upper camel case: `ClusterIdMap` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashSet` [INFO] [stdout] --> src/generate_sorted_fastq_for_cluster.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use std::collections::HashSet; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `read_ids` should have an upper camel case name [INFO] [stdout] --> src/structs.rs:5:5 [INFO] [stdout] | [INFO] [stdout] 5 | read_ids(HashSet), [INFO] [stdout] | ^^^^^^^^ help: convert the identifier to upper camel case: `ReadIds` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_camel_case_types)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `mini_seqs` should have an upper camel case name [INFO] [stdout] --> src/structs.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | mini_seqs(HashSet), [INFO] [stdout] | ^^^^^^^^^ help: convert the identifier to upper camel case: `MiniSeqs` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `Minimizer_hashed` should have an upper camel case name [INFO] [stdout] --> src/structs.rs:20:12 [INFO] [stdout] | [INFO] [stdout] 20 | pub struct Minimizer_hashed { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: convert the identifier to upper camel case: `MinimizerHashed` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `Coord_obj` should have an upper camel case name [INFO] [stdout] --> src/structs.rs:48:19 [INFO] [stdout] | [INFO] [stdout] 48 | pub(crate) struct Coord_obj{ [INFO] [stdout] | ^^^^^^^^^ help: convert the identifier to upper camel case: `CoordObj` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `FastqRecord_isoncl_init` should have an upper camel case name [INFO] [stdout] --> src/structs.rs:103:19 [INFO] [stdout] | [INFO] [stdout] 103 | pub(crate) struct FastqRecord_isoncl_init { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ help: convert the identifier to upper camel case: `FastqRecordIsonclInit` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `internal_gff` should have an upper camel case name [INFO] [stdout] --> src/structs.rs:111:19 [INFO] [stdout] | [INFO] [stdout] 111 | pub(crate) struct internal_gff { [INFO] [stdout] | ^^^^^^^^^^^^ help: convert the identifier to upper camel case: `InternalGff` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io::Read` [INFO] [stdout] --> src/main.rs:32:5 [INFO] [stdout] | [INFO] [stdout] 32 | use std::io::Read; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `Seed_Map` should have an upper camel case name [INFO] [stdout] --> src/main.rs:43:6 [INFO] [stdout] | [INFO] [stdout] 43 | type Seed_Map = FxHashMap>; // Change here to any other hash table implementation, e.g., HashMap, nohash_has... [INFO] [stdout] | ^^^^^^^^ help: convert the identifier to upper camel case: `SeedMap` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `Cluster_ID_Map` should have an upper camel case name [INFO] [stdout] --> src/main.rs:44:6 [INFO] [stdout] | [INFO] [stdout] 44 | type Cluster_ID_Map = FxHashMap>; // Change here to any other hash table implementation, e.g., HashMap,nohas... [INFO] [stdout] | ^^^^^^^^^^^^^^ help: convert the identifier to upper camel case: `ClusterIdMap` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rayon::prelude` [INFO] [stdout] --> src/clustering.rs:5:5 [INFO] [stdout] | [INFO] [stdout] 5 | use rayon::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rayon::prelude` [INFO] [stdout] --> src/seeding_and_filtering_seeds.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use rayon::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rayon::prelude` [INFO] [stdout] --> src/gff_handling.rs:9:5 [INFO] [stdout] | [INFO] [stdout] 9 | use rayon::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `BufRead` [INFO] [stdout] --> src/gff_handling.rs:3:26 [INFO] [stdout] | [INFO] [stdout] 3 | use std::io::{BufReader, BufRead}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rayon::prelude` [INFO] [stdout] --> src/write_output.rs:9:5 [INFO] [stdout] | [INFO] [stdout] 9 | use rayon::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `quality_header` is never read [INFO] [stdout] --> src/file_actions.rs:78:9 [INFO] [stdout] | [INFO] [stdout] 78 | quality_header = quality_header.trim().to_owned(); [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] = note: `#[warn(unused_assignments)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `quality_header` is never read [INFO] [stdout] --> src/file_actions.rs:121:9 [INFO] [stdout] | [INFO] [stdout] 121 | quality_header = quality_header.trim().to_owned(); [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/clustering.rs:97:17 [INFO] [stdout] | [INFO] [stdout] 97 | let mut shared_perc: f64; [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/clustering.rs:179:17 [INFO] [stdout] | [INFO] [stdout] 179 | let mut cl_vec= clusters_map.get_mut(seed_hash).unwrap(); [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `verbose` [INFO] [stdout] --> src/clustering.rs:192:209 [INFO] [stdout] | [INFO] [stdout] 192 | ...seed_infos_vec: &mut [i32], verbose:bool ){ [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_verbose` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rayon::prelude` [INFO] [stdout] --> src/clustering.rs:5:5 [INFO] [stdout] | [INFO] [stdout] 5 | use rayon::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rayon::prelude` [INFO] [stdout] --> src/seeding_and_filtering_seeds.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use rayon::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rayon::prelude` [INFO] [stdout] --> src/gff_handling.rs:9:5 [INFO] [stdout] | [INFO] [stdout] 9 | use rayon::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `BufRead` [INFO] [stdout] --> src/gff_handling.rs:3:26 [INFO] [stdout] | [INFO] [stdout] 3 | use std::io::{BufReader, BufRead}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rayon::prelude` [INFO] [stdout] --> src/write_output.rs:9:5 [INFO] [stdout] | [INFO] [stdout] 9 | use rayon::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `min_shared_minis` [INFO] [stdout] --> src/clustering.rs:268:90 [INFO] [stdout] | [INFO] [stdout] 268 | ...ap: &mut Seed_Map, min_shared_minis:f64, shared_seed_infos_vec: &mut Vec, verbose: bool){ [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_shared_minis` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `quality_header` is never read [INFO] [stdout] --> src/file_actions.rs:78:9 [INFO] [stdout] | [INFO] [stdout] 78 | quality_header = quality_header.trim().to_owned(); [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] = note: `#[warn(unused_assignments)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `quality_header` is never read [INFO] [stdout] --> src/file_actions.rs:121:9 [INFO] [stdout] | [INFO] [stdout] 121 | quality_header = quality_header.trim().to_owned(); [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seq_len` [INFO] [stdout] --> src/seeding_and_filtering_seeds.rs:349:13 [INFO] [stdout] | [INFO] [stdout] 349 | let seq_len= seq.len(); [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_seq_len` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/clustering.rs:97:17 [INFO] [stdout] | [INFO] [stdout] 97 | let mut shared_perc: f64; [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/clustering.rs:179:17 [INFO] [stdout] | [INFO] [stdout] 179 | let mut cl_vec= clusters_map.get_mut(seed_hash).unwrap(); [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `verbose` [INFO] [stdout] --> src/clustering.rs:192:209 [INFO] [stdout] | [INFO] [stdout] 192 | ...seed_infos_vec: &mut [i32], verbose:bool ){ [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_verbose` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `min_shared_minis` [INFO] [stdout] --> src/clustering.rs:268:90 [INFO] [stdout] | [INFO] [stdout] 268 | ...ap: &mut Seed_Map, min_shared_minis:f64, shared_seed_infos_vec: &mut Vec, verbose: bool){ [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_shared_minis` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/generate_sorted_fastq_for_cluster.rs:116:9 [INFO] [stdout] | [INFO] [stdout] 116 | let mut reader = fastq::Reader::from_file(Path::new(&in_file_path)).expect("We expect the file to exist"); [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `internal_id` is assigned to, but never used [INFO] [stdout] --> src/gff_handling.rs:46:17 [INFO] [stdout] | [INFO] [stdout] 46 | let mut internal_id=0; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_internal_id` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/gff_handling.rs:42:9 [INFO] [stdout] | [INFO] [stdout] 42 | let mut reader = fasta::Reader::from_file(Path::new(path)).expect("We expect the file to exist"); [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/gff_handling.rs:88:13 [INFO] [stdout] | [INFO] [stdout] 88 | let mut rec = record.ok().expect("Error reading record."); [INFO] [stdout] | ----^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `seq_len` [INFO] [stdout] --> src/seeding_and_filtering_seeds.rs:349:13 [INFO] [stdout] | [INFO] [stdout] 349 | let seq_len= seq.len(); [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_seq_len` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `is_gene` is assigned to, but never used [INFO] [stdout] --> src/gff_handling.rs:168:17 [INFO] [stdout] | [INFO] [stdout] 168 | let mut is_gene= false; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_is_gene` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `is_gene` is never read [INFO] [stdout] --> src/gff_handling.rs:178:21 [INFO] [stdout] | [INFO] [stdout] 178 | is_gene = true; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `is_gene` is never read [INFO] [stdout] --> src/gff_handling.rs:214:21 [INFO] [stdout] | [INFO] [stdout] 214 | is_gene = false; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `is_gene` is never read [INFO] [stdout] --> src/gff_handling.rs:224:21 [INFO] [stdout] | [INFO] [stdout] 224 | is_gene = true; [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/write_output.rs:70:21 [INFO] [stdout] | [INFO] [stdout] 70 | let mut id_vec: &mut Vec = cluster_map.get_mut(cluster_id).unwrap(); [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `cl_id` [INFO] [stdout] --> src/write_output.rs:88:10 [INFO] [stdout] | [INFO] [stdout] 88 | for (cl_id, records) in cluster_map.into_iter(){ [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_cl_id` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/generate_sorted_fastq_for_cluster.rs:116:9 [INFO] [stdout] | [INFO] [stdout] 116 | let mut reader = fastq::Reader::from_file(Path::new(&in_file_path)).expect("We expect the file to exist"); [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `internal_id` is assigned to, but never used [INFO] [stdout] --> src/gff_handling.rs:46:17 [INFO] [stdout] | [INFO] [stdout] 46 | let mut internal_id=0; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_internal_id` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/gff_handling.rs:42:9 [INFO] [stdout] | [INFO] [stdout] 42 | let mut reader = fasta::Reader::from_file(Path::new(path)).expect("We expect the file to exist"); [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/gff_handling.rs:88:13 [INFO] [stdout] | [INFO] [stdout] 88 | let mut rec = record.ok().expect("Error reading record."); [INFO] [stdout] | ----^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `is_gene` is assigned to, but never used [INFO] [stdout] --> src/gff_handling.rs:168:17 [INFO] [stdout] | [INFO] [stdout] 168 | let mut is_gene= false; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_is_gene` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `is_gene` is never read [INFO] [stdout] --> src/gff_handling.rs:178:21 [INFO] [stdout] | [INFO] [stdout] 178 | is_gene = true; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `is_gene` is never read [INFO] [stdout] --> src/gff_handling.rs:214:21 [INFO] [stdout] | [INFO] [stdout] 214 | is_gene = false; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `is_gene` is never read [INFO] [stdout] --> src/gff_handling.rs:224:21 [INFO] [stdout] | [INFO] [stdout] 224 | is_gene = true; [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/write_output.rs:70:21 [INFO] [stdout] | [INFO] [stdout] 70 | let mut id_vec: &mut Vec = cluster_map.get_mut(cluster_id).unwrap(); [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `cl_id` [INFO] [stdout] --> src/write_output.rs:88:10 [INFO] [stdout] | [INFO] [stdout] 88 | for (cl_id, records) in cluster_map.into_iter(){ [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_cl_id` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `annotation_based` is assigned to, but never used [INFO] [stdout] --> src/main.rs:313:13 [INFO] [stdout] | [INFO] [stdout] 313 | let mut annotation_based= false; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_annotation_based` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `annotation_based` is never read [INFO] [stdout] --> src/main.rs:326:13 [INFO] [stdout] | [INFO] [stdout] 326 | annotation_based = true; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `now3` [INFO] [stdout] --> src/main.rs:372:17 [INFO] [stdout] | [INFO] [stdout] 372 | let now3 = Instant::now(); [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_now3` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `compute_d` is never used [INFO] [stdout] --> src/main.rs:46:4 [INFO] [stdout] | [INFO] [stdout] 46 | fn compute_d() -> [f64; 128] { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `expected_number_errornous_kmers` is never used [INFO] [stdout] --> src/main.rs:59:4 [INFO] [stdout] | [INFO] [stdout] 59 | fn expected_number_errornous_kmers(quality_string: &str, k: usize, d:&[f64;128]) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_error_rate` is never used [INFO] [stdout] --> src/main.rs:86:4 [INFO] [stdout] | [INFO] [stdout] 86 | fn calculate_error_rate(qual: &str, d_no_min: &[f64; 128]) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `get_sorted_entries` is never used [INFO] [stdout] --> src/main.rs:102:4 [INFO] [stdout] | [INFO] [stdout] 102 | fn get_sorted_entries(mini_map_filtered: FxHashMap>)->Vec<(i32, Vec)>{ [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `filter_fastq_records` is never used [INFO] [stdout] --> src/main.rs:116:4 [INFO] [stdout] | [INFO] [stdout] 116 | fn filter_fastq_records(mut fastq_records:Vec,d_no_min:[f64;128], q_threshold:f64,k:usize,d :[f64;128])->Vec src/main.rs:134:4 [INFO] [stdout] | [INFO] [stdout] 134 | fn convert_cl_id(v: usize) -> Option { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parse_fasta` is never used [INFO] [stdout] --> src/file_actions.rs:9:15 [INFO] [stdout] | [INFO] [stdout] 9 | pub(crate) fn parse_fasta(file_path: &str) -> Result, std::io::Error> { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `new_Fx_hashset` is never used [INFO] [stdout] --> src/clustering.rs:28:4 [INFO] [stdout] | [INFO] [stdout] 28 | fn new_Fx_hashset()->FxHashSet{ [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `detect_whether_shared` is never used [INFO] [stdout] --> src/clustering.rs:33:4 [INFO] [stdout] | [INFO] [stdout] 33 | fn detect_whether_shared(min_shared_minis:f64, shared_seed_infos: &FxHashMap, minimizers: &[Minimizer_hashed]) -> (bool, i32) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `cow_to_string` is never used [INFO] [stdout] --> src/seeding_and_filtering_seeds.rs:34:4 [INFO] [stdout] | [INFO] [stdout] 34 | fn cow_to_string(cow: Cow<'_, [u8]>) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `get_canonical_kmer_minimizers_hashed` is never used [INFO] [stdout] --> src/seeding_and_filtering_seeds.rs:43:8 [INFO] [stdout] | [INFO] [stdout] 43 | pub fn get_canonical_kmer_minimizers_hashed(seq: &[u8], k_size: usize, w_size: usize, this_minimizers: &mut Vec) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `get_kmer_minimizers_hashed` is never used [INFO] [stdout] --> src/seeding_and_filtering_seeds.rs:138:8 [INFO] [stdout] | [INFO] [stdout] 138 | pub fn get_kmer_minimizers_hashed(seq: &[u8], k_size: usize, w_size: usize, this_minimizers: &mut Vec) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `average` is never used [INFO] [stdout] --> src/seeding_and_filtering_seeds.rs:277:4 [INFO] [stdout] | [INFO] [stdout] 277 | fn average(numbers: &[f64]) -> f64 { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `expected_number_errornous_kmers` is never used [INFO] [stdout] --> src/generate_sorted_fastq_for_cluster.rs:34:4 [INFO] [stdout] | [INFO] [stdout] 34 | fn expected_number_errornous_kmers(quality_string: &str, k: usize, d:&[f64;128]) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `compute_d` is never used [INFO] [stdout] --> src/generate_sorted_fastq_for_cluster.rs:82:4 [INFO] [stdout] | [INFO] [stdout] 82 | fn compute_d() -> [f64; 128] { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `print_statistics` is never used [INFO] [stdout] --> src/generate_sorted_fastq_for_cluster.rs:195:4 [INFO] [stdout] | [INFO] [stdout] 195 | fn print_statistics(fastq_records: &[FastqRecord_isoncl_init]){ [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `detect_overlaps` is never used [INFO] [stdout] --> src/gff_handling.rs:23:4 [INFO] [stdout] | [INFO] [stdout] 23 | fn detect_overlaps(gene_map: &FxHashMap>, this_gene_id:&i32, this_coords: &Vec, overlap_ctr: &mut i32){ [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parse_fasta_and_gen_clusters` is never used [INFO] [stdout] --> src/gff_handling.rs:39:4 [INFO] [stdout] | [INFO] [stdout] 39 | fn parse_fasta_and_gen_clusters(fasta_path: Option<&str>, coords: FxHashMap>>, clusters: &mut Cluster... [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parse_gtf_and_collect_coords` is never used [INFO] [stdout] --> src/gff_handling.rs:82:4 [INFO] [stdout] | [INFO] [stdout] 82 | fn parse_gtf_and_collect_coords(gtf_path: Option<&str>, coords:&mut FxHashMap>>){ [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `resolve_gff` is never used [INFO] [stdout] --> src/gff_handling.rs:134:15 [INFO] [stdout] | [INFO] [stdout] 134 | pub(crate) fn resolve_gff(gff_path: Option<&str>, fasta_path: Option<&str>,clusters: &mut Cluster_ID_Map, cluster_map: &mut Seed_Map,k:us... [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: enum `Cluster` is never used [INFO] [stdout] --> src/structs.rs:4:10 [INFO] [stdout] | [INFO] [stdout] 4 | pub enum Cluster { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `Minimizer` is never constructed [INFO] [stdout] --> src/structs.rs:13:12 [INFO] [stdout] | [INFO] [stdout] 13 | pub struct Minimizer { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `GtfEntry` is never constructed [INFO] [stdout] --> src/structs.rs:29:19 [INFO] [stdout] | [INFO] [stdout] 29 | pub(crate) struct GtfEntry { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `Coord_obj` is never constructed [INFO] [stdout] --> src/structs.rs:48:19 [INFO] [stdout] | [INFO] [stdout] 48 | pub(crate) struct Coord_obj{ [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `overlaps_with` is never used [INFO] [stdout] --> src/structs.rs:59:12 [INFO] [stdout] | [INFO] [stdout] 58 | impl Coord_obj{ [INFO] [stdout] | -------------- method in this implementation [INFO] [stdout] 59 | pub fn overlaps_with(&self,other:&Coord_obj)-> bool{ [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `FastaRecord` is never constructed [INFO] [stdout] --> src/structs.rs:73:19 [INFO] [stdout] | [INFO] [stdout] 73 | pub(crate) struct FastaRecord { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `FastqRecord` is never constructed [INFO] [stdout] --> src/structs.rs:88:19 [INFO] [stdout] | [INFO] [stdout] 88 | pub(crate) struct FastqRecord { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `score` and `error_rate` are never read [INFO] [stdout] --> src/structs.rs:108:9 [INFO] [stdout] | [INFO] [stdout] 103 | pub(crate) struct FastqRecord_isoncl_init { [INFO] [stdout] | ----------------------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 108 | pub score: f64, [INFO] [stdout] | ^^^^^ [INFO] [stdout] 109 | pub error_rate:f64, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `internal_gff` is never constructed [INFO] [stdout] --> src/structs.rs:111:19 [INFO] [stdout] | [INFO] [stdout] 111 | pub(crate) struct internal_gff { [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `get_err_rate`, `set_error_rate`, and `set_score` are never used [INFO] [stdout] --> src/structs.rs:132:12 [INFO] [stdout] | [INFO] [stdout] 118 | impl FastqRecord_isoncl_init{ [INFO] [stdout] | ---------------------------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 132 | pub fn get_err_rate(&self)->&f64{&self.error_rate} [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 133 | pub fn set_error_rate(&mut self, new_error_rate: f64){ self.error_rate = new_error_rate } [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] 134 | pub fn set_score(&mut self, new_score: f64) { self.score = new_score } [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: module `Parallelization_side` should have a snake case name [INFO] [stdout] --> src/main.rs:18:5 [INFO] [stdout] | [INFO] [stdout] 18 | mod Parallelization_side; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ help: convert the identifier to snake case: `parallelization_side` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_snake_case)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `new_Fx_hashset` should have a snake case name [INFO] [stdout] --> src/clustering.rs:28:4 [INFO] [stdout] | [INFO] [stdout] 28 | fn new_Fx_hashset()->FxHashSet{ [INFO] [stdout] | ^^^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): `new_fx_hashset` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `annotation_based` is assigned to, but never used [INFO] [stdout] --> src/main.rs:313:13 [INFO] [stdout] | [INFO] [stdout] 313 | let mut annotation_based= false; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_annotation_based` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `annotation_based` is never read [INFO] [stdout] --> src/main.rs:326:13 [INFO] [stdout] | [INFO] [stdout] 326 | annotation_based = true; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `now3` [INFO] [stdout] --> src/main.rs:372:17 [INFO] [stdout] | [INFO] [stdout] 372 | let now3 = Instant::now(); [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_now3` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `compute_d` is never used [INFO] [stdout] --> src/main.rs:46:4 [INFO] [stdout] | [INFO] [stdout] 46 | fn compute_d() -> [f64; 128] { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `expected_number_errornous_kmers` is never used [INFO] [stdout] --> src/main.rs:59:4 [INFO] [stdout] | [INFO] [stdout] 59 | fn expected_number_errornous_kmers(quality_string: &str, k: usize, d:&[f64;128]) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_error_rate` is never used [INFO] [stdout] --> src/main.rs:86:4 [INFO] [stdout] | [INFO] [stdout] 86 | fn calculate_error_rate(qual: &str, d_no_min: &[f64; 128]) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `get_sorted_entries` is never used [INFO] [stdout] --> src/main.rs:102:4 [INFO] [stdout] | [INFO] [stdout] 102 | fn get_sorted_entries(mini_map_filtered: FxHashMap>)->Vec<(i32, Vec)>{ [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `filter_fastq_records` is never used [INFO] [stdout] --> src/main.rs:116:4 [INFO] [stdout] | [INFO] [stdout] 116 | fn filter_fastq_records(mut fastq_records:Vec,d_no_min:[f64;128], q_threshold:f64,k:usize,d :[f64;128])->Vec src/main.rs:134:4 [INFO] [stdout] | [INFO] [stdout] 134 | fn convert_cl_id(v: usize) -> Option { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parse_fasta` is never used [INFO] [stdout] --> src/file_actions.rs:9:15 [INFO] [stdout] | [INFO] [stdout] 9 | pub(crate) fn parse_fasta(file_path: &str) -> Result, std::io::Error> { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `new_Fx_hashset` is never used [INFO] [stdout] --> src/clustering.rs:28:4 [INFO] [stdout] | [INFO] [stdout] 28 | fn new_Fx_hashset()->FxHashSet{ [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `detect_whether_shared` is never used [INFO] [stdout] --> src/clustering.rs:33:4 [INFO] [stdout] | [INFO] [stdout] 33 | fn detect_whether_shared(min_shared_minis:f64, shared_seed_infos: &FxHashMap, minimizers: &[Minimizer_hashed]) -> (bool, i32) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `cow_to_string` is never used [INFO] [stdout] --> src/seeding_and_filtering_seeds.rs:34:4 [INFO] [stdout] | [INFO] [stdout] 34 | fn cow_to_string(cow: Cow<'_, [u8]>) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `get_canonical_kmer_minimizers_hashed` is never used [INFO] [stdout] --> src/seeding_and_filtering_seeds.rs:43:8 [INFO] [stdout] | [INFO] [stdout] 43 | pub fn get_canonical_kmer_minimizers_hashed(seq: &[u8], k_size: usize, w_size: usize, this_minimizers: &mut Vec) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `get_kmer_minimizers_hashed` is never used [INFO] [stdout] --> src/seeding_and_filtering_seeds.rs:138:8 [INFO] [stdout] | [INFO] [stdout] 138 | pub fn get_kmer_minimizers_hashed(seq: &[u8], k_size: usize, w_size: usize, this_minimizers: &mut Vec) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `average` is never used [INFO] [stdout] --> src/seeding_and_filtering_seeds.rs:277:4 [INFO] [stdout] | [INFO] [stdout] 277 | fn average(numbers: &[f64]) -> f64 { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `expected_number_errornous_kmers` is never used [INFO] [stdout] --> src/generate_sorted_fastq_for_cluster.rs:34:4 [INFO] [stdout] | [INFO] [stdout] 34 | fn expected_number_errornous_kmers(quality_string: &str, k: usize, d:&[f64;128]) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `compute_d` is never used [INFO] [stdout] --> src/generate_sorted_fastq_for_cluster.rs:82:4 [INFO] [stdout] | [INFO] [stdout] 82 | fn compute_d() -> [f64; 128] { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `print_statistics` is never used [INFO] [stdout] --> src/generate_sorted_fastq_for_cluster.rs:195:4 [INFO] [stdout] | [INFO] [stdout] 195 | fn print_statistics(fastq_records: &[FastqRecord_isoncl_init]){ [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `detect_overlaps` is never used [INFO] [stdout] --> src/gff_handling.rs:23:4 [INFO] [stdout] | [INFO] [stdout] 23 | fn detect_overlaps(gene_map: &FxHashMap>, this_gene_id:&i32, this_coords: &Vec, overlap_ctr: &mut i32){ [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parse_fasta_and_gen_clusters` is never used [INFO] [stdout] --> src/gff_handling.rs:39:4 [INFO] [stdout] | [INFO] [stdout] 39 | fn parse_fasta_and_gen_clusters(fasta_path: Option<&str>, coords: FxHashMap>>, clusters: &mut Cluster... [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parse_gtf_and_collect_coords` is never used [INFO] [stdout] --> src/gff_handling.rs:82:4 [INFO] [stdout] | [INFO] [stdout] 82 | fn parse_gtf_and_collect_coords(gtf_path: Option<&str>, coords:&mut FxHashMap>>){ [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `resolve_gff` is never used [INFO] [stdout] --> src/gff_handling.rs:134:15 [INFO] [stdout] | [INFO] [stdout] 134 | pub(crate) fn resolve_gff(gff_path: Option<&str>, fasta_path: Option<&str>,clusters: &mut Cluster_ID_Map, cluster_map: &mut Seed_Map,k:us... [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: enum `Cluster` is never used [INFO] [stdout] --> src/structs.rs:4:10 [INFO] [stdout] | [INFO] [stdout] 4 | pub enum Cluster { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `Minimizer` is never constructed [INFO] [stdout] --> src/structs.rs:13:12 [INFO] [stdout] | [INFO] [stdout] 13 | pub struct Minimizer { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `GtfEntry` is never constructed [INFO] [stdout] --> src/structs.rs:29:19 [INFO] [stdout] | [INFO] [stdout] 29 | pub(crate) struct GtfEntry { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `Coord_obj` is never constructed [INFO] [stdout] --> src/structs.rs:48:19 [INFO] [stdout] | [INFO] [stdout] 48 | pub(crate) struct Coord_obj{ [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `overlaps_with` is never used [INFO] [stdout] --> src/structs.rs:59:12 [INFO] [stdout] | [INFO] [stdout] 58 | impl Coord_obj{ [INFO] [stdout] | -------------- method in this implementation [INFO] [stdout] 59 | pub fn overlaps_with(&self,other:&Coord_obj)-> bool{ [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `FastaRecord` is never constructed [INFO] [stdout] --> src/structs.rs:73:19 [INFO] [stdout] | [INFO] [stdout] 73 | pub(crate) struct FastaRecord { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `FastqRecord` is never constructed [INFO] [stdout] --> src/structs.rs:88:19 [INFO] [stdout] | [INFO] [stdout] 88 | pub(crate) struct FastqRecord { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `score` and `error_rate` are never read [INFO] [stdout] --> src/structs.rs:108:9 [INFO] [stdout] | [INFO] [stdout] 103 | pub(crate) struct FastqRecord_isoncl_init { [INFO] [stdout] | ----------------------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 108 | pub score: f64, [INFO] [stdout] | ^^^^^ [INFO] [stdout] 109 | pub error_rate:f64, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `internal_gff` is never constructed [INFO] [stdout] --> src/structs.rs:111:19 [INFO] [stdout] | [INFO] [stdout] 111 | pub(crate) struct internal_gff { [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `get_err_rate`, `set_error_rate`, and `set_score` are never used [INFO] [stdout] --> src/structs.rs:132:12 [INFO] [stdout] | [INFO] [stdout] 118 | impl FastqRecord_isoncl_init{ [INFO] [stdout] | ---------------------------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 132 | pub fn get_err_rate(&self)->&f64{&self.error_rate} [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 133 | pub fn set_error_rate(&mut self, new_error_rate: f64){ self.error_rate = new_error_rate } [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] 134 | pub fn set_score(&mut self, new_score: f64) { self.score = new_score } [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: module `Parallelization_side` should have a snake case name [INFO] [stdout] --> src/main.rs:18:5 [INFO] [stdout] | [INFO] [stdout] 18 | mod Parallelization_side; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ help: convert the identifier to snake case: `parallelization_side` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_snake_case)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `new_Fx_hashset` should have a snake case name [INFO] [stdout] --> src/clustering.rs:28:4 [INFO] [stdout] | [INFO] [stdout] 28 | fn new_Fx_hashset()->FxHashSet{ [INFO] [stdout] | ^^^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): `new_fx_hashset` [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 40.45s [INFO] running `Command { std: "docker" "inspect" "e8c467e10319c54b8a347ea2e68fa33bbd2e9c5c690555698466890a559e83b4", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "e8c467e10319c54b8a347ea2e68fa33bbd2e9c5c690555698466890a559e83b4", kill_on_drop: false }` [INFO] [stdout] e8c467e10319c54b8a347ea2e68fa33bbd2e9c5c690555698466890a559e83b4