[INFO] cloning repository https://github.com/SorenHeidelbach/rustymotif [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/SorenHeidelbach/rustymotif" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FSorenHeidelbach%2Frustymotif", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FSorenHeidelbach%2Frustymotif'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] c6d71f49c1f683cc86f0d9967026db610f02ba20 [INFO] checking SorenHeidelbach/rustymotif against master#4068bafedd8ba724e332a5221c06a6fa531a30d2 for pr-146978 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FSorenHeidelbach%2Frustymotif" "/workspace/builds/worker-7-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-7-tc1/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/SorenHeidelbach/rustymotif [INFO] finished tweaking git repo https://github.com/SorenHeidelbach/rustymotif [INFO] tweaked toml for git repo https://github.com/SorenHeidelbach/rustymotif written to /workspace/builds/worker-7-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/SorenHeidelbach/rustymotif on toolchain 4068bafedd8ba724e332a5221c06a6fa531a30d2 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+4068bafedd8ba724e332a5221c06a6fa531a30d2" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/SorenHeidelbach/rustymotif 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" "+4068bafedd8ba724e332a5221c06a6fa531a30d2" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... 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"/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+4068bafedd8ba724e332a5221c06a6fa531a30d2" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 93650d59246b1cdbfb9ca5cfa4850c628e9d4111dc094f33cc3c62f9f02bf159 [INFO] running `Command { std: "docker" "start" "-a" 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"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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+4068bafedd8ba724e332a5221c06a6fa531a30d2" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 653b085024fee0ca393289720dae512532fe88ef5d53f91ba088a131388bb6c0 [INFO] running `Command { std: "docker" "start" "-a" "653b085024fee0ca393289720dae512532fe88ef5d53f91ba088a131388bb6c0", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.93 [INFO] [stderr] Compiling libc v0.2.169 [INFO] [stderr] Compiling target-lexicon v0.13.2 [INFO] [stderr] Compiling glob v0.3.2 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling 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[INFO] [stderr] Checking multimap v0.10.0 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking bv v0.11.1 [INFO] [stderr] Checking csv v1.3.1 [INFO] [stderr] Checking serde_json v1.0.140 [INFO] [stderr] Checking seq_io v0.3.4 [INFO] [stderr] Checking statrs v0.18.0 [INFO] [stderr] Checking bio v2.3.0 [INFO] [stderr] Checking rust-htslib v0.49.0 [INFO] [stderr] Checking rustymotif v0.3.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused imports: `SerializeStruct` and `Serialize` [INFO] [stdout] --> src/lib/motif.rs:3:18 [INFO] [stdout] | [INFO] [stdout] 3 | use serde::ser::{Serialize, Serializer, SerializeStruct}; [INFO] [stdout] | ^^^^^^^^^ ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ToString` [INFO] [stdout] --> src/lib/pileup.rs:6:30 [INFO] [stdout] | [INFO] [stdout] 6 | use strum_macros::{EnumIter, ToString}; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `debug`, `info`, and `warn` [INFO] [stdout] --> src/lib/pileup.rs:9:11 [INFO] [stdout] | [INFO] [stdout] 9 | use log::{debug, info, warn}; [INFO] [stdout] | ^^^^^ ^^^^ ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `motif::Motif` [INFO] [stdout] --> src/lib/preprocess.rs:3:31 [INFO] [stdout] | [INFO] [stdout] 3 | use crate::{modtype::ModType, motif::Motif, pileup, strand::Strand}; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `debug` [INFO] [stdout] --> src/lib/preprocess.rs:5:11 [INFO] [stdout] | [INFO] [stdout] 5 | use log::{debug, info, warn}; [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `PyList` [INFO] [stdout] --> src/lib/preprocess.rs:9:27 [INFO] [stdout] | [INFO] [stdout] 9 | use pyo3::types::{PyDict, PyList}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `SerializeStruct` and `Serialize` [INFO] [stdout] --> src/lib/motif.rs:3:18 [INFO] [stdout] | [INFO] [stdout] 3 | use serde::ser::{Serialize, Serializer, SerializeStruct}; [INFO] [stdout] | ^^^^^^^^^ ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ToString` [INFO] [stdout] --> src/lib/pileup.rs:6:30 [INFO] [stdout] | [INFO] [stdout] 6 | use strum_macros::{EnumIter, ToString}; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `debug`, `info`, and `warn` [INFO] [stdout] --> src/lib/pileup.rs:9:11 [INFO] [stdout] | [INFO] [stdout] 9 | use log::{debug, info, warn}; [INFO] [stdout] | ^^^^^ ^^^^ ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `motif::Motif` [INFO] [stdout] --> src/lib/preprocess.rs:3:31 [INFO] [stdout] | [INFO] [stdout] 3 | use crate::{modtype::ModType, motif::Motif, pileup, strand::Strand}; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `debug` [INFO] [stdout] --> src/lib/preprocess.rs:5:11 [INFO] [stdout] | [INFO] [stdout] 5 | use log::{debug, info, warn}; [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `PyList` [INFO] [stdout] --> src/lib/preprocess.rs:9:27 [INFO] [stdout] | [INFO] [stdout] 9 | use pyo3::types::{PyDict, PyList}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `strum::IntoEnumIterator` [INFO] [stdout] --> src/lib/iupac.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use strum::IntoEnumIterator; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `strum::IntoEnumIterator` [INFO] [stdout] --> src/lib/iupac.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use strum::IntoEnumIterator; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `e` [INFO] [stdout] --> src/lib/pileup.rs:400:21 [INFO] [stdout] | [INFO] [stdout] 400 | Err(e) => continue, // Skip invalid records [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_e` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `line_to_byterecord` is never used [INFO] [stdout] --> src/lib/pileup.rs:532:4 [INFO] [stdout] | [INFO] [stdout] 532 | fn line_to_byterecord(line: &[u8]) -> ByteRecord { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `e` [INFO] [stdout] --> src/lib/pileup.rs:400:21 [INFO] [stdout] | [INFO] [stdout] 400 | Err(e) => continue, // Skip invalid records [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_e` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `line_to_byterecord` is never used [INFO] [stdout] --> src/lib/pileup.rs:532:4 [INFO] [stdout] | [INFO] [stdout] 532 | fn line_to_byterecord(line: &[u8]) -> ByteRecord { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ValueEnum` [INFO] [stdout] --> src/bin/preprocess/cli.rs:2:20 [INFO] [stdout] | [INFO] [stdout] 2 | use clap::{Parser, ValueEnum}; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs` [INFO] [stdout] --> src/bin/preprocess/io.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use std::fs; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `motif::Motif` [INFO] [stdout] --> src/bin/preprocess/io.rs:7:24 [INFO] [stdout] | [INFO] [stdout] 7 | use rustymotif_utils::{motif::Motif, pileup::PileupRecord}; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io` [INFO] [stdout] --> src/bin/preprocess/io.rs:11:5 [INFO] [stdout] | [INFO] [stdout] 11 | use std::io; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ValueEnum` [INFO] [stdout] --> src/bin/preprocess/cli.rs:2:20 [INFO] [stdout] | [INFO] [stdout] 2 | use clap::{Parser, ValueEnum}; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs` [INFO] [stdout] --> src/bin/preprocess/io.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use std::fs; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `motif::Motif` [INFO] [stdout] --> src/bin/preprocess/io.rs:7:24 [INFO] [stdout] | [INFO] [stdout] 7 | use rustymotif_utils::{motif::Motif, pileup::PileupRecord}; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io` [INFO] [stdout] --> src/bin/preprocess/io.rs:11:5 [INFO] [stdout] | [INFO] [stdout] 11 | use std::io; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `debug` and `warn` [INFO] [stdout] --> src/bin/motif_summary/main.rs:3:17 [INFO] [stdout] | [INFO] [stdout] 3 | use log::{info, debug, warn}; [INFO] [stdout] | ^^^^^ ^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `verbose` should have an upper camel case name [INFO] [stdout] --> src/bin/motif_summary/cli.rs:75:5 [INFO] [stdout] | [INFO] [stdout] 75 | verbose, [INFO] [stdout] | ^^^^^^^ help: convert the identifier to upper camel case (notice the capitalization): `Verbose` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_camel_case_types)]` (part of `#[warn(nonstandard_style)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `normal` should have an upper camel case name [INFO] [stdout] --> src/bin/motif_summary/cli.rs:76:5 [INFO] [stdout] | [INFO] [stdout] 76 | normal, [INFO] [stdout] | ^^^^^^ help: convert the identifier to upper camel case: `Normal` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `silent` should have an upper camel case name [INFO] [stdout] --> src/bin/motif_summary/cli.rs:77:5 [INFO] [stdout] | [INFO] [stdout] 77 | silent, [INFO] [stdout] | ^^^^^^ help: convert the identifier to upper camel case (notice the capitalization): `Silent` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `pileup` [INFO] [stdout] --> src/bin/motif_summary/data.rs:5:56 [INFO] [stdout] | [INFO] [stdout] 5 | use rustymotif_utils::{modtype::ModType, motif::Motif, pileup, strand::Strand}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `info` [INFO] [stdout] --> src/bin/motif_summary/data.rs:6:18 [INFO] [stdout] | [INFO] [stdout] 6 | use log::{debug, info}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `anyhow` [INFO] [stdout] --> src/bin/motif_summary/data.rs:7:14 [INFO] [stdout] | [INFO] [stdout] 7 | use anyhow::{anyhow, Ok}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::sequence::Contig` [INFO] [stdout] --> src/bin/motif_summary/fasta_reader.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use crate::sequence::Contig; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashSet` [INFO] [stdout] --> src/bin/motif_summary/sequence.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use std::collections::HashSet; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `anyhow::anyhow` [INFO] [stdout] --> src/bin/motif_summary/sequence.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use anyhow::anyhow; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs` [INFO] [stdout] --> src/bin/motif_summary/io.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use std::fs; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `debug`, `info`, and `warn` [INFO] [stdout] --> src/bin/motif_summary/io.rs:9:11 [INFO] [stdout] | [INFO] [stdout] 9 | use log::{info, debug, warn}; [INFO] [stdout] | ^^^^ ^^^^^ ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `WriterBuilder` [INFO] [stdout] --> src/bin/motif_summary/motif_summary.rs:10:11 [INFO] [stdout] | [INFO] [stdout] 10 | use csv::{WriterBuilder}; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `verbose` should have an upper camel case name [INFO] [stdout] --> src/bin/rustymotif/cli.rs:81:5 [INFO] [stdout] | [INFO] [stdout] 81 | verbose, [INFO] [stdout] | ^^^^^^^ help: convert the identifier to upper camel case (notice the capitalization): `Verbose` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_camel_case_types)]` (part of `#[warn(nonstandard_style)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `normal` should have an upper camel case name [INFO] [stdout] --> src/bin/rustymotif/cli.rs:82:5 [INFO] [stdout] | [INFO] [stdout] 82 | normal, [INFO] [stdout] | ^^^^^^ help: convert the identifier to upper camel case: `Normal` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `silent` should have an upper camel case name [INFO] [stdout] --> src/bin/rustymotif/cli.rs:83:5 [INFO] [stdout] | [INFO] [stdout] 83 | silent, [INFO] [stdout] | ^^^^^^ help: convert the identifier to upper camel case (notice the capitalization): `Silent` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::sequence::MethylationThresholds` [INFO] [stdout] --> src/bin/rustymotif/data.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use crate::sequence::MethylationThresholds; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashSet` [INFO] [stdout] --> src/bin/rustymotif/data.rs:5:5 [INFO] [stdout] | [INFO] [stdout] 5 | use std::collections::HashSet; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::sequence::Contig` [INFO] [stdout] --> src/bin/rustymotif/fasta_reader.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use crate::sequence::Contig; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::sequence::MethylationThresholds` [INFO] [stdout] --> src/bin/rustymotif/fasta_reader.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use crate::sequence::MethylationThresholds; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bail` [INFO] [stdout] --> src/bin/rustymotif/motif_discovery.rs:2:14 [INFO] [stdout] | [INFO] [stdout] 2 | use anyhow::{bail, Result}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bio::bio_types::annot::contig` [INFO] [stdout] --> src/bin/rustymotif/motif_discovery.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use bio::bio_types::annot::contig; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `motif::MotifLike`, `motif`, and `strand::Strand` [INFO] [stdout] --> src/bin/rustymotif/motif_discovery.rs:6:24 [INFO] [stdout] | [INFO] [stdout] 6 | use rustymotif_utils::{motif, motif::MotifLike, pileup, strand::Strand}; [INFO] [stdout] | ^^^^^ ^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `collections::HashSet` and `hash::Hash` [INFO] [stdout] --> src/bin/rustymotif/search.rs:1:11 [INFO] [stdout] | [INFO] [stdout] 1 | use std::{collections::HashSet, hash::Hash}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bio::bio_types::annot::contig` [INFO] [stdout] --> src/bin/rustymotif/search.rs:9:5 [INFO] [stdout] | [INFO] [stdout] 9 | use bio::bio_types::annot::contig; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ordered_float::OrderedFloat` [INFO] [stdout] --> src/bin/rustymotif/search.rs:12:5 [INFO] [stdout] | [INFO] [stdout] 12 | use ordered_float::OrderedFloat; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `algo::min_spanning_tree` [INFO] [stdout] --> src/bin/rustymotif/search.rs:14:5 [INFO] [stdout] | [INFO] [stdout] 14 | algo::min_spanning_tree, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `pileup` [INFO] [stdout] --> src/bin/rustymotif/search.rs:20:80 [INFO] [stdout] | [INFO] [stdout] 20 | iupac::IupacBase, modtype::ModType, motif, motif::Motif, motif::MotifLike, pileup, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Deserialize` [INFO] [stdout] --> src/bin/rustymotif/search.rs:23:13 [INFO] [stdout] | [INFO] [stdout] 23 | use serde::{Deserialize, Serialize}; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `anyhow::anyhow` [INFO] [stdout] --> src/bin/rustymotif/sequence.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use anyhow::anyhow; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ValueEnum` [INFO] [stdout] --> src/bin/mixedmotif/cli.rs:2:20 [INFO] [stdout] | [INFO] [stdout] 2 | use clap::{Parser, ValueEnum}; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::sequence::MethylationThresholds` [INFO] [stdout] --> src/bin/mixedmotif/data.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use crate::sequence::MethylationThresholds; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::sequence::Contig` [INFO] [stdout] --> src/bin/mixedmotif/fasta_reader.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use crate::sequence::Contig; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `score_motifs` [INFO] [stdout] --> src/bin/mixedmotif/motif_discovery.rs:1:56 [INFO] [stdout] | [INFO] [stdout] 1 | use crate::{cli, data, fasta_reader, search, sequence, score_motifs}; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bail` [INFO] [stdout] --> src/bin/mixedmotif/motif_discovery.rs:2:14 [INFO] [stdout] | [INFO] [stdout] 2 | use anyhow::{bail, Result}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bio::bio_types::annot::contig` [INFO] [stdout] --> src/bin/mixedmotif/motif_discovery.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use bio::bio_types::annot::contig; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `itertools::concat` [INFO] [stdout] --> src/bin/mixedmotif/motif_discovery.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use itertools::concat; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `motif::MotifLike`, `motif`, and `strand::Strand` [INFO] [stdout] --> src/bin/mixedmotif/motif_discovery.rs:7:24 [INFO] [stdout] | [INFO] [stdout] 7 | use rustymotif_utils::{motif, motif::MotifLike, pileup, strand::Strand}; [INFO] [stdout] | ^^^^^ ^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::search::MotifNode` [INFO] [stdout] --> src/bin/mixedmotif/sequence.rs:5:5 [INFO] [stdout] | [INFO] [stdout] 5 | use crate::search::MotifNode; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `anyhow::anyhow` [INFO] [stdout] --> src/bin/mixedmotif/sequence.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | use anyhow::anyhow; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bio::io::fasta` [INFO] [stdout] --> src/bin/mixedmotif/sequence.rs:10:5 [INFO] [stdout] | [INFO] [stdout] 10 | use bio::io::fasta; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `hash::Hash` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:1:43 [INFO] [stdout] | [INFO] [stdout] 1 | use std::{collections::HashSet, fs::File, hash::Hash}; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `BetaBernoulliModel`, `EqualLengthDNASet`, and `fit_true_beta_model_em` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:5:9 [INFO] [stdout] | [INFO] [stdout] 5 | fit_true_beta_model_em, Beta, BetaBernoulliModel, BetaMixture [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] 6 | }, [INFO] [stdout] 7 | sequence::{Contig, EqualLengthDNASet}, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `HashMap` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:9:13 [INFO] [stdout] | [INFO] [stdout] 9 | use ahash::{HashMap, HashMapExt}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `strum_macros::EnumIter` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:12:5 [INFO] [stdout] | [INFO] [stdout] 12 | use strum_macros::EnumIter; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `info` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:14:18 [INFO] [stdout] | [INFO] [stdout] 14 | use log::{debug, info}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ordered_float::OrderedFloat` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:15:5 [INFO] [stdout] | [INFO] [stdout] 15 | use ordered_float::OrderedFloat; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Direction`, `Graph`, `NodeIndex`, and `algo::min_spanning_tree` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:17:5 [INFO] [stdout] | [INFO] [stdout] 17 | algo::min_spanning_tree, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] 18 | graph::{Graph, NodeIndex}, [INFO] [stdout] | ^^^^^ ^^^^^^^^^ [INFO] [stdout] 19 | Direction, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `cmp::Ordering` and `collections::BinaryHeap` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:21:11 [INFO] [stdout] | [INFO] [stdout] 21 | use std::{cmp::Ordering, collections::BinaryHeap}; [INFO] [stdout] | ^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `IupacBase`, `MotifLike`, `modtype::ModType`, `pileup`, `self`, `self`, and `strand::Strand` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:23:13 [INFO] [stdout] | [INFO] [stdout] 23 | iupac::{self, IupacBase}, modtype::ModType, motif::{self, Motif, MotifLike}, pileup, [INFO] [stdout] | ^^^^ ^^^^^^^^^ ^^^^^^^^^^^^^^^^ ^^^^ ^^^^^^^^^ ^^^^^^ [INFO] [stdout] 24 | strand::Strand, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Deserialize` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:26:13 [INFO] [stdout] | [INFO] [stdout] 26 | use serde::{Deserialize, Serialize}; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `debug` and `warn` [INFO] [stdout] --> src/bin/motif_summary/main.rs:3:17 [INFO] [stdout] | [INFO] [stdout] 3 | use log::{info, debug, warn}; [INFO] [stdout] | ^^^^^ ^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `verbose` should have an upper camel case name [INFO] [stdout] --> src/bin/motif_summary/cli.rs:75:5 [INFO] [stdout] | [INFO] [stdout] 75 | verbose, [INFO] [stdout] | ^^^^^^^ help: convert the identifier to upper camel case (notice the capitalization): `Verbose` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_camel_case_types)]` (part of `#[warn(nonstandard_style)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `normal` should have an upper camel case name [INFO] [stdout] --> src/bin/motif_summary/cli.rs:76:5 [INFO] [stdout] | [INFO] [stdout] 76 | normal, [INFO] [stdout] | ^^^^^^ help: convert the identifier to upper camel case: `Normal` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `silent` should have an upper camel case name [INFO] [stdout] --> src/bin/motif_summary/cli.rs:77:5 [INFO] [stdout] | [INFO] [stdout] 77 | silent, [INFO] [stdout] | ^^^^^^ help: convert the identifier to upper camel case (notice the capitalization): `Silent` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `pileup` [INFO] [stdout] --> src/bin/motif_summary/data.rs:5:56 [INFO] [stdout] | [INFO] [stdout] 5 | use rustymotif_utils::{modtype::ModType, motif::Motif, pileup, strand::Strand}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `info` [INFO] [stdout] --> src/bin/motif_summary/data.rs:6:18 [INFO] [stdout] | [INFO] [stdout] 6 | use log::{debug, info}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `anyhow` [INFO] [stdout] --> src/bin/motif_summary/data.rs:7:14 [INFO] [stdout] | [INFO] [stdout] 7 | use anyhow::{anyhow, Ok}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::sequence::Contig` [INFO] [stdout] --> src/bin/motif_summary/fasta_reader.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use crate::sequence::Contig; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashSet` [INFO] [stdout] --> src/bin/motif_summary/sequence.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use std::collections::HashSet; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `anyhow::anyhow` [INFO] [stdout] --> src/bin/motif_summary/sequence.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use anyhow::anyhow; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bio::bio_types::annot::contig` [INFO] [stdout] --> src/bin/motif_summary/sequence.rs:320:9 [INFO] [stdout] | [INFO] [stdout] 320 | use bio::bio_types::annot::contig; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `debug`, `info`, and `warn` [INFO] [stdout] --> src/bin/motif_summary/io.rs:9:11 [INFO] [stdout] | [INFO] [stdout] 9 | use log::{info, debug, warn}; [INFO] [stdout] | ^^^^ ^^^^^ ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs::File` [INFO] [stdout] --> src/bin/motif_summary/io.rs:234:9 [INFO] [stdout] | [INFO] [stdout] 234 | use std::fs::File; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashMap` [INFO] [stdout] --> src/bin/motif_summary/io.rs:237:9 [INFO] [stdout] | [INFO] [stdout] 237 | use std::collections::HashMap; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `WriterBuilder` [INFO] [stdout] --> src/bin/motif_summary/motif_summary.rs:10:11 [INFO] [stdout] | [INFO] [stdout] 10 | use csv::{WriterBuilder}; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `verbose` should have an upper camel case name [INFO] [stdout] --> src/bin/rustymotif/cli.rs:81:5 [INFO] [stdout] | [INFO] [stdout] 81 | verbose, [INFO] [stdout] | ^^^^^^^ help: convert the identifier to upper camel case (notice the capitalization): `Verbose` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_camel_case_types)]` (part of `#[warn(nonstandard_style)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `normal` should have an upper camel case name [INFO] [stdout] --> src/bin/rustymotif/cli.rs:82:5 [INFO] [stdout] | [INFO] [stdout] 82 | normal, [INFO] [stdout] | ^^^^^^ help: convert the identifier to upper camel case: `Normal` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `silent` should have an upper camel case name [INFO] [stdout] --> src/bin/rustymotif/cli.rs:83:5 [INFO] [stdout] | [INFO] [stdout] 83 | silent, [INFO] [stdout] | ^^^^^^ help: convert the identifier to upper camel case (notice the capitalization): `Silent` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashSet` [INFO] [stdout] --> src/bin/rustymotif/data.rs:5:5 [INFO] [stdout] | [INFO] [stdout] 5 | use std::collections::HashSet; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `MethylationLevel` [INFO] [stdout] --> src/bin/rustymotif/data.rs:48:35 [INFO] [stdout] | [INFO] [stdout] 48 | use crate::sequence::{Contig, MethylationLevel}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ahash::HashSet` [INFO] [stdout] --> src/bin/rustymotif/data.rs:49:9 [INFO] [stdout] | [INFO] [stdout] 49 | use ahash::HashSet; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::sequence::Contig` [INFO] [stdout] --> src/bin/rustymotif/fasta_reader.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use crate::sequence::Contig; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::sequence::MethylationThresholds` [INFO] [stdout] --> src/bin/rustymotif/fasta_reader.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use crate::sequence::MethylationThresholds; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bail` [INFO] [stdout] --> src/bin/rustymotif/motif_discovery.rs:2:14 [INFO] [stdout] | [INFO] [stdout] 2 | use anyhow::{bail, Result}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bio::bio_types::annot::contig` [INFO] [stdout] --> src/bin/rustymotif/motif_discovery.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use bio::bio_types::annot::contig; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `motif::MotifLike`, `motif`, and `strand::Strand` [INFO] [stdout] --> src/bin/rustymotif/motif_discovery.rs:6:24 [INFO] [stdout] | [INFO] [stdout] 6 | use rustymotif_utils::{motif, motif::MotifLike, pileup, strand::Strand}; [INFO] [stdout] | ^^^^^ ^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `collections::HashSet` and `hash::Hash` [INFO] [stdout] --> src/bin/rustymotif/search.rs:1:11 [INFO] [stdout] | [INFO] [stdout] 1 | use std::{collections::HashSet, hash::Hash}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bio::bio_types::annot::contig` [INFO] [stdout] --> src/bin/rustymotif/search.rs:9:5 [INFO] [stdout] | [INFO] [stdout] 9 | use bio::bio_types::annot::contig; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ordered_float::OrderedFloat` [INFO] [stdout] --> src/bin/rustymotif/search.rs:12:5 [INFO] [stdout] | [INFO] [stdout] 12 | use ordered_float::OrderedFloat; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `algo::min_spanning_tree` [INFO] [stdout] --> src/bin/rustymotif/search.rs:14:5 [INFO] [stdout] | [INFO] [stdout] 14 | algo::min_spanning_tree, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `pileup` [INFO] [stdout] --> src/bin/rustymotif/search.rs:20:80 [INFO] [stdout] | [INFO] [stdout] 20 | iupac::IupacBase, modtype::ModType, motif, motif::Motif, motif::MotifLike, pileup, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Deserialize` [INFO] [stdout] --> src/bin/rustymotif/search.rs:23:13 [INFO] [stdout] | [INFO] [stdout] 23 | use serde::{Deserialize, Serialize}; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `anyhow::anyhow` [INFO] [stdout] --> src/bin/rustymotif/sequence.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use anyhow::anyhow; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bio::bio_types::annot::contig` [INFO] [stdout] --> src/bin/rustymotif/sequence.rs:374:9 [INFO] [stdout] | [INFO] [stdout] 374 | use bio::bio_types::annot::contig; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ValueEnum` [INFO] [stdout] --> src/bin/mixedmotif/cli.rs:2:20 [INFO] [stdout] | [INFO] [stdout] 2 | use clap::{Parser, ValueEnum}; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::sequence::Contig` [INFO] [stdout] --> src/bin/mixedmotif/fasta_reader.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use crate::sequence::Contig; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `score_motifs` [INFO] [stdout] --> src/bin/mixedmotif/motif_discovery.rs:1:56 [INFO] [stdout] | [INFO] [stdout] 1 | use crate::{cli, data, fasta_reader, search, sequence, score_motifs}; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bail` [INFO] [stdout] --> src/bin/mixedmotif/motif_discovery.rs:2:14 [INFO] [stdout] | [INFO] [stdout] 2 | use anyhow::{bail, Result}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bio::bio_types::annot::contig` [INFO] [stdout] --> src/bin/mixedmotif/motif_discovery.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use bio::bio_types::annot::contig; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `itertools::concat` [INFO] [stdout] --> src/bin/mixedmotif/motif_discovery.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use itertools::concat; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `motif::MotifLike`, `motif`, and `strand::Strand` [INFO] [stdout] --> src/bin/mixedmotif/motif_discovery.rs:7:24 [INFO] [stdout] | [INFO] [stdout] 7 | use rustymotif_utils::{motif, motif::MotifLike, pileup, strand::Strand}; [INFO] [stdout] | ^^^^^ ^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::search::MotifNode` [INFO] [stdout] --> src/bin/mixedmotif/sequence.rs:5:5 [INFO] [stdout] | [INFO] [stdout] 5 | use crate::search::MotifNode; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `anyhow::anyhow` [INFO] [stdout] --> src/bin/mixedmotif/sequence.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | use anyhow::anyhow; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bio::io::fasta` [INFO] [stdout] --> src/bin/mixedmotif/sequence.rs:10:5 [INFO] [stdout] | [INFO] [stdout] 10 | use bio::io::fasta; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bio::bio_types::annot::contig` [INFO] [stdout] --> src/bin/mixedmotif/sequence.rs:452:9 [INFO] [stdout] | [INFO] [stdout] 452 | use bio::bio_types::annot::contig; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `hash::Hash` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:1:43 [INFO] [stdout] | [INFO] [stdout] 1 | use std::{collections::HashSet, fs::File, hash::Hash}; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `BetaBernoulliModel`, `EqualLengthDNASet`, and `fit_true_beta_model_em` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:5:9 [INFO] [stdout] | [INFO] [stdout] 5 | fit_true_beta_model_em, Beta, BetaBernoulliModel, BetaMixture [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] 6 | }, [INFO] [stdout] 7 | sequence::{Contig, EqualLengthDNASet}, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `HashMap` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:9:13 [INFO] [stdout] | [INFO] [stdout] 9 | use ahash::{HashMap, HashMapExt}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `strum_macros::EnumIter` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:12:5 [INFO] [stdout] | [INFO] [stdout] 12 | use strum_macros::EnumIter; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `info` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:14:18 [INFO] [stdout] | [INFO] [stdout] 14 | use log::{debug, info}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ordered_float::OrderedFloat` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:15:5 [INFO] [stdout] | [INFO] [stdout] 15 | use ordered_float::OrderedFloat; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Direction`, `Graph`, `NodeIndex`, and `algo::min_spanning_tree` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:17:5 [INFO] [stdout] | [INFO] [stdout] 17 | algo::min_spanning_tree, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] 18 | graph::{Graph, NodeIndex}, [INFO] [stdout] | ^^^^^ ^^^^^^^^^ [INFO] [stdout] 19 | Direction, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `cmp::Ordering` and `collections::BinaryHeap` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:21:11 [INFO] [stdout] | [INFO] [stdout] 21 | use std::{cmp::Ordering, collections::BinaryHeap}; [INFO] [stdout] | ^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `IupacBase`, `MotifLike`, `modtype::ModType`, `pileup`, `self`, `self`, and `strand::Strand` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:23:13 [INFO] [stdout] | [INFO] [stdout] 23 | iupac::{self, IupacBase}, modtype::ModType, motif::{self, Motif, MotifLike}, pileup, [INFO] [stdout] | ^^^^ ^^^^^^^^^ ^^^^^^^^^^^^^^^^ ^^^^ ^^^^^^^^^ ^^^^^^ [INFO] [stdout] 24 | strand::Strand, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Deserialize` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:26:13 [INFO] [stdout] | [INFO] [stdout] 26 | use serde::{Deserialize, Serialize}; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `write_header` is never used [INFO] [stdout] --> src/bin/preprocess/io.rs:16:8 [INFO] [stdout] | [INFO] [stdout] 15 | pub trait MethylBedWriter { [INFO] [stdout] | --------------- method in this trait [INFO] [stdout] 16 | fn write_header(&mut self) -> Result<()>; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `write_records_iter` is never used [INFO] [stdout] --> src/bin/preprocess/io.rs:35:12 [INFO] [stdout] | [INFO] [stdout] 25 | impl RecordWriter { [INFO] [stdout] | ----------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 35 | pub fn write_records_iter<'a, I>(&mut self, records: I) -> Result<()> [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `write_records_iter` is never used [INFO] [stdout] --> src/bin/preprocess/io.rs:78:12 [INFO] [stdout] | [INFO] [stdout] 73 | impl BgzippedRecordWriter { [INFO] [stdout] | ------------------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 78 | pub fn write_records_iter<'a, I>(&mut self, records: I) -> Result<()> [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `write_header` is never used [INFO] [stdout] --> src/bin/preprocess/io.rs:16:8 [INFO] [stdout] | [INFO] [stdout] 15 | pub trait MethylBedWriter { [INFO] [stdout] | --------------- method in this trait [INFO] [stdout] 16 | fn write_header(&mut self) -> Result<()>; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `write_records_iter` is never used [INFO] [stdout] --> src/bin/preprocess/io.rs:35:12 [INFO] [stdout] | [INFO] [stdout] 25 | impl RecordWriter { [INFO] [stdout] | ----------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 35 | pub fn write_records_iter<'a, I>(&mut self, records: I) -> Result<()> [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `write_records_iter` is never used [INFO] [stdout] --> src/bin/preprocess/io.rs:78:12 [INFO] [stdout] | [INFO] [stdout] 73 | impl BgzippedRecordWriter { [INFO] [stdout] | ------------------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 78 | pub fn write_records_iter<'a, I>(&mut self, records: I) -> Result<()> [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mod_type` [INFO] [stdout] --> src/bin/motif_summary/io.rs:215:15 [INFO] [stdout] | [INFO] [stdout] 215 | for ((mod_type, strand), data) in summary.summary.into_iter() { [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mod_type` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `strand` [INFO] [stdout] --> src/bin/motif_summary/io.rs:215:25 [INFO] [stdout] | [INFO] [stdout] 215 | for ((mod_type, strand), data) in summary.summary.into_iter() { [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_strand` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `extract_subsequences` and `remove_record_at_motif_indices` are never used [INFO] [stdout] --> src/bin/motif_summary/sequence.rs:59:12 [INFO] [stdout] | [INFO] [stdout] 22 | impl Contig { [INFO] [stdout] | ----------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 59 | pub fn extract_subsequences(&self, indices: &[usize], flank_size: usize) -> Result> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 86 | pub fn remove_record_at_motif_indices( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `EqualLengthDNASet` is never constructed [INFO] [stdout] --> src/bin/motif_summary/sequence.rs:107:12 [INFO] [stdout] | [INFO] [stdout] 107 | pub struct EqualLengthDNASet { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: multiple associated items are never used [INFO] [stdout] --> src/bin/motif_summary/sequence.rs:113:12 [INFO] [stdout] | [INFO] [stdout] 112 | impl EqualLengthDNASet { [INFO] [stdout] | ---------------------- associated items in this implementation [INFO] [stdout] 113 | pub fn new_empty(length: usize) -> Result { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 120 | pub fn new(sequences: Vec) -> Result { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 132 | pub fn len(&self) -> usize { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 136 | pub fn add_other(&mut self, other: &Self) -> Result<()> { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 144 | pub fn reverse_complement(&self) -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 161 | pub fn pssm(&self, pseudocount: f64) -> PSSM { [INFO] [stdout] | ^^^^ [INFO] [stdout] ... [INFO] [stdout] 196 | pub fn get_motif_matching_sequences(&self, motif: &Motif) -> Result { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 228 | pub fn remove_motif_matching_sequences(&self, motif: &Motif) -> Result { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `PSSM` is never constructed [INFO] [stdout] --> src/bin/motif_summary/sequence.rs:269:12 [INFO] [stdout] | [INFO] [stdout] 269 | pub struct PSSM { [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `new`, `length`, `kl_divergence`, and `bases_above_freq` are never used [INFO] [stdout] --> src/bin/motif_summary/sequence.rs:275:12 [INFO] [stdout] | [INFO] [stdout] 274 | impl PSSM { [INFO] [stdout] | --------- associated items in this implementation [INFO] [stdout] 275 | pub fn new(pssm: Vec>) -> Self { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 280 | pub fn length(&self) -> usize { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 284 | pub fn kl_divergence(&self, other: &PSSM) -> Result> { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 302 | pub fn bases_above_freq(&self, position: u8, min_freq: f64) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `file` is never read [INFO] [stdout] --> src/bin/motif_summary/io.rs:171:5 [INFO] [stdout] | [INFO] [stdout] 170 | pub struct AnnotatedRecordSummaryWriter { [INFO] [stdout] | ---------------------------- field in this struct [INFO] [stdout] 171 | file: File, [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: using `.clone()` on a double reference, which returns `&PileupRecord` instead of cloning the inner type [INFO] [stdout] --> src/bin/motif_summary/motif_summary.rs:112:43 [INFO] [stdout] | [INFO] [stdout] 112 | ... record.clone().clone(), [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(suspicious_double_ref_op)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io::Write` [INFO] [stdout] --> src/bin/motif_summary/io.rs:235:9 [INFO] [stdout] | [INFO] [stdout] 235 | use std::io::Write; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `strum::IntoEnumIterator` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:11:5 [INFO] [stdout] | [INFO] [stdout] 11 | use strum::IntoEnumIterator; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `itertools::Itertools` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:13:5 [INFO] [stdout] | [INFO] [stdout] 13 | use itertools::Itertools; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `HashMapExt` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:9:22 [INFO] [stdout] | [INFO] [stdout] 9 | use ahash::{HashMap, HashMapExt}; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Serialize` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:26:26 [INFO] [stdout] | [INFO] [stdout] 26 | use serde::{Deserialize, Serialize}; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function `new` is never used [INFO] [stdout] --> src/bin/rustymotif/model.rs:10:12 [INFO] [stdout] | [INFO] [stdout] 8 | impl BetaBernoulliModel { [INFO] [stdout] | ----------------------- associated function in this implementation [INFO] [stdout] 9 | /// Create a new Beta-Bernoulli model with alpha=1.0, beta=1.0 [INFO] [stdout] 10 | pub fn new() -> Self { [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `check_node` and `neighbors` are never used [INFO] [stdout] --> src/bin/rustymotif/search.rs:424:12 [INFO] [stdout] | [INFO] [stdout] 398 | impl MotifGraph { [INFO] [stdout] | --------------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 424 | pub fn check_node(&self, motif: &motif::Motif) -> bool { [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 461 | pub fn neighbors(&self, motif: &motif::Motif) -> Option> { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `score_log_odds_ratio` and `score_log_odds_ratio_z_score` are never used [INFO] [stdout] --> src/bin/rustymotif/search.rs:496:8 [INFO] [stdout] | [INFO] [stdout] 491 | impl ScoreCalculator { [INFO] [stdout] | -------------------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 496 | fn score_log_odds_ratio( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 511 | fn score_log_odds_ratio_z_score( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `priority_log_odds_ratio` and `priority_log_odds_ratio_z_score` are never used [INFO] [stdout] --> src/bin/rustymotif/search.rs:572:8 [INFO] [stdout] | [INFO] [stdout] 554 | impl PriorityCalculator { [INFO] [stdout] | ----------------------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 572 | fn priority_log_odds_ratio( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 586 | fn priority_log_odds_ratio_z_score( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `log_odds_ratio` is never used [INFO] [stdout] --> src/bin/rustymotif/search.rs:601:4 [INFO] [stdout] | [INFO] [stdout] 601 | fn log_odds_ratio(p1: f64, p2: f64, q1: f64, q2: f64, psudo_count: f64) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `log_odds_ratio_z_score` is never used [INFO] [stdout] --> src/bin/rustymotif/search.rs:607:4 [INFO] [stdout] | [INFO] [stdout] 607 | fn log_odds_ratio_z_score(p1: f64, p2: f64, q1: f64, q2: f64, psudo_count: f64) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function `default` is never used [INFO] [stdout] --> src/bin/rustymotif/sequence.rs:32:12 [INFO] [stdout] | [INFO] [stdout] 27 | impl MethylationThresholds { [INFO] [stdout] | -------------------------- associated function in this implementation [INFO] [stdout] ... [INFO] [stdout] 32 | pub fn default() -> Self { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `length` is never used [INFO] [stdout] --> src/bin/rustymotif/sequence.rs:334:12 [INFO] [stdout] | [INFO] [stdout] 328 | impl PSSM { [INFO] [stdout] | --------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 334 | pub fn length(&self) -> usize { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `iter` [INFO] [stdout] --> src/bin/mixedmotif/model.rs:395:9 [INFO] [stdout] | [INFO] [stdout] 395 | for iter in 0..max_iter { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_iter` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mix` [INFO] [stdout] --> src/bin/mixedmotif/model.rs:415:17 [INFO] [stdout] | [INFO] [stdout] 415 | let mix = log_mix.exp(); // Stable mixture probability. [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_mix` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `log_lik_old` is never read [INFO] [stdout] --> src/bin/mixedmotif/model.rs:443:13 [INFO] [stdout] | [INFO] [stdout] 443 | log_lik_old = log_lik; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mod_type` [INFO] [stdout] --> src/bin/motif_summary/io.rs:215:15 [INFO] [stdout] | [INFO] [stdout] 215 | for ((mod_type, strand), data) in summary.summary.into_iter() { [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mod_type` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `strand` [INFO] [stdout] --> src/bin/motif_summary/io.rs:215:25 [INFO] [stdout] | [INFO] [stdout] 215 | for ((mod_type, strand), data) in summary.summary.into_iter() { [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_strand` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bin/mixedmotif/motif_discovery.rs:54:21 [INFO] [stdout] | [INFO] [stdout] 54 | let mut genome_work_space = builder.build(); [INFO] [stdout] | ----^^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `strum::IntoEnumIterator` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:11:5 [INFO] [stdout] | [INFO] [stdout] 11 | use strum::IntoEnumIterator; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `itertools::Itertools` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:13:5 [INFO] [stdout] | [INFO] [stdout] 13 | use itertools::Itertools; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `HashMapExt` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:9:22 [INFO] [stdout] | [INFO] [stdout] 9 | use ahash::{HashMap, HashMapExt}; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Serialize` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:26:26 [INFO] [stdout] | [INFO] [stdout] 26 | use serde::{Deserialize, Serialize}; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `min_base_probability` [INFO] [stdout] --> src/bin/mixedmotif/search.rs:42:5 [INFO] [stdout] | [INFO] [stdout] 42 | min_base_probability: f64, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_base_probability` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `kl_divergence` [INFO] [stdout] --> src/bin/mixedmotif/search.rs:228:21 [INFO] [stdout] | [INFO] [stdout] 228 | let kl_divergence = pssm_methylated.kl_divergence(&pssm_background)?; [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_kl_divergence` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `remove_record_at_motif_indices` is never used [INFO] [stdout] --> src/bin/motif_summary/sequence.rs:86:12 [INFO] [stdout] | [INFO] [stdout] 22 | impl Contig { [INFO] [stdout] | ----------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 86 | pub fn remove_record_at_motif_indices( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `add_other` and `remove_motif_matching_sequences` are never used [INFO] [stdout] --> src/bin/motif_summary/sequence.rs:136:12 [INFO] [stdout] | [INFO] [stdout] 112 | impl EqualLengthDNASet { [INFO] [stdout] | ---------------------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 136 | pub fn add_other(&mut self, other: &Self) -> Result<()> { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 228 | pub fn remove_motif_matching_sequences(&self, motif: &Motif) -> Result { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `length` and `bases_above_freq` are never used [INFO] [stdout] --> src/bin/motif_summary/sequence.rs:280:12 [INFO] [stdout] | [INFO] [stdout] 274 | impl PSSM { [INFO] [stdout] | --------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 280 | pub fn length(&self) -> usize { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 302 | pub fn bases_above_freq(&self, position: u8, min_freq: f64) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `file` is never read [INFO] [stdout] --> src/bin/motif_summary/io.rs:171:5 [INFO] [stdout] | [INFO] [stdout] 170 | pub struct AnnotatedRecordSummaryWriter { [INFO] [stdout] | ---------------------------- field in this struct [INFO] [stdout] 171 | file: File, [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: using `.clone()` on a double reference, which returns `&PileupRecord` instead of cloning the inner type [INFO] [stdout] --> src/bin/motif_summary/motif_summary.rs:112:43 [INFO] [stdout] | [INFO] [stdout] 112 | ... record.clone().clone(), [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(suspicious_double_ref_op)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function `new` is never used [INFO] [stdout] --> src/bin/rustymotif/model.rs:10:12 [INFO] [stdout] | [INFO] [stdout] 8 | impl BetaBernoulliModel { [INFO] [stdout] | ----------------------- associated function in this implementation [INFO] [stdout] 9 | /// Create a new Beta-Bernoulli model with alpha=1.0, beta=1.0 [INFO] [stdout] 10 | pub fn new() -> Self { [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `check_node` and `neighbors` are never used [INFO] [stdout] --> src/bin/rustymotif/search.rs:424:12 [INFO] [stdout] | [INFO] [stdout] 398 | impl MotifGraph { [INFO] [stdout] | --------------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 424 | pub fn check_node(&self, motif: &motif::Motif) -> bool { [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 461 | pub fn neighbors(&self, motif: &motif::Motif) -> Option> { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `score_log_odds_ratio` and `score_log_odds_ratio_z_score` are never used [INFO] [stdout] --> src/bin/rustymotif/search.rs:496:8 [INFO] [stdout] | [INFO] [stdout] 491 | impl ScoreCalculator { [INFO] [stdout] | -------------------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 496 | fn score_log_odds_ratio( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 511 | fn score_log_odds_ratio_z_score( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `priority_log_odds_ratio` and `priority_log_odds_ratio_z_score` are never used [INFO] [stdout] --> src/bin/rustymotif/search.rs:572:8 [INFO] [stdout] | [INFO] [stdout] 554 | impl PriorityCalculator { [INFO] [stdout] | ----------------------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 572 | fn priority_log_odds_ratio( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 586 | fn priority_log_odds_ratio_z_score( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `log_odds_ratio` is never used [INFO] [stdout] --> src/bin/rustymotif/search.rs:601:4 [INFO] [stdout] | [INFO] [stdout] 601 | fn log_odds_ratio(p1: f64, p2: f64, q1: f64, q2: f64, psudo_count: f64) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `log_odds_ratio_z_score` is never used [INFO] [stdout] --> src/bin/rustymotif/search.rs:607:4 [INFO] [stdout] | [INFO] [stdout] 607 | fn log_odds_ratio_z_score(p1: f64, p2: f64, q1: f64, q2: f64, psudo_count: f64) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `length` is never used [INFO] [stdout] --> src/bin/rustymotif/sequence.rs:334:12 [INFO] [stdout] | [INFO] [stdout] 328 | impl PSSM { [INFO] [stdout] | --------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 334 | pub fn length(&self) -> usize { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `motif_reverse_index_set` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:57:9 [INFO] [stdout] | [INFO] [stdout] 57 | let motif_reverse_index_set: HashSet = motif_reverse_index.iter().cloned().collect(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_motif_reverse_index_set` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `iter` [INFO] [stdout] --> src/bin/mixedmotif/model.rs:395:9 [INFO] [stdout] | [INFO] [stdout] 395 | for iter in 0..max_iter { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_iter` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mix` [INFO] [stdout] --> src/bin/mixedmotif/model.rs:415:17 [INFO] [stdout] | [INFO] [stdout] 415 | let mix = log_mix.exp(); // Stable mixture probability. [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_mix` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `log_lik_old` is never read [INFO] [stdout] --> src/bin/mixedmotif/model.rs:443:13 [INFO] [stdout] | [INFO] [stdout] 443 | log_lik_old = log_lik; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `BetaBernoulliModel` is never constructed [INFO] [stdout] --> src/bin/mixedmotif/model.rs:8:12 [INFO] [stdout] | [INFO] [stdout] 8 | pub struct BetaBernoulliModel { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bin/mixedmotif/motif_discovery.rs:54:21 [INFO] [stdout] | [INFO] [stdout] 54 | let mut genome_work_space = builder.build(); [INFO] [stdout] | ----^^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `new`, `new_with_params`, `update`, `mean`, and `standard_deviation` are never used [INFO] [stdout] --> src/bin/mixedmotif/model.rs:15:12 [INFO] [stdout] | [INFO] [stdout] 13 | impl BetaBernoulliModel { [INFO] [stdout] | ----------------------- associated items in this implementation [INFO] [stdout] 14 | /// Create a new Beta-Bernoulli model with alpha=1.0, beta=1.0 [INFO] [stdout] 15 | pub fn new() -> Self { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 22 | pub fn new_with_params(alpha: f64, beta: f64) -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 27 | pub fn update(&mut self, n_meth: usize, n_nonmeth: usize) { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 33 | pub fn mean(&self) -> f64 { [INFO] [stdout] | ^^^^ [INFO] [stdout] ... [INFO] [stdout] 38 | pub fn standard_deviation(&self) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `variance`, `standard_deviation`, and `pdf` are never used [INFO] [stdout] --> src/bin/mixedmotif/model.rs:82:12 [INFO] [stdout] | [INFO] [stdout] 52 | impl Beta { [INFO] [stdout] | --------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 82 | pub fn variance(&self) -> f64 { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 88 | pub fn standard_deviation(&self) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 102 | pub fn pdf(&self, x: f64) -> f64 { [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `log_pdf` is never used [INFO] [stdout] --> src/bin/mixedmotif/model.rs:125:12 [INFO] [stdout] | [INFO] [stdout] 116 | impl BetaMixture { [INFO] [stdout] | ---------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 125 | pub fn log_pdf(&self, x: f64) -> f64 { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `mean`, `variance`, and `log_likelihoods` are never used [INFO] [stdout] --> src/bin/mixedmotif/model.rs:134:12 [INFO] [stdout] | [INFO] [stdout] 133 | impl BetaMixture { [INFO] [stdout] | ---------------- methods in this implementation [INFO] [stdout] 134 | pub fn mean(&self) -> f64 { [INFO] [stdout] | ^^^^ [INFO] [stdout] ... [INFO] [stdout] 138 | pub fn variance(&self) -> f64 { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 148 | pub fn log_likelihoods( [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `weighted_beta_fit_degrees_with_prior` is never used [INFO] [stdout] --> src/bin/mixedmotif/model.rs:314:4 [INFO] [stdout] | [INFO] [stdout] 314 | fn weighted_beta_fit_degrees_with_prior(degrees: &[f64], weights: &[f64], prior_alpha: f64, prior_beta: f64) -> Option { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `fit_true_beta_model_em` is never used [INFO] [stdout] --> src/bin/mixedmotif/model.rs:365:8 [INFO] [stdout] | [INFO] [stdout] 365 | pub fn fit_true_beta_model_em( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `all_unique_combinations` is never used [INFO] [stdout] --> src/bin/mixedmotif/search.rs:24:4 [INFO] [stdout] | [INFO] [stdout] 24 | fn all_unique_combinations(bases: Vec) -> Result>> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function `new` is never used [INFO] [stdout] --> src/bin/mixedmotif/search.rs:351:12 [INFO] [stdout] | [INFO] [stdout] 350 | impl MotifResult { [INFO] [stdout] | ---------------- associated function in this implementation [INFO] [stdout] 351 | pub fn new( [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `update_node`, `neighbors`, and `highest_scoring_node` are never used [INFO] [stdout] --> src/bin/mixedmotif/search.rs:463:12 [INFO] [stdout] | [INFO] [stdout] 432 | impl MotifGraph { [INFO] [stdout] | --------------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 463 | pub fn update_node(&mut self, motif: &motif::Motif, priority: f64, score: f64) -> bool { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 496 | pub fn neighbors(&self, motif: &motif::Motif) -> Option> { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 507 | pub fn highest_scoring_node(&self) -> Option<&MotifNode> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function `default` is never used [INFO] [stdout] --> src/bin/mixedmotif/sequence.rs:35:12 [INFO] [stdout] | [INFO] [stdout] 30 | impl MethylationThresholds { [INFO] [stdout] | -------------------------- associated function in this implementation [INFO] [stdout] ... [INFO] [stdout] 35 | pub fn default() -> Self { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `remove_record_at_motif_indices` is never used [INFO] [stdout] --> src/bin/mixedmotif/sequence.rs:120:12 [INFO] [stdout] | [INFO] [stdout] 52 | impl Contig { [INFO] [stdout] | ----------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 120 | pub fn remove_record_at_motif_indices( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `length` and `bases_above_freq` are never used [INFO] [stdout] --> src/bin/mixedmotif/sequence.rs:412:12 [INFO] [stdout] | [INFO] [stdout] 406 | impl PSSM { [INFO] [stdout] | --------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 412 | pub fn length(&self) -> usize { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 434 | pub fn bases_above_freq(&self, position: u8, min_freq: f64) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `score_motif` is never used [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:30:8 [INFO] [stdout] | [INFO] [stdout] 30 | pub fn score_motif( [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `min_base_probability` [INFO] [stdout] --> src/bin/mixedmotif/search.rs:42:5 [INFO] [stdout] | [INFO] [stdout] 42 | min_base_probability: f64, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_base_probability` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `kl_divergence` [INFO] [stdout] --> src/bin/mixedmotif/search.rs:228:21 [INFO] [stdout] | [INFO] [stdout] 228 | let kl_divergence = pssm_methylated.kl_divergence(&pssm_background)?; [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_kl_divergence` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `motif_reverse_index_set` [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:57:9 [INFO] [stdout] | [INFO] [stdout] 57 | let motif_reverse_index_set: HashSet = motif_reverse_index.iter().cloned().collect(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_motif_reverse_index_set` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `BetaBernoulliModel` is never constructed [INFO] [stdout] --> src/bin/mixedmotif/model.rs:8:12 [INFO] [stdout] | [INFO] [stdout] 8 | pub struct BetaBernoulliModel { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `new`, `new_with_params`, `update`, `mean`, and `standard_deviation` are never used [INFO] [stdout] --> src/bin/mixedmotif/model.rs:15:12 [INFO] [stdout] | [INFO] [stdout] 13 | impl BetaBernoulliModel { [INFO] [stdout] | ----------------------- associated items in this implementation [INFO] [stdout] 14 | /// Create a new Beta-Bernoulli model with alpha=1.0, beta=1.0 [INFO] [stdout] 15 | pub fn new() -> Self { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 22 | pub fn new_with_params(alpha: f64, beta: f64) -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 27 | pub fn update(&mut self, n_meth: usize, n_nonmeth: usize) { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 33 | pub fn mean(&self) -> f64 { [INFO] [stdout] | ^^^^ [INFO] [stdout] ... [INFO] [stdout] 38 | pub fn standard_deviation(&self) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `variance`, `standard_deviation`, and `pdf` are never used [INFO] [stdout] --> src/bin/mixedmotif/model.rs:82:12 [INFO] [stdout] | [INFO] [stdout] 52 | impl Beta { [INFO] [stdout] | --------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 82 | pub fn variance(&self) -> f64 { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 88 | pub fn standard_deviation(&self) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 102 | pub fn pdf(&self, x: f64) -> f64 { [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `log_pdf` is never used [INFO] [stdout] --> src/bin/mixedmotif/model.rs:125:12 [INFO] [stdout] | [INFO] [stdout] 116 | impl BetaMixture { [INFO] [stdout] | ---------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 125 | pub fn log_pdf(&self, x: f64) -> f64 { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `mean`, `variance`, and `log_likelihoods` are never used [INFO] [stdout] --> src/bin/mixedmotif/model.rs:134:12 [INFO] [stdout] | [INFO] [stdout] 133 | impl BetaMixture { [INFO] [stdout] | ---------------- methods in this implementation [INFO] [stdout] 134 | pub fn mean(&self) -> f64 { [INFO] [stdout] | ^^^^ [INFO] [stdout] ... [INFO] [stdout] 138 | pub fn variance(&self) -> f64 { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 148 | pub fn log_likelihoods( [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `weighted_beta_fit_degrees_with_prior` is never used [INFO] [stdout] --> src/bin/mixedmotif/model.rs:314:4 [INFO] [stdout] | [INFO] [stdout] 314 | fn weighted_beta_fit_degrees_with_prior(degrees: &[f64], weights: &[f64], prior_alpha: f64, prior_beta: f64) -> Option { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `fit_true_beta_model_em` is never used [INFO] [stdout] --> src/bin/mixedmotif/model.rs:365:8 [INFO] [stdout] | [INFO] [stdout] 365 | pub fn fit_true_beta_model_em( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `all_unique_combinations` is never used [INFO] [stdout] --> src/bin/mixedmotif/search.rs:24:4 [INFO] [stdout] | [INFO] [stdout] 24 | fn all_unique_combinations(bases: Vec) -> Result>> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function `new` is never used [INFO] [stdout] --> src/bin/mixedmotif/search.rs:351:12 [INFO] [stdout] | [INFO] [stdout] 350 | impl MotifResult { [INFO] [stdout] | ---------------- associated function in this implementation [INFO] [stdout] 351 | pub fn new( [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `update_node`, `neighbors`, and `highest_scoring_node` are never used [INFO] [stdout] --> src/bin/mixedmotif/search.rs:463:12 [INFO] [stdout] | [INFO] [stdout] 432 | impl MotifGraph { [INFO] [stdout] | --------------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 463 | pub fn update_node(&mut self, motif: &motif::Motif, priority: f64, score: f64) -> bool { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 496 | pub fn neighbors(&self, motif: &motif::Motif) -> Option> { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 507 | pub fn highest_scoring_node(&self) -> Option<&MotifNode> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `remove_record_at_motif_indices` is never used [INFO] [stdout] --> src/bin/mixedmotif/sequence.rs:120:12 [INFO] [stdout] | [INFO] [stdout] 52 | impl Contig { [INFO] [stdout] | ----------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 120 | pub fn remove_record_at_motif_indices( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `length` and `bases_above_freq` are never used [INFO] [stdout] --> src/bin/mixedmotif/sequence.rs:412:12 [INFO] [stdout] | [INFO] [stdout] 406 | impl PSSM { [INFO] [stdout] | --------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 412 | pub fn length(&self) -> usize { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 434 | pub fn bases_above_freq(&self, position: u8, min_freq: f64) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `score_motif` is never used [INFO] [stdout] --> src/bin/mixedmotif/score_motifs.rs:30:8 [INFO] [stdout] | [INFO] [stdout] 30 | pub fn score_motif( [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 40.87s [INFO] running `Command { std: "docker" "inspect" "653b085024fee0ca393289720dae512532fe88ef5d53f91ba088a131388bb6c0", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "653b085024fee0ca393289720dae512532fe88ef5d53f91ba088a131388bb6c0", kill_on_drop: false }` [INFO] [stdout] 653b085024fee0ca393289720dae512532fe88ef5d53f91ba088a131388bb6c0