[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] testing SorenHeidelbach/rustymotif against try#2440211fe03bc45c89b6dc1a3df18382ce91e32b for pr-146098-1 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FSorenHeidelbach%2Frustymotif" "/workspace/builds/worker-0-tc2/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc2/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-0-tc2/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/SorenHeidelbach/rustymotif on toolchain 2440211fe03bc45c89b6dc1a3df18382ce91e32b [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+2440211fe03bc45c89b6dc1a3df18382ce91e32b" "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" "+2440211fe03bc45c89b6dc1a3df18382ce91e32b" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/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" "+2440211fe03bc45c89b6dc1a3df18382ce91e32b" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 26a890aa573fcb1d7568e1e2f84e364b53deed7e76aa5c6e45aeba1630c53c74 [INFO] running `Command { std: "docker" "start" "-a" "26a890aa573fcb1d7568e1e2f84e364b53deed7e76aa5c6e45aeba1630c53c74", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "26a890aa573fcb1d7568e1e2f84e364b53deed7e76aa5c6e45aeba1630c53c74", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "26a890aa573fcb1d7568e1e2f84e364b53deed7e76aa5c6e45aeba1630c53c74", kill_on_drop: false }` [INFO] [stdout] 26a890aa573fcb1d7568e1e2f84e364b53deed7e76aa5c6e45aeba1630c53c74 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+2440211fe03bc45c89b6dc1a3df18382ce91e32b" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 13a79de5716b91fb39c9adee1f1b6d4a4b4ae38ad09a8125aae29a99a092b16e [INFO] running `Command { std: "docker" "start" "-a" "13a79de5716b91fb39c9adee1f1b6d4a4b4ae38ad09a8125aae29a99a092b16e", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.93 [INFO] [stderr] Compiling unicode-ident v1.0.14 [INFO] [stderr] Compiling libc v0.2.169 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bytecount v0.6.8 [INFO] [stderr] Compiling scoped_threadpool v0.1.9 [INFO] [stderr] Compiling fastrand v2.3.0 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling strum v0.26.3 [INFO] [stderr] Compiling tempfile v3.20.0 [INFO] [stderr] Compiling clap v4.5.40 [INFO] [stderr] Compiling seq_io v0.3.4 [INFO] [stderr] Compiling strum_macros v0.27.1 [INFO] [stderr] Compiling atoi v2.0.0 [INFO] [stderr] Compiling ordered-float v4.6.0 [INFO] [stderr] Compiling strum v0.27.1 [INFO] [stderr] Compiling statrs v0.18.0 [INFO] [stderr] Compiling env_logger v0.11.8 [INFO] [stderr] Compiling bio v2.3.0 [INFO] [stderr] Compiling rust-htslib v0.49.0 [INFO] [stderr] Compiling 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 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 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/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: 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: 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 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: 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: 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: 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: 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: `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 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: `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: `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: 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: `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: 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: 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 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: `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: `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: 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] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 3m 18s [INFO] running `Command { std: "docker" "inspect" "13a79de5716b91fb39c9adee1f1b6d4a4b4ae38ad09a8125aae29a99a092b16e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "13a79de5716b91fb39c9adee1f1b6d4a4b4ae38ad09a8125aae29a99a092b16e", kill_on_drop: false }` [INFO] [stdout] 13a79de5716b91fb39c9adee1f1b6d4a4b4ae38ad09a8125aae29a99a092b16e [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+2440211fe03bc45c89b6dc1a3df18382ce91e32b" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 721ef4a73f7dad401cbfaf82c6a88938a5ff063ed4c7fe525b9f96647713b601 [INFO] running `Command { std: "docker" "start" "-a" "721ef4a73f7dad401cbfaf82c6a88938a5ff063ed4c7fe525b9f96647713b601", kill_on_drop: false }` [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 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] [stderr] Compiling rustymotif v0.3.0 (/opt/rustwide/workdir) [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: 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: 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: 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 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 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: 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: 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: 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 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: `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: 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 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: `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 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: `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] [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] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 3.80s [INFO] running `Command { std: "docker" "inspect" "721ef4a73f7dad401cbfaf82c6a88938a5ff063ed4c7fe525b9f96647713b601", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "721ef4a73f7dad401cbfaf82c6a88938a5ff063ed4c7fe525b9f96647713b601", kill_on_drop: false }` [INFO] [stdout] 721ef4a73f7dad401cbfaf82c6a88938a5ff063ed4c7fe525b9f96647713b601 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+2440211fe03bc45c89b6dc1a3df18382ce91e32b" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] 5b8211546a24a63a0bae11d0b95a7fef531eeb5ebe8b53b43158ffde6f11ae9d [INFO] running `Command { std: "docker" "start" "-a" "5b8211546a24a63a0bae11d0b95a7fef531eeb5ebe8b53b43158ffde6f11ae9d", kill_on_drop: false }` [INFO] [stderr] warning: unused imports: `SerializeStruct` and `Serialize` [INFO] [stderr] --> src/lib/motif.rs:3:18 [INFO] [stderr] | [INFO] [stderr] 3 | use serde::ser::{Serialize, Serializer, SerializeStruct}; [INFO] [stderr] | ^^^^^^^^^ ^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: unused import: `ToString` [INFO] [stderr] --> src/lib/pileup.rs:6:30 [INFO] [stderr] | [INFO] [stderr] 6 | use strum_macros::{EnumIter, ToString}; [INFO] [stderr] | ^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused imports: `debug`, `info`, and `warn` [INFO] [stderr] --> src/lib/pileup.rs:9:11 [INFO] [stderr] | [INFO] [stderr] 9 | use log::{debug, info, warn}; [INFO] [stderr] | ^^^^^ ^^^^ ^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `motif::Motif` [INFO] [stderr] --> src/lib/preprocess.rs:3:31 [INFO] [stderr] | [INFO] [stderr] 3 | use crate::{modtype::ModType, motif::Motif, pileup, strand::Strand}; [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `debug` [INFO] [stderr] --> src/lib/preprocess.rs:5:11 [INFO] [stderr] | [INFO] [stderr] 5 | use log::{debug, info, warn}; [INFO] [stderr] | ^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `PyList` [INFO] [stderr] --> src/lib/preprocess.rs:9:27 [INFO] [stderr] | [INFO] [stderr] 9 | use pyo3::types::{PyDict, PyList}; [INFO] [stderr] | ^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `strum::IntoEnumIterator` [INFO] [stderr] --> src/lib/iupac.rs:4:5 [INFO] [stderr] | [INFO] [stderr] 4 | use strum::IntoEnumIterator; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused variable: `e` [INFO] [stderr] --> src/lib/pileup.rs:400:21 [INFO] [stderr] | [INFO] [stderr] 400 | Err(e) => continue, // Skip invalid records [INFO] [stderr] | ^ help: if this is intentional, prefix it with an underscore: `_e` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: function `line_to_byterecord` is never used [INFO] [stderr] --> src/lib/pileup.rs:532:4 [INFO] [stderr] | [INFO] [stderr] 532 | fn line_to_byterecord(line: &[u8]) -> ByteRecord { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: `rustymotif` (lib) generated 9 warnings (run `cargo fix --lib -p rustymotif` to apply 6 suggestions) [INFO] [stderr] warning: `rustymotif` (lib test) generated 9 warnings (9 duplicates) [INFO] [stderr] warning: unused import: `ValueEnum` [INFO] [stderr] --> src/bin/preprocess/cli.rs:2:20 [INFO] [stderr] | [INFO] [stderr] 2 | use clap::{Parser, ValueEnum}; [INFO] [stderr] | ^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: unused import: `std::fs` [INFO] [stderr] --> src/bin/preprocess/io.rs:4:5 [INFO] [stderr] | [INFO] [stderr] 4 | use std::fs; [INFO] [stderr] | ^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `motif::Motif` [INFO] [stderr] --> src/bin/preprocess/io.rs:7:24 [INFO] [stderr] | [INFO] [stderr] 7 | use rustymotif_utils::{motif::Motif, pileup::PileupRecord}; [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `std::io` [INFO] [stderr] --> src/bin/preprocess/io.rs:11:5 [INFO] [stderr] | [INFO] [stderr] 11 | use std::io; [INFO] [stderr] | ^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: method `write_header` is never used [INFO] [stderr] --> src/bin/preprocess/io.rs:16:8 [INFO] [stderr] | [INFO] [stderr] 15 | pub trait MethylBedWriter { [INFO] [stderr] | --------------- method in this trait [INFO] [stderr] 16 | fn write_header(&mut self) -> Result<()>; [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: method `write_records_iter` is never used [INFO] [stderr] --> src/bin/preprocess/io.rs:35:12 [INFO] [stderr] | [INFO] [stderr] 25 | impl RecordWriter { [INFO] [stderr] | ----------------- method in this implementation [INFO] [stderr] ... [INFO] [stderr] 35 | pub fn write_records_iter<'a, I>(&mut self, records: I) -> Result<()> [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: method `write_records_iter` is never used [INFO] [stderr] --> src/bin/preprocess/io.rs:78:12 [INFO] [stderr] | [INFO] [stderr] 73 | impl BgzippedRecordWriter { [INFO] [stderr] | ------------------------- method in this implementation [INFO] [stderr] ... [INFO] [stderr] 78 | pub fn write_records_iter<'a, I>(&mut self, records: I) -> Result<()> [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `ValueEnum` [INFO] [stderr] --> src/bin/mixedmotif/cli.rs:2:20 [INFO] [stderr] | [INFO] [stderr] 2 | use clap::{Parser, ValueEnum}; [INFO] [stderr] | ^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: unused import: `crate::sequence::Contig` [INFO] [stderr] --> src/bin/mixedmotif/fasta_reader.rs:1:5 [INFO] [stderr] | [INFO] [stderr] 1 | use crate::sequence::Contig; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `score_motifs` [INFO] [stderr] --> src/bin/mixedmotif/motif_discovery.rs:1:56 [INFO] [stderr] | [INFO] [stderr] 1 | use crate::{cli, data, fasta_reader, search, sequence, score_motifs}; [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `bail` [INFO] [stderr] --> src/bin/mixedmotif/motif_discovery.rs:2:14 [INFO] [stderr] | [INFO] [stderr] 2 | use anyhow::{bail, Result}; [INFO] [stderr] | ^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `bio::bio_types::annot::contig` [INFO] [stderr] --> src/bin/mixedmotif/motif_discovery.rs:3:5 [INFO] [stderr] | [INFO] [stderr] 3 | use bio::bio_types::annot::contig; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `itertools::concat` [INFO] [stderr] --> src/bin/mixedmotif/motif_discovery.rs:4:5 [INFO] [stderr] | [INFO] [stderr] 4 | use itertools::concat; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused imports: `motif::MotifLike`, `motif`, and `strand::Strand` [INFO] [stderr] --> src/bin/mixedmotif/motif_discovery.rs:7:24 [INFO] [stderr] | [INFO] [stderr] 7 | use rustymotif_utils::{motif, motif::MotifLike, pileup, strand::Strand}; [INFO] [stderr] | ^^^^^ ^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `crate::search::MotifNode` [INFO] [stderr] --> src/bin/mixedmotif/sequence.rs:5:5 [INFO] [stderr] | [INFO] [stderr] 5 | use crate::search::MotifNode; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `anyhow::anyhow` [INFO] [stderr] --> src/bin/mixedmotif/sequence.rs:7:5 [INFO] [stderr] | [INFO] [stderr] 7 | use anyhow::anyhow; [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `bio::io::fasta` [INFO] [stderr] --> src/bin/mixedmotif/sequence.rs:10:5 [INFO] [stderr] | [INFO] [stderr] 10 | use bio::io::fasta; [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `bio::bio_types::annot::contig` [INFO] [stderr] --> src/bin/mixedmotif/sequence.rs:452:9 [INFO] [stderr] | [INFO] [stderr] 452 | use bio::bio_types::annot::contig; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `hash::Hash` [INFO] [stderr] --> src/bin/mixedmotif/score_motifs.rs:1:43 [INFO] [stderr] | [INFO] [stderr] 1 | use std::{collections::HashSet, fs::File, hash::Hash}; [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused imports: `BetaBernoulliModel`, `EqualLengthDNASet`, and `fit_true_beta_model_em` [INFO] [stderr] --> src/bin/mixedmotif/score_motifs.rs:5:9 [INFO] [stderr] | [INFO] [stderr] 5 | fit_true_beta_model_em, Beta, BetaBernoulliModel, BetaMixture [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^ [INFO] [stderr] 6 | }, [INFO] [stderr] 7 | sequence::{Contig, EqualLengthDNASet}, [INFO] [stderr] | ^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `HashMap` [INFO] [stderr] --> src/bin/mixedmotif/score_motifs.rs:9:13 [INFO] [stderr] | [INFO] [stderr] 9 | use ahash::{HashMap, HashMapExt}; [INFO] [stderr] | ^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `strum_macros::EnumIter` [INFO] [stderr] --> src/bin/mixedmotif/score_motifs.rs:12:5 [INFO] [stderr] | [INFO] [stderr] 12 | use strum_macros::EnumIter; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `info` [INFO] [stderr] --> src/bin/mixedmotif/score_motifs.rs:14:18 [INFO] [stderr] | [INFO] [stderr] 14 | use log::{debug, info}; [INFO] [stderr] | ^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `ordered_float::OrderedFloat` [INFO] [stderr] --> src/bin/mixedmotif/score_motifs.rs:15:5 [INFO] [stderr] | [INFO] [stderr] 15 | use ordered_float::OrderedFloat; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused imports: `Direction`, `Graph`, `NodeIndex`, and `algo::min_spanning_tree` [INFO] [stderr] --> src/bin/mixedmotif/score_motifs.rs:17:5 [INFO] [stderr] | [INFO] [stderr] 17 | algo::min_spanning_tree, [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] 18 | graph::{Graph, NodeIndex}, [INFO] [stderr] | ^^^^^ ^^^^^^^^^ [INFO] [stderr] 19 | Direction, [INFO] [stderr] | ^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused imports: `cmp::Ordering` and `collections::BinaryHeap` [INFO] [stderr] --> src/bin/mixedmotif/score_motifs.rs:21:11 [INFO] [stderr] | [INFO] [stderr] 21 | use std::{cmp::Ordering, collections::BinaryHeap}; [INFO] [stderr] | ^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused imports: `IupacBase`, `MotifLike`, `modtype::ModType`, `pileup`, `self`, `self`, and `strand::Strand` [INFO] [stderr] --> src/bin/mixedmotif/score_motifs.rs:23:13 [INFO] [stderr] | [INFO] [stderr] 23 | iupac::{self, IupacBase}, modtype::ModType, motif::{self, Motif, MotifLike}, pileup, [INFO] [stderr] | ^^^^ ^^^^^^^^^ ^^^^^^^^^^^^^^^^ ^^^^ ^^^^^^^^^ ^^^^^^ [INFO] [stderr] 24 | strand::Strand, [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `Deserialize` [INFO] [stderr] --> src/bin/mixedmotif/score_motifs.rs:26:13 [INFO] [stderr] | [INFO] [stderr] 26 | use serde::{Deserialize, Serialize}; [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `strum::IntoEnumIterator` [INFO] [stderr] --> src/bin/mixedmotif/score_motifs.rs:11:5 [INFO] [stderr] | [INFO] [stderr] 11 | use strum::IntoEnumIterator; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `itertools::Itertools` [INFO] [stderr] --> src/bin/mixedmotif/score_motifs.rs:13:5 [INFO] [stderr] | [INFO] [stderr] 13 | use itertools::Itertools; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `HashMapExt` [INFO] [stderr] --> src/bin/mixedmotif/score_motifs.rs:9:22 [INFO] [stderr] | [INFO] [stderr] 9 | use ahash::{HashMap, HashMapExt}; [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `Serialize` [INFO] [stderr] --> src/bin/mixedmotif/score_motifs.rs:26:26 [INFO] [stderr] | [INFO] [stderr] 26 | use serde::{Deserialize, Serialize}; [INFO] [stderr] | ^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused variable: `iter` [INFO] [stderr] --> src/bin/mixedmotif/model.rs:395:9 [INFO] [stderr] | [INFO] [stderr] 395 | for iter in 0..max_iter { [INFO] [stderr] | ^^^^ help: if this is intentional, prefix it with an underscore: `_iter` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: unused variable: `mix` [INFO] [stderr] --> src/bin/mixedmotif/model.rs:415:17 [INFO] [stderr] | [INFO] [stderr] 415 | let mix = log_mix.exp(); // Stable mixture probability. [INFO] [stderr] | ^^^ help: if this is intentional, prefix it with an underscore: `_mix` [INFO] [stderr] [INFO] [stderr] warning: value assigned to `log_lik_old` is never read [INFO] [stderr] --> src/bin/mixedmotif/model.rs:443:13 [INFO] [stderr] | [INFO] [stderr] 443 | log_lik_old = log_lik; [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = help: maybe it is overwritten before being read? [INFO] [stderr] = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/bin/mixedmotif/motif_discovery.rs:54:21 [INFO] [stderr] | [INFO] [stderr] 54 | let mut genome_work_space = builder.build(); [INFO] [stderr] | ----^^^^^^^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: unused variable: `kl_divergence` [INFO] [stderr] --> src/bin/mixedmotif/search.rs:228:21 [INFO] [stderr] | [INFO] [stderr] 228 | let kl_divergence = pssm_methylated.kl_divergence(&pssm_background)?; [INFO] [stderr] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_kl_divergence` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `min_base_probability` [INFO] [stderr] --> src/bin/mixedmotif/search.rs:42:5 [INFO] [stderr] | [INFO] [stderr] 42 | min_base_probability: f64, [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_base_probability` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `motif_reverse_index_set` [INFO] [stderr] --> src/bin/mixedmotif/score_motifs.rs:57:9 [INFO] [stderr] | [INFO] [stderr] 57 | let motif_reverse_index_set: HashSet = motif_reverse_index.iter().cloned().collect(); [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_motif_reverse_index_set` [INFO] [stderr] [INFO] [stderr] warning: struct `BetaBernoulliModel` is never constructed [INFO] [stderr] --> src/bin/mixedmotif/model.rs:8:12 [INFO] [stderr] | [INFO] [stderr] 8 | pub struct BetaBernoulliModel { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: associated items `new`, `new_with_params`, `update`, `mean`, and `standard_deviation` are never used [INFO] [stderr] --> src/bin/mixedmotif/model.rs:15:12 [INFO] [stderr] | [INFO] [stderr] 13 | impl BetaBernoulliModel { [INFO] [stderr] | ----------------------- associated items in this implementation [INFO] [stderr] 14 | /// Create a new Beta-Bernoulli model with alpha=1.0, beta=1.0 [INFO] [stderr] 15 | pub fn new() -> Self { [INFO] [stderr] | ^^^ [INFO] [stderr] ... [INFO] [stderr] 22 | pub fn new_with_params(alpha: f64, beta: f64) -> Self { [INFO] [stderr] | ^^^^^^^^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 27 | pub fn update(&mut self, n_meth: usize, n_nonmeth: usize) { [INFO] [stderr] | ^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 33 | pub fn mean(&self) -> f64 { [INFO] [stderr] | ^^^^ [INFO] [stderr] ... [INFO] [stderr] 38 | pub fn standard_deviation(&self) -> f64 { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: methods `variance`, `standard_deviation`, and `pdf` are never used [INFO] [stderr] --> src/bin/mixedmotif/model.rs:82:12 [INFO] [stderr] | [INFO] [stderr] 52 | impl Beta { [INFO] [stderr] | --------- methods in this implementation [INFO] [stderr] ... [INFO] [stderr] 82 | pub fn variance(&self) -> f64 { [INFO] [stderr] | ^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 88 | pub fn standard_deviation(&self) -> f64 { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 102 | pub fn pdf(&self, x: f64) -> f64 { [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: method `log_pdf` is never used [INFO] [stderr] --> src/bin/mixedmotif/model.rs:125:12 [INFO] [stderr] | [INFO] [stderr] 116 | impl BetaMixture { [INFO] [stderr] | ---------------- method in this implementation [INFO] [stderr] ... [INFO] [stderr] 125 | pub fn log_pdf(&self, x: f64) -> f64 { [INFO] [stderr] | ^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: methods `mean`, `variance`, and `log_likelihoods` are never used [INFO] [stderr] --> src/bin/mixedmotif/model.rs:134:12 [INFO] [stderr] | [INFO] [stderr] 133 | impl BetaMixture { [INFO] [stderr] | ---------------- methods in this implementation [INFO] [stderr] 134 | pub fn mean(&self) -> f64 { [INFO] [stderr] | ^^^^ [INFO] [stderr] ... [INFO] [stderr] 138 | pub fn variance(&self) -> f64 { [INFO] [stderr] | ^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 148 | pub fn log_likelihoods( [INFO] [stderr] | ^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `weighted_beta_fit_degrees_with_prior` is never used [INFO] [stderr] --> src/bin/mixedmotif/model.rs:314:4 [INFO] [stderr] | [INFO] [stderr] 314 | fn weighted_beta_fit_degrees_with_prior(degrees: &[f64], weights: &[f64], prior_alpha: f64, prior_beta: f64) -> Option { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `fit_true_beta_model_em` is never used [INFO] [stderr] --> src/bin/mixedmotif/model.rs:365:8 [INFO] [stderr] | [INFO] [stderr] 365 | pub fn fit_true_beta_model_em( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `all_unique_combinations` is never used [INFO] [stderr] --> src/bin/mixedmotif/search.rs:24:4 [INFO] [stderr] | [INFO] [stderr] 24 | fn all_unique_combinations(bases: Vec) -> Result>> { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: associated function `new` is never used [INFO] [stderr] --> src/bin/mixedmotif/search.rs:351:12 [INFO] [stderr] | [INFO] [stderr] 350 | impl MotifResult { [INFO] [stderr] | ---------------- associated function in this implementation [INFO] [stderr] 351 | pub fn new( [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: methods `update_node`, `neighbors`, and `highest_scoring_node` are never used [INFO] [stderr] --> src/bin/mixedmotif/search.rs:463:12 [INFO] [stderr] | [INFO] [stderr] 432 | impl MotifGraph { [INFO] [stderr] | --------------- methods in this implementation [INFO] [stderr] ... [INFO] [stderr] 463 | pub fn update_node(&mut self, motif: &motif::Motif, priority: f64, score: f64) -> bool { [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 496 | pub fn neighbors(&self, motif: &motif::Motif) -> Option> { [INFO] [stderr] | ^^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 507 | pub fn highest_scoring_node(&self) -> Option<&MotifNode> { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: method `remove_record_at_motif_indices` is never used [INFO] [stderr] --> src/bin/mixedmotif/sequence.rs:120:12 [INFO] [stderr] | [INFO] [stderr] 52 | impl Contig { [INFO] [stderr] | ----------- method in this implementation [INFO] [stderr] ... [INFO] [stderr] 120 | pub fn remove_record_at_motif_indices( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: methods `length` and `bases_above_freq` are never used [INFO] [stderr] --> src/bin/mixedmotif/sequence.rs:412:12 [INFO] [stderr] | [INFO] [stderr] 406 | impl PSSM { [INFO] [stderr] | --------- methods in this implementation [INFO] [stderr] ... [INFO] [stderr] 412 | pub fn length(&self) -> usize { [INFO] [stderr] | ^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 434 | pub fn bases_above_freq(&self, position: u8, min_freq: f64) -> Vec { [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `score_motif` is never used [INFO] [stderr] --> src/bin/mixedmotif/score_motifs.rs:30:8 [INFO] [stderr] | [INFO] [stderr] 30 | pub fn score_motif( [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: variant `verbose` should have an upper camel case name [INFO] [stderr] --> src/bin/rustymotif/cli.rs:81:5 [INFO] [stderr] | [INFO] [stderr] 81 | verbose, [INFO] [stderr] | ^^^^^^^ help: convert the identifier to upper camel case (notice the capitalization): `Verbose` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(non_camel_case_types)]` (part of `#[warn(nonstandard_style)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: variant `normal` should have an upper camel case name [INFO] [stderr] --> src/bin/rustymotif/cli.rs:82:5 [INFO] [stderr] | [INFO] [stderr] 82 | normal, [INFO] [stderr] | ^^^^^^ help: convert the identifier to upper camel case: `Normal` [INFO] [stderr] [INFO] [stderr] warning: variant `silent` should have an upper camel case name [INFO] [stderr] --> src/bin/rustymotif/cli.rs:83:5 [INFO] [stderr] | [INFO] [stderr] 83 | silent, [INFO] [stderr] | ^^^^^^ help: convert the identifier to upper camel case (notice the capitalization): `Silent` [INFO] [stderr] [INFO] [stderr] warning: unused import: `std::collections::HashSet` [INFO] [stderr] --> src/bin/rustymotif/data.rs:5:5 [INFO] [stderr] | [INFO] [stderr] 5 | use std::collections::HashSet; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: unused import: `MethylationLevel` [INFO] [stderr] --> src/bin/rustymotif/data.rs:48:35 [INFO] [stderr] | [INFO] [stderr] 48 | use crate::sequence::{Contig, MethylationLevel}; [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `ahash::HashSet` [INFO] [stderr] --> src/bin/rustymotif/data.rs:49:9 [INFO] [stderr] | [INFO] [stderr] 49 | use ahash::HashSet; [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `crate::sequence::Contig` [INFO] [stderr] --> src/bin/rustymotif/fasta_reader.rs:1:5 [INFO] [stderr] | [INFO] [stderr] 1 | use crate::sequence::Contig; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `crate::sequence::MethylationThresholds` [INFO] [stderr] --> src/bin/rustymotif/fasta_reader.rs:2:5 [INFO] [stderr] | [INFO] [stderr] 2 | use crate::sequence::MethylationThresholds; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `bail` [INFO] [stderr] --> src/bin/rustymotif/motif_discovery.rs:2:14 [INFO] [stderr] | [INFO] [stderr] 2 | use anyhow::{bail, Result}; [INFO] [stderr] | ^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `bio::bio_types::annot::contig` [INFO] [stderr] --> src/bin/rustymotif/motif_discovery.rs:3:5 [INFO] [stderr] | [INFO] [stderr] 3 | use bio::bio_types::annot::contig; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused imports: `motif::MotifLike`, `motif`, and `strand::Strand` [INFO] [stderr] --> src/bin/rustymotif/motif_discovery.rs:6:24 [INFO] [stderr] | [INFO] [stderr] 6 | use rustymotif_utils::{motif, motif::MotifLike, pileup, strand::Strand}; [INFO] [stderr] | ^^^^^ ^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused imports: `collections::HashSet` and `hash::Hash` [INFO] [stderr] --> src/bin/rustymotif/search.rs:1:11 [INFO] [stderr] | [INFO] [stderr] 1 | use std::{collections::HashSet, hash::Hash}; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `bio::bio_types::annot::contig` [INFO] [stderr] --> src/bin/rustymotif/search.rs:9:5 [INFO] [stderr] | [INFO] [stderr] 9 | use bio::bio_types::annot::contig; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `ordered_float::OrderedFloat` [INFO] [stderr] --> src/bin/rustymotif/search.rs:12:5 [INFO] [stderr] | [INFO] [stderr] 12 | use ordered_float::OrderedFloat; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `algo::min_spanning_tree` [INFO] [stderr] --> src/bin/rustymotif/search.rs:14:5 [INFO] [stderr] | [INFO] [stderr] 14 | algo::min_spanning_tree, [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `pileup` [INFO] [stderr] --> src/bin/rustymotif/search.rs:20:80 [INFO] [stderr] | [INFO] [stderr] 20 | iupac::IupacBase, modtype::ModType, motif, motif::Motif, motif::MotifLike, pileup, [INFO] [stderr] | ^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `Deserialize` [INFO] [stderr] --> src/bin/rustymotif/search.rs:23:13 [INFO] [stderr] | [INFO] [stderr] 23 | use serde::{Deserialize, Serialize}; [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `anyhow::anyhow` [INFO] [stderr] --> src/bin/rustymotif/sequence.rs:6:5 [INFO] [stderr] | [INFO] [stderr] 6 | use anyhow::anyhow; [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `bio::bio_types::annot::contig` [INFO] [stderr] --> src/bin/rustymotif/sequence.rs:374:9 [INFO] [stderr] | [INFO] [stderr] 374 | use bio::bio_types::annot::contig; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: associated function `new` is never used [INFO] [stderr] --> src/bin/rustymotif/model.rs:10:12 [INFO] [stderr] | [INFO] [stderr] 8 | impl BetaBernoulliModel { [INFO] [stderr] | ----------------------- associated function in this implementation [INFO] [stderr] 9 | /// Create a new Beta-Bernoulli model with alpha=1.0, beta=1.0 [INFO] [stderr] 10 | pub fn new() -> Self { [INFO] [stderr] | ^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: methods `check_node` and `neighbors` are never used [INFO] [stderr] --> src/bin/rustymotif/search.rs:424:12 [INFO] [stderr] | [INFO] [stderr] 398 | impl MotifGraph { [INFO] [stderr] | --------------- methods in this implementation [INFO] [stderr] ... [INFO] [stderr] 424 | pub fn check_node(&self, motif: &motif::Motif) -> bool { [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 461 | pub fn neighbors(&self, motif: &motif::Motif) -> Option> { [INFO] [stderr] | ^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: methods `score_log_odds_ratio` and `score_log_odds_ratio_z_score` are never used [INFO] [stderr] --> src/bin/rustymotif/search.rs:496:8 [INFO] [stderr] | [INFO] [stderr] 491 | impl ScoreCalculator { [INFO] [stderr] | -------------------- methods in this implementation [INFO] [stderr] ... [INFO] [stderr] 496 | fn score_log_odds_ratio( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 511 | fn score_log_odds_ratio_z_score( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: methods `priority_log_odds_ratio` and `priority_log_odds_ratio_z_score` are never used [INFO] [stderr] --> src/bin/rustymotif/search.rs:572:8 [INFO] [stderr] | [INFO] [stderr] 554 | impl PriorityCalculator { [INFO] [stderr] | ----------------------- methods in this implementation [INFO] [stderr] ... [INFO] [stderr] 572 | fn priority_log_odds_ratio( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 586 | fn priority_log_odds_ratio_z_score( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `log_odds_ratio` is never used [INFO] [stderr] --> src/bin/rustymotif/search.rs:601:4 [INFO] [stderr] | [INFO] [stderr] 601 | fn log_odds_ratio(p1: f64, p2: f64, q1: f64, q2: f64, psudo_count: f64) -> f64 { [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `log_odds_ratio_z_score` is never used [INFO] [stderr] --> src/bin/rustymotif/search.rs:607:4 [INFO] [stderr] | [INFO] [stderr] 607 | fn log_odds_ratio_z_score(p1: f64, p2: f64, q1: f64, q2: f64, psudo_count: f64) -> f64 { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: method `length` is never used [INFO] [stderr] --> src/bin/rustymotif/sequence.rs:334:12 [INFO] [stderr] | [INFO] [stderr] 328 | impl PSSM { [INFO] [stderr] | --------- method in this implementation [INFO] [stderr] ... [INFO] [stderr] 334 | pub fn length(&self) -> usize { [INFO] [stderr] | ^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused imports: `debug` and `warn` [INFO] [stderr] --> src/bin/motif_summary/main.rs:3:17 [INFO] [stderr] | [INFO] [stderr] 3 | use log::{info, debug, warn}; [INFO] [stderr] | ^^^^^ ^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: variant `verbose` should have an upper camel case name [INFO] [stderr] --> src/bin/motif_summary/cli.rs:75:5 [INFO] [stderr] | [INFO] [stderr] 75 | verbose, [INFO] [stderr] | ^^^^^^^ help: convert the identifier to upper camel case (notice the capitalization): `Verbose` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(non_camel_case_types)]` (part of `#[warn(nonstandard_style)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: variant `normal` should have an upper camel case name [INFO] [stderr] --> src/bin/motif_summary/cli.rs:76:5 [INFO] [stderr] | [INFO] [stderr] 76 | normal, [INFO] [stderr] | ^^^^^^ help: convert the identifier to upper camel case: `Normal` [INFO] [stderr] [INFO] [stderr] warning: variant `silent` should have an upper camel case name [INFO] [stderr] --> src/bin/motif_summary/cli.rs:77:5 [INFO] [stderr] | [INFO] [stderr] 77 | silent, [INFO] [stderr] | ^^^^^^ help: convert the identifier to upper camel case (notice the capitalization): `Silent` [INFO] [stderr] [INFO] [stderr] warning: unused import: `pileup` [INFO] [stderr] --> src/bin/motif_summary/data.rs:5:56 [INFO] [stderr] | [INFO] [stderr] 5 | use rustymotif_utils::{modtype::ModType, motif::Motif, pileup, strand::Strand}; [INFO] [stderr] | ^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `info` [INFO] [stderr] --> src/bin/motif_summary/data.rs:6:18 [INFO] [stderr] | [INFO] [stderr] 6 | use log::{debug, info}; [INFO] [stderr] | ^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `anyhow` [INFO] [stderr] --> src/bin/motif_summary/data.rs:7:14 [INFO] [stderr] | [INFO] [stderr] 7 | use anyhow::{anyhow, Ok}; [INFO] [stderr] | ^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `crate::sequence::Contig` [INFO] [stderr] --> src/bin/motif_summary/fasta_reader.rs:1:5 [INFO] [stderr] | [INFO] [stderr] 1 | use crate::sequence::Contig; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `std::collections::HashSet` [INFO] [stderr] --> src/bin/motif_summary/sequence.rs:1:5 [INFO] [stderr] | [INFO] [stderr] 1 | use std::collections::HashSet; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `anyhow::anyhow` [INFO] [stderr] --> src/bin/motif_summary/sequence.rs:6:5 [INFO] [stderr] | [INFO] [stderr] 6 | use anyhow::anyhow; [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `bio::bio_types::annot::contig` [INFO] [stderr] --> src/bin/motif_summary/sequence.rs:320:9 [INFO] [stderr] | [INFO] [stderr] 320 | use bio::bio_types::annot::contig; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused imports: `debug`, `info`, and `warn` [INFO] [stderr] --> src/bin/motif_summary/io.rs:9:11 [INFO] [stderr] | [INFO] [stderr] 9 | use log::{info, debug, warn}; [INFO] [stderr] | ^^^^ ^^^^^ ^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `std::fs::File` [INFO] [stderr] --> src/bin/motif_summary/io.rs:234:9 [INFO] [stderr] | [INFO] [stderr] 234 | use std::fs::File; [INFO] [stderr] | ^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `std::collections::HashMap` [INFO] [stderr] --> src/bin/motif_summary/io.rs:237:9 [INFO] [stderr] | [INFO] [stderr] 237 | use std::collections::HashMap; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `WriterBuilder` [INFO] [stderr] --> src/bin/motif_summary/motif_summary.rs:10:11 [INFO] [stderr] | [INFO] [stderr] 10 | use csv::{WriterBuilder}; [INFO] [stderr] | ^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `std::io::Write` [INFO] [stderr] --> src/bin/motif_summary/io.rs:235:9 [INFO] [stderr] | [INFO] [stderr] 235 | use std::io::Write; [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused variable: `mod_type` [INFO] [stderr] --> src/bin/motif_summary/io.rs:215:15 [INFO] [stderr] | [INFO] [stderr] 215 | for ((mod_type, strand), data) in summary.summary.into_iter() { [INFO] [stderr] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mod_type` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: unused variable: `strand` [INFO] [stderr] --> src/bin/motif_summary/io.rs:215:25 [INFO] [stderr] | [INFO] [stderr] 215 | for ((mod_type, strand), data) in summary.summary.into_iter() { [INFO] [stderr] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_strand` [INFO] [stderr] [INFO] [stderr] warning: method `remove_record_at_motif_indices` is never used [INFO] [stderr] --> src/bin/motif_summary/sequence.rs:86:12 [INFO] [stderr] | [INFO] [stderr] 22 | impl Contig { [INFO] [stderr] | ----------- method in this implementation [INFO] [stderr] ... [INFO] [stderr] 86 | pub fn remove_record_at_motif_indices( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: methods `add_other` and `remove_motif_matching_sequences` are never used [INFO] [stderr] --> src/bin/motif_summary/sequence.rs:136:12 [INFO] [stderr] | [INFO] [stderr] 112 | impl EqualLengthDNASet { [INFO] [stderr] | ---------------------- methods in this implementation [INFO] [stderr] ... [INFO] [stderr] 136 | pub fn add_other(&mut self, other: &Self) -> Result<()> { [INFO] [stderr] | ^^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 228 | pub fn remove_motif_matching_sequences(&self, motif: &Motif) -> Result { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: methods `length` and `bases_above_freq` are never used [INFO] [stderr] --> src/bin/motif_summary/sequence.rs:280:12 [INFO] [stderr] | [INFO] [stderr] 274 | impl PSSM { [INFO] [stderr] | --------- methods in this implementation [INFO] [stderr] ... [INFO] [stderr] 280 | pub fn length(&self) -> usize { [INFO] [stderr] | ^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 302 | pub fn bases_above_freq(&self, position: u8, min_freq: f64) -> Vec { [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: field `file` is never read [INFO] [stderr] --> src/bin/motif_summary/io.rs:171:5 [INFO] [stderr] | [INFO] [stderr] 170 | pub struct AnnotatedRecordSummaryWriter { [INFO] [stderr] | ---------------------------- field in this struct [INFO] [stderr] 171 | file: File, [INFO] [stderr] | ^^^^ [INFO] [stderr] [INFO] [stderr] warning: using `.clone()` on a double reference, which returns `&PileupRecord` instead of cloning the inner type [INFO] [stderr] --> src/bin/motif_summary/motif_summary.rs:112:43 [INFO] [stderr] | [INFO] [stderr] 112 | ... record.clone().clone(), [INFO] [stderr] | ^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(suspicious_double_ref_op)]` on by default [INFO] [stderr] [INFO] [stderr] warning: `rustymotif` (bin "preprocess" test) generated 7 warnings (run `cargo fix --bin "preprocess" --tests` to apply 4 suggestions) [INFO] [stderr] warning: `rustymotif` (bin "mixedmotif" test) generated 45 warnings (run `cargo fix --bin "mixedmotif" --tests` to apply 22 suggestions) [INFO] [stderr] warning: `rustymotif` (bin "rustymotif" test) generated 26 warnings (run `cargo fix --bin "rustymotif" --tests` to apply 16 suggestions) [INFO] [stderr] warning: `rustymotif` (bin "motif_summary" test) generated 23 warnings (run `cargo fix --bin "motif_summary" --tests` to apply 12 suggestions) [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.32s [INFO] [stderr] Running unittests src/lib/lib.rs (/opt/rustwide/target/debug/deps/rustymotif_utils-994175f20d39e974) [INFO] [stdout] [INFO] [stdout] running 26 tests [INFO] [stdout] test iupac::tests::test_complement ... ok [INFO] [stdout] test modtype::tests::test_display ... ok [INFO] [stdout] test modtype::tests::test_from_str ... ok [INFO] [stdout] test modtype::tests::test_to_pileup_code ... ok [INFO] [stdout] test modtype::tests::test_from_str_error ... ok [INFO] [stdout] test motif::tests::test_motif_grow_motif_at ... ok [INFO] [stdout] test motif::tests::test_motif_pair_new ... ok [INFO] [stdout] test pileup::tests::test_new_pileup_record ... ok [INFO] [stdout] test iupac::tests::test_to_regex ... ok [INFO] [stdout] test pileup::tests::test_pileup_record_to_bed_fields ... ok [INFO] [stdout] test pileup::tests::test_parse_and_validate_record ... ok [INFO] [stdout] test preprocess::tests::test_add_record_and_get ... ok [INFO] [stdout] test preprocess::tests::test_add_records_reference_mismatch_panics ... ok [INFO] [stdout] test preprocess::tests::test_filter_chunk_coverage_filtering ... ok [INFO] [stdout] test preprocess::tests::test_from_chunk ... ok [INFO] [stdout] test preprocess::tests::test_new_empty_hashmap ... ok [INFO] [stdout] test preprocess::tests::test_remove_windows_with_high_methylation ... ok [INFO] [stdout] test pileup::tests::test_new_pileup_chunk_reader ... ok [INFO] [stdout] test pileup::tests::test_n_chunks ... ok [INFO] [stdout] test preprocess::tests::test_remove_windows_with_high_methylation_close_windows ... ok [INFO] [stdout] test motif::tests::test_reverse_complement ... ok [INFO] [stdout] test preprocess::tests::test_retain_max_mod_per_pos_strand ... ok [INFO] [stdout] test pileup::tests::test_with_tempfile ... ok [INFO] [stdout] test pileup::tests::test_low_coverage_filtering ... ok [INFO] [stdout] test motif::tests::test_new ... ok [INFO] [stdout] test pileup::tests::test_new_pileup_chunk ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 26 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.02s [INFO] [stdout] [INFO] [stderr] Running unittests src/bin/mixedmotif/main.rs (/opt/rustwide/target/debug/deps/mixedmotif-4efd3512c6c857e9) [INFO] [stdout] [INFO] [stdout] running 12 tests [INFO] [stdout] test sequence::tests::test_contig_add_records ... ok [INFO] [stdout] test data::tests::test_genome_workspace_builder ... ok [INFO] [stdout] test sequence::tests::test_contig_find_motif_indices ... ok [INFO] [stdout] test sequence::tests::test_contig_populate_methylation_levels ... ok [INFO] [stdout] test sequence::tests::test_contig_extract_subsequences ... ok [INFO] [stdout] test sequence::tests::test_pssm_kl_divergence ... ok [INFO] [stdout] test sequence::tests::test_equal_length_dna_set_empty ... ok [INFO] [stdout] test sequence::tests::test_equal_length_dna_set_new ... ok [INFO] [stdout] test sequence::tests::test_equal_length_dna_set_pssm ... ok [INFO] [stdout] test sequence::tests::test_contig_add_record ... ok [INFO] [stdout] test sequence::tests::test_equal_length_dna_set_get_motif_matching_sequences ... ok [INFO] [stdout] test sequence::tests::test_equal_length_dna_set_reverse_complement ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 12 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s [INFO] [stdout] [INFO] [stderr] Running unittests src/bin/motif_summary/main.rs (/opt/rustwide/target/debug/deps/motif_summary-4c6ee816ef54358b) [INFO] [stdout] [INFO] [stdout] running 16 tests [INFO] [stdout] test io::tests::test_load_bin_motifs ... ok [INFO] [stdout] test sequence::tests::test_contig_add_records ... ok [INFO] [stdout] test sequence::tests::test_contig_extract_subsequences ... ok [INFO] [stdout] test sequence::tests::test_contig_add_record ... ok [INFO] [stdout] test sequence::tests::test_equal_length_dna_set_empty ... ok [INFO] [stdout] test io::tests::test_load_contig_bin ... ok [INFO] [stdout] test sequence::tests::test_contig_find_motif_indices ... ok [INFO] [stdout] test sequence::tests::test_equal_length_dna_set_pssm ... ok [INFO] [stdout] test data::tests::test_genome_workspace_builder ... ok [INFO] [stdout] test sequence::tests::test_equal_length_dna_set_reverse_complement ... ok [INFO] [stdout] test sequence::tests::test_pssm_kl_divergence ... ok [INFO] [stdout] test io::tests::test_annotated_record_writer ... FAILED [INFO] [stdout] test sequence::tests::test_equal_length_dna_set_new ... ok [INFO] [stdout] test io::tests::test_annotated_record_writer_multiple_records ... FAILED [INFO] [stdout] test sequence::tests::test_equal_length_dna_set_get_motif_matching_sequences ... ok [INFO] [stdout] test io::tests::test_annotated_record_writer_empty_motifs ... FAILED [INFO] [stdout] [INFO] [stdout] failures: [INFO] [stdout] [INFO] [stdout] ---- io::tests::test_annotated_record_writer stdout ---- [INFO] [stdout] [INFO] [stdout] thread 'io::tests::test_annotated_record_writer' (59) panicked at src/bin/motif_summary/io.rs:261:64: [INFO] [stdout] Failed to create writer: Read-only file system (os error 30) [INFO] [stdout] [INFO] [stdout] Stack backtrace: [INFO] [stdout] 0: anyhow::error:: for anyhow::Error>::from [INFO] [stdout] at /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/anyhow-1.0.98/src/backtrace.rs:27:14 [INFO] [stdout] 1: as core::ops::try_trait::FromResidual>>::from_residual [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/result.rs:2177:27 [INFO] [stdout] 2: motif_summary::io::AnnotatedRecordWriter::new [INFO] [stdout] at ./src/bin/motif_summary/io.rs:107:20 [INFO] [stdout] 3: motif_summary::io::tests::test_annotated_record_writer [INFO] [stdout] at ./src/bin/motif_summary/io.rs:261:26 [INFO] [stdout] 4: motif_summary::io::tests::test_annotated_record_writer::{{closure}} [INFO] [stdout] at ./src/bin/motif_summary/io.rs:259:38 [INFO] [stdout] 5: core::ops::function::FnOnce::call_once [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 6: core::ops::function::FnOnce::call_once [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 7: test::__rust_begin_short_backtrace [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:663:18 [INFO] [stdout] 8: test::run_test_in_process::{{closure}} [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:686:74 [INFO] [stdout] 9: as core::ops::function::FnOnce<()>>::call_once [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/panic/unwind_safe.rs:274:9 [INFO] [stdout] 10: std::panicking::catch_unwind::do_call [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:590:40 [INFO] [stdout] 11: std::panicking::catch_unwind [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:553:19 [INFO] [stdout] 12: std::panic::catch_unwind [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panic.rs:359:14 [INFO] [stdout] 13: test::run_test_in_process [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:686:27 [INFO] [stdout] 14: test::run_test::{{closure}} [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:607:43 [INFO] [stdout] 15: test::run_test::{{closure}} [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:637:41 [INFO] [stdout] 16: std::sys::backtrace::__rust_begin_short_backtrace [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/backtrace.rs:158:18 [INFO] [stdout] 17: std::thread::Builder::spawn_unchecked_::{{closure}}::{{closure}} [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/thread/mod.rs:559:17 [INFO] [stdout] 18: as core::ops::function::FnOnce<()>>::call_once [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/panic/unwind_safe.rs:274:9 [INFO] [stdout] 19: std::panicking::catch_unwind::do_call [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:590:40 [INFO] [stdout] 20: std::panicking::catch_unwind [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:553:19 [INFO] [stdout] 21: std::panic::catch_unwind [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panic.rs:359:14 [INFO] [stdout] 22: std::thread::Builder::spawn_unchecked_::{{closure}} [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/thread/mod.rs:557:30 [INFO] [stdout] 23: core::ops::function::FnOnce::call_once{{vtable.shim}} [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 24: as core::ops::function::FnOnce>::call_once [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/alloc/src/boxed.rs:1973:9 [INFO] [stdout] 25: std::sys::thread::unix::Thread::new::thread_start [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/thread/unix.rs:126:17 [INFO] [stdout] 26: [INFO] [stdout] 27: clone [INFO] [stdout] stack backtrace: [INFO] [stdout] 0: 0x5b05007f79f2 - std::backtrace_rs::backtrace::libunwind::trace::h22a6a535a50603c6 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/../../backtrace/src/backtrace/libunwind.rs:117:9 [INFO] [stdout] 1: 0x5b05007f79f2 - std::backtrace_rs::backtrace::trace_unsynchronized::h2503a4f30dbfbaa2 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/../../backtrace/src/backtrace/mod.rs:66:14 [INFO] [stdout] 2: 0x5b05007f79f2 - std::sys::backtrace::_print_fmt::hec54e31f36456895 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/backtrace.rs:66:9 [INFO] [stdout] 3: 0x5b05007f79f2 - ::fmt::hb1988e8b50fa5f19 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/backtrace.rs:39:26 [INFO] [stdout] 4: 0x5b0500808d2f - core::fmt::rt::Argument::fmt::h3118a66e1a57a586 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/fmt/rt.rs:173:76 [INFO] [stdout] 5: 0x5b0500808d2f - core::fmt::write::hcd056e06a609f600 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/fmt/mod.rs:1468:25 [INFO] [stdout] 6: 0x5b05007c34c1 - std::io::default_write_fmt::hdabc5d6505cb374b [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/io/mod.rs:639:11 [INFO] [stdout] 7: 0x5b05007c34c1 - std::io::Write::write_fmt::h18c82179fdc1f9d2 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/io/mod.rs:1954:13 [INFO] [stdout] 8: 0x5b05007cf912 - std::sys::backtrace::BacktraceLock::print::h69f50ba7cfff8317 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/backtrace.rs:42:9 [INFO] [stdout] 9: 0x5b05007d4dff - std::panicking::default_hook::{{closure}}::hfa978eb2255ab3ab [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:301:27 [INFO] [stdout] 10: 0x5b05007d4c91 - std::panicking::default_hook::h09da2eaf8f1deadd [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:325:9 [INFO] [stdout] 11: 0x5b05004cd30e - as core::ops::function::Fn>::call::h1697e4d80f236ef6 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/alloc/src/boxed.rs:1987:9 [INFO] [stdout] 12: 0x5b05004cd30e - test::test_main_with_exit_callback::{{closure}}::h8f63929ca9fd483b [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:145:21 [INFO] [stdout] 13: 0x5b05007d54bf - as core::ops::function::Fn>::call::hba67e0dc3e3fc548 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/alloc/src/boxed.rs:1987:9 [INFO] [stdout] 14: 0x5b05007d54bf - std::panicking::panic_with_hook::h13c40d280d130fd3 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:842:13 [INFO] [stdout] 15: 0x5b05007d531a - std::panicking::panic_handler::{{closure}}::hd79d22e8a1d3b951 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:707:13 [INFO] [stdout] 16: 0x5b05007cfa49 - std::sys::backtrace::__rust_end_short_backtrace::h83414d1ec69cf3a6 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/backtrace.rs:174:18 [INFO] [stdout] 17: 0x5b05007b740d - __rustc[b78aa6c7b08e5dc4]::rust_begin_unwind [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:698:5 [INFO] [stdout] 18: 0x5b0500812d70 - core::panicking::panic_fmt::h326b75cf8ee01b13 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/panicking.rs:78:14 [INFO] [stdout] 19: 0x5b0500812106 - core::result::unwrap_failed::h38baee32fdec5ac8 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/result.rs:1855:5 [INFO] [stdout] 20: 0x5b050049a2b3 - core::result::Result::expect::hb5d56a4bcb687b9c [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/result.rs:1178:23 [INFO] [stdout] 21: 0x5b05004887ee - motif_summary::io::tests::test_annotated_record_writer::h5b7f4be3d68eb737 [INFO] [stdout] at /opt/rustwide/workdir/src/bin/motif_summary/io.rs:261:64 [INFO] [stdout] 22: 0x5b05004890a7 - motif_summary::io::tests::test_annotated_record_writer::{{closure}}::h50b372ee7fd17084 [INFO] [stdout] at /opt/rustwide/workdir/src/bin/motif_summary/io.rs:259:38 [INFO] [stdout] 23: 0x5b05004a8c06 - core::ops::function::FnOnce::call_once::h10f025896a04ab89 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 24: 0x5b05004cd0eb - core::ops::function::FnOnce::call_once::he420dad47d9aac14 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 25: 0x5b05004cd0eb - test::__rust_begin_short_backtrace::h51976f55c263f7c2 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:663:18 [INFO] [stdout] 26: 0x5b05004e2d15 - test::run_test_in_process::{{closure}}::h6aa4339396d33320 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:686:74 [INFO] [stdout] 27: 0x5b05004e2d15 - as core::ops::function::FnOnce<()>>::call_once::h5bd0ba3863a53529 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/panic/unwind_safe.rs:274:9 [INFO] [stdout] 28: 0x5b05004e2d15 - std::panicking::catch_unwind::do_call::h5c710722c40c5839 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:590:40 [INFO] [stdout] 29: 0x5b05004e2d15 - std::panicking::catch_unwind::hf41b5be070ce0f19 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:553:19 [INFO] [stdout] 30: 0x5b05004e2d15 - std::panic::catch_unwind::h4559aa103e6f16d6 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panic.rs:359:14 [INFO] [stdout] 31: 0x5b05004e2d15 - test::run_test_in_process::he6fd763a772ff213 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:686:27 [INFO] [stdout] 32: 0x5b05004e2d15 - test::run_test::{{closure}}::he46f5435849feb5b [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:607:43 [INFO] [stdout] 33: 0x5b05004b9524 - test::run_test::{{closure}}::h12a66289c31b502a [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:637:41 [INFO] [stdout] 34: 0x5b05004b9524 - std::sys::backtrace::__rust_begin_short_backtrace::h614a7925ed7b2f5e [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/backtrace.rs:158:18 [INFO] [stdout] 35: 0x5b05004bceca - std::thread::Builder::spawn_unchecked_::{{closure}}::{{closure}}::hbc654088c5dbff36 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/thread/mod.rs:559:17 [INFO] [stdout] 36: 0x5b05004bceca - as core::ops::function::FnOnce<()>>::call_once::h3f631d2ca531b61d [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/panic/unwind_safe.rs:274:9 [INFO] [stdout] 37: 0x5b05004bceca - std::panicking::catch_unwind::do_call::hd2548748db0aa717 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:590:40 [INFO] [stdout] 38: 0x5b05004bceca - std::panicking::catch_unwind::hf7d8620d84df48e2 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:553:19 [INFO] [stdout] 39: 0x5b05004bceca - std::panic::catch_unwind::hdde75b8543fcb96b [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panic.rs:359:14 [INFO] [stdout] 40: 0x5b05004bceca - std::thread::Builder::spawn_unchecked_::{{closure}}::h991e7d03b432cf3f [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/thread/mod.rs:557:30 [INFO] [stdout] 41: 0x5b05004bceca - core::ops::function::FnOnce::call_once{{vtable.shim}}::hebddb40255441657 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 42: 0x5b05007cab8f - as core::ops::function::FnOnce>::call_once::h55e8930dc7db99a5 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/alloc/src/boxed.rs:1973:9 [INFO] [stdout] 43: 0x5b05007cab8f - std::sys::thread::unix::Thread::new::thread_start::he23d038ee4fa004e [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/thread/unix.rs:126:17 [INFO] [stdout] 44: 0x7d80742eeaa4 - [INFO] [stdout] 45: 0x7d807437ba34 - clone [INFO] [stdout] 46: 0x0 - [INFO] [stdout] [INFO] [stdout] ---- io::tests::test_annotated_record_writer_multiple_records stdout ---- [INFO] [stdout] [INFO] [stdout] thread 'io::tests::test_annotated_record_writer_multiple_records' (61) panicked at src/bin/motif_summary/io.rs:325:64: [INFO] [stdout] Failed to create writer: Read-only file system (os error 30) [INFO] [stdout] [INFO] [stdout] Stack backtrace: [INFO] [stdout] 0: anyhow::error:: for anyhow::Error>::from [INFO] [stdout] at /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/anyhow-1.0.98/src/backtrace.rs:27:14 [INFO] [stdout] 1: as core::ops::try_trait::FromResidual>>::from_residual [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/result.rs:2177:27 [INFO] [stdout] 2: motif_summary::io::AnnotatedRecordWriter::new [INFO] [stdout] at ./src/bin/motif_summary/io.rs:107:20 [INFO] [stdout] 3: motif_summary::io::tests::test_annotated_record_writer_multiple_records [INFO] [stdout] at ./src/bin/motif_summary/io.rs:325:26 [INFO] [stdout] 4: motif_summary::io::tests::test_annotated_record_writer_multiple_records::{{closure}} [INFO] [stdout] at ./src/bin/motif_summary/io.rs:323:55 [INFO] [stdout] 5: core::ops::function::FnOnce::call_once [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 6: core::ops::function::FnOnce::call_once [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 7: test::__rust_begin_short_backtrace [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:663:18 [INFO] [stdout] 8: test::run_test_in_process::{{closure}} [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:686:74 [INFO] [stdout] 9: as core::ops::function::FnOnce<()>>::call_once [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/panic/unwind_safe.rs:274:9 [INFO] [stdout] 10: std::panicking::catch_unwind::do_call [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:590:40 [INFO] [stdout] 11: std::panicking::catch_unwind [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:553:19 [INFO] [stdout] 12: std::panic::catch_unwind [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panic.rs:359:14 [INFO] [stdout] 13: test::run_test_in_process [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:686:27 [INFO] [stdout] 14: test::run_test::{{closure}} [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:607:43 [INFO] [stdout] 15: test::run_test::{{closure}} [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:637:41 [INFO] [stdout] 16: std::sys::backtrace::__rust_begin_short_backtrace [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/backtrace.rs:158:18 [INFO] [stdout] 17: std::thread::Builder::spawn_unchecked_::{{closure}}::{{closure}} [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/thread/mod.rs:559:17 [INFO] [stdout] 18: as core::ops::function::FnOnce<()>>::call_once [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/panic/unwind_safe.rs:274:9 [INFO] [stdout] 19: std::panicking::catch_unwind::do_call [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:590:40 [INFO] [stdout] 20: std::panicking::catch_unwind [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:553:19 [INFO] [stdout] 21: std::panic::catch_unwind [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panic.rs:359:14 [INFO] [stdout] 22: std::thread::Builder::spawn_unchecked_::{{closure}} [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/thread/mod.rs:557:30 [INFO] [stdout] 23: core::ops::function::FnOnce::call_once{{vtable.shim}} [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 24: as core::ops::function::FnOnce>::call_once [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/alloc/src/boxed.rs:1973:9 [INFO] [stdout] 25: std::sys::thread::unix::Thread::new::thread_start [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/thread/unix.rs:126:17 [INFO] [stdout] 26: [INFO] [stdout] 27: clone [INFO] [stdout] stack backtrace: [INFO] [stdout] 0: 0x5b05007f79f2 - std::backtrace_rs::backtrace::libunwind::trace::h22a6a535a50603c6 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/../../backtrace/src/backtrace/libunwind.rs:117:9 [INFO] [stdout] 1: 0x5b05007f79f2 - std::backtrace_rs::backtrace::trace_unsynchronized::h2503a4f30dbfbaa2 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/../../backtrace/src/backtrace/mod.rs:66:14 [INFO] [stdout] 2: 0x5b05007f79f2 - std::sys::backtrace::_print_fmt::hec54e31f36456895 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/backtrace.rs:66:9 [INFO] [stdout] 3: 0x5b05007f79f2 - ::fmt::hb1988e8b50fa5f19 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/backtrace.rs:39:26 [INFO] [stdout] 4: 0x5b0500808d2f - core::fmt::rt::Argument::fmt::h3118a66e1a57a586 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/fmt/rt.rs:173:76 [INFO] [stdout] 5: 0x5b0500808d2f - core::fmt::write::hcd056e06a609f600 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/fmt/mod.rs:1468:25 [INFO] [stdout] 6: 0x5b05007c34c1 - std::io::default_write_fmt::hdabc5d6505cb374b [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/io/mod.rs:639:11 [INFO] [stdout] 7: 0x5b05007c34c1 - std::io::Write::write_fmt::h18c82179fdc1f9d2 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/io/mod.rs:1954:13 [INFO] [stdout] 8: 0x5b05007cf912 - std::sys::backtrace::BacktraceLock::print::h69f50ba7cfff8317 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/backtrace.rs:42:9 [INFO] [stdout] 9: 0x5b05007d4dff - std::panicking::default_hook::{{closure}}::hfa978eb2255ab3ab [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:301:27 [INFO] [stdout] 10: 0x5b05007d4c91 - std::panicking::default_hook::h09da2eaf8f1deadd [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:325:9 [INFO] [stdout] 11: 0x5b05004cd30e - as core::ops::function::Fn>::call::h1697e4d80f236ef6 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/alloc/src/boxed.rs:1987:9 [INFO] [stdout] 12: 0x5b05004cd30e - test::test_main_with_exit_callback::{{closure}}::h8f63929ca9fd483b [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:145:21 [INFO] [stdout] 13: 0x5b05007d54bf - as core::ops::function::Fn>::call::hba67e0dc3e3fc548 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/alloc/src/boxed.rs:1987:9 [INFO] [stdout] 14: 0x5b05007d54bf - std::panicking::panic_with_hook::h13c40d280d130fd3 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:842:13 [INFO] [stdout] 15: 0x5b05007d531a - std::panicking::panic_handler::{{closure}}::hd79d22e8a1d3b951 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:707:13 [INFO] [stdout] 16: 0x5b05007cfa49 - std::sys::backtrace::__rust_end_short_backtrace::h83414d1ec69cf3a6 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/backtrace.rs:174:18 [INFO] [stdout] 17: 0x5b05007b740d - __rustc[b78aa6c7b08e5dc4]::rust_begin_unwind [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:698:5 [INFO] [stdout] 18: 0x5b0500812d70 - core::panicking::panic_fmt::h326b75cf8ee01b13 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/panicking.rs:78:14 [INFO] [stdout] 19: 0x5b0500812106 - core::result::unwrap_failed::h38baee32fdec5ac8 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/result.rs:1855:5 [INFO] [stdout] 20: 0x5b050049a2b3 - core::result::Result::expect::hb5d56a4bcb687b9c [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/result.rs:1178:23 [INFO] [stdout] 21: 0x5b0500489886 - motif_summary::io::tests::test_annotated_record_writer_multiple_records::h333dbf105ee405f1 [INFO] [stdout] at /opt/rustwide/workdir/src/bin/motif_summary/io.rs:325:64 [INFO] [stdout] 22: 0x5b050048a6b7 - motif_summary::io::tests::test_annotated_record_writer_multiple_records::{{closure}}::h0ac8a7e5c896d70d [INFO] [stdout] at /opt/rustwide/workdir/src/bin/motif_summary/io.rs:323:55 [INFO] [stdout] 23: 0x5b05004a9156 - core::ops::function::FnOnce::call_once::h9400779a7e17a9d1 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 24: 0x5b05004cd0eb - core::ops::function::FnOnce::call_once::he420dad47d9aac14 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 25: 0x5b05004cd0eb - test::__rust_begin_short_backtrace::h51976f55c263f7c2 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:663:18 [INFO] [stdout] 26: 0x5b05004e2d15 - test::run_test_in_process::{{closure}}::h6aa4339396d33320 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:686:74 [INFO] [stdout] 27: 0x5b05004e2d15 - as core::ops::function::FnOnce<()>>::call_once::h5bd0ba3863a53529 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/panic/unwind_safe.rs:274:9 [INFO] [stdout] 28: 0x5b05004e2d15 - std::panicking::catch_unwind::do_call::h5c710722c40c5839 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:590:40 [INFO] [stdout] 29: 0x5b05004e2d15 - std::panicking::catch_unwind::hf41b5be070ce0f19 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:553:19 [INFO] [stdout] 30: 0x5b05004e2d15 - std::panic::catch_unwind::h4559aa103e6f16d6 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panic.rs:359:14 [INFO] [stdout] 31: 0x5b05004e2d15 - test::run_test_in_process::he6fd763a772ff213 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:686:27 [INFO] [stdout] 32: 0x5b05004e2d15 - test::run_test::{{closure}}::he46f5435849feb5b [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:607:43 [INFO] [stdout] 33: 0x5b05004b9524 - test::run_test::{{closure}}::h12a66289c31b502a [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:637:41 [INFO] [stdout] 34: 0x5b05004b9524 - std::sys::backtrace::__rust_begin_short_backtrace::h614a7925ed7b2f5e [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/backtrace.rs:158:18 [INFO] [stdout] 35: 0x5b05004bceca - std::thread::Builder::spawn_unchecked_::{{closure}}::{{closure}}::hbc654088c5dbff36 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/thread/mod.rs:559:17 [INFO] [stdout] 36: 0x5b05004bceca - as core::ops::function::FnOnce<()>>::call_once::h3f631d2ca531b61d [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/panic/unwind_safe.rs:274:9 [INFO] [stdout] 37: 0x5b05004bceca - std::panicking::catch_unwind::do_call::hd2548748db0aa717 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:590:40 [INFO] [stdout] 38: 0x5b05004bceca - std::panicking::catch_unwind::hf7d8620d84df48e2 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:553:19 [INFO] [stdout] 39: 0x5b05004bceca - std::panic::catch_unwind::hdde75b8543fcb96b [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panic.rs:359:14 [INFO] [stdout] 40: 0x5b05004bceca - std::thread::Builder::spawn_unchecked_::{{closure}}::h991e7d03b432cf3f [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/thread/mod.rs:557:30 [INFO] [stdout] 41: 0x5b05004bceca - core::ops::function::FnOnce::call_once{{vtable.shim}}::hebddb40255441657 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 42: 0x5b05007cab8f - as core::ops::function::FnOnce>::call_once::h55e8930dc7db99a5 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/alloc/src/boxed.rs:1973:9 [INFO] [stdout] 43: 0x5b05007cab8f - std::sys::thread::unix::Thread::new::thread_start::he23d038ee4fa004e [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/thread/unix.rs:126:17 [INFO] [stdout] 44: 0x7d80742eeaa4 - [INFO] [stdout] 45: 0x7d807437ba34 - clone [INFO] [stdout] 46: 0x0 - [INFO] [stdout] [INFO] [stdout] ---- io::tests::test_annotated_record_writer_empty_motifs stdout ---- [INFO] [stdout] [INFO] [stdout] thread 'io::tests::test_annotated_record_writer_empty_motifs' (60) panicked at src/bin/motif_summary/io.rs:293:64: [INFO] [stdout] Failed to create writer: Read-only file system (os error 30) [INFO] [stdout] [INFO] [stdout] Stack backtrace: [INFO] [stdout] 0: anyhow::error:: for anyhow::Error>::from [INFO] [stdout] at /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/anyhow-1.0.98/src/backtrace.rs:27:14 [INFO] [stdout] 1: as core::ops::try_trait::FromResidual>>::from_residual [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/result.rs:2177:27 [INFO] [stdout] 2: motif_summary::io::AnnotatedRecordWriter::new [INFO] [stdout] at ./src/bin/motif_summary/io.rs:107:20 [INFO] [stdout] 3: motif_summary::io::tests::test_annotated_record_writer_empty_motifs [INFO] [stdout] at ./src/bin/motif_summary/io.rs:293:26 [INFO] [stdout] 4: motif_summary::io::tests::test_annotated_record_writer_empty_motifs::{{closure}} [INFO] [stdout] at ./src/bin/motif_summary/io.rs:291:51 [INFO] [stdout] 5: core::ops::function::FnOnce::call_once [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 6: core::ops::function::FnOnce::call_once [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 7: test::__rust_begin_short_backtrace [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:663:18 [INFO] [stdout] 8: test::run_test_in_process::{{closure}} [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:686:74 [INFO] [stdout] 9: as core::ops::function::FnOnce<()>>::call_once [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/panic/unwind_safe.rs:274:9 [INFO] [stdout] 10: std::panicking::catch_unwind::do_call [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:590:40 [INFO] [stdout] 11: std::panicking::catch_unwind [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:553:19 [INFO] [stderr] error: test failed, to rerun pass `--bin motif_summary` [INFO] [stdout] 12: std::panic::catch_unwind [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panic.rs:359:14 [INFO] [stdout] 13: test::run_test_in_process [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:686:27 [INFO] [stdout] 14: test::run_test::{{closure}} [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:607:43 [INFO] [stdout] 15: test::run_test::{{closure}} [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:637:41 [INFO] [stdout] 16: std::sys::backtrace::__rust_begin_short_backtrace [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/backtrace.rs:158:18 [INFO] [stdout] 17: std::thread::Builder::spawn_unchecked_::{{closure}}::{{closure}} [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/thread/mod.rs:559:17 [INFO] [stdout] 18: as core::ops::function::FnOnce<()>>::call_once [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/panic/unwind_safe.rs:274:9 [INFO] [stdout] 19: std::panicking::catch_unwind::do_call [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:590:40 [INFO] [stdout] 20: std::panicking::catch_unwind [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:553:19 [INFO] [stdout] 21: std::panic::catch_unwind [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panic.rs:359:14 [INFO] [stdout] 22: std::thread::Builder::spawn_unchecked_::{{closure}} [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/thread/mod.rs:557:30 [INFO] [stdout] 23: core::ops::function::FnOnce::call_once{{vtable.shim}} [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 24: as core::ops::function::FnOnce>::call_once [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/alloc/src/boxed.rs:1973:9 [INFO] [stdout] 25: std::sys::thread::unix::Thread::new::thread_start [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/thread/unix.rs:126:17 [INFO] [stdout] 26: [INFO] [stdout] 27: clone [INFO] [stdout] stack backtrace: [INFO] [stdout] 0: 0x5b05007f79f2 - std::backtrace_rs::backtrace::libunwind::trace::h22a6a535a50603c6 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/../../backtrace/src/backtrace/libunwind.rs:117:9 [INFO] [stdout] 1: 0x5b05007f79f2 - std::backtrace_rs::backtrace::trace_unsynchronized::h2503a4f30dbfbaa2 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/../../backtrace/src/backtrace/mod.rs:66:14 [INFO] [stdout] 2: 0x5b05007f79f2 - std::sys::backtrace::_print_fmt::hec54e31f36456895 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/backtrace.rs:66:9 [INFO] [stdout] 3: 0x5b05007f79f2 - ::fmt::hb1988e8b50fa5f19 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/backtrace.rs:39:26 [INFO] [stdout] 4: 0x5b0500808d2f - core::fmt::rt::Argument::fmt::h3118a66e1a57a586 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/fmt/rt.rs:173:76 [INFO] [stdout] 5: 0x5b0500808d2f - core::fmt::write::hcd056e06a609f600 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/fmt/mod.rs:1468:25 [INFO] [stdout] 6: 0x5b05007c34c1 - std::io::default_write_fmt::hdabc5d6505cb374b [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/io/mod.rs:639:11 [INFO] [stdout] 7: 0x5b05007c34c1 - std::io::Write::write_fmt::h18c82179fdc1f9d2 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/io/mod.rs:1954:13 [INFO] [stdout] 8: 0x5b05007cf912 - std::sys::backtrace::BacktraceLock::print::h69f50ba7cfff8317 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/backtrace.rs:42:9 [INFO] [stdout] 9: 0x5b05007d4dff - std::panicking::default_hook::{{closure}}::hfa978eb2255ab3ab [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:301:27 [INFO] [stdout] 10: 0x5b05007d4c91 - std::panicking::default_hook::h09da2eaf8f1deadd [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:325:9 [INFO] [stdout] 11: 0x5b05004cd30e - as core::ops::function::Fn>::call::h1697e4d80f236ef6 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/alloc/src/boxed.rs:1987:9 [INFO] [stdout] 12: 0x5b05004cd30e - test::test_main_with_exit_callback::{{closure}}::h8f63929ca9fd483b [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:145:21 [INFO] [stdout] 13: 0x5b05007d54bf - as core::ops::function::Fn>::call::hba67e0dc3e3fc548 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/alloc/src/boxed.rs:1987:9 [INFO] [stdout] 14: 0x5b05007d54bf - std::panicking::panic_with_hook::h13c40d280d130fd3 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:842:13 [INFO] [stdout] 15: 0x5b05007d531a - std::panicking::panic_handler::{{closure}}::hd79d22e8a1d3b951 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:707:13 [INFO] [stdout] 16: 0x5b05007cfa49 - std::sys::backtrace::__rust_end_short_backtrace::h83414d1ec69cf3a6 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/backtrace.rs:174:18 [INFO] [stdout] 17: 0x5b05007b740d - __rustc[b78aa6c7b08e5dc4]::rust_begin_unwind [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:698:5 [INFO] [stdout] 18: 0x5b0500812d70 - core::panicking::panic_fmt::h326b75cf8ee01b13 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/panicking.rs:78:14 [INFO] [stdout] 19: 0x5b0500812106 - core::result::unwrap_failed::h38baee32fdec5ac8 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/result.rs:1855:5 [INFO] [stdout] 20: 0x5b050049a2b3 - core::result::Result::expect::hb5d56a4bcb687b9c [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/result.rs:1178:23 [INFO] [stdout] 21: 0x5b050048914e - motif_summary::io::tests::test_annotated_record_writer_empty_motifs::hb9b2b8601bc9d1e0 [INFO] [stdout] at /opt/rustwide/workdir/src/bin/motif_summary/io.rs:293:64 [INFO] [stdout] 22: 0x5b05004897d7 - motif_summary::io::tests::test_annotated_record_writer_empty_motifs::{{closure}}::h2c6e3ffcac3e0953 [INFO] [stdout] at /opt/rustwide/workdir/src/bin/motif_summary/io.rs:291:51 [INFO] [stdout] 23: 0x5b05004a8e56 - core::ops::function::FnOnce::call_once::h3f60d052788f086a [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 24: 0x5b05004cd0eb - core::ops::function::FnOnce::call_once::he420dad47d9aac14 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 25: 0x5b05004cd0eb - test::__rust_begin_short_backtrace::h51976f55c263f7c2 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:663:18 [INFO] [stdout] 26: 0x5b05004e2d15 - test::run_test_in_process::{{closure}}::h6aa4339396d33320 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:686:74 [INFO] [stdout] 27: 0x5b05004e2d15 - as core::ops::function::FnOnce<()>>::call_once::h5bd0ba3863a53529 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/panic/unwind_safe.rs:274:9 [INFO] [stdout] 28: 0x5b05004e2d15 - std::panicking::catch_unwind::do_call::h5c710722c40c5839 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:590:40 [INFO] [stdout] 29: 0x5b05004e2d15 - std::panicking::catch_unwind::hf41b5be070ce0f19 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:553:19 [INFO] [stdout] 30: 0x5b05004e2d15 - std::panic::catch_unwind::h4559aa103e6f16d6 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panic.rs:359:14 [INFO] [stdout] 31: 0x5b05004e2d15 - test::run_test_in_process::he6fd763a772ff213 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:686:27 [INFO] [stdout] 32: 0x5b05004e2d15 - test::run_test::{{closure}}::he46f5435849feb5b [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:607:43 [INFO] [stdout] 33: 0x5b05004b9524 - test::run_test::{{closure}}::h12a66289c31b502a [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/test/src/lib.rs:637:41 [INFO] [stdout] 34: 0x5b05004b9524 - std::sys::backtrace::__rust_begin_short_backtrace::h614a7925ed7b2f5e [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/backtrace.rs:158:18 [INFO] [stdout] 35: 0x5b05004bceca - std::thread::Builder::spawn_unchecked_::{{closure}}::{{closure}}::hbc654088c5dbff36 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/thread/mod.rs:559:17 [INFO] [stdout] 36: 0x5b05004bceca - as core::ops::function::FnOnce<()>>::call_once::h3f631d2ca531b61d [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/panic/unwind_safe.rs:274:9 [INFO] [stdout] 37: 0x5b05004bceca - std::panicking::catch_unwind::do_call::hd2548748db0aa717 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:590:40 [INFO] [stdout] 38: 0x5b05004bceca - std::panicking::catch_unwind::hf7d8620d84df48e2 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panicking.rs:553:19 [INFO] [stdout] 39: 0x5b05004bceca - std::panic::catch_unwind::hdde75b8543fcb96b [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/panic.rs:359:14 [INFO] [stdout] 40: 0x5b05004bceca - std::thread::Builder::spawn_unchecked_::{{closure}}::h991e7d03b432cf3f [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/thread/mod.rs:557:30 [INFO] [stdout] 41: 0x5b05004bceca - core::ops::function::FnOnce::call_once{{vtable.shim}}::hebddb40255441657 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 42: 0x5b05007cab8f - as core::ops::function::FnOnce>::call_once::h55e8930dc7db99a5 [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/alloc/src/boxed.rs:1973:9 [INFO] [stdout] 43: 0x5b05007cab8f - std::sys::thread::unix::Thread::new::thread_start::he23d038ee4fa004e [INFO] [stdout] at /rustc/2440211fe03bc45c89b6dc1a3df18382ce91e32b/library/std/src/sys/thread/unix.rs:126:17 [INFO] [stdout] 44: 0x7d80742eeaa4 - [INFO] [stdout] 45: 0x7d807437ba34 - clone [INFO] [stdout] 46: 0x0 - [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] failures: [INFO] [stdout] io::tests::test_annotated_record_writer [INFO] [stdout] io::tests::test_annotated_record_writer_empty_motifs [INFO] [stdout] io::tests::test_annotated_record_writer_multiple_records [INFO] [stdout] [INFO] [stdout] test result: FAILED. 13 passed; 3 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.20s [INFO] [stdout] [INFO] running `Command { std: "docker" "inspect" "5b8211546a24a63a0bae11d0b95a7fef531eeb5ebe8b53b43158ffde6f11ae9d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "5b8211546a24a63a0bae11d0b95a7fef531eeb5ebe8b53b43158ffde6f11ae9d", kill_on_drop: false }` [INFO] [stdout] 5b8211546a24a63a0bae11d0b95a7fef531eeb5ebe8b53b43158ffde6f11ae9d