[INFO] cloning repository https://github.com/Cardosaum/cdr3-parser [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/Cardosaum/cdr3-parser" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FCardosaum%2Fcdr3-parser", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FCardosaum%2Fcdr3-parser'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] b81c2de33c73591b1139b36bc29a83edf1040601 [INFO] testing Cardosaum/cdr3-parser against master#432e145bd5a974c5b6f4dd9b352891bd7502b69d for pr-87041 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FCardosaum%2Fcdr3-parser" "/workspace/builds/worker-0/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-0/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/Cardosaum/cdr3-parser on toolchain 432e145bd5a974c5b6f4dd9b352891bd7502b69d [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+432e145bd5a974c5b6f4dd9b352891bd7502b69d" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/Cardosaum/cdr3-parser [INFO] finished tweaking git repo https://github.com/Cardosaum/cdr3-parser [INFO] tweaked toml for git repo https://github.com/Cardosaum/cdr3-parser written to /workspace/builds/worker-0/source/Cargo.toml [INFO] crate git repo https://github.com/Cardosaum/cdr3-parser already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+432e145bd5a974c5b6f4dd9b352891bd7502b69d" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/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@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+432e145bd5a974c5b6f4dd9b352891bd7502b69d" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 6b48bb5499cf094d97624f32b14e28e82a646a74ba51e371780415eafe337d80 [INFO] running `Command { std: "docker" "start" "-a" "6b48bb5499cf094d97624f32b14e28e82a646a74ba51e371780415eafe337d80", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "6b48bb5499cf094d97624f32b14e28e82a646a74ba51e371780415eafe337d80", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "6b48bb5499cf094d97624f32b14e28e82a646a74ba51e371780415eafe337d80", kill_on_drop: false }` [INFO] [stdout] 6b48bb5499cf094d97624f32b14e28e82a646a74ba51e371780415eafe337d80 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+432e145bd5a974c5b6f4dd9b352891bd7502b69d" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] a6678897e8741dbc54c35dcfd1ee801bf92a4dda867a5138e9b5e47ccb940b11 [INFO] running `Command { std: "docker" "start" "-a" "a6678897e8741dbc54c35dcfd1ee801bf92a4dda867a5138e9b5e47ccb940b11", kill_on_drop: false }` [INFO] [stderr] Compiling syn v1.0.73 [INFO] [stderr] Compiling libm v0.2.1 [INFO] [stderr] Compiling libc v0.2.97 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling ident_case v1.0.1 [INFO] [stderr] Compiling rawpointer v0.2.1 [INFO] [stderr] Compiling unicode-segmentation v1.7.1 [INFO] [stderr] Compiling rayon-core v1.9.1 [INFO] [stderr] Compiling cc v1.0.68 [INFO] [stderr] Compiling fs_extra v1.2.0 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling scopeguard v1.1.0 [INFO] [stderr] Compiling regex-automata v0.1.10 [INFO] [stderr] Compiling ndarray v0.14.0 [INFO] [stderr] Compiling rustversion v1.0.5 [INFO] [stderr] Compiling hashbrown v0.9.1 [INFO] [stderr] Compiling regex-syntax v0.6.25 [INFO] [stderr] Compiling fixedbitset v0.2.0 [INFO] [stderr] Compiling bio v0.34.0 [INFO] [stderr] Compiling unicode-width v0.1.8 [INFO] [stderr] Compiling array-macro v1.0.5 [INFO] [stderr] Compiling bit-vec v0.6.3 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling triple_accel v0.3.4 [INFO] [stderr] Compiling num-traits v0.2.14 [INFO] [stderr] Compiling num-integer v0.1.44 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling memoffset v0.6.4 [INFO] [stderr] Compiling num-rational v0.2.4 [INFO] [stderr] Compiling num-bigint v0.4.0 [INFO] [stderr] Compiling indexmap v1.6.2 [INFO] [stderr] Compiling num-iter v0.1.42 [INFO] [stderr] Compiling num-rational v0.4.0 [INFO] [stderr] Compiling rayon v1.5.1 [INFO] [stderr] Compiling itertools v0.9.0 [INFO] [stderr] Compiling fxhash v0.2.1 [INFO] [stderr] Compiling matrixmultiply v0.2.4 [INFO] [stderr] Compiling crossbeam-utils v0.8.5 [INFO] [stderr] Compiling aho-corasick v0.7.18 [INFO] [stderr] Compiling csv-core v0.1.10 [INFO] [stderr] Compiling generic-array v0.13.3 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling bit-set v0.5.2 [INFO] [stderr] Compiling heck v0.3.3 [INFO] [stderr] Compiling crossbeam-channel v0.5.1 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling crossbeam-epoch v0.9.5 [INFO] [stderr] Compiling jemalloc-sys v0.3.2 [INFO] [stderr] Compiling petgraph v0.5.1 [INFO] [stderr] Compiling crossbeam-deque v0.8.0 [INFO] [stderr] Compiling getrandom v0.1.16 [INFO] [stderr] Compiling term_size v0.3.2 [INFO] [stderr] Compiling num_cpus v1.13.0 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling textwrap v0.11.0 [INFO] [stderr] Compiling rand_core v0.5.1 [INFO] [stderr] Compiling rand_chacha v0.2.2 [INFO] [stderr] Compiling approx v0.3.2 [INFO] [stderr] Compiling num-complex v0.3.1 [INFO] [stderr] Compiling ordered-float v1.1.1 [INFO] [stderr] Compiling num-complex v0.4.0 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling regex v1.5.4 [INFO] [stderr] Compiling rand v0.7.3 [INFO] [stderr] Compiling alga v0.9.3 [INFO] [stderr] Compiling rand_distr v0.2.2 [INFO] [stderr] Compiling nalgebra v0.19.0 [INFO] [stderr] Compiling num v0.4.0 [INFO] [stderr] Compiling darling_core v0.13.0 [INFO] [stderr] Compiling velcro_core v0.5.2 [INFO] [stderr] Compiling serde_derive v1.0.126 [INFO] [stderr] Compiling thiserror-impl v1.0.25 [INFO] [stderr] Compiling strum_macros v0.20.1 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling enum-map-derive v0.4.6 [INFO] [stderr] Compiling velcro_macros v0.5.2 [INFO] [stderr] Compiling getset v0.0.9 [INFO] [stderr] Compiling darling_macro v0.13.0 [INFO] [stderr] Compiling enum-map v0.6.4 [INFO] [stderr] Compiling velcro v0.5.3 [INFO] [stderr] Compiling thiserror v1.0.25 [INFO] [stderr] Compiling bio-types v0.11.0 [INFO] [stderr] Compiling darling v0.13.0 [INFO] [stderr] Compiling serde_with_macros v1.4.2 [INFO] [stderr] Compiling serde v1.0.126 [INFO] [stderr] Compiling bstr v0.2.16 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling multimap v0.8.3 [INFO] [stderr] Compiling serde_with v1.9.3 [INFO] [stderr] Compiling serde_json v1.0.64 [INFO] [stderr] Compiling clap v2.33.3 [INFO] [stderr] Compiling statrs v0.13.0 [INFO] [stderr] Compiling csv v1.1.6 [INFO] [stderr] Compiling jemallocator v0.3.2 [INFO] [stderr] Compiling cdr3-parser v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `Arg` [INFO] [stdout] --> src/app.rs:1:45 [INFO] [stdout] | [INFO] [stdout] 1 | use clap::{crate_version, App, AppSettings, Arg}; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `App`, `Arg`, `Error`, `SubCommand` [INFO] [stdout] --> src/cdr3/cdr3.rs:1:12 [INFO] [stdout] | [INFO] [stdout] 1 | use clap::{App, Arg, Error, SubCommand}; [INFO] [stdout] | ^^^ ^^^ ^^^^^ ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `csv::Writer` [INFO] [stdout] --> src/cdr3/cdr3.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use csv::Writer; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Deserialize` [INFO] [stdout] --> src/cdr3/cdr3.rs:6:13 [INFO] [stdout] | [INFO] [stdout] 6 | use serde::{Deserialize, Serialize}; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `OpenOptions`, `self` [INFO] [stdout] --> src/cdr3/cdr3.rs:10:15 [INFO] [stdout] | [INFO] [stdout] 10 | use std::fs::{self, File, OpenOptions}; [INFO] [stdout] | ^^^^ ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Path` [INFO] [stdout] --> src/cdr3/cdr3.rs:13:17 [INFO] [stdout] | [INFO] [stdout] 13 | use std::path::{Path, PathBuf}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `env` [INFO] [stdout] --> src/cdr3/cdr3.rs:14:11 [INFO] [stdout] | [INFO] [stdout] 14 | use std::{env, str}; [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `num::pow` [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:33:5 [INFO] [stdout] | [INFO] [stdout] 33 | use num::pow; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `num::pow` [INFO] [stdout] --> src/cdr3/protein_analysis.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use num::pow; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `serde_json::json` [INFO] [stdout] --> src/cdr3/protein_analysis.rs:10:5 [INFO] [stdout] | [INFO] [stdout] 10 | use serde_json::json; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `HashSet` [INFO] [stdout] --> src/cdr3/protein_analysis.rs:11:33 [INFO] [stdout] | [INFO] [stdout] 11 | use std::collections::{HashMap, HashSet}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `App`, `Arg`, `Error`, `SubCommand` [INFO] [stdout] --> src/main.rs:13:12 [INFO] [stdout] | [INFO] [stdout] 13 | use clap::{App, Arg, Error, SubCommand}; [INFO] [stdout] | ^^^ ^^^ ^^^^^ ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `csv::Writer` [INFO] [stdout] --> src/main.rs:14:5 [INFO] [stdout] | [INFO] [stdout] 14 | use csv::Writer; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `serde_json::json` [INFO] [stdout] --> src/main.rs:15:5 [INFO] [stdout] | [INFO] [stdout] 15 | use serde_json::json; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `File`, `OpenOptions`, `self` [INFO] [stdout] --> src/main.rs:16:15 [INFO] [stdout] | [INFO] [stdout] 16 | use std::fs::{self, File, OpenOptions}; [INFO] [stdout] | ^^^^ ^^^^ ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `BufReader`, `prelude::*`, `self` [INFO] [stdout] --> src/main.rs:17:15 [INFO] [stdout] | [INFO] [stdout] 17 | use std::io::{self, prelude::*, BufReader}; [INFO] [stdout] | ^^^^ ^^^^^^^^^^ ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::iter::FromIterator` [INFO] [stdout] --> src/main.rs:18:5 [INFO] [stdout] | [INFO] [stdout] 18 | use std::iter::FromIterator; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `str` [INFO] [stdout] --> src/main.rs:20:16 [INFO] [stdout] | [INFO] [stdout] 20 | use std::{env, str}; [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `output_file` [INFO] [stdout] --> src/main.rs:55:9 [INFO] [stdout] | [INFO] [stdout] 55 | let output_file = PathBuf::from( [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_output_file` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `aa` [INFO] [stdout] --> src/cdr3/cdr3.rs:92:13 [INFO] [stdout] | [INFO] [stdout] 92 | let aa = match monoisotopic_protein_weights.get_key_value(&str::from_utf8(&[c]).unwrap()) { [INFO] [stdout] | ^^ help: if this is intentional, prefix it with an underscore: `_aa` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `sequence` [INFO] [stdout] --> src/cdr3/cdr3.rs:122:24 [INFO] [stdout] | [INFO] [stdout] 122 | pub fn aa_groups<'seq>(sequence: String) -> BTreeMap> { [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_sequence` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `n` [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:151:21 [INFO] [stdout] | [INFO] [stdout] 151 | if let Some(n) = pKnterminal.get_mut(&nterm) {} [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_n` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `v` [INFO] [stdout] --> src/cdr3/protein_analysis.rs:252:22 [INFO] [stdout] | [INFO] [stdout] 252 | for (aa, v) in &self.amino_acids_content { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_v` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `v` [INFO] [stdout] --> src/cdr3/protein_analysis.rs:288:26 [INFO] [stdout] | [INFO] [stdout] 288 | .filter(|(k, v)| **k == 'Y' || **k == 'W' || **k == 'F') [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_v` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `k` [INFO] [stdout] --> src/cdr3/protein_analysis.rs:289:20 [INFO] [stdout] | [INFO] [stdout] 289 | .map(|(k, v)| *v) [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_k` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `aromatic_aas` [INFO] [stdout] --> src/cdr3/protein_analysis.rs:283:13 [INFO] [stdout] | [INFO] [stdout] 283 | let aromatic_aas = "YWF"; [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_aromatic_aas` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `aromaticity` [INFO] [stdout] --> src/cdr3/protein_analysis.rs:284:13 [INFO] [stdout] | [INFO] [stdout] 284 | let aromaticity: f64 = 0.0; [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_aromaticity` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/app.rs:10:9 [INFO] [stdout] | [INFO] [stdout] 10 | let mut app = App::new("cdr3-parser") [INFO] [stdout] | ----^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/cdr3/cdr3.rs:262:15 [INFO] [stdout] | [INFO] [stdout] 262 | fn parse_file(mut input_file: PathBuf) -> Vec { [INFO] [stdout] | ----^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/cdr3/cdr3.rs:284:22 [INFO] [stdout] | [INFO] [stdout] 284 | pub fn pipeline_cdr3(mut input_file: PathBuf) -> Result<(), Box> { [INFO] [stdout] | ----^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:135:13 [INFO] [stdout] | [INFO] [stdout] 135 | let mut pos_pKs: HashMap = POSITIVE_PKS.clone(); [INFO] [stdout] | ----^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:136:13 [INFO] [stdout] | [INFO] [stdout] 136 | let mut neg_pKs: HashMap = NEGATIVE_PKS.clone(); [INFO] [stdout] | ----^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `molecular_weight` [INFO] [stdout] --> src/cdr3/cdr3.rs:62:8 [INFO] [stdout] | [INFO] [stdout] 62 | pub fn molecular_weight(sequence: &str) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `aromaticity` [INFO] [stdout] --> src/cdr3/cdr3.rs:104:8 [INFO] [stdout] | [INFO] [stdout] 104 | pub fn aromaticity(sequence: &str) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `create_cdr3_dict` [INFO] [stdout] --> src/cdr3/cdr3.rs:111:8 [INFO] [stdout] | [INFO] [stdout] 111 | pub fn create_cdr3_dict(cdr3_sequence: Vec) -> BTreeMap { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `aa_groups` [INFO] [stdout] --> src/cdr3/cdr3.rs:122:8 [INFO] [stdout] | [INFO] [stdout] 122 | pub fn aa_groups<'seq>(sequence: String) -> BTreeMap> { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `build_cdr3_struct` [INFO] [stdout] --> src/cdr3/cdr3.rs:153:8 [INFO] [stdout] | [INFO] [stdout] 153 | pub fn build_cdr3_struct(cdr3: String) -> CDR3Prop { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `get_cdr3_sequences_attributes` [INFO] [stdout] --> src/cdr3/cdr3.rs:199:8 [INFO] [stdout] | [INFO] [stdout] 199 | pub fn get_cdr3_sequences_attributes(cdr3_dict: BTreeMap) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/main.rs:62:5 [INFO] [stdout] | [INFO] [stdout] 62 | pipeline_cdr3(input_file); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_must_use)]` on by default [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `MW` should have a snake case name [INFO] [stdout] --> src/cdr3/cdr3.rs:25:9 [INFO] [stdout] | [INFO] [stdout] 25 | pub MW: f64, [INFO] [stdout] | ^^ help: convert the identifier to snake case: `mw` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_snake_case)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `AV` should have a snake case name [INFO] [stdout] --> src/cdr3/cdr3.rs:26:9 [INFO] [stdout] | [INFO] [stdout] 26 | pub AV: f64, [INFO] [stdout] | ^^ help: convert the identifier to snake case: `av` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `IP` should have a snake case name [INFO] [stdout] --> src/cdr3/cdr3.rs:27:5 [INFO] [stdout] | [INFO] [stdout] 27 | IP: f64, [INFO] [stdout] | ^^ help: convert the identifier to snake case: `ip` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `P` should have a snake case name [INFO] [stdout] --> src/cdr3/cdr3.rs:243:9 [INFO] [stdout] | [INFO] [stdout] 243 | let P = ProteinAnalysis::new(sequence); [INFO] [stdout] | ^ help: convert the identifier to snake case: `p` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/cdr3/cdr3.rs:287:5 [INFO] [stdout] | [INFO] [stdout] 287 | write_cdr3_header(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/cdr3/cdr3.rs:289:9 [INFO] [stdout] | [INFO] [stdout] 289 | write_cdr3_attributes(s); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `pos_pKs` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:94:5 [INFO] [stdout] | [INFO] [stdout] 94 | pos_pKs: HashMap, [INFO] [stdout] | ^^^^^^^ help: convert the identifier to snake case: `pos_p_ks` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `neg_pKs` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:95:5 [INFO] [stdout] | [INFO] [stdout] 95 | neg_pKs: HashMap, [INFO] [stdout] | ^^^^^^^ help: convert the identifier to snake case: `neg_p_ks` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `charge_at_pH` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:98:9 [INFO] [stdout] | [INFO] [stdout] 98 | pub charge_at_pH: f64, [INFO] [stdout] | ^^^^^^^^^^^^ help: convert the identifier to snake case: `charge_at_p_h` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pH` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:102:32 [INFO] [stdout] | [INFO] [stdout] 102 | pub fn new(sequence: &str, pH: Option) -> Self { [INFO] [stdout] | ^^ help: convert the identifier to snake case: `p_h` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `pK_table` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:134:8 [INFO] [stdout] | [INFO] [stdout] 134 | fn pK_table(sequence: &String) -> (HashMap, HashMap) { [INFO] [stdout] | ^^^^^^^^ help: convert the identifier to snake case: `p_k_table` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pos_pKs` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:135:17 [INFO] [stdout] | [INFO] [stdout] 135 | let mut pos_pKs: HashMap = POSITIVE_PKS.clone(); [INFO] [stdout] | ^^^^^^^ help: convert the identifier to snake case: `pos_p_ks` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `neg_pKs` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:136:17 [INFO] [stdout] | [INFO] [stdout] 136 | let mut neg_pKs: HashMap = NEGATIVE_PKS.clone(); [INFO] [stdout] | ^^^^^^^ help: convert the identifier to snake case: `neg_p_ks` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pKnterminal` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:148:17 [INFO] [stdout] | [INFO] [stdout] 148 | let mut pKnterminal = PKNTERMINAL.clone(); [INFO] [stdout] | ^^^^^^^^^^^ help: convert the identifier to snake case: `p_knterminal` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pKcterminal` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:149:17 [INFO] [stdout] | [INFO] [stdout] 149 | let mut pKcterminal = PKCTERMINAL.clone(); [INFO] [stdout] | ^^^^^^^^^^^ help: convert the identifier to snake case: `p_kcterminal` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `charge_at_pH` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:171:12 [INFO] [stdout] | [INFO] [stdout] 171 | pub fn charge_at_pH(&self, pH: f64) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^ help: convert the identifier to snake case: `charge_at_p_h` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pH` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:171:32 [INFO] [stdout] | [INFO] [stdout] 171 | pub fn charge_at_pH(&self, pH: f64) -> f64 { [INFO] [stdout] | ^^ help: convert the identifier to snake case: `p_h` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pK` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:173:18 [INFO] [stdout] | [INFO] [stdout] 173 | for (aa, pK) in &self.pos_pKs { [INFO] [stdout] | ^^ help: convert the identifier to snake case: `p_k` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pK` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:183:18 [INFO] [stdout] | [INFO] [stdout] 183 | for (aa, pK) in &self.neg_pKs { [INFO] [stdout] | ^^ help: convert the identifier to snake case: `p_k` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pH` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:194:22 [INFO] [stdout] | [INFO] [stdout] 194 | fn pi(&self, mut pH: Option, mut min_: Option, mut max_: Option) -> f64 { [INFO] [stdout] | ^^ help: convert the identifier to snake case: `p_h` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `H` should have a snake case name [INFO] [stdout] --> src/cdr3/protein_analysis.rs:68:13 [INFO] [stdout] | [INFO] [stdout] 68 | let H: HashMap> = [INFO] [stdout] | ^ help: convert the identifier to snake case: `h` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `charge_at_pH` should have a snake case name [INFO] [stdout] --> src/cdr3/protein_analysis.rs:205:9 [INFO] [stdout] | [INFO] [stdout] 205 | pub charge_at_pH: f64, [INFO] [stdout] | ^^^^^^^^^^^^ help: convert the identifier to snake case: `charge_at_p_h` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `PA` should have a snake case name [INFO] [stdout] --> src/cdr3/protein_analysis.rs:212:17 [INFO] [stdout] | [INFO] [stdout] 212 | let mut PA = ProteinAnalysis { [INFO] [stdout] | ^^ help: convert the identifier to snake case: `pa` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `charge_at_pH` should have a snake case name [INFO] [stdout] --> src/cdr3/protein_analysis.rs:348:8 [INFO] [stdout] | [INFO] [stdout] 348 | fn charge_at_pH(&mut self, pH: Option) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^ help: convert the identifier to snake case: `charge_at_p_h` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pH` should have a snake case name [INFO] [stdout] --> src/cdr3/protein_analysis.rs:348:32 [INFO] [stdout] | [INFO] [stdout] 348 | fn charge_at_pH(&mut self, pH: Option) -> f64 { [INFO] [stdout] | ^^ help: convert the identifier to snake case: `p_h` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 64 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 54.33s [INFO] running `Command { std: "docker" "inspect" "a6678897e8741dbc54c35dcfd1ee801bf92a4dda867a5138e9b5e47ccb940b11", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "a6678897e8741dbc54c35dcfd1ee801bf92a4dda867a5138e9b5e47ccb940b11", kill_on_drop: false }` [INFO] [stdout] a6678897e8741dbc54c35dcfd1ee801bf92a4dda867a5138e9b5e47ccb940b11 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+432e145bd5a974c5b6f4dd9b352891bd7502b69d" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] b445a704b88838e20678218900834b39b669d21b2844a308db3ec138c625bdf9 [INFO] running `Command { std: "docker" "start" "-a" "b445a704b88838e20678218900834b39b669d21b2844a308db3ec138c625bdf9", kill_on_drop: false }` [INFO] [stderr] Compiling cdr3-parser v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `Arg` [INFO] [stdout] --> src/app.rs:1:45 [INFO] [stdout] | [INFO] [stdout] 1 | use clap::{crate_version, App, AppSettings, Arg}; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `App`, `Arg`, `Error`, `SubCommand` [INFO] [stdout] --> src/cdr3/cdr3.rs:1:12 [INFO] [stdout] | [INFO] [stdout] 1 | use clap::{App, Arg, Error, SubCommand}; [INFO] [stdout] | ^^^ ^^^ ^^^^^ ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `csv::Writer` [INFO] [stdout] --> src/cdr3/cdr3.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use csv::Writer; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Deserialize` [INFO] [stdout] --> src/cdr3/cdr3.rs:6:13 [INFO] [stdout] | [INFO] [stdout] 6 | use serde::{Deserialize, Serialize}; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `OpenOptions`, `self` [INFO] [stdout] --> src/cdr3/cdr3.rs:10:15 [INFO] [stdout] | [INFO] [stdout] 10 | use std::fs::{self, File, OpenOptions}; [INFO] [stdout] | ^^^^ ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Path` [INFO] [stdout] --> src/cdr3/cdr3.rs:13:17 [INFO] [stdout] | [INFO] [stdout] 13 | use std::path::{Path, PathBuf}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `env` [INFO] [stdout] --> src/cdr3/cdr3.rs:14:11 [INFO] [stdout] | [INFO] [stdout] 14 | use std::{env, str}; [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `num::pow` [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:33:5 [INFO] [stdout] | [INFO] [stdout] 33 | use num::pow; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `num::pow` [INFO] [stdout] --> src/cdr3/protein_analysis.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use num::pow; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `serde_json::json` [INFO] [stdout] --> src/cdr3/protein_analysis.rs:10:5 [INFO] [stdout] | [INFO] [stdout] 10 | use serde_json::json; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `HashSet` [INFO] [stdout] --> src/cdr3/protein_analysis.rs:11:33 [INFO] [stdout] | [INFO] [stdout] 11 | use std::collections::{HashMap, HashSet}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `App`, `Arg`, `Error`, `SubCommand` [INFO] [stdout] --> src/main.rs:13:12 [INFO] [stdout] | [INFO] [stdout] 13 | use clap::{App, Arg, Error, SubCommand}; [INFO] [stdout] | ^^^ ^^^ ^^^^^ ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `csv::Writer` [INFO] [stdout] --> src/main.rs:14:5 [INFO] [stdout] | [INFO] [stdout] 14 | use csv::Writer; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `serde_json::json` [INFO] [stdout] --> src/main.rs:15:5 [INFO] [stdout] | [INFO] [stdout] 15 | use serde_json::json; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `File`, `OpenOptions`, `self` [INFO] [stdout] --> src/main.rs:16:15 [INFO] [stdout] | [INFO] [stdout] 16 | use std::fs::{self, File, OpenOptions}; [INFO] [stdout] | ^^^^ ^^^^ ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `BufReader`, `prelude::*`, `self` [INFO] [stdout] --> src/main.rs:17:15 [INFO] [stdout] | [INFO] [stdout] 17 | use std::io::{self, prelude::*, BufReader}; [INFO] [stdout] | ^^^^ ^^^^^^^^^^ ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::iter::FromIterator` [INFO] [stdout] --> src/main.rs:18:5 [INFO] [stdout] | [INFO] [stdout] 18 | use std::iter::FromIterator; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `str` [INFO] [stdout] --> src/main.rs:20:16 [INFO] [stdout] | [INFO] [stdout] 20 | use std::{env, str}; [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `output_file` [INFO] [stdout] --> src/main.rs:55:9 [INFO] [stdout] | [INFO] [stdout] 55 | let output_file = PathBuf::from( [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_output_file` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `aa` [INFO] [stdout] --> src/cdr3/cdr3.rs:92:13 [INFO] [stdout] | [INFO] [stdout] 92 | let aa = match monoisotopic_protein_weights.get_key_value(&str::from_utf8(&[c]).unwrap()) { [INFO] [stdout] | ^^ help: if this is intentional, prefix it with an underscore: `_aa` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `sequence` [INFO] [stdout] --> src/cdr3/cdr3.rs:122:24 [INFO] [stdout] | [INFO] [stdout] 122 | pub fn aa_groups<'seq>(sequence: String) -> BTreeMap> { [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_sequence` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `n` [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:151:21 [INFO] [stdout] | [INFO] [stdout] 151 | if let Some(n) = pKnterminal.get_mut(&nterm) {} [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_n` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `v` [INFO] [stdout] --> src/cdr3/protein_analysis.rs:252:22 [INFO] [stdout] | [INFO] [stdout] 252 | for (aa, v) in &self.amino_acids_content { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_v` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `v` [INFO] [stdout] --> src/cdr3/protein_analysis.rs:288:26 [INFO] [stdout] | [INFO] [stdout] 288 | .filter(|(k, v)| **k == 'Y' || **k == 'W' || **k == 'F') [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_v` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `k` [INFO] [stdout] --> src/cdr3/protein_analysis.rs:289:20 [INFO] [stdout] | [INFO] [stdout] 289 | .map(|(k, v)| *v) [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_k` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `aromatic_aas` [INFO] [stdout] --> src/cdr3/protein_analysis.rs:283:13 [INFO] [stdout] | [INFO] [stdout] 283 | let aromatic_aas = "YWF"; [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_aromatic_aas` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `aromaticity` [INFO] [stdout] --> src/cdr3/protein_analysis.rs:284:13 [INFO] [stdout] | [INFO] [stdout] 284 | let aromaticity: f64 = 0.0; [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_aromaticity` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/app.rs:10:9 [INFO] [stdout] | [INFO] [stdout] 10 | let mut app = App::new("cdr3-parser") [INFO] [stdout] | ----^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/cdr3/cdr3.rs:262:15 [INFO] [stdout] | [INFO] [stdout] 262 | fn parse_file(mut input_file: PathBuf) -> Vec { [INFO] [stdout] | ----^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/cdr3/cdr3.rs:284:22 [INFO] [stdout] | [INFO] [stdout] 284 | pub fn pipeline_cdr3(mut input_file: PathBuf) -> Result<(), Box> { [INFO] [stdout] | ----^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:135:13 [INFO] [stdout] | [INFO] [stdout] 135 | let mut pos_pKs: HashMap = POSITIVE_PKS.clone(); [INFO] [stdout] | ----^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:136:13 [INFO] [stdout] | [INFO] [stdout] 136 | let mut neg_pKs: HashMap = NEGATIVE_PKS.clone(); [INFO] [stdout] | ----^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `molecular_weight` [INFO] [stdout] --> src/cdr3/cdr3.rs:62:8 [INFO] [stdout] | [INFO] [stdout] 62 | pub fn molecular_weight(sequence: &str) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `aromaticity` [INFO] [stdout] --> src/cdr3/cdr3.rs:104:8 [INFO] [stdout] | [INFO] [stdout] 104 | pub fn aromaticity(sequence: &str) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `create_cdr3_dict` [INFO] [stdout] --> src/cdr3/cdr3.rs:111:8 [INFO] [stdout] | [INFO] [stdout] 111 | pub fn create_cdr3_dict(cdr3_sequence: Vec) -> BTreeMap { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `aa_groups` [INFO] [stdout] --> src/cdr3/cdr3.rs:122:8 [INFO] [stdout] | [INFO] [stdout] 122 | pub fn aa_groups<'seq>(sequence: String) -> BTreeMap> { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `build_cdr3_struct` [INFO] [stdout] --> src/cdr3/cdr3.rs:153:8 [INFO] [stdout] | [INFO] [stdout] 153 | pub fn build_cdr3_struct(cdr3: String) -> CDR3Prop { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `get_cdr3_sequences_attributes` [INFO] [stdout] --> src/cdr3/cdr3.rs:199:8 [INFO] [stdout] | [INFO] [stdout] 199 | pub fn get_cdr3_sequences_attributes(cdr3_dict: BTreeMap) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/main.rs:62:5 [INFO] [stdout] | [INFO] [stdout] 62 | pipeline_cdr3(input_file); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_must_use)]` on by default [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `MW` should have a snake case name [INFO] [stdout] --> src/cdr3/cdr3.rs:25:9 [INFO] [stdout] | [INFO] [stdout] 25 | pub MW: f64, [INFO] [stdout] | ^^ help: convert the identifier to snake case: `mw` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_snake_case)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `AV` should have a snake case name [INFO] [stdout] --> src/cdr3/cdr3.rs:26:9 [INFO] [stdout] | [INFO] [stdout] 26 | pub AV: f64, [INFO] [stdout] | ^^ help: convert the identifier to snake case: `av` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `IP` should have a snake case name [INFO] [stdout] --> src/cdr3/cdr3.rs:27:5 [INFO] [stdout] | [INFO] [stdout] 27 | IP: f64, [INFO] [stdout] | ^^ help: convert the identifier to snake case: `ip` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `P` should have a snake case name [INFO] [stdout] --> src/cdr3/cdr3.rs:243:9 [INFO] [stdout] | [INFO] [stdout] 243 | let P = ProteinAnalysis::new(sequence); [INFO] [stdout] | ^ help: convert the identifier to snake case: `p` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/cdr3/cdr3.rs:287:5 [INFO] [stdout] | [INFO] [stdout] 287 | write_cdr3_header(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/cdr3/cdr3.rs:289:9 [INFO] [stdout] | [INFO] [stdout] 289 | write_cdr3_attributes(s); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `pos_pKs` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:94:5 [INFO] [stdout] | [INFO] [stdout] 94 | pos_pKs: HashMap, [INFO] [stdout] | ^^^^^^^ help: convert the identifier to snake case: `pos_p_ks` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `neg_pKs` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:95:5 [INFO] [stdout] | [INFO] [stdout] 95 | neg_pKs: HashMap, [INFO] [stdout] | ^^^^^^^ help: convert the identifier to snake case: `neg_p_ks` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `charge_at_pH` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:98:9 [INFO] [stdout] | [INFO] [stdout] 98 | pub charge_at_pH: f64, [INFO] [stdout] | ^^^^^^^^^^^^ help: convert the identifier to snake case: `charge_at_p_h` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pH` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:102:32 [INFO] [stdout] | [INFO] [stdout] 102 | pub fn new(sequence: &str, pH: Option) -> Self { [INFO] [stdout] | ^^ help: convert the identifier to snake case: `p_h` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `pK_table` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:134:8 [INFO] [stdout] | [INFO] [stdout] 134 | fn pK_table(sequence: &String) -> (HashMap, HashMap) { [INFO] [stdout] | ^^^^^^^^ help: convert the identifier to snake case: `p_k_table` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pos_pKs` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:135:17 [INFO] [stdout] | [INFO] [stdout] 135 | let mut pos_pKs: HashMap = POSITIVE_PKS.clone(); [INFO] [stdout] | ^^^^^^^ help: convert the identifier to snake case: `pos_p_ks` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `neg_pKs` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:136:17 [INFO] [stdout] | [INFO] [stdout] 136 | let mut neg_pKs: HashMap = NEGATIVE_PKS.clone(); [INFO] [stdout] | ^^^^^^^ help: convert the identifier to snake case: `neg_p_ks` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pKnterminal` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:148:17 [INFO] [stdout] | [INFO] [stdout] 148 | let mut pKnterminal = PKNTERMINAL.clone(); [INFO] [stdout] | ^^^^^^^^^^^ help: convert the identifier to snake case: `p_knterminal` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pKcterminal` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:149:17 [INFO] [stdout] | [INFO] [stdout] 149 | let mut pKcterminal = PKCTERMINAL.clone(); [INFO] [stdout] | ^^^^^^^^^^^ help: convert the identifier to snake case: `p_kcterminal` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `charge_at_pH` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:171:12 [INFO] [stdout] | [INFO] [stdout] 171 | pub fn charge_at_pH(&self, pH: f64) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^ help: convert the identifier to snake case: `charge_at_p_h` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pH` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:171:32 [INFO] [stdout] | [INFO] [stdout] 171 | pub fn charge_at_pH(&self, pH: f64) -> f64 { [INFO] [stdout] | ^^ help: convert the identifier to snake case: `p_h` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pK` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:173:18 [INFO] [stdout] | [INFO] [stdout] 173 | for (aa, pK) in &self.pos_pKs { [INFO] [stdout] | ^^ help: convert the identifier to snake case: `p_k` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pK` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:183:18 [INFO] [stdout] | [INFO] [stdout] 183 | for (aa, pK) in &self.neg_pKs { [INFO] [stdout] | ^^ help: convert the identifier to snake case: `p_k` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pH` should have a snake case name [INFO] [stdout] --> src/cdr3/isoelectric_point.rs:194:22 [INFO] [stdout] | [INFO] [stdout] 194 | fn pi(&self, mut pH: Option, mut min_: Option, mut max_: Option) -> f64 { [INFO] [stdout] | ^^ help: convert the identifier to snake case: `p_h` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `H` should have a snake case name [INFO] [stdout] --> src/cdr3/protein_analysis.rs:68:13 [INFO] [stdout] | [INFO] [stdout] 68 | let H: HashMap> = [INFO] [stdout] | ^ help: convert the identifier to snake case: `h` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `charge_at_pH` should have a snake case name [INFO] [stdout] --> src/cdr3/protein_analysis.rs:205:9 [INFO] [stdout] | [INFO] [stdout] 205 | pub charge_at_pH: f64, [INFO] [stdout] | ^^^^^^^^^^^^ help: convert the identifier to snake case: `charge_at_p_h` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `PA` should have a snake case name [INFO] [stdout] --> src/cdr3/protein_analysis.rs:212:17 [INFO] [stdout] | [INFO] [stdout] 212 | let mut PA = ProteinAnalysis { [INFO] [stdout] | ^^ help: convert the identifier to snake case: `pa` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `charge_at_pH` should have a snake case name [INFO] [stdout] --> src/cdr3/protein_analysis.rs:348:8 [INFO] [stdout] | [INFO] [stdout] 348 | fn charge_at_pH(&mut self, pH: Option) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^ help: convert the identifier to snake case: `charge_at_p_h` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pH` should have a snake case name [INFO] [stdout] --> src/cdr3/protein_analysis.rs:348:32 [INFO] [stdout] | [INFO] [stdout] 348 | fn charge_at_pH(&mut self, pH: Option) -> f64 { [INFO] [stdout] | ^^ help: convert the identifier to snake case: `p_h` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 64 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished test [unoptimized + debuginfo] target(s) in 2.85s [INFO] running `Command { std: "docker" "inspect" "b445a704b88838e20678218900834b39b669d21b2844a308db3ec138c625bdf9", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "b445a704b88838e20678218900834b39b669d21b2844a308db3ec138c625bdf9", kill_on_drop: false }` [INFO] [stdout] b445a704b88838e20678218900834b39b669d21b2844a308db3ec138c625bdf9 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+432e145bd5a974c5b6f4dd9b352891bd7502b69d" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] b582d65d69b74e487bd6ec462d13292253d5342e76474085137fb8b2ad20899c [INFO] running `Command { std: "docker" "start" "-a" "b582d65d69b74e487bd6ec462d13292253d5342e76474085137fb8b2ad20899c", kill_on_drop: false }` [INFO] [stderr] warning: unused import: `Arg` [INFO] [stderr] --> src/app.rs:1:45 [INFO] [stderr] | [INFO] [stderr] 1 | use clap::{crate_version, App, AppSettings, Arg}; [INFO] [stderr] | ^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_imports)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused imports: `App`, `Arg`, `Error`, `SubCommand` [INFO] [stderr] --> src/cdr3/cdr3.rs:1:12 [INFO] [stderr] | [INFO] [stderr] 1 | use clap::{App, Arg, Error, SubCommand}; [INFO] [stderr] | ^^^ ^^^ ^^^^^ ^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `csv::Writer` [INFO] [stderr] --> src/cdr3/cdr3.rs:2:5 [INFO] [stderr] | [INFO] [stderr] 2 | use csv::Writer; [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `Deserialize` [INFO] [stderr] --> src/cdr3/cdr3.rs:6:13 [INFO] [stderr] | [INFO] [stderr] 6 | use serde::{Deserialize, Serialize}; [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused imports: `OpenOptions`, `self` [INFO] [stderr] --> src/cdr3/cdr3.rs:10:15 [INFO] [stderr] | [INFO] [stderr] 10 | use std::fs::{self, File, OpenOptions}; [INFO] [stderr] | ^^^^ ^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `Path` [INFO] [stderr] --> src/cdr3/cdr3.rs:13:17 [INFO] [stderr] | [INFO] [stderr] 13 | use std::path::{Path, PathBuf}; [INFO] [stderr] | ^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `env` [INFO] [stderr] --> src/cdr3/cdr3.rs:14:11 [INFO] [stderr] | [INFO] [stderr] 14 | use std::{env, str}; [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `num::pow` [INFO] [stderr] --> src/cdr3/isoelectric_point.rs:33:5 [INFO] [stderr] | [INFO] [stderr] 33 | use num::pow; [INFO] [stderr] | ^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `num::pow` [INFO] [stderr] --> src/cdr3/protein_analysis.rs:8:5 [INFO] [stderr] | [INFO] [stderr] 8 | use num::pow; [INFO] [stderr] | ^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `serde_json::json` [INFO] [stderr] --> src/cdr3/protein_analysis.rs:10:5 [INFO] [stderr] | [INFO] [stderr] 10 | use serde_json::json; [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `HashSet` [INFO] [stderr] --> src/cdr3/protein_analysis.rs:11:33 [INFO] [stderr] | [INFO] [stderr] 11 | use std::collections::{HashMap, HashSet}; [INFO] [stderr] | ^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused imports: `App`, `Arg`, `Error`, `SubCommand` [INFO] [stderr] --> src/main.rs:13:12 [INFO] [stderr] | [INFO] [stderr] 13 | use clap::{App, Arg, Error, SubCommand}; [INFO] [stderr] | ^^^ ^^^ ^^^^^ ^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `csv::Writer` [INFO] [stderr] --> src/main.rs:14:5 [INFO] [stderr] | [INFO] [stderr] 14 | use csv::Writer; [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `serde_json::json` [INFO] [stderr] --> src/main.rs:15:5 [INFO] [stderr] | [INFO] [stderr] 15 | use serde_json::json; [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused imports: `File`, `OpenOptions`, `self` [INFO] [stderr] --> src/main.rs:16:15 [INFO] [stderr] | [INFO] [stderr] 16 | use std::fs::{self, File, OpenOptions}; [INFO] [stderr] | ^^^^ ^^^^ ^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused imports: `BufReader`, `prelude::*`, `self` [INFO] [stderr] --> src/main.rs:17:15 [INFO] [stderr] | [INFO] [stderr] 17 | use std::io::{self, prelude::*, BufReader}; [INFO] [stderr] | ^^^^ ^^^^^^^^^^ ^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `std::iter::FromIterator` [INFO] [stderr] --> src/main.rs:18:5 [INFO] [stderr] | [INFO] [stderr] 18 | use std::iter::FromIterator; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `str` [INFO] [stderr] --> src/main.rs:20:16 [INFO] [stderr] | [INFO] [stderr] 20 | use std::{env, str}; [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: unused variable: `output_file` [INFO] [stderr] --> src/main.rs:55:9 [INFO] [stderr] | [INFO] [stderr] 55 | let output_file = PathBuf::from( [INFO] [stderr] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_output_file` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_variables)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused variable: `aa` [INFO] [stderr] --> src/cdr3/cdr3.rs:92:13 [INFO] [stderr] | [INFO] [stderr] 92 | let aa = match monoisotopic_protein_weights.get_key_value(&str::from_utf8(&[c]).unwrap()) { [INFO] [stderr] | ^^ help: if this is intentional, prefix it with an underscore: `_aa` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `sequence` [INFO] [stderr] --> src/cdr3/cdr3.rs:122:24 [INFO] [stderr] | [INFO] [stderr] 122 | pub fn aa_groups<'seq>(sequence: String) -> BTreeMap> { [INFO] [stderr] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_sequence` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `n` [INFO] [stderr] --> src/cdr3/isoelectric_point.rs:151:21 [INFO] [stderr] | [INFO] [stderr] 151 | if let Some(n) = pKnterminal.get_mut(&nterm) {} [INFO] [stderr] | ^ help: if this is intentional, prefix it with an underscore: `_n` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `v` [INFO] [stderr] --> src/cdr3/protein_analysis.rs:252:22 [INFO] [stderr] | [INFO] [stderr] 252 | for (aa, v) in &self.amino_acids_content { [INFO] [stderr] | ^ help: if this is intentional, prefix it with an underscore: `_v` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `v` [INFO] [stderr] --> src/cdr3/protein_analysis.rs:288:26 [INFO] [stderr] | [INFO] [stderr] 288 | .filter(|(k, v)| **k == 'Y' || **k == 'W' || **k == 'F') [INFO] [stderr] | ^ help: if this is intentional, prefix it with an underscore: `_v` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `k` [INFO] [stderr] --> src/cdr3/protein_analysis.rs:289:20 [INFO] [stderr] | [INFO] [stderr] 289 | .map(|(k, v)| *v) [INFO] [stderr] | ^ help: if this is intentional, prefix it with an underscore: `_k` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `aromatic_aas` [INFO] [stderr] --> src/cdr3/protein_analysis.rs:283:13 [INFO] [stderr] | [INFO] [stderr] 283 | let aromatic_aas = "YWF"; [INFO] [stderr] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_aromatic_aas` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `aromaticity` [INFO] [stderr] --> src/cdr3/protein_analysis.rs:284:13 [INFO] [stderr] | [INFO] [stderr] 284 | let aromaticity: f64 = 0.0; [INFO] [stderr] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_aromaticity` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/app.rs:10:9 [INFO] [stderr] | [INFO] [stderr] 10 | let mut app = App::new("cdr3-parser") [INFO] [stderr] | ----^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_mut)]` on by default [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/cdr3/cdr3.rs:262:15 [INFO] [stderr] | [INFO] [stderr] 262 | fn parse_file(mut input_file: PathBuf) -> Vec { [INFO] [stderr] | ----^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/cdr3/cdr3.rs:284:22 [INFO] [stderr] | [INFO] [stderr] 284 | pub fn pipeline_cdr3(mut input_file: PathBuf) -> Result<(), Box> { [INFO] [stderr] | ----^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/cdr3/isoelectric_point.rs:135:13 [INFO] [stderr] | [INFO] [stderr] 135 | let mut pos_pKs: HashMap = POSITIVE_PKS.clone(); [INFO] [stderr] | ----^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/cdr3/isoelectric_point.rs:136:13 [INFO] [stderr] | [INFO] [stderr] 136 | let mut neg_pKs: HashMap = NEGATIVE_PKS.clone(); [INFO] [stderr] | ----^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: function is never used: `molecular_weight` [INFO] [stderr] --> src/cdr3/cdr3.rs:62:8 [INFO] [stderr] | [INFO] [stderr] 62 | pub fn molecular_weight(sequence: &str) -> f64 { [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` on by default [INFO] [stderr] [INFO] [stderr] warning: function is never used: `aromaticity` [INFO] [stderr] --> src/cdr3/cdr3.rs:104:8 [INFO] [stderr] | [INFO] [stderr] 104 | pub fn aromaticity(sequence: &str) -> f64 { [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function is never used: `create_cdr3_dict` [INFO] [stderr] --> src/cdr3/cdr3.rs:111:8 [INFO] [stderr] | [INFO] [stderr] 111 | pub fn create_cdr3_dict(cdr3_sequence: Vec) -> BTreeMap { [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function is never used: `aa_groups` [INFO] [stderr] --> src/cdr3/cdr3.rs:122:8 [INFO] [stderr] | [INFO] [stderr] 122 | pub fn aa_groups<'seq>(sequence: String) -> BTreeMap> { [INFO] [stderr] | ^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function is never used: `build_cdr3_struct` [INFO] [stderr] --> src/cdr3/cdr3.rs:153:8 [INFO] [stderr] | [INFO] [stderr] 153 | pub fn build_cdr3_struct(cdr3: String) -> CDR3Prop { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function is never used: `get_cdr3_sequences_attributes` [INFO] [stderr] --> src/cdr3/cdr3.rs:199:8 [INFO] [stderr] | [INFO] [stderr] 199 | pub fn get_cdr3_sequences_attributes(cdr3_dict: BTreeMap) -> Vec { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused `Result` that must be used [INFO] [stderr] --> src/main.rs:62:5 [INFO] [stderr] | [INFO] [stderr] 62 | pipeline_cdr3(input_file); [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_must_use)]` on by default [INFO] [stderr] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stderr] [INFO] [stderr] warning: structure field `MW` should have a snake case name [INFO] [stderr] --> src/cdr3/cdr3.rs:25:9 [INFO] [stderr] | [INFO] [stderr] 25 | pub MW: f64, [INFO] [stderr] | ^^ help: convert the identifier to snake case: `mw` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(non_snake_case)]` on by default [INFO] [stderr] [INFO] [stderr] warning: structure field `AV` should have a snake case name [INFO] [stderr] --> src/cdr3/cdr3.rs:26:9 [INFO] [stderr] | [INFO] [stderr] 26 | pub AV: f64, [INFO] [stderr] | ^^ help: convert the identifier to snake case: `av` [INFO] [stderr] [INFO] [stderr] warning: structure field `IP` should have a snake case name [INFO] [stderr] --> src/cdr3/cdr3.rs:27:5 [INFO] [stderr] | [INFO] [stderr] 27 | IP: f64, [INFO] [stderr] | ^^ help: convert the identifier to snake case: `ip` [INFO] [stderr] [INFO] [stderr] warning: variable `P` should have a snake case name [INFO] [stderr] --> src/cdr3/cdr3.rs:243:9 [INFO] [stderr] | [INFO] [stderr] 243 | let P = ProteinAnalysis::new(sequence); [INFO] [stderr] | ^ help: convert the identifier to snake case: `p` [INFO] [stderr] [INFO] [stderr] warning: unused `Result` that must be used [INFO] [stderr] --> src/cdr3/cdr3.rs:287:5 [INFO] [stderr] | [INFO] [stderr] 287 | write_cdr3_header(); [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stderr] [INFO] [stderr] warning: unused `Result` that must be used [INFO] [stderr] --> src/cdr3/cdr3.rs:289:9 [INFO] [stderr] | [INFO] [stderr] 289 | write_cdr3_attributes(s); [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stderr] [INFO] [stderr] warning: structure field `pos_pKs` should have a snake case name [INFO] [stderr] --> src/cdr3/isoelectric_point.rs:94:5 [INFO] [stderr] | [INFO] [stderr] 94 | pos_pKs: HashMap, [INFO] [stderr] | ^^^^^^^ help: convert the identifier to snake case: `pos_p_ks` [INFO] [stderr] [INFO] [stderr] warning: structure field `neg_pKs` should have a snake case name [INFO] [stderr] --> src/cdr3/isoelectric_point.rs:95:5 [INFO] [stderr] | [INFO] [stderr] 95 | neg_pKs: HashMap, [INFO] [stderr] | ^^^^^^^ help: convert the identifier to snake case: `neg_p_ks` [INFO] [stderr] [INFO] [stderr] warning: structure field `charge_at_pH` should have a snake case name [INFO] [stderr] --> src/cdr3/isoelectric_point.rs:98:9 [INFO] [stderr] | [INFO] [stderr] 98 | pub charge_at_pH: f64, [INFO] [stderr] | ^^^^^^^^^^^^ help: convert the identifier to snake case: `charge_at_p_h` [INFO] [stderr] [INFO] [stderr] warning: variable `pH` should have a snake case name [INFO] [stderr] --> src/cdr3/isoelectric_point.rs:102:32 [INFO] [stderr] | [INFO] [stderr] 102 | pub fn new(sequence: &str, pH: Option) -> Self { [INFO] [stderr] | ^^ help: convert the identifier to snake case: `p_h` [INFO] [stderr] [INFO] [stderr] warning: method `pK_table` should have a snake case name [INFO] [stderr] --> src/cdr3/isoelectric_point.rs:134:8 [INFO] [stderr] | [INFO] [stderr] 134 | fn pK_table(sequence: &String) -> (HashMap, HashMap) { [INFO] [stderr] | ^^^^^^^^ help: convert the identifier to snake case: `p_k_table` [INFO] [stderr] [INFO] [stderr] warning: variable `pos_pKs` should have a snake case name [INFO] [stderr] --> src/cdr3/isoelectric_point.rs:135:17 [INFO] [stderr] | [INFO] [stderr] 135 | let mut pos_pKs: HashMap = POSITIVE_PKS.clone(); [INFO] [stderr] | ^^^^^^^ help: convert the identifier to snake case: `pos_p_ks` [INFO] [stderr] [INFO] [stderr] warning: variable `neg_pKs` should have a snake case name [INFO] [stderr] --> src/cdr3/isoelectric_point.rs:136:17 [INFO] [stderr] | [INFO] [stderr] 136 | let mut neg_pKs: HashMap = NEGATIVE_PKS.clone(); [INFO] [stderr] | ^^^^^^^ help: convert the identifier to snake case: `neg_p_ks` [INFO] [stderr] [INFO] [stderr] warning: variable `pKnterminal` should have a snake case name [INFO] [stderr] --> src/cdr3/isoelectric_point.rs:148:17 [INFO] [stderr] | [INFO] [stderr] 148 | let mut pKnterminal = PKNTERMINAL.clone(); [INFO] [stderr] | ^^^^^^^^^^^ help: convert the identifier to snake case: `p_knterminal` [INFO] [stderr] [INFO] [stderr] warning: variable `pKcterminal` should have a snake case name [INFO] [stderr] --> src/cdr3/isoelectric_point.rs:149:17 [INFO] [stderr] | [INFO] [stderr] 149 | let mut pKcterminal = PKCTERMINAL.clone(); [INFO] [stderr] | ^^^^^^^^^^^ help: convert the identifier to snake case: `p_kcterminal` [INFO] [stderr] [INFO] [stderr] warning: method `charge_at_pH` should have a snake case name [INFO] [stderr] --> src/cdr3/isoelectric_point.rs:171:12 [INFO] [stderr] | [INFO] [stderr] 171 | pub fn charge_at_pH(&self, pH: f64) -> f64 { [INFO] [stderr] | ^^^^^^^^^^^^ help: convert the identifier to snake case: `charge_at_p_h` [INFO] [stderr] [INFO] [stderr] warning: variable `pH` should have a snake case name [INFO] [stderr] --> src/cdr3/isoelectric_point.rs:171:32 [INFO] [stderr] | [INFO] [stderr] 171 | pub fn charge_at_pH(&self, pH: f64) -> f64 { [INFO] [stderr] | ^^ help: convert the identifier to snake case: `p_h` [INFO] [stderr] [INFO] [stderr] warning: variable `pK` should have a snake case name [INFO] [stderr] --> src/cdr3/isoelectric_point.rs:173:18 [INFO] [stderr] | [INFO] [stderr] 173 | for (aa, pK) in &self.pos_pKs { [INFO] [stderr] | ^^ help: convert the identifier to snake case: `p_k` [INFO] [stderr] [INFO] [stderr] warning: variable `pK` should have a snake case name [INFO] [stderr] --> src/cdr3/isoelectric_point.rs:183:18 [INFO] [stderr] | [INFO] [stderr] 183 | for (aa, pK) in &self.neg_pKs { [INFO] [stderr] | ^^ help: convert the identifier to snake case: `p_k` [INFO] [stderr] [INFO] [stderr] warning: variable `pH` should have a snake case name [INFO] [stderr] --> src/cdr3/isoelectric_point.rs:194:22 [INFO] [stderr] | [INFO] [stderr] 194 | fn pi(&self, mut pH: Option, mut min_: Option, mut max_: Option) -> f64 { [INFO] [stderr] | ^^ help: convert the identifier to snake case: `p_h` [INFO] [stderr] [INFO] [stderr] warning: variable `H` should have a snake case name [INFO] [stderr] --> src/cdr3/protein_analysis.rs:68:13 [INFO] [stderr] | [INFO] [stderr] 68 | let H: HashMap> = [INFO] [stderr] | ^ help: convert the identifier to snake case: `h` [INFO] [stderr] [INFO] [stderr] warning: structure field `charge_at_pH` should have a snake case name [INFO] [stderr] --> src/cdr3/protein_analysis.rs:205:9 [INFO] [stderr] | [INFO] [stderr] 205 | pub charge_at_pH: f64, [INFO] [stderr] | ^^^^^^^^^^^^ help: convert the identifier to snake case: `charge_at_p_h` [INFO] [stderr] [INFO] [stderr] warning: variable `PA` should have a snake case name [INFO] [stderr] --> src/cdr3/protein_analysis.rs:212:17 [INFO] [stderr] | [INFO] [stderr] 212 | let mut PA = ProteinAnalysis { [INFO] [stderr] | ^^ help: convert the identifier to snake case: `pa` [INFO] [stderr] [INFO] [stderr] warning: method `charge_at_pH` should have a snake case name [INFO] [stderr] --> src/cdr3/protein_analysis.rs:348:8 [INFO] [stderr] | [INFO] [stderr] 348 | fn charge_at_pH(&mut self, pH: Option) -> f64 { [INFO] [stderr] | ^^^^^^^^^^^^ help: convert the identifier to snake case: `charge_at_p_h` [INFO] [stderr] [INFO] [stderr] warning: variable `pH` should have a snake case name [INFO] [stderr] --> src/cdr3/protein_analysis.rs:348:32 [INFO] [stderr] | [INFO] [stderr] 348 | fn charge_at_pH(&mut self, pH: Option) -> f64 { [INFO] [stderr] | ^^ help: convert the identifier to snake case: `p_h` [INFO] [stderr] [INFO] [stderr] warning: 64 warnings emitted [INFO] [stderr] [INFO] [stderr] Finished test [unoptimized + debuginfo] target(s) in 0.07s [INFO] [stdout] [INFO] [stderr] Running unittests (/opt/rustwide/target/debug/deps/cdr3_parser-8da7676fd6b1e708) [INFO] [stdout] running 0 tests [INFO] [stdout] [INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] running `Command { std: "docker" "inspect" "b582d65d69b74e487bd6ec462d13292253d5342e76474085137fb8b2ad20899c", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "b582d65d69b74e487bd6ec462d13292253d5342e76474085137fb8b2ad20899c", kill_on_drop: false }` [INFO] [stdout] b582d65d69b74e487bd6ec462d13292253d5342e76474085137fb8b2ad20899c