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[INFO] [stderr] Downloaded seq_io v0.3.1 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:923055f121b5182466d55868a8b05e67af8ba4a3a3f6bad814e953ca3cd3ac2a" "/opt/rustwide/cargo-home/bin/cargo" "+1f12b9b0fdbe735968ac002792a720f0ba4faca6" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 7f4ca1e4e3c2257b89278fe0c0bba863da847d4ce37b1d6d8d08dfb053d1b305 [INFO] running `Command { std: "docker" "start" "-a" "7f4ca1e4e3c2257b89278fe0c0bba863da847d4ce37b1d6d8d08dfb053d1b305", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "7f4ca1e4e3c2257b89278fe0c0bba863da847d4ce37b1d6d8d08dfb053d1b305", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "7f4ca1e4e3c2257b89278fe0c0bba863da847d4ce37b1d6d8d08dfb053d1b305", kill_on_drop: false }` [INFO] [stdout] 7f4ca1e4e3c2257b89278fe0c0bba863da847d4ce37b1d6d8d08dfb053d1b305 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:923055f121b5182466d55868a8b05e67af8ba4a3a3f6bad814e953ca3cd3ac2a" "/opt/rustwide/cargo-home/bin/cargo" "+1f12b9b0fdbe735968ac002792a720f0ba4faca6" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 721825e40171c88433b9138c5dd87ee9e103b6e718b5d9822e91326aeb82c229 [INFO] running `Command { std: "docker" "start" "-a" "721825e40171c88433b9138c5dd87ee9e103b6e718b5d9822e91326aeb82c229", kill_on_drop: false }` [INFO] [stderr] Compiling autocfg v1.1.0 [INFO] [stderr] Compiling proc-macro2 v1.0.63 [INFO] [stderr] Compiling crossbeam-utils v0.8.16 [INFO] [stderr] Compiling unicode-ident v1.0.10 [INFO] [stderr] Compiling quote v1.0.29 [INFO] [stderr] Checking cfg-if v1.0.0 [INFO] [stderr] Compiling crossbeam-queue v0.3.8 [INFO] [stderr] Compiling serde v1.0.164 [INFO] [stderr] Checking scopeguard v1.1.0 [INFO] [stderr] Compiling memchr v2.5.0 [INFO] [stderr] Compiling serde_json v1.0.99 [INFO] [stderr] Checking safemem v0.3.3 [INFO] [stderr] Compiling unicode-xid v0.2.4 [INFO] [stderr] Checking ryu v1.0.13 [INFO] [stderr] Checking either v1.8.1 [INFO] [stderr] Checking scoped_threadpool v0.1.9 [INFO] [stderr] Checking itoa v1.0.6 [INFO] [stderr] Checking itertools v0.11.0 [INFO] [stderr] Compiling memoffset v0.9.0 [INFO] [stderr] Compiling crossbeam-epoch v0.9.15 [INFO] [stderr] Checking crossbeam-channel v0.5.8 [INFO] [stderr] Checking buf_redux v0.8.4 [INFO] [stderr] Checking crossbeam-deque v0.8.3 [INFO] [stderr] Checking crossbeam v0.8.2 [INFO] [stderr] Compiling syn v2.0.25 [INFO] [stderr] Compiling const_format_proc_macros v0.2.31 [INFO] [stderr] Checking const_format v0.2.31 [INFO] [stderr] Compiling serde_derive v1.0.171 [INFO] [stderr] Checking seq_io v0.3.1 [INFO] [stderr] Checking restrander-testing-rig v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused imports: `collections::HashSet`, `hash::Hash`, and `process::Command` [INFO] [stdout] --> src/main.rs:2:20 [INFO] [stdout] | [INFO] [stdout] 2 | use std::{env, fs, process::Command, collections::HashSet, hash::Hash}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `GenericProgramConfig` [INFO] [stdout] --> src/main.rs:4:79 [INFO] [stdout] | [INFO] [stdout] 4 | use config::{ProgramResult, PychopperConfig, SpecificProgramConfig, Protocol, GenericProgramConfig}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `paf::PafReads` [INFO] [stdout] --> src/main.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use paf::PafReads; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::fastq::CategorisedReads` [INFO] [stdout] --> src/main.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use crate::fastq::CategorisedReads; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `fmt::format` and `path::Path` [INFO] [stdout] --> src/json.rs:1:21 [INFO] [stdout] | [INFO] [stdout] 1 | use std::{fs::File, path::Path, io::Write, fmt::format}; [INFO] [stdout] | ^^^^^^^^^^ ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `iproduct` [INFO] [stdout] --> src/json.rs:3:17 [INFO] [stdout] | [INFO] [stdout] 3 | use itertools::{iproduct, Itertools}; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `error` [INFO] [stdout] --> src/json.rs:4:31 [INFO] [stdout] | [INFO] [stdout] 4 | use serde_json::{Value, json, error}; [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `constants` and `self` [INFO] [stdout] --> src/json.rs:6:13 [INFO] [stdout] | [INFO] [stdout] 6 | use crate::{constants, config::{Protocol, self}}; [INFO] [stdout] | ^^^^^^^^^ ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashMap` [INFO] [stdout] --> src/restrander.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use std::collections::HashMap; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs::remove_file` [INFO] [stdout] --> src/restrander.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use std::fs::remove_file; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::json::Config` [INFO] [stdout] --> src/restrander.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use crate::json::Config; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `PafRead` [INFO] [stdout] --> src/restrander.rs:7:18 [INFO] [stdout] | [INFO] [stdout] 7 | use crate::paf::{PafRead, PafReads}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `collections::HashMap` and `fs::remove_file` [INFO] [stdout] --> src/pychopper.rs:1:44 [INFO] [stdout] | [INFO] [stdout] 1 | use std::{time::Instant, process::Command, fs::remove_file, collections::HashMap}; [INFO] [stdout] | ^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `PafRead` [INFO] [stdout] --> src/pychopper.rs:3:139 [INFO] [stdout] | [INFO] [stdout] 3 | ...sult, ProgramConfig, PychopperConfig}, constants, fastq, paf::{PafRead, PafReads}}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::hash::Hash` [INFO] [stdout] --> src/paf.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use std::hash::Hash; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Config` and `Method` [INFO] [stdout] --> src/config.rs:1:43 [INFO] [stdout] | [INFO] [stdout] 1 | use crate::{fastq::AccuracyResult, json::{Config, Method}}; [INFO] [stdout] | ^^^^^^ ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `collections::HashSet`, `hash::Hash`, and `process::Command` [INFO] [stdout] --> src/main.rs:2:20 [INFO] [stdout] | [INFO] [stdout] 2 | use std::{env, fs, process::Command, collections::HashSet, hash::Hash}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `GenericProgramConfig` [INFO] [stdout] --> src/main.rs:4:79 [INFO] [stdout] | [INFO] [stdout] 4 | use config::{ProgramResult, PychopperConfig, SpecificProgramConfig, Protocol, GenericProgramConfig}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `paf::PafReads` [INFO] [stdout] --> src/main.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use paf::PafReads; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::fastq::CategorisedReads` [INFO] [stdout] --> src/main.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use crate::fastq::CategorisedReads; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `fmt::format` and `path::Path` [INFO] [stdout] --> src/json.rs:1:21 [INFO] [stdout] | [INFO] [stdout] 1 | use std::{fs::File, path::Path, io::Write, fmt::format}; [INFO] [stdout] | ^^^^^^^^^^ ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `iproduct` [INFO] [stdout] --> src/json.rs:3:17 [INFO] [stdout] | [INFO] [stdout] 3 | use itertools::{iproduct, Itertools}; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `error` [INFO] [stdout] --> src/json.rs:4:31 [INFO] [stdout] | [INFO] [stdout] 4 | use serde_json::{Value, json, error}; [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `constants` and `self` [INFO] [stdout] --> src/json.rs:6:13 [INFO] [stdout] | [INFO] [stdout] 6 | use crate::{constants, config::{Protocol, self}}; [INFO] [stdout] | ^^^^^^^^^ ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashMap` [INFO] [stdout] --> src/restrander.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use std::collections::HashMap; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs::remove_file` [INFO] [stdout] --> src/restrander.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use std::fs::remove_file; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::json::Config` [INFO] [stdout] --> src/restrander.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use crate::json::Config; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `PafRead` [INFO] [stdout] --> src/restrander.rs:7:18 [INFO] [stdout] | [INFO] [stdout] 7 | use crate::paf::{PafRead, PafReads}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `collections::HashMap` and `fs::remove_file` [INFO] [stdout] --> src/pychopper.rs:1:44 [INFO] [stdout] | [INFO] [stdout] 1 | use std::{time::Instant, process::Command, fs::remove_file, collections::HashMap}; [INFO] [stdout] | ^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `PafRead` [INFO] [stdout] --> src/pychopper.rs:3:139 [INFO] [stdout] | [INFO] [stdout] 3 | ...sult, ProgramConfig, PychopperConfig}, constants, fastq, paf::{PafRead, PafReads}}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::hash::Hash` [INFO] [stdout] --> src/paf.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use std::hash::Hash; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Config` and `Method` [INFO] [stdout] --> src/config.rs:1:43 [INFO] [stdout] | [INFO] [stdout] 1 | use crate::{fastq::AccuracyResult, json::{Config, Method}}; [INFO] [stdout] | ^^^^^^ ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `command` [INFO] [stdout] --> src/pychopper.rs:29:9 [INFO] [stdout] | [INFO] [stdout] 29 | let command = format!("{} run pychopper {} {} {}", constants::CONDA_PATH, backend_string, generic_config.clone().input, generic_confi... [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_command` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `paf_reads` [INFO] [stdout] --> src/pychopper.rs:65:5 [INFO] [stdout] | [INFO] [stdout] 65 | paf_reads: PafReads [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_paf_reads` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `command` [INFO] [stdout] --> src/pychopper.rs:29:9 [INFO] [stdout] | [INFO] [stdout] 29 | let command = format!("{} run pychopper {} {} {}", constants::CONDA_PATH, backend_string, generic_config.clone().input, generic_confi... [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_command` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `paf_reads` [INFO] [stdout] --> src/pychopper.rs:65:5 [INFO] [stdout] | [INFO] [stdout] 65 | paf_reads: PafReads [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_paf_reads` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function `new_from_args` is never used [INFO] [stdout] --> src/main.rs:135:12 [INFO] [stdout] | [INFO] [stdout] 134 | impl GridTestInput { [INFO] [stdout] | ------------------ associated function in this implementation [INFO] [stdout] 135 | pub fn new_from_args() -> GridTestInput { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `OUTPUT_FILENAME` is never used [INFO] [stdout] --> src/constants.rs:6:11 [INFO] [stdout] | [INFO] [stdout] 6 | pub const OUTPUT_FILENAME: &str = "/home/jakob/Documents/restrander-paper/error-rate-testing/temp.fq"; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `DEFAULT_ERROR_RATE`, `default_pipeline`, `default_config`, and `to_filename` are never used [INFO] [stdout] --> src/json.rs:18:11 [INFO] [stdout] | [INFO] [stdout] 17 | impl Config { [INFO] [stdout] | ----------- associated items in this implementation [INFO] [stdout] 18 | const DEFAULT_ERROR_RATE: f64 = 0.25; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 21 | fn default_pipeline(protocol: Protocol) -> Pipeline { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 28 | fn default_config() -> Config { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 49 | pub fn to_filename(self) -> String { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `Poly` is never constructed [INFO] [stdout] --> src/json.rs:61:5 [INFO] [stdout] | [INFO] [stdout] 60 | pub enum Method { [INFO] [stdout] | ------ variant in this enum [INFO] [stdout] 61 | Poly(u64, u64), [INFO] [stdout] | ^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Method` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `default_poly`, `default_primer`, and `to_filename` are never used [INFO] [stdout] --> src/json.rs:66:8 [INFO] [stdout] | [INFO] [stdout] 65 | impl Method { [INFO] [stdout] | ----------- associated items in this implementation [INFO] [stdout] 66 | fn default_poly() -> Method { [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 70 | fn default_primer() -> Method { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 98 | fn to_filename(self) -> String { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `make_desired_configs` is never used [INFO] [stdout] --> src/json.rs:109:8 [INFO] [stdout] | [INFO] [stdout] 109 | pub fn make_desired_configs(config_dir: String, protocol: Protocol) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `make_error_rate_config` is never used [INFO] [stdout] --> src/json.rs:152:4 [INFO] [stdout] | [INFO] [stdout] 152 | fn make_error_rate_config(error_rate: f64, protocol: Protocol) -> Config { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `make_search_size_config` is never used [INFO] [stdout] --> src/json.rs:168:4 [INFO] [stdout] | [INFO] [stdout] 168 | fn make_search_size_config(search_size: u64, protocol: Protocol) -> Config { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `make_no_primer_config` is never used [INFO] [stdout] --> src/json.rs:179:4 [INFO] [stdout] | [INFO] [stdout] 179 | fn make_no_primer_config() -> Config { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `make_no_poly_config` is never used [INFO] [stdout] --> src/json.rs:189:4 [INFO] [stdout] | [INFO] [stdout] 189 | fn make_no_poly_config(protocol: Protocol) -> Config { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `insert`, `get`, and `size` are never used [INFO] [stdout] --> src/paf.rs:24:12 [INFO] [stdout] | [INFO] [stdout] 19 | impl PafReads { [INFO] [stdout] | ------------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 24 | pub fn insert(mut self, read: PafRead) { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 39 | pub fn get(self, name: String) -> char { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 46 | pub fn size(self) -> i32 { [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `total` is never used [INFO] [stdout] --> src/fastq.rs:40:8 [INFO] [stdout] | [INFO] [stdout] 39 | impl AccuracyResultExact { [INFO] [stdout] | ------------------------ method in this implementation [INFO] [stdout] 40 | fn total(&self) -> u64 { [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parse_nanoprep` is never used [INFO] [stdout] --> src/fastq.rs:144:8 [INFO] [stdout] | [INFO] [stdout] 144 | pub fn parse_nanoprep (filename: String, paf_reads: &Vec) { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `PafRead` is never constructed [INFO] [stdout] --> src/paf.rs:8:12 [INFO] [stdout] | [INFO] [stdout] 8 | pub struct PafRead { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `PafRead` has a derived impl for the trait `Clone`, but this is intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `PafReads` is never constructed [INFO] [stdout] --> src/paf.rs:14:12 [INFO] [stdout] | [INFO] [stdout] 14 | pub struct PafReads { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `PafReads` has a derived impl for the trait `Clone`, but this is intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `new`, `insert`, `get`, and `size` are never used [INFO] [stdout] --> src/paf.rs:20:8 [INFO] [stdout] | [INFO] [stdout] 19 | impl PafReads { [INFO] [stdout] | ------------- associated items in this implementation [INFO] [stdout] 20 | fn new() -> PafReads { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 24 | pub fn insert(mut self, read: PafRead) { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 39 | pub fn get(self, name: String) -> char { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 46 | pub fn size(self) -> i32 { [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function `from_paf_line` is never used [INFO] [stdout] --> src/paf.rs:52:12 [INFO] [stdout] | [INFO] [stdout] 51 | impl PafRead { [INFO] [stdout] | ------------ associated function in this implementation [INFO] [stdout] 52 | pub fn from_paf_line (line: &Vec) -> PafRead { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parse` is never used [INFO] [stdout] --> src/paf.rs:90:8 [INFO] [stdout] | [INFO] [stdout] 90 | pub fn parse (filename: String) -> PafReads { [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `generic` is never read [INFO] [stdout] --> src/config.rs:27:9 [INFO] [stdout] | [INFO] [stdout] 25 | pub struct ProgramConfig { [INFO] [stdout] | ------------- field in this struct [INFO] [stdout] 26 | pub specific: SpecificProgramConfig, [INFO] [stdout] 27 | pub generic: GenericProgramConfig, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `ProgramConfig` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variants `Poly` and `Primer` are never constructed [INFO] [stdout] --> src/config.rs:68:5 [INFO] [stdout] | [INFO] [stdout] 67 | pub enum PipelineStep { [INFO] [stdout] | ------------ variants in this enum [INFO] [stdout] 68 | Poly(u64, u64), [INFO] [stdout] | ^^^^ [INFO] [stdout] 69 | Primer(Protocol), [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `PipelineStep` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function `new_from_args` is never used [INFO] [stdout] --> src/main.rs:135:12 [INFO] [stdout] | [INFO] [stdout] 134 | impl GridTestInput { [INFO] [stdout] | ------------------ associated function in this implementation [INFO] [stdout] 135 | pub fn new_from_args() -> GridTestInput { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `OUTPUT_FILENAME` is never used [INFO] [stdout] --> src/constants.rs:6:11 [INFO] [stdout] | [INFO] [stdout] 6 | pub const OUTPUT_FILENAME: &str = "/home/jakob/Documents/restrander-paper/error-rate-testing/temp.fq"; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `DEFAULT_ERROR_RATE`, `default_pipeline`, `default_config`, and `to_filename` are never used [INFO] [stdout] --> src/json.rs:18:11 [INFO] [stdout] | [INFO] [stdout] 17 | impl Config { [INFO] [stdout] | ----------- associated items in this implementation [INFO] [stdout] 18 | const DEFAULT_ERROR_RATE: f64 = 0.25; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 21 | fn default_pipeline(protocol: Protocol) -> Pipeline { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 28 | fn default_config() -> Config { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 49 | pub fn to_filename(self) -> String { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `Poly` is never constructed [INFO] [stdout] --> src/json.rs:61:5 [INFO] [stdout] | [INFO] [stdout] 60 | pub enum Method { [INFO] [stdout] | ------ variant in this enum [INFO] [stdout] 61 | Poly(u64, u64), [INFO] [stdout] | ^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Method` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `default_poly`, `default_primer`, and `to_filename` are never used [INFO] [stdout] --> src/json.rs:66:8 [INFO] [stdout] | [INFO] [stdout] 65 | impl Method { [INFO] [stdout] | ----------- associated items in this implementation [INFO] [stdout] 66 | fn default_poly() -> Method { [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 70 | fn default_primer() -> Method { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 98 | fn to_filename(self) -> String { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `make_desired_configs` is never used [INFO] [stdout] --> src/json.rs:109:8 [INFO] [stdout] | [INFO] [stdout] 109 | pub fn make_desired_configs(config_dir: String, protocol: Protocol) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `make_error_rate_config` is never used [INFO] [stdout] --> src/json.rs:152:4 [INFO] [stdout] | [INFO] [stdout] 152 | fn make_error_rate_config(error_rate: f64, protocol: Protocol) -> Config { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `make_search_size_config` is never used [INFO] [stdout] --> src/json.rs:168:4 [INFO] [stdout] | [INFO] [stdout] 168 | fn make_search_size_config(search_size: u64, protocol: Protocol) -> Config { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `make_no_primer_config` is never used [INFO] [stdout] --> src/json.rs:179:4 [INFO] [stdout] | [INFO] [stdout] 179 | fn make_no_primer_config() -> Config { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `make_no_poly_config` is never used [INFO] [stdout] --> src/json.rs:189:4 [INFO] [stdout] | [INFO] [stdout] 189 | fn make_no_poly_config(protocol: Protocol) -> Config { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `insert`, `get`, and `size` are never used [INFO] [stdout] --> src/paf.rs:24:12 [INFO] [stdout] | [INFO] [stdout] 19 | impl PafReads { [INFO] [stdout] | ------------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 24 | pub fn insert(mut self, read: PafRead) { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 39 | pub fn get(self, name: String) -> char { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 46 | pub fn size(self) -> i32 { [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `total` is never used [INFO] [stdout] --> src/fastq.rs:40:8 [INFO] [stdout] | [INFO] [stdout] 39 | impl AccuracyResultExact { [INFO] [stdout] | ------------------------ method in this implementation [INFO] [stdout] 40 | fn total(&self) -> u64 { [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parse_nanoprep` is never used [INFO] [stdout] --> src/fastq.rs:144:8 [INFO] [stdout] | [INFO] [stdout] 144 | pub fn parse_nanoprep (filename: String, paf_reads: &Vec) { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `PafRead` is never constructed [INFO] [stdout] --> src/paf.rs:8:12 [INFO] [stdout] | [INFO] [stdout] 8 | pub struct PafRead { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `PafRead` has a derived impl for the trait `Clone`, but this is intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `PafReads` is never constructed [INFO] [stdout] --> src/paf.rs:14:12 [INFO] [stdout] | [INFO] [stdout] 14 | pub struct PafReads { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `PafReads` has a derived impl for the trait `Clone`, but this is intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `new`, `insert`, `get`, and `size` are never used [INFO] [stdout] --> src/paf.rs:20:8 [INFO] [stdout] | [INFO] [stdout] 19 | impl PafReads { [INFO] [stdout] | ------------- associated items in this implementation [INFO] [stdout] 20 | fn new() -> PafReads { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 24 | pub fn insert(mut self, read: PafRead) { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 39 | pub fn get(self, name: String) -> char { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 46 | pub fn size(self) -> i32 { [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function `from_paf_line` is never used [INFO] [stdout] --> src/paf.rs:52:12 [INFO] [stdout] | [INFO] [stdout] 51 | impl PafRead { [INFO] [stdout] | ------------ associated function in this implementation [INFO] [stdout] 52 | pub fn from_paf_line (line: &Vec) -> PafRead { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parse` is never used [INFO] [stdout] --> src/paf.rs:90:8 [INFO] [stdout] | [INFO] [stdout] 90 | pub fn parse (filename: String) -> PafReads { [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `generic` is never read [INFO] [stdout] --> src/config.rs:27:9 [INFO] [stdout] | [INFO] [stdout] 25 | pub struct ProgramConfig { [INFO] [stdout] | ------------- field in this struct [INFO] [stdout] 26 | pub specific: SpecificProgramConfig, [INFO] [stdout] 27 | pub generic: GenericProgramConfig, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `ProgramConfig` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variants `Poly` and `Primer` are never constructed [INFO] [stdout] --> src/config.rs:68:5 [INFO] [stdout] | [INFO] [stdout] 67 | pub enum PipelineStep { [INFO] [stdout] | ------------ variants in this enum [INFO] [stdout] 68 | Poly(u64, u64), [INFO] [stdout] | ^^^^ [INFO] [stdout] 69 | Primer(Protocol), [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `PipelineStep` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 38 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 38 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 3.81s [INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: buf_redux v0.8.4 [INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1` [INFO] running `Command { std: "docker" "inspect" "721825e40171c88433b9138c5dd87ee9e103b6e718b5d9822e91326aeb82c229", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "721825e40171c88433b9138c5dd87ee9e103b6e718b5d9822e91326aeb82c229", kill_on_drop: false }` [INFO] [stdout] 721825e40171c88433b9138c5dd87ee9e103b6e718b5d9822e91326aeb82c229