[INFO] cloning repository https://github.com/clinico-omics/preqc-pack [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/clinico-omics/preqc-pack" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fclinico-omics%2Fpreqc-pack", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fclinico-omics%2Fpreqc-pack'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] b4dc6def64d046417c317becefadc86c81bb2e14 [INFO] testing clinico-omics/preqc-pack against try#1b74e096b9bfb06f84a3007193dcd2f059cbdf6a for pr-96025 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fclinico-omics%2Fpreqc-pack" "/workspace/builds/worker-10/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-10/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/clinico-omics/preqc-pack on toolchain 1b74e096b9bfb06f84a3007193dcd2f059cbdf6a [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1b74e096b9bfb06f84a3007193dcd2f059cbdf6a" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/clinico-omics/preqc-pack [INFO] finished tweaking git repo https://github.com/clinico-omics/preqc-pack [INFO] tweaked toml for git repo https://github.com/clinico-omics/preqc-pack written to /workspace/builds/worker-10/source/Cargo.toml [INFO] crate git repo https://github.com/clinico-omics/preqc-pack already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1b74e096b9bfb06f84a3007193dcd2f059cbdf6a" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-10/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-10/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:b0c94ce3c1162fcb8e57cac5b65ec2f72eabb1eebea4fcc35e269e823f681646" "/opt/rustwide/cargo-home/bin/cargo" "+1b74e096b9bfb06f84a3007193dcd2f059cbdf6a" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] c63257aca5188c1c354622b9a92a48dc33840ee60c913118c2317a1e9005ebf3 [INFO] running `Command { std: "docker" "start" "-a" "c63257aca5188c1c354622b9a92a48dc33840ee60c913118c2317a1e9005ebf3", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "c63257aca5188c1c354622b9a92a48dc33840ee60c913118c2317a1e9005ebf3", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "c63257aca5188c1c354622b9a92a48dc33840ee60c913118c2317a1e9005ebf3", kill_on_drop: false }` [INFO] [stdout] c63257aca5188c1c354622b9a92a48dc33840ee60c913118c2317a1e9005ebf3 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-10/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-10/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:b0c94ce3c1162fcb8e57cac5b65ec2f72eabb1eebea4fcc35e269e823f681646" "/opt/rustwide/cargo-home/bin/cargo" "+1b74e096b9bfb06f84a3007193dcd2f059cbdf6a" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 841175a3e5cbce1f4378b98a54588a30bc0e7b910170fa846e33473f759bf8a6 [INFO] running `Command { std: "docker" "start" "-a" "841175a3e5cbce1f4378b98a54588a30bc0e7b910170fa846e33473f759bf8a6", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.98 [INFO] [stderr] Compiling autocfg v1.0.1 [INFO] [stderr] Compiling cfg-if v1.0.0 [INFO] [stderr] Compiling proc-macro2 v1.0.28 [INFO] 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v0.3.1 [INFO] [stderr] Compiling chrono v0.4.19 [INFO] [stderr] Compiling rust-ini v0.16.1 [INFO] [stderr] Compiling webpki v0.21.4 [INFO] [stderr] Compiling sct v0.6.1 [INFO] [stderr] Compiling rustls v0.19.1 [INFO] [stderr] Compiling webpki-roots v0.19.0 [INFO] [stderr] Compiling rustls v0.18.1 [INFO] [stderr] Compiling webpki-roots v0.21.1 [INFO] [stderr] Compiling stderrlog v0.4.3 [INFO] [stderr] Compiling tokio-macros v1.3.0 [INFO] [stderr] Compiling thiserror-impl v1.0.26 [INFO] [stderr] Compiling maybe-async v0.2.6 [INFO] [stderr] Compiling structopt-derive v0.4.15 [INFO] [stderr] Compiling thiserror v1.0.26 [INFO] [stderr] Compiling structopt v0.3.22 [INFO] [stderr] Compiling tokio-util v0.6.7 [INFO] [stderr] Compiling tokio-rustls v0.22.0 [INFO] [stderr] Compiling tokio-stream v0.1.7 [INFO] [stderr] Compiling futures-executor v0.3.16 [INFO] [stderr] Compiling futures v0.3.16 [INFO] [stderr] Compiling h2 v0.3.3 [INFO] [stderr] Compiling lz4 v1.23.2 [INFO] [stderr] Compiling fastq v0.6.0 [INFO] [stderr] Compiling serde_urlencoded v0.7.0 [INFO] [stderr] Compiling serde-xml-rs v0.4.1 [INFO] [stderr] Compiling uuid v0.8.2 [INFO] [stderr] Compiling serde_bytes v0.11.5 [INFO] [stderr] Compiling attohttpc v0.16.3 [INFO] [stderr] Compiling bson v2.1.0 [INFO] [stderr] Compiling hyper v0.14.11 [INFO] [stderr] Compiling aws-creds v0.26.0 [INFO] [stderr] Compiling hyper-rustls v0.22.1 [INFO] [stderr] Compiling reqwest v0.11.4 [INFO] [stderr] Compiling rust-s3 v0.27.0-rc4 [INFO] [stderr] Compiling preqc-pack v0.1.2 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `blake2::Blake2b` [INFO] [stdout] --> src/qc/mislabeling.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use blake2::Blake2b; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `md5::Md5` [INFO] [stdout] --> src/qc/mislabeling.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use md5::Md5; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Deserialize`, `Serialize` [INFO] [stdout] --> src/qc/util.rs:1:13 [INFO] [stdout] | [INFO] [stdout] 1 | use serde::{Deserialize, Serialize}; [INFO] [stdout] | ^^^^^^^^^^^ ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `log::*` [INFO] [stdout] --> src/qc/hasher.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use log::*; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `add_to_a_count` [INFO] [stdout] --> src/qc/fastqc.rs:528:6 [INFO] [stdout] | [INFO] [stdout] 528 | fn add_to_a_count(&mut self, a_count: usize) { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `add_to_t_count` [INFO] [stdout] --> src/qc/fastqc.rs:532:6 [INFO] [stdout] | [INFO] [stdout] 532 | fn add_to_t_count(&mut self, t_count: usize) { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `add_to_c_count` [INFO] [stdout] --> src/qc/fastqc.rs:536:6 [INFO] [stdout] | [INFO] [stdout] 536 | fn add_to_c_count(&mut self, c_count: usize) { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `add_to_g_count` [INFO] [stdout] --> src/qc/fastqc.rs:540:6 [INFO] [stdout] | [INFO] [stdout] 540 | fn add_to_g_count(&mut self, g_count: usize) { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `add_to_n_count` [INFO] [stdout] --> src/qc/fastqc.rs:544:6 [INFO] [stdout] | [INFO] [stdout] 544 | fn add_to_n_count(&mut self, n_count: usize) { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `length` [INFO] [stdout] --> src/qc/mislabeling.rs:14:3 [INFO] [stdout] | [INFO] [stdout] 14 | length: usize, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: `VAFMatrix` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] --> src/qc/mislabeling.rs:11:10 [INFO] [stdout] | [INFO] [stdout] 11 | #[derive(Debug, Serialize, Deserialize, Clone)] [INFO] [stdout] | ^^^^^ ^^^^^ [INFO] [stdout] = note: this warning originates in the derive macro `Debug` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `hash` [INFO] [stdout] --> src/qc/mislabeling.rs:149:6 [INFO] [stdout] | [INFO] [stdout] 149 | fn hash(&self, seq: &[u8]) -> String [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 11 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 31.91s [INFO] running `Command { std: "docker" "inspect" "841175a3e5cbce1f4378b98a54588a30bc0e7b910170fa846e33473f759bf8a6", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "841175a3e5cbce1f4378b98a54588a30bc0e7b910170fa846e33473f759bf8a6", kill_on_drop: false }` [INFO] [stdout] 841175a3e5cbce1f4378b98a54588a30bc0e7b910170fa846e33473f759bf8a6 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-10/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-10/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:b0c94ce3c1162fcb8e57cac5b65ec2f72eabb1eebea4fcc35e269e823f681646" "/opt/rustwide/cargo-home/bin/cargo" "+1b74e096b9bfb06f84a3007193dcd2f059cbdf6a" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] eaf38d90f0159977603f37feb2871222a62df251d6ec5391996f6373a1a3b7e6 [INFO] running `Command { std: "docker" "start" "-a" "eaf38d90f0159977603f37feb2871222a62df251d6ec5391996f6373a1a3b7e6", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stdout] warning: unused import: `blake2::Blake2b` [INFO] [stdout] --> src/qc/mislabeling.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use blake2::Blake2b; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `md5::Md5` [INFO] [stdout] --> src/qc/mislabeling.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use md5::Md5; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Deserialize`, `Serialize` [INFO] [stdout] --> src/qc/util.rs:1:13 [INFO] [stdout] | [INFO] [stdout] 1 | use serde::{Deserialize, Serialize}; [INFO] [stdout] | ^^^^^^^^^^^ ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `log::*` [INFO] [stdout] --> src/qc/hasher.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use log::*; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `add_to_a_count` [INFO] [stdout] --> src/qc/fastqc.rs:528:6 [INFO] [stdout] | [INFO] [stdout] 528 | fn add_to_a_count(&mut self, a_count: usize) { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `add_to_t_count` [INFO] [stdout] --> src/qc/fastqc.rs:532:6 [INFO] [stdout] | [INFO] [stdout] 532 | fn add_to_t_count(&mut self, t_count: usize) { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `add_to_c_count` [INFO] [stdout] --> src/qc/fastqc.rs:536:6 [INFO] [stdout] | [INFO] [stdout] 536 | fn add_to_c_count(&mut self, c_count: usize) { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `add_to_g_count` [INFO] [stdout] --> src/qc/fastqc.rs:540:6 [INFO] [stdout] | [INFO] [stdout] 540 | fn add_to_g_count(&mut self, g_count: usize) { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `add_to_n_count` [INFO] [stdout] --> src/qc/fastqc.rs:544:6 [INFO] [stdout] | [INFO] [stdout] 544 | fn add_to_n_count(&mut self, n_count: usize) { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `length` [INFO] [stdout] --> src/qc/mislabeling.rs:14:3 [INFO] [stdout] | [INFO] [stdout] 14 | length: usize, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: `VAFMatrix` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] --> src/qc/mislabeling.rs:11:10 [INFO] [stdout] | [INFO] [stdout] 11 | #[derive(Debug, Serialize, Deserialize, Clone)] [INFO] [stdout] | ^^^^^ ^^^^^ [INFO] [stdout] = note: this warning originates in the derive macro `Debug` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Compiling preqc-pack v0.1.2 (/opt/rustwide/workdir) [INFO] [stdout] warning: associated function is never used: `hash` [INFO] [stdout] --> src/qc/mislabeling.rs:149:6 [INFO] [stdout] | [INFO] [stdout] 149 | fn hash(&self, seq: &[u8]) -> String [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 11 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `indexes` [INFO] [stdout] --> examples/mislabeling.rs:5:18 [INFO] [stdout] | [INFO] [stdout] 5 | let (patterns, indexes, count) = VAFMatrix::read_patterns("data/patterns.bson"); [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_indexes` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `blake2::Blake2b` [INFO] [stdout] --> src/qc/mislabeling.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use blake2::Blake2b; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `md5::Md5` [INFO] [stdout] --> src/qc/mislabeling.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use md5::Md5; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Deserialize`, `Serialize` [INFO] [stdout] --> src/qc/util.rs:1:13 [INFO] [stdout] | [INFO] [stdout] 1 | use serde::{Deserialize, Serialize}; [INFO] [stdout] | ^^^^^^^^^^^ ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `log::*` [INFO] [stdout] --> src/qc/hasher.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use log::*; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `add_to_a_count` [INFO] [stdout] --> src/qc/fastqc.rs:528:6 [INFO] [stdout] | [INFO] [stdout] 528 | fn add_to_a_count(&mut self, a_count: usize) { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `add_to_t_count` [INFO] [stdout] --> src/qc/fastqc.rs:532:6 [INFO] [stdout] | [INFO] [stdout] 532 | fn add_to_t_count(&mut self, t_count: usize) { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `add_to_c_count` [INFO] [stdout] --> src/qc/fastqc.rs:536:6 [INFO] [stdout] | [INFO] [stdout] 536 | fn add_to_c_count(&mut self, c_count: usize) { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `add_to_g_count` [INFO] [stdout] --> src/qc/fastqc.rs:540:6 [INFO] [stdout] | [INFO] [stdout] 540 | fn add_to_g_count(&mut self, g_count: usize) { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `add_to_n_count` [INFO] [stdout] --> src/qc/fastqc.rs:544:6 [INFO] [stdout] | [INFO] [stdout] 544 | fn add_to_n_count(&mut self, n_count: usize) { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `length` [INFO] [stdout] --> src/qc/mislabeling.rs:14:3 [INFO] [stdout] | [INFO] [stdout] 14 | length: usize, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] note: `VAFMatrix` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] --> src/qc/mislabeling.rs:11:10 [INFO] [stdout] | [INFO] [stdout] 11 | #[derive(Debug, Serialize, Deserialize, Clone)] [INFO] [stdout] | ^^^^^ ^^^^^ [INFO] [stdout] = note: this warning originates in the derive macro `Debug` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `hash` [INFO] [stdout] --> src/qc/mislabeling.rs:149:6 [INFO] [stdout] | [INFO] [stdout] 149 | fn hash(&self, seq: &[u8]) -> String [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 1 warning emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 11 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished test [unoptimized + debuginfo] target(s) in 1.55s [INFO] [stderr] Executable unittests src/lib.rs (/opt/rustwide/target/debug/deps/preqc_pack-63857da2bd62c670) [INFO] [stderr] Executable unittests src/bin/preqc-pack.rs (/opt/rustwide/target/debug/deps/preqc_pack-a58d36d02f87c642) [INFO] running `Command { std: "docker" "inspect" "eaf38d90f0159977603f37feb2871222a62df251d6ec5391996f6373a1a3b7e6", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "eaf38d90f0159977603f37feb2871222a62df251d6ec5391996f6373a1a3b7e6", kill_on_drop: false }` [INFO] [stdout] eaf38d90f0159977603f37feb2871222a62df251d6ec5391996f6373a1a3b7e6 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-10/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-10/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:b0c94ce3c1162fcb8e57cac5b65ec2f72eabb1eebea4fcc35e269e823f681646" "/opt/rustwide/cargo-home/bin/cargo" "+1b74e096b9bfb06f84a3007193dcd2f059cbdf6a" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] cc3416f4126580cf3ff8399235fdfcba4f711929e67eab326b2e6c3eb5d033bf [INFO] running `Command { std: "docker" "start" "-a" "cc3416f4126580cf3ff8399235fdfcba4f711929e67eab326b2e6c3eb5d033bf", kill_on_drop: false }` [INFO] [stderr] warning: unused import: `blake2::Blake2b` [INFO] [stderr] --> src/qc/mislabeling.rs:1:5 [INFO] [stderr] | [INFO] [stderr] 1 | use blake2::Blake2b; [INFO] [stderr] | ^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_imports)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused import: `md5::Md5` [INFO] [stderr] --> src/qc/mislabeling.rs:2:5 [INFO] [stderr] | [INFO] [stderr] 2 | use md5::Md5; [INFO] [stderr] | ^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused imports: `Deserialize`, `Serialize` [INFO] [stderr] --> src/qc/util.rs:1:13 [INFO] [stderr] | [INFO] [stderr] 1 | use serde::{Deserialize, Serialize}; [INFO] [stderr] | ^^^^^^^^^^^ ^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `log::*` [INFO] [stderr] --> src/qc/hasher.rs:3:5 [INFO] [stderr] | [INFO] [stderr] 3 | use log::*; [INFO] [stderr] | ^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: associated function is never used: `add_to_a_count` [INFO] [stderr] --> src/qc/fastqc.rs:528:6 [INFO] [stderr] | [INFO] [stderr] 528 | fn add_to_a_count(&mut self, a_count: usize) { [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` on by default [INFO] [stderr] [INFO] [stderr] warning: associated function is never used: `add_to_t_count` [INFO] [stderr] --> src/qc/fastqc.rs:532:6 [INFO] [stderr] | [INFO] [stderr] 532 | fn add_to_t_count(&mut self, t_count: usize) { [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: associated function is never used: `add_to_c_count` [INFO] [stderr] --> src/qc/fastqc.rs:536:6 [INFO] [stderr] | [INFO] [stderr] 536 | fn add_to_c_count(&mut self, c_count: usize) { [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: associated function is never used: `add_to_g_count` [INFO] [stderr] --> src/qc/fastqc.rs:540:6 [INFO] [stderr] | [INFO] [stderr] 540 | fn add_to_g_count(&mut self, g_count: usize) { [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: associated function is never used: `add_to_n_count` [INFO] [stderr] --> src/qc/fastqc.rs:544:6 [INFO] [stderr] | [INFO] [stderr] 544 | fn add_to_n_count(&mut self, n_count: usize) { [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: field is never read: `length` [INFO] [stderr] --> src/qc/mislabeling.rs:14:3 [INFO] [stderr] | [INFO] [stderr] 14 | length: usize, [INFO] [stderr] | ^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] note: `VAFMatrix` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stderr] --> src/qc/mislabeling.rs:11:10 [INFO] [stderr] | [INFO] [stderr] 11 | #[derive(Debug, Serialize, Deserialize, Clone)] [INFO] [stderr] | ^^^^^ ^^^^^ [INFO] [stderr] = note: this warning originates in the derive macro `Debug` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stderr] [INFO] [stderr] warning: associated function is never used: `hash` [INFO] [stderr] --> src/qc/mislabeling.rs:149:6 [INFO] [stderr] | [INFO] [stderr] 149 | fn hash(&self, seq: &[u8]) -> String [INFO] [stderr] | ^^^^ [INFO] [stderr] [INFO] [stderr] warning: `preqc-pack` (lib) generated 11 warnings [INFO] [stderr] warning: `preqc-pack` (lib test) generated 11 warnings (11 duplicates) [INFO] [stderr] warning: unused variable: `indexes` [INFO] [stderr] --> examples/mislabeling.rs:5:18 [INFO] [stderr] | [INFO] [stderr] 5 | let (patterns, indexes, count) = VAFMatrix::read_patterns("data/patterns.bson"); [INFO] [stderr] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_indexes` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_variables)]` on by default [INFO] [stderr] [INFO] [stderr] warning: `preqc-pack` (example "mislabeling") generated 1 warning [INFO] [stderr] Finished test [unoptimized + debuginfo] target(s) in 0.19s [INFO] [stderr] Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/preqc_pack-63857da2bd62c670) [INFO] [stdout] [INFO] [stdout] running 3 tests [INFO] [stderr] Running unittests src/bin/preqc-pack.rs (/opt/rustwide/target/debug/deps/preqc_pack-a58d36d02f87c642) [INFO] [stdout] test qc::fastqc::phred_encoding_tests::test_get_fastq_encoding_offset ... ok [INFO] [stdout] test qc::fastqc::phred_encoding_tests::test_convert_probability_to_old_illumina_phred ... ok [INFO] [stdout] test qc::fastqc::phred_encoding_tests::test_phred_encoding ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 3 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.02s [INFO] [stdout] [INFO] [stdout] [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 0.02s [INFO] [stdout] [INFO] [stderr] Doc-tests preqc-pack [INFO] [stdout] [INFO] [stdout] running 4 tests [INFO] [stdout] test src/qc/hasher.rs - qc::hasher::process_remote (line 78) - compile ... ok [INFO] [stdout] test src/qc/fastqc.rs - qc::fastqc::FastQC::process_sequence (line 648) ... ok [INFO] [stdout] test src/qc/fastqc.rs - qc::fastqc::FastQC::merge (line 705) ... ok [INFO] [stdout] test src/qc/mislabeling.rs - qc::mislabeling::VAFMatrix::read_patterns (line 37) ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 4 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 5.14s [INFO] [stdout] [INFO] running `Command { std: "docker" "inspect" "cc3416f4126580cf3ff8399235fdfcba4f711929e67eab326b2e6c3eb5d033bf", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "cc3416f4126580cf3ff8399235fdfcba4f711929e67eab326b2e6c3eb5d033bf", kill_on_drop: false }` [INFO] [stdout] cc3416f4126580cf3ff8399235fdfcba4f711929e67eab326b2e6c3eb5d033bf