[INFO] cloning repository https://github.com/pangenome/vcfbub [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/pangenome/vcfbub" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fpangenome%2Fvcfbub", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fpangenome%2Fvcfbub'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 77289654b246a4e3422902d04277e258d9fabe9a [INFO] linting pangenome/vcfbub against nightly for clippy-nonminimal_bool-denied [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fpangenome%2Fvcfbub" "/workspace/builds/worker-5-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-5-tc1/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/pangenome/vcfbub [INFO] finished tweaking git repo https://github.com/pangenome/vcfbub [INFO] tweaked toml for git repo https://github.com/pangenome/vcfbub written to /workspace/builds/worker-5-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/pangenome/vcfbub on toolchain nightly [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+nightly" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/pangenome/vcfbub already has a lockfile, it will not be regenerated [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+nightly" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded derive-new v0.6.0 [INFO] [stderr] Downloaded custom_derive v0.1.7 [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded bio-types v1.0.4 [INFO] [stderr] Downloaded rust-htslib v0.46.0 [INFO] [stderr] Downloaded cc v1.2.26 [INFO] [stderr] Downloaded syn v2.0.102 [INFO] [stderr] Downloaded hts-sys v2.2.0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+nightly" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 8c9d4a5744801730a90a8ee5f0239af5b49c9166016891740db85cfabd3d1a36 [INFO] running `Command { std: "docker" "start" "-a" "8c9d4a5744801730a90a8ee5f0239af5b49c9166016891740db85cfabd3d1a36", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "8c9d4a5744801730a90a8ee5f0239af5b49c9166016891740db85cfabd3d1a36", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "8c9d4a5744801730a90a8ee5f0239af5b49c9166016891740db85cfabd3d1a36", kill_on_drop: false }` [INFO] [stdout] 8c9d4a5744801730a90a8ee5f0239af5b49c9166016891740db85cfabd3d1a36 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+nightly" "clippy" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 87745846f05efc22bdca2135292e3928ac9be9e74c1db4c87a24ff5e5a1d17cd [INFO] running `Command { std: "docker" "start" "-a" "87745846f05efc22bdca2135292e3928ac9be9e74c1db4c87a24ff5e5a1d17cd", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.95 [INFO] [stderr] Compiling libc v0.2.172 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Checking memchr v2.7.5 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Checking smallvec v1.15.1 [INFO] [stderr] Compiling rustversion v1.0.21 [INFO] [stderr] Compiling glob v0.3.2 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Checking percent-encoding v2.3.1 [INFO] [stderr] Checking cfg-if v1.0.1 [INFO] [stderr] Checking textwrap v0.11.0 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Checking crc32fast v1.4.2 [INFO] [stderr] Checking form_urlencoded v1.2.1 [INFO] [stderr] Checking flate2 v1.1.2 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Checking aho-corasick v1.1.3 [INFO] [stderr] Compiling jobserver v0.1.33 [INFO] [stderr] Compiling quote v1.0.40 [INFO] [stderr] Compiling cc v1.2.26 [INFO] [stderr] Checking atty v0.2.14 [INFO] [stderr] Checking clap v2.34.0 [INFO] [stderr] Compiling syn v2.0.102 [INFO] [stderr] Checking regex-automata v0.4.9 [INFO] [stderr] Compiling cmake v0.1.54 [INFO] [stderr] Compiling libz-sys v1.1.22 [INFO] [stderr] Compiling hts-sys v2.2.0 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling synstructure v0.13.2 [INFO] [stderr] Compiling zerofrom-derive v0.1.6 [INFO] [stderr] Compiling yoke-derive v0.8.0 [INFO] [stderr] Compiling zerovec-derive v0.11.1 [INFO] [stderr] Compiling displaydoc v0.2.5 [INFO] [stderr] Compiling thiserror-impl v1.0.69 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling derive-new v0.6.0 [INFO] [stderr] Checking zerofrom v0.1.6 [INFO] [stderr] Checking yoke v0.8.0 [INFO] [stderr] Checking zerovec v0.11.2 [INFO] [stderr] Checking zerotrie v0.2.2 [INFO] [stderr] Checking thiserror v1.0.69 [INFO] [stderr] Checking regex v1.11.1 [INFO] [stderr] Checking bio-types v1.0.4 [INFO] [stderr] Checking tinystr v0.8.1 [INFO] [stderr] Checking potential_utf v0.1.2 [INFO] [stderr] Checking icu_collections v2.0.0 [INFO] [stderr] Checking icu_locale_core v2.0.0 [INFO] [stderr] Checking icu_provider v2.0.0 [INFO] [stderr] Checking icu_properties v2.0.1 [INFO] [stderr] Checking icu_normalizer v2.0.0 [INFO] [stderr] Checking idna_adapter v1.2.1 [INFO] [stderr] Checking idna v1.0.3 [INFO] [stderr] Checking url v2.5.4 [INFO] [stderr] Checking rust-htslib v0.46.0 [INFO] [stderr] Checking vcfbub v0.1.2 (/opt/rustwide/workdir) [INFO] [stdout] warning: casting to the same type is unnecessary (`i32` -> `i32`) [INFO] [stdout] --> src/main.rs:34:5 [INFO] [stdout] | [INFO] [stdout] 34 | lv_int as i32 [INFO] [stdout] | ^^^^^^^^^^^^^ help: try: `lv_int` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast [INFO] [stdout] = note: `#[warn(clippy::unnecessary_cast)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: used `unwrap()` on `Some` value [INFO] [stdout] --> src/main.rs:45:35 [INFO] [stdout] | [INFO] [stdout] 45 | Some(ps_array) => Some(String::from_utf8_lossy(&*ps_array[0]).to_string()).unwrap(), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_literal_unwrap [INFO] [stdout] = note: `#[warn(clippy::unnecessary_literal_unwrap)]` on by default [INFO] [stdout] help: remove the `Some` and `unwrap()` [INFO] [stdout] | [INFO] [stdout] 45 - Some(ps_array) => Some(String::from_utf8_lossy(&*ps_array[0]).to_string()).unwrap(), [INFO] [stdout] 45 + Some(ps_array) => String::from_utf8_lossy(&*ps_array[0]).to_string(), [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: deref on an immutable reference [INFO] [stdout] --> src/main.rs:45:64 [INFO] [stdout] | [INFO] [stdout] 45 | Some(ps_array) => Some(String::from_utf8_lossy(&*ps_array[0]).to_string()).unwrap(), [INFO] [stdout] | ^^^^^^^^^^^^^ help: if you would like to reborrow, try removing `&*`: `ps_array[0]` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#borrow_deref_ref [INFO] [stdout] = note: `#[warn(clippy::borrow_deref_ref)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: using `clone` on type `usize` which implements the `Copy` trait [INFO] [stdout] --> src/main.rs:71:5 [INFO] [stdout] | [INFO] [stdout] 71 | allele_lengths.iter().max().unwrap().clone() [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try dereferencing it: `*allele_lengths.iter().max().unwrap()` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy [INFO] [stdout] = note: `#[warn(clippy::clone_on_copy)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: this boolean expression can be simplified [INFO] [stdout] --> src/main.rs:187:12 [INFO] [stdout] | [INFO] [stdout] 187 | if keep_record[idx] // we keep records when they're marked to keep [INFO] [stdout] | ____________^ [INFO] [stdout] 188 | | // or if they're marked don't-keep but their parent was popped and they weren't popped [INFO] [stdout] 189 | | || (!keep_record[idx] [INFO] [stdout] 190 | | && popped_bubbles.contains(&parent_snarl) [INFO] [stdout] 191 | | && !popped_bubbles.contains(&snarl_id)) [INFO] [stdout] | |_______________________________________________________^ [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#nonminimal_bool [INFO] [stdout] = note: `#[warn(clippy::nonminimal_bool)]` on by default [INFO] [stdout] help: try [INFO] [stdout] | [INFO] [stdout] 187 - if keep_record[idx] // we keep records when they're marked to keep [INFO] [stdout] 188 - // or if they're marked don't-keep but their parent was popped and they weren't popped [INFO] [stdout] 189 - || (!keep_record[idx] [INFO] [stdout] 190 - && popped_bubbles.contains(&parent_snarl) [INFO] [stdout] 191 - && !popped_bubbles.contains(&snarl_id)) [INFO] [stdout] 187 + if (!popped_bubbles.contains(&snarl_id) || keep_record[idx]) && (popped_bubbles.contains(&parent_snarl) || keep_record[idx]) [INFO] [stdout] | [INFO] [stdout] 187 - if keep_record[idx] // we keep records when they're marked to keep [INFO] [stdout] 188 - // or if they're marked don't-keep but their parent was popped and they weren't popped [INFO] [stdout] 189 - || (!keep_record[idx] [INFO] [stdout] 190 - && popped_bubbles.contains(&parent_snarl) [INFO] [stdout] 191 - && !popped_bubbles.contains(&snarl_id)) [INFO] [stdout] 187 + if keep_record[idx] || popped_bubbles.contains(&parent_snarl) && !popped_bubbles.contains(&snarl_id) [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: this expression creates a reference which is immediately dereferenced by the compiler [INFO] [stdout] --> src/main.rs:193:19 [INFO] [stdout] | [INFO] [stdout] 193 | writer.write(&vcf_record).unwrap() [INFO] [stdout] | ^^^^^^^^^^^ help: change this to: `vcf_record` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow [INFO] [stdout] = note: `#[warn(clippy::needless_borrow)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: casting to the same type is unnecessary (`i32` -> `i32`) [INFO] [stdout] --> src/main.rs:34:5 [INFO] [stdout] | [INFO] [stdout] 34 | lv_int as i32 [INFO] [stdout] | ^^^^^^^^^^^^^ help: try: `lv_int` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast [INFO] [stdout] = note: `#[warn(clippy::unnecessary_cast)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: used `unwrap()` on `Some` value [INFO] [stdout] --> src/main.rs:45:35 [INFO] [stdout] | [INFO] [stdout] 45 | Some(ps_array) => Some(String::from_utf8_lossy(&*ps_array[0]).to_string()).unwrap(), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_literal_unwrap [INFO] [stdout] = note: `#[warn(clippy::unnecessary_literal_unwrap)]` on by default [INFO] [stdout] help: remove the `Some` and `unwrap()` [INFO] [stdout] | [INFO] [stdout] 45 - Some(ps_array) => Some(String::from_utf8_lossy(&*ps_array[0]).to_string()).unwrap(), [INFO] [stdout] 45 + Some(ps_array) => String::from_utf8_lossy(&*ps_array[0]).to_string(), [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: deref on an immutable reference [INFO] [stdout] --> src/main.rs:45:64 [INFO] [stdout] | [INFO] [stdout] 45 | Some(ps_array) => Some(String::from_utf8_lossy(&*ps_array[0]).to_string()).unwrap(), [INFO] [stdout] | ^^^^^^^^^^^^^ help: if you would like to reborrow, try removing `&*`: `ps_array[0]` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#borrow_deref_ref [INFO] [stdout] = note: `#[warn(clippy::borrow_deref_ref)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: using `clone` on type `usize` which implements the `Copy` trait [INFO] [stdout] --> src/main.rs:71:5 [INFO] [stdout] | [INFO] [stdout] 71 | allele_lengths.iter().max().unwrap().clone() [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try dereferencing it: `*allele_lengths.iter().max().unwrap()` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy [INFO] [stdout] = note: `#[warn(clippy::clone_on_copy)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: this boolean expression can be simplified [INFO] [stdout] --> src/main.rs:187:12 [INFO] [stdout] | [INFO] [stdout] 187 | if keep_record[idx] // we keep records when they're marked to keep [INFO] [stdout] | ____________^ [INFO] [stdout] 188 | | // or if they're marked don't-keep but their parent was popped and they weren't popped [INFO] [stdout] 189 | | || (!keep_record[idx] [INFO] [stdout] 190 | | && popped_bubbles.contains(&parent_snarl) [INFO] [stdout] 191 | | && !popped_bubbles.contains(&snarl_id)) [INFO] [stdout] | |_______________________________________________________^ [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#nonminimal_bool [INFO] [stdout] = note: `#[warn(clippy::nonminimal_bool)]` on by default [INFO] [stdout] help: try [INFO] [stdout] | [INFO] [stdout] 187 - if keep_record[idx] // we keep records when they're marked to keep [INFO] [stdout] 188 - // or if they're marked don't-keep but their parent was popped and they weren't popped [INFO] [stdout] 189 - || (!keep_record[idx] [INFO] [stdout] 190 - && popped_bubbles.contains(&parent_snarl) [INFO] [stdout] 191 - && !popped_bubbles.contains(&snarl_id)) [INFO] [stdout] 187 + if (!popped_bubbles.contains(&snarl_id) || keep_record[idx]) && (popped_bubbles.contains(&parent_snarl) || keep_record[idx]) [INFO] [stdout] | [INFO] [stdout] 187 - if keep_record[idx] // we keep records when they're marked to keep [INFO] [stdout] 188 - // or if they're marked don't-keep but their parent was popped and they weren't popped [INFO] [stdout] 189 - || (!keep_record[idx] [INFO] [stdout] 190 - && popped_bubbles.contains(&parent_snarl) [INFO] [stdout] 191 - && !popped_bubbles.contains(&snarl_id)) [INFO] [stdout] 187 + if keep_record[idx] || popped_bubbles.contains(&parent_snarl) && !popped_bubbles.contains(&snarl_id) [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: this expression creates a reference which is immediately dereferenced by the compiler [INFO] [stdout] --> src/main.rs:193:19 [INFO] [stdout] | [INFO] [stdout] 193 | writer.write(&vcf_record).unwrap() [INFO] [stdout] | ^^^^^^^^^^^ help: change this to: `vcf_record` [INFO] [stdout] | [INFO] [stdout] = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow [INFO] [stdout] = note: `#[warn(clippy::needless_borrow)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 20.87s [INFO] running `Command { std: "docker" "inspect" "87745846f05efc22bdca2135292e3928ac9be9e74c1db4c87a24ff5e5a1d17cd", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "87745846f05efc22bdca2135292e3928ac9be9e74c1db4c87a24ff5e5a1d17cd", kill_on_drop: false }` [INFO] [stdout] 87745846f05efc22bdca2135292e3928ac9be9e74c1db4c87a24ff5e5a1d17cd