[INFO] cloning repository https://github.com/Euphrasiologist/nu_plugin_bio [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/Euphrasiologist/nu_plugin_bio" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FEuphrasiologist%2Fnu_plugin_bio", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FEuphrasiologist%2Fnu_plugin_bio'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 49ab34152f2a8e42eeae0fb9f762e2f695339f5c [INFO] checking Euphrasiologist/nu_plugin_bio against master#5dbf4069dc98bbbca98dd600a65f50c258fbfd56 for pr-148477-1 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FEuphrasiologist%2Fnu_plugin_bio" "/workspace/builds/worker-4-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-4-tc1/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/Euphrasiologist/nu_plugin_bio [INFO] finished tweaking git repo https://github.com/Euphrasiologist/nu_plugin_bio [INFO] tweaked toml for git repo https://github.com/Euphrasiologist/nu_plugin_bio written to /workspace/builds/worker-4-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/Euphrasiologist/nu_plugin_bio on toolchain 5dbf4069dc98bbbca98dd600a65f50c258fbfd56 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+5dbf4069dc98bbbca98dd600a65f50c258fbfd56" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/Euphrasiologist/nu_plugin_bio 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" "+5dbf4069dc98bbbca98dd600a65f50c258fbfd56" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded strip-ansi-escapes v0.2.0 [INFO] [stderr] Downloaded ghost v0.1.6 [INFO] [stderr] Downloaded inventory v0.3.3 [INFO] [stderr] Downloaded typetag-impl v0.2.5 [INFO] [stderr] Downloaded nu-utils v0.104.1 [INFO] [stderr] Downloaded nu-glob v0.104.1 [INFO] [stderr] Downloaded typetag v0.2.5 [INFO] [stderr] Downloaded erased-serde v0.3.23 [INFO] [stderr] Downloaded lexical-core v1.0.5 [INFO] [stderr] Downloaded lexical-parse-integer v1.0.5 [INFO] [stderr] Downloaded nu-system v0.104.1 [INFO] [stderr] Downloaded vte_generate_state_changes v0.1.1 [INFO] [stderr] Downloaded noodles-core v0.17.0 [INFO] [stderr] Downloaded noodles-fasta v0.54.0 [INFO] [stderr] Downloaded noodles v0.99.0 [INFO] [stderr] Downloaded noodles-gff v0.50.0 [INFO] [stderr] Downloaded noodles-bam v0.81.0 [INFO] [stderr] Downloaded noodles-bcf v0.76.0 [INFO] [stderr] Downloaded noodles-cram v0.84.0 [INFO] [stderr] Downloaded noodles-vcf v0.79.0 [INFO] [stderr] Downloaded nu-engine v0.104.1 [INFO] [stderr] Downloaded lexical-parse-float v1.0.5 [INFO] [stderr] Downloaded interprocess v2.2.3 [INFO] [stderr] Downloaded pure-rust-locales v0.8.1 [INFO] [stderr] Downloaded cxx-build v1.0.82 [INFO] [stderr] Downloaded procfs-core v0.17.0 [INFO] [stderr] Downloaded procfs v0.17.0 [INFO] [stderr] Downloaded cxx v1.0.82 [INFO] [stderr] Downloaded noodles-sam v0.77.0 [INFO] [stderr] Downloaded libproc v0.14.10 [INFO] [stderr] Downloaded cxxbridge-macro v1.0.82 [INFO] [stderr] Downloaded syn v1.0.104 [INFO] [stderr] Downloaded lexical-write-float v1.0.5 [INFO] [stderr] Downloaded lexical-util v1.0.6 [INFO] [stderr] Downloaded lexical-write-integer v1.0.5 [INFO] [stderr] Downloaded noodles-csi v0.49.0 [INFO] [stderr] Downloaded nu-plugin-core v0.104.1 [INFO] [stderr] Downloaded nu-plugin v0.104.1 [INFO] [stderr] Downloaded nu-path v0.104.1 [INFO] [stderr] Downloaded vte v0.11.1 [INFO] [stderr] Downloaded nu-plugin-protocol v0.104.1 [INFO] [stderr] Downloaded nu-derive-value v0.104.1 [INFO] [stderr] Downloaded omnipath v0.1.1 [INFO] [stderr] Downloaded lscolors v0.17.0 [INFO] [stderr] Downloaded noodles-bed v0.26.0 [INFO] [stderr] Downloaded noodles-tabix v0.55.0 [INFO] [stderr] Downloaded noodles-fastq v0.19.0 [INFO] [stderr] Downloaded noodles-bgzf v0.41.0 [INFO] [stderr] Downloaded pwd v1.4.0 [INFO] [stderr] Downloaded cxxbridge-flags v1.0.82 [INFO] [stderr] Downloaded nu-protocol v0.104.1 [INFO] [stderr] Downloaded gfa v0.10.1 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+5dbf4069dc98bbbca98dd600a65f50c258fbfd56" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 32febada04c6053b819cc6a64b5981a1a6194c5ecf8697105fab13b1e96630fe [INFO] running `Command { std: "docker" "start" "-a" "32febada04c6053b819cc6a64b5981a1a6194c5ecf8697105fab13b1e96630fe", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "32febada04c6053b819cc6a64b5981a1a6194c5ecf8697105fab13b1e96630fe", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "32febada04c6053b819cc6a64b5981a1a6194c5ecf8697105fab13b1e96630fe", kill_on_drop: false }` [INFO] [stdout] 32febada04c6053b819cc6a64b5981a1a6194c5ecf8697105fab13b1e96630fe [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+5dbf4069dc98bbbca98dd600a65f50c258fbfd56" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] ae20f890ed8fe62171b9881c399d259f3d55c5754e6c80d6f8dca631f702ab49 [INFO] running `Command { std: "docker" "start" "-a" "ae20f890ed8fe62171b9881c399d259f3d55c5754e6c80d6f8dca631f702ab49", kill_on_drop: false }` [INFO] [stderr] Checking regex-syntax v0.8.5 [INFO] [stderr] Checking zlib-rs v0.5.1 [INFO] [stderr] Checking bitflags v2.4.0 [INFO] [stderr] Compiling proc-macro2 v1.0.95 [INFO] [stderr] Compiling syn v1.0.104 [INFO] [stderr] Compiling num-traits v0.2.15 [INFO] [stderr] Checking hashbrown v0.15.4 [INFO] [stderr] Checking lexical-util v1.0.6 [INFO] [stderr] Compiling rustix v0.38.44 [INFO] [stderr] Compiling lock_api v0.4.13 [INFO] [stderr] Checking pure-rust-locales v0.8.1 [INFO] [stderr] Compiling cc v1.0.77 [INFO] [stderr] Checking linux-raw-sys v0.4.15 [INFO] [stderr] Compiling nix v0.29.0 [INFO] [stderr] Compiling rustix v1.0.7 [INFO] [stderr] Checking either v1.8.0 [INFO] [stderr] Checking parking_lot_core 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v0.54.0 [INFO] [stderr] Checking bytemuck v1.12.3 [INFO] [stderr] Checking gfa v0.10.1 [INFO] [stderr] Checking noodles-tabix v0.55.0 [INFO] [stderr] Checking noodles-sam v0.77.0 [INFO] [stderr] Checking noodles-gff v0.50.0 [INFO] [stderr] Checking serde v1.0.219 [INFO] [stderr] Checking noodles-vcf v0.79.0 [INFO] [stderr] Checking noodles-bed v0.26.0 [INFO] [stderr] Checking noodles-bam v0.81.0 [INFO] [stderr] Checking noodles-bcf v0.76.0 [INFO] [stderr] Checking noodles-cram v0.84.0 [INFO] [stderr] Checking chrono v0.4.41 [INFO] [stderr] Checking serde_json v1.0.140 [INFO] [stderr] Checking rmp-serde v1.3.0 [INFO] [stderr] Checking typetag v0.2.5 [INFO] [stderr] Checking nu-utils v0.104.1 [INFO] [stderr] Checking noodles v0.99.0 [INFO] [stderr] Checking procfs-core v0.17.0 [INFO] [stderr] Checking chrono-humanize v0.2.3 [INFO] [stderr] Checking nu-system v0.104.1 [INFO] [stderr] Checking nu-protocol v0.104.1 [INFO] [stderr] Checking nu-plugin-protocol v0.104.1 [INFO] [stderr] Checking nu-engine v0.104.1 [INFO] [stderr] Checking nu-plugin-core v0.104.1 [INFO] [stderr] Checking nu-plugin v0.104.1 [INFO] [stderr] Checking nu_plugin_bio v0.104.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `Cursor` [INFO] [stdout] --> src/bio_format/bcf.rs:10:35 [INFO] [stdout] | [INFO] [stdout] 10 | use std::io::{BufRead, BufReader, Cursor}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Record` [INFO] [stdout] --> src/bio_format/bed.rs:4:19 [INFO] [stdout] | [INFO] [stdout] 4 | use nu_protocol::{Record, Value}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `super::SpanExt` [INFO] [stdout] --> src/bio_format/bed.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use super::SpanExt; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Cursor` [INFO] [stdout] --> src/bio_format/fasta.rs:1:35 [INFO] [stdout] | [INFO] [stdout] 1 | use std::io::{BufRead, BufReader, Cursor}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Cursor` [INFO] [stdout] --> src/bio_format/gfa.rs:12:35 [INFO] [stdout] | [INFO] [stdout] 12 | use std::io::{BufRead, BufReader, Cursor}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Record` [INFO] [stdout] --> src/bio_format/gff.rs:5:19 [INFO] [stdout] | [INFO] [stdout] 5 | use nu_protocol::{Record, Value}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `super::SpanExt` [INFO] [stdout] --> src/bio_format/gff.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | use super::SpanExt; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Cursor` [INFO] [stdout] --> src/bio_format/bcf.rs:10:35 [INFO] [stdout] | [INFO] [stdout] 10 | use std::io::{BufRead, BufReader, Cursor}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Record` [INFO] [stdout] --> src/bio_format/bed.rs:4:19 [INFO] [stdout] | [INFO] [stdout] 4 | use nu_protocol::{Record, Value}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `super::SpanExt` [INFO] [stdout] --> src/bio_format/bed.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use super::SpanExt; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Cursor` [INFO] [stdout] --> src/bio_format/fasta.rs:1:35 [INFO] [stdout] | [INFO] [stdout] 1 | use std::io::{BufRead, BufReader, Cursor}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Cursor` [INFO] [stdout] --> src/bio_format/gfa.rs:12:35 [INFO] [stdout] | [INFO] [stdout] 12 | use std::io::{BufRead, BufReader, Cursor}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Record` [INFO] [stdout] --> src/bio_format/gff.rs:5:19 [INFO] [stdout] | [INFO] [stdout] 5 | use nu_protocol::{Record, Value}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `super::SpanExt` [INFO] [stdout] --> src/bio_format/gff.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | use super::SpanExt; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `read_name` [INFO] [stdout] --> src/bio_format/bam.rs:144:9 [INFO] [stdout] | [INFO] [stdout] 144 | let read_name = r [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_name` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `r` [INFO] [stdout] --> src/bio_format/bcf.rs:177:37 [INFO] [stdout] | [INFO] [stdout] 177 | fn add_record(call: &EvaluatedCall, r: vcf::Record, vec_vals: &mut Vec) { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_r` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/bcf.rs:241:13 [INFO] [stdout] | [INFO] [stdout] 241 | let mut vec_vals = Vec::new(); [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `header` [INFO] [stdout] --> src/bio_format/bcf.rs:228:5 [INFO] [stdout] | [INFO] [stdout] 228 | header: vcf::Header, [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_header` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `r` [INFO] [stdout] --> src/bio_format/bcf.rs:234:13 [INFO] [stdout] | [INFO] [stdout] 234 | let r = match record { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_r` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/bcf.rs:345:13 [INFO] [stdout] | [INFO] [stdout] 345 | let mut vec_vals = Vec::new(); [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `header` [INFO] [stdout] --> src/bio_format/bcf.rs:333:5 [INFO] [stdout] | [INFO] [stdout] 333 | header: vcf::Header, [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_header` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `r` [INFO] [stdout] --> src/bio_format/bcf.rs:338:13 [INFO] [stdout] | [INFO] [stdout] 338 | let r = match record { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_r` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/bed.rs:28:9 [INFO] [stdout] | [INFO] [stdout] 28 | let mut reader: bed::io::Reader<3, &[u8]> = bed::io::Reader::new(bytes.as_slice()); [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/bio_format/bed.rs:30:9 [INFO] [stdout] | [INFO] [stdout] 30 | let mut records = Vec::new(); [INFO] [stdout] | ----^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `call` [INFO] [stdout] --> src/bio_format/bed.rs:21:23 [INFO] [stdout] | [INFO] [stdout] 21 | pub fn from_bed_inner(call: &EvaluatedCall, input: Value) -> Result, LabeledError> { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_call` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `reader` [INFO] [stdout] --> src/bio_format/bed.rs:28:9 [INFO] [stdout] | [INFO] [stdout] 28 | let mut reader: bed::io::Reader<3, &[u8]> = bed::io::Reader::new(bytes.as_slice()); [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_reader` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `read_name` [INFO] [stdout] --> src/bio_format/bam.rs:144:9 [INFO] [stdout] | [INFO] [stdout] 144 | let read_name = r [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_name` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `call` [INFO] [stdout] --> src/bio_format/gfa.rs:28:5 [INFO] [stdout] | [INFO] [stdout] 28 | call: &EvaluatedCall, [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_call` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `r` [INFO] [stdout] --> src/bio_format/bcf.rs:177:37 [INFO] [stdout] | [INFO] [stdout] 177 | fn add_record(call: &EvaluatedCall, r: vcf::Record, vec_vals: &mut Vec) { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_r` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/bcf.rs:241:13 [INFO] [stdout] | [INFO] [stdout] 241 | let mut vec_vals = Vec::new(); [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `header` [INFO] [stdout] --> src/bio_format/bcf.rs:228:5 [INFO] [stdout] | [INFO] [stdout] 228 | header: vcf::Header, [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_header` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `r` [INFO] [stdout] --> src/bio_format/bcf.rs:234:13 [INFO] [stdout] | [INFO] [stdout] 234 | let r = match record { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_r` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/bcf.rs:345:13 [INFO] [stdout] | [INFO] [stdout] 345 | let mut vec_vals = Vec::new(); [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `header` [INFO] [stdout] --> src/bio_format/bcf.rs:333:5 [INFO] [stdout] | [INFO] [stdout] 333 | header: vcf::Header, [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_header` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `r` [INFO] [stdout] --> src/bio_format/bcf.rs:338:13 [INFO] [stdout] | [INFO] [stdout] 338 | let r = match record { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_r` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/bed.rs:28:9 [INFO] [stdout] | [INFO] [stdout] 28 | let mut reader: bed::io::Reader<3, &[u8]> = bed::io::Reader::new(bytes.as_slice()); [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/bio_format/bed.rs:30:9 [INFO] [stdout] | [INFO] [stdout] 30 | let mut records = Vec::new(); [INFO] [stdout] | ----^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `call` [INFO] [stdout] --> src/bio_format/bed.rs:21:23 [INFO] [stdout] | [INFO] [stdout] 21 | pub fn from_bed_inner(call: &EvaluatedCall, input: Value) -> Result, LabeledError> { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_call` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `reader` [INFO] [stdout] --> src/bio_format/bed.rs:28:9 [INFO] [stdout] | [INFO] [stdout] 28 | let mut reader: bed::io::Reader<3, &[u8]> = bed::io::Reader::new(bytes.as_slice()); [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_reader` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/gff.rs:31:9 [INFO] [stdout] | [INFO] [stdout] 31 | let mut reader = gff::io::Reader::new(stream); [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/bio_format/gff.rs:33:9 [INFO] [stdout] | [INFO] [stdout] 33 | let mut value_records = Vec::new(); [INFO] [stdout] | ----^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `call` [INFO] [stdout] --> src/bio_format/gff.rs:23:23 [INFO] [stdout] | [INFO] [stdout] 23 | pub fn from_gff_inner(call: &EvaluatedCall, input: &Value) -> Result, LabeledError> { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_call` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `reader` [INFO] [stdout] --> src/bio_format/gff.rs:31:9 [INFO] [stdout] | [INFO] [stdout] 31 | let mut reader = gff::io::Reader::new(stream); [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_reader` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `call` [INFO] [stdout] --> src/bio_format/gfa.rs:28:5 [INFO] [stdout] | [INFO] [stdout] 28 | call: &EvaluatedCall, [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_call` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `add_record` is never used [INFO] [stdout] --> src/bio_format/bcf.rs:177:4 [INFO] [stdout] | [INFO] [stdout] 177 | fn add_record(call: &EvaluatedCall, r: vcf::Record, vec_vals: &mut Vec) { [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `BED_COLUMN_NUMBER` is never used [INFO] [stdout] --> src/bio_format/bed.rs:9:7 [INFO] [stdout] | [INFO] [stdout] 9 | const BED_COLUMN_NUMBER: u8 = 3; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `BED_COLUMNS` is never used [INFO] [stdout] --> src/bio_format/bed.rs:12:11 [INFO] [stdout] | [INFO] [stdout] 12 | pub const BED_COLUMNS: &[&str] = &[ [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `GFF_COLUMNS` is never used [INFO] [stdout] --> src/bio_format/gff.rs:10:7 [INFO] [stdout] | [INFO] [stdout] 10 | const GFF_COLUMNS: &[&str] = &[ [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/gff.rs:31:9 [INFO] [stdout] | [INFO] [stdout] 31 | let mut reader = gff::io::Reader::new(stream); [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/bio_format/gff.rs:33:9 [INFO] [stdout] | [INFO] [stdout] 33 | let mut value_records = Vec::new(); [INFO] [stdout] | ----^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `call` [INFO] [stdout] --> src/bio_format/gff.rs:23:23 [INFO] [stdout] | [INFO] [stdout] 23 | pub fn from_gff_inner(call: &EvaluatedCall, input: &Value) -> Result, LabeledError> { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_call` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `reader` [INFO] [stdout] --> src/bio_format/gff.rs:31:9 [INFO] [stdout] | [INFO] [stdout] 31 | let mut reader = gff::io::Reader::new(stream); [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_reader` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `add_record` is never used [INFO] [stdout] --> src/bio_format/bcf.rs:177:4 [INFO] [stdout] | [INFO] [stdout] 177 | fn add_record(call: &EvaluatedCall, r: vcf::Record, vec_vals: &mut Vec) { [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `BED_COLUMN_NUMBER` is never used [INFO] [stdout] --> src/bio_format/bed.rs:9:7 [INFO] [stdout] | [INFO] [stdout] 9 | const BED_COLUMN_NUMBER: u8 = 3; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `BED_COLUMNS` is never used [INFO] [stdout] --> src/bio_format/bed.rs:12:11 [INFO] [stdout] | [INFO] [stdout] 12 | pub const BED_COLUMNS: &[&str] = &[ [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `GFF_COLUMNS` is never used [INFO] [stdout] --> src/bio_format/gff.rs:10:7 [INFO] [stdout] | [INFO] [stdout] 10 | const GFF_COLUMNS: &[&str] = &[ [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 28.96s [INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nom v5.1.2 [INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 3` [INFO] running `Command { std: "docker" "inspect" "ae20f890ed8fe62171b9881c399d259f3d55c5754e6c80d6f8dca631f702ab49", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "ae20f890ed8fe62171b9881c399d259f3d55c5754e6c80d6f8dca631f702ab49", kill_on_drop: false }` [INFO] [stdout] ae20f890ed8fe62171b9881c399d259f3d55c5754e6c80d6f8dca631f702ab49