[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#82dd3cb008233bfe50ba6b8d6618e6bbd6054eb1 for pr-150408
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FEuphrasiologist%2Fnu_plugin_bio" "/workspace/builds/worker-0-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-0-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-0-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/Euphrasiologist/nu_plugin_bio on toolchain 82dd3cb008233bfe50ba6b8d6618e6bbd6054eb1
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+82dd3cb008233bfe50ba6b8d6618e6bbd6054eb1" "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" "+82dd3cb008233bfe50ba6b8d6618e6bbd6054eb1" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded typetag-impl v0.2.5
[INFO] [stderr]   Downloaded typetag v0.2.5
[INFO] [stderr]   Downloaded num-format v0.4.3
[INFO] [stderr]   Downloaded strip-ansi-escapes v0.2.0
[INFO] [stderr]   Downloaded ghost v0.1.6
[INFO] [stderr]   Downloaded nu-utils v0.104.1
[INFO] [stderr]   Downloaded rmp-serde v1.3.0
[INFO] [stderr]   Downloaded inventory v0.3.3
[INFO] [stderr]   Downloaded lexical-write-integer v1.0.5
[INFO] [stderr]   Downloaded noodles-fastq v0.19.0
[INFO] [stderr]   Downloaded nu-path v0.104.1
[INFO] [stderr]   Downloaded lexical-core v1.0.5
[INFO] [stderr]   Downloaded doctest-file v1.0.0
[INFO] [stderr]   Downloaded recvmsg v1.0.0
[INFO] [stderr]   Downloaded noodles v0.99.0
[INFO] [stderr]   Downloaded noodles-gff v0.50.0
[INFO] [stderr]   Downloaded lexical-write-float v1.0.5
[INFO] [stderr]   Downloaded libproc v0.14.10
[INFO] [stderr]   Downloaded lexical-parse-float v1.0.5
[INFO] [stderr]   Downloaded lexical-util v1.0.6
[INFO] [stderr]   Downloaded zlib-rs v0.5.1
[INFO] [stderr]   Downloaded noodles-bam v0.81.0
[INFO] [stderr]   Downloaded nu-engine v0.104.1
[INFO] [stderr]   Downloaded noodles-bcf v0.76.0
[INFO] [stderr]   Downloaded noodles-sam v0.77.0
[INFO] [stderr]   Downloaded noodles-cram v0.84.0
[INFO] [stderr]   Downloaded noodles-vcf v0.79.0
[INFO] [stderr]   Downloaded pure-rust-locales v0.8.1
[INFO] [stderr]   Downloaded nu-protocol v0.104.1
[INFO] [stderr]   Downloaded interprocess v2.2.3
[INFO] [stderr]   Downloaded nu-plugin-protocol v0.104.1
[INFO] [stderr]   Downloaded fancy-regex v0.14.0
[INFO] [stderr]   Downloaded lexical-parse-integer v1.0.5
[INFO] [stderr]   Downloaded noodles-bgzf v0.41.0
[INFO] [stderr]   Downloaded noodles-csi v0.49.0
[INFO] [stderr]   Downloaded nu-plugin v0.104.1
[INFO] [stderr]   Downloaded nu-glob v0.104.1
[INFO] [stderr]   Downloaded lscolors v0.17.0
[INFO] [stderr]   Downloaded noodles-bed v0.26.0
[INFO] [stderr]   Downloaded noodles-fasta v0.54.0
[INFO] [stderr]   Downloaded noodles-core v0.17.0
[INFO] [stderr]   Downloaded noodles-tabix v0.55.0
[INFO] [stderr]   Downloaded nu-plugin-core v0.104.1
[INFO] [stderr]   Downloaded libz-rs-sys v0.5.1
[INFO] [stderr]   Downloaded nu-system v0.104.1
[INFO] [stderr]   Downloaded gfa v0.10.1
[INFO] [stderr]   Downloaded pwd v1.4.0
[INFO] [stderr]   Downloaded vte_generate_state_changes v0.1.1
[INFO] [stderr]   Downloaded nu-derive-value v0.104.1
[INFO] [stderr]   Downloaded omnipath v0.1.1
[INFO] [stderr]   Downloaded vte v0.11.1
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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@sha256:845e597a41426bbf2703be69acdb67d10b6de511142d05cba7bbe119c898b2c7" "/opt/rustwide/cargo-home/bin/cargo" "+82dd3cb008233bfe50ba6b8d6618e6bbd6054eb1" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] ce9f082b76e91059321d1a4d365ad336a4e1620db6dc5a1337f6d480dc532f0c
[INFO] running `Command { std: "docker" "start" "-a" "ce9f082b76e91059321d1a4d365ad336a4e1620db6dc5a1337f6d480dc532f0c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "ce9f082b76e91059321d1a4d365ad336a4e1620db6dc5a1337f6d480dc532f0c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "ce9f082b76e91059321d1a4d365ad336a4e1620db6dc5a1337f6d480dc532f0c", kill_on_drop: false }`
[INFO] [stdout] ce9f082b76e91059321d1a4d365ad336a4e1620db6dc5a1337f6d480dc532f0c
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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@sha256:845e597a41426bbf2703be69acdb67d10b6de511142d05cba7bbe119c898b2c7" "/opt/rustwide/cargo-home/bin/cargo" "+82dd3cb008233bfe50ba6b8d6618e6bbd6054eb1" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 263edf3b39f0854a7fe11014357ef4b93de4d5e77e06a1806536412871093e4d
[INFO] running `Command { std: "docker" "start" "-a" "263edf3b39f0854a7fe11014357ef4b93de4d5e77e06a1806536412871093e4d", kill_on_drop: false }`
[INFO] [stderr]     Checking memchr v2.7.5
[INFO] [stderr]    Compiling proc-macro2 v1.0.95
[INFO] [stderr]     Checking regex-syntax v0.8.5
[INFO] [stderr]     Checking zlib-rs v0.5.1
[INFO] [stderr]     Checking miniz_oxide v0.8.9
[INFO] [stderr]     Checking bitflags v2.4.0
[INFO] [stderr]     Checking bit-vec v0.8.0
[INFO] [stderr]     Checking hashbrown v0.15.4
[INFO] [stderr]    Compiling num-traits v0.2.15
[INFO] [stderr]     Checking crossbeam-channel v0.5.6
[INFO] [stderr]     Checking indexmap v2.10.0
[INFO] [stderr]     Checking lexical-util v1.0.6
[INFO] [stderr]    Compiling quote v1.0.40
[INFO] [stderr]     Checking aho-corasick v1.1.3
[INFO] [stderr]    Compiling syn v2.0.104
[INFO] [stderr]    Compiling syn v1.0.104
[INFO] [stderr]    Compiling rustix v0.38.44
[INFO] [stderr]     Checking crossbeam-epoch v0.9.13
[INFO] [stderr]    Compiling lock_api v0.4.13
[INFO] [stderr]    Compiling cc v1.0.77
[INFO] [stderr]    Compiling signal-hook v0.3.18
[INFO] [stderr]    Compiling parking_lot_core v0.9.11
[INFO] [stderr]     Checking linux-raw-sys v0.4.15
[INFO] [stderr]     Checking libz-rs-sys v0.5.1
[INFO] [stderr]     Checking pure-rust-locales v0.8.1
[INFO] [stderr]     Checking flate2 v1.1.2
[INFO] [stderr]    Compiling pkg-config v0.3.26
[INFO] [stderr]     Checking iana-time-zone v0.1.53
[INFO] [stderr]     Checking regex-automata v0.4.9
[INFO] [stderr]     Checking noodles-bgzf v0.41.0
[INFO] [stderr]    Compiling nix v0.29.0
[INFO] [stderr]     Checking crossbeam-deque v0.8.2
[INFO] [stderr]    Compiling rustix v1.0.7
[INFO] [stderr]     Checking either v1.8.0
[INFO] [stderr]    Compiling thiserror v1.0.49
[INFO] [stderr]     Checking smallvec v1.15.1
[INFO] [stderr]     Checking rayon-core v1.12.1
[INFO] [stderr]     Checking mio v1.0.4
[INFO] [stderr]     Checking lexical-parse-integer v1.0.5
[INFO] [stderr]     Checking lexical-write-integer v1.0.5
[INFO] [stderr]    Compiling vte_generate_state_changes v0.1.1
[INFO] [stderr]    Compiling procfs v0.17.0
[INFO] [stderr]    Compiling owo-colors v4.2.2
[INFO] [stderr]    Compiling erased-serde v0.3.23
[INFO] [stderr]    Compiling ref-cast v1.0.24
[INFO] [stderr]     Checking itoa v1.0.4
[INFO] [stderr]     Checking utf8parse v0.2.0
[INFO] [stderr]     Checking dirs-sys v0.4.1
[INFO] [stderr]     Checking vte v0.11.1
[INFO] [stderr]     Checking lexical-write-float v1.0.5
[INFO] [stderr]     Checking signal-hook-mio v0.2.4
[INFO] [stderr]     Checking lexical-parse-float v1.0.5
[INFO] [stderr]     Checking bstr v1.12.0
[INFO] [stderr]     Checking rayon v1.10.0
[INFO] [stderr]     Checking parking_lot v0.12.4
[INFO] [stderr]    Compiling proc-macro-error-attr2 v2.0.0
[INFO] [stderr]     Checking bit-set v0.8.0
[INFO] [stderr]    Compiling serde_derive v1.0.219
[INFO] [stderr]    Compiling thiserror-impl v1.0.49
[INFO] [stderr]    Compiling ref-cast-impl v1.0.24
[INFO] [stderr]    Compiling ghost v0.1.6
[INFO] [stderr]     Checking noodles-core v0.17.0
[INFO] [stderr]     Checking noodles-csi v0.49.0
[INFO] [stderr]    Compiling ctor v0.1.26
[INFO] [stderr]     Checking nu-ansi-term v0.50.1
[INFO] [stderr]     Checking arrayvec v0.7.2
[INFO] [stderr]    Compiling paste v1.0.9
[INFO] [stderr]     Checking unicode-width v0.2.1
[INFO] [stderr]     Checking is_ci v1.2.0
[INFO] [stderr]     Checking supports-color v3.0.2
[INFO] [stderr]     Checking inventory v0.3.3
[INFO] [stderr]     Checking textwrap v0.16.2
[INFO] [stderr]     Checking lscolors v0.17.0
[INFO] [stderr]     Checking rmp v0.8.14
[INFO] [stderr]     Checking num-format v0.4.3
[INFO] [stderr]    Compiling typetag-impl v0.2.5
[INFO] [stderr]    Compiling proc-macro-error2 v2.0.1
[INFO] [stderr]     Checking pwd v1.4.0
[INFO] [stderr]     Checking fancy-regex v0.14.0
[INFO] [stderr]    Compiling thiserror-impl v2.0.12
[INFO] [stderr]    Compiling miette-derive v7.6.0
[INFO] [stderr]     Checking crossterm v0.28.1
[INFO] [stderr]     Checking strip-ansi-escapes v0.2.0
[INFO] [stderr]     Checking terminal_size v0.4.2
[INFO] [stderr]     Checking lexical-core v1.0.5
[INFO] [stderr]     Checking dirs v5.0.1
[INFO] [stderr]     Checking itertools v0.13.0
[INFO] [stderr]     Checking sys-locale v0.3.1
[INFO] [stderr]     Checking supports-hyperlinks v3.1.0
[INFO] [stderr]     Checking sysinfo v0.33.1
[INFO] [stderr]     Checking supports-unicode v3.0.0
[INFO] [stderr]     Checking web-time v1.1.0
[INFO] [stderr]     Checking nu-path v0.104.1
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]    Compiling nu-derive-value v0.104.1
[INFO] [stderr]     Checking miette v7.6.0
[INFO] [stderr]    Compiling lzma-sys v0.1.20
[INFO] [stderr]     Checking thiserror v2.0.12
[INFO] [stderr]    Compiling bzip2-sys v0.1.13+1.0.8
[INFO] [stderr]     Checking lru v0.12.5
[INFO] [stderr]     Checking os_pipe v1.2.2
[INFO] [stderr]     Checking strum v0.26.3
[INFO] [stderr]     Checking heck v0.5.0
[INFO] [stderr]     Checking nu-glob v0.104.1
[INFO] [stderr]    Compiling semver v1.0.26
[INFO] [stderr]     Checking noodles-tabix v0.55.0
[INFO] [stderr]    Compiling lexical-core v0.7.6
[INFO] [stderr]     Checking percent-encoding v2.2.0
[INFO] [stderr]     Checking noodles-sam v0.77.0
[INFO] [stderr]    Compiling nom v5.1.2
[INFO] [stderr]    Compiling doctest-file v1.0.0
[INFO] [stderr]    Compiling anyhow v1.0.66
[INFO] [stderr]     Checking xz2 v0.1.7
[INFO] [stderr]     Checking interprocess v2.2.3
[INFO] [stderr]     Checking noodles-vcf v0.79.0
[INFO] [stderr]     Checking md-5 v0.10.5
[INFO] [stderr]     Checking noodles-fasta v0.54.0
[INFO] [stderr]     Checking noodles-bam v0.81.0
[INFO] [stderr]    Compiling bytemuck_derive v1.3.0
[INFO] [stderr]     Checking bzip2 v0.5.2
[INFO] [stderr]     Checking serde v1.0.219
[INFO] [stderr]     Checking aho-corasick v0.7.20
[INFO] [stderr]     Checking regex-syntax v0.6.28
[INFO] [stderr]     Checking noodles-bed v0.26.0
[INFO] [stderr]     Checking noodles-gff v0.50.0
[INFO] [stderr]     Checking noodles-cram v0.84.0
[INFO] [stderr]     Checking bytemuck v1.12.3
[INFO] [stderr]     Checking noodles-fastq v0.19.0
[INFO] [stderr]     Checking bstr v0.2.17
[INFO] [stderr]     Checking memmap v0.7.0
[INFO] [stderr]     Checking noodles-bcf v0.76.0
[INFO] [stderr]     Checking regex v1.7.0
[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 gfa v0.10.1
[INFO] [stderr]     Checking noodles v0.99.0
[INFO] [stderr]     Checking typetag v0.2.5
[INFO] [stderr]     Checking nu-utils v0.104.1
[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<Value>) {
[INFO] [stdout]     |                                     ^ help: if this is intentional, prefix it with an underscore: `_r`
[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<Value>) {
[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<Vec<Value>, 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: value assigned to `value_records` is never read
[INFO] [stdout]   --> src/bio_format/cram.rs:41:29
[INFO] [stdout]    |
[INFO] [stdout] 41 |     let mut value_records = Vec::new();
[INFO] [stdout]    |                             ^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: maybe it is overwritten before being read?
[INFO] [stdout]    = note: `#[warn(unused_assignments)]` (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: 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<Vec<Value>, 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: 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: 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<Value>) {
[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: 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: 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: 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<Vec<Value>, 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: value assigned to `value_records` is never read
[INFO] [stdout]   --> src/bio_format/cram.rs:41:29
[INFO] [stdout]    |
[INFO] [stdout] 41 |     let mut value_records = Vec::new();
[INFO] [stdout]    |                             ^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: maybe it is overwritten before being read?
[INFO] [stdout]    = note: `#[warn(unused_assignments)]` (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: 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<Vec<Value>, 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<Value>) {
[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 1m 39s
[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" "263edf3b39f0854a7fe11014357ef4b93de4d5e77e06a1806536412871093e4d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "263edf3b39f0854a7fe11014357ef4b93de4d5e77e06a1806536412871093e4d", kill_on_drop: false }`
[INFO] [stdout] 263edf3b39f0854a7fe11014357ef4b93de4d5e77e06a1806536412871093e4d
