[INFO] cloning repository https://github.com/2lambda123/nextclade
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/2lambda123/nextclade" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2F2lambda123%2Fnextclade", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2F2lambda123%2Fnextclade'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 5b830c1f07ae453577313d6e6ed5759eed1a372b
[INFO] documenting 2lambda123/nextclade against 1.75.0 for beta-1.76-rustdoc-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2F2lambda123%2Fnextclade" "/workspace/builds/worker-7-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-7-tc1/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/2lambda123/nextclade on toolchain 1.75.0
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.75.0" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] removed /workspace/builds/worker-7-tc1/source/.cargo/config.toml
[INFO] removed /workspace/builds/worker-7-tc1/source/rust-toolchain.toml
[INFO] started tweaking git repo https://github.com/2lambda123/nextclade
[INFO] finished tweaking git repo https://github.com/2lambda123/nextclade
[INFO] tweaked toml for git repo https://github.com/2lambda123/nextclade written to /workspace/builds/worker-7-tc1/source/Cargo.toml
[INFO] crate git repo https://github.com/2lambda123/nextclade 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" "+1.75.0" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr] warning: virtual workspace defaulting to `resolver = "1"` despite one or more workspace members being on edition 2021 which implies `resolver = "2"`
[INFO] [stderr] note: to keep the current resolver, specify `workspace.resolver = "1"` in the workspace root's manifest
[INFO] [stderr] note: to use the edition 2021 resolver, specify `workspace.resolver = "2"` in the workspace root's manifest
[INFO] [stderr] note: for more details see https://doc.rust-lang.org/cargo/reference/resolver.html#resolver-versions
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded validator v0.16.1
[INFO] [stderr]   Downloaded strum_macros v0.25.0
[INFO] [stderr]   Downloaded editdistancek v1.0.2
[INFO] [stderr]   Downloaded validator_derive v0.16.0
[INFO] [stderr]   Downloaded schemars_derive v0.8.12
[INFO] [stderr]   Downloaded dotenv_codegen v0.15.0
[INFO] [stderr]   Downloaded serde_yaml v0.9.22
[INFO] [stderr]   Downloaded dotenv_codegen_implementation v0.15.0
[INFO] [stderr]   Downloaded serde_stacker v0.1.8
[INFO] [stderr]   Downloaded auto_ops v0.3.0
[INFO] [stderr]   Downloaded optfield v0.3.0
[INFO] [stderr]   Downloaded schemars v0.8.12
[INFO] [stderr]   Downloaded comfy-table v7.0.1
[INFO] [stderr]   Downloaded bio v1.3.1
[INFO] [stderr]   Downloaded traversal v0.1.2
[INFO] [stderr]   Downloaded clap-markdown v0.1.3
[INFO] [stderr]   Downloaded ctor v0.2.2
[INFO] [stderr]   Downloaded intervallum v1.4.0
[INFO] [stderr]   Downloaded ordered-float v3.9.1
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+1.75.0" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] e2c752f4e75d3de5ca8721efebc97294d34cfcd57ce649a95c9c4337631367e5
[INFO] running `Command { std: "docker" "start" "-a" "e2c752f4e75d3de5ca8721efebc97294d34cfcd57ce649a95c9c4337631367e5", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "e2c752f4e75d3de5ca8721efebc97294d34cfcd57ce649a95c9c4337631367e5", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "e2c752f4e75d3de5ca8721efebc97294d34cfcd57ce649a95c9c4337631367e5", kill_on_drop: false }`
[INFO] [stdout] e2c752f4e75d3de5ca8721efebc97294d34cfcd57ce649a95c9c4337631367e5
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+1.75.0" "doc" "--frozen" "--no-deps" "--document-private-items" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] ebb24071decf8862f21d038c13303014a103d49657135b340644e8ae8a5e893d
[INFO] running `Command { std: "docker" "start" "-a" "ebb24071decf8862f21d038c13303014a103d49657135b340644e8ae8a5e893d", kill_on_drop: false }`
[INFO] [stderr] warning: virtual workspace defaulting to `resolver = "1"` despite one or more workspace members being on edition 2021 which implies `resolver = "2"`
[INFO] [stderr] note: to keep the current resolver, specify `workspace.resolver = "1"` in the workspace root's manifest
[INFO] [stderr] note: to use the edition 2021 resolver, specify `workspace.resolver = "2"` in the workspace root's manifest
[INFO] [stderr] note: for more details see https://doc.rust-lang.org/cargo/reference/resolver.html#resolver-versions
[INFO] [stderr] warning: output filename collision.
[INFO] [stderr] The bin target `nextclade` in package `nextclade-cli v3.0.0-alpha.0 (/opt/rustwide/workdir/packages_rs/nextclade-cli)` has the same output filename as the lib target `nextclade` in package `nextclade v3.0.0-alpha.0 (/opt/rustwide/workdir/packages_rs/nextclade)`.
[INFO] [stderr] Colliding filename is: /opt/rustwide/target/doc/nextclade/index.html
[INFO] [stderr] The targets should have unique names.
[INFO] [stderr] This is a known bug where multiple crates with the same name use
[INFO] [stderr] the same path; see <https://github.com/rust-lang/cargo/issues/6313>.
[INFO] [stderr]    Compiling proc-macro2 v1.0.63
[INFO] [stderr]    Compiling quote v1.0.29
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[INFO] [stderr]    Compiling libc v0.2.147
[INFO] [stderr]    Compiling serde v1.0.164
[INFO] [stderr]    Compiling libm v0.2.7
[INFO] [stderr]    Compiling num-traits v0.2.15
[INFO] [stderr]    Compiling syn v1.0.109
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[INFO] [stderr]     Checking itoa v1.0.6
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[INFO] [stderr]    Compiling validator_derive v0.16.0
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[INFO] [stderr]    Compiling strum_macros v0.25.0
[INFO] [stderr]    Compiling getset v0.1.2
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[INFO] [stderr]     Checking rand v0.8.5
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[INFO] [stderr]    Compiling dotenv v0.15.0
[INFO] [stderr]     Checking base64 v0.21.2
[INFO] [stderr]    Compiling dotenv_codegen_implementation v0.15.0
[INFO] [stderr]     Checking rustls-pemfile v1.0.3
[INFO] [stderr]     Checking crossterm v0.26.1
[INFO] [stderr]     Checking webpki-roots v0.22.6
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[INFO] [stderr]     Checking hyper-rustls v0.24.0
[INFO] [stderr]     Checking tokio-socks v0.5.1
[INFO] [stderr]     Checking js-sys v0.3.64
[INFO] [stderr]     Checking serde_urlencoded v0.7.1
[INFO] [stderr]     Checking encoding_rs v0.8.32
[INFO] [stderr]     Checking mime v0.3.17
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[INFO] [stderr]     Checking dotenv_codegen v0.15.0
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[INFO] [stderr]     Checking console_error_panic_hook v0.1.7
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[INFO] [stderr]     Checking bzip2 v0.4.4
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[INFO] [stderr]     Checking web-sys v0.3.64
[INFO] [stderr]     Checking serde-wasm-bindgen v0.5.0
[INFO] [stderr]    Compiling xz2 v0.1.7
[INFO] [stderr]     Checking zstd v0.12.3+zstd.1.5.2
[INFO] [stderr]     Checking nextclade v3.0.0-alpha.0 (/opt/rustwide/workdir/packages_rs/nextclade)
[INFO] [stderr]  Documenting nextclade v3.0.0-alpha.0 (/opt/rustwide/workdir/packages_rs/nextclade)
[INFO] [stderr]     Checking wasm-logger v0.2.0
[INFO] [stdout] warning: unused import: `Stripe`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/backtrace.rs:1:37
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::align::band_2d::{Band2d, Stripe};
[INFO] [stdout]   |                                     ^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::utils::vec2d::Vec2d`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/backtrace.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::utils::vec2d::Vec2d;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `log::warn`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/backtrace.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use log::warn;
[INFO] [stdout]   |     ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::cmp`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/backtrace.rs:7:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | use std::cmp;
[INFO] [stdout]   |     ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::coord::range::NucRefGlobalRange`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/gap_open.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::coord::range::NucRefGlobalRange;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `color_eyre::SectionExt`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/insertions_strip.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use color_eyre::SectionExt;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `eyre::Report`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/insertions_strip.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use eyre::Report;
[INFO] [stdout]   |     ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `serde::de::Error`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/insertions_strip.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use serde::de::Error;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Deserializer`, `Serializer`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/insertions_strip.rs:9:26
[INFO] [stdout]   |
[INFO] [stdout] 9 | use serde::{Deserialize, Deserializer, Serialize, Serializer};
[INFO] [stdout]   |                          ^^^^^^^^^^^^             ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::str::FromStr`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/insertions_strip.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use std::str::FromStr;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::align::band_2d::full_matrix`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/seed_alignment.rs:1:5
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::align::band_2d::full_matrix;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::align::params::AlignPairwiseParams`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/seed_alignment.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::align::params::AlignPairwiseParams;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::align::seed_match::seed_match`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/seed_alignment.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::align::seed_match::seed_match;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `CodonSpacedIndex`, `get_seed_matches2`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/seed_alignment.rs:5:33
[INFO] [stdout]   |
[INFO] [stdout] 5 | use crate::align::seed_match2::{get_seed_matches2, CodonSpacedIndex, SeedMatch2};
[INFO] [stdout]   |                                 ^^^^^^^^^^^^^^^^^  ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::alphabet::nuc::Nuc`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/seed_alignment.rs:7:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | use crate::alphabet::nuc::Nuc;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::coord::position::LocalSpace`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/seed_alignment.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use crate::coord::position::LocalSpace;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::make_error`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/seed_alignment.rs:9:5
[INFO] [stdout]   |
[INFO] [stdout] 9 | use crate::make_error;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::utils::collections::first`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/seed_alignment.rs:10:5
[INFO] [stdout]    |
[INFO] [stdout] 10 | use crate::utils::collections::first;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `eyre::Report`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/seed_alignment.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use eyre::Report;
[INFO] [stdout]    |     ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `num_traits::clamp_min`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/seed_alignment.rs:15:5
[INFO] [stdout]    |
[INFO] [stdout] 15 | use num_traits::clamp_min;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::collections::BTreeMap`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/seed_alignment.rs:18:5
[INFO] [stdout]    |
[INFO] [stdout] 18 | use std::collections::BTreeMap;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::align::seed_alignment::write_matches_to_file`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/seed_match2.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | use crate::align::seed_alignment::write_matches_to_file;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Bounded`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/seed_match2.rs:12:25
[INFO] [stdout]    |
[INFO] [stdout] 12 | use gcollections::ops::{Bounded, Intersection, IsEmpty, Union};
[INFO] [stdout]    |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Deserializer`, `Serializer`
[INFO] [stdout]  --> packages_rs/nextclade/src/alphabet/aa.rs:5:26
[INFO] [stdout]   |
[INFO] [stdout] 5 | use serde::{Deserialize, Deserializer, Serialize, Serializer};
[INFO] [stdout]   |                          ^^^^^^^^^^^^             ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Deserializer`, `Serializer`
[INFO] [stdout]  --> packages_rs/nextclade/src/alphabet/nuc.rs:5:26
[INFO] [stdout]   |
[INFO] [stdout] 5 | use serde::{Deserialize, Deserializer, Serialize, Serializer};
[INFO] [stdout]   |                          ^^^^^^^^^^^^             ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `from_aa`
[INFO] [stdout]  --> packages_rs/nextclade/src/analyze/aa_del.rs:1:27
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::alphabet::aa::{from_aa, Aa};
[INFO] [stdout]   |                           ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::str::FromStr`
[INFO] [stdout]  --> packages_rs/nextclade/src/analyze/nuc_del.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use std::str::FromStr;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Stripe`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/backtrace.rs:1:37
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::align::band_2d::{Band2d, Stripe};
[INFO] [stdout]   |                                     ^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::utils::vec2d::Vec2d`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/backtrace.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::utils::vec2d::Vec2d;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `log::warn`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/backtrace.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use log::warn;
[INFO] [stdout]   |     ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::cmp`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/backtrace.rs:7:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | use std::cmp;
[INFO] [stdout]   |     ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::coord::range::NucRefGlobalRange`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/gap_open.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::coord::range::NucRefGlobalRange;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `color_eyre::SectionExt`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/insertions_strip.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use color_eyre::SectionExt;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `eyre::Report`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/insertions_strip.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use eyre::Report;
[INFO] [stdout]   |     ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `serde::de::Error`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/insertions_strip.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use serde::de::Error;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Deserializer`, `Serializer`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/insertions_strip.rs:9:26
[INFO] [stdout]   |
[INFO] [stdout] 9 | use serde::{Deserialize, Deserializer, Serialize, Serializer};
[INFO] [stdout]   |                          ^^^^^^^^^^^^             ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::str::FromStr`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/insertions_strip.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use std::str::FromStr;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `CoordsMarker`, `SeqTypeMarker`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/coord_map.rs:4:35
[INFO] [stdout]   |
[INFO] [stdout] 4 |   AaRefPosition, AlignmentCoords, CoordsMarker, NucRefLocalPosition, NucSpace, Position, PositionLike, ReferenceCoords,
[INFO] [stdout]   |                                   ^^^^^^^^^^^^
[INFO] [stdout] 5 |   SeqTypeMarker, SpaceMarker,
[INFO] [stdout]   |   ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `itertools::Itertools`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/coord_map.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use itertools::Itertools;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Deserialize`, `Serialize`
[INFO] [stdout]   --> packages_rs/nextclade/src/coord/coord_map.rs:10:13
[INFO] [stdout]    |
[INFO] [stdout] 10 | use serde::{Deserialize, Serialize};
[INFO] [stdout]    |             ^^^^^^^^^^^  ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::alphabet::letter::Letter`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/coord_map_cds_to_global.rs:1:5
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::alphabet::letter::Letter;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `CoordsMarker`, `SeqTypeMarker`, `SpaceMarker`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/coord_map_cds_to_global.rs:3:18
[INFO] [stdout]   |
[INFO] [stdout] 3 |   AaRefPosition, CoordsMarker, NucRefGlobalPosition, NucRefLocalPosition, PositionLike, SeqTypeMarker, SpaceMarker,
[INFO] [stdout]   |                  ^^^^^^^^^^^^                                                           ^^^^^^^^^^^^^  ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::gene::cds_segment::WrappingPart`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/coord_map_cds_to_global.rs:7:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | use crate::gene::cds_segment::WrappingPart;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Deserialize`, `Serialize`
[INFO] [stdout]   --> packages_rs/nextclade/src/coord/coord_map_cds_to_global.rs:11:13
[INFO] [stdout]    |
[INFO] [stdout] 11 | use serde::{Deserialize, Serialize};
[INFO] [stdout]    |             ^^^^^^^^^^^  ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `itertools::Itertools`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/coord_map_global.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use itertools::Itertools;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::coord::coord_map_global::CoordMapGlobal`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/coord_map_local.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::coord::coord_map_global::CoordMapGlobal;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::align::band_2d::full_matrix`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/seed_alignment.rs:1:5
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::align::band_2d::full_matrix;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::align::params::AlignPairwiseParams`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/seed_alignment.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::align::params::AlignPairwiseParams;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::align::seed_match::seed_match`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/seed_alignment.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::align::seed_match::seed_match;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `CodonSpacedIndex`, `get_seed_matches2`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/seed_alignment.rs:5:33
[INFO] [stdout]   |
[INFO] [stdout] 5 | use crate::align::seed_match2::{get_seed_matches2, CodonSpacedIndex, SeedMatch2};
[INFO] [stdout]   |                                 ^^^^^^^^^^^^^^^^^  ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::alphabet::nuc::Nuc`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/seed_alignment.rs:7:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | use crate::alphabet::nuc::Nuc;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::coord::position::LocalSpace`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/seed_alignment.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use crate::coord::position::LocalSpace;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::make_error`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/seed_alignment.rs:9:5
[INFO] [stdout]   |
[INFO] [stdout] 9 | use crate::make_error;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::utils::collections::first`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/seed_alignment.rs:10:5
[INFO] [stdout]    |
[INFO] [stdout] 10 | use crate::utils::collections::first;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `eyre::Report`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/seed_alignment.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use eyre::Report;
[INFO] [stdout]    |     ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `num_traits::clamp_min`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/seed_alignment.rs:15:5
[INFO] [stdout]    |
[INFO] [stdout] 15 | use num_traits::clamp_min;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::collections::BTreeMap`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/seed_alignment.rs:18:5
[INFO] [stdout]    |
[INFO] [stdout] 18 | use std::collections::BTreeMap;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::align::seed_alignment::write_matches_to_file`
[INFO] [stdout]  --> packages_rs/nextclade/src/align/seed_match2.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | use crate::align::seed_alignment::write_matches_to_file;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Bounded`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/seed_match2.rs:12:25
[INFO] [stdout]    |
[INFO] [stdout] 12 | use gcollections::ops::{Bounded, Intersection, IsEmpty, Union};
[INFO] [stdout]    |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Deserializer`, `Serializer`
[INFO] [stdout]  --> packages_rs/nextclade/src/alphabet/aa.rs:5:26
[INFO] [stdout]   |
[INFO] [stdout] 5 | use serde::{Deserialize, Deserializer, Serialize, Serializer};
[INFO] [stdout]   |                          ^^^^^^^^^^^^             ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Deserializer`, `Serializer`
[INFO] [stdout]  --> packages_rs/nextclade/src/alphabet/nuc.rs:5:26
[INFO] [stdout]   |
[INFO] [stdout] 5 | use serde::{Deserialize, Deserializer, Serialize, Serializer};
[INFO] [stdout]   |                          ^^^^^^^^^^^^             ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `from_aa`
[INFO] [stdout]  --> packages_rs/nextclade/src/analyze/aa_del.rs:1:27
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::alphabet::aa::{from_aa, Aa};
[INFO] [stdout]   |                           ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::str::FromStr`
[INFO] [stdout]  --> packages_rs/nextclade/src/analyze/nuc_del.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use std::str::FromStr;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fmt::Display`
[INFO] [stdout]   --> packages_rs/nextclade/src/gene/cds.rs:16:5
[INFO] [stdout]    |
[INFO] [stdout] 16 | use std::fmt::Display;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `CoordsMarker`, `SeqTypeMarker`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/coord_map.rs:4:35
[INFO] [stdout]   |
[INFO] [stdout] 4 |   AaRefPosition, AlignmentCoords, CoordsMarker, NucRefLocalPosition, NucSpace, Position, PositionLike, ReferenceCoords,
[INFO] [stdout]   |                                   ^^^^^^^^^^^^
[INFO] [stdout] 5 |   SeqTypeMarker, SpaceMarker,
[INFO] [stdout]   |   ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fmt::Display`
[INFO] [stdout]   --> packages_rs/nextclade/src/gene/gene_map.rs:19:5
[INFO] [stdout]    |
[INFO] [stdout] 19 | use std::fmt::Display;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `itertools::Itertools`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/coord_map.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use itertools::Itertools;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Deserialize`, `Serialize`
[INFO] [stdout]   --> packages_rs/nextclade/src/coord/coord_map.rs:10:13
[INFO] [stdout]    |
[INFO] [stdout] 10 | use serde::{Deserialize, Serialize};
[INFO] [stdout]    |             ^^^^^^^^^^^  ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::alphabet::letter::Letter`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/coord_map_cds_to_global.rs:1:5
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::alphabet::letter::Letter;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `CoordsMarker`, `SeqTypeMarker`, `SpaceMarker`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/coord_map_cds_to_global.rs:3:18
[INFO] [stdout]   |
[INFO] [stdout] 3 |   AaRefPosition, CoordsMarker, NucRefGlobalPosition, NucRefLocalPosition, PositionLike, SeqTypeMarker, SpaceMarker,
[INFO] [stdout]   |                  ^^^^^^^^^^^^                                                           ^^^^^^^^^^^^^  ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::gene::cds_segment::WrappingPart`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/coord_map_cds_to_global.rs:7:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | use crate::gene::cds_segment::WrappingPart;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Deserialize`, `Serialize`
[INFO] [stdout]   --> packages_rs/nextclade/src/coord/coord_map_cds_to_global.rs:11:13
[INFO] [stdout]    |
[INFO] [stdout] 11 | use serde::{Deserialize, Serialize};
[INFO] [stdout]    |             ^^^^^^^^^^^  ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `itertools::Itertools`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/coord_map_global.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use itertools::Itertools;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::coord::coord_map_global::CoordMapGlobal`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/coord_map_local.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::coord::coord_map_global::CoordMapGlobal;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Display`
[INFO] [stdout]  --> packages_rs/nextclade/src/graph/node.rs:3:24
[INFO] [stdout]   |
[INFO] [stdout] 3 | use core::fmt::{Debug, Display};
[INFO] [stdout]   |                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fmt::Display`
[INFO] [stdout]   --> packages_rs/nextclade/src/gene/cds.rs:16:5
[INFO] [stdout]    |
[INFO] [stdout] 16 | use std::fmt::Display;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fmt::Display`
[INFO] [stdout]   --> packages_rs/nextclade/src/gene/gene_map.rs:19:5
[INFO] [stdout]    |
[INFO] [stdout] 19 | use std::fmt::Display;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fmt::Display`
[INFO] [stdout]   --> packages_rs/nextclade/src/io/fasta.rs:13:5
[INFO] [stdout]    |
[INFO] [stdout] 13 | use std::fmt::Display;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fmt::Debug`
[INFO] [stdout]  --> packages_rs/nextclade/src/io/file.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use std::fmt::Debug;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `WrapErr`
[INFO] [stdout]  --> packages_rs/nextclade/src/io/gff3.rs:7:26
[INFO] [stdout]   |
[INFO] [stdout] 7 | use eyre::{eyre, Report, WrapErr};
[INFO] [stdout]   |                          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::borrow::BorrowMut`
[INFO] [stdout]   --> packages_rs/nextclade/src/io/gff3.rs:10:5
[INFO] [stdout]    |
[INFO] [stdout] 10 | use std::borrow::BorrowMut;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::hash::Hash`
[INFO] [stdout]   --> packages_rs/nextclade/src/io/gff3.rs:13:5
[INFO] [stdout]    |
[INFO] [stdout] 13 | use std::hash::Hash;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::io::Read`
[INFO] [stdout]   --> packages_rs/nextclade/src/io/gff3.rs:14:5
[INFO] [stdout]    |
[INFO] [stdout] 14 | use std::io::Read;
[INFO] [stdout]    |     ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Display`
[INFO] [stdout]  --> packages_rs/nextclade/src/graph/node.rs:3:24
[INFO] [stdout]   |
[INFO] [stdout] 3 | use core::fmt::{Debug, Display};
[INFO] [stdout]   |                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fmt::Debug`
[INFO] [stdout]  --> packages_rs/nextclade/src/io/ndjson.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use std::fmt::Debug;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fmt::Display`
[INFO] [stdout]   --> packages_rs/nextclade/src/io/fasta.rs:13:5
[INFO] [stdout]    |
[INFO] [stdout] 13 | use std::fmt::Display;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fmt::Debug`
[INFO] [stdout]  --> packages_rs/nextclade/src/io/file.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use std::fmt::Debug;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `WrapErr`
[INFO] [stdout]  --> packages_rs/nextclade/src/io/gff3.rs:7:26
[INFO] [stdout]   |
[INFO] [stdout] 7 | use eyre::{eyre, Report, WrapErr};
[INFO] [stdout]   |                          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::borrow::BorrowMut`
[INFO] [stdout]   --> packages_rs/nextclade/src/io/gff3.rs:10:5
[INFO] [stdout]    |
[INFO] [stdout] 10 | use std::borrow::BorrowMut;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::hash::Hash`
[INFO] [stdout]   --> packages_rs/nextclade/src/io/gff3.rs:13:5
[INFO] [stdout]    |
[INFO] [stdout] 13 | use std::hash::Hash;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::io::Read`
[INFO] [stdout]   --> packages_rs/nextclade/src/io/gff3.rs:14:5
[INFO] [stdout]    |
[INFO] [stdout] 14 | use std::io::Read;
[INFO] [stdout]    |     ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fmt::Debug`
[INFO] [stdout]  --> packages_rs/nextclade/src/io/ndjson.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use std::fmt::Debug;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `QcConfig`
[INFO] [stdout]  --> packages_rs/nextclade/src/qc/qc_rule_mixed_sites.rs:3:28
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::qc::qc_config::{QcConfig, QcRulesConfigMixedSites};
[INFO] [stdout]   |                            ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `make_error`, `o`
[INFO] [stdout]  --> packages_rs/nextclade/src/run/params.rs:5:13
[INFO] [stdout]   |
[INFO] [stdout] 5 | use crate::{make_error, o};
[INFO] [stdout]   |             ^^^^^^^^^^  ^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `itertools::Itertools`
[INFO] [stdout]  --> packages_rs/nextclade/src/run/params.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use itertools::Itertools;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::collections::BTreeMap`
[INFO] [stdout]   --> packages_rs/nextclade/src/run/params.rs:10:5
[INFO] [stdout]    |
[INFO] [stdout] 10 | use std::collections::BTreeMap;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `QcConfig`
[INFO] [stdout]  --> packages_rs/nextclade/src/qc/qc_rule_mixed_sites.rs:3:28
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::qc::qc_config::{QcConfig, QcRulesConfigMixedSites};
[INFO] [stdout]   |                            ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `make_error`, `o`
[INFO] [stdout]  --> packages_rs/nextclade/src/run/params.rs:5:13
[INFO] [stdout]   |
[INFO] [stdout] 5 | use crate::{make_error, o};
[INFO] [stdout]   |             ^^^^^^^^^^  ^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `itertools::Itertools`
[INFO] [stdout]  --> packages_rs/nextclade/src/run/params.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use itertools::Itertools;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::collections::BTreeMap`
[INFO] [stdout]   --> packages_rs/nextclade/src/run/params.rs:10:5
[INFO] [stdout]    |
[INFO] [stdout] 10 | use std::collections::BTreeMap;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::hash::Hash`
[INFO] [stdout]   --> packages_rs/nextclade/src/tree/split_muts.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use std::hash::Hash;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::analyze::nuc_del::NucDel`
[INFO] [stdout]  --> packages_rs/nextclade/src/tree/split_muts2.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::analyze::nuc_del::NucDel;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::hash::Hash`
[INFO] [stdout]   --> packages_rs/nextclade/src/tree/split_muts.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use std::hash::Hash;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::analyze::nuc_del::NucDel`
[INFO] [stdout]  --> packages_rs/nextclade/src/tree/split_muts2.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::analyze::nuc_del::NucDel;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Range`
[INFO] [stdout]  --> packages_rs/nextclade/src/tree/tree_find_nearest_node.rs:5:46
[INFO] [stdout]   |
[INFO] [stdout] 5 | use crate::coord::range::{NucRefGlobalRange, Range};
[INFO] [stdout]   |                                              ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `TreeNodeAttr`
[INFO] [stdout]  --> packages_rs/nextclade/src/tree/tree_find_nearest_node.rs:7:64
[INFO] [stdout]   |
[INFO] [stdout] 7 | use crate::tree::tree::{AuspiceGraph, AuspiceGraphNodePayload, TreeNodeAttr};
[INFO] [stdout]   |                                                                ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::analyze::nuc_del::NucDel`
[INFO] [stdout]  --> packages_rs/nextclade/src/tree/tree_preprocess.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use crate::analyze::nuc_del::NucDel;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Range`
[INFO] [stdout]  --> packages_rs/nextclade/src/tree/tree_find_nearest_node.rs:5:46
[INFO] [stdout]   |
[INFO] [stdout] 5 | use crate::coord::range::{NucRefGlobalRange, Range};
[INFO] [stdout]   |                                              ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `TreeNodeAttr`
[INFO] [stdout]  --> packages_rs/nextclade/src/tree/tree_find_nearest_node.rs:7:64
[INFO] [stdout]   |
[INFO] [stdout] 7 | use crate::tree::tree::{AuspiceGraph, AuspiceGraphNodePayload, TreeNodeAttr};
[INFO] [stdout]   |                                                                ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::analyze::nuc_del::NucDel`
[INFO] [stdout]  --> packages_rs/nextclade/src/tree/tree_preprocess.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use crate::analyze::nuc_del::NucDel;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Write`
[INFO] [stdout]  --> packages_rs/nextclade/src/utils/vec2d.rs:1:43
[INFO] [stdout]   |
[INFO] [stdout] 1 | use std::fmt::{Debug, Display, Formatter, Write};
[INFO] [stdout]   |                                           ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Write`
[INFO] [stdout]  --> packages_rs/nextclade/src/utils/vec2d.rs:1:43
[INFO] [stdout]   |
[INFO] [stdout] 1 | use std::fmt::{Debug, Display, Formatter, Write};
[INFO] [stdout]   |                                           ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `itertools::Itertools`
[INFO] [stdout]  --> packages_rs/nextclade/src/utils/error.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use itertools::Itertools;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `itertools::Itertools`
[INFO] [stdout]  --> packages_rs/nextclade/src/analyze/is_sequenced.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use itertools::Itertools;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `num_traits::real::Real`
[INFO] [stdout]  --> packages_rs/nextclade/src/analyze/phenotype.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use num_traits::real::Real;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::str::FromStr`
[INFO] [stdout]   --> packages_rs/nextclade/src/analyze/virus_properties.rs:21:5
[INFO] [stdout]    |
[INFO] [stdout] 21 | use std::str::FromStr;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `SaturatingAdd`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/position.rs:4:60
[INFO] [stdout]   |
[INFO] [stdout] 4 | use num_traits::{clamp, clamp_max, clamp_min, AsPrimitive, SaturatingAdd, SaturatingMul, SaturatingSub};
[INFO] [stdout]   |                                                            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `SaturatingSub`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/position.rs:4:90
[INFO] [stdout]   |
[INFO] [stdout] 4 | use num_traits::{clamp, clamp_max, clamp_min, AsPrimitive, SaturatingAdd, SaturatingMul, SaturatingSub};
[INFO] [stdout]   |                                                                                          ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `SaturatingMul`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/position.rs:4:75
[INFO] [stdout]   |
[INFO] [stdout] 4 | use num_traits::{clamp, clamp_max, clamp_min, AsPrimitive, SaturatingAdd, SaturatingMul, SaturatingSub};
[INFO] [stdout]   |                                                                           ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `itertools::Itertools`
[INFO] [stdout]  --> packages_rs/nextclade/src/utils/error.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use itertools::Itertools;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::str::FromStr`
[INFO] [stdout]   --> packages_rs/nextclade/src/tree/tree.rs:17:5
[INFO] [stdout]    |
[INFO] [stdout] 17 | use std::str::FromStr;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `regex::internal::Input`
[INFO] [stdout]   --> packages_rs/nextclade/src/gene/gene_map.rs:16:5
[INFO] [stdout]    |
[INFO] [stdout] 16 | use regex::internal::Input;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `itertools::Itertools`
[INFO] [stdout]  --> packages_rs/nextclade/src/analyze/is_sequenced.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use itertools::Itertools;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Read`
[INFO] [stdout]   --> packages_rs/nextclade/src/io/fasta.rs:14:35
[INFO] [stdout]    |
[INFO] [stdout] 14 | use std::io::{BufRead, BufReader, Read};
[INFO] [stdout]    |                                   ^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::io::Write`
[INFO] [stdout]   --> packages_rs/nextclade/src/io/nextclade_csv.rs:30:5
[INFO] [stdout]    |
[INFO] [stdout] 30 | use std::io::Write;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `itertools::Itertools`
[INFO] [stdout]  --> packages_rs/nextclade/src/io/nwk_writer.rs:7:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | use itertools::Itertools;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::str::FromStr`
[INFO] [stdout]   --> packages_rs/nextclade/src/run/nextclade_wasm.rs:27:5
[INFO] [stdout]    |
[INFO] [stdout] 27 | use std::str::FromStr;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `num_traits::real::Real`
[INFO] [stdout]  --> packages_rs/nextclade/src/analyze/phenotype.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use num_traits::real::Real;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::str::FromStr`
[INFO] [stdout]   --> packages_rs/nextclade/src/analyze/virus_properties.rs:21:5
[INFO] [stdout]    |
[INFO] [stdout] 21 | use std::str::FromStr;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `SaturatingAdd`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/position.rs:4:60
[INFO] [stdout]   |
[INFO] [stdout] 4 | use num_traits::{clamp, clamp_max, clamp_min, AsPrimitive, SaturatingAdd, SaturatingMul, SaturatingSub};
[INFO] [stdout]   |                                                            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `SaturatingSub`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/position.rs:4:90
[INFO] [stdout]   |
[INFO] [stdout] 4 | use num_traits::{clamp, clamp_max, clamp_min, AsPrimitive, SaturatingAdd, SaturatingMul, SaturatingSub};
[INFO] [stdout]   |                                                                                          ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `SaturatingMul`
[INFO] [stdout]  --> packages_rs/nextclade/src/coord/position.rs:4:75
[INFO] [stdout]   |
[INFO] [stdout] 4 | use num_traits::{clamp, clamp_max, clamp_min, AsPrimitive, SaturatingAdd, SaturatingMul, SaturatingSub};
[INFO] [stdout]   |                                                                           ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::str::FromStr`
[INFO] [stdout]   --> packages_rs/nextclade/src/tree/tree.rs:17:5
[INFO] [stdout]    |
[INFO] [stdout] 17 | use std::str::FromStr;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `regex::internal::Input`
[INFO] [stdout]   --> packages_rs/nextclade/src/gene/gene_map.rs:16:5
[INFO] [stdout]    |
[INFO] [stdout] 16 | use regex::internal::Input;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Read`
[INFO] [stdout]   --> packages_rs/nextclade/src/io/fasta.rs:14:35
[INFO] [stdout]    |
[INFO] [stdout] 14 | use std::io::{BufRead, BufReader, Read};
[INFO] [stdout]    |                                   ^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::io::Write`
[INFO] [stdout]   --> packages_rs/nextclade/src/io/nextclade_csv.rs:30:5
[INFO] [stdout]    |
[INFO] [stdout] 30 | use std::io::Write;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `itertools::Itertools`
[INFO] [stdout]  --> packages_rs/nextclade/src/io/nwk_writer.rs:7:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | use itertools::Itertools;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::str::FromStr`
[INFO] [stdout]   --> packages_rs/nextclade/src/run/nextclade_wasm.rs:27:5
[INFO] [stdout]    |
[INFO] [stdout] 27 | use std::str::FromStr;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `qry_len`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/backtrace.rs:30:7
[INFO] [stdout]    |
[INFO] [stdout] 30 |   let qry_len = qry_seq.len() as i32;
[INFO] [stdout]    |       ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_qry_len`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `ref_len`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/backtrace.rs:31:7
[INFO] [stdout]    |
[INFO] [stdout] 31 |   let ref_len = ref_seq.len() as i32;
[INFO] [stdout]    |       ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `qry_len_i32`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/band_2d.rs:59:7
[INFO] [stdout]    |
[INFO] [stdout] 59 |   let qry_len_i32 = qry_len.to_i32().unwrap();
[INFO] [stdout]    |       ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_qry_len_i32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/band_2d.rs:60:7
[INFO] [stdout]    |
[INFO] [stdout] 60 |   for i in 0..=ref_len_i32 {
[INFO] [stdout]    |       ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `qry_len`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/backtrace.rs:30:7
[INFO] [stdout]    |
[INFO] [stdout] 30 |   let qry_len = qry_seq.len() as i32;
[INFO] [stdout]    |       ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_qry_len`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `ref_len`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/backtrace.rs:31:7
[INFO] [stdout]    |
[INFO] [stdout] 31 |   let ref_len = ref_seq.len() as i32;
[INFO] [stdout]    |       ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `qry_len_i32`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/band_2d.rs:59:7
[INFO] [stdout]    |
[INFO] [stdout] 59 |   let qry_len_i32 = qry_len.to_i32().unwrap();
[INFO] [stdout]    |       ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_qry_len_i32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/band_2d.rs:60:7
[INFO] [stdout]    |
[INFO] [stdout] 60 |   for i in 0..=ref_len_i32 {
[INFO] [stdout]    |       ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `tmp_match`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/score_matrix.rs:92:11
[INFO] [stdout]    |
[INFO] [stdout] 92 |       let tmp_match: i32;
[INFO] [stdout]    |           ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_tmp_match`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `current_seed_end`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/seed_alignment.rs:68:7
[INFO] [stdout]    |
[INFO] [stdout] 68 |   let current_seed_end = (current_seed.ref_pos + current_seed.length) as isize;
[INFO] [stdout]    |       ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_current_seed_end`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `tmp_match`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/score_matrix.rs:92:11
[INFO] [stdout]    |
[INFO] [stdout] 92 |       let tmp_match: i32;
[INFO] [stdout]    |           ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_tmp_match`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `current_seed_end`
[INFO] [stdout]   --> packages_rs/nextclade/src/align/seed_alignment.rs:68:7
[INFO] [stdout]    |
[INFO] [stdout] 68 |   let current_seed_end = (current_seed.ref_pos + current_seed.length) as isize;
[INFO] [stdout]    |       ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_current_seed_end`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `params`
[INFO] [stdout]   --> packages_rs/nextclade/src/analyze/divergence.rs:68:81
[INFO] [stdout]    |
[INFO] [stdout] 68 | pub fn score_nuc_muts(nuc_muts: &[NucSub], masked_ranges: &[NucRefGlobalRange], params: &TreeBuilderParams) -> f64 {
[INFO] [stdout]    |                                                                                 ^^^^^^ help: if this is intentional, prefix it with an underscore: `_params`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `params`
[INFO] [stdout]   --> packages_rs/nextclade/src/analyze/divergence.rs:68:81
[INFO] [stdout]    |
[INFO] [stdout] 68 | pub fn score_nuc_muts(nuc_muts: &[NucSub], masked_ranges: &[NucRefGlobalRange], params: &TreeBuilderParams) -> f64 {
[INFO] [stdout]    |                                                                                 ^^^^^^ help: if this is intentional, prefix it with an underscore: `_params`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `ref_seq`
[INFO] [stdout]    --> packages_rs/nextclade/src/analyze/find_private_aa_mutations.rs:203:3
[INFO] [stdout]     |
[INFO] [stdout] 203 |   ref_seq: &[Aa],
[INFO] [stdout]     |   ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_seq`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `ref_seq`
[INFO] [stdout]    --> packages_rs/nextclade/src/analyze/find_private_aa_mutations.rs:203:3
[INFO] [stdout]     |
[INFO] [stdout] 203 |   ref_seq: &[Aa],
[INFO] [stdout]     |   ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_seq`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> packages_rs/nextclade/src/align/seed_match2.rs:19:17
[INFO] [stdout]    |
[INFO] [stdout] 19 | /// Copied from https://stackoverflow.com/a/75084739/7483211
[INFO] [stdout]    |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://stackoverflow.com/a/75084739/7483211>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout]    = note: `#[warn(rustdoc::bare_urls)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> packages_rs/nextclade/src/coord/position.rs:423:10
[INFO] [stdout]     |
[INFO] [stdout] 423 | ///    - https://github.com/carbotaniuman/auto_ops/blob/74d97b4fb0f39e73c7fd63934c877c91a2c4a031/README.md?plain=1#L47-L48
[INFO] [stdout]     |          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/carbotaniuman/auto_ops/blob/74d97b4fb0f39e73c7fd63934c877c91a2c4a031/README.md?plain=1#L47-L48>`
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> packages_rs/nextclade/src/coord/position.rs:424:10
[INFO] [stdout]     |
[INFO] [stdout] 424 | ///    - https://github.com/carbotaniuman/auto_ops/issues/2
[INFO] [stdout]     |          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/carbotaniuman/auto_ops/issues/2>`
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> packages_rs/nextclade/src/coord/position.rs:426:10
[INFO] [stdout]     |
[INFO] [stdout] 426 | ///    - https://rust-lang.github.io/rfcs/1210-impl-specialization.html
[INFO] [stdout]     |          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://rust-lang.github.io/rfcs/1210-impl-specialization.html>`
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> packages_rs/nextclade/src/coord/position.rs:428:10
[INFO] [stdout]     |
[INFO] [stdout] 428 | ///    - https://github.com/carbotaniuman/auto_ops/pull/14
[INFO] [stdout]     |          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/carbotaniuman/auto_ops/pull/14>`
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> packages_rs/nextclade/src/io/json.rs:19:9
[INFO] [stdout]    |
[INFO] [stdout] 19 | /// See https://github.com/serde-rs/json/issues/334
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/serde-rs/json/issues/334>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> packages_rs/nextclade/src/utils/collections.rs:35:14
[INFO] [stdout]    |
[INFO] [stdout] 35 | /// Credits: https://sts10.github.io/2019/06/06/is-all-equal-function.html
[INFO] [stdout]    |              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://sts10.github.io/2019/06/06/is-all-equal-function.html>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> packages_rs/nextclade/src/utils/option.rs:24:7
[INFO] [stdout]    |
[INFO] [stdout] 24 |   /// https://github.com/ammongit/rust-ref-map/blob/4b1251c6d2fd192d89a114395b36aeeab5c5433c/src/option.rs
[INFO] [stdout]    |       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/ammongit/rust-ref-map/blob/4b1251c6d2fd192d89a114395b36aeeab5c5433c/src/option.rs>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> packages_rs/nextclade/src/utils/option.rs:47:7
[INFO] [stdout]    |
[INFO] [stdout] 47 |   /// https://github.com/ammongit/rust-ref-map/blob/4b1251c6d2fd192d89a114395b36aeeab5c5433c/src/option.rs
[INFO] [stdout]    |       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/ammongit/rust-ref-map/blob/4b1251c6d2fd192d89a114395b36aeeab5c5433c/src/option.rs>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `T`
[INFO] [stdout]   --> packages_rs/nextclade/src/utils/vec2d.rs:90:33
[INFO] [stdout]    |
[INFO] [stdout] 90 | /// Allows to pretty-print Vec2d<T>
[INFO] [stdout]    |                                 ^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(rustdoc::invalid_html_tags)]` on by default
[INFO] [stdout] help: try marking as source code
[INFO] [stdout]    |
[INFO] [stdout] 90 | /// Allows to pretty-print `Vec2d<T>`
[INFO] [stdout]    |                            +        +
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `id`
[INFO] [stdout]   --> packages_rs/nextclade/src/features/feature_group.rs:40:14
[INFO] [stdout]    |
[INFO] [stdout] 40 |   pub fn new(id: &str, features: &[Feature]) -> Self {
[INFO] [stdout]    |              ^^ help: if this is intentional, prefix it with an underscore: `_id`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `content_end`
[INFO] [stdout]   --> packages_rs/nextclade/src/features/feature_tree.rs:90:43
[INFO] [stdout]    |
[INFO] [stdout] 90 |     .map(|(index,(content, content_begin, content_end))| {
[INFO] [stdout]    |                                           ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_content_end`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `height`
[INFO] [stdout]    --> packages_rs/nextclade/src/features/feature_tree_format.rs:106:21
[INFO] [stdout]     |
[INFO] [stdout] 106 |     .try_for_each(|(height, feature_group)| -> Result<(), Report> {
[INFO] [stdout]     |                     ^^^^^^ help: if this is intentional, prefix it with an underscore: `_height`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `id`
[INFO] [stdout]   --> packages_rs/nextclade/src/features/feature_group.rs:40:14
[INFO] [stdout]    |
[INFO] [stdout] 40 |   pub fn new(id: &str, features: &[Feature]) -> Self {
[INFO] [stdout]    |              ^^ help: if this is intentional, prefix it with an underscore: `_id`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `content_end`
[INFO] [stdout]   --> packages_rs/nextclade/src/features/feature_tree.rs:90:43
[INFO] [stdout]    |
[INFO] [stdout] 90 |     .map(|(index,(content, content_begin, content_end))| {
[INFO] [stdout]    |                                           ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_content_end`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `height`
[INFO] [stdout]    --> packages_rs/nextclade/src/features/feature_tree_format.rs:106:21
[INFO] [stdout]     |
[INFO] [stdout] 106 |     .try_for_each(|(height, feature_group)| -> Result<(), Report> {
[INFO] [stdout]     |                     ^^^^^^ help: if this is intentional, prefix it with an underscore: `_height`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]    --> packages_rs/nextclade/src/io/gff3.rs:172:15
[INFO] [stdout]     |
[INFO] [stdout] 172 |     .filter(|(i, record)| {
[INFO] [stdout]     |               ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `column`
[INFO] [stdout]    --> packages_rs/nextclade/src/io/nextclade_csv.rs:238:17
[INFO] [stdout]     |
[INFO] [stdout] 238 |       .filter(|(column, enabled)| **enabled)
[INFO] [stdout]     |                 ^^^^^^ help: if this is intentional, prefix it with an underscore: `_column`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `name`
[INFO] [stdout]    --> packages_rs/nextclade/src/io/nextclade_csv.rs:805:10
[INFO] [stdout]     |
[INFO] [stdout] 805 |          name,
[INFO] [stdout]     |          ^^^^ help: try ignoring the field: `name: _`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]    --> packages_rs/nextclade/src/io/results_json.rs:132:10
[INFO] [stdout]     |
[INFO] [stdout] 132 |     for (i, output_or_error) in output_or_errors {
[INFO] [stdout]     |          ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `total`
[INFO] [stdout]   --> packages_rs/nextclade/src/qc/qc_rule_mixed_sites.rs:35:20
[INFO] [stdout]    |
[INFO] [stdout] 35 |     .filter(|(nuc, total)| !(nuc.is_acgtn() || nuc.is_gap()))
[INFO] [stdout]    |                    ^^^^^ help: if this is intentional, prefix it with an underscore: `_total`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]    --> packages_rs/nextclade/src/io/gff3.rs:172:15
[INFO] [stdout]     |
[INFO] [stdout] 172 |     .filter(|(i, record)| {
[INFO] [stdout]     |               ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 10 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `column`
[INFO] [stdout]    --> packages_rs/nextclade/src/io/nextclade_csv.rs:238:17
[INFO] [stdout]     |
[INFO] [stdout] 238 |       .filter(|(column, enabled)| **enabled)
[INFO] [stdout]     |                 ^^^^^^ help: if this is intentional, prefix it with an underscore: `_column`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `name`
[INFO] [stdout]    --> packages_rs/nextclade/src/io/nextclade_csv.rs:805:10
[INFO] [stdout]     |
[INFO] [stdout] 805 |          name,
[INFO] [stdout]     |          ^^^^ help: try ignoring the field: `name: _`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]    --> packages_rs/nextclade/src/io/results_json.rs:132:10
[INFO] [stdout]     |
[INFO] [stdout] 132 |     for (i, output_or_error) in output_or_errors {
[INFO] [stdout]     |          ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `total`
[INFO] [stdout]   --> packages_rs/nextclade/src/qc/qc_rule_mixed_sites.rs:35:20
[INFO] [stdout]    |
[INFO] [stdout] 35 |     .filter(|(nuc, total)| !(nuc.is_acgtn() || nuc.is_gap()))
[INFO] [stdout]    |                    ^^^^^ help: if this is intentional, prefix it with an underscore: `_total`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> packages_rs/nextclade/src/tree/tree_builder.rs:393:9
[INFO] [stdout]     |
[INFO] [stdout] 393 |     let mut target_node_auspice = target_node.payload_mut();
[INFO] [stdout]     |         ----^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_mut)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `current_exe`
[INFO] [stdout]   --> packages_rs/nextclade/src/utils/global_init.rs:45:11
[INFO] [stdout]    |
[INFO] [stdout] 45 |       let current_exe = get_current_exe_filename().unwrap_or_default().dimmed().to_string();
[INFO] [stdout]    |           ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_current_exe`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> packages_rs/nextclade/src/tree/tree_builder.rs:393:9
[INFO] [stdout]     |
[INFO] [stdout] 393 |     let mut target_node_auspice = target_node.payload_mut();
[INFO] [stdout]     |         ----^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_mut)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `current_exe`
[INFO] [stdout]   --> packages_rs/nextclade/src/utils/global_init.rs:45:11
[INFO] [stdout]    |
[INFO] [stdout] 45 |       let current_exe = get_current_exe_filename().unwrap_or_default().dimmed().to_string();
[INFO] [stdout]    |           ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_current_exe`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `index_to_shift` is never used
[INFO] [stdout]  --> packages_rs/nextclade/src/align/backtrace.rs:9:10
[INFO] [stdout]   |
[INFO] [stdout] 9 | const fn index_to_shift(si: i32, band_width: i32, mean_shift: i32) -> i32 {
[INFO] [stdout]   |          ^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_map_to_good_positions` is never used
[INFO] [stdout]   --> packages_rs/nextclade/src/align/seed_alignment.rs:22:4
[INFO] [stdout]    |
[INFO] [stdout] 22 | fn get_map_to_good_positions<L: Letter<L>>(qry_seq: &[L], seed_length: usize) -> Vec<usize> {
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `trace_stripe_stats` is never used
[INFO] [stdout]    --> packages_rs/nextclade/src/align/seed_alignment.rs:249:4
[INFO] [stdout]     |
[INFO] [stdout] 249 | fn trace_stripe_stats(stripes: &[Stripe]) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `trace_matches` is never used
[INFO] [stdout]    --> packages_rs/nextclade/src/align/seed_alignment.rs:266:4
[INFO] [stdout]     |
[INFO] [stdout] 266 | fn trace_matches(matches: &[SeedMatch2]) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `write_stripes_to_file` is never used
[INFO] [stdout]    --> packages_rs/nextclade/src/align/seed_alignment.rs:278:4
[INFO] [stdout]     |
[INFO] [stdout] 278 | fn write_stripes_to_file(stripes: &[Stripe], filename: &str) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `muts`, `masked_muts`, and `other_muts` are never read
[INFO] [stdout]  --> packages_rs/nextclade/src/analyze/divergence.rs:7:3
[INFO] [stdout]   |
[INFO] [stdout] 6 | pub struct NucMutsCounted<'a> {
[INFO] [stdout]   |            -------------- fields in this struct
[INFO] [stdout] 7 |   muts: Vec<&'a NucSub>,
[INFO] [stdout]   |   ^^^^
[INFO] [stdout] 8 |   masked_muts: Vec<&'a NucSub>,
[INFO] [stdout]   |   ^^^^^^^^^^^
[INFO] [stdout] 9 |   other_muts: Vec<&'a NucSub>,
[INFO] [stdout]   |   ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `PASS_ICON` is never used
[INFO] [stdout]   --> packages_rs/nextclade/src/features/feature_tree_format.rs:88:7
[INFO] [stdout]    |
[INFO] [stdout] 88 | const PASS_ICON: &str = "│  ";
[INFO] [stdout]    |       ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `FORK_ICON` is never used
[INFO] [stdout]   --> packages_rs/nextclade/src/features/feature_tree_format.rs:89:7
[INFO] [stdout]    |
[INFO] [stdout] 89 | const FORK_ICON: &str = "├──";
[INFO] [stdout]    |       ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `IMPASSE_ICON` is never used
[INFO] [stdout]   --> packages_rs/nextclade/src/features/feature_tree_format.rs:90:7
[INFO] [stdout]    |
[INFO] [stdout] 90 | const IMPASSE_ICON: &str = "└──";
[INFO] [stdout]    |       ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_records_by_feature_type` is never used
[INFO] [stdout]    --> packages_rs/nextclade/src/io/gff3.rs:166:4
[INFO] [stdout]     |
[INFO] [stdout] 166 | fn get_records_by_feature_type<'r>(
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `present_genes` is never read
[INFO] [stdout]   --> packages_rs/nextclade/src/run/nextclade_run_one.rs:49:3
[INFO] [stdout]    |
[INFO] [stdout] 39 | struct NextcladeResultWithAa {
[INFO] [stdout]    |        --------------------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 49 |   present_genes: HashSet<String>,
[INFO] [stdout]    |   ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `index_to_shift` is never used
[INFO] [stdout]  --> packages_rs/nextclade/src/align/backtrace.rs:9:10
[INFO] [stdout]   |
[INFO] [stdout] 9 | const fn index_to_shift(si: i32, band_width: i32, mean_shift: i32) -> i32 {
[INFO] [stdout]   |          ^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_map_to_good_positions` is never used
[INFO] [stdout]   --> packages_rs/nextclade/src/align/seed_alignment.rs:22:4
[INFO] [stdout]    |
[INFO] [stdout] 22 | fn get_map_to_good_positions<L: Letter<L>>(qry_seq: &[L], seed_length: usize) -> Vec<usize> {
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `trace_stripe_stats` is never used
[INFO] [stdout]    --> packages_rs/nextclade/src/align/seed_alignment.rs:249:4
[INFO] [stdout]     |
[INFO] [stdout] 249 | fn trace_stripe_stats(stripes: &[Stripe]) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `trace_matches` is never used
[INFO] [stdout]    --> packages_rs/nextclade/src/align/seed_alignment.rs:266:4
[INFO] [stdout]     |
[INFO] [stdout] 266 | fn trace_matches(matches: &[SeedMatch2]) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `write_stripes_to_file` is never used
[INFO] [stdout]    --> packages_rs/nextclade/src/align/seed_alignment.rs:278:4
[INFO] [stdout]     |
[INFO] [stdout] 278 | fn write_stripes_to_file(stripes: &[Stripe], filename: &str) {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `muts`, `masked_muts`, and `other_muts` are never read
[INFO] [stdout]  --> packages_rs/nextclade/src/analyze/divergence.rs:7:3
[INFO] [stdout]   |
[INFO] [stdout] 6 | pub struct NucMutsCounted<'a> {
[INFO] [stdout]   |            -------------- fields in this struct
[INFO] [stdout] 7 |   muts: Vec<&'a NucSub>,
[INFO] [stdout]   |   ^^^^
[INFO] [stdout] 8 |   masked_muts: Vec<&'a NucSub>,
[INFO] [stdout]   |   ^^^^^^^^^^^
[INFO] [stdout] 9 |   other_muts: Vec<&'a NucSub>,
[INFO] [stdout]   |   ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `PASS_ICON` is never used
[INFO] [stdout]   --> packages_rs/nextclade/src/features/feature_tree_format.rs:88:7
[INFO] [stdout]    |
[INFO] [stdout] 88 | const PASS_ICON: &str = "│  ";
[INFO] [stdout]    |       ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `FORK_ICON` is never used
[INFO] [stdout]   --> packages_rs/nextclade/src/features/feature_tree_format.rs:89:7
[INFO] [stdout]    |
[INFO] [stdout] 89 | const FORK_ICON: &str = "├──";
[INFO] [stdout]    |       ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `IMPASSE_ICON` is never used
[INFO] [stdout]   --> packages_rs/nextclade/src/features/feature_tree_format.rs:90:7
[INFO] [stdout]    |
[INFO] [stdout] 90 | const IMPASSE_ICON: &str = "└──";
[INFO] [stdout]    |       ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_records_by_feature_type` is never used
[INFO] [stdout]    --> packages_rs/nextclade/src/io/gff3.rs:166:4
[INFO] [stdout]     |
[INFO] [stdout] 166 | fn get_records_by_feature_type<'r>(
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `present_genes` is never read
[INFO] [stdout]   --> packages_rs/nextclade/src/run/nextclade_run_one.rs:49:3
[INFO] [stdout]    |
[INFO] [stdout] 39 | struct NextcladeResultWithAa {
[INFO] [stdout]    |        --------------------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 49 |   present_genes: HashSet<String>,
[INFO] [stdout]    |   ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 98 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Checking nextclade-cli v3.0.0-alpha.0 (/opt/rustwide/workdir/packages_rs/nextclade-cli)
[INFO] [stderr]  Documenting nextclade-cli v3.0.0-alpha.0 (/opt/rustwide/workdir/packages_rs/nextclade-cli)
[INFO] [stdout] error: proc-macro derive panicked
[INFO] [stdout]   --> packages_rs/nextclade-cli/src/cli/nextclade_cli.rs:29:32
[INFO] [stdout]    |
[INFO] [stdout] 29 | const DATA_FULL_DOMAIN: &str = getenv!("DATA_FULL_DOMAIN");
[INFO] [stdout]    |                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: message: Error loading .env file: path not found
[INFO] [stdout]    = note: this error originates in the macro `dotenv_codegen::dotenv` which comes from the expansion of the macro `getenv` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error: proc-macro derive panicked
[INFO] [stdout]   --> packages_rs/nextclade-cli/src/cli/nextclade_cli.rs:29:32
[INFO] [stdout]    |
[INFO] [stdout] 29 | const DATA_FULL_DOMAIN: &str = getenv!("DATA_FULL_DOMAIN");
[INFO] [stdout]    |                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: message: Error loading .env file: path not found
[INFO] [stdout]    = note: this error originates in the macro `dotenv_codegen::dotenv` which comes from the expansion of the macro `getenv` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error: cannot find macro `proc_macro_call` in this scope
[INFO] [stdout]   --> packages_rs/nextclade-cli/src/cli/nextclade_cli.rs:29:32
[INFO] [stdout]    |
[INFO] [stdout] 29 | const DATA_FULL_DOMAIN: &str = getenv!("DATA_FULL_DOMAIN");
[INFO] [stdout]    |                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: this error originates in the macro `dotenv_codegen::dotenv` which comes from the expansion of the macro `getenv` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error: cannot find macro `proc_macro_call` in this scope
[INFO] [stdout]   --> packages_rs/nextclade-cli/src/cli/nextclade_cli.rs:29:32
[INFO] [stdout]    |
[INFO] [stdout] 29 | const DATA_FULL_DOMAIN: &str = getenv!("DATA_FULL_DOMAIN");
[INFO] [stdout]    |                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: this error originates in the macro `dotenv_codegen::dotenv` which comes from the expansion of the macro `getenv` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Generator`
[INFO] [stdout]   --> packages_rs/nextclade-cli/src/cli/nextclade_cli.rs:11:31
[INFO] [stdout]    |
[INFO] [stdout] 11 | use clap_complete::{generate, Generator, Shell};
[INFO] [stdout]    |                               ^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 2 previous errors
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr] error: could not document `nextclade-cli`
[INFO] [stderr] 
[INFO] [stderr] Caused by:
[INFO] [stderr]   process didn't exit successfully: `/opt/rustwide/rustup-home/toolchains/1.75.0-x86_64-unknown-linux-gnu/bin/rustdoc --edition=2021 --crate-type lib --crate-name nextclade_cli packages_rs/nextclade-cli/src/lib.rs -o /opt/rustwide/target/doc --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --document-private-items -C metadata=31b5d9ced25d0749 -L dependency=/opt/rustwide/target/debug/deps --extern assert2=/opt/rustwide/target/debug/deps/libassert2-522e945f275c92b0.rmeta --extern clap=/opt/rustwide/target/debug/deps/libclap-ca692e6f3a9a10e0.rmeta --extern clap_markdown=/opt/rustwide/target/debug/deps/libclap_markdown-a0df1714ab2210d3.rmeta --extern clap_complete=/opt/rustwide/target/debug/deps/libclap_complete-61cf874865b57427.rmeta --extern clap_complete_fig=/opt/rustwide/target/debug/deps/libclap_complete_fig-c983e9833326ce89.rmeta --extern color_eyre=/opt/rustwide/target/debug/deps/libcolor_eyre-ef92514a990dfc19.rmeta --extern comfy_table=/opt/rustwide/target/debug/deps/libcomfy_table-a8016eec6425c912.rmeta --extern crossbeam=/opt/rustwide/target/debug/deps/libcrossbeam-833dbaa19a6d2d54.rmeta --extern crossbeam_channel=/opt/rustwide/target/debug/deps/libcrossbeam_channel-381e7d2640192fd2.rmeta --extern ctor=/opt/rustwide/target/debug/deps/libctor-d2b2d1987cef190d.so --extern dotenv=/opt/rustwide/target/debug/deps/libdotenv-5c7b155fb9ea380a.rmeta --extern dotenv_codegen=/opt/rustwide/target/debug/deps/libdotenv_codegen-e0122fb8f4a27a9f.rmeta --extern eyre=/opt/rustwide/target/debug/deps/libeyre-340c1b64073526b8.rmeta --extern indexmap=/opt/rustwide/target/debug/deps/libindexmap-ee1bd4a169c14dc0.rmeta --extern itertools=/opt/rustwide/target/debug/deps/libitertools-df1c8772faf6b77b.rmeta --extern lazy_static=/opt/rustwide/target/debug/deps/liblazy_static-e7445b4e8703c20b.rmeta --extern log=/opt/rustwide/target/debug/deps/liblog-e31d57e8ecf90e98.rmeta --extern nextclade=/opt/rustwide/target/debug/deps/libnextclade-d3f877bc5d27c9ef.rmeta --extern num_cpus=/opt/rustwide/target/debug/deps/libnum_cpus-3aa8d7b073bd91ee.rmeta --extern ordered_float=/opt/rustwide/target/debug/deps/libordered_float-147b5f00562a5db1.rmeta --extern owo_colors=/opt/rustwide/target/debug/deps/libowo_colors-71927e04e8b19f1d.rmeta --extern pretty_assertions=/opt/rustwide/target/debug/deps/libpretty_assertions-d29f17d9b87d0a08.rmeta --extern rayon=/opt/rustwide/target/debug/deps/librayon-3d31c2ab0df9dc04.rmeta --extern regex=/opt/rustwide/target/debug/deps/libregex-a6a7c58205cdd988.rmeta --extern reqwest=/opt/rustwide/target/debug/deps/libreqwest-420210fa736148b4.rmeta --extern schemars=/opt/rustwide/target/debug/deps/libschemars-71e1be00d933b4c8.rmeta --extern semver=/opt/rustwide/target/debug/deps/libsemver-bee38f98805d6da1.rmeta --extern serde=/opt/rustwide/target/debug/deps/libserde-7a9c60faf7796a6c.rmeta --extern serde_json=/opt/rustwide/target/debug/deps/libserde_json-9b4757d3a69dc305.rmeta --extern strum=/opt/rustwide/target/debug/deps/libstrum-a0f1e7c96a0fb5f5.rmeta --extern strum_macros=/opt/rustwide/target/debug/deps/libstrum_macros-11fe28d472db831e.so --extern tinytemplate=/opt/rustwide/target/debug/deps/libtinytemplate-f53eda9522b590f4.rmeta --extern url=/opt/rustwide/target/debug/deps/liburl-1adc59651666bd6c.rmeta --extern zip=/opt/rustwide/target/debug/deps/libzip-ff23306d24994c48.rmeta --cap-lints=warn --crate-version 3.0.0-alpha.0` (exit status: 1)
[INFO] [stderr] warning: build failed, waiting for other jobs to finish...
[INFO] [stdout] warning: unused import: `std::hash::Hasher`
[INFO] [stdout]   --> packages_rs/nextclade-cli/src/cli/nextclade_ordered_writer.rs:21:5
[INFO] [stdout]    |
[INFO] [stdout] 21 | use std::hash::Hasher;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::str::FromStr`
[INFO] [stdout]   --> packages_rs/nextclade-cli/src/dataset/dataset_download.rs:22:5
[INFO] [stdout]    |
[INFO] [stdout] 22 | use std::str::FromStr;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rayon::iter::ParallelIterator`
[INFO] [stdout]   --> packages_rs/nextclade-cli/src/dataset/dataset_download.rs:17:5
[INFO] [stdout]    |
[INFO] [stdout] 17 | use rayon::iter::ParallelIterator;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `itertools::Itertools`
[INFO] [stdout]  --> packages_rs/nextclade-cli/src/dataset/dataset_download.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 5 | use itertools::Itertools;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 2 previous errors; 5 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `nextclade-cli` (lib) due to 3 previous errors; 5 warnings emitted
[INFO] [stdout] warning: 98 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "ebb24071decf8862f21d038c13303014a103d49657135b340644e8ae8a5e893d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "ebb24071decf8862f21d038c13303014a103d49657135b340644e8ae8a5e893d", kill_on_drop: false }`
[INFO] [stdout] ebb24071decf8862f21d038c13303014a103d49657135b340644e8ae8a5e893d
