[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] 7d190705ebd011d57fc79868254a0f19771f00d2 [INFO] checking 2lambda123/nextclade against master#af4a5a13a15fa0c60e06321077ef452f769b42fd for pr-122960-3 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2F2lambda123%2Fnextclade" "/workspace/builds/worker-2-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-2-tc1/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/2lambda123/nextclade on toolchain af4a5a13a15fa0c60e06321077ef452f769b42fd [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+af4a5a13a15fa0c60e06321077ef452f769b42fd" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] removed /workspace/builds/worker-2-tc1/source/.cargo/config.toml [INFO] removed /workspace/builds/worker-2-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-2-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" "+af4a5a13a15fa0c60e06321077ef452f769b42fd" "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 traversal v0.1.2 [INFO] [stderr] Downloaded unsafe-libyaml v0.2.10 [INFO] [stderr] Downloaded serde_stacker v0.1.8 [INFO] [stderr] Downloaded wasm-logger v0.2.0 [INFO] [stderr] Downloaded rstest_reuse v0.5.0 [INFO] [stderr] Downloaded strum_macros v0.25.0 [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded serde_yaml v0.9.22 [INFO] [stderr] Downloaded assert2-macros v0.3.11 [INFO] [stderr] Downloaded assert2 v0.3.11 [INFO] [stderr] Downloaded clap-markdown v0.1.3 [INFO] [stderr] Downloaded triple_accel v0.4.0 [INFO] [stderr] Downloaded comfy-table v7.0.1 [INFO] [stderr] Downloaded safe_arch v0.7.0 [INFO] [stderr] Downloaded rustls v0.21.2 [INFO] [stderr] Downloaded rustix v0.38.1 [INFO] [stderr] Downloaded bio v1.3.1 [INFO] [stderr] Downloaded csv v1.2.2 [INFO] [stderr] Downloaded wide v0.7.10 [INFO] [stderr] Downloaded auto_ops v0.3.0 [INFO] [stderr] Downloaded editdistancek v1.0.2 [INFO] [stderr] Downloaded clap_complete v4.4.1 [INFO] [stderr] Downloaded bio-types v1.0.0 [INFO] [stderr] Downloaded clap_complete_fig v4.4.0 [INFO] [stderr] Downloaded ctor v0.2.2 [INFO] [stderr] Downloaded gcollections v1.5.0 [INFO] [stderr] Downloaded intervallum v1.4.0 [INFO] [stderr] Downloaded optfield v0.3.0 [INFO] [stderr] Downloaded edit-distance v2.1.0 [INFO] [stderr] Downloaded trilean v1.1.0 [INFO] [stderr] Downloaded zstd-safe v6.0.5+zstd.1.5.4 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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" "+af4a5a13a15fa0c60e06321077ef452f769b42fd" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] c03e27fa62fd69391327bae3e26ed38b1f02484b920bc849fa218787c829fd0c [INFO] running `Command { std: "docker" "start" "-a" "c03e27fa62fd69391327bae3e26ed38b1f02484b920bc849fa218787c829fd0c", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "c03e27fa62fd69391327bae3e26ed38b1f02484b920bc849fa218787c829fd0c", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "c03e27fa62fd69391327bae3e26ed38b1f02484b920bc849fa218787c829fd0c", kill_on_drop: false }` [INFO] [stdout] c03e27fa62fd69391327bae3e26ed38b1f02484b920bc849fa218787c829fd0c [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+af4a5a13a15fa0c60e06321077ef452f769b42fd" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] d05fa8e04d92f5aaf2a0ccd2ac2afd1023ea2b79b292464502f2ed38084b3c58 [INFO] running `Command { std: "docker" "start" "-a" "d05fa8e04d92f5aaf2a0ccd2ac2afd1023ea2b79b292464502f2ed38084b3c58", 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] Compiling proc-macro2 v1.0.63 [INFO] [stderr] Compiling unicode-ident v1.0.9 [INFO] [stderr] Compiling quote v1.0.29 [INFO] [stderr] Compiling libc v0.2.153 [INFO] [stderr] Compiling autocfg v1.1.0 [INFO] [stderr] Compiling serde v1.0.164 [INFO] [stderr] Compiling version_check v0.9.4 [INFO] [stderr] Compiling libm v0.2.7 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Compiling memchr v2.5.0 [INFO] [stderr] Compiling cfg-if v1.0.0 [INFO] [stderr] Compiling num-traits v0.2.15 [INFO] [stderr] Compiling typenum v1.16.0 [INFO] [stderr] Compiling generic-array v0.14.7 [INFO] [stderr] Compiling num-integer v0.1.45 [INFO] [stderr] Compiling serde_json v1.0.99 [INFO] [stderr] Compiling pkg-config v0.3.27 [INFO] [stderr] Compiling syn v2.0.22 [INFO] [stderr] Checking itoa v1.0.6 [INFO] [stderr] Compiling once_cell v1.18.0 [INFO] [stderr] Checking equivalent v1.0.0 [INFO] [stderr] Checking hashbrown v0.14.0 [INFO] [stderr] Compiling crossbeam-utils v0.8.16 [INFO] [stderr] Compiling semver v1.0.17 [INFO] [stderr] Checking ryu v1.0.13 [INFO] [stderr] Checking pin-project-lite v0.2.10 [INFO] [stderr] Checking indexmap v2.0.0 [INFO] [stderr] Compiling wasm-bindgen-shared v0.2.87 [INFO] [stderr] Compiling jobserver v0.1.26 [INFO] [stderr] Compiling unicase v2.7.0 [INFO] [stderr] Compiling cc v1.0.79 [INFO] [stderr] Compiling memoffset v0.9.0 [INFO] [stderr] Compiling num-bigint v0.4.3 [INFO] [stderr] Checking log v0.4.19 [INFO] [stderr] Compiling bumpalo v3.13.0 [INFO] [stderr] Compiling ident_case v1.0.1 [INFO] [stderr] Compiling fnv v1.0.7 [INFO] [stderr] Compiling num-rational v0.4.1 [INFO] [stderr] Compiling crossbeam-epoch v0.9.15 [INFO] [stderr] Compiling matrixmultiply v0.3.7 [INFO] [stderr] Compiling indexmap v1.9.3 [INFO] [stderr] Compiling lazy_static v1.4.0 [INFO] [stderr] Compiling paste v1.0.12 [INFO] [stderr] Compiling rustix v0.38.1 [INFO] [stderr] Compiling wasm-bindgen v0.2.87 [INFO] [stderr] Compiling getrandom v0.2.10 [INFO] [stderr] Checking num_cpus v1.16.0 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Compiling rustversion v1.0.12 [INFO] [stderr] Compiling thiserror v1.0.40 [INFO] [stderr] Compiling crc32fast v1.3.2 [INFO] [stderr] Compiling zstd-sys v2.0.8+zstd.1.5.5 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Compiling futures-core v0.3.28 [INFO] [stderr] Compiling wasm-bindgen-backend v0.2.87 [INFO] [stderr] Compiling darling_core v0.20.1 [INFO] [stderr] Compiling psm v0.1.21 [INFO] [stderr] Compiling bzip2-sys v0.1.11+1.0.8 [INFO] [stderr] Compiling serde_derive_internals v0.26.0 [INFO] [stderr] Compiling aho-corasick v1.0.2 [INFO] [stderr] Checking tracing-core v0.1.31 [INFO] [stderr] Compiling schemars v0.8.12 [INFO] [stderr] Checking either v1.8.1 [INFO] [stderr] Compiling wasm-bindgen-macro-support v0.2.87 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling regex-syntax v0.7.2 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling serde_derive v1.0.164 [INFO] [stderr] Compiling wasm-bindgen-macro v0.2.87 [INFO] [stderr] Compiling thiserror-impl v1.0.40 [INFO] [stderr] Compiling clap_derive v4.4.2 [INFO] [stderr] Compiling schemars_derive v0.8.12 [INFO] [stderr] Compiling darling_macro v0.20.1 [INFO] [stderr] Compiling nalgebra-macros v0.1.0 [INFO] [stderr] Compiling regex v1.8.4 [INFO] [stderr] Compiling darling v0.20.1 [INFO] [stderr] Compiling enumset_derive v0.8.1 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling rayon-core v1.11.0 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Compiling strum_macros v0.24.3 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Checking tracing v0.1.37 [INFO] [stderr] Checking crypto-common v0.1.6 [INFO] [stderr] Compiling backtrace v0.3.68 [INFO] [stderr] Compiling stacker v0.1.15 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling slab v0.4.8 [INFO] [stderr] Compiling num-iter v0.1.43 [INFO] [stderr] Compiling eyre v0.6.8 [INFO] [stderr] Compiling anyhow v1.0.71 [INFO] [stderr] Compiling futures-task v0.3.28 [INFO] [stderr] Compiling ppv-lite86 v0.2.17 [INFO] [stderr] Compiling zstd-safe v6.0.5+zstd.1.5.4 [INFO] [stderr] Compiling futures-channel v0.3.28 [INFO] [stderr] Checking futures-sink v0.3.28 [INFO] [stderr] Checking anstyle-parse v0.2.1 [INFO] [stderr] Compiling enum-map-derive v0.6.0 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Checking adler v1.0.2 [INFO] [stderr] Checking subtle v2.5.0 [INFO] [stderr] Checking anstyle-query v1.0.0 [INFO] [stderr] Checking unicode-width v0.1.10 [INFO] [stderr] Checking anstyle v1.0.1 [INFO] [stderr] Compiling futures-util v0.3.28 [INFO] [stderr] Checking anstream v0.5.0 [INFO] [stderr] Checking miniz_oxide v0.7.1 [INFO] [stderr] Compiling futures-macro v0.3.28 [INFO] [stderr] Compiling validator_types v0.16.0 [INFO] [stderr] Checking block-buffer v0.10.4 [INFO] [stderr] Checking num-complex v0.4.3 [INFO] [stderr] Checking tinyvec_macros v0.1.1 [INFO] [stderr] Compiling if_chain v1.0.2 [INFO] [stderr] Checking clap_lex v0.5.0 [INFO] [stderr] Checking bytemuck v1.13.1 [INFO] [stderr] Checking futures-io v0.3.28 [INFO] [stderr] Checking clap_builder v4.4.2 [INFO] [stderr] Checking tinyvec v1.6.0 [INFO] [stderr] Checking safe_arch v0.7.0 [INFO] [stderr] Compiling validator_derive v0.16.0 [INFO] [stderr] Checking digest v0.10.7 [INFO] [stderr] Compiling getset v0.1.2 [INFO] [stderr] Compiling strum_macros v0.25.0 [INFO] [stderr] Checking mio v0.8.11 [INFO] [stderr] Checking bitflags v2.3.3 [INFO] [stderr] Checking hashbrown v0.12.3 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Checking cpufeatures v0.2.8 [INFO] [stderr] Checking percent-encoding v2.3.0 [INFO] [stderr] Checking linux-raw-sys v0.4.3 [INFO] [stderr] Checking form_urlencoded v1.2.0 [INFO] [stderr] Checking clap v4.4.2 [INFO] [stderr] Checking crossbeam-deque v0.8.3 [INFO] [stderr] Checking unicode-normalization v0.1.22 [INFO] [stderr] Checking wide v0.7.10 [INFO] [stderr] Checking crossbeam-channel v0.5.8 [INFO] [stderr] Checking rand_core v0.6.4 [INFO] [stderr] Checking sharded-slab v0.1.4 [INFO] [stderr] Checking rand_chacha v0.3.1 [INFO] [stderr] Checking rand v0.8.5 [INFO] [stderr] Compiling ring v0.16.20 [INFO] [stderr] Checking approx v0.5.1 [INFO] [stderr] Checking thread_local v1.1.7 [INFO] [stderr] Checking unicode-bidi v0.3.13 [INFO] [stderr] Checking bytes v1.4.0 [INFO] [stderr] Compiling convert_case v0.4.0 [INFO] [stderr] Checking iana-time-zone v0.1.57 [INFO] [stderr] Checking bit-vec v0.6.3 [INFO] [stderr] Checking chrono v0.4.26 [INFO] [stderr] Checking bit-set v0.5.3 [INFO] [stderr] Checking simba v0.6.0 [INFO] [stderr] Compiling derive_more v0.99.17 [INFO] [stderr] Compiling rustc_version v0.4.0 [INFO] [stderr] Checking rand_distr v0.4.3 [INFO] [stderr] Checking idna v0.4.0 [INFO] [stderr] Compiling assert2-macros v0.3.11 [INFO] [stderr] Checking tracing-subscriber v0.3.17 [INFO] [stderr] Checking flate2 v1.0.26 [INFO] [stderr] Checking is-terminal v0.4.8 [INFO] [stderr] Checking enumset v1.1.2 [INFO] [stderr] Compiling serde_repr v0.1.12 [INFO] [stderr] Compiling optfield v0.3.0 [INFO] [stderr] Compiling ctor v0.2.2 [INFO] [stderr] Checking inout v0.1.3 [INFO] [stderr] Compiling tokio v1.29.1 [INFO] [stderr] Checking byteorder v1.4.3 [INFO] [stderr] Checking base64ct v1.6.0 [INFO] [stderr] Checking gimli v0.27.3 [INFO] [stderr] Checking dyn-clone v1.0.11 [INFO] [stderr] Checking password-hash v0.4.2 [INFO] [stderr] Checking cipher v0.4.4 [INFO] [stderr] Checking tracing-error v0.2.0 [INFO] [stderr] Checking url v2.4.0 [INFO] [stderr] Checking sha2 v0.10.7 [INFO] [stderr] Checking hmac v0.12.1 [INFO] [stderr] Checking socket2 v0.4.9 [INFO] [stderr] Checking object v0.31.1 [INFO] [stderr] Checking csv-core v0.1.10 [INFO] [stderr] Checking indenter v0.3.3 [INFO] [stderr] Checking spin v0.5.2 [INFO] [stderr] Checking fixedbitset v0.4.2 [INFO] [stderr] Checking rustc-demangle v0.1.23 [INFO] [stderr] Checking untrusted v0.7.1 [INFO] [stderr] Checking time-core v0.1.1 [INFO] [stderr] Checking owo-colors v3.5.0 [INFO] [stderr] Checking trilean v1.1.0 [INFO] [stderr] Checking yansi v0.5.1 [INFO] [stderr] Checking gcollections v1.5.0 [INFO] [stderr] Checking time v0.3.22 [INFO] [stderr] Checking petgraph v0.6.3 [INFO] [stderr] Checking color-spantrace v0.2.0 [INFO] [stderr] Checking csv v1.2.2 [INFO] [stderr] Checking rayon v1.7.0 [INFO] [stderr] Checking pbkdf2 v0.11.0 [INFO] [stderr] Checking addr2line v0.20.0 [INFO] [stderr] Checking ordered-float v3.9.1 [INFO] [stderr] Checking aes v0.8.3 [INFO] [stderr] Checking fxhash v0.2.1 [INFO] [stderr] Checking tinytemplate v1.2.1 [INFO] [stderr] Checking bio-types v1.0.0 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking multimap v0.8.3 [INFO] [stderr] Checking ndarray v0.15.6 [INFO] [stderr] Checking clap_complete v4.4.1 [INFO] [stderr] Checking sha1 v0.10.5 [INFO] [stderr] Checking enum-map v1.1.1 [INFO] [stderr] Checking nalgebra v0.29.0 [INFO] [stderr] Checking itertools v0.11.0 [INFO] [stderr] Checking itertools-num v0.1.3 [INFO] [stderr] Checking triple_accel v0.4.0 [INFO] [stderr] Checking termcolor v1.2.0 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking unsafe-libyaml v0.2.10 [INFO] [stderr] Checking editdistancek v1.0.2 [INFO] [stderr] Checking constant_time_eq v0.1.5 [INFO] [stderr] Checking diff v0.1.13 [INFO] [stderr] Checking humantime v2.1.0 [INFO] [stderr] Checking bytecount v0.6.3 [INFO] [stderr] Checking strum v0.25.0 [INFO] [stderr] Checking pretty_assertions v1.3.0 [INFO] [stderr] Checking env_logger v0.10.0 [INFO] [stderr] Checking color-eyre v0.6.2 [INFO] [stderr] Checking num v0.4.0 [INFO] [stderr] Checking clap_complete_fig v4.4.0 [INFO] [stderr] Checking serde_stacker v0.1.8 [INFO] [stderr] Checking intervallum v1.4.0 [INFO] [stderr] Checking assert2 v0.3.11 [INFO] [stderr] Checking validator v0.16.1 [INFO] [stderr] Checking serde_yaml v0.9.22 [INFO] [stderr] Checking atty v0.2.14 [INFO] [stderr] Checking urlencoding v2.1.2 [INFO] [stderr] Checking auto_ops v0.3.0 [INFO] [stderr] Checking traversal v0.1.2 [INFO] [stderr] Compiling utf8parse v0.2.1 [INFO] [stderr] Checking edit-distance v2.1.0 [INFO] [stderr] Checking maplit v1.0.2 [INFO] [stderr] Compiling colorchoice v1.0.0 [INFO] [stderr] Checking http v0.2.9 [INFO] [stderr] Compiling rstest_macros v0.17.0 [INFO] [stderr] Compiling lock_api v0.4.10 [INFO] [stderr] Compiling scopeguard v1.1.0 [INFO] [stderr] Compiling signal-hook v0.3.15 [INFO] [stderr] Compiling parking_lot_core v0.9.8 [INFO] [stderr] Checking half v1.8.2 [INFO] [stderr] Checking ciborium-io v0.2.1 [INFO] [stderr] Compiling rustls v0.21.2 [INFO] [stderr] Checking alloc-no-stdlib v2.0.4 [INFO] [stderr] Checking plotters-backend v0.3.5 [INFO] [stderr] Compiling httparse v1.8.0 [INFO] [stderr] Compiling strsim v0.10.0 [INFO] [stderr] Checking plotters-svg v0.3.5 [INFO] [stderr] Checking alloc-stdlib v0.2.2 [INFO] [stderr] Checking ciborium-ll v0.2.1 [INFO] [stderr] Checking tokio-util v0.7.8 [INFO] [stderr] Checking sct v0.7.0 [INFO] [stderr] Checking rustls-webpki v0.100.1 [INFO] [stderr] 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Compiling crossbeam-queue v0.3.8 [INFO] [stderr] Checking httpdate v1.0.2 [INFO] [stderr] Checking tower-service v0.3.2 [INFO] [stderr] Checking anes v0.1.6 [INFO] [stderr] Checking rstest v0.17.0 [INFO] [stderr] Checking criterion v0.5.1 [INFO] [stderr] Checking hyper v0.14.27 [INFO] [stderr] Checking brotli v3.3.4 [INFO] [stderr] Checking tokio-rustls v0.24.1 [INFO] [stderr] Checking parking_lot v0.12.1 [INFO] [stderr] Checking signal-hook-mio v0.2.3 [INFO] [stderr] Checking webpki v0.22.0 [INFO] [stderr] Checking bitflags v1.3.2 [INFO] [stderr] Checking base64 v0.21.2 [INFO] [stderr] Compiling dotenv v0.15.0 [INFO] [stderr] Checking rustls-pemfile v1.0.3 [INFO] [stderr] Checking crossterm v0.26.1 [INFO] [stderr] Checking async-compression v0.4.0 [INFO] [stderr] Compiling dotenv_codegen_implementation v0.15.0 [INFO] [stderr] Checking webpki-roots v0.22.6 [INFO] [stderr] Checking hyper-rustls v0.24.0 [INFO] [stderr] Checking tokio-socks v0.5.1 [INFO] [stderr] Checking serde_urlencoded 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(/opt/rustwide/workdir/packages_rs/nextclade) [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 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: `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: `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/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: the item `strum` is imported redundantly [INFO] [stdout] --> packages_rs/nextclade/src/io/nextclade_csv.rs:33:5 [INFO] [stdout] | [INFO] [stdout] 33 | use strum; [INFO] [stdout] | ^^^^^ the item `strum` is already defined by prelude [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: `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: the item `Report` is imported redundantly [INFO] [stdout] --> packages_rs/nextclade/src/align/align.rs:148:7 [INFO] [stdout] | [INFO] [stdout] 143 | use super::*; [INFO] [stdout] | -------- the item `Report` is already imported here [INFO] [stdout] ... [INFO] [stdout] 148 | use eyre::Report; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [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] [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::align::score_matrix` [INFO] [stdout] --> packages_rs/nextclade/src/align/backtrace.rs:111:7 [INFO] [stdout] | [INFO] [stdout] 111 | use crate::align::score_matrix; [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: the item `NucRefGlobalRange` is imported redundantly [INFO] [stdout] --> packages_rs/nextclade/src/align/gap_open.rs:51:29 [INFO] [stdout] | [INFO] [stdout] 49 | use super::*; [INFO] [stdout] | -------- the item `NucRefGlobalRange` is already imported here [INFO] [stdout] 50 | use crate::coord::position::Position; [INFO] [stdout] 51 | use crate::coord::range::{NucRefGlobalRange, Range}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `GeneStrand` is imported redundantly [INFO] [stdout] --> packages_rs/nextclade/src/align/gap_open.rs:56:33 [INFO] [stdout] | [INFO] [stdout] 49 | use super::*; [INFO] [stdout] | -------- the item `GeneStrand` is already imported here [INFO] [stdout] ... [INFO] [stdout] 56 | use crate::gene::gene::{Gene, GeneStrand}; [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: the item `Report` is imported redundantly [INFO] [stdout] --> packages_rs/nextclade/src/align/insertions_strip.rs:148:7 [INFO] [stdout] | [INFO] [stdout] 146 | use super::*; [INFO] [stdout] | -------- the item `Report` is already imported here [INFO] [stdout] 147 | use crate::alphabet::nuc::to_nuc_seq; [INFO] [stdout] 148 | use eyre::Report; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::align::score_matrix` [INFO] [stdout] --> packages_rs/nextclade/src/align/score_matrix.rs:207:7 [INFO] [stdout] | [INFO] [stdout] 207 | use crate::align::score_matrix; [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: the item `Report` is imported redundantly [INFO] [stdout] --> packages_rs/nextclade/src/align/seed_alignment.rs:299:7 [INFO] [stdout] | [INFO] [stdout] 298 | use super::*; [INFO] [stdout] | -------- the item `Report` is already imported here [INFO] [stdout] 299 | use eyre::Report; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `from_nuc_seq` [INFO] [stdout] --> packages_rs/nextclade/src/align/seed_match.rs:69:30 [INFO] [stdout] | [INFO] [stdout] 69 | use crate::alphabet::nuc::{from_nuc_seq, to_nuc_seq}; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `fixture` [INFO] [stdout] --> packages_rs/nextclade/src/align/seed_match.rs:72:16 [INFO] [stdout] | [INFO] [stdout] 72 | use rstest::{fixture, rstest}; [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: the item `Report` is imported redundantly [INFO] [stdout] --> packages_rs/nextclade/src/align/seed_match2.rs:541:7 [INFO] [stdout] | [INFO] [stdout] 539 | use super::*; [INFO] [stdout] | -------- the item `Report` is already imported here [INFO] [stdout] 540 | use crate::alphabet::nuc::to_nuc_seq; [INFO] [stdout] 541 | use eyre::Report; [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 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: the item `WrappingPart` is imported redundantly [INFO] [stdout] --> packages_rs/nextclade/src/coord/coord_map_cds_to_global.rs:83:46 [INFO] [stdout] | [INFO] [stdout] 80 | use super::*; [INFO] [stdout] | -------- the item `WrappingPart` is already imported here [INFO] [stdout] ... [INFO] [stdout] 83 | use crate::gene::cds_segment::{CdsSegment, WrappingPart}; [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: `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: the item `Report` is imported redundantly [INFO] [stdout] --> packages_rs/nextclade/src/gene/gene_map.rs:266:7 [INFO] [stdout] | [INFO] [stdout] 265 | use super::*; [INFO] [stdout] | -------- the item `Report` is already imported here [INFO] [stdout] 266 | use eyre::Report; [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/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: the item `strum` is imported redundantly [INFO] [stdout] --> packages_rs/nextclade/src/io/nextclade_csv.rs:33:5 [INFO] [stdout] | [INFO] [stdout] 33 | use strum; [INFO] [stdout] | ^^^^^ the item `strum` is already defined by prelude [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: the item `WrappingPart` is imported redundantly [INFO] [stdout] --> packages_rs/nextclade/src/translate/extract.rs:69:46 [INFO] [stdout] | [INFO] [stdout] 65 | use super::*; [INFO] [stdout] | -------- the item `WrappingPart` is already imported here [INFO] [stdout] ... [INFO] [stdout] 69 | use crate::gene::cds_segment::{CdsSegment, WrappingPart}; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `Itertools` is imported redundantly [INFO] [stdout] --> packages_rs/nextclade/src/translate/extract.rs:73:7 [INFO] [stdout] | [INFO] [stdout] 65 | use super::*; [INFO] [stdout] | -------- the item `Itertools` is already imported here [INFO] [stdout] ... [INFO] [stdout] 73 | use itertools::Itertools; [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: the item `Report` is imported redundantly [INFO] [stdout] --> packages_rs/nextclade/src/tree/split_muts.rs:335:7 [INFO] [stdout] | [INFO] [stdout] 333 | use super::*; [INFO] [stdout] | -------- the item `Report` is already imported here [INFO] [stdout] 334 | use crate::analyze::nuc_sub::NucSub; [INFO] [stdout] 335 | use eyre::Report; [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: the item `Nuc` is imported redundantly [INFO] [stdout] --> packages_rs/nextclade/src/tree/tree_find_nearest_node.rs:128:7 [INFO] [stdout] | [INFO] [stdout] 128 | use crate::alphabet::nuc::Nuc; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 131 | use super::*; [INFO] [stdout] | -------- the item `Nuc` is already imported here [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `Report` is imported redundantly [INFO] [stdout] --> packages_rs/nextclade/src/tree/tree_find_nearest_node.rs:133:7 [INFO] [stdout] | [INFO] [stdout] 131 | use super::*; [INFO] [stdout] | -------- the item `Report` is already imported here [INFO] [stdout] 132 | use crate::coord::position::NucRefGlobalPosition; [INFO] [stdout] 133 | use eyre::Report; [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: `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 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: `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: `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/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: the item `strum` is imported redundantly [INFO] [stdout] --> packages_rs/nextclade/src/io/nextclade_csv.rs:33:5 [INFO] [stdout] | [INFO] [stdout] 33 | use strum; [INFO] [stdout] | ^^^^^ the item `strum` is already defined by prelude [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: `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: `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: `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 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: `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: `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: `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: `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: `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: `ctx` [INFO] [stdout] --> packages_rs/nextclade/src/align/backtrace.rs:143:21 [INFO] [stdout] | [INFO] [stdout] 143 | fn test_backtrace(ctx: Context) -> Result<(), Report> { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_ctx` [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: `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: `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: `max_indel` [INFO] [stdout] --> packages_rs/nextclade/src/align/seed_alignment.rs:322:9 [INFO] [stdout] | [INFO] [stdout] 322 | let max_indel = 100; [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_max_indel` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `result` [INFO] [stdout] --> packages_rs/nextclade/src/align/seed_alignment.rs:326:9 [INFO] [stdout] | [INFO] [stdout] 326 | let result = create_alignment_band( [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_result` [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 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: `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: `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: `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: `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: `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: `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: `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: `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: `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: `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: `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: `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: `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: 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: 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: `foo` [INFO] [stdout] --> packages_rs/nextclade/src/translate/extract.rs:79:9 [INFO] [stdout] | [INFO] [stdout] 79 | let foo = 0; [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_foo` [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: fields `params`, `gene_map`, and `gap_open_close` are never read [INFO] [stdout] --> packages_rs/nextclade/src/align/backtrace.rs:119:5 [INFO] [stdout] | [INFO] [stdout] 118 | struct Context { [INFO] [stdout] | ------- fields in this struct [INFO] [stdout] 119 | params: AlignPairwiseParams, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] 120 | gene_map: GeneMap, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 121 | gap_open_close: GapScoreMap, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `gene_map` is never read [INFO] [stdout] --> packages_rs/nextclade/src/align/score_matrix.rs:216:5 [INFO] [stdout] | [INFO] [stdout] 214 | struct Context { [INFO] [stdout] | ------- field in this struct [INFO] [stdout] 215 | params: AlignPairwiseParams, [INFO] [stdout] 216 | gene_map: GeneMap, [INFO] [stdout] | ^^^^^^^^ [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>(qry_seq: &[L], seed_length: usize) -> Vec { [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, [INFO] [stdout] | ^^^^^^^^^^^^^ [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>(qry_seq: &[L], seed_length: usize) -> Vec { [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, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 120 warnings emitted [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>(qry_seq: &[L], seed_length: usize) -> Vec { [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, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 99 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Checking 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] 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] 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] 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] warning: unused variable: `writer` [INFO] [stdout] --> packages_rs/nextclade-cli/src/cli/nextclade_loop.rs:114:9 [INFO] [stdout] | [INFO] [stdout] 114 | let writer = s.spawn(move || { [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_writer` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `genome_size` [INFO] [stdout] --> packages_rs/nextclade-cli/src/cli/nextclade_loop.rs:118:9 [INFO] [stdout] | [INFO] [stdout] 118 | genome_size, [INFO] [stdout] | ^^^^^^^^^^^- [INFO] [stdout] | | [INFO] [stdout] | help: try removing the field [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `gene_map` [INFO] [stdout] --> packages_rs/nextclade-cli/src/cli/nextclade_loop.rs:119:9 [INFO] [stdout] | [INFO] [stdout] 119 | gene_map, [INFO] [stdout] | ^^^^^^^^- [INFO] [stdout] | | [INFO] [stdout] | help: try removing the field [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `insertions` [INFO] [stdout] --> packages_rs/nextclade-cli/src/cli/nextclade_ordered_writer.rs:136:11 [INFO] [stdout] | [INFO] [stdout] 136 | insertions, [INFO] [stdout] | ^^^^^^^^^^- [INFO] [stdout] | | [INFO] [stdout] | help: try removing the field [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `aa_insertions` [INFO] [stdout] --> packages_rs/nextclade-cli/src/cli/nextclade_ordered_writer.rs:137:11 [INFO] [stdout] | [INFO] [stdout] 137 | aa_insertions, [INFO] [stdout] | ^^^^^^^^^^^^^- [INFO] [stdout] | | [INFO] [stdout] | help: try removing the field [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `missing_genes` [INFO] [stdout] --> packages_rs/nextclade-cli/src/cli/nextclade_ordered_writer.rs:138:11 [INFO] [stdout] | [INFO] [stdout] 138 | missing_genes, [INFO] [stdout] | ^^^^^^^^^^^^^- [INFO] [stdout] | | [INFO] [stdout] | help: try removing the field [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `writer` [INFO] [stdout] --> packages_rs/nextclade-cli/src/cli/nextclade_loop.rs:114:9 [INFO] [stdout] | [INFO] [stdout] 114 | let writer = s.spawn(move || { [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_writer` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `genome_size` [INFO] [stdout] --> packages_rs/nextclade-cli/src/cli/nextclade_loop.rs:118:9 [INFO] [stdout] | [INFO] [stdout] 118 | genome_size, [INFO] [stdout] | ^^^^^^^^^^^- [INFO] [stdout] | | [INFO] [stdout] | help: try removing the field [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `gene_map` [INFO] [stdout] --> packages_rs/nextclade-cli/src/cli/nextclade_loop.rs:119:9 [INFO] [stdout] | [INFO] [stdout] 119 | gene_map, [INFO] [stdout] | ^^^^^^^^- [INFO] [stdout] | | [INFO] [stdout] | help: try removing the field [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `writer` [INFO] [stdout] --> packages_rs/nextclade-cli/src/cli/nextclade_seq_sort.rs:130:9 [INFO] [stdout] | [INFO] [stdout] 130 | let writer = s.spawn(move || { [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_writer` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `insertions` [INFO] [stdout] --> packages_rs/nextclade-cli/src/cli/nextclade_ordered_writer.rs:136:11 [INFO] [stdout] | [INFO] [stdout] 136 | insertions, [INFO] [stdout] | ^^^^^^^^^^- [INFO] [stdout] | | [INFO] [stdout] | help: try removing the field [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `aa_insertions` [INFO] [stdout] --> packages_rs/nextclade-cli/src/cli/nextclade_ordered_writer.rs:137:11 [INFO] [stdout] | [INFO] [stdout] 137 | aa_insertions, [INFO] [stdout] | ^^^^^^^^^^^^^- [INFO] [stdout] | | [INFO] [stdout] | help: try removing the field [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `missing_genes` [INFO] [stdout] --> packages_rs/nextclade-cli/src/cli/nextclade_ordered_writer.rs:138:11 [INFO] [stdout] | [INFO] [stdout] 138 | missing_genes, [INFO] [stdout] | ^^^^^^^^^^^^^- [INFO] [stdout] | | [INFO] [stdout] | help: try removing the field [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `writer` [INFO] [stdout] --> packages_rs/nextclade-cli/src/cli/nextclade_seq_sort.rs:130:9 [INFO] [stdout] | [INFO] [stdout] 130 | let writer = s.spawn(move || { [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_writer` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to 2 previous errors; 12 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to 2 previous errors; 12 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: could not compile `nextclade-cli` (lib test) due to 3 previous errors; 12 warnings emitted [INFO] [stderr] warning: build failed, waiting for other jobs to finish... [INFO] [stderr] error: could not compile `nextclade-cli` (lib) due to 3 previous errors; 12 warnings emitted [INFO] [stdout] warning: 99 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] running `Command { std: "docker" "inspect" "d05fa8e04d92f5aaf2a0ccd2ac2afd1023ea2b79b292464502f2ed38084b3c58", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "d05fa8e04d92f5aaf2a0ccd2ac2afd1023ea2b79b292464502f2ed38084b3c58", kill_on_drop: false }` [INFO] [stdout] d05fa8e04d92f5aaf2a0ccd2ac2afd1023ea2b79b292464502f2ed38084b3c58 [INFO] checking 2lambda123/nextclade against try#36dbcaee1a55543dfc181be52a69d99ff46ff62f for pr-122960-3 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2F2lambda123%2Fnextclade" "/workspace/builds/worker-2-tc2/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-2-tc2/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/2lambda123/nextclade on toolchain 36dbcaee1a55543dfc181be52a69d99ff46ff62f [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+36dbcaee1a55543dfc181be52a69d99ff46ff62f" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] removed /workspace/builds/worker-2-tc2/source/.cargo/config.toml [INFO] removed /workspace/builds/worker-2-tc2/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-2-tc2/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" "+36dbcaee1a55543dfc181be52a69d99ff46ff62f" "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] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/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" "+36dbcaee1a55543dfc181be52a69d99ff46ff62f" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 75c34a6b17dc4c1b4ffab5997471b85ccc7d6ee4e442a351be7757251092c1fa [INFO] running `Command { std: "docker" "start" "-a" "75c34a6b17dc4c1b4ffab5997471b85ccc7d6ee4e442a351be7757251092c1fa", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "75c34a6b17dc4c1b4ffab5997471b85ccc7d6ee4e442a351be7757251092c1fa", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "75c34a6b17dc4c1b4ffab5997471b85ccc7d6ee4e442a351be7757251092c1fa", kill_on_drop: false }` [INFO] [stdout] 75c34a6b17dc4c1b4ffab5997471b85ccc7d6ee4e442a351be7757251092c1fa [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+36dbcaee1a55543dfc181be52a69d99ff46ff62f" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 5316ca3719f2fa166fa7f1fbc30ba44b456cdb7cb204a4560aa34bb24822adcf [INFO] running `Command { std: "docker" "start" "-a" "5316ca3719f2fa166fa7f1fbc30ba44b456cdb7cb204a4560aa34bb24822adcf", kill_on_drop: false }` [INFO] [stderr] Copying to /tmp/fixit [INFO] [stderr] no edition found in manifest, probably 2015, skipping [INFO] running `Command { std: "docker" "inspect" "5316ca3719f2fa166fa7f1fbc30ba44b456cdb7cb204a4560aa34bb24822adcf", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "5316ca3719f2fa166fa7f1fbc30ba44b456cdb7cb204a4560aa34bb24822adcf", kill_on_drop: false }` [INFO] [stdout] 5316ca3719f2fa166fa7f1fbc30ba44b456cdb7cb204a4560aa34bb24822adcf