[INFO] cloning repository https://github.com/mladen5000/strain_ahsp
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/mladen5000/strain_ahsp" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fmladen5000%2Fstrain_ahsp", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fmladen5000%2Fstrain_ahsp'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] c295f025db344377d82d603c756a23d30301f98a
[INFO] checking mladen5000/strain_ahsp against try#1779a8680dcd39c56ed600627cf6742ef07ed78c for pr-149045
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fmladen5000%2Fstrain_ahsp" "/workspace/builds/worker-6-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-6-tc2/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/mladen5000/strain_ahsp
[INFO] removed 0 missing examples
[INFO] finished tweaking git repo https://github.com/mladen5000/strain_ahsp
[INFO] tweaked toml for git repo https://github.com/mladen5000/strain_ahsp written to /workspace/builds/worker-6-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/mladen5000/strain_ahsp on toolchain 1779a8680dcd39c56ed600627cf6742ef07ed78c
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1779a8680dcd39c56ed600627cf6742ef07ed78c" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/mladen5000/strain_ahsp 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" "+1779a8680dcd39c56ed600627cf6742ef07ed78c" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr] warning: unused manifest key: example.0.required_features
[INFO] [stderr] warning: unused manifest key: example.1.required_features
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded redox_syscall v0.5.11
[INFO] [stderr]   Downloaded miniz_oxide v0.8.7
[INFO] [stderr]   Downloaded nthash v0.5.1
[INFO] [stderr]   Downloaded bytecount v0.6.8
[INFO] [stderr]   Downloaded sprs v0.11.3
[INFO] [stderr]   Downloaded cc v1.2.18
[INFO] [stderr]   Downloaded buffer-redux v1.0.2
[INFO] [stderr]   Downloaded strum v0.20.0
[INFO] [stderr]   Downloaded newtype_derive v0.1.6
[INFO] [stderr]   Downloaded semver v0.1.20
[INFO] [stderr]   Downloaded enum-map v0.6.6
[INFO] [stderr]   Downloaded enum-map-derive v0.4.6
[INFO] [stderr]   Downloaded array-macro v1.0.5
[INFO] [stderr]   Downloaded rustc_version v0.1.7
[INFO] [stderr]   Downloaded liblzma v0.3.6
[INFO] [stderr]   Downloaded itertools-num v0.1.3
[INFO] [stderr]   Downloaded bio-types v1.0.4
[INFO] [stderr]   Downloaded derive-new v0.6.0
[INFO] [stderr]   Downloaded triple_accel v0.3.4
[INFO] [stderr]   Downloaded jiff-static v0.2.5
[INFO] [stderr]   Downloaded clap v4.5.35
[INFO] [stderr]   Downloaded statrs v0.18.0
[INFO] [stderr]   Downloaded openssl-sys v0.9.107
[INFO] [stderr]   Downloaded rand v0.9.0
[INFO] [stderr]   Downloaded tokio-util v0.7.14
[INFO] [stderr]   Downloaded linfa v0.7.0
[INFO] [stderr]   Downloaded rustix v1.0.5
[INFO] [stderr]   Downloaded quick-xml v0.37.4
[INFO] [stderr]   Downloaded clap_builder v4.5.35
[INFO] [stderr]   Downloaded bio v2.2.0
[INFO] [stderr]   Downloaded rustls v0.23.26
[INFO] [stderr]   Downloaded sled v0.34.7
[INFO] [stderr]   Downloaded needletail v0.6.3
[INFO] [stderr]   Downloaded jiff v0.2.5
[INFO] [stderr]   Downloaded rustls-webpki v0.103.1
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[INFO] [stderr]   Downloaded mockito v1.7.0
[INFO] [stderr]   Downloaded editdistancek v1.0.2
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+1779a8680dcd39c56ed600627cf6742ef07ed78c" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] fe807b2bb56310e0f14cffce6ac204e054ca9a1620529c997f5997a3821b9101
[INFO] running `Command { std: "docker" "start" "-a" "fe807b2bb56310e0f14cffce6ac204e054ca9a1620529c997f5997a3821b9101", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "fe807b2bb56310e0f14cffce6ac204e054ca9a1620529c997f5997a3821b9101", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "fe807b2bb56310e0f14cffce6ac204e054ca9a1620529c997f5997a3821b9101", kill_on_drop: false }`
[INFO] [stdout] fe807b2bb56310e0f14cffce6ac204e054ca9a1620529c997f5997a3821b9101
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+1779a8680dcd39c56ed600627cf6742ef07ed78c" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 1336871fc0aa69db22195b2eabf0088200098888806205ec07c075537b743ddd
[INFO] running `Command { std: "docker" "start" "-a" "1336871fc0aa69db22195b2eabf0088200098888806205ec07c075537b743ddd", kill_on_drop: false }`
[INFO] [stderr] warning: unused manifest key: example.0.required_features
[INFO] [stderr] warning: unused manifest key: example.1.required_features
[INFO] [stderr]    Compiling libc v0.2.171
[INFO] [stderr]    Compiling proc-macro2 v1.0.94
[INFO] [stderr]    Compiling autocfg v1.4.0
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[INFO] [stderr]     Checking smallvec v1.15.0
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[INFO] [stderr]     Checking writeable v0.5.5
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[INFO] [stderr]    Compiling icu_locid_transform_data v1.5.1
[INFO] [stderr]    Compiling getrandom v0.3.2
[INFO] [stderr]    Compiling icu_properties_data v1.5.1
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[INFO] [stderr]     Checking hashbrown v0.15.2
[INFO] [stderr]     Checking futures-io v0.3.31
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling lock_api v0.4.12
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[INFO] [stderr]    Compiling syn v2.0.100
[INFO] [stderr]     Checking parking_lot_core v0.9.10
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[INFO] [stderr]    Compiling zstd-sys v2.0.15+zstd.1.5.7
[INFO] [stderr]    Compiling bzip2-sys v0.1.13+1.0.8
[INFO] [stderr]    Compiling serde_json v1.0.140
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling liblzma-sys v0.3.13
[INFO] [stderr]     Checking regex v1.11.1
[INFO] [stderr]    Compiling native-tls v0.2.14
[INFO] [stderr]     Checking wide v0.7.32
[INFO] [stderr]     Checking anstyle-parse v0.2.6
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[INFO] [stderr]     Checking rand_core v0.9.3
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[INFO] [stderr]    Compiling indexmap v1.9.3
[INFO] [stderr]     Checking is_terminal_polyfill v1.70.1
[INFO] [stderr]    Compiling zstd-safe v7.2.4
[INFO] [stderr]    Compiling feature-probe v0.1.1
[INFO] [stderr]     Checking anstyle v1.0.10
[INFO] [stderr]     Checking anstyle-query v1.1.2
[INFO] [stderr]     Checking colorchoice v1.0.3
[INFO] [stderr]    Compiling parking_lot_core v0.8.6
[INFO] [stderr]    Compiling bv v0.11.1
[INFO] [stderr]     Checking anstream v0.6.18
[INFO] [stderr]     Checking rayon-core v1.12.1
[INFO] [stderr]     Checking rand_chacha v0.9.0
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking simba v0.9.0
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking tokio-util v0.7.14
[INFO] [stderr]    Compiling synstructure v0.13.1
[INFO] [stderr]     Checking num-rational v0.4.2
[INFO] [stderr]     Checking h2 v0.4.8
[INFO] [stderr]     Checking approx v0.3.2
[INFO] [stderr]     Checking crc32fast v1.4.2
[INFO] [stderr]     Checking instant v0.1.13
[INFO] [stderr]    Compiling rustix v1.0.5
[INFO] [stderr]     Checking hashbrown v0.12.3
[INFO] [stderr]    Compiling anyhow v1.0.97
[INFO] [stderr]     Checking adler2 v2.0.0
[INFO] [stderr]     Checking miniz_oxide v0.8.7
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]    Compiling serde_derive v1.0.219
[INFO] [stderr]    Compiling zerofrom-derive v0.1.6
[INFO] [stderr]    Compiling yoke-derive v0.7.5
[INFO] [stderr]    Compiling zerovec-derive v0.10.3
[INFO] [stderr]    Compiling displaydoc v0.2.5
[INFO] [stderr]     Checking zerofrom v0.1.6
[INFO] [stderr]     Checking yoke v0.7.5
[INFO] [stderr]    Compiling icu_provider_macros v1.5.0
[INFO] [stderr]    Compiling openssl-macros v0.1.1
[INFO] [stderr]    Compiling thiserror-impl v1.0.69
[INFO] [stderr]     Checking hyper v1.6.0
[INFO] [stderr]     Checking zerovec v0.10.4
[INFO] [stderr]     Checking tinystr v0.7.6
[INFO] [stderr]     Checking icu_locid v1.5.0
[INFO] [stderr]     Checking icu_collections v1.5.0
[INFO] [stderr]     Checking thiserror v1.0.69
[INFO] [stderr]    Compiling nalgebra-macros v0.2.2
[INFO] [stderr]     Checking hyper-util v0.1.11
[INFO] [stderr]     Checking icu_provider v1.5.0
[INFO] [stderr]    Compiling enum-map-derive v0.4.6
[INFO] [stderr]     Checking nalgebra v0.33.2
[INFO] [stderr]     Checking icu_locid_transform v1.5.0
[INFO] [stderr]    Compiling thiserror-impl v2.0.12
[INFO] [stderr]     Checking icu_properties v1.5.1
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]     Checking tokio-native-tls v0.3.1
[INFO] [stderr]     Checking alga v0.9.3
[INFO] [stderr]     Checking rayon v1.10.0
[INFO] [stderr]     Checking rand v0.9.0
[INFO] [stderr]     Checking approx v0.4.0
[INFO] [stderr]     Checking num_cpus v1.16.0
[INFO] [stderr]     Checking sync_wrapper v1.0.2
[INFO] [stderr]     Checking csv-core v0.1.12
[INFO] [stderr]     Checking clap_lex v0.7.4
[INFO] [stderr]    Compiling virtue v0.0.18
[INFO] [stderr]     Checking linux-raw-sys v0.9.3
[INFO] [stderr]     Checking bytecount v0.6.8
[INFO] [stderr]    Compiling linfa v0.7.0
[INFO] [stderr]     Checking icu_normalizer v1.5.0
[INFO] [stderr]     Checking strsim v0.11.1
[INFO] [stderr]     Checking rustls-pki-types v1.11.0
[INFO] [stderr]     Checking bit-vec v0.8.0
[INFO] [stderr]     Checking fixedbitset v0.2.0
[INFO] [stderr]     Checking array-macro v1.0.5
[INFO] [stderr]     Checking idna_adapter v1.2.0
[INFO] [stderr]     Checking ndarray v0.16.1
[INFO] [stderr]     Checking serde_urlencoded v0.7.1
[INFO] [stderr]     Checking tower v0.5.2
[INFO] [stderr]     Checking idna v1.0.3
[INFO] [stderr]     Checking petgraph v0.5.1
[INFO] [stderr]     Checking url v2.5.4
[INFO] [stderr]     Checking enum-map v0.6.6
[INFO] [stderr]     Checking assert-json-diff v2.0.2
[INFO] [stderr]    Compiling bincode_derive v2.0.1
[INFO] [stderr]     Checking multimap v0.8.3
[INFO] [stderr]     Checking csv v1.3.1
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking rustls-pemfile v2.2.0
[INFO] [stderr]     Checking bit-set v0.8.0
[INFO] [stderr]     Checking clap_builder v4.5.35
[INFO] [stderr]     Checking bio-types v1.0.4
[INFO] [stderr]     Checking ndarray v0.15.6
[INFO] [stderr]     Checking hyper-tls v0.6.0
[INFO] [stderr]     Checking parking_lot v0.11.2
[INFO] [stderr]     Checking thiserror v2.0.12
[INFO] [stderr]     Checking liblzma v0.3.6
[INFO] [stderr]    Compiling clap_derive v4.5.32
[INFO] [stderr]     Checking flate2 v1.1.1
[INFO] [stderr]     Checking bzip2 v0.4.4
[INFO] [stderr]     Checking colored v2.2.0
[INFO] [stderr]     Checking sprs v0.11.3
[INFO] [stderr]     Checking env_filter v0.1.3
[INFO] [stderr]     Checking itertools v0.14.0
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking ordered-float v5.0.0
[INFO] [stderr]     Checking fs2 v0.4.3
[INFO] [stderr]     Checking buffer-redux v1.0.2
[INFO] [stderr]     Checking encoding_rs v0.8.35
[INFO] [stderr]     Checking triple_accel v0.3.4
[INFO] [stderr]     Checking similar v2.7.0
[INFO] [stderr]     Checking strum v0.20.0
[INFO] [stderr]     Checking statrs v0.18.0
[INFO] [stderr]     Checking unty v0.0.4
[INFO] [stderr]     Checking fastrand v2.3.0
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking jiff v0.2.5
[INFO] [stderr]     Checking editdistancek v1.0.2
[INFO] [stderr]     Checking ipnet v2.11.0
[INFO] [stderr]     Checking tempfile v3.19.1
[INFO] [stderr]     Checking bincode v2.0.1
[INFO] [stderr]     Checking mockito v1.7.0
[INFO] [stderr]     Checking reqwest v0.12.15
[INFO] [stderr]     Checking clap v4.5.35
[INFO] [stderr]     Checking sled v0.34.7
[INFO] [stderr]     Checking bio v2.2.0
[INFO] [stderr]     Checking quick-xml v0.37.4
[INFO] [stderr]     Checking nthash v0.5.1
[INFO] [stderr]     Checking bzip2 v0.5.2
[INFO] [stderr]     Checking urlencoding v2.1.3
[INFO] [stderr]     Checking zstd v0.13.3
[INFO] [stderr]     Checking needletail v0.6.3
[INFO] [stderr]     Checking env_logger v0.11.8
[INFO] [stderr]     Checking strain_ahsp v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] error[E0433]: cannot find module or crate `plotters` in this scope
[INFO] [stdout]  --> src/visualization/plotter.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use plotters::prelude::*;
[INFO] [stdout]   |     ^^^^^^^^ use of unresolved module or unlinked crate `plotters`
[INFO] [stdout]   |
[INFO] [stdout]   = help: if you wanted to use a crate named `plotters`, use `cargo add plotters` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `crate::pipeline::processor::ClassificationResults`
[INFO] [stdout]   --> src/visualization/plotter.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use crate::pipeline::processor::ClassificationResults;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ no `ClassificationResults` in `pipeline::processor`
[INFO] [stdout]    |
[INFO] [stdout] help: consider importing this struct instead
[INFO] [stdout]    |
[INFO] [stdout] 11 - use crate::pipeline::processor::ClassificationResults;
[INFO] [stdout] 11 + use crate::pipeline::qc::ClassificationResults;
[INFO] [stdout]    |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find module or crate `plotters` in this scope
[INFO] [stdout]  --> src/visualization/plotter.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use plotters::prelude::*;
[INFO] [stdout]   |     ^^^^^^^^ use of unresolved module or unlinked crate `plotters`
[INFO] [stdout]   |
[INFO] [stdout]   = help: if you wanted to use a crate named `plotters`, use `cargo add plotters` to add it to your `Cargo.toml`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0432]: unresolved import `crate::pipeline::processor::ClassificationResults`
[INFO] [stdout]   --> src/visualization/plotter.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use crate::pipeline::processor::ClassificationResults;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ no `ClassificationResults` in `pipeline::processor`
[INFO] [stdout]    |
[INFO] [stdout] help: consider importing this struct instead
[INFO] [stdout]    |
[INFO] [stdout] 11 - use crate::pipeline::processor::ClassificationResults;
[INFO] [stdout] 11 + use crate::pipeline::qc::ClassificationResults;
[INFO] [stdout]    |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `WHITE` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:441:20
[INFO] [stdout]     |
[INFO] [stdout] 441 |         root.fill(&WHITE)?;
[INFO] [stdout]     |                    ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `BLACK` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:514:29
[INFO] [stdout]     |
[INFO] [stdout] 514 |                     .color(&BLACK)
[INFO] [stdout]     |                             ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `WHITE` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:552:20
[INFO] [stdout]     |
[INFO] [stdout] 552 |         root.fill(&WHITE)?;
[INFO] [stdout]     |                    ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `BLACK` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:574:29
[INFO] [stdout]     |
[INFO] [stdout] 574 |                     .color(&BLACK)
[INFO] [stdout]     |                             ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Text` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:637:51
[INFO] [stdout]     |
[INFO] [stdout] 637 |                 chart.draw_series(std::iter::once(Text::new(
[INFO] [stdout]     |                                                   ^^^^ use of undeclared type `Text`
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing one of these items
[INFO] [stdout]     |
[INFO] [stdout]   1 + use bio::utils::Text;
[INFO] [stdout]     |
[INFO] [stdout]   1 + use quick_xml::de::Text;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `BLACK` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:640:61
[INFO] [stdout]     |
[INFO] [stdout] 640 |                     ("sans-serif", 15.0).into_font().color(&BLACK).rotate(45.0),
[INFO] [stdout]     |                                                             ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Text` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:646:51
[INFO] [stdout]     |
[INFO] [stdout] 646 |                 chart.draw_series(std::iter::once(Text::new(
[INFO] [stdout]     |                                                   ^^^^ use of undeclared type `Text`
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing one of these items
[INFO] [stdout]     |
[INFO] [stdout]   1 + use bio::utils::Text;
[INFO] [stdout]     |
[INFO] [stdout]   1 + use quick_xml::de::Text;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `BLACK` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:649:61
[INFO] [stdout]     |
[INFO] [stdout] 649 |                     ("sans-serif", 15.0).into_font().color(&BLACK),
[INFO] [stdout]     |                                                             ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `WHITE` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:674:20
[INFO] [stdout]     |
[INFO] [stdout] 674 |         root.fill(&WHITE)?;
[INFO] [stdout]     |                    ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `BLACK` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:727:29
[INFO] [stdout]     |
[INFO] [stdout] 727 |                     .color(&BLACK)
[INFO] [stdout]     |                             ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Text` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:772:51
[INFO] [stdout]     |
[INFO] [stdout] 772 |                 chart.draw_series(std::iter::once(Text::new(
[INFO] [stdout]     |                                                   ^^^^ use of undeclared type `Text`
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing one of these items
[INFO] [stdout]     |
[INFO] [stdout]   1 + use bio::utils::Text;
[INFO] [stdout]     |
[INFO] [stdout]   1 + use quick_xml::de::Text;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `BLACK` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:775:61
[INFO] [stdout]     |
[INFO] [stdout] 775 |                     ("sans-serif", 15.0).into_font().color(&BLACK),
[INFO] [stdout]     |                                                             ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Text` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:781:51
[INFO] [stdout]     |
[INFO] [stdout] 781 |                 chart.draw_series(std::iter::once(Text::new(
[INFO] [stdout]     |                                                   ^^^^ use of undeclared type `Text`
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing one of these items
[INFO] [stdout]     |
[INFO] [stdout]   1 + use bio::utils::Text;
[INFO] [stdout]     |
[INFO] [stdout]   1 + use quick_xml::de::Text;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `BLACK` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:784:61
[INFO] [stdout]     |
[INFO] [stdout] 784 |                     ("sans-serif", 15.0).into_font().color(&BLACK),
[INFO] [stdout]     |                                                             ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `WHITE` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:816:20
[INFO] [stdout]     |
[INFO] [stdout] 816 |         root.fill(&WHITE)?;
[INFO] [stdout]     |                    ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `BLACK` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:833:25
[INFO] [stdout]     |
[INFO] [stdout] 833 |                 .color(&BLACK)
[INFO] [stdout]     |                         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find type `FastqProcessor` in module `crate::pipeline::processor`
[INFO] [stdout]    --> src/visualization/plotter.rs:845:34
[INFO] [stdout]     |
[INFO] [stdout] 845 | impl crate::pipeline::processor::FastqProcessor {
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^ not found in `crate::pipeline::processor`
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this struct through its public re-export
[INFO] [stdout]     |
[INFO] [stdout]   1 + use crate::pipeline::FastqProcessor;
[INFO] [stdout]     |
[INFO] [stdout] help: if you import `FastqProcessor`, refer to it directly
[INFO] [stdout]     |
[INFO] [stdout] 845 - impl crate::pipeline::processor::FastqProcessor {
[INFO] [stdout] 845 + impl FastqProcessor {
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find type `ClassificationResults` in this scope
[INFO] [stdout]   --> src/visualization/mod.rs:25:19
[INFO] [stdout]    |
[INFO] [stdout] 25 |         results: &ClassificationResults,
[INFO] [stdout]    |                   ^^^^^^^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]    |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]    |
[INFO] [stdout]  4 + use crate::pipeline::qc::ClassificationResults;
[INFO] [stdout]    |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find type `ClassificationResults` in this scope
[INFO] [stdout]   --> src/visualization/mod.rs:34:19
[INFO] [stdout]    |
[INFO] [stdout] 34 |         results: &ClassificationResults,
[INFO] [stdout]    |                   ^^^^^^^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]    |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]    |
[INFO] [stdout]  4 + use crate::pipeline::qc::ClassificationResults;
[INFO] [stdout]    |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find type `ClassificationResults` in this scope
[INFO] [stdout]   --> src/visualization/mod.rs:42:20
[INFO] [stdout]    |
[INFO] [stdout] 42 |         results: &[ClassificationResults],
[INFO] [stdout]    |                    ^^^^^^^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]    |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]    |
[INFO] [stdout]  4 + use crate::pipeline::qc::ClassificationResults;
[INFO] [stdout]    |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Array` and `Axis`
[INFO] [stdout]  --> src/count_table.rs:8:15
[INFO] [stdout]   |
[INFO] [stdout] 8 | use ndarray::{Array, Array2, Axis}; // Using ndarray for matrix operations
[INFO] [stdout]   |               ^^^^^          ^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `BytesStart`
[INFO] [stdout]   --> src/database/downloader.rs:12:25
[INFO] [stdout]    |
[INFO] [stdout] 12 | use quick_xml::events::{BytesStart, Event}; // Added BytesStart, Event
[INFO] [stdout]    |                         ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `ArrayView1` and `s`
[INFO] [stdout]   --> src/normalization.rs:10:15
[INFO] [stdout]    |
[INFO] [stdout] 10 | use ndarray::{s, Array1, ArrayView1, Axis};
[INFO] [stdout]    |               ^          ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `needletail::parser::FastaReader`
[INFO] [stdout]   --> src/sketch/adaptive.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use needletail::parser::FastaReader; // Add this import at the top with other imports
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `bio::io::fasta::Record as SequenceRecord2`
[INFO] [stdout]   --> src/sketch/minhash.rs:14:5
[INFO] [stdout]    |
[INFO] [stdout] 14 | use bio::io::fasta::Record as SequenceRecord2;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `needletail::FastxReader`
[INFO] [stdout]   --> src/sketch/minhash.rs:16:5
[INFO] [stdout]    |
[INFO] [stdout] 16 | use needletail::FastxReader;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::collections::hash_map::DefaultHasher`
[INFO] [stdout]  --> src/sketch/signature.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use std::collections::hash_map::DefaultHasher;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `KmerSignature`
[INFO] [stdout]   --> src/sketch/mod.rs:13:17
[INFO] [stdout]    |
[INFO] [stdout] 13 | use signature::{KmerSignature, KmerSignatureBuilder};
[INFO] [stdout]    |                 ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Sequence`
[INFO] [stdout]   --> src/sketch/mod.rs:22:36
[INFO] [stdout]    |
[INFO] [stdout] 22 | use needletail::{parse_fastx_file, Sequence};
[INFO] [stdout]    |                                    ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition value: `random`
[INFO] [stdout]  --> src/stats/bayesian.rs:4:7
[INFO] [stdout]   |
[INFO] [stdout] 4 | #[cfg(feature = "random")]
[INFO] [stdout]   |       ^^^^^^^^^^^^^^^^^^ help: remove the condition
[INFO] [stdout]   |
[INFO] [stdout]   = note: no expected values for `feature`
[INFO] [stdout]   = help: consider adding `random` as a feature in `Cargo.toml`
[INFO] [stdout]   = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout]   = note: `#[warn(unexpected_cfgs)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition value: `random`
[INFO] [stdout]   --> src/stats/bayesian.rs:44:15
[INFO] [stdout]    |
[INFO] [stdout] 44 |         #[cfg(feature = "random")]
[INFO] [stdout]    |               ^^^^^^^^^^^^^^^^^^ help: remove the condition
[INFO] [stdout]    |
[INFO] [stdout]    = note: no expected values for `feature`
[INFO] [stdout]    = help: consider adding `random` as a feature in `Cargo.toml`
[INFO] [stdout]    = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition value: `random`
[INFO] [stdout]   --> src/stats/bayesian.rs:47:19
[INFO] [stdout]    |
[INFO] [stdout] 47 |         #[cfg(not(feature = "random"))]
[INFO] [stdout]    |                   ^^^^^^^^^^^^^^^^^^ help: remove the condition
[INFO] [stdout]    |
[INFO] [stdout]    = note: no expected values for `feature`
[INFO] [stdout]    = help: consider adding `random` as a feature in `Cargo.toml`
[INFO] [stdout]    = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition value: `random`
[INFO] [stdout]  --> src/stats/deconvolution.rs:5:7
[INFO] [stdout]   |
[INFO] [stdout] 5 | #[cfg(feature = "random")]
[INFO] [stdout]   |       ^^^^^^^^^^^^^^^^^^ help: remove the condition
[INFO] [stdout]   |
[INFO] [stdout]   = note: no expected values for `feature`
[INFO] [stdout]   = help: consider adding `random` as a feature in `Cargo.toml`
[INFO] [stdout]   = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition value: `random`
[INFO] [stdout]   --> src/stats/deconvolution.rs:86:15
[INFO] [stdout]    |
[INFO] [stdout] 86 |         #[cfg(feature = "random")]
[INFO] [stdout]    |               ^^^^^^^^^^^^^^^^^^ help: remove the condition
[INFO] [stdout]    |
[INFO] [stdout]    = note: no expected values for `feature`
[INFO] [stdout]    = help: consider adding `random` as a feature in `Cargo.toml`
[INFO] [stdout]    = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition value: `random`
[INFO] [stdout]   --> src/stats/deconvolution.rs:89:19
[INFO] [stdout]    |
[INFO] [stdout] 89 |         #[cfg(not(feature = "random"))]
[INFO] [stdout]    |                   ^^^^^^^^^^^^^^^^^^ help: remove the condition
[INFO] [stdout]    |
[INFO] [stdout]    = note: no expected values for `feature`
[INFO] [stdout]    = help: consider adding `random` as a feature in `Cargo.toml`
[INFO] [stdout]    = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::count_table::CountTable`
[INFO] [stdout]   --> src/strain_method.rs:10:5
[INFO] [stdout]    |
[INFO] [stdout] 10 | use crate::count_table::CountTable; // Might use count data as input
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::midas_db::MidasData`
[INFO] [stdout]   --> src/strain_method.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use crate::midas_db::MidasData; // Might use MIDAS data for markers/references
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `serde::Serialize`
[INFO] [stdout]  --> src/visualization/plotter.rs:7:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | use serde::Serialize;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Classification`
[INFO] [stdout]   --> src/visualization/plotter.rs:10:35
[INFO] [stdout]    |
[INFO] [stdout] 10 | use crate::adaptive::classifier::{Classification, TaxonomicLevel};
[INFO] [stdout]    |                                   ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unreachable statement
[INFO] [stdout]   --> src/cli.rs:60:13
[INFO] [stdout]    |
[INFO] [stdout] 59 |             let results = todo!();
[INFO] [stdout]    |                           ------- any code following this expression is unreachable
[INFO] [stdout] 60 |             let report = generate_report(&results)?;
[INFO] [stdout]    |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ unreachable statement
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unreachable_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unreachable statement
[INFO] [stdout]    --> src/cli.rs:148:13
[INFO] [stdout]     |
[INFO] [stdout] 146 |             let comparison_results = todo!();
[INFO] [stdout]     |                                      ------- any code following this expression is unreachable
[INFO] [stdout] 147 |
[INFO] [stdout] 148 |             println!("Comparison results: {:?}", comparison_results);
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ unreachable statement
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unreachable statement
[INFO] [stdout]    --> src/cli.rs:155:13
[INFO] [stdout]     |
[INFO] [stdout] 154 |             let results = todo!();
[INFO] [stdout]     |                           ------- any code following this expression is unreachable
[INFO] [stdout] 155 |             let report = generate_report(&results)?;
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ unreachable statement
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `WHITE` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:441:20
[INFO] [stdout]     |
[INFO] [stdout] 441 |         root.fill(&WHITE)?;
[INFO] [stdout]     |                    ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `BLACK` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:514:29
[INFO] [stdout]     |
[INFO] [stdout] 514 |                     .color(&BLACK)
[INFO] [stdout]     |                             ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `WHITE` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:552:20
[INFO] [stdout]     |
[INFO] [stdout] 552 |         root.fill(&WHITE)?;
[INFO] [stdout]     |                    ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `BLACK` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:574:29
[INFO] [stdout]     |
[INFO] [stdout] 574 |                     .color(&BLACK)
[INFO] [stdout]     |                             ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Text` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:637:51
[INFO] [stdout]     |
[INFO] [stdout] 637 |                 chart.draw_series(std::iter::once(Text::new(
[INFO] [stdout]     |                                                   ^^^^ use of undeclared type `Text`
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing one of these items
[INFO] [stdout]     |
[INFO] [stdout]   1 + use bio::utils::Text;
[INFO] [stdout]     |
[INFO] [stdout]   1 + use quick_xml::de::Text;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `BLACK` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:640:61
[INFO] [stdout]     |
[INFO] [stdout] 640 |                     ("sans-serif", 15.0).into_font().color(&BLACK).rotate(45.0),
[INFO] [stdout]     |                                                             ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Text` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:646:51
[INFO] [stdout]     |
[INFO] [stdout] 646 |                 chart.draw_series(std::iter::once(Text::new(
[INFO] [stdout]     |                                                   ^^^^ use of undeclared type `Text`
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing one of these items
[INFO] [stdout]     |
[INFO] [stdout]   1 + use bio::utils::Text;
[INFO] [stdout]     |
[INFO] [stdout]   1 + use quick_xml::de::Text;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `BLACK` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:649:61
[INFO] [stdout]     |
[INFO] [stdout] 649 |                     ("sans-serif", 15.0).into_font().color(&BLACK),
[INFO] [stdout]     |                                                             ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `WHITE` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:674:20
[INFO] [stdout]     |
[INFO] [stdout] 674 |         root.fill(&WHITE)?;
[INFO] [stdout]     |                    ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `BLACK` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:727:29
[INFO] [stdout]     |
[INFO] [stdout] 727 |                     .color(&BLACK)
[INFO] [stdout]     |                             ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `generate_quality_plots` found for struct `FastqProcessor` in the current scope
[INFO] [stdout]    --> src/pipeline/report.rs:324:23
[INFO] [stdout]     |
[INFO] [stdout] 324 |             processor.generate_quality_plots(&results, &output)?;
[INFO] [stdout]     |                       ^^^^^^^^^^^^^^^^^^^^^^ method not found in `FastqProcessor`
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/pipeline/qc.rs:107:1
[INFO] [stdout]     |
[INFO] [stdout] 107 | pub struct FastqProcessor {
[INFO] [stdout]     | ------------------------- method `generate_quality_plots` not found for this struct
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Text` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:772:51
[INFO] [stdout]     |
[INFO] [stdout] 772 |                 chart.draw_series(std::iter::once(Text::new(
[INFO] [stdout]     |                                                   ^^^^ use of undeclared type `Text`
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing one of these items
[INFO] [stdout]     |
[INFO] [stdout]   1 + use bio::utils::Text;
[INFO] [stdout]     |
[INFO] [stdout]   1 + use quick_xml::de::Text;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `BLACK` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:775:61
[INFO] [stdout]     |
[INFO] [stdout] 775 |                     ("sans-serif", 15.0).into_font().color(&BLACK),
[INFO] [stdout]     |                                                             ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Text` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:781:51
[INFO] [stdout]     |
[INFO] [stdout] 781 |                 chart.draw_series(std::iter::once(Text::new(
[INFO] [stdout]     |                                                   ^^^^ use of undeclared type `Text`
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing one of these items
[INFO] [stdout]     |
[INFO] [stdout]   1 + use bio::utils::Text;
[INFO] [stdout]     |
[INFO] [stdout]   1 + use quick_xml::de::Text;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `BLACK` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:784:61
[INFO] [stdout]     |
[INFO] [stdout] 784 |                     ("sans-serif", 15.0).into_font().color(&BLACK),
[INFO] [stdout]     |                                                             ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `WHITE` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:816:20
[INFO] [stdout]     |
[INFO] [stdout] 816 |         root.fill(&WHITE)?;
[INFO] [stdout]     |                    ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find value `BLACK` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:833:25
[INFO] [stdout]     |
[INFO] [stdout] 833 |                 .color(&BLACK)
[INFO] [stdout]     |                         ^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find type `FastqProcessor` in module `crate::pipeline::processor`
[INFO] [stdout]    --> src/visualization/plotter.rs:845:34
[INFO] [stdout]     |
[INFO] [stdout] 845 | impl crate::pipeline::processor::FastqProcessor {
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^ not found in `crate::pipeline::processor`
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this struct through its public re-export
[INFO] [stdout]     |
[INFO] [stdout]   1 + use crate::pipeline::FastqProcessor;
[INFO] [stdout]     |
[INFO] [stdout] help: if you import `FastqProcessor`, refer to it directly
[INFO] [stdout]     |
[INFO] [stdout] 845 - impl crate::pipeline::processor::FastqProcessor {
[INFO] [stdout] 845 + impl FastqProcessor {
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find type `ClassificationResults` in this scope
[INFO] [stdout]   --> src/visualization/mod.rs:25:19
[INFO] [stdout]    |
[INFO] [stdout] 25 |         results: &ClassificationResults,
[INFO] [stdout]    |                   ^^^^^^^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]    |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]    |
[INFO] [stdout]  4 + use crate::pipeline::qc::ClassificationResults;
[INFO] [stdout]    |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find type `ClassificationResults` in this scope
[INFO] [stdout]   --> src/visualization/mod.rs:34:19
[INFO] [stdout]    |
[INFO] [stdout] 34 |         results: &ClassificationResults,
[INFO] [stdout]    |                   ^^^^^^^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]    |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]    |
[INFO] [stdout]  4 + use crate::pipeline::qc::ClassificationResults;
[INFO] [stdout]    |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find type `ClassificationResults` in this scope
[INFO] [stdout]   --> src/visualization/mod.rs:42:20
[INFO] [stdout]    |
[INFO] [stdout] 42 |         results: &[ClassificationResults],
[INFO] [stdout]    |                    ^^^^^^^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]    |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]    |
[INFO] [stdout]  4 + use crate::pipeline::qc::ClassificationResults;
[INFO] [stdout]    |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::collections::HashSet`
[INFO] [stdout]    --> src/bio/signature.rs:125:9
[INFO] [stdout]     |
[INFO] [stdout] 125 |     use std::collections::HashSet;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Array` and `Axis`
[INFO] [stdout]  --> src/count_table.rs:8:15
[INFO] [stdout]   |
[INFO] [stdout] 8 | use ndarray::{Array, Array2, Axis}; // Using ndarray for matrix operations
[INFO] [stdout]   |               ^^^^^          ^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `ndarray::arr2`
[INFO] [stdout]    --> src/count_table.rs:137:9
[INFO] [stdout]     |
[INFO] [stdout] 137 |     use ndarray::arr2;
[INFO] [stdout]     |         ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `BytesStart`
[INFO] [stdout]   --> src/database/downloader.rs:12:25
[INFO] [stdout]    |
[INFO] [stdout] 12 | use quick_xml::events::{BytesStart, Event}; // Added BytesStart, Event
[INFO] [stdout]    |                         ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::sketch::signature::MultiResolutionSignature`
[INFO] [stdout]     --> src/database/downloader.rs:1032:9
[INFO] [stdout]      |
[INFO] [stdout] 1032 |     use crate::sketch::signature::MultiResolutionSignature;
[INFO] [stdout]      |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::sketch::SignatureBuilder`
[INFO] [stdout]     --> src/database/downloader.rs:1033:9
[INFO] [stdout]      |
[INFO] [stdout] 1033 |     use crate::sketch::SignatureBuilder;
[INFO] [stdout]      |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::io::Write`
[INFO] [stdout]     --> src/database/downloader.rs:1244:9
[INFO] [stdout]      |
[INFO] [stdout] 1244 |     use std::io::Write;
[INFO] [stdout]      |         ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::path::PathBuf`
[INFO] [stdout]   --> src/midas_db.rs:71:9
[INFO] [stdout]    |
[INFO] [stdout] 71 |     use std::path::PathBuf;
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `ArrayView1` and `s`
[INFO] [stdout]   --> src/normalization.rs:10:15
[INFO] [stdout]    |
[INFO] [stdout] 10 | use ndarray::{s, Array1, ArrayView1, Axis};
[INFO] [stdout]    |               ^          ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Array2` and `Axis`
[INFO] [stdout]    --> src/normalization.rs:189:25
[INFO] [stdout]     |
[INFO] [stdout] 189 |     use ndarray::{arr2, Array2, Axis}; // For float comparisons
[INFO] [stdout]     |                         ^^^^^^  ^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `needletail::parser::FastaReader`
[INFO] [stdout]   --> src/sketch/adaptive.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use needletail::parser::FastaReader; // Add this import at the top with other imports
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `parse_fastx_file`
[INFO] [stdout]    --> src/sketch/adaptive.rs:107:22
[INFO] [stdout]     |
[INFO] [stdout] 107 |     use needletail::{parse_fastx_file, parser::SequenceRecord};
[INFO] [stdout]     |                      ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::io::Cursor`
[INFO] [stdout]    --> src/sketch/adaptive.rs:108:9
[INFO] [stdout]     |
[INFO] [stdout] 108 |     use std::io::Cursor;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Seek` and `Write`
[INFO] [stdout]    --> src/sketch/adaptive.rs:109:19
[INFO] [stdout]     |
[INFO] [stdout] 109 |     use std::io::{Seek, Write}; // For writing to tempfile in tests
[INFO] [stdout]     |                   ^^^^  ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `bio::io::fasta::Record as SequenceRecord2`
[INFO] [stdout]   --> src/sketch/minhash.rs:14:5
[INFO] [stdout]    |
[INFO] [stdout] 14 | use bio::io::fasta::Record as SequenceRecord2;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `needletail::FastxReader`
[INFO] [stdout]   --> src/sketch/minhash.rs:16:5
[INFO] [stdout]    |
[INFO] [stdout] 16 | use needletail::FastxReader;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::collections::hash_map::DefaultHasher`
[INFO] [stdout]  --> src/sketch/signature.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 8 | use std::collections::hash_map::DefaultHasher;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `KmerSignature`
[INFO] [stdout]   --> src/sketch/mod.rs:13:17
[INFO] [stdout]    |
[INFO] [stdout] 13 | use signature::{KmerSignature, KmerSignatureBuilder};
[INFO] [stdout]    |                 ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Sequence`
[INFO] [stdout]   --> src/sketch/mod.rs:22:36
[INFO] [stdout]    |
[INFO] [stdout] 22 | use needletail::{parse_fastx_file, Sequence};
[INFO] [stdout]    |                                    ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition value: `random`
[INFO] [stdout]  --> src/stats/bayesian.rs:4:7
[INFO] [stdout]   |
[INFO] [stdout] 4 | #[cfg(feature = "random")]
[INFO] [stdout]   |       ^^^^^^^^^^^^^^^^^^ help: remove the condition
[INFO] [stdout]   |
[INFO] [stdout]   = note: no expected values for `feature`
[INFO] [stdout]   = help: consider adding `random` as a feature in `Cargo.toml`
[INFO] [stdout]   = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout]   = note: `#[warn(unexpected_cfgs)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition value: `random`
[INFO] [stdout]   --> src/stats/bayesian.rs:44:15
[INFO] [stdout]    |
[INFO] [stdout] 44 |         #[cfg(feature = "random")]
[INFO] [stdout]    |               ^^^^^^^^^^^^^^^^^^ help: remove the condition
[INFO] [stdout]    |
[INFO] [stdout]    = note: no expected values for `feature`
[INFO] [stdout]    = help: consider adding `random` as a feature in `Cargo.toml`
[INFO] [stdout]    = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition value: `random`
[INFO] [stdout]   --> src/stats/bayesian.rs:47:19
[INFO] [stdout]    |
[INFO] [stdout] 47 |         #[cfg(not(feature = "random"))]
[INFO] [stdout]    |                   ^^^^^^^^^^^^^^^^^^ help: remove the condition
[INFO] [stdout]    |
[INFO] [stdout]    = note: no expected values for `feature`
[INFO] [stdout]    = help: consider adding `random` as a feature in `Cargo.toml`
[INFO] [stdout]    = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition value: `random`
[INFO] [stdout]  --> src/stats/deconvolution.rs:5:7
[INFO] [stdout]   |
[INFO] [stdout] 5 | #[cfg(feature = "random")]
[INFO] [stdout]   |       ^^^^^^^^^^^^^^^^^^ help: remove the condition
[INFO] [stdout]   |
[INFO] [stdout]   = note: no expected values for `feature`
[INFO] [stdout]   = help: consider adding `random` as a feature in `Cargo.toml`
[INFO] [stdout]   = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition value: `random`
[INFO] [stdout]   --> src/stats/deconvolution.rs:86:15
[INFO] [stdout]    |
[INFO] [stdout] 86 |         #[cfg(feature = "random")]
[INFO] [stdout]    |               ^^^^^^^^^^^^^^^^^^ help: remove the condition
[INFO] [stdout]    |
[INFO] [stdout]    = note: no expected values for `feature`
[INFO] [stdout]    = help: consider adding `random` as a feature in `Cargo.toml`
[INFO] [stdout]    = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition value: `random`
[INFO] [stdout]   --> src/stats/deconvolution.rs:89:19
[INFO] [stdout]    |
[INFO] [stdout] 89 |         #[cfg(not(feature = "random"))]
[INFO] [stdout]    |                   ^^^^^^^^^^^^^^^^^^ help: remove the condition
[INFO] [stdout]    |
[INFO] [stdout]    = note: no expected values for `feature`
[INFO] [stdout]    = help: consider adding `random` as a feature in `Cargo.toml`
[INFO] [stdout]    = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::count_table::CountTable`
[INFO] [stdout]   --> src/strain_method.rs:10:5
[INFO] [stdout]    |
[INFO] [stdout] 10 | use crate::count_table::CountTable; // Might use count data as input
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::midas_db::MidasData`
[INFO] [stdout]   --> src/strain_method.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use crate::midas_db::MidasData; // Might use MIDAS data for markers/references
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `serde::Serialize`
[INFO] [stdout]  --> src/visualization/plotter.rs:7:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | use serde::Serialize;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Classification`
[INFO] [stdout]   --> src/visualization/plotter.rs:10:35
[INFO] [stdout]    |
[INFO] [stdout] 10 | use crate::adaptive::classifier::{Classification, TaxonomicLevel};
[INFO] [stdout]    |                                   ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `generate_taxonomy_plots` found for struct `FastqProcessor` in the current scope
[INFO] [stdout]    --> src/pipeline/report.rs:325:23
[INFO] [stdout]     |
[INFO] [stdout] 325 |             processor.generate_taxonomy_plots(&results, &output)?;
[INFO] [stdout]     |                       ^^^^^^^^^^^^^^^^^^^^^^^ method not found in `FastqProcessor`
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/pipeline/qc.rs:107:1
[INFO] [stdout]     |
[INFO] [stdout] 107 | pub struct FastqProcessor {
[INFO] [stdout]     | ------------------------- method `generate_taxonomy_plots` not found for this struct
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `rand::Rng::gen_range`: Renamed to `random_range`
[INFO] [stdout]    --> src/stats/deconvolution.rs:146:48
[INFO] [stdout]     |
[INFO] [stdout] 146 |                 let mut new_val = a + self.rng.gen_range(-perturbation_scale..perturbation_scale);
[INFO] [stdout]     |                                                ^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(deprecated)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unreachable statement
[INFO] [stdout]   --> src/cli.rs:60:13
[INFO] [stdout]    |
[INFO] [stdout] 59 |             let results = todo!();
[INFO] [stdout]    |                           ------- any code following this expression is unreachable
[INFO] [stdout] 60 |             let report = generate_report(&results)?;
[INFO] [stdout]    |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ unreachable statement
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unreachable_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unreachable statement
[INFO] [stdout]    --> src/cli.rs:148:13
[INFO] [stdout]     |
[INFO] [stdout] 146 |             let comparison_results = todo!();
[INFO] [stdout]     |                                      ------- any code following this expression is unreachable
[INFO] [stdout] 147 |
[INFO] [stdout] 148 |             println!("Comparison results: {:?}", comparison_results);
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ unreachable statement
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unreachable statement
[INFO] [stdout]    --> src/cli.rs:155:13
[INFO] [stdout]     |
[INFO] [stdout] 154 |             let results = todo!();
[INFO] [stdout]     |                           ------- any code following this expression is unreachable
[INFO] [stdout] 155 |             let report = generate_report(&results)?;
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ unreachable statement
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `generate_quality_plots` found for struct `FastqProcessor` in the current scope
[INFO] [stdout]    --> src/pipeline/report.rs:324:23
[INFO] [stdout]     |
[INFO] [stdout] 324 |             processor.generate_quality_plots(&results, &output)?;
[INFO] [stdout]     |                       ^^^^^^^^^^^^^^^^^^^^^^ method not found in `FastqProcessor`
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/pipeline/qc.rs:107:1
[INFO] [stdout]     |
[INFO] [stdout] 107 | pub struct FastqProcessor {
[INFO] [stdout]     | ------------------------- method `generate_quality_plots` not found for this struct
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `generate_taxonomy_plots` found for struct `FastqProcessor` in the current scope
[INFO] [stdout]    --> src/pipeline/report.rs:325:23
[INFO] [stdout]     |
[INFO] [stdout] 325 |             processor.generate_taxonomy_plots(&results, &output)?;
[INFO] [stdout]     |                       ^^^^^^^^^^^^^^^^^^^^^^^ method not found in `FastqProcessor`
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/pipeline/qc.rs:107:1
[INFO] [stdout]     |
[INFO] [stdout] 107 | pub struct FastqProcessor {
[INFO] [stdout]     | ------------------------- method `generate_taxonomy_plots` not found for this struct
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `rand::Rng::gen_range`: Renamed to `random_range`
[INFO] [stdout]    --> src/stats/deconvolution.rs:146:48
[INFO] [stdout]     |
[INFO] [stdout] 146 |                 let mut new_val = a + self.rng.gen_range(-perturbation_scale..perturbation_scale);
[INFO] [stdout]     |                                                ^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(deprecated)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `SVGBackend` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:440:20
[INFO] [stdout]     |
[INFO] [stdout] 440 |         let root = SVGBackend::new(&output_file, (width, height)).into_drawing_area();
[INFO] [stdout]     |                    ^^^^^^^^^^ use of undeclared type `SVGBackend`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ChartBuilder` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:445:25
[INFO] [stdout]     |
[INFO] [stdout] 445 |         let mut chart = ChartBuilder::on(&root)
[INFO] [stdout]     |                         ^^^^^^^^^^^^ use of undeclared type `ChartBuilder`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function, tuple struct or tuple variant `RGBColor` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:475:29
[INFO] [stdout]     |
[INFO] [stdout] 475 |                 let color = RGBColor(
[INFO] [stdout]     |                             ^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Polygon` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:486:32
[INFO] [stdout]     |
[INFO] [stdout] 486 |                     root.draw(&Polygon::new(
[INFO] [stdout]     |                                ^^^^^^^ use of undeclared type `Polygon`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `step` found for struct `std::ops::RangeInclusive<Idx>` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:488:30
[INFO] [stdout]     |
[INFO] [stdout] 487 | /                         (start_angle..=end_angle)
[INFO] [stdout] 488 | |                             .step(0.1)
[INFO] [stdout]     | |                             -^^^^ method not found in `std::ops::RangeInclusive<f64>`
[INFO] [stdout]     | |_____________________________|
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `step` found for struct `std::ops::RangeInclusive<Idx>` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:495:62
[INFO] [stdout]     |
[INFO] [stdout] 495 | ...                   .chain((start_angle..=end_angle).step(0.1).rev().map(|angle| {
[INFO] [stdout]     |                                                        ^^^^ method not found in `std::ops::RangeInclusive<f64>`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `TextStyle` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:513:29
[INFO] [stdout]     |
[INFO] [stdout] 513 |                 let style = TextStyle::from(("sans-serif", 12).into_font())
[INFO] [stdout]     |                             ^^^^^^^^^ use of undeclared type `TextStyle`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `into_font` found for tuple `(&str, {integer})` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:513:64
[INFO] [stdout]     |
[INFO] [stdout] 513 |                 let style = TextStyle::from(("sans-serif", 12).into_font())
[INFO] [stdout]     |                                                                ^^^^^^^^^ method not found in `(&str, {integer})`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `TextAlignment` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:517:25
[INFO] [stdout]     |
[INFO] [stdout] 517 |                         TextAlignment::right()
[INFO] [stdout]     |                         ^^^^^^^^^^^^^ use of undeclared type `TextAlignment`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `TextAlignment` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:519:25
[INFO] [stdout]     |
[INFO] [stdout] 519 |                         TextAlignment::left()
[INFO] [stdout]     |                         ^^^^^^^^^^^^^ use of undeclared type `TextAlignment`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `SVGBackend` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:551:20
[INFO] [stdout]     |
[INFO] [stdout] 551 |         let root = SVGBackend::new(&output_file, (width, height)).into_drawing_area();
[INFO] [stdout]     |                    ^^^^^^^^^^ use of undeclared type `SVGBackend`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ChartBuilder` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:563:29
[INFO] [stdout]     |
[INFO] [stdout] 563 |             let mut chart = ChartBuilder::on(&root)
[INFO] [stdout]     |                             ^^^^^^^^^^^^ use of undeclared type `ChartBuilder`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `TextStyle` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:573:18
[INFO] [stdout]     |
[INFO] [stdout] 573 |                 &TextStyle::from(("sans-serif", 20).into_font())
[INFO] [stdout]     |                  ^^^^^^^^^ use of undeclared type `TextStyle`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `into_font` found for tuple `(&str, {integer})` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:573:53
[INFO] [stdout]     |
[INFO] [stdout] 573 |                 &TextStyle::from(("sans-serif", 20).into_font())
[INFO] [stdout]     |                                                     ^^^^^^^^^ method not found in `(&str, {integer})`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `TextAlignment` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:576:29
[INFO] [stdout]     |
[INFO] [stdout] 576 |                     .anchor(TextAlignment::center()),
[INFO] [stdout]     |                             ^^^^^^^^^^^^^ use of undeclared type `TextAlignment`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ChartBuilder` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:600:29
[INFO] [stdout]     |
[INFO] [stdout] 600 |             let mut chart = ChartBuilder::on(&root)
[INFO] [stdout]     |                             ^^^^^^^^^^^^ use of undeclared type `ChartBuilder`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function, tuple struct or tuple variant `RGBColor` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:619:29
[INFO] [stdout]     |
[INFO] [stdout] 619 |                 let color = RGBColor(
[INFO] [stdout]     |                             ^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Rectangle` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:630:31
[INFO] [stdout]     |
[INFO] [stdout] 630 |                 let mut bar = Rectangle::new([(i, 0.0), (i + 1, value)], color.mix(0.8).filled());
[INFO] [stdout]     |                               ^^^^^^^^^ use of undeclared type `Rectangle`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `into_font` found for tuple `(&str, {float})` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:640:42
[INFO] [stdout]     |
[INFO] [stdout] 640 |                     ("sans-serif", 15.0).into_font().color(&BLACK).rotate(45.0),
[INFO] [stdout]     |                                          ^^^^^^^^^ method not found in `(&str, {float})`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `into_font` found for tuple `(&str, {float})` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:649:42
[INFO] [stdout]     |
[INFO] [stdout] 649 |                     ("sans-serif", 15.0).into_font().color(&BLACK),
[INFO] [stdout]     |                                          ^^^^^^^^^ method not found in `(&str, {float})`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `SVGBackend` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:673:20
[INFO] [stdout]     |
[INFO] [stdout] 673 |         let root = SVGBackend::new(&output_file, (width, height)).into_drawing_area();
[INFO] [stdout]     |                    ^^^^^^^^^^ use of undeclared type `SVGBackend`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ChartBuilder` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:716:29
[INFO] [stdout]     |
[INFO] [stdout] 716 |             let mut chart = ChartBuilder::on(&root)
[INFO] [stdout]     |                             ^^^^^^^^^^^^ use of undeclared type `ChartBuilder`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `TextStyle` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:726:18
[INFO] [stdout]     |
[INFO] [stdout] 726 |                 &TextStyle::from(("sans-serif", 20).into_font())
[INFO] [stdout]     |                  ^^^^^^^^^ use of undeclared type `TextStyle`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `into_font` found for tuple `(&str, {integer})` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:726:53
[INFO] [stdout]     |
[INFO] [stdout] 726 |                 &TextStyle::from(("sans-serif", 20).into_font())
[INFO] [stdout]     |                                                     ^^^^^^^^^ method not found in `(&str, {integer})`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `TextAlignment` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:729:29
[INFO] [stdout]     |
[INFO] [stdout] 729 |                     .anchor(TextAlignment::center()),
[INFO] [stdout]     |                             ^^^^^^^^^^^^^ use of undeclared type `TextAlignment`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ChartBuilder` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:740:29
[INFO] [stdout]     |
[INFO] [stdout] 740 |             let mut chart = ChartBuilder::on(&root)
[INFO] [stdout]     |                             ^^^^^^^^^^^^ use of undeclared type `ChartBuilder`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function, tuple struct or tuple variant `RGBColor` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:758:21
[INFO] [stdout]     |
[INFO] [stdout] 758 |                     RGBColor(255, 50, 50)
[INFO] [stdout]     |                     ^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function, tuple struct or tuple variant `RGBColor` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:760:21
[INFO] [stdout]     |
[INFO] [stdout] 760 |                     RGBColor(255, 200, 50)
[INFO] [stdout]     |                     ^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function, tuple struct or tuple variant `RGBColor` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:762:21
[INFO] [stdout]     |
[INFO] [stdout] 762 |                     RGBColor(50, 200, 50)
[INFO] [stdout]     |                     ^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Rectangle` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:765:31
[INFO] [stdout]     |
[INFO] [stdout] 765 |                 let mut bar = Rectangle::new([(0.0, i), (value, i + 1)], color.mix(0.8).filled());
[INFO] [stdout]     |                               ^^^^^^^^^ use of undeclared type `Rectangle`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `into_font` found for tuple `(&str, {float})` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:775:42
[INFO] [stdout]     |
[INFO] [stdout] 775 |                     ("sans-serif", 15.0).into_font().color(&BLACK),
[INFO] [stdout]     |                                          ^^^^^^^^^ method not found in `(&str, {float})`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `into_font` found for tuple `(&str, {float})` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:784:42
[INFO] [stdout]     |
[INFO] [stdout] 784 |                     ("sans-serif", 15.0).into_font().color(&BLACK),
[INFO] [stdout]     |                                          ^^^^^^^^^ method not found in `(&str, {float})`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `SVGBackend` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:815:20
[INFO] [stdout]     |
[INFO] [stdout] 815 |         let root = SVGBackend::new(&output_file, (width, height)).into_drawing_area();
[INFO] [stdout]     |                    ^^^^^^^^^^ use of undeclared type `SVGBackend`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ChartBuilder` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:819:25
[INFO] [stdout]     |
[INFO] [stdout] 819 |         let mut chart = ChartBuilder::on(&root)
[INFO] [stdout]     |                         ^^^^^^^^^^^^ use of undeclared type `ChartBuilder`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `TextStyle` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:832:14
[INFO] [stdout]     |
[INFO] [stdout] 832 |             &TextStyle::from(("sans-serif", 20).into_font())
[INFO] [stdout]     |              ^^^^^^^^^ use of undeclared type `TextStyle`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `into_font` found for tuple `(&str, {integer})` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:832:49
[INFO] [stdout]     |
[INFO] [stdout] 832 |             &TextStyle::from(("sans-serif", 20).into_font())
[INFO] [stdout]     |                                                 ^^^^^^^^^ method not found in `(&str, {integer})`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `TextAlignment` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:835:25
[INFO] [stdout]     |
[INFO] [stdout] 835 |                 .anchor(TextAlignment::center()),
[INFO] [stdout]     |                         ^^^^^^^^^^^^^ use of undeclared type `TextAlignment`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Hasher`
[INFO] [stdout]   --> src/sketch/signature.rs:11:23
[INFO] [stdout]    |
[INFO] [stdout] 11 | use std::hash::{Hash, Hasher};
[INFO] [stdout]    |                       ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `sample_name`
[INFO] [stdout]   --> src/count_table.rs:72:9
[INFO] [stdout]    |
[INFO] [stdout] 72 |         sample_name: &str, /* sample_counts: AppropriateDataStructure */
[INFO] [stdout]    |         ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_sample_name`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `builder_kmer_size`
[INFO] [stdout]    --> src/database/downloader.rs:872:9
[INFO] [stdout]     |
[INFO] [stdout] 872 |         builder_kmer_size: usize,    // Sketch size for builder setup
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_builder_kmer_size`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `builder_sketch_size`
[INFO] [stdout]    --> src/database/downloader.rs:873:9
[INFO] [stdout]     |
[INFO] [stdout] 873 |         builder_sketch_size: usize,
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_builder_sketch_size`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/normalization.rs:112:9
[INFO] [stdout]     |
[INFO] [stdout] 112 |     let mut normalized_counts = table.counts_matrix_mut();
[INFO] [stdout]     |         ----^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/normalization.rs:137:9
[INFO] [stdout]     |
[INFO] [stdout] 137 |     let mut counts = table.counts_matrix_mut();
[INFO] [stdout]     |         ----^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `table`
[INFO] [stdout]    --> src/normalization.rs:170:5
[INFO] [stdout]     |
[INFO] [stdout] 170 |     table: &mut CountTable, /*, feature_lengths: &[f64] or HashMap<String, f64> */
[INFO] [stdout]     |     ^^^^^ help: if this is intentional, prefix it with an underscore: `_table`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/sketch/signature.rs:439:13
[INFO] [stdout]     |
[INFO] [stdout] 439 |         let mut signature = KmerSignature {
[INFO] [stdout]     |             ----^^^^^^^^^
[INFO] [stdout]     |             |
[INFO] [stdout]     |             help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/sketch/mod.rs:96:13
[INFO] [stdout]    |
[INFO] [stdout] 96 |         let mut reader = parse_fastx_file(file_path.as_ref())?;
[INFO] [stdout]    |             ----^^^^^^
[INFO] [stdout]    |             |
[INFO] [stdout]    |             help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/sketch/mod.rs:107:17
[INFO] [stdout]     |
[INFO] [stdout] 107 |             let mut level_sig =
[INFO] [stdout]     |                 ----^^^^^^^^^
[INFO] [stdout]     |                 |
[INFO] [stdout]     |                 help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `reader`
[INFO] [stdout]   --> src/sketch/mod.rs:96:13
[INFO] [stdout]    |
[INFO] [stdout] 96 |         let mut reader = parse_fastx_file(file_path.as_ref())?;
[INFO] [stdout]    |             ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_reader`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `observed`
[INFO] [stdout]   --> src/stats/bayesian.rs:65:9
[INFO] [stdout]    |
[INFO] [stdout] 65 |         observed: &Array1<f64>,
[INFO] [stdout]    |         ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_observed`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]   --> src/stats/bayesian.rs:72:14
[INFO] [stdout]    |
[INFO] [stdout] 72 |         for (i, id) in self.strain_ids.iter().enumerate() {
[INFO] [stdout]    |              ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `SVGBackend` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:440:20
[INFO] [stdout]     |
[INFO] [stdout] 440 |         let root = SVGBackend::new(&output_file, (width, height)).into_drawing_area();
[INFO] [stdout]     |                    ^^^^^^^^^^ use of undeclared type `SVGBackend`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ChartBuilder` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:445:25
[INFO] [stdout]     |
[INFO] [stdout] 445 |         let mut chart = ChartBuilder::on(&root)
[INFO] [stdout]     |                         ^^^^^^^^^^^^ use of undeclared type `ChartBuilder`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0425, E0432, E0433, E0599.
[INFO] [stdout] 
[INFO] [stdout] For more information about an error, try `rustc --explain E0425`.
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `strain_ahsp` (lib) due to 61 previous errors; 36 warnings emitted
[INFO] [stderr] warning: build failed, waiting for other jobs to finish...
[INFO] [stdout] error[E0425]: cannot find function, tuple struct or tuple variant `RGBColor` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:475:29
[INFO] [stdout]     |
[INFO] [stdout] 475 |                 let color = RGBColor(
[INFO] [stdout]     |                             ^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Polygon` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:486:32
[INFO] [stdout]     |
[INFO] [stdout] 486 |                     root.draw(&Polygon::new(
[INFO] [stdout]     |                                ^^^^^^^ use of undeclared type `Polygon`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `step` found for struct `std::ops::RangeInclusive<Idx>` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:488:30
[INFO] [stdout]     |
[INFO] [stdout] 487 | /                         (start_angle..=end_angle)
[INFO] [stdout] 488 | |                             .step(0.1)
[INFO] [stdout]     | |                             -^^^^ method not found in `std::ops::RangeInclusive<f64>`
[INFO] [stdout]     | |_____________________________|
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `step` found for struct `std::ops::RangeInclusive<Idx>` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:495:62
[INFO] [stdout]     |
[INFO] [stdout] 495 | ...                   .chain((start_angle..=end_angle).step(0.1).rev().map(|angle| {
[INFO] [stdout]     |                                                        ^^^^ method not found in `std::ops::RangeInclusive<f64>`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `TextStyle` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:513:29
[INFO] [stdout]     |
[INFO] [stdout] 513 |                 let style = TextStyle::from(("sans-serif", 12).into_font())
[INFO] [stdout]     |                             ^^^^^^^^^ use of undeclared type `TextStyle`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `into_font` found for tuple `(&str, {integer})` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:513:64
[INFO] [stdout]     |
[INFO] [stdout] 513 |                 let style = TextStyle::from(("sans-serif", 12).into_font())
[INFO] [stdout]     |                                                                ^^^^^^^^^ method not found in `(&str, {integer})`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `TextAlignment` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:517:25
[INFO] [stdout]     |
[INFO] [stdout] 517 |                         TextAlignment::right()
[INFO] [stdout]     |                         ^^^^^^^^^^^^^ use of undeclared type `TextAlignment`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `TextAlignment` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:519:25
[INFO] [stdout]     |
[INFO] [stdout] 519 |                         TextAlignment::left()
[INFO] [stdout]     |                         ^^^^^^^^^^^^^ use of undeclared type `TextAlignment`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `SVGBackend` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:551:20
[INFO] [stdout]     |
[INFO] [stdout] 551 |         let root = SVGBackend::new(&output_file, (width, height)).into_drawing_area();
[INFO] [stdout]     |                    ^^^^^^^^^^ use of undeclared type `SVGBackend`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ChartBuilder` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:563:29
[INFO] [stdout]     |
[INFO] [stdout] 563 |             let mut chart = ChartBuilder::on(&root)
[INFO] [stdout]     |                             ^^^^^^^^^^^^ use of undeclared type `ChartBuilder`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `TextStyle` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:573:18
[INFO] [stdout]     |
[INFO] [stdout] 573 |                 &TextStyle::from(("sans-serif", 20).into_font())
[INFO] [stdout]     |                  ^^^^^^^^^ use of undeclared type `TextStyle`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `into_font` found for tuple `(&str, {integer})` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:573:53
[INFO] [stdout]     |
[INFO] [stdout] 573 |                 &TextStyle::from(("sans-serif", 20).into_font())
[INFO] [stdout]     |                                                     ^^^^^^^^^ method not found in `(&str, {integer})`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `TextAlignment` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:576:29
[INFO] [stdout]     |
[INFO] [stdout] 576 |                     .anchor(TextAlignment::center()),
[INFO] [stdout]     |                             ^^^^^^^^^^^^^ use of undeclared type `TextAlignment`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ChartBuilder` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:600:29
[INFO] [stdout]     |
[INFO] [stdout] 600 |             let mut chart = ChartBuilder::on(&root)
[INFO] [stdout]     |                             ^^^^^^^^^^^^ use of undeclared type `ChartBuilder`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function, tuple struct or tuple variant `RGBColor` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:619:29
[INFO] [stdout]     |
[INFO] [stdout] 619 |                 let color = RGBColor(
[INFO] [stdout]     |                             ^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Rectangle` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:630:31
[INFO] [stdout]     |
[INFO] [stdout] 630 |                 let mut bar = Rectangle::new([(i, 0.0), (i + 1, value)], color.mix(0.8).filled());
[INFO] [stdout]     |                               ^^^^^^^^^ use of undeclared type `Rectangle`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `into_font` found for tuple `(&str, {float})` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:640:42
[INFO] [stdout]     |
[INFO] [stdout] 640 |                     ("sans-serif", 15.0).into_font().color(&BLACK).rotate(45.0),
[INFO] [stdout]     |                                          ^^^^^^^^^ method not found in `(&str, {float})`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `into_font` found for tuple `(&str, {float})` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:649:42
[INFO] [stdout]     |
[INFO] [stdout] 649 |                     ("sans-serif", 15.0).into_font().color(&BLACK),
[INFO] [stdout]     |                                          ^^^^^^^^^ method not found in `(&str, {float})`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `SVGBackend` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:673:20
[INFO] [stdout]     |
[INFO] [stdout] 673 |         let root = SVGBackend::new(&output_file, (width, height)).into_drawing_area();
[INFO] [stdout]     |                    ^^^^^^^^^^ use of undeclared type `SVGBackend`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ChartBuilder` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:716:29
[INFO] [stdout]     |
[INFO] [stdout] 716 |             let mut chart = ChartBuilder::on(&root)
[INFO] [stdout]     |                             ^^^^^^^^^^^^ use of undeclared type `ChartBuilder`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `TextStyle` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:726:18
[INFO] [stdout]     |
[INFO] [stdout] 726 |                 &TextStyle::from(("sans-serif", 20).into_font())
[INFO] [stdout]     |                  ^^^^^^^^^ use of undeclared type `TextStyle`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `into_font` found for tuple `(&str, {integer})` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:726:53
[INFO] [stdout]     |
[INFO] [stdout] 726 |                 &TextStyle::from(("sans-serif", 20).into_font())
[INFO] [stdout]     |                                                     ^^^^^^^^^ method not found in `(&str, {integer})`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `TextAlignment` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:729:29
[INFO] [stdout]     |
[INFO] [stdout] 729 |                     .anchor(TextAlignment::center()),
[INFO] [stdout]     |                             ^^^^^^^^^^^^^ use of undeclared type `TextAlignment`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ChartBuilder` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:740:29
[INFO] [stdout]     |
[INFO] [stdout] 740 |             let mut chart = ChartBuilder::on(&root)
[INFO] [stdout]     |                             ^^^^^^^^^^^^ use of undeclared type `ChartBuilder`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function, tuple struct or tuple variant `RGBColor` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:758:21
[INFO] [stdout]     |
[INFO] [stdout] 758 |                     RGBColor(255, 50, 50)
[INFO] [stdout]     |                     ^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function, tuple struct or tuple variant `RGBColor` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:760:21
[INFO] [stdout]     |
[INFO] [stdout] 760 |                     RGBColor(255, 200, 50)
[INFO] [stdout]     |                     ^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function, tuple struct or tuple variant `RGBColor` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:762:21
[INFO] [stdout]     |
[INFO] [stdout] 762 |                     RGBColor(50, 200, 50)
[INFO] [stdout]     |                     ^^^^^^^^ not found in this scope
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `Rectangle` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:765:31
[INFO] [stdout]     |
[INFO] [stdout] 765 |                 let mut bar = Rectangle::new([(0.0, i), (value, i + 1)], color.mix(0.8).filled());
[INFO] [stdout]     |                               ^^^^^^^^^ use of undeclared type `Rectangle`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `into_font` found for tuple `(&str, {float})` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:775:42
[INFO] [stdout]     |
[INFO] [stdout] 775 |                     ("sans-serif", 15.0).into_font().color(&BLACK),
[INFO] [stdout]     |                                          ^^^^^^^^^ method not found in `(&str, {float})`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `into_font` found for tuple `(&str, {float})` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:784:42
[INFO] [stdout]     |
[INFO] [stdout] 784 |                     ("sans-serif", 15.0).into_font().color(&BLACK),
[INFO] [stdout]     |                                          ^^^^^^^^^ method not found in `(&str, {float})`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `SVGBackend` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:815:20
[INFO] [stdout]     |
[INFO] [stdout] 815 |         let root = SVGBackend::new(&output_file, (width, height)).into_drawing_area();
[INFO] [stdout]     |                    ^^^^^^^^^^ use of undeclared type `SVGBackend`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `ChartBuilder` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:819:25
[INFO] [stdout]     |
[INFO] [stdout] 819 |         let mut chart = ChartBuilder::on(&root)
[INFO] [stdout]     |                         ^^^^^^^^^^^^ use of undeclared type `ChartBuilder`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `TextStyle` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:832:14
[INFO] [stdout]     |
[INFO] [stdout] 832 |             &TextStyle::from(("sans-serif", 20).into_font())
[INFO] [stdout]     |              ^^^^^^^^^ use of undeclared type `TextStyle`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `into_font` found for tuple `(&str, {integer})` in the current scope
[INFO] [stdout]    --> src/visualization/plotter.rs:832:49
[INFO] [stdout]     |
[INFO] [stdout] 832 |             &TextStyle::from(("sans-serif", 20).into_font())
[INFO] [stdout]     |                                                 ^^^^^^^^^ method not found in `(&str, {integer})`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: cannot find type `TextAlignment` in this scope
[INFO] [stdout]    --> src/visualization/plotter.rs:835:25
[INFO] [stdout]     |
[INFO] [stdout] 835 |                 .anchor(TextAlignment::center()),
[INFO] [stdout]     |                         ^^^^^^^^^^^^^ use of undeclared type `TextAlignment`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `needletail::parser::FastxReader`
[INFO] [stdout]    --> src/bio/kmers.rs:216:9
[INFO] [stdout]     |
[INFO] [stdout] 216 |     use needletail::parser::FastxReader;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Hasher`
[INFO] [stdout]   --> src/sketch/signature.rs:11:23
[INFO] [stdout]    |
[INFO] [stdout] 11 | use std::hash::{Hash, Hasher};
[INFO] [stdout]    |                       ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `sample_name`
[INFO] [stdout]   --> src/count_table.rs:72:9
[INFO] [stdout]    |
[INFO] [stdout] 72 |         sample_name: &str, /* sample_counts: AppropriateDataStructure */
[INFO] [stdout]    |         ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_sample_name`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `builder_kmer_size`
[INFO] [stdout]    --> src/database/downloader.rs:872:9
[INFO] [stdout]     |
[INFO] [stdout] 872 |         builder_kmer_size: usize,    // Sketch size for builder setup
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_builder_kmer_size`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `builder_sketch_size`
[INFO] [stdout]    --> src/database/downloader.rs:873:9
[INFO] [stdout]     |
[INFO] [stdout] 873 |         builder_sketch_size: usize,
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_builder_sketch_size`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/normalization.rs:112:9
[INFO] [stdout]     |
[INFO] [stdout] 112 |     let mut normalized_counts = table.counts_matrix_mut();
[INFO] [stdout]     |         ----^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/normalization.rs:137:9
[INFO] [stdout]     |
[INFO] [stdout] 137 |     let mut counts = table.counts_matrix_mut();
[INFO] [stdout]     |         ----^^^^^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `table`
[INFO] [stdout]    --> src/normalization.rs:170:5
[INFO] [stdout]     |
[INFO] [stdout] 170 |     table: &mut CountTable, /*, feature_lengths: &[f64] or HashMap<String, f64> */
[INFO] [stdout]     |     ^^^^^ help: if this is intentional, prefix it with an underscore: `_table`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/sketch/signature.rs:439:13
[INFO] [stdout]     |
[INFO] [stdout] 439 |         let mut signature = KmerSignature {
[INFO] [stdout]     |             ----^^^^^^^^^
[INFO] [stdout]     |             |
[INFO] [stdout]     |             help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/sketch/mod.rs:96:13
[INFO] [stdout]    |
[INFO] [stdout] 96 |         let mut reader = parse_fastx_file(file_path.as_ref())?;
[INFO] [stdout]    |             ----^^^^^^
[INFO] [stdout]    |             |
[INFO] [stdout]    |             help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/sketch/mod.rs:107:17
[INFO] [stdout]     |
[INFO] [stdout] 107 |             let mut level_sig =
[INFO] [stdout]     |                 ----^^^^^^^^^
[INFO] [stdout]     |                 |
[INFO] [stdout]     |                 help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `reader`
[INFO] [stdout]   --> src/sketch/mod.rs:96:13
[INFO] [stdout]    |
[INFO] [stdout] 96 |         let mut reader = parse_fastx_file(file_path.as_ref())?;
[INFO] [stdout]    |             ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_reader`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `observed`
[INFO] [stdout]   --> src/stats/bayesian.rs:65:9
[INFO] [stdout]    |
[INFO] [stdout] 65 |         observed: &Array1<f64>,
[INFO] [stdout]    |         ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_observed`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]   --> src/stats/bayesian.rs:72:14
[INFO] [stdout]    |
[INFO] [stdout] 72 |         for (i, id) in self.strain_ids.iter().enumerate() {
[INFO] [stdout]    |              ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0425, E0432, E0433, E0599.
[INFO] [stdout] 
[INFO] [stdout] For more information about an error, try `rustc --explain E0425`.
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `strain_ahsp` (lib test) due to 61 previous errors; 47 warnings emitted
[INFO] running `Command { std: "docker" "inspect" "1336871fc0aa69db22195b2eabf0088200098888806205ec07c075537b743ddd", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "1336871fc0aa69db22195b2eabf0088200098888806205ec07c075537b743ddd", kill_on_drop: false }`
[INFO] [stdout] 1336871fc0aa69db22195b2eabf0088200098888806205ec07c075537b743ddd
