[INFO] fetching crate scrubby 0.4.0... [INFO] testing scrubby-0.4.0 against try#b83b707f97d809763b7861afa7638871f3339a33 for pr-145838-1 [INFO] extracting crate scrubby 0.4.0 into /workspace/builds/worker-5-tc2/source [INFO] started tweaking crates.io crate scrubby 0.4.0 [INFO] finished tweaking crates.io crate scrubby 0.4.0 [INFO] tweaked toml for crates.io crate scrubby 0.4.0 written to /workspace/builds/worker-5-tc2/source/Cargo.toml [INFO] validating manifest of crates.io crate scrubby 0.4.0 on toolchain b83b707f97d809763b7861afa7638871f3339a33 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+b83b707f97d809763b7861afa7638871f3339a33" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate crates.io crate scrubby 0.4.0 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" "+b83b707f97d809763b7861afa7638871f3339a33" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+b83b707f97d809763b7861afa7638871f3339a33" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 36e7ce37f1f5967bff0abd0ded61e11d1a72190d6490f54c1403411a8b4fd750 [INFO] running `Command { std: "docker" "start" "-a" "36e7ce37f1f5967bff0abd0ded61e11d1a72190d6490f54c1403411a8b4fd750", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "36e7ce37f1f5967bff0abd0ded61e11d1a72190d6490f54c1403411a8b4fd750", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "36e7ce37f1f5967bff0abd0ded61e11d1a72190d6490f54c1403411a8b4fd750", kill_on_drop: false }` [INFO] [stdout] 36e7ce37f1f5967bff0abd0ded61e11d1a72190d6490f54c1403411a8b4fd750 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+b83b707f97d809763b7861afa7638871f3339a33" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 373d7afda391228ac1a8b7a1f330dba4cfa8cf3f96b41926789dbd37e94b916e [INFO] running `Command { std: "docker" "start" "-a" "373d7afda391228ac1a8b7a1f330dba4cfa8cf3f96b41926789dbd37e94b916e", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.159 [INFO] [stderr] Compiling pkg-config v0.3.30 [INFO] [stderr] Compiling proc-macro2 v1.0.86 [INFO] [stderr] Compiling memchr v2.7.4 [INFO] [stderr] Compiling autocfg v1.3.0 [INFO] [stderr] Compiling pin-project-lite v0.2.14 [INFO] [stderr] Compiling bytes v1.7.2 [INFO] [stderr] Compiling once_cell v1.19.0 [INFO] [stderr] Compiling itoa v1.0.11 [INFO] [stderr] Compiling futures-core v0.3.30 [INFO] [stderr] Compiling bitflags v2.6.0 [INFO] [stderr] Compiling futures-sink v0.3.30 [INFO] [stderr] Compiling slab v0.4.9 [INFO] [stderr] Compiling tracing-core v0.1.32 [INFO] [stderr] Compiling quote v1.0.36 [INFO] [stderr] Compiling syn v2.0.72 [INFO] [stderr] Compiling http v1.1.0 [INFO] [stderr] Compiling jobserver v0.1.32 [INFO] [stderr] Compiling mio v1.0.2 [INFO] [stderr] Compiling socket2 v0.5.7 [INFO] [stderr] Compiling hashbrown v0.14.5 [INFO] [stderr] Compiling futures-io v0.3.30 [INFO] [stderr] Compiling cc v1.1.6 [INFO] [stderr] Compiling crossbeam-utils v0.8.20 [INFO] [stderr] Compiling tokio v1.40.0 [INFO] [stderr] Compiling openssl v0.10.66 [INFO] [stderr] Compiling log v0.4.22 [INFO] [stderr] Compiling httparse v1.9.4 [INFO] [stderr] Compiling futures-task v0.3.30 [INFO] [stderr] Compiling openssl-src v300.3.1+3.3.1 [INFO] [stderr] Compiling serde v1.0.204 [INFO] [stderr] Compiling futures-util v0.3.30 [INFO] [stderr] Compiling indexmap v2.5.0 [INFO] [stderr] Compiling http-body v1.0.1 [INFO] [stderr] Compiling tracing v0.1.40 [INFO] [stderr] Compiling tinyvec_macros v0.1.1 [INFO] [stderr] Compiling adler v1.0.2 [INFO] [stderr] Compiling rustix v0.38.37 [INFO] [stderr] Compiling native-tls v0.2.12 [INFO] [stderr] Compiling utf8parse v0.2.2 [INFO] [stderr] Compiling miniz_oxide v0.7.4 [INFO] [stderr] Compiling anstyle-parse v0.2.5 [INFO] [stderr] Compiling tinyvec v1.8.0 [INFO] [stderr] Compiling openssl-sys v0.9.103 [INFO] [stderr] Compiling zstd-sys v2.0.12+zstd.1.5.6 [INFO] [stderr] Compiling bzip2-sys v0.1.11+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling aho-corasick v1.1.3 [INFO] [stderr] Compiling futures-channel v0.3.30 [INFO] [stderr] Compiling crc32fast v1.4.2 [INFO] [stderr] Compiling linux-raw-sys v0.4.14 [INFO] [stderr] Compiling smallvec v1.13.2 [INFO] [stderr] Compiling colorchoice v1.0.2 [INFO] [stderr] Compiling regex-syntax v0.8.4 [INFO] [stderr] Compiling is_terminal_polyfill v1.70.1 [INFO] [stderr] Compiling zstd-safe v6.0.6 [INFO] [stderr] Compiling thiserror v1.0.63 [INFO] [stderr] Compiling anstyle v1.0.7 [INFO] [stderr] Compiling anstyle-query v1.1.1 [INFO] [stderr] Compiling openssl-probe v0.1.5 [INFO] [stderr] Compiling anstream v0.6.15 [INFO] [stderr] Compiling openssl-macros v0.1.1 [INFO] [stderr] Compiling serde_derive v1.0.204 [INFO] [stderr] Compiling tokio-util v0.7.12 [INFO] [stderr] Compiling thiserror-impl v1.0.63 [INFO] [stderr] Compiling h2 v0.4.6 [INFO] [stderr] Compiling regex-automata v0.4.7 [INFO] [stderr] Compiling flate2 v1.0.30 [INFO] [stderr] Compiling crossbeam-epoch v0.9.18 [INFO] [stderr] Compiling unicode-normalization v0.1.23 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling unicode-bidi v0.3.15 [INFO] [stderr] Compiling xz2 v0.1.7 [INFO] [stderr] Compiling crossbeam-deque v0.8.5 [INFO] [stderr] Compiling bzip2 v0.4.4 [INFO] [stderr] Compiling regex v1.10.5 [INFO] [stderr] Compiling idna v0.5.0 [INFO] [stderr] Compiling hyper v1.4.1 [INFO] [stderr] Compiling http-body-util v0.1.2 [INFO] [stderr] Compiling clap_lex v0.7.2 [INFO] [stderr] Compiling anyhow v1.0.86 [INFO] [stderr] Compiling rustls-pki-types v1.9.0 [INFO] [stderr] Compiling serde_json v1.0.121 [INFO] [stderr] Compiling strsim v0.11.1 [INFO] [stderr] Compiling rustls-pemfile v2.1.3 [INFO] [stderr] Compiling hyper-util v0.1.9 [INFO] [stderr] Compiling clap_builder v4.5.13 [INFO] [stderr] Compiling clap_derive v4.5.13 [INFO] [stderr] Compiling bgzip v0.2.2 [INFO] [stderr] Compiling url v2.5.2 [INFO] [stderr] Compiling env_filter v0.1.2 [INFO] [stderr] Compiling serde_urlencoded v0.7.1 [INFO] [stderr] Compiling xattr v1.3.1 [INFO] [stderr] Compiling rayon-core v1.12.1 [INFO] [stderr] Compiling filetime v0.2.25 [INFO] [stderr] Compiling buffer-redux v1.0.2 [INFO] [stderr] Compiling csv-core v0.1.11 [INFO] [stderr] Compiling sync_wrapper v1.0.1 [INFO] [stderr] Compiling encoding_rs v0.8.34 [INFO] [stderr] Compiling bytecount v0.6.8 [INFO] [stderr] Compiling fastrand v2.1.1 [INFO] [stderr] Compiling humantime v2.1.0 [INFO] [stderr] Compiling either v1.13.0 [INFO] [stderr] Compiling iana-time-zone v0.1.60 [INFO] [stderr] Compiling ipnet v2.10.0 [INFO] [stderr] Compiling tempfile v3.13.0 [INFO] [stderr] Compiling chrono v0.4.38 [INFO] [stderr] Compiling env_logger v0.11.5 [INFO] [stderr] Compiling rayon v1.10.0 [INFO] [stderr] Compiling needletail v0.5.1 [INFO] [stderr] Compiling clap v4.5.13 [INFO] [stderr] Compiling csv v1.3.0 [INFO] [stderr] Compiling tar v0.4.42 [INFO] [stderr] Compiling termcolor v1.4.1 [INFO] [stderr] Compiling zstd v0.12.4 [INFO] [stderr] Compiling niffler v2.5.0 [INFO] [stderr] Compiling tokio-native-tls v0.3.1 [INFO] [stderr] Compiling hyper-tls v0.6.0 [INFO] [stderr] Compiling reqwest v0.12.7 [INFO] [stderr] Compiling scrubby v0.4.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 4m 51s [INFO] running `Command { std: "docker" "inspect" "373d7afda391228ac1a8b7a1f330dba4cfa8cf3f96b41926789dbd37e94b916e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "373d7afda391228ac1a8b7a1f330dba4cfa8cf3f96b41926789dbd37e94b916e", kill_on_drop: false }` [INFO] [stdout] 373d7afda391228ac1a8b7a1f330dba4cfa8cf3f96b41926789dbd37e94b916e [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+b83b707f97d809763b7861afa7638871f3339a33" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 1f7382dacf6bf054a6897ef95e400b2b6fa938ddfae06bd51ffd2a86d95db84e [INFO] running `Command { std: "docker" "start" "-a" "1f7382dacf6bf054a6897ef95e400b2b6fa938ddfae06bd51ffd2a86d95db84e", kill_on_drop: false }` [INFO] [stderr] Compiling scrubby v0.4.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 2.45s [INFO] running `Command { std: "docker" "inspect" "1f7382dacf6bf054a6897ef95e400b2b6fa938ddfae06bd51ffd2a86d95db84e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "1f7382dacf6bf054a6897ef95e400b2b6fa938ddfae06bd51ffd2a86d95db84e", kill_on_drop: false }` [INFO] [stdout] 1f7382dacf6bf054a6897ef95e400b2b6fa938ddfae06bd51ffd2a86d95db84e [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+b83b707f97d809763b7861afa7638871f3339a33" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] 619edcfbcb7a6b18548845b742755d7e00ba4c199b01dae41a95e055526c8765 [INFO] running `Command { std: "docker" "start" "-a" "619edcfbcb7a6b18548845b742755d7e00ba4c199b01dae41a95e055526c8765", kill_on_drop: false }` [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.21s [INFO] [stderr] Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/scrubby-115b0476c074b6a8) [INFO] [stdout] [INFO] [stdout] running 0 tests [INFO] [stderr] Running unittests src/main.rs (/opt/rustwide/target/debug/deps/scrubby-a04574a5392f60c8) [INFO] [stdout] [INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] running 0 tests [INFO] [stdout] [INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] [stderr] Doc-tests scrubby [INFO] [stdout] [INFO] [stdout] running 80 tests [INFO] [stdout] test src/classifier.rs - classifier::KrakenReportRecord::from_str (line 446) ... FAILED [INFO] [stdout] test src/classifier.rs - classifier::get_tax_level (line 342) ... FAILED [INFO] [stdout] test src/classifier.rs - classifier::KrakenReadRecord::from_str (line 398) ... FAILED [INFO] [stdout] test src/classifier.rs - classifier::MetabuliReadRecord::from_str (line 494) ... FAILED [INFO] [stdout] test src/classifier.rs - classifier::get_taxids_from_report (line 121) ... FAILED [INFO] [stdout] test src/classifier.rs - classifier::get_taxid_reads_metabuli (line 305) ... FAILED [INFO] [stdout] test src/classifier.rs - classifier::TaxonCounts::update (line 88) ... FAILED [INFO] [stdout] test src/classifier.rs - classifier::TaxonCounts::new (line 68) ... FAILED [INFO] [stdout] test src/cleaner.rs - cleaner::Cleaner::run_aligner_output (line 201) ... FAILED [INFO] [stdout] test src/classifier.rs - classifier::get_taxid_reads_kraken (line 267) ... FAILED [INFO] [stdout] test src/cleaner.rs - cleaner::Cleaner::from_scrubby (line 102) ... FAILED [INFO] [stdout] test src/cleaner.rs - cleaner::Cleaner::clean_reads (line 230) ... FAILED [INFO] [stdout] test src/cleaner.rs - cleaner::FastqCleaner::clean_reads (line 727) ... FAILED [INFO] [stdout] test src/cleaner.rs - cleaner::Cleaner::run_classifier (line 153) ... FAILED [INFO] [stdout] test src/cleaner.rs - cleaner::SamtoolsConfig::from_scrubby (line 43) ... FAILED [INFO] [stdout] test src/cleaner.rs - cleaner::Cleaner::run_aligner (line 129) ... FAILED [INFO] [stdout] test src/download.rs - download::ScrubbyDownloader::download_index (line 160) ... FAILED [INFO] [stdout] test src/cleaner.rs - cleaner::Cleaner::run_classifier_output (line 172) ... FAILED [INFO] [stdout] test src/cleaner.rs - cleaner::FastqCleaner::from (line 706) ... FAILED [INFO] [stdout] test src/download.rs - download::ScrubbyDownloader::download (line 237) ... FAILED [INFO] [stdout] test src/download.rs - download::ScrubbyDownloader::builder (line 118) ... FAILED [INFO] [stdout] test src/cleaner.rs - cleaner::SamtoolsConfig::get_pipeline (line 75) ... FAILED [INFO] [stdout] test src/download.rs - download::ScrubbyDownloader::unpack (line 206) ... FAILED [INFO] [stdout] test src/download.rs - download::ScrubbyDownloader::list (line 130) ... FAILED [INFO] [stdout] test src/download.rs - download::ScrubbyDownloaderBuilder::aligner (line 307) ... FAILED [INFO] [stdout] test src/download.rs - download::ScrubbyDownloader::new (line 101) ... FAILED [INFO] [stdout] test src/download.rs - download::ScrubbyDownloaderBuilder::base_url (line 352) ... FAILED [INFO] [stdout] test src/download.rs - download::ScrubbyDownloaderBuilder::build (line 397) ... FAILED [INFO] [stdout] test src/download.rs - download::ScrubbyDownloaderBuilder::new (line 282) ... FAILED [INFO] [stdout] test src/download.rs - download::ScrubbyDownloaderBuilder::timeout (line 337) ... FAILED [INFO] [stdout] test src/download.rs - download::ScrubbyDownloaderBuilder::classifier (line 322) ... FAILED [INFO] [stdout] test src/download.rs - download::ScrubbyDownloaderBuilder::password (line 382) ... FAILED [INFO] [stdout] test src/download.rs - download::ScrubbyIndex::classifier_name (line 44) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::Scrubby::new (line 193) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::aligner (line 500) ... FAILED [INFO] [stdout] test src/download.rs - download::ScrubbyDownloaderBuilder::username (line 367) ... FAILED [INFO] [stdout] test src/download.rs - download::ScrubbyIndex::fmt (line 63) ... FAILED [INFO] [stdout] test src/download.rs - download::ScrubbyIndex::aligner_name (line 28) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::Scrubby::builder (line 228) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::Scrubby::clean (line 249) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::aligner_args (line 705) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::aligner_index (line 638) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::classifier_args (line 692) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::classifier_index (line 652) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::classifier (line 583) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::alignment_format (line 527) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::command (line 420) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::build_classifier (line 967) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::build_alignment (line 1008) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::alignment (line 513) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::build (line 802) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::extract (line 448) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::min_mapq (line 569) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::index (line 624) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::keep (line 461) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::min_query_length (line 541) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::needletail_parallel (line 731) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::json (line 406) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::min_query_coverage (line 555) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::reads (line 596) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::preset (line 744) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::new (line 337) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::read_ids (line 392) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::taxa_direct (line 679) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::report (line 610) ... FAILED [INFO] [stdout] test src/terminal.rs - terminal::AlignmentArgs::validate_and_build (line 406) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::unpaired (line 474) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::samtools_threads (line 718) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::taxa (line 666) ... FAILED [INFO] [stdout] test src/terminal.rs - terminal::DiffArgs::validate_and_build (line 540) ... FAILED [INFO] [stdout] test src/terminal.rs - terminal::ClassifierArgs::validate_and_build (line 294) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::threads (line 487) ... FAILED [INFO] [stdout] test src/scrubby.rs - scrubby::ScrubbyBuilder::workdir (line 434) ... FAILED [INFO] [stdout] test src/utils.rs - utils::get_id (line 88) ... FAILED [INFO] [stdout] test src/utils.rs - utils::get_fastx_writer (line 53) ... FAILED [INFO] [stdout] test src/utils.rs - utils::ReadDifferenceBuilder::json (line 323) ... FAILED [INFO] [stdout] test src/utils.rs - utils::ReadDifferenceBuilder::read_ids (line 309) ... FAILED [INFO] [stdout] test src/terminal.rs - terminal::DownloadArgs::validate_and_build (line 475) ... FAILED [INFO] [stdout] test src/terminal.rs - terminal::ReadsArgs::validate_and_build (line 172) ... FAILED [INFO] [stdout] test src/utils.rs - utils::niffler::compression::Format::from_path (line 24) ... FAILED [INFO] [stdout] [INFO] [stdout] failures: [INFO] [stdout] [INFO] [stdout] ---- src/classifier.rs - classifier::KrakenReportRecord::from_str (line 446) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `KrakenReportRecord` [INFO] [stdout] --> src/classifier.rs:447:14 [INFO] [stdout] | [INFO] [stdout] 3 | let record = KrakenReportRecord::from_str("0.05\t100\t50\tS\t12345\ttaxon_name".to_string()).unwrap(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ use of undeclared type `KrakenReportRecord` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::classifier::KrakenReportRecord; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0433`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/classifier.rs - classifier::get_tax_level (line 342) stdout ---- [INFO] [stdout] error[E0425]: cannot find function `get_tax_level` in this scope [INFO] [stdout] --> src/classifier.rs:343:17 [INFO] [stdout] | [INFO] [stdout] 3 | let tax_level = get_tax_level(&record); [INFO] [stdout] | ^^^^^^^^^^^^^ not found in this scope [INFO] [stdout] | [INFO] [stdout] help: consider importing this function [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::classifier::get_tax_level; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `record` in this scope [INFO] [stdout] --> src/classifier.rs:343:32 [INFO] [stdout] | [INFO] [stdout] 3 | let tax_level = get_tax_level(&record); [INFO] [stdout] | ^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 2 previous errors [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/classifier.rs - classifier::KrakenReadRecord::from_str (line 398) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `KrakenReadRecord` [INFO] [stdout] --> src/classifier.rs:399:14 [INFO] [stdout] | [INFO] [stdout] 3 | let record = KrakenReadRecord::from_str("C\tread1\t12345\t100\tannotation".to_string()).unwrap(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^ use of undeclared type `KrakenReadRecord` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::classifier::KrakenReadRecord; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0433`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/classifier.rs - classifier::MetabuliReadRecord::from_str (line 494) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `MetabuliReadRecord` [INFO] [stdout] --> src/classifier.rs:495:14 [INFO] [stdout] | [INFO] [stdout] 3 | let record = MetabuliReadRecord::from_str("1\tread1\t12345\t100\t80.5\tgenus\tannotation".to_string()).unwrap(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ use of undeclared type `MetabuliReadRecord` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::classifier::MetabuliReadRecord; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0433`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/classifier.rs - classifier::get_taxids_from_report (line 121) stdout ---- [INFO] [stdout] error[E0425]: cannot find function `get_taxids_from_report` in this scope [INFO] [stdout] --> src/classifier.rs:122:14 [INFO] [stdout] | [INFO] [stdout] 3 | let taxids = get_taxids_from_report(&report_path, &vec!["Eukaryota".to_string()], &vec![]).unwrap(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ not found in this scope [INFO] [stdout] | [INFO] [stdout] help: consider importing this function [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::classifier::get_taxids_from_report; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `report_path` in this scope [INFO] [stdout] --> src/classifier.rs:122:38 [INFO] [stdout] | [INFO] [stdout] 3 | let taxids = get_taxids_from_report(&report_path, &vec!["Eukaryota".to_string()], &vec![]).unwrap(); [INFO] [stdout] | ^^^^^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 2 previous errors [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/classifier.rs - classifier::get_taxid_reads_metabuli (line 305) stdout ---- [INFO] [stdout] error[E0425]: cannot find function `get_taxid_reads_metabuli` in this scope [INFO] [stdout] --> src/classifier.rs:306:16 [INFO] [stdout] | [INFO] [stdout] 3 | let read_ids = get_taxid_reads_metabuli(taxids, &reads_path).unwrap(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ not found in this scope [INFO] [stdout] | [INFO] [stdout] help: consider importing this function [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::classifier::get_taxid_reads_metabuli; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `taxids` in this scope [INFO] [stdout] --> src/classifier.rs:306:41 [INFO] [stdout] | [INFO] [stdout] 3 | let read_ids = get_taxid_reads_metabuli(taxids, &reads_path).unwrap(); [INFO] [stdout] | ^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `reads_path` in this scope [INFO] [stdout] --> src/classifier.rs:306:50 [INFO] [stdout] | [INFO] [stdout] 3 | let read_ids = get_taxid_reads_metabuli(taxids, &reads_path).unwrap(); [INFO] [stdout] | ^^^^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/classifier.rs - classifier::TaxonCounts::update (line 88) stdout ---- [INFO] [stdout] error[E0425]: cannot find value `taxon_counts` in this scope [INFO] [stdout] --> src/classifier.rs:89:1 [INFO] [stdout] | [INFO] [stdout] 3 | taxon_counts.update("GenusA".to_string(), "FamilyA".to_string(), 10); [INFO] [stdout] | ^^^^^^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/classifier.rs - classifier::TaxonCounts::new (line 68) stdout ---- [INFO] [stdout] error[E0432]: unresolved import `scrubby::TaxonCounts` [INFO] [stdout] --> src/classifier.rs:70:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::TaxonCounts; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ no `TaxonCounts` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::classifier::TaxonCounts; [INFO] [stdout] | ++++++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/cleaner.rs - cleaner::Cleaner::run_aligner_output (line 201) stdout ---- [INFO] [stdout] error[E0425]: cannot find value `cleaner` in this scope [INFO] [stdout] --> src/cleaner.rs:202:1 [INFO] [stdout] | [INFO] [stdout] 3 | cleaner.run_aligner_output().unwrap(); [INFO] [stdout] | ^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/classifier.rs - classifier::get_taxid_reads_kraken (line 267) stdout ---- [INFO] [stdout] error[E0425]: cannot find function `get_taxid_reads_kraken` in this scope [INFO] [stdout] --> src/classifier.rs:268:16 [INFO] [stdout] | [INFO] [stdout] 3 | let read_ids = get_taxid_reads_kraken(taxids, &reads_path).unwrap(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ not found in this scope [INFO] [stdout] | [INFO] [stdout] help: consider importing this function [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::classifier::get_taxid_reads_kraken; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `taxids` in this scope [INFO] [stdout] --> src/classifier.rs:268:39 [INFO] [stdout] | [INFO] [stdout] 3 | let read_ids = get_taxid_reads_kraken(taxids, &reads_path).unwrap(); [INFO] [stdout] | ^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `reads_path` in this scope [INFO] [stdout] --> src/classifier.rs:268:48 [INFO] [stdout] | [INFO] [stdout] 3 | let read_ids = get_taxid_reads_kraken(taxids, &reads_path).unwrap(); [INFO] [stdout] | ^^^^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/cleaner.rs - cleaner::Cleaner::from_scrubby (line 102) stdout ---- [INFO] [stdout] error[E0432]: unresolved import `scrubby::Cleaner` [INFO] [stdout] --> src/cleaner.rs:104:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::Cleaner; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ no `Cleaner` in the root [INFO] [stdout] | [INFO] [stdout] help: a similar name exists in the module (notice the capitalization) [INFO] [stdout] | [INFO] [stdout] 5 - use scrubby::Cleaner; [INFO] [stdout] 5 + use scrubby::cleaner; [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::cleaner::Cleaner; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `scrubby_instance` in this scope [INFO] [stdout] --> src/cleaner.rs:105:38 [INFO] [stdout] | [INFO] [stdout] 6 | let cleaner = Cleaner::from_scrubby(&scrubby_instance).unwrap(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 2 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0425, E0432. [INFO] [stdout] For more information about an error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/cleaner.rs - cleaner::Cleaner::clean_reads (line 230) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `HashSet` [INFO] [stdout] --> src/cleaner.rs:231:16 [INFO] [stdout] | [INFO] [stdout] 3 | let read_ids = HashSet::new(); [INFO] [stdout] | ^^^^^^^ use of undeclared type `HashSet` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use std::collections::HashSet; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `cleaner` in this scope [INFO] [stdout] --> src/cleaner.rs:232:1 [INFO] [stdout] | [INFO] [stdout] 4 | cleaner.clean_reads(&read_ids).unwrap(); [INFO] [stdout] | ^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 2 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0425, E0433. [INFO] [stdout] For more information about an error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/cleaner.rs - cleaner::FastqCleaner::clean_reads (line 727) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `HashSet` [INFO] [stdout] --> src/cleaner.rs:728:16 [INFO] [stdout] | [INFO] [stdout] 3 | let read_ids = HashSet::new(); [INFO] [stdout] | ^^^^^^^ use of undeclared type `HashSet` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use std::collections::HashSet; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `cleaner` in this scope [INFO] [stdout] --> src/cleaner.rs:729:1 [INFO] [stdout] | [INFO] [stdout] 4 | cleaner.clean_reads(&read_ids, false).unwrap(); [INFO] [stdout] | ^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 2 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0425, E0433. [INFO] [stdout] For more information about an error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/cleaner.rs - cleaner::Cleaner::run_classifier (line 153) stdout ---- [INFO] [stdout] error[E0425]: cannot find value `cleaner` in this scope [INFO] [stdout] --> src/cleaner.rs:154:1 [INFO] [stdout] | [INFO] [stdout] 3 | cleaner.run_classifier().unwrap(); [INFO] [stdout] | ^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/cleaner.rs - cleaner::SamtoolsConfig::from_scrubby (line 43) stdout ---- [INFO] [stdout] error[E0432]: unresolved import `scrubby::SamtoolsConfig` [INFO] [stdout] --> src/cleaner.rs:45:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::SamtoolsConfig; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `SamtoolsConfig` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::cleaner::SamtoolsConfig; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `scrubby_instance` in this scope [INFO] [stdout] --> src/cleaner.rs:46:53 [INFO] [stdout] | [INFO] [stdout] 6 | let samtools_config = SamtoolsConfig::from_scrubby(&scrubby_instance); [INFO] [stdout] | ^^^^^^^^^^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 2 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0425, E0432. [INFO] [stdout] For more information about an error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/cleaner.rs - cleaner::Cleaner::run_aligner (line 129) stdout ---- [INFO] [stdout] error[E0425]: cannot find value `cleaner` in this scope [INFO] [stdout] --> src/cleaner.rs:130:1 [INFO] [stdout] | [INFO] [stdout] 3 | cleaner.run_aligner().unwrap(); [INFO] [stdout] | ^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloader::download_index (line 160) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyDownloader` [INFO] [stdout] --> src/download.rs:161:18 [INFO] [stdout] | [INFO] [stdout] 3 | let downloader = ScrubbyDownloader::new(outdir, indices); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloader` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyDownloader; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope [INFO] [stdout] --> src/download.rs:161:41 [INFO] [stdout] | [INFO] [stdout] 3 | let downloader = ScrubbyDownloader::new(outdir, indices); [INFO] [stdout] | ^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `indices` in this scope [INFO] [stdout] --> src/download.rs:161:49 [INFO] [stdout] | [INFO] [stdout] 3 | let downloader = ScrubbyDownloader::new(outdir, indices); [INFO] [stdout] | ^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0425, E0433. [INFO] [stdout] For more information about an error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/cleaner.rs - cleaner::Cleaner::run_classifier_output (line 172) stdout ---- [INFO] [stdout] error[E0425]: cannot find value `cleaner` in this scope [INFO] [stdout] --> src/cleaner.rs:173:1 [INFO] [stdout] | [INFO] [stdout] 3 | cleaner.run_classifier_output().unwrap(); [INFO] [stdout] | ^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/cleaner.rs - cleaner::FastqCleaner::from (line 706) stdout ---- [INFO] [stdout] error[E0432]: unresolved import `scrubby::FastqCleaner` [INFO] [stdout] --> src/cleaner.rs:708:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::FastqCleaner; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ no `FastqCleaner` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::cleaner::FastqCleaner; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `input_path` in this scope [INFO] [stdout] --> src/cleaner.rs:709:35 [INFO] [stdout] | [INFO] [stdout] 6 | let cleaner = FastqCleaner::from(&input_path, &output_path); [INFO] [stdout] | ^^^^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `output_path` in this scope [INFO] [stdout] --> src/cleaner.rs:709:48 [INFO] [stdout] | [INFO] [stdout] 6 | let cleaner = FastqCleaner::from(&input_path, &output_path); [INFO] [stdout] | ^^^^^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0425, E0432. [INFO] [stdout] For more information about an error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloader::download (line 237) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyDownloader` [INFO] [stdout] --> src/download.rs:238:18 [INFO] [stdout] | [INFO] [stdout] 3 | let downloader = ScrubbyDownloader::new(outdir, indices); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloader` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyDownloader; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope [INFO] [stdout] --> src/download.rs:238:41 [INFO] [stdout] | [INFO] [stdout] 3 | let downloader = ScrubbyDownloader::new(outdir, indices); [INFO] [stdout] | ^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `indices` in this scope [INFO] [stdout] --> src/download.rs:238:49 [INFO] [stdout] | [INFO] [stdout] 3 | let downloader = ScrubbyDownloader::new(outdir, indices); [INFO] [stdout] | ^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0423]: expected value, found built-in attribute `path` [INFO] [stdout] --> src/download.rs:239:42 [INFO] [stdout] | [INFO] [stdout] 4 | downloader.download("file_name.tar.xz", &path); [INFO] [stdout] | ^^^^ not a value [INFO] [stdout] [INFO] [stdout] error: aborting due to 4 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0423, E0425, E0433. [INFO] [stdout] For more information about an error, try `rustc --explain E0423`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloader::builder (line 118) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `PathBuf` [INFO] [stdout] --> src/download.rs:119:14 [INFO] [stdout] | [INFO] [stdout] 3 | let outdir = PathBuf::from("/path/to/output"); [INFO] [stdout] | ^^^^^^^ use of undeclared type `PathBuf` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use std::path::PathBuf; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyIndex` [INFO] [stdout] --> src/download.rs:120:20 [INFO] [stdout] | [INFO] [stdout] 4 | let indices = vec![ScrubbyIndex::Chm13v2]; [INFO] [stdout] | ^^^^^^^^^^^^ use of undeclared type `ScrubbyIndex` [INFO] [stdout] | [INFO] [stdout] help: consider importing this enum [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyIndex; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyDownloader` [INFO] [stdout] --> src/download.rs:121:15 [INFO] [stdout] | [INFO] [stdout] 5 | let builder = ScrubbyDownloader::builder(outdir, indices); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloader` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyDownloader; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0433`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/cleaner.rs - cleaner::SamtoolsConfig::get_pipeline (line 75) stdout ---- [INFO] [stdout] error[E0425]: cannot find value `samtools_config` in this scope [INFO] [stdout] --> src/cleaner.rs:76:16 [INFO] [stdout] | [INFO] [stdout] 3 | let pipeline = samtools_config.get_pipeline(); [INFO] [stdout] | ^^^^^^^^^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloader::unpack (line 206) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyDownloader` [INFO] [stdout] --> src/download.rs:207:18 [INFO] [stdout] | [INFO] [stdout] 3 | let downloader = ScrubbyDownloader::new(outdir, indices); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloader` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyDownloader; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope [INFO] [stdout] --> src/download.rs:207:41 [INFO] [stdout] | [INFO] [stdout] 3 | let downloader = ScrubbyDownloader::new(outdir, indices); [INFO] [stdout] | ^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `indices` in this scope [INFO] [stdout] --> src/download.rs:207:49 [INFO] [stdout] | [INFO] [stdout] 3 | let downloader = ScrubbyDownloader::new(outdir, indices); [INFO] [stdout] | ^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `download_path` in this scope [INFO] [stdout] --> src/download.rs:208:20 [INFO] [stdout] | [INFO] [stdout] 4 | downloader.unpack(&download_path, &outdir); [INFO] [stdout] | ^^^^^^^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope [INFO] [stdout] --> src/download.rs:208:36 [INFO] [stdout] | [INFO] [stdout] 4 | downloader.unpack(&download_path, &outdir); [INFO] [stdout] | ^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 5 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0425, E0433. [INFO] [stdout] For more information about an error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloader::list (line 130) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyDownloader` [INFO] [stdout] --> src/download.rs:131:18 [INFO] [stdout] | [INFO] [stdout] 3 | let downloader = ScrubbyDownloader::new(outdir, indices); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloader` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyDownloader; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope [INFO] [stdout] --> src/download.rs:131:41 [INFO] [stdout] | [INFO] [stdout] 3 | let downloader = ScrubbyDownloader::new(outdir, indices); [INFO] [stdout] | ^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `indices` in this scope [INFO] [stdout] --> src/download.rs:131:49 [INFO] [stdout] | [INFO] [stdout] 3 | let downloader = ScrubbyDownloader::new(outdir, indices); [INFO] [stdout] | ^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0425, E0433. [INFO] [stdout] For more information about an error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloaderBuilder::aligner (line 307) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyDownloaderBuilder` [INFO] [stdout] --> src/download.rs:308:15 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).aligner(vec![Aligner::Bowtie2]); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloaderBuilder` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyDownloaderBuilder; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope [INFO] [stdout] --> src/download.rs:308:45 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).aligner(vec![Aligner::Bowtie2]); [INFO] [stdout] | ^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `indices` in this scope [INFO] [stdout] --> src/download.rs:308:53 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).aligner(vec![Aligner::Bowtie2]); [INFO] [stdout] | ^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `Aligner` [INFO] [stdout] --> src/download.rs:308:75 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).aligner(vec![Aligner::Bowtie2]); [INFO] [stdout] | ^^^^^^^ use of undeclared type `Aligner` [INFO] [stdout] | [INFO] [stdout] help: consider importing this enum [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::Aligner; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error: aborting due to 4 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0425, E0433. [INFO] [stdout] For more information about an error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloader::new (line 101) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `PathBuf` [INFO] [stdout] --> src/download.rs:102:14 [INFO] [stdout] | [INFO] [stdout] 3 | let outdir = PathBuf::from("/path/to/output"); [INFO] [stdout] | ^^^^^^^ use of undeclared type `PathBuf` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use std::path::PathBuf; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyIndex` [INFO] [stdout] --> src/download.rs:103:20 [INFO] [stdout] | [INFO] [stdout] 4 | let indices = vec![ScrubbyIndex::Chm13v2]; [INFO] [stdout] | ^^^^^^^^^^^^ use of undeclared type `ScrubbyIndex` [INFO] [stdout] | [INFO] [stdout] help: consider importing this enum [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyIndex; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyDownloader` [INFO] [stdout] --> src/download.rs:104:18 [INFO] [stdout] | [INFO] [stdout] 5 | let downloader = ScrubbyDownloader::new(outdir, indices); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloader` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyDownloader; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0433`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloaderBuilder::base_url (line 352) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyDownloaderBuilder` [INFO] [stdout] --> src/download.rs:353:15 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).base_url("https://example.com"); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloaderBuilder` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyDownloaderBuilder; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope [INFO] [stdout] --> src/download.rs:353:45 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).base_url("https://example.com"); [INFO] [stdout] | ^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `indices` in this scope [INFO] [stdout] --> src/download.rs:353:53 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).base_url("https://example.com"); [INFO] [stdout] | ^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0425, E0433. [INFO] [stdout] For more information about an error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloaderBuilder::build (line 397) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyDownloaderBuilder` [INFO] [stdout] --> src/download.rs:398:15 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloaderBuilder` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyDownloaderBuilder; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope [INFO] [stdout] --> src/download.rs:398:45 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices); [INFO] [stdout] | ^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `indices` in this scope [INFO] [stdout] --> src/download.rs:398:53 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices); [INFO] [stdout] | ^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0425, E0433. [INFO] [stdout] For more information about an error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloaderBuilder::new (line 282) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `PathBuf` [INFO] [stdout] --> src/download.rs:283:14 [INFO] [stdout] | [INFO] [stdout] 3 | let outdir = PathBuf::from("/path/to/output"); [INFO] [stdout] | ^^^^^^^ use of undeclared type `PathBuf` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use std::path::PathBuf; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyIndex` [INFO] [stdout] --> src/download.rs:284:20 [INFO] [stdout] | [INFO] [stdout] 4 | let indices = vec![ScrubbyIndex::Chm13v2]; [INFO] [stdout] | ^^^^^^^^^^^^ use of undeclared type `ScrubbyIndex` [INFO] [stdout] | [INFO] [stdout] help: consider importing this enum [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyIndex; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyDownloaderBuilder` [INFO] [stdout] --> src/download.rs:285:15 [INFO] [stdout] | [INFO] [stdout] 5 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloaderBuilder` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyDownloaderBuilder; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0433`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloaderBuilder::timeout (line 337) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyDownloaderBuilder` [INFO] [stdout] --> src/download.rs:338:15 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).timeout(60); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloaderBuilder` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyDownloaderBuilder; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope [INFO] [stdout] --> src/download.rs:338:45 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).timeout(60); [INFO] [stdout] | ^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `indices` in this scope [INFO] [stdout] --> src/download.rs:338:53 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).timeout(60); [INFO] [stdout] | ^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0425, E0433. [INFO] [stdout] For more information about an error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloaderBuilder::classifier (line 322) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyDownloaderBuilder` [INFO] [stdout] --> src/download.rs:323:15 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).classifier(vec![Classifier::new()]); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloaderBuilder` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyDownloaderBuilder; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope [INFO] [stdout] --> src/download.rs:323:45 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).classifier(vec![Classifier::new()]); [INFO] [stdout] | ^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `indices` in this scope [INFO] [stdout] --> src/download.rs:323:53 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).classifier(vec![Classifier::new()]); [INFO] [stdout] | ^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `Classifier` [INFO] [stdout] --> src/download.rs:323:78 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).classifier(vec![Classifier::new()]); [INFO] [stdout] | ^^^^^^^^^^ use of undeclared type `Classifier` [INFO] [stdout] | [INFO] [stdout] help: consider importing this enum [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::Classifier; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error: aborting due to 4 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0425, E0433. [INFO] [stdout] For more information about an error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloaderBuilder::password (line 382) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyDownloaderBuilder` [INFO] [stdout] --> src/download.rs:383:15 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).password("pass"); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloaderBuilder` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyDownloaderBuilder; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope [INFO] [stdout] --> src/download.rs:383:45 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).password("pass"); [INFO] [stdout] | ^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `indices` in this scope [INFO] [stdout] --> src/download.rs:383:53 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).password("pass"); [INFO] [stdout] | ^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0425, E0433. [INFO] [stdout] For more information about an error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/download.rs - download::ScrubbyIndex::classifier_name (line 44) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyIndex` [INFO] [stdout] --> src/download.rs:45:13 [INFO] [stdout] | [INFO] [stdout] 3 | let index = ScrubbyIndex::Chm13v2; [INFO] [stdout] | ^^^^^^^^^^^^ use of undeclared type `ScrubbyIndex` [INFO] [stdout] | [INFO] [stdout] help: consider importing this enum [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyIndex; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `Classifier` [INFO] [stdout] --> src/download.rs:46:18 [INFO] [stdout] | [INFO] [stdout] 4 | let classifier = Classifier::new(); [INFO] [stdout] | ^^^^^^^^^^ use of undeclared type `Classifier` [INFO] [stdout] | [INFO] [stdout] help: consider importing this enum [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::Classifier; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error: aborting due to 2 previous errors [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0433`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::Scrubby::new (line 193) stdout ---- [INFO] [stdout] error: unexpected closing delimiter: `)` [INFO] [stdout] --> src/scrubby.rs:203:2 [INFO] [stdout] | [INFO] [stdout] 1 | use scrubby::{Scrubby, Aligner, Classifier}; [INFO] [stdout] | - this opening brace... - ...matches this closing brace [INFO] [stdout] ... [INFO] [stdout] 10 | )).unwrap(); [INFO] [stdout] | ^ unexpected closing delimiter [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::aligner (line 500) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:504:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).aligner(Aligner::Minimap2); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).aligner(Aligner::Minimap2); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).aligner(Aligner::Minimap2); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).aligner(Aligner::Minimap2); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..=).aligner(Aligner::Minimap2); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:504:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).aligner(Aligner::Minimap2); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).aligner(Aligner::Minimap2); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).aligner(Aligner::Minimap2); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved imports `scrubby::ScrubbyBuilder`, `scrubby::Aligner` [INFO] [stdout] --> src/scrubby.rs:502:15 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::{ScrubbyBuilder, Aligner}; [INFO] [stdout] | ^^^^^^^^^^^^^^ ^^^^^^^ no `Aligner` in the root [INFO] [stdout] | | [INFO] [stdout] | no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] = help: consider importing this struct instead: [INFO] [stdout] scrubby::prelude::ScrubbyBuilder [INFO] [stdout] = help: consider importing this enum instead: [INFO] [stdout] scrubby::prelude::Aligner [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/download.rs - download::ScrubbyDownloaderBuilder::username (line 367) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyDownloaderBuilder` [INFO] [stdout] --> src/download.rs:368:15 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).username("user"); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ use of undeclared type `ScrubbyDownloaderBuilder` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyDownloaderBuilder; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `outdir` in this scope [INFO] [stdout] --> src/download.rs:368:45 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).username("user"); [INFO] [stdout] | ^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `indices` in this scope [INFO] [stdout] --> src/download.rs:368:53 [INFO] [stdout] | [INFO] [stdout] 3 | let builder = ScrubbyDownloaderBuilder::new(outdir, indices).username("user"); [INFO] [stdout] | ^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0425, E0433. [INFO] [stdout] For more information about an error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/download.rs - download::ScrubbyIndex::fmt (line 63) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyIndex` [INFO] [stdout] --> src/download.rs:64:13 [INFO] [stdout] | [INFO] [stdout] 3 | let index = ScrubbyIndex::Chm13v2; [INFO] [stdout] | ^^^^^^^^^^^^ use of undeclared type `ScrubbyIndex` [INFO] [stdout] | [INFO] [stdout] help: consider importing this enum [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyIndex; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0433`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/download.rs - download::ScrubbyIndex::aligner_name (line 28) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ScrubbyIndex` [INFO] [stdout] --> src/download.rs:29:13 [INFO] [stdout] | [INFO] [stdout] 3 | let index = ScrubbyIndex::Chm13v2; [INFO] [stdout] | ^^^^^^^^^^^^ use of undeclared type `ScrubbyIndex` [INFO] [stdout] | [INFO] [stdout] help: consider importing this enum [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::ScrubbyIndex; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `Aligner` [INFO] [stdout] --> src/download.rs:30:15 [INFO] [stdout] | [INFO] [stdout] 4 | let aligner = Aligner::new(); [INFO] [stdout] | ^^^^^^^ use of undeclared type `Aligner` [INFO] [stdout] | [INFO] [stdout] help: consider importing this enum [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::prelude::Aligner; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error: aborting due to 2 previous errors [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0433`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::Scrubby::builder (line 228) stdout ---- [INFO] [stdout] error[E0432]: unresolved import `scrubby::Scrubby` [INFO] [stdout] --> src/scrubby.rs:230:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::Scrubby; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ no `Scrubby` in the root [INFO] [stdout] | [INFO] [stdout] help: a similar name exists in the module (notice the capitalization) [INFO] [stdout] | [INFO] [stdout] 5 - use scrubby::Scrubby; [INFO] [stdout] 5 + use scrubby::scrubby; [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::Scrubby; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::Scrubby::clean (line 249) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:253:28 [INFO] [stdout] | [INFO] [stdout] 7 | let scrubby = Scrubby::new(...).unwrap(); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let scrubby = Scrubby::new(...).unwrap(); [INFO] [stdout] 7 + let scrubby = Scrubby::new(..).unwrap(); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let scrubby = Scrubby::new(...).unwrap(); [INFO] [stdout] 7 + let scrubby = Scrubby::new(..=).unwrap(); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:253:28 [INFO] [stdout] | [INFO] [stdout] 7 | let scrubby = Scrubby::new(...).unwrap(); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 7 - let scrubby = Scrubby::new(...).unwrap(); [INFO] [stdout] 7 + let scrubby = Scrubby::new(..).unwrap(); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::Scrubby` [INFO] [stdout] --> src/scrubby.rs:251:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::Scrubby; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ no `Scrubby` in the root [INFO] [stdout] | [INFO] [stdout] help: a similar name exists in the module (notice the capitalization) [INFO] [stdout] | [INFO] [stdout] 5 - use scrubby::Scrubby; [INFO] [stdout] 5 + use scrubby::scrubby; [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::Scrubby; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::aligner_args (line 705) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:709:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).aligner_args("aligner_args".to_string()); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).aligner_args("aligner_args".to_string()); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).aligner_args("aligner_args".to_string()); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).aligner_args("aligner_args".to_string()); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..=).aligner_args("aligner_args".to_string()); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:709:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).aligner_args("aligner_args".to_string()); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).aligner_args("aligner_args".to_string()); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).aligner_args("aligner_args".to_string()); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:707:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::aligner_index (line 638) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:643:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).aligner_index(PathBuf::from("aligner_index")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).aligner_index(PathBuf::from("aligner_index")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).aligner_index(PathBuf::from("aligner_index")); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).aligner_index(PathBuf::from("aligner_index")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..=).aligner_index(PathBuf::from("aligner_index")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:643:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).aligner_index(PathBuf::from("aligner_index")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).aligner_index(PathBuf::from("aligner_index")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).aligner_index(PathBuf::from("aligner_index")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:640:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::classifier_args (line 692) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:696:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).classifier_args("classifier_args".to_string()); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).classifier_args("classifier_args".to_string()); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).classifier_args("classifier_args".to_string()); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).classifier_args("classifier_args".to_string()); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..=).classifier_args("classifier_args".to_string()); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:696:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).classifier_args("classifier_args".to_string()); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).classifier_args("classifier_args".to_string()); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).classifier_args("classifier_args".to_string()); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:694:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::classifier_index (line 652) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:657:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).classifier_index(PathBuf::from("classifier_index")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).classifier_index(PathBuf::from("classifier_index")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).classifier_index(PathBuf::from("classifier_index")); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).classifier_index(PathBuf::from("classifier_index")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..=).classifier_index(PathBuf::from("classifier_index")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:657:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).classifier_index(PathBuf::from("classifier_index")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).classifier_index(PathBuf::from("classifier_index")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).classifier_index(PathBuf::from("classifier_index")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:654:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::classifier (line 583) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:587:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).classifier(Classifier::Kraken2); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).classifier(Classifier::Kraken2); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).classifier(Classifier::Kraken2); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).classifier(Classifier::Kraken2); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..=).classifier(Classifier::Kraken2); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:587:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).classifier(Classifier::Kraken2); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).classifier(Classifier::Kraken2); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).classifier(Classifier::Kraken2); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved imports `scrubby::ScrubbyBuilder`, `scrubby::Classifier` [INFO] [stdout] --> src/scrubby.rs:585:15 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::{ScrubbyBuilder, Classifier}; [INFO] [stdout] | ^^^^^^^^^^^^^^ ^^^^^^^^^^ [INFO] [stdout] | | | [INFO] [stdout] | | no `Classifier` in the root [INFO] [stdout] | | help: a similar name exists in the module (notice the capitalization): `classifier` [INFO] [stdout] | no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] = help: consider importing this struct instead: [INFO] [stdout] scrubby::prelude::ScrubbyBuilder [INFO] [stdout] = help: consider importing one of these items instead: [INFO] [stdout] scrubby::prelude::Classifier [INFO] [stdout] scrubby::terminal::Commands::Classifier [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::alignment_format (line 527) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:532:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).alignment_format(AlignmentFormat::Bam); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).alignment_format(AlignmentFormat::Bam); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).alignment_format(AlignmentFormat::Bam); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).alignment_format(AlignmentFormat::Bam); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..=).alignment_format(AlignmentFormat::Bam); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:532:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).alignment_format(AlignmentFormat::Bam); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).alignment_format(AlignmentFormat::Bam); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).alignment_format(AlignmentFormat::Bam); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved imports `scrubby::ScrubbyBuilder`, `scrubby::AlignmentFormat` [INFO] [stdout] --> src/scrubby.rs:529:15 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::{ScrubbyBuilder, AlignmentFormat}; [INFO] [stdout] | ^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^ no `AlignmentFormat` in the root [INFO] [stdout] | | [INFO] [stdout] | no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] = help: consider importing this struct instead: [INFO] [stdout] scrubby::prelude::ScrubbyBuilder [INFO] [stdout] = help: consider importing this enum instead: [INFO] [stdout] scrubby::prelude::AlignmentFormat [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::command (line 420) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:425:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).command("scrubby clean ..."); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).command("scrubby clean ..."); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).command("scrubby clean ..."); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).command("scrubby clean ..."); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..=).command("scrubby clean ..."); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:425:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).command("scrubby clean ..."); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).command("scrubby clean ..."); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).command("scrubby clean ..."); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:422:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::build_classifier (line 967) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:971:35 [INFO] [stdout] | [INFO] [stdout] 7 | let scrubby = ScrubbyBuilder::new(...).build_classifier().unwrap(); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let scrubby = ScrubbyBuilder::new(...).build_classifier().unwrap(); [INFO] [stdout] 7 + let scrubby = ScrubbyBuilder::new(..).build_classifier().unwrap(); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let scrubby = ScrubbyBuilder::new(...).build_classifier().unwrap(); [INFO] [stdout] 7 + let scrubby = ScrubbyBuilder::new(..=).build_classifier().unwrap(); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:971:35 [INFO] [stdout] | [INFO] [stdout] 7 | let scrubby = ScrubbyBuilder::new(...).build_classifier().unwrap(); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 7 - let scrubby = ScrubbyBuilder::new(...).build_classifier().unwrap(); [INFO] [stdout] 7 + let scrubby = ScrubbyBuilder::new(..).build_classifier().unwrap(); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:969:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::build_alignment (line 1008) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:1012:35 [INFO] [stdout] | [INFO] [stdout] 7 | let scrubby = ScrubbyBuilder::new(...).build_alignment().unwrap(); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let scrubby = ScrubbyBuilder::new(...).build_alignment().unwrap(); [INFO] [stdout] 7 + let scrubby = ScrubbyBuilder::new(..).build_alignment().unwrap(); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let scrubby = ScrubbyBuilder::new(...).build_alignment().unwrap(); [INFO] [stdout] 7 + let scrubby = ScrubbyBuilder::new(..=).build_alignment().unwrap(); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:1012:35 [INFO] [stdout] | [INFO] [stdout] 7 | let scrubby = ScrubbyBuilder::new(...).build_alignment().unwrap(); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 7 - let scrubby = ScrubbyBuilder::new(...).build_alignment().unwrap(); [INFO] [stdout] 7 + let scrubby = ScrubbyBuilder::new(..).build_alignment().unwrap(); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:1010:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::alignment (line 513) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:518:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).alignment(PathBuf::from("alignment.paf")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).alignment(PathBuf::from("alignment.paf")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).alignment(PathBuf::from("alignment.paf")); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).alignment(PathBuf::from("alignment.paf")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..=).alignment(PathBuf::from("alignment.paf")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:518:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).alignment(PathBuf::from("alignment.paf")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).alignment(PathBuf::from("alignment.paf")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).alignment(PathBuf::from("alignment.paf")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:515:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::build (line 802) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:806:35 [INFO] [stdout] | [INFO] [stdout] 7 | let scrubby = ScrubbyBuilder::new(...).build().unwrap(); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let scrubby = ScrubbyBuilder::new(...).build().unwrap(); [INFO] [stdout] 7 + let scrubby = ScrubbyBuilder::new(..).build().unwrap(); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let scrubby = ScrubbyBuilder::new(...).build().unwrap(); [INFO] [stdout] 7 + let scrubby = ScrubbyBuilder::new(..=).build().unwrap(); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:806:35 [INFO] [stdout] | [INFO] [stdout] 7 | let scrubby = ScrubbyBuilder::new(...).build().unwrap(); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 7 - let scrubby = ScrubbyBuilder::new(...).build().unwrap(); [INFO] [stdout] 7 + let scrubby = ScrubbyBuilder::new(..).build().unwrap(); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:804:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::extract (line 448) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:452:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).extract(true); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).extract(true); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).extract(true); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).extract(true); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..=).extract(true); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:452:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).extract(true); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).extract(true); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).extract(true); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:450:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::min_mapq (line 569) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:574:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).min_mapq(50); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).min_mapq(50); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).min_mapq(50); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).min_mapq(50); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..=).min_mapq(50); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:574:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).min_mapq(50); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).min_mapq(50); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).min_mapq(50); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:571:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::index (line 624) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:629:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).index(PathBuf::from("index")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).index(PathBuf::from("index")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).index(PathBuf::from("index")); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).index(PathBuf::from("index")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..=).index(PathBuf::from("index")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:629:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).index(PathBuf::from("index")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).index(PathBuf::from("index")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).index(PathBuf::from("index")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:626:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::keep (line 461) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:465:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).keep(true); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).keep(true); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).keep(true); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).keep(true); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..=).keep(true); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:465:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).keep(true); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).keep(true); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).keep(true); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:463:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::min_query_length (line 541) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:546:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).min_query_length(50); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).min_query_length(50); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).min_query_length(50); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).min_query_length(50); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..=).min_query_length(50); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:546:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).min_query_length(50); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).min_query_length(50); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).min_query_length(50); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:543:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::needletail_parallel (line 731) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:735:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).needletail_parallel(true); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).needletail_parallel(true); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).needletail_parallel(true); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).needletail_parallel(true); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..=).needletail_parallel(true); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:735:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).needletail_parallel(true); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).needletail_parallel(true); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).needletail_parallel(true); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:733:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::json (line 406) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:411:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).json(PathBuf::from("report.json")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).json(PathBuf::from("report.json")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).json(PathBuf::from("report.json")); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).json(PathBuf::from("report.json")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..=).json(PathBuf::from("report.json")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:411:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).json(PathBuf::from("report.json")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).json(PathBuf::from("report.json")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).json(PathBuf::from("report.json")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:408:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::min_query_coverage (line 555) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:560:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).min_query_coverage(0.5); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).min_query_coverage(0.5); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).min_query_coverage(0.5); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).min_query_coverage(0.5); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..=).min_query_coverage(0.5); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:560:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).min_query_coverage(0.5); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).min_query_coverage(0.5); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).min_query_coverage(0.5); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:557:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::reads (line 596) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:601:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).reads(PathBuf::from("read_classifications.tsv")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).reads(PathBuf::from("read_classifications.tsv")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).reads(PathBuf::from("read_classifications.tsv")); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).reads(PathBuf::from("read_classifications.tsv")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..=).reads(PathBuf::from("read_classifications.tsv")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:601:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).reads(PathBuf::from("read_classifications.tsv")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).reads(PathBuf::from("read_classifications.tsv")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).reads(PathBuf::from("read_classifications.tsv")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:598:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::preset (line 744) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:749:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).preset(Preset::MapOnt); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).preset(Preset::MapOnt); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).preset(Preset::MapOnt); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).preset(Preset::MapOnt); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..=).preset(Preset::MapOnt); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:749:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).preset(Preset::MapOnt); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).preset(Preset::MapOnt); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).preset(Preset::MapOnt); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:746:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::Preset` [INFO] [stdout] --> src/scrubby.rs:747:5 [INFO] [stdout] | [INFO] [stdout] 6 | use scrubby::Preset; [INFO] [stdout] | ^^^^^^^^^^^^^^^ no `Preset` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this enum instead [INFO] [stdout] | [INFO] [stdout] 6 | use scrubby::prelude::Preset; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 4 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::new (line 337) stdout ---- [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:339:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::read_ids (line 392) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:397:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).read_ids(PathBuf::from("depleted_reads.fastq")); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..=).read_ids(PathBuf::from("depleted_reads.fastq")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:397:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).read_ids(PathBuf::from("depleted_reads.fastq")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:394:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::taxa_direct (line 679) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:683:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).taxa_direct(vec!["taxon_direct1", "taxon_direct2"]); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).taxa_direct(vec!["taxon_direct1", "taxon_direct2"]); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).taxa_direct(vec!["taxon_direct1", "taxon_direct2"]); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).taxa_direct(vec!["taxon_direct1", "taxon_direct2"]); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..=).taxa_direct(vec!["taxon_direct1", "taxon_direct2"]); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:683:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).taxa_direct(vec!["taxon_direct1", "taxon_direct2"]); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).taxa_direct(vec!["taxon_direct1", "taxon_direct2"]); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).taxa_direct(vec!["taxon_direct1", "taxon_direct2"]); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:681:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::report (line 610) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:615:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).report(PathBuf::from("classifier_report.tsv")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).report(PathBuf::from("classifier_report.tsv")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).report(PathBuf::from("classifier_report.tsv")); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).report(PathBuf::from("classifier_report.tsv")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..=).report(PathBuf::from("classifier_report.tsv")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:615:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).report(PathBuf::from("classifier_report.tsv")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).report(PathBuf::from("classifier_report.tsv")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).report(PathBuf::from("classifier_report.tsv")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:612:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/terminal.rs - terminal::AlignmentArgs::validate_and_build (line 406) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `AlignmentArgs` [INFO] [stdout] --> src/terminal.rs:410:16 [INFO] [stdout] | [INFO] [stdout] 7 | let aln_args = AlignmentArgs::parse(); [INFO] [stdout] | ^^^^^^^^^^^^^ use of undeclared type `AlignmentArgs` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::terminal::AlignmentArgs; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0433`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::unpaired (line 474) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:478:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).unpaired(true); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).unpaired(true); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).unpaired(true); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).unpaired(true); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..=).unpaired(true); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:478:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).unpaired(true); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).unpaired(true); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).unpaired(true); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:476:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::samtools_threads (line 718) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:722:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).samtools_threads(4); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).samtools_threads(4); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).samtools_threads(4); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).samtools_threads(4); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..=).samtools_threads(4); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:722:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).samtools_threads(4); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).samtools_threads(4); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).samtools_threads(4); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:720:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::taxa (line 666) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:670:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).taxa(vec!["taxon1", "taxon2"]); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).taxa(vec!["taxon1", "taxon2"]); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).taxa(vec!["taxon1", "taxon2"]); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).taxa(vec!["taxon1", "taxon2"]); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..=).taxa(vec!["taxon1", "taxon2"]); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:670:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).taxa(vec!["taxon1", "taxon2"]); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).taxa(vec!["taxon1", "taxon2"]); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).taxa(vec!["taxon1", "taxon2"]); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:668:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/terminal.rs - terminal::DiffArgs::validate_and_build (line 540) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `DifferenceArgs` [INFO] [stdout] --> src/terminal.rs:543:17 [INFO] [stdout] | [INFO] [stdout] 5 | let diff_args = DifferenceArgs::parse(); [INFO] [stdout] | ^^^^^^^^^^^^^^ use of undeclared type `DifferenceArgs` [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0433`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/terminal.rs - terminal::ClassifierArgs::validate_and_build (line 294) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ClassifierArgs` [INFO] [stdout] --> src/terminal.rs:298:18 [INFO] [stdout] | [INFO] [stdout] 7 | let class_args = ClassifierArgs::parse(); [INFO] [stdout] | ^^^^^^^^^^^^^^ use of undeclared type `ClassifierArgs` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::terminal::ClassifierArgs; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0433`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::threads (line 487) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:491:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).threads(8); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).threads(8); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).threads(8); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).threads(8); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..=).threads(8); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:491:35 [INFO] [stdout] | [INFO] [stdout] 7 | let builder = ScrubbyBuilder::new(...).threads(8); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 7 - let builder = ScrubbyBuilder::new(...).threads(8); [INFO] [stdout] 7 + let builder = ScrubbyBuilder::new(..).threads(8); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:489:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/scrubby.rs - scrubby::ScrubbyBuilder::workdir (line 434) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/scrubby.rs:439:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).workdir(PathBuf::from("workdir")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).workdir(PathBuf::from("workdir")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).workdir(PathBuf::from("workdir")); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).workdir(PathBuf::from("workdir")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..=).workdir(PathBuf::from("workdir")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/scrubby.rs:439:35 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ScrubbyBuilder::new(...).workdir(PathBuf::from("workdir")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ScrubbyBuilder::new(...).workdir(PathBuf::from("workdir")); [INFO] [stdout] 8 + let builder = ScrubbyBuilder::new(..).workdir(PathBuf::from("workdir")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ScrubbyBuilder` [INFO] [stdout] --> src/scrubby.rs:436:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ScrubbyBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `ScrubbyBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ScrubbyBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/utils.rs - utils::get_id (line 88) stdout ---- [INFO] [stdout] error[E0425]: cannot find function `get_id` in this scope [INFO] [stdout] --> src/utils.rs:89:10 [INFO] [stdout] | [INFO] [stdout] 3 | let id = get_id(b"@read1 description").unwrap(); [INFO] [stdout] | ^^^^^^ not found in this scope [INFO] [stdout] | [INFO] [stdout] help: consider importing this function [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::utils::get_id; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/utils.rs - utils::get_fastx_writer (line 53) stdout ---- [INFO] [stdout] error[E0425]: cannot find value `output_path` in this scope [INFO] [stdout] --> src/utils.rs:54:57 [INFO] [stdout] | [INFO] [stdout] 3 | let (reader, writer) = get_niffler_fastx_reader_writer(&output_path, niffler::compression::Level::Six, None).unwrap(); [INFO] [stdout] | ^^^^^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `get_niffler_fastx_reader_writer` in this scope [INFO] [stdout] --> src/utils.rs:54:24 [INFO] [stdout] | [INFO] [stdout] 3 | let (reader, writer) = get_niffler_fastx_reader_writer(&output_path, niffler::compression::Level::Six, None).unwrap(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ not found in this scope [INFO] [stdout] [INFO] [stdout] error: aborting due to 2 previous errors [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/utils.rs - utils::ReadDifferenceBuilder::json (line 323) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/utils.rs:328:42 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ReadDifferenceBuilder::new(...).json(PathBuf::from("report.json")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ReadDifferenceBuilder::new(...).json(PathBuf::from("report.json")); [INFO] [stdout] 8 + let builder = ReadDifferenceBuilder::new(..).json(PathBuf::from("report.json")); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ReadDifferenceBuilder::new(...).json(PathBuf::from("report.json")); [INFO] [stdout] 8 + let builder = ReadDifferenceBuilder::new(..=).json(PathBuf::from("report.json")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/utils.rs:328:42 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ReadDifferenceBuilder::new(...).json(PathBuf::from("report.json")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ReadDifferenceBuilder::new(...).json(PathBuf::from("report.json")); [INFO] [stdout] 8 + let builder = ReadDifferenceBuilder::new(..).json(PathBuf::from("report.json")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ReadDifferenceBuilder` [INFO] [stdout] --> src/utils.rs:325:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ReadDifferenceBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ no `ReadDifferenceBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ReadDifferenceBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/utils.rs - utils::ReadDifferenceBuilder::read_ids (line 309) stdout ---- [INFO] [stdout] error: unexpected token: `...` [INFO] [stdout] --> src/utils.rs:314:42 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ReadDifferenceBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] help: use `..` for an exclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ReadDifferenceBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq")); [INFO] [stdout] 8 + let builder = ReadDifferenceBuilder::new(..).read_ids(PathBuf::from("depleted_reads.fastq")); [INFO] [stdout] | [INFO] [stdout] help: or `..=` for an inclusive range [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ReadDifferenceBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq")); [INFO] [stdout] 8 + let builder = ReadDifferenceBuilder::new(..=).read_ids(PathBuf::from("depleted_reads.fastq")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0586]: inclusive range with no end [INFO] [stdout] --> src/utils.rs:314:42 [INFO] [stdout] | [INFO] [stdout] 8 | let builder = ReadDifferenceBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq")); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: inclusive ranges must be bounded at the end (`..=b` or `a..=b`) [INFO] [stdout] help: use `..` instead [INFO] [stdout] | [INFO] [stdout] 8 - let builder = ReadDifferenceBuilder::new(...).read_ids(PathBuf::from("depleted_reads.fastq")); [INFO] [stdout] 8 + let builder = ReadDifferenceBuilder::new(..).read_ids(PathBuf::from("depleted_reads.fastq")); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `scrubby::ReadDifferenceBuilder` [INFO] [stdout] --> src/utils.rs:311:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::ReadDifferenceBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ no `ReadDifferenceBuilder` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::prelude::ReadDifferenceBuilder; [INFO] [stdout] | +++++++++ [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0586. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/terminal.rs - terminal::DownloadArgs::validate_and_build (line 475) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `Download` [INFO] [stdout] --> src/terminal.rs:478:15 [INFO] [stdout] | [INFO] [stdout] 5 | let dl_args = Download::parse(); [INFO] [stdout] | ^^^^^^^^ use of undeclared type `Download` [INFO] [stdout] | [INFO] [stdout] help: there is an enum variant `scrubby::terminal::Commands::Download`; try using the variant's enum [INFO] [stdout] | [INFO] [stdout] 5 - let dl_args = Download::parse(); [INFO] [stdout] 5 + let dl_args = scrubby::terminal::Commands::parse(); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0433`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/terminal.rs - terminal::ReadsArgs::validate_and_build (line 172) stdout ---- [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `ReadsArgs` [INFO] [stdout] --> src/terminal.rs:176:18 [INFO] [stdout] | [INFO] [stdout] 7 | let reads_Args = ReadsArgs::parse(); [INFO] [stdout] | ^^^^^^^^^ use of undeclared type `ReadsArgs` [INFO] [stdout] | [INFO] [stdout] help: consider importing this struct [INFO] [stdout] | [INFO] [stdout] 2 + use scrubby::terminal::ReadsArgs; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0433`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/utils.rs - utils::niffler::compression::Format::from_path (line 24) stdout ---- [INFO] [stdout] error[E0432]: unresolved import `scrubby::CompressionExt` [INFO] [stdout] --> src/utils.rs:26:5 [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::CompressionExt; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ no `CompressionExt` in the root [INFO] [stdout] | [INFO] [stdout] help: consider importing this trait instead [INFO] [stdout] | [INFO] [stdout] 5 | use scrubby::utils::CompressionExt; [INFO] [stdout] | +++++++ [INFO] [stdout] [INFO] [stdout] error[E0599]: no variant or associated item named `from_path` found for enum `niffler::Format` in the current scope [INFO] [stdout] --> src/utils.rs:27:44 [INFO] [stdout] | [INFO] [stdout] 6 | let format = niffler::compression::Format::from_path("file.gz"); [INFO] [stdout] | ^^^^^^^^^ variant or associated item not found in `niffler::Format` [INFO] [stdout] | [INFO] [stdout] = help: items from traits can only be used if the trait is in scope [INFO] [stdout] help: trait `CompressionExt` which provides `from_path` is implemented but not in scope; perhaps you want to import it [INFO] [stdout] | [INFO] [stdout] 2 + use crate::scrubby::utils::CompressionExt; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error: aborting due to 2 previous errors [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0599. [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] [INFO] [stdout] failures: [INFO] [stdout] src/classifier.rs - classifier::KrakenReadRecord::from_str (line 398) [INFO] [stdout] src/classifier.rs - classifier::KrakenReportRecord::from_str (line 446) [INFO] [stdout] src/classifier.rs - classifier::MetabuliReadRecord::from_str (line 494) [INFO] [stdout] src/classifier.rs - classifier::TaxonCounts::new (line 68) [INFO] [stdout] src/classifier.rs - classifier::TaxonCounts::update (line 88) [INFO] [stdout] src/classifier.rs - classifier::get_tax_level (line 342) [INFO] [stdout] src/classifier.rs - classifier::get_taxid_reads_kraken (line 267) [INFO] [stdout] src/classifier.rs - classifier::get_taxid_reads_metabuli (line 305) [INFO] [stdout] src/classifier.rs - classifier::get_taxids_from_report (line 121) [INFO] [stdout] src/cleaner.rs - cleaner::Cleaner::clean_reads (line 230) [INFO] [stdout] src/cleaner.rs - cleaner::Cleaner::from_scrubby (line 102) [INFO] [stdout] src/cleaner.rs - cleaner::Cleaner::run_aligner (line 129) [INFO] [stdout] src/cleaner.rs - cleaner::Cleaner::run_aligner_output (line 201) [INFO] [stdout] src/cleaner.rs - cleaner::Cleaner::run_classifier (line 153) [INFO] [stdout] src/cleaner.rs - cleaner::Cleaner::run_classifier_output (line 172) [INFO] [stdout] src/cleaner.rs - cleaner::FastqCleaner::clean_reads (line 727) [INFO] [stdout] src/cleaner.rs - cleaner::FastqCleaner::from (line 706) [INFO] [stdout] src/cleaner.rs - cleaner::SamtoolsConfig::from_scrubby (line 43) [INFO] [stdout] src/cleaner.rs - cleaner::SamtoolsConfig::get_pipeline (line 75) [INFO] [stdout] src/download.rs - download::ScrubbyDownloader::builder (line 118) [INFO] [stdout] src/download.rs - download::ScrubbyDownloader::download (line 237) [INFO] [stdout] src/download.rs - download::ScrubbyDownloader::download_index (line 160) [INFO] [stdout] src/download.rs - download::ScrubbyDownloader::list (line 130) [INFO] [stdout] src/download.rs - download::ScrubbyDownloader::new (line 101) [INFO] [stdout] src/download.rs - download::ScrubbyDownloader::unpack (line 206) [INFO] [stdout] src/download.rs - download::ScrubbyDownloaderBuilder::aligner (line 307) [INFO] [stdout] src/download.rs - download::ScrubbyDownloaderBuilder::base_url (line 352) [INFO] [stdout] src/download.rs - download::ScrubbyDownloaderBuilder::build (line 397) [INFO] [stdout] src/download.rs - download::ScrubbyDownloaderBuilder::classifier (line 322) [INFO] [stdout] src/download.rs - download::ScrubbyDownloaderBuilder::new (line 282) [INFO] [stdout] src/download.rs - download::ScrubbyDownloaderBuilder::password (line 382) [INFO] [stdout] src/download.rs - download::ScrubbyDownloaderBuilder::timeout (line 337) [INFO] [stdout] src/download.rs - download::ScrubbyDownloaderBuilder::username (line 367) [INFO] [stdout] src/download.rs - download::ScrubbyIndex::aligner_name (line 28) [INFO] [stdout] src/download.rs - download::ScrubbyIndex::classifier_name (line 44) [INFO] [stdout] src/download.rs - download::ScrubbyIndex::fmt (line 63) [INFO] [stdout] src/scrubby.rs - scrubby::Scrubby::builder (line 228) [INFO] [stdout] src/scrubby.rs - scrubby::Scrubby::clean (line 249) [INFO] [stdout] src/scrubby.rs - scrubby::Scrubby::new (line 193) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::aligner (line 500) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::aligner_args (line 705) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::aligner_index (line 638) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::alignment (line 513) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::alignment_format (line 527) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::build (line 802) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::build_alignment (line 1008) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::build_classifier (line 967) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::classifier (line 583) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::classifier_args (line 692) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::classifier_index (line 652) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::command (line 420) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::extract (line 448) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::index (line 624) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::json (line 406) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::keep (line 461) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::min_mapq (line 569) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::min_query_coverage (line 555) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::min_query_length (line 541) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::needletail_parallel (line 731) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::new (line 337) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::preset (line 744) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::read_ids (line 392) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::reads (line 596) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::report (line 610) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::samtools_threads (line 718) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::taxa (line 666) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::taxa_direct (line 679) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::threads (line 487) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::unpaired (line 474) [INFO] [stdout] src/scrubby.rs - scrubby::ScrubbyBuilder::workdir (line 434) [INFO] [stdout] src/terminal.rs - terminal::AlignmentArgs::validate_and_build (line 406) [INFO] [stdout] src/terminal.rs - terminal::ClassifierArgs::validate_and_build (line 294) [INFO] [stdout] src/terminal.rs - terminal::DiffArgs::validate_and_build (line 540) [INFO] [stdout] src/terminal.rs - terminal::DownloadArgs::validate_and_build (line 475) [INFO] [stdout] src/terminal.rs - terminal::ReadsArgs::validate_and_build (line 172) [INFO] [stdout] src/utils.rs - utils::ReadDifferenceBuilder::json (line 323) [INFO] [stdout] src/utils.rs - utils::ReadDifferenceBuilder::read_ids (line 309) [INFO] [stdout] src/utils.rs - utils::get_fastx_writer (line 53) [INFO] [stdout] src/utils.rs - utils::get_id (line 88) [INFO] [stdout] src/utils.rs - utils::niffler::compression::Format::from_path (line 24) [INFO] [stdout] [INFO] [stdout] test result: FAILED. 0 passed; 80 failed; 0 ignored; 0 measured; 0 filtered out; finished in 6.96s [INFO] [stdout] [INFO] [stderr] error: doctest failed, to rerun pass `--doc` [INFO] running `Command { std: "docker" "inspect" "619edcfbcb7a6b18548845b742755d7e00ba4c199b01dae41a95e055526c8765", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "619edcfbcb7a6b18548845b742755d7e00ba4c199b01dae41a95e055526c8765", kill_on_drop: false }` [INFO] [stdout] 619edcfbcb7a6b18548845b742755d7e00ba4c199b01dae41a95e055526c8765