[INFO] cloning repository https://github.com/lleyton/sequence-analysis-rust [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/lleyton/sequence-analysis-rust" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Flleyton%2Fsequence-analysis-rust", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Flleyton%2Fsequence-analysis-rust'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] cc2ce38fcfa7ebd245f30c1b157d1d69c08a0fed [INFO] checking lleyton/sequence-analysis-rust against master#af4a5a13a15fa0c60e06321077ef452f769b42fd for pr-122960-3 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Flleyton%2Fsequence-analysis-rust" "/workspace/builds/worker-6-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-6-tc1/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/lleyton/sequence-analysis-rust on toolchain af4a5a13a15fa0c60e06321077ef452f769b42fd [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+af4a5a13a15fa0c60e06321077ef452f769b42fd" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/lleyton/sequence-analysis-rust [INFO] finished tweaking git repo https://github.com/lleyton/sequence-analysis-rust [INFO] tweaked toml for git repo https://github.com/lleyton/sequence-analysis-rust written to /workspace/builds/worker-6-tc1/source/Cargo.toml [INFO] crate git repo https://github.com/lleyton/sequence-analysis-rust already has a lockfile, it will not be regenerated [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+af4a5a13a15fa0c60e06321077ef452f769b42fd" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded bio-types v0.12.1 [INFO] [stderr] Downloaded triple_accel v0.4.0 [INFO] [stderr] Downloaded enum-map-derive v0.6.0 [INFO] [stderr] Downloaded enum-map v1.1.1 [INFO] [stderr] Downloaded bio v0.41.0 [INFO] [stderr] Downloaded ndarray v0.15.4 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+af4a5a13a15fa0c60e06321077ef452f769b42fd" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 4ab90e73699a4822b3bad5026f49564b28976c3f78432c2e7d19669c80535d4f [INFO] running `Command { std: "docker" "start" "-a" "4ab90e73699a4822b3bad5026f49564b28976c3f78432c2e7d19669c80535d4f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "4ab90e73699a4822b3bad5026f49564b28976c3f78432c2e7d19669c80535d4f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "4ab90e73699a4822b3bad5026f49564b28976c3f78432c2e7d19669c80535d4f", kill_on_drop: false }` [INFO] [stdout] 4ab90e73699a4822b3bad5026f49564b28976c3f78432c2e7d19669c80535d4f [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+af4a5a13a15fa0c60e06321077ef452f769b42fd" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 83a98fa16a80419bacf6e5534b031d4f33ab86f07f31924e21a1c02cd626586a [INFO] running `Command { std: "docker" "start" "-a" "83a98fa16a80419bacf6e5534b031d4f33ab86f07f31924e21a1c02cd626586a", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.39 [INFO] [stderr] Compiling unicode-ident v1.0.0 [INFO] [stderr] Compiling syn v1.0.95 [INFO] [stderr] Compiling libm v0.2.2 [INFO] [stderr] Compiling libc v0.2.126 [INFO] [stderr] Compiling serde_derive v1.0.137 [INFO] [stderr] Compiling num-traits v0.2.15 [INFO] [stderr] Compiling serde v1.0.137 [INFO] [stderr] Compiling num-integer v0.1.45 [INFO] [stderr] Compiling num-rational v0.4.0 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Compiling rustversion v1.0.6 [INFO] [stderr] Checking matrixmultiply v0.3.2 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling indexmap v1.8.2 [INFO] [stderr] Compiling paste v1.0.7 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling unicode-segmentation v1.9.0 [INFO] [stderr] Compiling quote v1.0.18 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Checking getrandom v0.2.6 [INFO] [stderr] Checking rand_core v0.6.3 [INFO] [stderr] Compiling heck v0.3.3 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Checking rand_chacha v0.3.1 [INFO] [stderr] Checking typenum v1.15.0 [INFO] [stderr] Checking aho-corasick v0.7.18 [INFO] [stderr] Checking hashbrown v0.11.2 [INFO] [stderr] Checking rand v0.8.5 [INFO] [stderr] Checking num-complex v0.4.1 [INFO] [stderr] Checking approx v0.5.1 [INFO] [stderr] Compiling anyhow v1.0.57 [INFO] [stderr] Checking regex-syntax v0.6.26 [INFO] [stderr] Checking simba v0.5.1 [INFO] [stderr] Checking csv-core v0.1.10 [INFO] [stderr] Checking rand_distr v0.4.3 [INFO] [stderr] Checking either v1.6.1 [INFO] [stderr] Checking byteorder v1.4.3 [INFO] [stderr] Checking ryu v1.0.10 [INFO] [stderr] Checking fixedbitset v0.4.1 [INFO] [stderr] Checking itoa v0.4.8 [INFO] [stderr] Checking bit-vec v0.6.3 [INFO] [stderr] Checking petgraph v0.6.2 [INFO] [stderr] Checking itertools v0.10.3 [INFO] [stderr] Checking fxhash v0.2.1 [INFO] [stderr] Checking ndarray v0.15.4 [INFO] [stderr] Checking bit-set v0.5.2 [INFO] [stderr] Checking ordered-float v1.1.1 [INFO] [stderr] Checking itertools-num v0.1.3 [INFO] [stderr] Checking bytecount v0.6.3 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking strum v0.23.0 [INFO] [stderr] Checking triple_accel v0.4.0 [INFO] [stderr] Checking regex v1.5.6 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Compiling nalgebra-macros v0.1.0 [INFO] [stderr] Compiling thiserror-impl v1.0.31 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling strum_macros v0.23.1 [INFO] [stderr] Compiling enum-map-derive v0.6.0 [INFO] [stderr] Compiling getset v0.1.2 [INFO] [stderr] Checking enum-map v1.1.1 [INFO] [stderr] Checking thiserror v1.0.31 [INFO] [stderr] Checking bio-types v0.12.1 [INFO] [stderr] Checking nalgebra v0.27.1 [INFO] [stderr] Checking bstr v0.2.17 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking multimap v0.8.3 [INFO] [stderr] Checking csv v1.1.6 [INFO] [stderr] Checking statrs v0.15.0 [INFO] [stderr] Checking bio v0.41.0 [INFO] [stderr] Checking sequence-analysis-rust v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused imports: `BackwardSearchResult`, `FMIndexable`, `levenshtein`, `self`, `simd` [INFO] [stdout] --> src/lib.rs:1:33 [INFO] [stdout] | [INFO] [stdout] 1 | ...t, self}, data_structures::{suffix_array::suffix_array, bwt::{bwt, less, Occ}, fmindex::{FMIndex, BackwardSearchResult, FMIndexable}}, alignment::distance::{simd, levenshtein... [INFO] [stdout] | ^^^^ ^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^ ^^^^ ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `build_fm_index` is never used [INFO] [stdout] --> src/lib.rs:3:4 [INFO] [stdout] | [INFO] [stdout] 3 | fn build_fm_index<'a>(text: &'a [u8], alphabet: &'a Alphabet) -> (FMIndex, Vec, Occ>, Vec) { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 2 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 12.30s [INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nalgebra v0.27.1 [INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 3` [INFO] running `Command { std: "docker" "inspect" "83a98fa16a80419bacf6e5534b031d4f33ab86f07f31924e21a1c02cd626586a", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "83a98fa16a80419bacf6e5534b031d4f33ab86f07f31924e21a1c02cd626586a", kill_on_drop: false }` [INFO] [stdout] 83a98fa16a80419bacf6e5534b031d4f33ab86f07f31924e21a1c02cd626586a [INFO] checking lleyton/sequence-analysis-rust against try#36dbcaee1a55543dfc181be52a69d99ff46ff62f for pr-122960-3 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Flleyton%2Fsequence-analysis-rust" "/workspace/builds/worker-6-tc2/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-6-tc2/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/lleyton/sequence-analysis-rust on toolchain 36dbcaee1a55543dfc181be52a69d99ff46ff62f [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+36dbcaee1a55543dfc181be52a69d99ff46ff62f" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/lleyton/sequence-analysis-rust [INFO] finished tweaking git repo https://github.com/lleyton/sequence-analysis-rust [INFO] tweaked toml for git repo https://github.com/lleyton/sequence-analysis-rust written to /workspace/builds/worker-6-tc2/source/Cargo.toml [INFO] crate git repo https://github.com/lleyton/sequence-analysis-rust already has a lockfile, it will not be regenerated [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+36dbcaee1a55543dfc181be52a69d99ff46ff62f" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+36dbcaee1a55543dfc181be52a69d99ff46ff62f" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] cab154bb9cd6ffb7859b4aa5c9b52a1c8e3bf44abc93bb76e569acbc33a2f1d5 [INFO] running `Command { std: "docker" "start" "-a" "cab154bb9cd6ffb7859b4aa5c9b52a1c8e3bf44abc93bb76e569acbc33a2f1d5", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "cab154bb9cd6ffb7859b4aa5c9b52a1c8e3bf44abc93bb76e569acbc33a2f1d5", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "cab154bb9cd6ffb7859b4aa5c9b52a1c8e3bf44abc93bb76e569acbc33a2f1d5", kill_on_drop: false }` [INFO] [stdout] cab154bb9cd6ffb7859b4aa5c9b52a1c8e3bf44abc93bb76e569acbc33a2f1d5 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+36dbcaee1a55543dfc181be52a69d99ff46ff62f" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] d53dfd4993502cb5c9c34751351c843e3c052affafc2e4981f8b10a071507111 [INFO] running `Command { std: "docker" "start" "-a" "d53dfd4993502cb5c9c34751351c843e3c052affafc2e4981f8b10a071507111", kill_on_drop: false }` [INFO] [stderr] Copying to /tmp/fixit [INFO] [stderr] Running `cargo fix --edition` [INFO] [stderr] Compiling proc-macro2 v1.0.39 [INFO] [stderr] Compiling unicode-ident v1.0.0 [INFO] [stderr] Compiling syn v1.0.95 [INFO] [stderr] Compiling libm v0.2.2 [INFO] [stderr] Compiling libc v0.2.126 [INFO] [stderr] Compiling serde_derive v1.0.137 [INFO] [stderr] Compiling num-traits v0.2.15 [INFO] [stderr] Compiling serde v1.0.137 [INFO] [stderr] Compiling num-integer v0.1.45 [INFO] [stderr] Compiling num-rational v0.4.0 [INFO] [stderr] Compiling rustversion v1.0.6 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Checking matrixmultiply v0.3.2 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling indexmap v1.8.2 [INFO] [stderr] Compiling paste v1.0.7 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling unicode-segmentation v1.9.0 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling quote v1.0.18 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Checking getrandom v0.2.6 [INFO] [stderr] Checking rand_core v0.6.3 [INFO] [stderr] Compiling heck v0.3.3 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Checking typenum v1.15.0 [INFO] [stderr] Checking rand_chacha v0.3.1 [INFO] [stderr] Checking aho-corasick v0.7.18 [INFO] [stderr] Checking hashbrown v0.11.2 [INFO] [stderr] Checking rand v0.8.5 [INFO] [stderr] Checking num-complex v0.4.1 [INFO] [stderr] Checking approx v0.5.1 [INFO] [stderr] Checking regex-automata v0.1.10 [INFO] [stderr] Checking regex-syntax v0.6.26 [INFO] [stderr] Compiling anyhow v1.0.57 [INFO] [stderr] Checking simba v0.5.1 [INFO] [stderr] Checking csv-core v0.1.10 [INFO] [stderr] Checking rand_distr v0.4.3 [INFO] [stderr] Checking byteorder v1.4.3 [INFO] [stderr] Checking bit-vec v0.6.3 [INFO] [stderr] Checking ryu v1.0.10 [INFO] [stderr] Checking itoa v0.4.8 [INFO] [stderr] Checking either v1.6.1 [INFO] [stderr] Checking fixedbitset v0.4.1 [INFO] [stderr] Checking bit-set v0.5.2 [INFO] [stderr] Checking fxhash v0.2.1 [INFO] [stderr] Checking itertools v0.10.3 [INFO] [stderr] Checking petgraph v0.6.2 [INFO] [stderr] Checking ndarray v0.15.4 [INFO] [stderr] Checking ordered-float v1.1.1 [INFO] [stderr] Checking itertools-num v0.1.3 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking bytecount v0.6.3 [INFO] [stderr] Checking strum v0.23.0 [INFO] [stderr] Checking triple_accel v0.4.0 [INFO] [stderr] Checking regex v1.5.6 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Compiling nalgebra-macros v0.1.0 [INFO] [stderr] Compiling thiserror-impl v1.0.31 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling enum-map-derive v0.6.0 [INFO] [stderr] Compiling strum_macros v0.23.1 [INFO] [stderr] Checking enum-map v1.1.1 [INFO] [stderr] Compiling getset v0.1.2 [INFO] [stderr] Checking thiserror v1.0.31 [INFO] [stderr] Checking bio-types v0.12.1 [INFO] [stderr] Checking nalgebra v0.27.1 [INFO] [stderr] Checking bstr v0.2.17 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking multimap v0.8.3 [INFO] [stderr] Checking csv v1.1.6 [INFO] [stderr] Checking statrs v0.15.0 [INFO] [stderr] Checking bio v0.41.0 [INFO] [stderr] Checking sequence-analysis-rust v0.1.0 (/tmp/fixit) [INFO] [stderr] Migrating src/lib.rs from 2021 edition to 2024 [INFO] [stdout] warning: function `build_fm_index` is never used [INFO] [stdout] --> src/lib.rs:3:4 [INFO] [stdout] | [INFO] [stdout] 3 | fn build_fm_index<'a>(text: &'a [u8], alphabet: &'a Alphabet) -> (FMIndex, Vec, Occ>, Vec) { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Fixed src/lib.rs (1 fix) [INFO] [stdout] warning: 1 warning emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared crate or module `alphabets` [INFO] [stdout] --> src/lib.rs:18:20 [INFO] [stdout] | [INFO] [stdout] 18 | let alphabet = alphabets::dna::alphabet(); [INFO] [stdout] | ^^^^^^^^^ use of undeclared crate or module `alphabets` [INFO] [stdout] | [INFO] [stdout] help: consider importing this module [INFO] [stdout] | [INFO] [stdout] 1 + use bio::alphabets::dna; [INFO] [stdout] | [INFO] [stdout] help: if you import `dna`, refer to it directly [INFO] [stdout] | [INFO] [stdout] 18 - let alphabet = alphabets::dna::alphabet(); [INFO] [stdout] 18 + let alphabet = dna::alphabet(); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `BackwardSearchResult` [INFO] [stdout] --> src/lib.rs:25:9 [INFO] [stdout] | [INFO] [stdout] 25 | BackwardSearchResult::Complete(saint) => saint.occ(&sa), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ use of undeclared type `BackwardSearchResult` [INFO] [stdout] | [INFO] [stdout] help: consider importing this enum [INFO] [stdout] | [INFO] [stdout] 1 + use bio::data_structures::fmindex::BackwardSearchResult; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `BackwardSearchResult` [INFO] [stdout] --> src/lib.rs:26:9 [INFO] [stdout] | [INFO] [stdout] 26 | BackwardSearchResult::Partial(saint, l) => { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ use of undeclared type `BackwardSearchResult` [INFO] [stdout] | [INFO] [stdout] help: consider importing this enum [INFO] [stdout] | [INFO] [stdout] 1 + use bio::data_structures::fmindex::BackwardSearchResult; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `BackwardSearchResult` [INFO] [stdout] --> src/lib.rs:30:9 [INFO] [stdout] | [INFO] [stdout] 30 | BackwardSearchResult::Absent => Vec::new(), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ use of undeclared type `BackwardSearchResult` [INFO] [stdout] | [INFO] [stdout] help: consider importing this enum [INFO] [stdout] | [INFO] [stdout] 1 + use bio::data_structures::fmindex::BackwardSearchResult; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared crate or module `alphabets` [INFO] [stdout] --> src/lib.rs:43:20 [INFO] [stdout] | [INFO] [stdout] 43 | let alphabet = alphabets::dna::alphabet(); [INFO] [stdout] | ^^^^^^^^^ use of undeclared crate or module `alphabets` [INFO] [stdout] | [INFO] [stdout] help: consider importing this module [INFO] [stdout] | [INFO] [stdout] 1 + use bio::alphabets::dna; [INFO] [stdout] | [INFO] [stdout] help: if you import `dna`, refer to it directly [INFO] [stdout] | [INFO] [stdout] 43 - let alphabet = alphabets::dna::alphabet(); [INFO] [stdout] 43 + let alphabet = dna::alphabet(); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `BackwardSearchResult` [INFO] [stdout] --> src/lib.rs:50:9 [INFO] [stdout] | [INFO] [stdout] 50 | BackwardSearchResult::Complete(saint) => saint.occ(&sa), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ use of undeclared type `BackwardSearchResult` [INFO] [stdout] | [INFO] [stdout] help: consider importing this enum [INFO] [stdout] | [INFO] [stdout] 1 + use bio::data_structures::fmindex::BackwardSearchResult; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `BackwardSearchResult` [INFO] [stdout] --> src/lib.rs:51:9 [INFO] [stdout] | [INFO] [stdout] 51 | BackwardSearchResult::Partial(saint, l) => { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ use of undeclared type `BackwardSearchResult` [INFO] [stdout] | [INFO] [stdout] help: consider importing this enum [INFO] [stdout] | [INFO] [stdout] 1 + use bio::data_structures::fmindex::BackwardSearchResult; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `BackwardSearchResult` [INFO] [stdout] --> src/lib.rs:55:9 [INFO] [stdout] | [INFO] [stdout] 55 | BackwardSearchResult::Absent => Vec::new(), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ use of undeclared type `BackwardSearchResult` [INFO] [stdout] | [INFO] [stdout] help: consider importing this enum [INFO] [stdout] | [INFO] [stdout] 1 + use bio::data_structures::fmindex::BackwardSearchResult; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `levenshtein` in this scope [INFO] [stdout] --> src/lib.rs:68:17 [INFO] [stdout] | [INFO] [stdout] 68 | let ldist = levenshtein(a, b); [INFO] [stdout] | ^^^^^^^^^^^ not found in this scope [INFO] [stdout] | [INFO] [stdout] help: consider importing one of these items [INFO] [stdout] | [INFO] [stdout] 1 + use bio::alignment::distance::levenshtein; [INFO] [stdout] | [INFO] [stdout] 1 + use bio::alignment::distance::simd::levenshtein; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared crate or module `simd` [INFO] [stdout] --> src/lib.rs:78:17 [INFO] [stdout] | [INFO] [stdout] 78 | let ldist = simd::levenshtein(a, b); [INFO] [stdout] | ^^^^ use of undeclared crate or module `simd` [INFO] [stdout] | [INFO] [stdout] help: consider importing this module [INFO] [stdout] | [INFO] [stdout] 1 + use bio::alignment::distance::simd; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared crate or module `simd` [INFO] [stdout] --> src/lib.rs:89:17 [INFO] [stdout] | [INFO] [stdout] 89 | let ldist = simd::bounded_levenshtein(a, b, 5); [INFO] [stdout] | ^^^^ use of undeclared crate or module `simd` [INFO] [stdout] | [INFO] [stdout] help: consider importing this module [INFO] [stdout] | [INFO] [stdout] 1 + use bio::alignment::distance::simd; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `levenshtein` in this scope [INFO] [stdout] --> src/lib.rs:93:17 [INFO] [stdout] | [INFO] [stdout] 93 | None => levenshtein(a, b), [INFO] [stdout] | ^^^^^^^^^^^ not found in this scope [INFO] [stdout] | [INFO] [stdout] help: consider importing one of these items [INFO] [stdout] | [INFO] [stdout] 1 + use bio::alignment::distance::levenshtein; [INFO] [stdout] | [INFO] [stdout] 1 + use bio::alignment::distance::simd::levenshtein; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `backward_search` found for struct `FMIndex` in the current scope [INFO] [stdout] --> src/lib.rs:21:28 [INFO] [stdout] | [INFO] [stdout] 21 | let interval = fmindex.backward_search(pattern.iter()); [INFO] [stdout] | ^^^^^^^^^^^^^^^ method not found in `FMIndex, Vec, Occ>` [INFO] [stdout] | [INFO] [stdout] ::: /opt/rustwide/cargo-home/registry/src/index.crates.io-6f17d22bba15001f/bio-0.41.0/src/data_structures/fmindex.rs:142:8 [INFO] [stdout] | [INFO] [stdout] 142 | fn backward_search<'b, P: Iterator + DoubleEndedIterator>( [INFO] [stdout] | --------------- the method is available for `FMIndex, Vec, Occ>` here [INFO] [stdout] | [INFO] [stdout] = help: items from traits can only be used if the trait is in scope [INFO] [stdout] help: trait `FMIndexable` which provides `backward_search` is implemented but not in scope; perhaps you want to import it [INFO] [stdout] | [INFO] [stdout] 1 + use bio::data_structures::fmindex::FMIndexable; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `backward_search` found for struct `FMIndex` in the current scope [INFO] [stdout] --> src/lib.rs:46:28 [INFO] [stdout] | [INFO] [stdout] 46 | let interval = fmindex.backward_search(pattern.iter()); [INFO] [stdout] | ^^^^^^^^^^^^^^^ method not found in `FMIndex, Vec, Occ>` [INFO] [stdout] | [INFO] [stdout] ::: /opt/rustwide/cargo-home/registry/src/index.crates.io-6f17d22bba15001f/bio-0.41.0/src/data_structures/fmindex.rs:142:8 [INFO] [stdout] | [INFO] [stdout] 142 | fn backward_search<'b, P: Iterator + DoubleEndedIterator>( [INFO] [stdout] | --------------- the method is available for `FMIndex, Vec, Occ>` here [INFO] [stdout] | [INFO] [stdout] = help: items from traits can only be used if the trait is in scope [INFO] [stdout] help: trait `FMIndexable` which provides `backward_search` is implemented but not in scope; perhaps you want to import it [INFO] [stdout] | [INFO] [stdout] 1 + use bio::data_structures::fmindex::FMIndexable; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to 14 previous errors [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0425, E0433, E0599. [INFO] [stdout] [INFO] [stdout] For more information about an error, try `rustc --explain E0425`. [INFO] [stdout] [INFO] [stderr] error: could not compile `sequence-analysis-rust` (lib test) due to 15 previous errors [INFO] [stderr] error: failed to migrate to next edition [INFO] [stderr] [INFO] [stderr] Caused by: [INFO] [stderr] process didn't exit successfully: `cargo fix --edition --allow-no-vcs --allow-dirty --frozen --all --all-targets --message-format=json` (exit status: 101) [INFO] running `Command { std: "docker" "inspect" "d53dfd4993502cb5c9c34751351c843e3c052affafc2e4981f8b10a071507111", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "d53dfd4993502cb5c9c34751351c843e3c052affafc2e4981f8b10a071507111", kill_on_drop: false }` [INFO] [stdout] d53dfd4993502cb5c9c34751351c843e3c052affafc2e4981f8b10a071507111