[INFO] cloning repository https://github.com/Euphrasiologist/nu_plugin_bio [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/Euphrasiologist/nu_plugin_bio" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FEuphrasiologist%2Fnu_plugin_bio", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FEuphrasiologist%2Fnu_plugin_bio'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 49ab34152f2a8e42eeae0fb9f762e2f695339f5c [INFO] building Euphrasiologist/nu_plugin_bio against master#ad85bc524b1ad696e42061ad8338d382dffbdbe5 for pr-146237-1 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FEuphrasiologist%2Fnu_plugin_bio" "/workspace/builds/worker-4-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-4-tc1/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/Euphrasiologist/nu_plugin_bio [INFO] finished tweaking git repo https://github.com/Euphrasiologist/nu_plugin_bio [INFO] tweaked toml for git repo https://github.com/Euphrasiologist/nu_plugin_bio written to /workspace/builds/worker-4-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/Euphrasiologist/nu_plugin_bio on toolchain ad85bc524b1ad696e42061ad8338d382dffbdbe5 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/Euphrasiologist/nu_plugin_bio 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" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded wasm-bindgen-shared v0.2.83 [INFO] [stderr] Downloaded wasm-bindgen-backend v0.2.83 [INFO] [stderr] Downloaded bumpalo v3.11.1 [INFO] [stderr] Downloaded supports-color v3.0.2 [INFO] [stderr] Downloaded recvmsg v1.0.0 [INFO] [stderr] Downloaded lexical-parse-integer v1.0.5 [INFO] [stderr] Downloaded cxx v1.0.82 [INFO] [stderr] Downloaded bytemuck_derive v1.3.0 [INFO] [stderr] Downloaded bzip2 v0.5.2 [INFO] [stderr] Downloaded anyhow v1.0.66 [INFO] [stderr] Downloaded bytemuck v1.12.3 [INFO] [stderr] Downloaded noodles-bam v0.81.0 [INFO] [stderr] Downloaded lexical-core v1.0.5 [INFO] [stderr] Downloaded noodles-cram v0.84.0 [INFO] [stderr] Downloaded lexical-write-float v1.0.5 [INFO] [stderr] Downloaded regex v1.7.0 [INFO] [stderr] Downloaded noodles-vcf v0.79.0 [INFO] [stderr] Downloaded nu-engine v0.104.1 [INFO] [stderr] Downloaded miette v7.6.0 [INFO] [stderr] Downloaded cxx-build v1.0.82 [INFO] [stderr] Downloaded ntapi v0.4.0 [INFO] [stderr] Downloaded fancy-regex v0.14.0 [INFO] [stderr] Downloaded noodles-fasta v0.54.0 [INFO] [stderr] Downloaded noodles-core v0.17.0 [INFO] [stderr] Downloaded supports-hyperlinks v3.1.0 [INFO] [stderr] Downloaded bstr v0.2.17 [INFO] [stderr] Downloaded terminal_size v0.4.2 [INFO] [stderr] Downloaded textwrap v0.16.2 [INFO] [stderr] Downloaded nu-derive-value v0.104.1 [INFO] [stderr] Downloaded ref-cast v1.0.24 [INFO] [stderr] Downloaded clang-sys v1.6.1 [INFO] [stderr] Downloaded mach2 v0.4.1 [INFO] [stderr] Downloaded iana-time-zone v0.1.53 [INFO] [stderr] Downloaded crossbeam-utils v0.8.14 [INFO] [stderr] Downloaded nu-system v0.104.1 [INFO] [stderr] Downloaded utf8parse v0.2.0 [INFO] [stderr] Downloaded arrayvec v0.7.2 [INFO] [stderr] Downloaded paste v1.0.9 [INFO] [stderr] Downloaded erased-serde v0.3.23 [INFO] [stderr] Downloaded typetag-impl v0.2.5 [INFO] [stderr] Downloaded bzip2-sys v0.1.13+1.0.8 [INFO] [stderr] Downloaded nu-plugin-protocol v0.104.1 [INFO] [stderr] Downloaded brotli v7.0.0 [INFO] [stderr] Downloaded libz-rs-sys v0.5.1 [INFO] [stderr] Downloaded crossbeam-epoch v0.9.13 [INFO] [stderr] Downloaded link-cplusplus v1.0.7 [INFO] [stderr] Downloaded noodles-csi v0.49.0 [INFO] [stderr] Downloaded lexical-util v1.0.6 [INFO] [stderr] Downloaded scratch v1.0.2 [INFO] [stderr] Downloaded windows-core v0.56.0 [INFO] [stderr] Downloaded regex-syntax v0.6.28 [INFO] [stderr] Downloaded cc v1.0.77 [INFO] [stderr] Downloaded js-sys v0.3.60 [INFO] [stderr] Downloaded pwd v1.4.0 [INFO] [stderr] Downloaded windows-implement v0.56.0 [INFO] [stderr] Downloaded interprocess v2.2.3 [INFO] [stderr] Downloaded noodles-fastq v0.19.0 [INFO] [stderr] Downloaded typetag v0.2.5 [INFO] [stderr] Downloaded wasm-bindgen-macro-support v0.2.83 [INFO] [stderr] Downloaded lexical-parse-float v1.0.5 [INFO] [stderr] Downloaded brotli-decompressor v4.0.3 [INFO] [stderr] Downloaded noodles-tabix v0.55.0 [INFO] [stderr] Downloaded noodles-sam v0.77.0 [INFO] [stderr] Downloaded ref-cast-impl v1.0.24 [INFO] [stderr] Downloaded omnipath v0.1.1 [INFO] [stderr] Downloaded getrandom v0.2.8 [INFO] [stderr] Downloaded procfs v0.17.0 [INFO] [stderr] Downloaded sysinfo v0.33.1 [INFO] [stderr] Downloaded wasm-bindgen v0.2.83 [INFO] [stderr] Downloaded aho-corasick v0.7.20 [INFO] [stderr] Downloaded nu-utils v0.104.1 [INFO] [stderr] Downloaded ghost v0.1.6 [INFO] [stderr] Downloaded gfa v0.10.1 [INFO] [stderr] Downloaded vte v0.11.1 [INFO] [stderr] Downloaded zlib-rs v0.5.1 [INFO] [stderr] Downloaded windows-interface v0.56.0 [INFO] [stderr] Downloaded nu-plugin v0.104.1 [INFO] [stderr] Downloaded nu-glob v0.104.1 [INFO] [stderr] Downloaded nom v7.1.1 [INFO] [stderr] Downloaded libproc v0.14.10 [INFO] [stderr] Downloaded md-5 v0.10.5 [INFO] [stderr] Downloaded inventory v0.3.3 [INFO] [stderr] Downloaded pkg-config v0.3.26 [INFO] [stderr] Downloaded ctor v0.1.26 [INFO] [stderr] Downloaded noodles v0.99.0 [INFO] [stderr] Downloaded noodles-bcf v0.76.0 [INFO] [stderr] Downloaded noodles-bed v0.26.0 [INFO] [stderr] Downloaded noodles-gff v0.50.0 [INFO] [stderr] Downloaded lexical-write-integer v1.0.5 [INFO] [stderr] Downloaded noodles-bgzf v0.41.0 [INFO] [stderr] Downloaded percent-encoding v2.2.0 [INFO] [stderr] Downloaded doctest-file v1.0.0 [INFO] [stderr] Downloaded nu-plugin-core v0.104.1 [INFO] [stderr] Downloaded miette-derive v7.6.0 [INFO] [stderr] Downloaded owo-colors v4.2.2 [INFO] [stderr] Downloaded thiserror-impl v1.0.49 [INFO] [stderr] Downloaded thiserror v1.0.49 [INFO] [stderr] Downloaded nu-path v0.104.1 [INFO] [stderr] Downloaded shlex v1.2.0 [INFO] [stderr] Downloaded cxxbridge-flags v1.0.82 [INFO] [stderr] Downloaded cxxbridge-macro v1.0.82 [INFO] [stderr] Downloaded iana-time-zone-haiku v0.1.1 [INFO] [stderr] Downloaded procfs-core v0.17.0 [INFO] [stderr] Downloaded vte_generate_state_changes v0.1.1 [INFO] [stderr] Downloaded num-format v0.4.3 [INFO] [stderr] Downloaded lscolors v0.17.0 [INFO] [stderr] Downloaded sys-locale v0.3.1 [INFO] [stderr] Downloaded syn v1.0.104 [INFO] [stderr] Downloaded nu-protocol v0.104.1 [INFO] [stderr] Downloaded bitflags v2.4.0 [INFO] [stderr] Downloaded os_pipe v1.2.2 [INFO] [stderr] Downloaded strip-ansi-escapes v0.2.0 [INFO] [stderr] Downloaded wasm-bindgen-macro v0.2.83 [INFO] [stderr] Downloaded windows v0.56.0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 163e224a593c5fd05e2b65156f39846f876fb3e5d5f50baf45cdd8af71df6808 [INFO] running `Command { std: "docker" "start" "-a" "163e224a593c5fd05e2b65156f39846f876fb3e5d5f50baf45cdd8af71df6808", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "163e224a593c5fd05e2b65156f39846f876fb3e5d5f50baf45cdd8af71df6808", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "163e224a593c5fd05e2b65156f39846f876fb3e5d5f50baf45cdd8af71df6808", kill_on_drop: false }` [INFO] [stdout] 163e224a593c5fd05e2b65156f39846f876fb3e5d5f50baf45cdd8af71df6808 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 1ca3f66476f48edd3ebbbc5562a3f75a5027dffdc4956a3025b944d3dc504709 [INFO] running `Command { std: "docker" "start" "-a" "1ca3f66476f48edd3ebbbc5562a3f75a5027dffdc4956a3025b944d3dc504709", kill_on_drop: false }` [INFO] [stderr] Compiling unicode-ident v1.0.5 [INFO] [stderr] Compiling memchr v2.7.5 [INFO] [stderr] Compiling libc v0.2.174 [INFO] [stderr] Compiling crossbeam-utils v0.8.14 [INFO] [stderr] Compiling regex-syntax v0.8.5 [INFO] [stderr] Compiling crc32fast v1.3.2 [INFO] [stderr] Compiling zlib-rs v0.5.1 [INFO] [stderr] Compiling bitflags v2.4.0 [INFO] [stderr] Compiling bit-vec v0.8.0 [INFO] [stderr] Compiling allocator-api2 v0.2.16 [INFO] [stderr] Compiling serde v1.0.219 [INFO] [stderr] Compiling miniz_oxide v0.8.9 [INFO] [stderr] Compiling syn v1.0.104 [INFO] [stderr] Compiling num-traits v0.2.15 [INFO] [stderr] Compiling memoffset v0.7.1 [INFO] [stderr] Compiling crossbeam-epoch v0.9.13 [INFO] [stderr] Compiling proc-macro2 v1.0.95 [INFO] [stderr] Compiling log v0.4.17 [INFO] [stderr] Compiling lexical-util v1.0.6 [INFO] [stderr] Compiling rustix v0.38.44 [INFO] [stderr] Compiling lock_api v0.4.13 [INFO] [stderr] Compiling pure-rust-locales v0.8.1 [INFO] [stderr] Compiling cc v1.0.77 [INFO] [stderr] Compiling ryu v1.0.11 [INFO] [stderr] Compiling linux-raw-sys v0.4.15 [INFO] [stderr] Compiling signal-hook v0.3.18 [INFO] [stderr] Compiling hashbrown v0.15.4 [INFO] [stderr] Compiling pkg-config v0.3.26 [INFO] [stderr] Compiling quote v1.0.40 [INFO] [stderr] Compiling iana-time-zone v0.1.53 [INFO] [stderr] Compiling aho-corasick v1.1.3 [INFO] [stderr] Compiling syn v2.0.104 [INFO] [stderr] Compiling crossbeam-channel v0.5.6 [INFO] [stderr] Compiling nix v0.29.0 [INFO] [stderr] Compiling thiserror v1.0.49 [INFO] [stderr] Compiling typenum v1.15.0 [INFO] [stderr] Compiling crossbeam-deque v0.8.2 [INFO] [stderr] Compiling either v1.8.0 [INFO] [stderr] Compiling indexmap v2.10.0 [INFO] [stderr] Compiling rustix v1.0.7 [INFO] [stderr] Compiling rayon-core v1.12.1 [INFO] [stderr] Compiling vte_generate_state_changes v0.1.1 [INFO] [stderr] Compiling lexical-parse-integer v1.0.5 [INFO] [stderr] Compiling lexical-write-integer v1.0.5 [INFO] [stderr] Compiling generic-array v0.14.6 [INFO] [stderr] Compiling itoa v1.0.4 [INFO] [stderr] Compiling ref-cast v1.0.24 [INFO] [stderr] Compiling linux-raw-sys v0.9.4 [INFO] [stderr] Compiling procfs v0.17.0 [INFO] [stderr] Compiling erased-serde v0.3.23 [INFO] [stderr] Compiling option-ext v0.2.0 [INFO] [stderr] Compiling owo-colors v4.2.2 [INFO] [stderr] Compiling utf8parse v0.2.0 [INFO] [stderr] Compiling rustversion v1.0.21 [INFO] [stderr] Compiling vte v0.11.1 [INFO] [stderr] Compiling rayon v1.10.0 [INFO] [stderr] Compiling lexical-write-float v1.0.5 [INFO] [stderr] Compiling lexical-parse-float v1.0.5 [INFO] [stderr] Compiling proc-macro-error-attr2 v2.0.0 [INFO] [stderr] Compiling signal-hook-registry v1.4.5 [INFO] [stderr] Compiling mio v1.0.4 [INFO] [stderr] Compiling parking_lot_core v0.9.11 [INFO] [stderr] Compiling regex-automata v0.4.9 [INFO] [stderr] Compiling parking_lot v0.12.4 [INFO] [stderr] Compiling dirs-sys v0.4.1 [INFO] [stderr] Compiling bit-set v0.8.0 [INFO] [stderr] Compiling signal-hook-mio v0.2.4 [INFO] [stderr] Compiling unicode-width v0.2.1 [INFO] [stderr] Compiling nu-ansi-term v0.50.1 [INFO] [stderr] Compiling unicode-linebreak v0.1.5 [INFO] [stderr] Compiling arrayvec v0.7.2 [INFO] [stderr] Compiling paste v1.0.9 [INFO] [stderr] Compiling thiserror v2.0.12 [INFO] [stderr] Compiling heck v0.5.0 [INFO] [stderr] Compiling is_ci v1.2.0 [INFO] [stderr] Compiling num-format v0.4.3 [INFO] [stderr] Compiling supports-color v3.0.2 [INFO] [stderr] Compiling rmp v0.8.14 [INFO] [stderr] Compiling proc-macro-error2 v2.0.1 [INFO] [stderr] Compiling textwrap v0.16.2 [INFO] [stderr] Compiling terminal_size v0.4.2 [INFO] [stderr] Compiling lscolors v0.17.0 [INFO] [stderr] Compiling dirs v5.0.1 [INFO] [stderr] Compiling strip-ansi-escapes v0.2.0 [INFO] [stderr] Compiling lexical-core v1.0.5 [INFO] [stderr] Compiling brotli-decompressor v4.0.3 [INFO] [stderr] Compiling itertools v0.13.0 [INFO] [stderr] Compiling sys-locale v0.3.1 [INFO] [stderr] Compiling supports-hyperlinks v3.1.0 [INFO] [stderr] Compiling libz-rs-sys v0.5.1 [INFO] [stderr] Compiling unicase v2.8.1 [INFO] [stderr] Compiling once_cell v1.21.3 [INFO] [stderr] Compiling supports-unicode v3.0.0 [INFO] [stderr] Compiling os_pipe v1.2.2 [INFO] [stderr] Compiling flate2 v1.1.2 [INFO] [stderr] Compiling bzip2-sys v0.1.13+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling lru v0.12.5 [INFO] [stderr] Compiling nu-glob v0.104.1 [INFO] [stderr] Compiling semver v1.0.26 [INFO] [stderr] Compiling serde_derive v1.0.219 [INFO] [stderr] Compiling thiserror-impl v1.0.49 [INFO] [stderr] Compiling ref-cast-impl v1.0.24 [INFO] [stderr] Compiling thiserror-impl v2.0.12 [INFO] [stderr] Compiling miette-derive v7.6.0 [INFO] [stderr] Compiling noodles-bgzf v0.41.0 [INFO] [stderr] Compiling sysinfo v0.33.1 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling nu-derive-value v0.104.1 [INFO] [stderr] Compiling strum v0.26.3 [INFO] [stderr] Compiling block-buffer v0.10.3 [INFO] [stderr] Compiling crypto-common v0.1.6 [INFO] [stderr] Compiling brotli v7.0.0 [INFO] [stderr] Compiling percent-encoding v2.2.0 [INFO] [stderr] Compiling pwd v1.4.0 [INFO] [stderr] Compiling ctor v0.1.26 [INFO] [stderr] Compiling ghost v0.1.6 [INFO] [stderr] Compiling typetag-impl v0.2.5 [INFO] [stderr] Compiling crossterm v0.28.1 [INFO] [stderr] Compiling nu-path v0.104.1 [INFO] [stderr] Compiling miette v7.6.0 [INFO] [stderr] Compiling digest v0.10.6 [INFO] [stderr] Compiling nom v5.1.2 [INFO] [stderr] Compiling doctest-file v1.0.0 [INFO] [stderr] Compiling anyhow v1.0.66 [INFO] [stderr] Compiling lexical-core v0.7.6 [INFO] [stderr] Compiling inventory v0.3.3 [INFO] [stderr] Compiling md-5 v0.10.5 [INFO] [stderr] Compiling bzip2 v0.5.2 [INFO] [stderr] Compiling xz2 v0.1.7 [INFO] [stderr] Compiling bstr v1.12.0 [INFO] [stderr] Compiling fancy-regex v0.14.0 [INFO] [stderr] Compiling bytemuck_derive v1.3.0 [INFO] [stderr] Compiling interprocess v2.2.3 [INFO] [stderr] Compiling noodles-core v0.17.0 [INFO] [stderr] Compiling aho-corasick v0.7.20 [INFO] [stderr] Compiling regex-syntax v0.6.28 [INFO] [stderr] Compiling noodles-csi v0.49.0 [INFO] [stderr] Compiling noodles-fasta v0.54.0 [INFO] [stderr] Compiling bytemuck v1.12.3 [INFO] [stderr] Compiling noodles-fastq v0.19.0 [INFO] [stderr] Compiling memmap v0.7.0 [INFO] [stderr] Compiling bstr v0.2.17 [INFO] [stderr] Compiling noodles-tabix v0.55.0 [INFO] [stderr] Compiling noodles-sam v0.77.0 [INFO] [stderr] Compiling noodles-gff v0.50.0 [INFO] [stderr] Compiling noodles-vcf v0.79.0 [INFO] [stderr] Compiling noodles-bed v0.26.0 [INFO] [stderr] Compiling noodles-bam v0.81.0 [INFO] [stderr] Compiling regex v1.7.0 [INFO] [stderr] Compiling noodles-cram v0.84.0 [INFO] [stderr] Compiling noodles-bcf v0.76.0 [INFO] [stderr] Compiling gfa v0.10.1 [INFO] [stderr] Compiling chrono v0.4.41 [INFO] [stderr] Compiling serde_json v1.0.140 [INFO] [stderr] Compiling rmp-serde v1.3.0 [INFO] [stderr] Compiling typetag v0.2.5 [INFO] [stderr] Compiling nu-utils v0.104.1 [INFO] [stderr] Compiling noodles v0.99.0 [INFO] [stderr] Compiling procfs-core v0.17.0 [INFO] [stderr] Compiling chrono-humanize v0.2.3 [INFO] [stderr] Compiling nu-system v0.104.1 [INFO] [stderr] Compiling nu-protocol v0.104.1 [INFO] [stderr] Compiling nu-plugin-protocol v0.104.1 [INFO] [stderr] Compiling nu-engine v0.104.1 [INFO] [stderr] Compiling nu-plugin-core v0.104.1 [INFO] [stderr] Compiling nu-plugin v0.104.1 [INFO] [stderr] Compiling nu_plugin_bio v0.104.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `Cursor` [INFO] [stdout] --> src/bio_format/bcf.rs:10:35 [INFO] [stdout] | [INFO] [stdout] 10 | use std::io::{BufRead, BufReader, Cursor}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Record` [INFO] [stdout] --> src/bio_format/bed.rs:4:19 [INFO] [stdout] | [INFO] [stdout] 4 | use nu_protocol::{Record, Value}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `super::SpanExt` [INFO] [stdout] --> src/bio_format/bed.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use super::SpanExt; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Cursor` [INFO] [stdout] --> src/bio_format/fasta.rs:1:35 [INFO] [stdout] | [INFO] [stdout] 1 | use std::io::{BufRead, BufReader, Cursor}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Cursor` [INFO] [stdout] --> src/bio_format/gfa.rs:12:35 [INFO] [stdout] | [INFO] [stdout] 12 | use std::io::{BufRead, BufReader, Cursor}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Record` [INFO] [stdout] --> src/bio_format/gff.rs:5:19 [INFO] [stdout] | [INFO] [stdout] 5 | use nu_protocol::{Record, Value}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `super::SpanExt` [INFO] [stdout] --> src/bio_format/gff.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | use super::SpanExt; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `read_name` [INFO] [stdout] --> src/bio_format/bam.rs:144:9 [INFO] [stdout] | [INFO] [stdout] 144 | let read_name = r [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_name` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `r` [INFO] [stdout] --> src/bio_format/bcf.rs:177:37 [INFO] [stdout] | [INFO] [stdout] 177 | fn add_record(call: &EvaluatedCall, r: vcf::Record, vec_vals: &mut Vec) { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_r` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `r` [INFO] [stdout] --> src/bio_format/bcf.rs:234:13 [INFO] [stdout] | [INFO] [stdout] 234 | let r = match record { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_r` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `header` [INFO] [stdout] --> src/bio_format/bcf.rs:228:5 [INFO] [stdout] | [INFO] [stdout] 228 | header: vcf::Header, [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_header` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/bcf.rs:241:13 [INFO] [stdout] | [INFO] [stdout] 241 | let mut vec_vals = Vec::new(); [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `r` [INFO] [stdout] --> src/bio_format/bcf.rs:338:13 [INFO] [stdout] | [INFO] [stdout] 338 | let r = match record { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_r` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `header` [INFO] [stdout] --> src/bio_format/bcf.rs:333:5 [INFO] [stdout] | [INFO] [stdout] 333 | header: vcf::Header, [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_header` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/bcf.rs:345:13 [INFO] [stdout] | [INFO] [stdout] 345 | let mut vec_vals = Vec::new(); [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `reader` [INFO] [stdout] --> src/bio_format/bed.rs:28:13 [INFO] [stdout] | [INFO] [stdout] 28 | let mut reader: bed::io::Reader<3, &[u8]> = bed::io::Reader::new(bytes.as_slice()); [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_reader` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `call` [INFO] [stdout] --> src/bio_format/bed.rs:21:23 [INFO] [stdout] | [INFO] [stdout] 21 | pub fn from_bed_inner(call: &EvaluatedCall, input: Value) -> Result, LabeledError> { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_call` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/bed.rs:28:9 [INFO] [stdout] | [INFO] [stdout] 28 | let mut reader: bed::io::Reader<3, &[u8]> = bed::io::Reader::new(bytes.as_slice()); [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/bed.rs:30:9 [INFO] [stdout] | [INFO] [stdout] 30 | let mut records = Vec::new(); [INFO] [stdout] | ----^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `value_records` is never read [INFO] [stdout] --> src/bio_format/cram.rs:41:13 [INFO] [stdout] | [INFO] [stdout] 41 | let mut value_records = Vec::new(); [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `call` [INFO] [stdout] --> src/bio_format/gfa.rs:28:5 [INFO] [stdout] | [INFO] [stdout] 28 | call: &EvaluatedCall, [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_call` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `reader` [INFO] [stdout] --> src/bio_format/gff.rs:31:13 [INFO] [stdout] | [INFO] [stdout] 31 | let mut reader = gff::io::Reader::new(stream); [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_reader` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `call` [INFO] [stdout] --> src/bio_format/gff.rs:23:23 [INFO] [stdout] | [INFO] [stdout] 23 | pub fn from_gff_inner(call: &EvaluatedCall, input: &Value) -> Result, LabeledError> { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_call` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/gff.rs:31:9 [INFO] [stdout] | [INFO] [stdout] 31 | let mut reader = gff::io::Reader::new(stream); [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/gff.rs:33:9 [INFO] [stdout] | [INFO] [stdout] 33 | let mut value_records = Vec::new(); [INFO] [stdout] | ----^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `add_record` is never used [INFO] [stdout] --> src/bio_format/bcf.rs:177:4 [INFO] [stdout] | [INFO] [stdout] 177 | fn add_record(call: &EvaluatedCall, r: vcf::Record, vec_vals: &mut Vec) { [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `BED_COLUMN_NUMBER` is never used [INFO] [stdout] --> src/bio_format/bed.rs:9:7 [INFO] [stdout] | [INFO] [stdout] 9 | const BED_COLUMN_NUMBER: u8 = 3; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `BED_COLUMNS` is never used [INFO] [stdout] --> src/bio_format/bed.rs:12:11 [INFO] [stdout] | [INFO] [stdout] 12 | pub const BED_COLUMNS: &[&str] = &[ [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `GFF_COLUMNS` is never used [INFO] [stdout] --> src/bio_format/gff.rs:10:7 [INFO] [stdout] | [INFO] [stdout] 10 | const GFF_COLUMNS: &[&str] = &[ [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 51s [INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nom v5.1.2 [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" "1ca3f66476f48edd3ebbbc5562a3f75a5027dffdc4956a3025b944d3dc504709", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "1ca3f66476f48edd3ebbbc5562a3f75a5027dffdc4956a3025b944d3dc504709", kill_on_drop: false }` [INFO] [stdout] 1ca3f66476f48edd3ebbbc5562a3f75a5027dffdc4956a3025b944d3dc504709 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] f3c0665fbfe9c1ce846c7679c9bea0f5ff7fa19d22661aaa1e771848cfd1cc62 [INFO] running `Command { std: "docker" "start" "-a" "f3c0665fbfe9c1ce846c7679c9bea0f5ff7fa19d22661aaa1e771848cfd1cc62", kill_on_drop: false }` [INFO] [stdout] warning: unused import: `Cursor` [INFO] [stdout] --> src/bio_format/bcf.rs:10:35 [INFO] [stdout] | [INFO] [stdout] 10 | use std::io::{BufRead, BufReader, Cursor}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Record` [INFO] [stdout] --> src/bio_format/bed.rs:4:19 [INFO] [stdout] | [INFO] [stdout] 4 | use nu_protocol::{Record, Value}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `super::SpanExt` [INFO] [stdout] --> src/bio_format/bed.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use super::SpanExt; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Cursor` [INFO] [stdout] --> src/bio_format/fasta.rs:1:35 [INFO] [stdout] | [INFO] [stdout] 1 | use std::io::{BufRead, BufReader, Cursor}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Cursor` [INFO] [stdout] --> src/bio_format/gfa.rs:12:35 [INFO] [stdout] | [INFO] [stdout] 12 | use std::io::{BufRead, BufReader, Cursor}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Record` [INFO] [stdout] --> src/bio_format/gff.rs:5:19 [INFO] [stdout] | [INFO] [stdout] 5 | use nu_protocol::{Record, Value}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `super::SpanExt` [INFO] [stdout] --> src/bio_format/gff.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | use super::SpanExt; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `read_name` [INFO] [stdout] --> src/bio_format/bam.rs:144:9 [INFO] [stdout] | [INFO] [stdout] 144 | let read_name = r [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_name` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `r` [INFO] [stdout] --> src/bio_format/bcf.rs:177:37 [INFO] [stdout] | [INFO] [stdout] 177 | fn add_record(call: &EvaluatedCall, r: vcf::Record, vec_vals: &mut Vec) { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_r` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `r` [INFO] [stdout] --> src/bio_format/bcf.rs:234:13 [INFO] [stdout] | [INFO] [stdout] 234 | let r = match record { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_r` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `header` [INFO] [stdout] --> src/bio_format/bcf.rs:228:5 [INFO] [stdout] | [INFO] [stdout] 228 | header: vcf::Header, [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_header` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/bcf.rs:241:13 [INFO] [stdout] | [INFO] [stdout] 241 | let mut vec_vals = Vec::new(); [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `r` [INFO] [stdout] --> src/bio_format/bcf.rs:338:13 [INFO] [stdout] | [INFO] [stdout] 338 | let r = match record { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_r` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `header` [INFO] [stdout] --> src/bio_format/bcf.rs:333:5 [INFO] [stdout] | [INFO] [stdout] 333 | header: vcf::Header, [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_header` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/bcf.rs:345:13 [INFO] [stdout] | [INFO] [stdout] 345 | let mut vec_vals = Vec::new(); [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `reader` [INFO] [stdout] --> src/bio_format/bed.rs:28:13 [INFO] [stdout] | [INFO] [stdout] 28 | let mut reader: bed::io::Reader<3, &[u8]> = bed::io::Reader::new(bytes.as_slice()); [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_reader` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `call` [INFO] [stdout] --> src/bio_format/bed.rs:21:23 [INFO] [stdout] | [INFO] [stdout] 21 | pub fn from_bed_inner(call: &EvaluatedCall, input: Value) -> Result, LabeledError> { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_call` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/bed.rs:28:9 [INFO] [stdout] | [INFO] [stdout] 28 | let mut reader: bed::io::Reader<3, &[u8]> = bed::io::Reader::new(bytes.as_slice()); [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/bed.rs:30:9 [INFO] [stdout] | [INFO] [stdout] 30 | let mut records = Vec::new(); [INFO] [stdout] | ----^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `value_records` is never read [INFO] [stdout] --> src/bio_format/cram.rs:41:13 [INFO] [stdout] | [INFO] [stdout] 41 | let mut value_records = Vec::new(); [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `call` [INFO] [stdout] --> src/bio_format/gfa.rs:28:5 [INFO] [stdout] | [INFO] [stdout] 28 | call: &EvaluatedCall, [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_call` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `reader` [INFO] [stdout] --> src/bio_format/gff.rs:31:13 [INFO] [stdout] | [INFO] [stdout] 31 | let mut reader = gff::io::Reader::new(stream); [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_reader` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `call` [INFO] [stdout] --> src/bio_format/gff.rs:23:23 [INFO] [stdout] | [INFO] [stdout] 23 | pub fn from_gff_inner(call: &EvaluatedCall, input: &Value) -> Result, LabeledError> { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_call` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/gff.rs:31:9 [INFO] [stdout] | [INFO] [stdout] 31 | let mut reader = gff::io::Reader::new(stream); [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/gff.rs:33:9 [INFO] [stdout] | [INFO] [stdout] 33 | let mut value_records = Vec::new(); [INFO] [stdout] | ----^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `add_record` is never used [INFO] [stdout] --> src/bio_format/bcf.rs:177:4 [INFO] [stdout] | [INFO] [stdout] 177 | fn add_record(call: &EvaluatedCall, r: vcf::Record, vec_vals: &mut Vec) { [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Compiling nu_plugin_bio v0.104.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: constant `BED_COLUMN_NUMBER` is never used [INFO] [stdout] --> src/bio_format/bed.rs:9:7 [INFO] [stdout] | [INFO] [stdout] 9 | const BED_COLUMN_NUMBER: u8 = 3; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `BED_COLUMNS` is never used [INFO] [stdout] --> src/bio_format/bed.rs:12:11 [INFO] [stdout] | [INFO] [stdout] 12 | pub const BED_COLUMNS: &[&str] = &[ [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `GFF_COLUMNS` is never used [INFO] [stdout] --> src/bio_format/gff.rs:10:7 [INFO] [stdout] | [INFO] [stdout] 10 | const GFF_COLUMNS: &[&str] = &[ [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Cursor` [INFO] [stdout] --> src/bio_format/bcf.rs:10:35 [INFO] [stdout] | [INFO] [stdout] 10 | use std::io::{BufRead, BufReader, Cursor}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Record` [INFO] [stdout] --> src/bio_format/bed.rs:4:19 [INFO] [stdout] | [INFO] [stdout] 4 | use nu_protocol::{Record, Value}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `super::SpanExt` [INFO] [stdout] --> src/bio_format/bed.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use super::SpanExt; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Cursor` [INFO] [stdout] --> src/bio_format/fasta.rs:1:35 [INFO] [stdout] | [INFO] [stdout] 1 | use std::io::{BufRead, BufReader, Cursor}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Cursor` [INFO] [stdout] --> src/bio_format/gfa.rs:12:35 [INFO] [stdout] | [INFO] [stdout] 12 | use std::io::{BufRead, BufReader, Cursor}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Record` [INFO] [stdout] --> src/bio_format/gff.rs:5:19 [INFO] [stdout] | [INFO] [stdout] 5 | use nu_protocol::{Record, Value}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `super::SpanExt` [INFO] [stdout] --> src/bio_format/gff.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | use super::SpanExt; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `read_name` [INFO] [stdout] --> src/bio_format/bam.rs:144:9 [INFO] [stdout] | [INFO] [stdout] 144 | let read_name = r [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_name` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `r` [INFO] [stdout] --> src/bio_format/bcf.rs:177:37 [INFO] [stdout] | [INFO] [stdout] 177 | fn add_record(call: &EvaluatedCall, r: vcf::Record, vec_vals: &mut Vec) { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_r` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `r` [INFO] [stdout] --> src/bio_format/bcf.rs:234:13 [INFO] [stdout] | [INFO] [stdout] 234 | let r = match record { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_r` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `header` [INFO] [stdout] --> src/bio_format/bcf.rs:228:5 [INFO] [stdout] | [INFO] [stdout] 228 | header: vcf::Header, [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_header` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/bcf.rs:241:13 [INFO] [stdout] | [INFO] [stdout] 241 | let mut vec_vals = Vec::new(); [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `r` [INFO] [stdout] --> src/bio_format/bcf.rs:338:13 [INFO] [stdout] | [INFO] [stdout] 338 | let r = match record { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_r` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `header` [INFO] [stdout] --> src/bio_format/bcf.rs:333:5 [INFO] [stdout] | [INFO] [stdout] 333 | header: vcf::Header, [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_header` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/bcf.rs:345:13 [INFO] [stdout] | [INFO] [stdout] 345 | let mut vec_vals = Vec::new(); [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `reader` [INFO] [stdout] --> src/bio_format/bed.rs:28:13 [INFO] [stdout] | [INFO] [stdout] 28 | let mut reader: bed::io::Reader<3, &[u8]> = bed::io::Reader::new(bytes.as_slice()); [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_reader` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `call` [INFO] [stdout] --> src/bio_format/bed.rs:21:23 [INFO] [stdout] | [INFO] [stdout] 21 | pub fn from_bed_inner(call: &EvaluatedCall, input: Value) -> Result, LabeledError> { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_call` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/bed.rs:28:9 [INFO] [stdout] | [INFO] [stdout] 28 | let mut reader: bed::io::Reader<3, &[u8]> = bed::io::Reader::new(bytes.as_slice()); [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/bed.rs:30:9 [INFO] [stdout] | [INFO] [stdout] 30 | let mut records = Vec::new(); [INFO] [stdout] | ----^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `value_records` is never read [INFO] [stdout] --> src/bio_format/cram.rs:41:13 [INFO] [stdout] | [INFO] [stdout] 41 | let mut value_records = Vec::new(); [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `call` [INFO] [stdout] --> src/bio_format/gfa.rs:28:5 [INFO] [stdout] | [INFO] [stdout] 28 | call: &EvaluatedCall, [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_call` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `reader` [INFO] [stdout] --> src/bio_format/gff.rs:31:13 [INFO] [stdout] | [INFO] [stdout] 31 | let mut reader = gff::io::Reader::new(stream); [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_reader` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `call` [INFO] [stdout] --> src/bio_format/gff.rs:23:23 [INFO] [stdout] | [INFO] [stdout] 23 | pub fn from_gff_inner(call: &EvaluatedCall, input: &Value) -> Result, LabeledError> { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_call` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/gff.rs:31:9 [INFO] [stdout] | [INFO] [stdout] 31 | let mut reader = gff::io::Reader::new(stream); [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bio_format/gff.rs:33:9 [INFO] [stdout] | [INFO] [stdout] 33 | let mut value_records = Vec::new(); [INFO] [stdout] | ----^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `add_record` is never used [INFO] [stdout] --> src/bio_format/bcf.rs:177:4 [INFO] [stdout] | [INFO] [stdout] 177 | fn add_record(call: &EvaluatedCall, r: vcf::Record, vec_vals: &mut Vec) { [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `BED_COLUMN_NUMBER` is never used [INFO] [stdout] --> src/bio_format/bed.rs:9:7 [INFO] [stdout] | [INFO] [stdout] 9 | const BED_COLUMN_NUMBER: u8 = 3; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `BED_COLUMNS` is never used [INFO] [stdout] --> src/bio_format/bed.rs:12:11 [INFO] [stdout] | [INFO] [stdout] 12 | pub const BED_COLUMNS: &[&str] = &[ [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `GFF_COLUMNS` is never used [INFO] [stdout] --> src/bio_format/gff.rs:10:7 [INFO] [stdout] | [INFO] [stdout] 10 | const GFF_COLUMNS: &[&str] = &[ [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 2.40s [INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nom v5.1.2 [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" "f3c0665fbfe9c1ce846c7679c9bea0f5ff7fa19d22661aaa1e771848cfd1cc62", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f3c0665fbfe9c1ce846c7679c9bea0f5ff7fa19d22661aaa1e771848cfd1cc62", kill_on_drop: false }` [INFO] [stdout] f3c0665fbfe9c1ce846c7679c9bea0f5ff7fa19d22661aaa1e771848cfd1cc62