[INFO] cloning repository https://github.com/arudhir/transdecoder-rust
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/arudhir/transdecoder-rust" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Farudhir%2Ftransdecoder-rust", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Farudhir%2Ftransdecoder-rust'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] b28e658d5c04de63c753d7d8b2a94f413557ecd7
[INFO] checking arudhir/transdecoder-rust against master#029c9e18dd1f4668e1d42bb187c1c263dfe20093 for pr-157562
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Farudhir%2Ftransdecoder-rust" "/workspace/builds/worker-5-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-5-tc1/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/arudhir/transdecoder-rust
[INFO] finished tweaking git repo https://github.com/arudhir/transdecoder-rust
[INFO] tweaked toml for git repo https://github.com/arudhir/transdecoder-rust written to /workspace/builds/worker-5-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/arudhir/transdecoder-rust on toolchain 029c9e18dd1f4668e1d42bb187c1c263dfe20093
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+029c9e18dd1f4668e1d42bb187c1c263dfe20093" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/arudhir/transdecoder-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" "+029c9e18dd1f4668e1d42bb187c1c263dfe20093" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded triple_accel v0.4.0
[INFO] [stderr]   Downloaded proc-macro2 v1.0.94
[INFO] [stderr]   Downloaded rustc_version v0.1.7
[INFO] [stderr]   Downloaded nalgebra-macros v0.1.0
[INFO] [stderr]   Downloaded itertools-num v0.1.3
[INFO] [stderr]   Downloaded semver v0.1.20
[INFO] [stderr]   Downloaded editdistancek v1.0.2
[INFO] [stderr]   Downloaded derive-new v0.6.0
[INFO] [stderr]   Downloaded newtype_derive v0.1.6
[INFO] [stderr]   Downloaded multimap v0.9.1
[INFO] [stderr]   Downloaded custom_derive v0.1.7
[INFO] [stderr]   Downloaded ordered-float v3.9.2
[INFO] [stderr]   Downloaded csv-core v0.1.12
[INFO] [stderr]   Downloaded statrs v0.16.1
[INFO] [stderr]   Downloaded bio-types v1.0.4
[INFO] [stderr]   Downloaded simba v0.6.0
[INFO] [stderr]   Downloaded matrixmultiply v0.3.9
[INFO] [stderr]   Downloaded anyhow v1.0.97
[INFO] [stderr]   Downloaded typenum v1.18.0
[INFO] [stderr]   Downloaded zerocopy-derive v0.8.24
[INFO] [stderr]   Downloaded bio v1.6.0
[INFO] [stderr]   Downloaded zerocopy v0.8.24
[INFO] [stderr]   Downloaded ndarray v0.15.6
[INFO] [stderr]   Downloaded nalgebra v0.29.0
[INFO] [stderr]   Downloaded petgraph v0.6.5
[INFO] [stderr]   Downloaded libc v0.2.171
[INFO] [stderr]   Downloaded csv v1.3.1
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,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" "-m" "1610612736" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:3e793bdf10248eb2ddbd6b0faebed8155c11b4589982e2893733958d93e8d540" "sleep" "infinity", kill_on_drop: false }`
[INFO] [stdout] 9d2a978bb3acc0046010badd73ae45e7e06f4797f96fdab62b737560a6adfdb8
[INFO] running `Command { std: "docker" "start" "9d2a978bb3acc0046010badd73ae45e7e06f4797f96fdab62b737560a6adfdb8", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-w" "/opt/rustwide/workdir" "--user" "0:0" "9d2a978bb3acc0046010badd73ae45e7e06f4797f96fdab62b737560a6adfdb8" "/opt/rustwide/cargo-home/bin/cargo" "+029c9e18dd1f4668e1d42bb187c1c263dfe20093" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "9d2a978bb3acc0046010badd73ae45e7e06f4797f96fdab62b737560a6adfdb8", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-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" "-w" "/opt/rustwide/workdir" "--user" "0:0" "9d2a978bb3acc0046010badd73ae45e7e06f4797f96fdab62b737560a6adfdb8" "/opt/rustwide/cargo-home/bin/cargo" "+029c9e18dd1f4668e1d42bb187c1c263dfe20093" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stderr]    Compiling proc-macro2 v1.0.94
[INFO] [stderr]    Compiling unicode-ident v1.0.18
[INFO] [stderr]    Compiling autocfg v1.4.0
[INFO] [stderr]    Compiling libm v0.2.11
[INFO] [stderr]    Compiling libc v0.2.171
[INFO] [stderr]    Compiling zerocopy v0.8.24
[INFO] [stderr]    Compiling serde v1.0.219
[INFO] [stderr]     Checking memchr v2.7.4
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]     Checking bytemuck v1.22.0
[INFO] [stderr]    Compiling rustversion v1.0.20
[INFO] [stderr]    Compiling typenum v1.18.0
[INFO] [stderr]     Checking safe_arch v0.7.4
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling matrixmultiply v0.3.9
[INFO] [stderr]    Compiling quote v1.0.40
[INFO] [stderr]    Compiling syn v2.0.100
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]     Checking wide v0.7.32
[INFO] [stderr]     Checking aho-corasick v1.1.3
[INFO] [stderr]     Checking regex-syntax v0.8.5
[INFO] [stderr]     Checking getrandom v0.2.15
[INFO] [stderr]     Checking rand_core v0.6.4
[INFO] [stderr]     Checking num-complex v0.4.6
[INFO] [stderr]     Checking num-integer v0.1.46
[INFO] [stderr]     Checking approx v0.5.1
[INFO] [stderr]    Compiling feature-probe v0.1.1
[INFO] [stderr]     Checking num-rational v0.4.2
[INFO] [stderr]    Compiling bv v0.11.1
[INFO] [stderr]     Checking ppv-lite86 v0.2.21
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling anyhow v1.0.97
[INFO] [stderr]     Checking hashbrown v0.15.2
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]     Checking csv-core v0.1.12
[INFO] [stderr]     Checking rand v0.8.5
[INFO] [stderr]     Checking simba v0.6.0
[INFO] [stderr]     Checking indexmap v2.9.0
[INFO] [stderr]     Checking ryu v1.0.20
[INFO] [stderr]     Checking itoa v1.0.15
[INFO] [stderr]     Checking either v1.15.0
[INFO] [stderr]     Checking bit-vec v0.6.3
[INFO] [stderr]     Checking regex-automata v0.4.9
[INFO] [stderr]    Compiling heck v0.4.1
[INFO] [stderr]     Checking fixedbitset v0.4.2
[INFO] [stderr]     Checking bit-set v0.5.3
[INFO] [stderr]     Checking itertools v0.11.0
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking petgraph v0.6.5
[INFO] [stderr]     Checking ndarray v0.15.6
[INFO] [stderr]     Checking ordered-float v3.9.2
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking strum v0.25.0
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking editdistancek v1.0.2
[INFO] [stderr]    Compiling serde_derive v1.0.219
[INFO] [stderr]    Compiling thiserror-impl v1.0.69
[INFO] [stderr]    Compiling enum-map-derive v0.17.0
[INFO] [stderr]     Checking regex v1.11.1
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]     Checking enum-map v2.7.3
[INFO] [stderr]    Compiling nalgebra-macros v0.1.0
[INFO] [stderr]    Compiling strum_macros v0.25.3
[INFO] [stderr]     Checking bytecount v0.6.8
[INFO] [stderr]     Checking thiserror v1.0.69
[INFO] [stderr]     Checking bio-types v1.0.4
[INFO] [stderr]     Checking nalgebra v0.29.0
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking multimap v0.9.1
[INFO] [stderr]     Checking csv v1.3.1
[INFO] [stderr]     Checking statrs v0.16.1
[INFO] [stderr]     Checking bio v1.6.0
[INFO] [stderr]     Checking transdecoder-rust v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/orf.rs:45:9
[INFO] [stdout]    |
[INFO] [stdout] 45 |     let mut orfs = Vec::new();  // A dynamic vector of ORFs as an accumulator, like orfs = [] in
[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: `seq`
[INFO] [stdout]   --> src/orf.rs:44:18
[INFO] [stdout]    |
[INFO] [stdout] 44 | pub fn find_orfs(seq: &str, strand: Strand) -> Vec<ORF> {
[INFO] [stdout]    |                  ^^^ help: if this is intentional, prefix it with an underscore: `_seq`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `strand`
[INFO] [stdout]   --> src/orf.rs:44:29
[INFO] [stdout]    |
[INFO] [stdout] 44 | pub fn find_orfs(seq: &str, strand: Strand) -> Vec<ORF> {
[INFO] [stdout]    |                             ^^^^^^ help: if this is intentional, prefix it with an underscore: `_strand`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `orf`
[INFO] [stdout]   --> src/orf.rs:92:17
[INFO] [stdout]    |
[INFO] [stdout] 92 | fn classify_orf(orf: &str) -> ORFType {
[INFO] [stdout]    |                 ^^^ help: if this is intentional, prefix it with an underscore: `_orf`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: enum `Strand` is never used
[INFO] [stdout]  --> src/types.rs:2:10
[INFO] [stdout]   |
[INFO] [stdout] 2 | pub enum Strand {
[INFO] [stdout]   |          ^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: enum `ORFType` is never used
[INFO] [stdout]  --> src/types.rs:9:10
[INFO] [stdout]   |
[INFO] [stdout] 9 | pub enum ORFType {
[INFO] [stdout]   |          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `ORF` is never constructed
[INFO] [stdout]   --> src/types.rs:17:12
[INFO] [stdout]    |
[INFO] [stdout] 17 | pub struct ORF {
[INFO] [stdout]    |            ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `make_codon_table` is never used
[INFO] [stdout]  --> src/orf.rs:4:8
[INFO] [stdout]   |
[INFO] [stdout] 4 | pub fn make_codon_table() -> HashMap<&'static str, char> {
[INFO] [stdout]   |        ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `find_orfs` is never used
[INFO] [stdout]   --> src/orf.rs:44:8
[INFO] [stdout]    |
[INFO] [stdout] 44 | pub fn find_orfs(seq: &str, strand: Strand) -> Vec<ORF> {
[INFO] [stdout]    |        ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `is_start` is never used
[INFO] [stdout]   --> src/orf.rs:65:4
[INFO] [stdout]    |
[INFO] [stdout] 65 | fn is_start(seq: &str) -> bool {
[INFO] [stdout]    |    ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `is_stop` is never used
[INFO] [stdout]   --> src/orf.rs:70:4
[INFO] [stdout]    |
[INFO] [stdout] 70 | fn is_stop(seq: &str) -> bool {
[INFO] [stdout]    |    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `translate` is never used
[INFO] [stdout]   --> src/orf.rs:75:4
[INFO] [stdout]    |
[INFO] [stdout] 75 | fn translate(seq: &str) -> String {
[INFO] [stdout]    |    ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `classify_orf` is never used
[INFO] [stdout]   --> src/orf.rs:92:4
[INFO] [stdout]    |
[INFO] [stdout] 92 | fn classify_orf(orf: &str) -> ORFType {
[INFO] [stdout]    |    ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `reverse_complement` is never used
[INFO] [stdout]   --> src/orf.rs:97:4
[INFO] [stdout]    |
[INFO] [stdout] 97 | fn reverse_complement(seq: &str) -> String {
[INFO] [stdout]    |    ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/orf.rs:45:9
[INFO] [stdout]    |
[INFO] [stdout] 45 |     let mut orfs = Vec::new();  // A dynamic vector of ORFs as an accumulator, like orfs = [] in
[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: `seq`
[INFO] [stdout]   --> src/orf.rs:44:18
[INFO] [stdout]    |
[INFO] [stdout] 44 | pub fn find_orfs(seq: &str, strand: Strand) -> Vec<ORF> {
[INFO] [stdout]    |                  ^^^ help: if this is intentional, prefix it with an underscore: `_seq`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `strand`
[INFO] [stdout]   --> src/orf.rs:44:29
[INFO] [stdout]    |
[INFO] [stdout] 44 | pub fn find_orfs(seq: &str, strand: Strand) -> Vec<ORF> {
[INFO] [stdout]    |                             ^^^^^^ help: if this is intentional, prefix it with an underscore: `_strand`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `orf`
[INFO] [stdout]   --> src/orf.rs:92:17
[INFO] [stdout]    |
[INFO] [stdout] 92 | fn classify_orf(orf: &str) -> ORFType {
[INFO] [stdout]    |                 ^^^ help: if this is intentional, prefix it with an underscore: `_orf`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `find_orfs` is never used
[INFO] [stdout]   --> src/orf.rs:44:8
[INFO] [stdout]    |
[INFO] [stdout] 44 | pub fn find_orfs(seq: &str, strand: Strand) -> Vec<ORF> {
[INFO] [stdout]    |        ^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `classify_orf` is never used
[INFO] [stdout]   --> src/orf.rs:92:4
[INFO] [stdout]    |
[INFO] [stdout] 92 | fn classify_orf(orf: &str) -> ORFType {
[INFO] [stdout]    |    ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 04s
[INFO] running `Command { std: "docker" "inspect" "9d2a978bb3acc0046010badd73ae45e7e06f4797f96fdab62b737560a6adfdb8", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "9d2a978bb3acc0046010badd73ae45e7e06f4797f96fdab62b737560a6adfdb8", kill_on_drop: false }`
[INFO] [stdout] 9d2a978bb3acc0046010badd73ae45e7e06f4797f96fdab62b737560a6adfdb8
