[INFO] cloning repository https://github.com/ARU-life-sciences/rep [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/ARU-life-sciences/rep" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FARU-life-sciences%2Frep", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FARU-life-sciences%2Frep'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 8f2a527dc31783e5c6351cd3eabadbeaefe7d997 [INFO] checking ARU-life-sciences/rep against master#1f12b9b0fdbe735968ac002792a720f0ba4faca6 for crater-rollup-uwu [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FARU-life-sciences%2Frep" "/workspace/builds/worker-1-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-1-tc1/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/ARU-life-sciences/rep on toolchain 1f12b9b0fdbe735968ac002792a720f0ba4faca6 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1f12b9b0fdbe735968ac002792a720f0ba4faca6" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/ARU-life-sciences/rep [INFO] finished tweaking git repo https://github.com/ARU-life-sciences/rep [INFO] tweaked toml for git repo https://github.com/ARU-life-sciences/rep written to /workspace/builds/worker-1-tc1/source/Cargo.toml [INFO] crate git repo https://github.com/ARU-life-sciences/rep 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" "+1f12b9b0fdbe735968ac002792a720f0ba4faca6" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded multimap v0.9.1 [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded itertools-num v0.1.3 [INFO] [stderr] Downloaded semver v0.1.20 [INFO] [stderr] Downloaded triple_accel v0.4.0 [INFO] [stderr] Downloaded editdistancek v1.0.2 [INFO] [stderr] Downloaded rustc_version v0.1.7 [INFO] [stderr] Downloaded bytecount v0.6.7 [INFO] [stderr] Downloaded bio-types v1.0.1 [INFO] [stderr] Downloaded bio v1.5.0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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@sha256:923055f121b5182466d55868a8b05e67af8ba4a3a3f6bad814e953ca3cd3ac2a" "/opt/rustwide/cargo-home/bin/cargo" "+1f12b9b0fdbe735968ac002792a720f0ba4faca6" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 975f5eda31a54f771e3a8b5cbf4a2e3511168007631e7255604fb58780d9f275 [INFO] running `Command { std: "docker" "start" "-a" "975f5eda31a54f771e3a8b5cbf4a2e3511168007631e7255604fb58780d9f275", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "975f5eda31a54f771e3a8b5cbf4a2e3511168007631e7255604fb58780d9f275", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "975f5eda31a54f771e3a8b5cbf4a2e3511168007631e7255604fb58780d9f275", kill_on_drop: false }` [INFO] [stdout] 975f5eda31a54f771e3a8b5cbf4a2e3511168007631e7255604fb58780d9f275 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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@sha256:923055f121b5182466d55868a8b05e67af8ba4a3a3f6bad814e953ca3cd3ac2a" "/opt/rustwide/cargo-home/bin/cargo" "+1f12b9b0fdbe735968ac002792a720f0ba4faca6" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 05fca9232963868bfa82ce18d394bef46e58c234d464ad445a4918704a1f9dbf [INFO] running `Command { std: "docker" "start" "-a" "05fca9232963868bfa82ce18d394bef46e58c234d464ad445a4918704a1f9dbf", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.79 [INFO] [stderr] Compiling libm v0.2.8 [INFO] [stderr] Compiling libc v0.2.153 [INFO] [stderr] Compiling num-traits v0.2.18 [INFO] [stderr] Compiling serde v1.0.197 [INFO] [stderr] Checking memchr v2.7.1 [INFO] [stderr] Compiling matrixmultiply v0.3.8 [INFO] [stderr] Compiling paste v1.0.14 [INFO] [stderr] Checking ppv-lite86 v0.2.17 [INFO] [stderr] Checking bytemuck v1.15.0 [INFO] [stderr] Compiling num-rational v0.4.1 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Checking safe_arch v0.7.1 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Compiling rustversion v1.0.14 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling quote v1.0.35 [INFO] [stderr] Checking wide v0.7.15 [INFO] [stderr] Checking aho-corasick v1.1.3 [INFO] [stderr] Compiling syn v2.0.53 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Checking getrandom v0.2.12 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Checking rand_core v0.6.4 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Checking rand_chacha v0.3.1 [INFO] [stderr] Compiling thiserror v1.0.58 [INFO] [stderr] Checking num-integer v0.1.46 [INFO] [stderr] Checking num-complex v0.4.5 [INFO] [stderr] Checking rand v0.8.5 [INFO] [stderr] Checking approx v0.5.1 [INFO] [stderr] Checking utf8parse v0.2.1 [INFO] [stderr] Checking regex-syntax v0.8.2 [INFO] [stderr] Checking anstyle-parse v0.2.3 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Checking simba v0.6.0 [INFO] [stderr] Checking rand_distr v0.4.3 [INFO] [stderr] Checking anstyle v1.0.6 [INFO] [stderr] Checking anstyle-query v1.0.2 [INFO] [stderr] Checking equivalent v1.0.1 [INFO] [stderr] Compiling anyhow v1.0.81 [INFO] [stderr] Checking hashbrown v0.14.3 [INFO] [stderr] Checking colorchoice v1.0.0 [INFO] [stderr] Checking anstream v0.6.13 [INFO] [stderr] Checking csv-core v0.1.11 [INFO] [stderr] Checking bit-vec v0.6.3 [INFO] [stderr] Checking clap_lex v0.7.0 [INFO] [stderr] Checking strsim v0.11.0 [INFO] [stderr] Checking fixedbitset v0.4.2 [INFO] [stderr] Checking indexmap v2.2.5 [INFO] [stderr] Checking itoa v1.0.10 [INFO] [stderr] Checking ryu v1.0.17 [INFO] [stderr] Checking either v1.10.0 [INFO] [stderr] Checking clap_builder v4.5.2 [INFO] [stderr] Checking regex-automata v0.4.6 [INFO] [stderr] Checking bit-set v0.5.3 [INFO] [stderr] Checking itertools v0.11.0 [INFO] [stderr] Checking fxhash v0.2.1 [INFO] [stderr] Checking petgraph v0.6.4 [INFO] [stderr] Checking ndarray v0.15.6 [INFO] [stderr] Compiling serde_derive v1.0.197 [INFO] [stderr] Compiling thiserror-impl v1.0.58 [INFO] [stderr] Compiling enum-map-derive v0.17.0 [INFO] [stderr] Compiling nalgebra-macros v0.1.0 [INFO] [stderr] Checking regex v1.10.3 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling strum_macros v0.25.3 [INFO] [stderr] Checking enum-map v2.7.3 [INFO] [stderr] Compiling getset v0.1.2 [INFO] [stderr] Checking itertools-num v0.1.3 [INFO] [stderr] Checking ordered-float v3.9.2 [INFO] [stderr] Checking bytecount v0.6.7 [INFO] [stderr] Checking triple_accel v0.4.0 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking strum v0.25.0 [INFO] [stderr] Checking editdistancek v1.0.2 [INFO] [stderr] Checking clap v4.5.2 [INFO] [stderr] Checking bio-types v1.0.1 [INFO] [stderr] Checking nalgebra v0.29.0 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking csv v1.3.0 [INFO] [stderr] Checking multimap v0.9.1 [INFO] [stderr] Checking statrs v0.16.0 [INFO] [stderr] Checking bio v1.5.0 [INFO] [stderr] Checking rep v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused variable: `flank` [INFO] [stdout] --> src/rm_curation_pipeline.rs:76:9 [INFO] [stdout] | [INFO] [stdout] 76 | let flank = 2000; [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_flank` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `maxhitdist` [INFO] [stdout] --> src/rm_curation_pipeline.rs:77:9 [INFO] [stdout] | [INFO] [stdout] 77 | let maxhitdist = 10000; [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_maxhitdist` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `minfrac` [INFO] [stdout] --> src/rm_curation_pipeline.rs:78:9 [INFO] [stdout] | [INFO] [stdout] 78 | let minfrac = 0.8; [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_minfrac` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `digits` [INFO] [stdout] --> src/rm_curation_pipeline.rs:79:9 [INFO] [stdout] | [INFO] [stdout] 79 | let digits = 5; [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_digits` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `temp_mafft` [INFO] [stdout] --> src/rm_curation_pipeline.rs:92:9 [INFO] [stdout] | [INFO] [stdout] 92 | let temp_mafft = matches.configure.join(INTERMEDIATE).join("tempMafft.txt"); [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_temp_mafft` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `flank` [INFO] [stdout] --> src/rm_curation_pipeline.rs:76:9 [INFO] [stdout] | [INFO] [stdout] 76 | let flank = 2000; [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_flank` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `maxhitdist` [INFO] [stdout] --> src/rm_curation_pipeline.rs:77:9 [INFO] [stdout] | [INFO] [stdout] 77 | let maxhitdist = 10000; [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_maxhitdist` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `minfrac` [INFO] [stdout] --> src/rm_curation_pipeline.rs:78:9 [INFO] [stdout] | [INFO] [stdout] 78 | let minfrac = 0.8; [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_minfrac` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `digits` [INFO] [stdout] --> src/rm_curation_pipeline.rs:79:9 [INFO] [stdout] | [INFO] [stdout] 79 | let digits = 5; [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_digits` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `temp_mafft` [INFO] [stdout] --> src/rm_curation_pipeline.rs:92:9 [INFO] [stdout] | [INFO] [stdout] 92 | let temp_mafft = matches.configure.join(INTERMEDIATE).join("tempMafft.txt"); [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_temp_mafft` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `rmdl_library_reader` [INFO] [stdout] --> src/rm_curation_pipeline.rs:189:9 [INFO] [stdout] | [INFO] [stdout] 189 | let rmdl_library_reader = fasta::Reader::from_file(rmdl_library)?; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_rmdl_library_reader` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `top_blast_hits` [INFO] [stdout] --> src/rm_curation_pipeline.rs:217:13 [INFO] [stdout] | [INFO] [stdout] 217 | let top_blast_hits = blast_hits.top_n(20); [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_top_blast_hits` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `rmdl_library_reader` [INFO] [stdout] --> src/rm_curation_pipeline.rs:189:9 [INFO] [stdout] | [INFO] [stdout] 189 | let rmdl_library_reader = fasta::Reader::from_file(rmdl_library)?; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_rmdl_library_reader` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `maxhitdist` [INFO] [stdout] --> src/rm_curation_pipeline.rs:154:5 [INFO] [stdout] | [INFO] [stdout] 154 | maxhitdist: i32, [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_maxhitdist` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `top_blast_hits` [INFO] [stdout] --> src/rm_curation_pipeline.rs:217:13 [INFO] [stdout] | [INFO] [stdout] 217 | let top_blast_hits = blast_hits.top_n(20); [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_top_blast_hits` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `minfrac` [INFO] [stdout] --> src/rm_curation_pipeline.rs:155:5 [INFO] [stdout] | [INFO] [stdout] 155 | minfrac: f64, [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_minfrac` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `maxhitdist` [INFO] [stdout] --> src/rm_curation_pipeline.rs:154:5 [INFO] [stdout] | [INFO] [stdout] 154 | maxhitdist: i32, [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_maxhitdist` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `minfrac` [INFO] [stdout] --> src/rm_curation_pipeline.rs:155:5 [INFO] [stdout] | [INFO] [stdout] 155 | minfrac: f64, [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_minfrac` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_hits_from_assembly` is never used [INFO] [stdout] --> src/rm_curation_pipeline.rs:150:4 [INFO] [stdout] | [INFO] [stdout] 150 | fn find_hits_from_assembly( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_hits_from_assembly` is never used [INFO] [stdout] --> src/rm_curation_pipeline.rs:150:4 [INFO] [stdout] | [INFO] [stdout] 150 | fn find_hits_from_assembly( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 10 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 10 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 16.10s [INFO] running `Command { std: "docker" "inspect" "05fca9232963868bfa82ce18d394bef46e58c234d464ad445a4918704a1f9dbf", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "05fca9232963868bfa82ce18d394bef46e58c234d464ad445a4918704a1f9dbf", kill_on_drop: false }` [INFO] [stdout] 05fca9232963868bfa82ce18d394bef46e58c234d464ad445a4918704a1f9dbf [INFO] checking ARU-life-sciences/rep against try#f9935d29d867449445ee008640ccca1bf1ae0889+rustflags=-Dtail_expr_drop_order for crater-rollup-uwu [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FARU-life-sciences%2Frep" "/workspace/builds/worker-1-tc2/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-1-tc2/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/ARU-life-sciences/rep on toolchain f9935d29d867449445ee008640ccca1bf1ae0889 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+f9935d29d867449445ee008640ccca1bf1ae0889" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/ARU-life-sciences/rep [INFO] finished tweaking git repo https://github.com/ARU-life-sciences/rep [INFO] tweaked toml for git repo https://github.com/ARU-life-sciences/rep written to /workspace/builds/worker-1-tc2/source/Cargo.toml [INFO] crate git repo https://github.com/ARU-life-sciences/rep 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" "+f9935d29d867449445ee008640ccca1bf1ae0889" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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@sha256:923055f121b5182466d55868a8b05e67af8ba4a3a3f6bad814e953ca3cd3ac2a" "/opt/rustwide/cargo-home/bin/cargo" "+f9935d29d867449445ee008640ccca1bf1ae0889" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 9588de60c5568919c568674449f72941bab4939fb309be5f1db7056c4dd3d16d [INFO] running `Command { std: "docker" "start" "-a" "9588de60c5568919c568674449f72941bab4939fb309be5f1db7056c4dd3d16d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "9588de60c5568919c568674449f72941bab4939fb309be5f1db7056c4dd3d16d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "9588de60c5568919c568674449f72941bab4939fb309be5f1db7056c4dd3d16d", kill_on_drop: false }` [INFO] [stdout] 9588de60c5568919c568674449f72941bab4939fb309be5f1db7056c4dd3d16d [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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 -Dtail_expr_drop_order" "-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@sha256:923055f121b5182466d55868a8b05e67af8ba4a3a3f6bad814e953ca3cd3ac2a" "/opt/rustwide/cargo-home/bin/cargo" "+f9935d29d867449445ee008640ccca1bf1ae0889" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 15adc68e3054ae74fcd272ffecb93d8ee6457e68904901980047d5cc76813d0d [INFO] running `Command { std: "docker" "start" "-a" "15adc68e3054ae74fcd272ffecb93d8ee6457e68904901980047d5cc76813d0d", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.79 [INFO] [stderr] Compiling libm v0.2.8 [INFO] [stderr] Compiling libc v0.2.153 [INFO] [stderr] Compiling num-traits v0.2.18 [INFO] [stderr] Checking memchr v2.7.1 [INFO] [stderr] Compiling serde v1.0.197 [INFO] [stderr] Compiling matrixmultiply v0.3.8 [INFO] [stderr] Compiling paste v1.0.14 [INFO] [stderr] Checking bytemuck v1.15.0 [INFO] [stderr] Checking ppv-lite86 v0.2.17 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Checking safe_arch v0.7.1 [INFO] [stderr] Compiling num-rational v0.4.1 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling rustversion v1.0.14 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Checking aho-corasick v1.1.3 [INFO] [stderr] Compiling quote v1.0.35 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Checking wide v0.7.15 [INFO] [stderr] Compiling syn v2.0.53 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Checking getrandom v0.2.12 [INFO] [stderr] Checking rand_core v0.6.4 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Checking rand_chacha v0.3.1 [INFO] [stderr] Checking regex-syntax v0.8.2 [INFO] [stderr] Checking utf8parse v0.2.1 [INFO] [stderr] Checking rand v0.8.5 [INFO] [stderr] Compiling thiserror v1.0.58 [INFO] [stderr] Checking num-integer v0.1.46 [INFO] [stderr] Checking num-complex v0.4.5 [INFO] [stderr] Checking approx v0.5.1 [INFO] [stderr] Checking anstyle-parse v0.2.3 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Checking rand_distr v0.4.3 [INFO] [stderr] Checking hashbrown v0.14.3 [INFO] [stderr] Checking simba v0.6.0 [INFO] [stderr] Checking anstyle-query v1.0.2 [INFO] [stderr] Checking colorchoice v1.0.0 [INFO] [stderr] Checking equivalent v1.0.1 [INFO] [stderr] Checking anstyle v1.0.6 [INFO] [stderr] Compiling anyhow v1.0.81 [INFO] [stderr] Checking anstream v0.6.13 [INFO] [stderr] Checking indexmap v2.2.5 [INFO] [stderr] Checking csv-core v0.1.11 [INFO] [stderr] Checking fixedbitset v0.4.2 [INFO] [stderr] Checking ryu v1.0.17 [INFO] [stderr] Checking bit-vec v0.6.3 [INFO] [stderr] Checking itoa v1.0.10 [INFO] [stderr] Checking either v1.10.0 [INFO] [stderr] Checking regex-automata v0.4.6 [INFO] [stderr] Checking clap_lex v0.7.0 [INFO] [stderr] Checking strsim v0.11.0 [INFO] [stderr] Checking itertools v0.11.0 [INFO] [stderr] Checking bit-set v0.5.3 [INFO] [stderr] Checking clap_builder v4.5.2 [INFO] [stderr] Checking petgraph v0.6.4 [INFO] [stderr] Checking fxhash v0.2.1 [INFO] [stderr] Checking ndarray v0.15.6 [INFO] [stderr] Checking ordered-float v3.9.2 [INFO] [stderr] Compiling serde_derive v1.0.197 [INFO] [stderr] Compiling thiserror-impl v1.0.58 [INFO] [stderr] Compiling enum-map-derive v0.17.0 [INFO] [stderr] Compiling strum_macros v0.25.3 [INFO] [stderr] Checking regex v1.10.3 [INFO] [stderr] Checking enum-map v2.7.3 [INFO] [stderr] Checking itertools-num v0.1.3 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking bytecount v0.6.7 [INFO] [stderr] Checking editdistancek v1.0.2 [INFO] [stderr] Checking triple_accel v0.4.0 [INFO] [stderr] Compiling nalgebra-macros v0.1.0 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling getset v0.1.2 [INFO] [stderr] Checking strum v0.25.0 [INFO] [stderr] Checking clap v4.5.2 [INFO] [stderr] Checking bio-types v1.0.1 [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 v1.3.0 [INFO] [stderr] Checking statrs v0.16.0 [INFO] [stderr] Checking bio v1.5.0 [INFO] [stderr] Checking rep v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused variable: `flank` [INFO] [stdout] --> src/rm_curation_pipeline.rs:76:9 [INFO] [stdout] | [INFO] [stdout] 76 | let flank = 2000; [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_flank` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `maxhitdist` [INFO] [stdout] --> src/rm_curation_pipeline.rs:77:9 [INFO] [stdout] | [INFO] [stdout] 77 | let maxhitdist = 10000; [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_maxhitdist` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `minfrac` [INFO] [stdout] --> src/rm_curation_pipeline.rs:78:9 [INFO] [stdout] | [INFO] [stdout] 78 | let minfrac = 0.8; [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_minfrac` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `digits` [INFO] [stdout] --> src/rm_curation_pipeline.rs:79:9 [INFO] [stdout] | [INFO] [stdout] 79 | let digits = 5; [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_digits` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `temp_mafft` [INFO] [stdout] --> src/rm_curation_pipeline.rs:92:9 [INFO] [stdout] | [INFO] [stdout] 92 | let temp_mafft = matches.configure.join(INTERMEDIATE).join("tempMafft.txt"); [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_temp_mafft` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `rmdl_library_reader` [INFO] [stdout] --> src/rm_curation_pipeline.rs:189:9 [INFO] [stdout] | [INFO] [stdout] 189 | let rmdl_library_reader = fasta::Reader::from_file(rmdl_library)?; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_rmdl_library_reader` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `top_blast_hits` [INFO] [stdout] --> src/rm_curation_pipeline.rs:217:13 [INFO] [stdout] | [INFO] [stdout] 217 | let top_blast_hits = blast_hits.top_n(20); [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_top_blast_hits` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `maxhitdist` [INFO] [stdout] --> src/rm_curation_pipeline.rs:154:5 [INFO] [stdout] | [INFO] [stdout] 154 | maxhitdist: i32, [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_maxhitdist` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `minfrac` [INFO] [stdout] --> src/rm_curation_pipeline.rs:155:5 [INFO] [stdout] | [INFO] [stdout] 155 | minfrac: f64, [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_minfrac` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_hits_from_assembly` is never used [INFO] [stdout] --> src/rm_curation_pipeline.rs:150:4 [INFO] [stdout] | [INFO] [stdout] 150 | fn find_hits_from_assembly( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: these values and local bindings have significant drop implementation that will have a different drop order from that of Edition 2021 [INFO] [stdout] --> src/error.rs:23:15 [INFO] [stdout] | [INFO] [stdout] 22 | pub(crate) fn new(kind: ErrorKind) -> Error { [INFO] [stdout] | --------------- these values have significant drop implementation and will observe changes in drop order under Edition 2024 [INFO] [stdout] 23 | Error(Box::new(kind)) [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this changes meaning in Rust 2024 [INFO] [stdout] = note: for more information, see issue #123739 [INFO] [stdout] = note: requested on the command line with `-D tail-expr-drop-order` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: these values and local bindings have significant drop implementation that will have a different drop order from that of Edition 2021 [INFO] [stdout] --> src/error.rs:67:20 [INFO] [stdout] | [INFO] [stdout] 66 | fn from(err: IOError) -> Error { [INFO] [stdout] | ------------ these values have significant drop implementation and will observe changes in drop order under Edition 2024 [INFO] [stdout] 67 | Error::new(ErrorKind::IO(err.kind())) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this changes meaning in Rust 2024 [INFO] [stdout] = note: for more information, see issue #123739 [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: these values and local bindings have significant drop implementation that will have a different drop order from that of Edition 2021 [INFO] [stdout] --> src/error.rs:73:20 [INFO] [stdout] | [INFO] [stdout] 72 | fn from(err: AnyhowError) -> Error { [INFO] [stdout] | ---------------- these values have significant drop implementation and will observe changes in drop order under Edition 2024 [INFO] [stdout] 73 | Error::new(ErrorKind::FastaReading(err)) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this changes meaning in Rust 2024 [INFO] [stdout] = note: for more information, see issue #123739 [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: these values and local bindings have significant drop implementation that will have a different drop order from that of Edition 2021 [INFO] [stdout] --> src/error.rs:91:20 [INFO] [stdout] | [INFO] [stdout] 90 | fn from(err: CsvError) -> Error { [INFO] [stdout] | ------------- these values have significant drop implementation and will observe changes in drop order under Edition 2024 [INFO] [stdout] 91 | Error::new(ErrorKind::BlastParse(err)) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this changes meaning in Rust 2024 [INFO] [stdout] = note: for more information, see issue #123739 [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `flank` [INFO] [stdout] --> src/rm_curation_pipeline.rs:76:9 [INFO] [stdout] | [INFO] [stdout] 76 | let flank = 2000; [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_flank` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `maxhitdist` [INFO] [stdout] --> src/rm_curation_pipeline.rs:77:9 [INFO] [stdout] | [INFO] [stdout] 77 | let maxhitdist = 10000; [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_maxhitdist` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `minfrac` [INFO] [stdout] --> src/rm_curation_pipeline.rs:78:9 [INFO] [stdout] | [INFO] [stdout] 78 | let minfrac = 0.8; [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_minfrac` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `digits` [INFO] [stdout] --> src/rm_curation_pipeline.rs:79:9 [INFO] [stdout] | [INFO] [stdout] 79 | let digits = 5; [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_digits` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `temp_mafft` [INFO] [stdout] --> src/rm_curation_pipeline.rs:92:9 [INFO] [stdout] | [INFO] [stdout] 92 | let temp_mafft = matches.configure.join(INTERMEDIATE).join("tempMafft.txt"); [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_temp_mafft` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to 4 previous errors; 10 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `rmdl_library_reader` [INFO] [stdout] --> src/rm_curation_pipeline.rs:189:9 [INFO] [stdout] | [INFO] [stdout] 189 | let rmdl_library_reader = fasta::Reader::from_file(rmdl_library)?; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_rmdl_library_reader` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `top_blast_hits` [INFO] [stdout] --> src/rm_curation_pipeline.rs:217:13 [INFO] [stdout] | [INFO] [stdout] 217 | let top_blast_hits = blast_hits.top_n(20); [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_top_blast_hits` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `maxhitdist` [INFO] [stdout] --> src/rm_curation_pipeline.rs:154:5 [INFO] [stdout] | [INFO] [stdout] 154 | maxhitdist: i32, [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_maxhitdist` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `minfrac` [INFO] [stdout] --> src/rm_curation_pipeline.rs:155:5 [INFO] [stdout] | [INFO] [stdout] 155 | minfrac: f64, [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_minfrac` [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: could not compile `rep` (lib) due to 5 previous errors; 10 warnings emitted [INFO] [stderr] warning: build failed, waiting for other jobs to finish... [INFO] [stdout] warning: function `find_hits_from_assembly` is never used [INFO] [stdout] --> src/rm_curation_pipeline.rs:150:4 [INFO] [stdout] | [INFO] [stdout] 150 | fn find_hits_from_assembly( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: these values and local bindings have significant drop implementation that will have a different drop order from that of Edition 2021 [INFO] [stdout] --> src/error.rs:23:15 [INFO] [stdout] | [INFO] [stdout] 22 | pub(crate) fn new(kind: ErrorKind) -> Error { [INFO] [stdout] | --------------- these values have significant drop implementation and will observe changes in drop order under Edition 2024 [INFO] [stdout] 23 | Error(Box::new(kind)) [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this changes meaning in Rust 2024 [INFO] [stdout] = note: for more information, see issue #123739 [INFO] [stdout] = note: requested on the command line with `-D tail-expr-drop-order` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: these values and local bindings have significant drop implementation that will have a different drop order from that of Edition 2021 [INFO] [stdout] --> src/error.rs:67:20 [INFO] [stdout] | [INFO] [stdout] 66 | fn from(err: IOError) -> Error { [INFO] [stdout] | ------------ these values have significant drop implementation and will observe changes in drop order under Edition 2024 [INFO] [stdout] 67 | Error::new(ErrorKind::IO(err.kind())) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this changes meaning in Rust 2024 [INFO] [stdout] = note: for more information, see issue #123739 [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: these values and local bindings have significant drop implementation that will have a different drop order from that of Edition 2021 [INFO] [stdout] --> src/error.rs:73:20 [INFO] [stdout] | [INFO] [stdout] 72 | fn from(err: AnyhowError) -> Error { [INFO] [stdout] | ---------------- these values have significant drop implementation and will observe changes in drop order under Edition 2024 [INFO] [stdout] 73 | Error::new(ErrorKind::FastaReading(err)) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this changes meaning in Rust 2024 [INFO] [stdout] = note: for more information, see issue #123739 [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: these values and local bindings have significant drop implementation that will have a different drop order from that of Edition 2021 [INFO] [stdout] --> src/error.rs:91:20 [INFO] [stdout] | [INFO] [stdout] 90 | fn from(err: CsvError) -> Error { [INFO] [stdout] | ------------- these values have significant drop implementation and will observe changes in drop order under Edition 2024 [INFO] [stdout] 91 | Error::new(ErrorKind::BlastParse(err)) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this changes meaning in Rust 2024 [INFO] [stdout] = note: for more information, see issue #123739 [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to 4 previous errors; 10 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: could not compile `rep` (lib test) due to 5 previous errors; 10 warnings emitted [INFO] running `Command { std: "docker" "inspect" "15adc68e3054ae74fcd272ffecb93d8ee6457e68904901980047d5cc76813d0d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "15adc68e3054ae74fcd272ffecb93d8ee6457e68904901980047d5cc76813d0d", kill_on_drop: false }` [INFO] [stdout] 15adc68e3054ae74fcd272ffecb93d8ee6457e68904901980047d5cc76813d0d