[INFO] cloning repository https://github.com/COMBINE-lab/simpleaf
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/COMBINE-lab/simpleaf" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FCOMBINE-lab%2Fsimpleaf", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FCOMBINE-lab%2Fsimpleaf'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 82b96d19a5221b58c34d047d05668f01bfadff73
[INFO] checking COMBINE-lab/simpleaf/82b96d19a5221b58c34d047d05668f01bfadff73 against master#ab869e094a907cc5d19b4080f22eccaf347f1f95 for pr-129604
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FCOMBINE-lab%2Fsimpleaf" "/workspace/builds/worker-3-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-3-tc1/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/COMBINE-lab/simpleaf on toolchain ab869e094a907cc5d19b4080f22eccaf347f1f95
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ab869e094a907cc5d19b4080f22eccaf347f1f95" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/COMBINE-lab/simpleaf
[INFO] finished tweaking git repo https://github.com/COMBINE-lab/simpleaf
[INFO] tweaked toml for git repo https://github.com/COMBINE-lab/simpleaf written to /workspace/builds/worker-3-tc1/source/Cargo.toml
[INFO] crate git repo https://github.com/COMBINE-lab/simpleaf 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" "+ab869e094a907cc5d19b4080f22eccaf347f1f95" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]     Updating git repository `https://github.com/COMBINE-lab/roers`
[INFO] [stderr]     Updating git repository `https://github.com/COMBINE-lab/seq_geom_parser`
[INFO] [stderr]     Updating git repository `https://github.com/COMBINE-lab/seq_geom_xform`
[INFO] [stderr]     Updating git repository `https://github.com/COMBINE-lab/grangers.git`
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded polars-error v0.34.2
[INFO] [stderr]   Downloaded peak_alloc v0.2.1
[INFO] [stderr]   Downloaded jrsonnet-cli v0.5.0-pre95
[INFO] [stderr]   Downloaded noodles v0.56.0
[INFO] [stderr]   Downloaded jrsonnet-interner v0.5.0-pre95
[INFO] [stderr]   Downloaded faccess v0.2.4
[INFO] [stderr]   Downloaded polars-row v0.34.2
[INFO] [stderr]   Downloaded jrsonnet-types v0.5.0-pre95
[INFO] [stderr]   Downloaded cmd_lib_macros v1.9.4
[INFO] [stderr]   Downloaded jrsonnet-macros v0.5.0-pre95
[INFO] [stderr]   Downloaded noodles-gtf v0.19.0
[INFO] [stderr]   Downloaded jrsonnet-stdlib v0.5.0-pre95
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[INFO] [stderr]   Downloaded cmd_lib v1.9.4
[INFO] [stderr]   Downloaded jrsonnet-evaluator v0.5.0-pre95
[INFO] [stderr]   Downloaded polars-io v0.34.2
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[INFO] [stderr]   Downloaded polars-lazy v0.34.2
[INFO] [stderr]   Downloaded sqlparser v0.38.0
[INFO] [stderr]   Downloaded polars-plan v0.34.2
[INFO] [stderr]   Downloaded polars-core v0.34.2
[INFO] [stderr]   Downloaded jrsonnet-gcmodule v0.3.7
[INFO] [stderr]   Downloaded minreq v2.11.2
[INFO] [stderr]   Downloaded polars-sql v0.34.2
[INFO] [stderr]   Downloaded polars v0.34.2
[INFO] [stderr]   Downloaded polars-arrow v0.34.2
[INFO] [stderr]   Downloaded peg-macros v0.8.3
[INFO] [stderr]   Downloaded lz4-sys v1.9.5
[INFO] [stderr]   Downloaded noodles-csi v0.26.0
[INFO] [stderr]   Downloaded peg v0.8.3
[INFO] [stderr]   Downloaded nutype_macros v0.3.1
[INFO] [stderr]   Downloaded nutype v0.3.1
[INFO] [stderr]   Downloaded noodles-gff v0.23.0
[INFO] [stderr]   Downloaded lz4 v1.25.0
[INFO] [stderr]   Downloaded polars-utils v0.34.2
[INFO] [stderr]   Downloaded polars-time v0.34.2
[INFO] [stderr]   Downloaded structdump v0.2.0
[INFO] [stderr]   Downloaded jrsonnet-parser v0.5.0-pre95
[INFO] [stderr]   Downloaded noodles-fasta v0.30.0
[INFO] [stderr]   Downloaded noodles-bgzf v0.25.0
[INFO] [stderr]   Downloaded noodles-core v0.12.0
[INFO] [stderr]   Downloaded oomfi v0.1.2
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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" "+ab869e094a907cc5d19b4080f22eccaf347f1f95" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] df6e8ea2aa8fd8bbd0f1103240691f1c26c5d270754cc47f98a4c400d6915fc3
[INFO] running `Command { std: "docker" "start" "-a" "df6e8ea2aa8fd8bbd0f1103240691f1c26c5d270754cc47f98a4c400d6915fc3", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "df6e8ea2aa8fd8bbd0f1103240691f1c26c5d270754cc47f98a4c400d6915fc3", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "df6e8ea2aa8fd8bbd0f1103240691f1c26c5d270754cc47f98a4c400d6915fc3", kill_on_drop: false }`
[INFO] [stdout] df6e8ea2aa8fd8bbd0f1103240691f1c26c5d270754cc47f98a4c400d6915fc3
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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" "+ab869e094a907cc5d19b4080f22eccaf347f1f95" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] da45c7da1d00c46aa18f4092ede327779c3e9e20a265aaac981afc814a616b21
[INFO] running `Command { std: "docker" "start" "-a" "da45c7da1d00c46aa18f4092ede327779c3e9e20a265aaac981afc814a616b21", kill_on_drop: false }`
[INFO] [stderr]    Compiling proc-macro2 v1.0.86
[INFO] [stderr]    Compiling unicode-ident v1.0.12
[INFO] [stderr]    Compiling version_check v0.9.4
[INFO] [stderr]    Compiling libc v0.2.155
[INFO] [stderr]     Checking cfg-if v1.0.0
[INFO] [stderr]    Compiling autocfg v1.3.0
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]     Checking once_cell v1.19.0
[INFO] [stderr]    Compiling cc v1.1.1
[INFO] [stderr]     Checking memchr v2.7.4
[INFO] [stderr]    Compiling parking_lot_core v0.9.10
[INFO] [stderr]    Compiling crossbeam-utils v0.8.20
[INFO] [stderr]    Compiling thiserror v1.0.62
[INFO] [stderr]     Checking zerocopy v0.7.35
[INFO] [stderr]     Checking static_assertions v1.1.0
[INFO] [stderr]    Compiling pkg-config v0.3.30
[INFO] [stderr]     Checking smallvec v1.13.2
[INFO] [stderr]     Checking either v1.13.0
[INFO] [stderr]    Compiling libm v0.2.8
[INFO] [stderr]    Compiling rayon-core v1.12.1
[INFO] [stderr]     Checking scopeguard v1.2.0
[INFO] [stderr]    Compiling ahash v0.8.11
[INFO] [stderr]     Checking regex-syntax v0.8.4
[INFO] [stderr]    Compiling lock_api v0.4.12
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling ppv-lite86 v0.2.17
[INFO] [stderr]    Compiling siphasher v0.3.11
[INFO] [stderr]     Checking bitflags v2.6.0
[INFO] [stderr]     Checking allocator-api2 v0.2.18
[INFO] [stderr]     Checking aho-corasick v1.1.3
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[INFO] [stderr]    Compiling target-features v0.1.6
[INFO] [stderr]    Compiling heck v0.5.0
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[INFO] [stderr]    Compiling quote v1.0.36
[INFO] [stderr]    Compiling proc-macro-hack v0.5.20+deprecated
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[INFO] [stderr]    Compiling vcpkg v0.2.15
[INFO] [stderr]    Compiling smartstring v1.0.1
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[INFO] [stderr]    Compiling rand_core v0.6.4
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[INFO] [stderr]    Compiling polars-utils v0.34.2
[INFO] [stderr]    Compiling rand_chacha v0.3.1
[INFO] [stderr]     Checking bytes v1.6.0
[INFO] [stderr]     Checking ryu v1.0.18
[INFO] [stderr]    Compiling serde v1.0.204
[INFO] [stderr]    Compiling libz-sys v1.1.18
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[INFO] [stderr]    Compiling rand v0.8.5
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[INFO] [stderr]     Checking foreign_vec v0.1.0
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[INFO] [stderr]    Compiling rustix v0.38.34
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[INFO] [stderr]     Checking chrono v0.4.38
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[INFO] [stderr]     Checking crossterm v0.27.0
[INFO] [stderr]    Compiling polars-core v0.34.2
[INFO] [stderr]    Compiling generic-array v0.14.7
[INFO] [stderr]     Checking linux-raw-sys v0.4.14
[INFO] [stderr]     Checking byteorder v1.5.0
[INFO] [stderr]    Compiling polars-ops v0.34.2
[INFO] [stderr]     Checking flate2 v1.0.30
[INFO] [stderr]    Compiling peg-macros v0.8.3
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[INFO] [stderr]     Checking argminmax v0.6.2
[INFO] [stderr]     Checking crossbeam-channel v0.5.13
[INFO] [stderr]     Checking percent-encoding v2.3.1
[INFO] [stderr]    Compiling heck v0.4.1
[INFO] [stderr]    Compiling phf_generator v0.10.0
[INFO] [stderr]     Checking utf8parse v0.2.2
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[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
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[INFO] [stderr]     Checking anstyle-query v1.1.0
[INFO] [stderr]     Checking noodles-core v0.12.0
[INFO] [stderr]     Checking colorchoice v1.0.1
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[INFO] [stderr]    Compiling hashbrown v0.13.2
[INFO] [stderr]     Checking lexical v6.1.1
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[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]    Compiling polars-plan v0.34.2
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[INFO] [stderr]    Compiling ucd-trie v0.1.6
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[INFO] [stderr]    Compiling rustc-hash v1.1.0
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[INFO] [stderr]    Compiling serde_json v1.0.120
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[INFO] [stderr]    Compiling phf_shared v0.11.2
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[INFO] [stderr]    Compiling rustls v0.21.12
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[INFO] [stderr]    Compiling thiserror-impl v1.0.62
[INFO] [stderr]    Compiling bytemuck_derive v1.7.0
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[INFO] [stderr]    Compiling serde_derive v1.0.204
[INFO] [stderr]    Compiling strum_macros v0.26.4
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[INFO] [stderr]    Compiling strum_macros v0.25.3
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[INFO] [stderr]     Checking bytemuck v1.16.1
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[INFO] [stderr]     Checking comfy-table v7.1.1
[INFO] [stderr]     Checking multiversion v0.7.4
[INFO] [stderr]     Checking polars-arrow v0.34.2
[INFO] [stderr]     Checking tabled v0.15.0
[INFO] [stderr]    Compiling pest_generator v2.7.11
[INFO] [stderr]    Compiling pest_derive v2.7.11
[INFO] [stderr]    Compiling jrsonnet-stdlib v0.5.0-pre95
[INFO] [stderr]     Checking seq_geom_parser v0.3.0 (https://github.com/COMBINE-lab/seq_geom_parser?branch=dev#f5f3f9f7)
[INFO] [stderr]     Checking nutype v0.3.1
[INFO] [stderr]     Checking seq_geom_xform v0.4.0 (https://github.com/COMBINE-lab/seq_geom_xform?branch=dev#445dab71)
[INFO] [stderr]     Checking jrsonnet-evaluator v0.5.0-pre95
[INFO] [stderr]     Checking serde_yaml_with_quirks v0.8.24
[INFO] [stderr]     Checking deranged v0.3.11
[INFO] [stderr]     Checking csv v1.3.0
[INFO] [stderr]     Checking time v0.3.36
[INFO] [stderr]     Checking polars-row v0.34.2
[INFO] [stderr]     Checking jrsonnet-cli v0.5.0-pre95
[INFO] [stderr]     Checking polars-time v0.34.2
[INFO] [stderr]     Checking polars-io v0.34.2
[INFO] [stderr]     Checking grangers v0.4.0 (https://github.com/COMBINE-lab/grangers.git?branch=main#1b0b0785)
[INFO] [stderr]     Checking roers v0.3.0 (https://github.com/COMBINE-lab/roers?branch=main#8ed7edc8)
[INFO] [stderr]     Checking simpleaf v0.17.2 (/opt/rustwide/workdir)
[INFO] [stdout] warning: field `af_home_path` is never read
[INFO] [stdout]    --> src/utils/workflow_utils.rs:548:9
[INFO] [stdout]     |
[INFO] [stdout] 547 | pub struct SimpleafWorkflow {
[INFO] [stdout]     |            ---------------- field in this struct
[INFO] [stdout] 548 |     pub af_home_path: PathBuf,
[INFO] [stdout]     |         ^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `active` is never read
[INFO] [stdout]    --> src/utils/workflow_utils.rs:998:9
[INFO] [stdout]     |
[INFO] [stdout] 996 | pub struct CommandRecord {
[INFO] [stdout]     |            ------------- field in this struct
[INFO] [stdout] 997 |     pub step: u64,
[INFO] [stdout] 998 |     pub active: bool,
[INFO] [stdout]     |         ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `af_home_path` is never read
[INFO] [stdout]    --> src/utils/workflow_utils.rs:548:9
[INFO] [stdout]     |
[INFO] [stdout] 547 | pub struct SimpleafWorkflow {
[INFO] [stdout]     |            ---------------- field in this struct
[INFO] [stdout] 548 |     pub af_home_path: PathBuf,
[INFO] [stdout]     |         ^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `active` is never read
[INFO] [stdout]    --> src/utils/workflow_utils.rs:998:9
[INFO] [stdout]     |
[INFO] [stdout] 996 | pub struct CommandRecord {
[INFO] [stdout]     |            ------------- field in this struct
[INFO] [stdout] 997 |     pub step: u64,
[INFO] [stdout] 998 |     pub active: bool,
[INFO] [stdout]     |         ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 2 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 2 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 10s
[INFO] running `Command { std: "docker" "inspect" "da45c7da1d00c46aa18f4092ede327779c3e9e20a265aaac981afc814a616b21", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "da45c7da1d00c46aa18f4092ede327779c3e9e20a265aaac981afc814a616b21", kill_on_drop: false }`
[INFO] [stdout] da45c7da1d00c46aa18f4092ede327779c3e9e20a265aaac981afc814a616b21