[INFO] cloning repository https://github.com/SorenHeidelbach/motif_methylation_state
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/SorenHeidelbach/motif_methylation_state" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FSorenHeidelbach%2Fmotif_methylation_state", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FSorenHeidelbach%2Fmotif_methylation_state'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 502ac26e1f766fdcfcd2e85ca0b1c888eb034027
[INFO] checking SorenHeidelbach/motif_methylation_state against try#d534db0721b23cf977073bf4cd306dbf501e6b4d for pr-138499
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FSorenHeidelbach%2Fmotif_methylation_state" "/workspace/builds/worker-3-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-3-tc2/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/SorenHeidelbach/motif_methylation_state on toolchain d534db0721b23cf977073bf4cd306dbf501e6b4d
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+d534db0721b23cf977073bf4cd306dbf501e6b4d" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/SorenHeidelbach/motif_methylation_state
[INFO] finished tweaking git repo https://github.com/SorenHeidelbach/motif_methylation_state
[INFO] tweaked toml for git repo https://github.com/SorenHeidelbach/motif_methylation_state written to /workspace/builds/worker-3-tc2/source/Cargo.toml
[INFO] crate git repo https://github.com/SorenHeidelbach/motif_methylation_state 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" "+d534db0721b23cf977073bf4cd306dbf501e6b4d" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]     Blocking waiting for file lock on package cache
[ERROR] error running command: no output for 300 seconds
[INFO] checking SorenHeidelbach/motif_methylation_state against try#d534db0721b23cf977073bf4cd306dbf501e6b4d for pr-138499
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FSorenHeidelbach%2Fmotif_methylation_state" "/workspace/builds/worker-3-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-3-tc2/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/SorenHeidelbach/motif_methylation_state on toolchain d534db0721b23cf977073bf4cd306dbf501e6b4d
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+d534db0721b23cf977073bf4cd306dbf501e6b4d" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/SorenHeidelbach/motif_methylation_state
[INFO] finished tweaking git repo https://github.com/SorenHeidelbach/motif_methylation_state
[INFO] tweaked toml for git repo https://github.com/SorenHeidelbach/motif_methylation_state written to /workspace/builds/worker-3-tc2/source/Cargo.toml
[INFO] crate git repo https://github.com/SorenHeidelbach/motif_methylation_state 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" "+d534db0721b23cf977073bf4cd306dbf501e6b4d" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded seq_io v0.3.2
[INFO] [stderr]   Downloaded bio-types v1.0.4
[INFO] [stderr]   Downloaded buffer-redux v1.0.2
[INFO] [stderr]   Downloaded bio v2.0.3
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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@sha256:1680c8fbd8dfb46fcd6d22e546df16ab0e007457dc29fcd9e987cdd5077fd1af" "/opt/rustwide/cargo-home/bin/cargo" "+d534db0721b23cf977073bf4cd306dbf501e6b4d" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 70fb025267197b479dd464734d633fa2cdcfeb1cc98c993f3adf639cc3f8a48d
[INFO] running `Command { std: "docker" "start" "-a" "70fb025267197b479dd464734d633fa2cdcfeb1cc98c993f3adf639cc3f8a48d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "70fb025267197b479dd464734d633fa2cdcfeb1cc98c993f3adf639cc3f8a48d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "70fb025267197b479dd464734d633fa2cdcfeb1cc98c993f3adf639cc3f8a48d", kill_on_drop: false }`
[INFO] [stdout] 70fb025267197b479dd464734d633fa2cdcfeb1cc98c993f3adf639cc3f8a48d
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:1680c8fbd8dfb46fcd6d22e546df16ab0e007457dc29fcd9e987cdd5077fd1af" "/opt/rustwide/cargo-home/bin/cargo" "+d534db0721b23cf977073bf4cd306dbf501e6b4d" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 01ce0d03e5b391e359e0685f49356c146550c4b0c1a2b5082d307996f5e79dbe
[INFO] running `Command { std: "docker" "start" "-a" "01ce0d03e5b391e359e0685f49356c146550c4b0c1a2b5082d307996f5e79dbe", kill_on_drop: false }`
[INFO] [stderr]    Compiling autocfg v1.4.0
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[INFO] [stderr]    Compiling syn v2.0.94
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[INFO] [stderr]    Compiling version_check v0.9.5
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[INFO] [stderr]    Compiling zerocopy-derive v0.7.35
[INFO] [stderr]    Compiling serde_derive v1.0.217
[INFO] [stderr]    Compiling nalgebra-macros v0.2.2
[INFO] [stderr]    Compiling thiserror-impl v1.0.69
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]    Compiling derive-new v0.6.0
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[INFO] [stderr]    Compiling clap_derive v4.5.18
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[INFO] [stderr]     Checking zerocopy v0.7.35
[INFO] [stderr]     Checking ppv-lite86 v0.2.20
[INFO] [stderr]     Checking clap v4.5.23
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]     Checking bio-types v1.0.4
[INFO] [stderr]     Checking rand v0.8.5
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking nalgebra v0.32.6
[INFO] [stderr]     Checking multimap v0.10.0
[INFO] [stderr]     Checking csv v1.3.1
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking seq_io v0.3.2
[INFO] [stderr]     Checking statrs v0.17.1
[INFO] [stderr]     Checking bio v2.0.3
[INFO] [stderr]     Checking memopair v0.1.6 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused imports: `debug`, `info`, and `warn`
[INFO] [stdout]  --> src/lib/pileup.rs:5:11
[INFO] [stdout]   |
[INFO] [stdout] 5 | use log::{debug, info, warn};
[INFO] [stdout]   |           ^^^^^  ^^^^  ^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `debug`, `info`, and `warn`
[INFO] [stdout]  --> src/lib/pileup.rs:5:11
[INFO] [stdout]   |
[INFO] [stdout] 5 | use log::{debug, info, warn};
[INFO] [stdout]   |           ^^^^^  ^^^^  ^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variant `verbose` should have an upper camel case name
[INFO] [stdout]   --> src/bin/memopair/cli.rs:63:5
[INFO] [stdout]    |
[INFO] [stdout] 63 |     verbose,
[INFO] [stdout]    |     ^^^^^^^ help: convert the identifier to upper camel case (notice the capitalization): `Verbose`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(non_camel_case_types)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variant `normal` should have an upper camel case name
[INFO] [stdout]   --> src/bin/memopair/cli.rs:64:5
[INFO] [stdout]    |
[INFO] [stdout] 64 |     normal,
[INFO] [stdout]    |     ^^^^^^ help: convert the identifier to upper camel case: `Normal`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variant `silent` should have an upper camel case name
[INFO] [stdout]   --> src/bin/memopair/cli.rs:65:5
[INFO] [stdout]    |
[INFO] [stdout] 65 |     silent,
[INFO] [stdout]    |     ^^^^^^ help: convert the identifier to upper camel case (notice the capitalization): `Silent`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variant `verbose` should have an upper camel case name
[INFO] [stdout]   --> src/bin/memopair/cli.rs:63:5
[INFO] [stdout]    |
[INFO] [stdout] 63 |     verbose,
[INFO] [stdout]    |     ^^^^^^^ help: convert the identifier to upper camel case (notice the capitalization): `Verbose`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(non_camel_case_types)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variant `normal` should have an upper camel case name
[INFO] [stdout]   --> src/bin/memopair/cli.rs:64:5
[INFO] [stdout]    |
[INFO] [stdout] 64 |     normal,
[INFO] [stdout]    |     ^^^^^^ help: convert the identifier to upper camel case: `Normal`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variant `silent` should have an upper camel case name
[INFO] [stdout]   --> src/bin/memopair/cli.rs:65:5
[INFO] [stdout]    |
[INFO] [stdout] 65 |     silent,
[INFO] [stdout]    |     ^^^^^^ help: convert the identifier to upper camel case (notice the capitalization): `Silent`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `refenrece_id`
[INFO] [stdout]   --> src/bin/memopair/methylated_motif_pair.rs:53:22
[INFO] [stdout]    |
[INFO] [stdout] 53 |                 for (refenrece_id, contig) in genome_work_space.contigs.into_iter() {
[INFO] [stdout]    |                      ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_refenrece_id`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `refenrece_id`
[INFO] [stdout]   --> src/bin/memopair/methylated_motif_pair.rs:53:22
[INFO] [stdout]    |
[INFO] [stdout] 53 |                 for (refenrece_id, contig) in genome_work_space.contigs.into_iter() {
[INFO] [stdout]    |                      ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_refenrece_id`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 12.38s
[INFO] running `Command { std: "docker" "inspect" "01ce0d03e5b391e359e0685f49356c146550c4b0c1a2b5082d307996f5e79dbe", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "01ce0d03e5b391e359e0685f49356c146550c4b0c1a2b5082d307996f5e79dbe", kill_on_drop: false }`
[INFO] [stdout] 01ce0d03e5b391e359e0685f49356c146550c4b0c1a2b5082d307996f5e79dbe