[INFO] fetching crate spdkit-surface 0.1.1...
[INFO] checking spdkit-surface-0.1.1 against master#8c32e313cccf7df531e2d49ffb8227bb92304aee for pr-145608-1
[INFO] extracting crate spdkit-surface 0.1.1 into /workspace/builds/worker-1-tc1/source
[INFO] started tweaking crates.io crate spdkit-surface 0.1.1
[INFO] finished tweaking crates.io crate spdkit-surface 0.1.1
[INFO] tweaked toml for crates.io crate spdkit-surface 0.1.1 written to /workspace/builds/worker-1-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate spdkit-surface 0.1.1 on toolchain 8c32e313cccf7df531e2d49ffb8227bb92304aee
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+8c32e313cccf7df531e2d49ffb8227bb92304aee" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+8c32e313cccf7df531e2d49ffb8227bb92304aee" "generate-lockfile" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]      Locking 232 packages to latest compatible versions
[INFO] [stderr]       Adding handlebars v4.0.1 (available: v4.5.0)
[INFO] [stderr]       Adding rand v0.8.5 (available: v0.9.2)
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+8c32e313cccf7df531e2d49ffb8227bb92304aee" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded vecfx v0.1.6
[INFO] [stderr]   Downloaded lazy-regex-proc_macros v2.4.1
[INFO] [stderr]   Downloaded gchemol-gut v0.4.4
[INFO] [stderr]   Downloaded lazy-regex v2.5.0
[INFO] [stderr]   Downloaded grep-cli v0.1.11
[INFO] [stderr]   Downloaded gchemol-graph v0.1.6
[INFO] [stderr]   Downloaded grep v0.3.2
[INFO] [stderr]   Downloaded gchemol-geometry v0.1.1
[INFO] [stderr]   Downloaded grep-reader v0.1.3
[INFO] [stderr]   Downloaded grep-printer v0.2.2
[INFO] [stderr]   Downloaded gchemol-readwrite v0.1.12
[INFO] [stderr]   Downloaded minijinja v1.0.22
[INFO] [stderr]   Downloaded uom v0.33.0
[INFO] [stderr]   Downloaded gchemol v0.1.7
[INFO] [stderr]   Downloaded gchemol-core v0.1.7
[INFO] [stderr]   Downloaded grep-printer v0.1.7
[INFO] [stderr]   Downloaded grep-regex v0.1.13
[INFO] [stderr]   Downloaded gchemol-parser v0.4.6
[INFO] [stderr]   Downloaded handlebars v4.0.1
[INFO] [stderr]   Downloaded extxyz v0.2.0
[INFO] [stderr]   Downloaded grep v0.2.13
[INFO] [stderr]   Downloaded gchemol-lattice v0.1.2
[INFO] [stderr]   Downloaded gchemol-neighbors v0.1.3
[INFO] [stderr]   Downloaded octree v0.1.0
[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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+8c32e313cccf7df531e2d49ffb8227bb92304aee" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 7ba5c472e0824ee5034630a9a135a1088623e4f860f577821ae1156bbc018b27
[INFO] running `Command { std: "docker" "start" "-a" "7ba5c472e0824ee5034630a9a135a1088623e4f860f577821ae1156bbc018b27", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "7ba5c472e0824ee5034630a9a135a1088623e4f860f577821ae1156bbc018b27", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "7ba5c472e0824ee5034630a9a135a1088623e4f860f577821ae1156bbc018b27", kill_on_drop: false }`
[INFO] [stdout] 7ba5c472e0824ee5034630a9a135a1088623e4f860f577821ae1156bbc018b27
[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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+8c32e313cccf7df531e2d49ffb8227bb92304aee" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] f58c69b220e3cd9be04b590b9c82881d7b30d58fc9f2dcc9ad87460883fb00b9
[INFO] running `Command { std: "docker" "start" "-a" "f58c69b220e3cd9be04b590b9c82881d7b30d58fc9f2dcc9ad87460883fb00b9", kill_on_drop: false }`
[INFO] [stderr]     Checking aho-corasick v1.1.3
[INFO] [stderr]    Compiling libm v0.2.15
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]    Compiling signal-hook v0.3.18
[INFO] [stderr]     Checking rand_core v0.6.4
[INFO] [stderr]    Compiling zerocopy v0.8.26
[INFO] [stderr]    Compiling serde v1.0.219
[INFO] [stderr]     Checking bytemuck v1.23.2
[INFO] [stderr]    Compiling matrixmultiply v0.3.10
[INFO] [stderr]     Checking grep-matcher v0.1.7
[INFO] [stderr]     Checking os_pipe v1.2.2
[INFO] [stderr]    Compiling thiserror-impl v2.0.16
[INFO] [stderr]     Checking winnow v0.5.40
[INFO] [stderr]     Checking encoding_rs_io v0.1.7
[INFO] [stderr]     Checking memmap2 v0.9.8
[INFO] [stderr]     Checking safe_arch v0.7.4
[INFO] [stderr]     Checking toml_datetime v0.6.11
[INFO] [stderr]     Checking sigchld v0.2.4
[INFO] [stderr]     Checking serde_spanned v0.6.9
[INFO] [stderr]     Checking clap_builder v4.5.47
[INFO] [stderr]    Compiling clap_derive v4.5.47
[INFO] [stderr]     Checking is-terminal v0.4.16
[INFO] [stderr]     Checking tempfile v3.21.0
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]     Checking time v0.3.43
[INFO] [stderr]     Checking shared_child v1.1.1
[INFO] [stderr]     Checking wide v0.7.33
[INFO] [stderr]     Checking rand v0.8.5
[INFO] [stderr]    Compiling ucd-trie v0.1.7
[INFO] [stderr]     Checking duct v0.13.7
[INFO] [stderr]    Compiling phf v0.11.3
[INFO] [stderr]    Compiling indexmap v1.9.3
[INFO] [stderr]     Checking phf_shared v0.11.3
[INFO] [stderr]     Checking base64 v0.20.0
[INFO] [stderr]     Checking petgraph v0.6.5
[INFO] [stderr]     Checking regex-automata v0.4.10
[INFO] [stderr]     Checking unic-ucd-segment v0.9.0
[INFO] [stderr]     Checking deunicode v1.6.2
[INFO] [stderr]     Checking str_indices v0.4.4
[INFO] [stderr]     Checking slug v0.1.6
[INFO] [stderr]     Checking humansize v2.1.3
[INFO] [stderr]     Checking ropey v1.6.1
[INFO] [stderr]     Checking bimap v0.6.3
[INFO] [stderr]     Checking envy v0.4.2
[INFO] [stderr]     Checking unic-segment v0.9.0
[INFO] [stderr]     Checking quick-error v2.0.1
[INFO] [stderr]     Checking xmlparser v0.13.6
[INFO] [stderr]     Checking minijinja v1.0.22
[INFO] [stderr]    Compiling thiserror v2.0.16
[INFO] [stderr]     Checking roxmltree v0.18.1
[INFO] [stderr]     Checking pest v2.8.1
[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 ppv-lite86 v0.2.21
[INFO] [stderr]     Checking toml_edit v0.19.15
[INFO] [stderr]     Checking ordered-float v3.9.2
[INFO] [stderr]     Checking chrono v0.4.41
[INFO] [stderr]     Checking num-rational v0.4.2
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking clap v4.5.47
[INFO] [stderr]     Checking gchemol-graph v0.1.6
[INFO] [stderr]     Checking uom v0.33.0
[INFO] [stderr]     Checking simba v0.7.3
[INFO] [stderr]    Compiling pest_meta v2.8.1
[INFO] [stderr]    Compiling nalgebra-macros v0.1.0
[INFO] [stderr]    Compiling pest_generator v2.8.1
[INFO] [stderr]     Checking toml v0.7.8
[INFO] [stderr]     Checking bstr v1.12.0
[INFO] [stderr]     Checking regex v1.11.2
[INFO] [stderr]     Checking env_logger v0.10.2
[INFO] [stderr]     Checking gchemol-gut v0.4.4
[INFO] [stderr]     Checking globset v0.4.16
[INFO] [stderr]     Checking grep-searcher v0.1.14
[INFO] [stderr]     Checking grep-regex v0.1.13
[INFO] [stderr]    Compiling pest_derive v2.8.1
[INFO] [stderr]    Compiling phf_generator v0.11.3
[INFO] [stderr]    Compiling phf_codegen v0.11.3
[INFO] [stderr]     Checking grep-printer v0.2.2
[INFO] [stderr]     Checking grep-printer v0.1.7
[INFO] [stderr]     Checking handlebars v4.0.1
[INFO] [stderr]     Checking grep-cli v0.1.11
[INFO] [stderr]     Checking ignore v0.4.23
[INFO] [stderr]     Checking globwalk v0.9.1
[INFO] [stderr]     Checking grep v0.3.2
[INFO] [stderr]     Checking grep v0.2.13
[INFO] [stderr]     Checking gchemol-parser v0.4.6
[INFO] [stderr]     Checking grep-reader v0.1.3
[INFO] [stderr]     Checking extxyz v0.2.0
[INFO] [stderr]    Compiling parse-zoneinfo v0.3.1
[INFO] [stderr]    Compiling chrono-tz-build v0.3.0
[INFO] [stderr]    Compiling lazy-regex-proc_macros v2.4.1
[INFO] [stderr]    Compiling chrono-tz v0.9.0
[INFO] [stderr]     Checking lazy-regex v2.5.0
[INFO] [stderr]     Checking nalgebra v0.31.4
[INFO] [stderr]     Checking tera v1.20.0
[INFO] [stderr]     Checking vecfx v0.1.6
[INFO] [stderr]     Checking gchemol-lattice v0.1.2
[INFO] [stderr]     Checking octree v0.1.0
[INFO] [stderr]     Checking gchemol-geometry v0.1.1
[INFO] [stderr]     Checking gchemol-neighbors v0.1.3
[INFO] [stderr]     Checking gchemol-core v0.1.7
[INFO] [stderr]     Checking gchemol-readwrite v0.1.12
[INFO] [stderr]     Checking gchemol v0.1.7
[INFO] [stderr]     Checking spdkit-surface v0.1.1 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `gchemol::Lattice`
[INFO] [stdout]  --> src/layers.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use gchemol::Lattice;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `gchemol::Lattice`
[INFO] [stdout]  --> src/layers.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use gchemol::Lattice;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `gchemol::prelude::*`
[INFO] [stdout]   --> src/lib.rs:11:13
[INFO] [stdout]    |
[INFO] [stdout] 11 |     pub use gchemol::prelude::*;
[INFO] [stdout]    |             ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `gchemol::Atom::label`: use get_label instead
[INFO] [stdout]   --> src/layers.rs:17:33
[INFO] [stdout]    |
[INFO] [stdout] 17 |     mol.atoms().find(|(_, a)| a.label() == format!("{i}")).is_some()
[INFO] [stdout]    |                                 ^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(deprecated)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `gchemol::Atom::label`: use get_label instead
[INFO] [stdout]   --> src/layers.rs:28:32
[INFO] [stdout]    |
[INFO] [stdout] 28 |     mol.atoms().map(|(_, a)| a.label().parse().unwrap()).collect()
[INFO] [stdout]    |                                ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `n_probes`
[INFO] [stdout]   --> src/probe.rs:71:59
[INFO] [stdout]    |
[INFO] [stdout] 71 | pub fn probe_surface_atoms(mol: &Molecule, r_cutoff: f64, n_probes: usize) -> Result<Vec<usize>> {
[INFO] [stdout]    |                                                           ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_n_probes`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `gchemol::Atom::label`: use get_label instead
[INFO] [stdout]   --> src/layers.rs:17:33
[INFO] [stdout]    |
[INFO] [stdout] 17 |     mol.atoms().find(|(_, a)| a.label() == format!("{i}")).is_some()
[INFO] [stdout]    |                                 ^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(deprecated)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `gchemol::Atom::label`: use get_label instead
[INFO] [stdout]   --> src/layers.rs:28:32
[INFO] [stdout]    |
[INFO] [stdout] 28 |     mol.atoms().map(|(_, a)| a.label().parse().unwrap()).collect()
[INFO] [stdout]    |                                ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `n_probes`
[INFO] [stdout]   --> src/probe.rs:71:59
[INFO] [stdout]    |
[INFO] [stdout] 71 | pub fn probe_surface_atoms(mol: &Molecule, r_cutoff: f64, n_probes: usize) -> Result<Vec<usize>> {
[INFO] [stdout]    |                                                           ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_n_probes`
[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 33.86s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: gchemol-core v0.1.7
[INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1`
[INFO] running `Command { std: "docker" "inspect" "f58c69b220e3cd9be04b590b9c82881d7b30d58fc9f2dcc9ad87460883fb00b9", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "f58c69b220e3cd9be04b590b9c82881d7b30d58fc9f2dcc9ad87460883fb00b9", kill_on_drop: false }`
[INFO] [stdout] f58c69b220e3cd9be04b590b9c82881d7b30d58fc9f2dcc9ad87460883fb00b9