[INFO] fetching crate spdkit-surface 0.1.1... [INFO] checking spdkit-surface-0.1.1 against master#af4a5a13a15fa0c60e06321077ef452f769b42fd for pr-122960-3 [INFO] extracting crate spdkit-surface 0.1.1 into /workspace/builds/worker-4-tc1/source [INFO] validating manifest of crates.io crate spdkit-surface 0.1.1 on toolchain af4a5a13a15fa0c60e06321077ef452f769b42fd [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+af4a5a13a15fa0c60e06321077ef452f769b42fd" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [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-4-tc1/source/Cargo.toml [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+af4a5a13a15fa0c60e06321077ef452f769b42fd" "generate-lockfile" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Locking 207 packages [INFO] [stderr] Adding base64 v0.20.0 (latest: v0.22.0) [INFO] [stderr] Adding bitflags v1.3.2 (latest: v2.5.0) [INFO] [stderr] Adding env_logger v0.10.2 (latest: v0.11.3) [INFO] [stderr] Adding fixedbitset v0.4.2 (latest: v0.5.6) [INFO] [stderr] Adding gchemol-parser v0.4.6 (latest: v0.5.1) [INFO] [stderr] Adding generic-array v0.14.7 (latest: v1.0.0) [INFO] [stderr] Adding globwalk v0.8.1 (latest: v0.9.1) [INFO] [stderr] Adding grep v0.2.13 (latest: v0.3.1) [INFO] [stderr] Adding grep-printer v0.1.7 (latest: v0.2.1) [INFO] [stderr] Adding handlebars v4.0.1 (latest: v5.1.2) [INFO] [stderr] Adding hashbrown v0.12.3 (latest: v0.14.3) [INFO] [stderr] Adding indexmap v1.9.3 (latest: v2.2.6) [INFO] [stderr] Adding itertools v0.10.5 (latest: v0.12.1) [INFO] [stderr] Adding lazy-regex v2.5.0 (latest: v3.1.0) [INFO] [stderr] Adding lazy-regex-proc_macros v2.4.1 (latest: v3.1.0) [INFO] [stderr] Adding linux-raw-sys v0.4.13 (latest: v0.6.4) [INFO] [stderr] Adding nalgebra v0.31.4 (latest: v0.32.5) [INFO] [stderr] Adding nalgebra-macros v0.1.0 (latest: v0.2.1) [INFO] [stderr] Adding ordered-float v3.9.2 (latest: v4.2.0) [INFO] [stderr] Adding roxmltree v0.18.1 (latest: v0.19.0) [INFO] [stderr] Adding simba v0.7.3 (latest: v0.8.1) [INFO] [stderr] Adding siphasher v0.3.11 (latest: v1.0.1) [INFO] [stderr] Adding syn v1.0.109 (latest: v2.0.57) [INFO] [stderr] Adding toml v0.7.8 (latest: v0.8.12) [INFO] [stderr] Adding toml_edit v0.19.15 (latest: v0.22.9) [INFO] [stderr] Adding uom v0.33.0 (latest: v0.36.0) [INFO] [stderr] Adding wasi v0.11.0+wasi-snapshot-preview1 (latest: v0.13.0+wasi-0.2.0) [INFO] [stderr] Adding windows-core v0.52.0 (latest: v0.55.0) [INFO] [stderr] Adding winnow v0.5.40 (latest: v0.6.5) [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+af4a5a13a15fa0c60e06321077ef452f769b42fd" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded grep-searcher v0.1.13 [INFO] [stderr] Downloaded grep v0.2.13 [INFO] [stderr] Downloaded grep v0.3.1 [INFO] [stderr] Downloaded grep-matcher v0.1.7 [INFO] [stderr] Downloaded grep-cli v0.1.10 [INFO] [stderr] Downloaded extxyz v0.2.0 [INFO] [stderr] Downloaded minijinja v1.0.16 [INFO] [stderr] Downloaded grep-printer v0.2.1 [INFO] [stderr] Downloaded grep-reader v0.1.3 [INFO] [stderr] Downloaded gchemol-core v0.1.7 [INFO] [stderr] Downloaded grep-printer v0.1.7 [INFO] [stderr] Downloaded grep-regex v0.1.12 [INFO] [stderr] Downloaded gchemol-parser v0.4.6 [INFO] [stderr] Downloaded handlebars v4.0.1 [INFO] [stderr] Downloaded gchemol-readwrite v0.1.11 [INFO] [stderr] Downloaded uom v0.33.0 [INFO] [stderr] Downloaded gchemol v0.1.7 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+af4a5a13a15fa0c60e06321077ef452f769b42fd" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 921f9e27905256d290eae38d7b57daed8516871e852de1eb2c4fd24e1345c67e [INFO] running `Command { std: "docker" "start" "-a" "921f9e27905256d290eae38d7b57daed8516871e852de1eb2c4fd24e1345c67e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "921f9e27905256d290eae38d7b57daed8516871e852de1eb2c4fd24e1345c67e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "921f9e27905256d290eae38d7b57daed8516871e852de1eb2c4fd24e1345c67e", kill_on_drop: false }` [INFO] [stdout] 921f9e27905256d290eae38d7b57daed8516871e852de1eb2c4fd24e1345c67e [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+af4a5a13a15fa0c60e06321077ef452f769b42fd" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] fdd8834515a1c7056eae8b9419008797b4cf6a98587da09ded3fabc09e94f4dc [INFO] running `Command { std: "docker" "start" "-a" "fdd8834515a1c7056eae8b9419008797b4cf6a98587da09ded3fabc09e94f4dc", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.153 [INFO] [stderr] Compiling autocfg v1.2.0 [INFO] [stderr] Checking memchr v2.7.2 [INFO] [stderr] Checking cfg-if v1.0.0 [INFO] [stderr] Checking regex-syntax v0.8.3 [INFO] [stderr] Checking log v0.4.21 [INFO] [stderr] Compiling libm v0.2.8 [INFO] [stderr] Compiling serde_json v1.0.115 [INFO] [stderr] Compiling crossbeam-utils v0.8.19 [INFO] [stderr] Checking ryu v1.0.17 [INFO] [stderr] Checking termcolor v1.4.1 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Checking ppv-lite86 v0.2.17 [INFO] [stderr] Compiling syn v2.0.57 [INFO] [stderr] Checking equivalent v1.0.1 [INFO] [stderr] Checking hashbrown v0.14.3 [INFO] [stderr] Compiling typenum v1.17.0 [INFO] [stderr] Compiling anyhow v1.0.81 [INFO] [stderr] Compiling paste v1.0.14 [INFO] [stderr] Checking utf8parse v0.2.1 [INFO] [stderr] Checking bytemuck v1.15.0 [INFO] [stderr] Checking anstyle-parse v0.2.3 [INFO] [stderr] Checking safe_arch v0.7.1 [INFO] [stderr] Compiling num-traits v0.2.18 [INFO] [stderr] Checking aho-corasick v1.1.3 [INFO] [stderr] Checking grep-matcher v0.1.7 [INFO] [stderr] Checking indexmap v2.2.6 [INFO] [stderr] Compiling num-rational v0.4.1 [INFO] [stderr] Checking crossbeam-epoch v0.9.18 [INFO] [stderr] Compiling matrixmultiply v0.3.8 [INFO] [stderr] Checking encoding_rs v0.8.33 [INFO] [stderr] Compiling siphasher v0.3.11 [INFO] [stderr] Compiling rayon-core v1.12.1 [INFO] [stderr] Compiling rustix v0.38.32 [INFO] [stderr] Checking crossbeam-deque v0.8.5 [INFO] [stderr] Checking colorchoice v1.0.0 [INFO] [stderr] Checking anstyle-query v1.0.2 [INFO] [stderr] Checking winnow v0.5.40 [INFO] [stderr] Checking either v1.10.0 [INFO] [stderr] Checking anstyle v1.0.6 [INFO] [stderr] Compiling phf_shared v0.11.2 [INFO] [stderr] Checking anstream v0.6.13 [INFO] [stderr] Checking wide v0.7.15 [INFO] [stderr] Checking bitflags v2.5.0 [INFO] [stderr] Checking linux-raw-sys v0.4.13 [INFO] [stderr] Compiling heck v0.5.0 [INFO] [stderr] Checking getrandom v0.2.12 [INFO] [stderr] Checking memmap2 v0.9.4 [INFO] [stderr] Checking strsim v0.11.0 [INFO] [stderr] Checking once_cell v1.19.0 [INFO] [stderr] Checking encoding_rs_io v0.1.7 [INFO] [stderr] Checking regex-automata v0.4.6 [INFO] [stderr] Checking clap_lex v0.7.0 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Checking shared_child v1.0.0 [INFO] [stderr] Checking os_pipe v1.1.5 [INFO] [stderr] Checking is-terminal v0.4.12 [INFO] [stderr] Checking num-integer v0.1.46 [INFO] [stderr] Checking approx v0.5.1 [INFO] [stderr] Checking clap_builder v4.5.2 [INFO] [stderr] Checking itertools v0.10.5 [INFO] [stderr] Checking humantime v2.1.0 [INFO] [stderr] Checking lazy_static v1.4.0 [INFO] [stderr] Checking fastrand v2.0.2 [INFO] [stderr] Checking time v0.3.34 [INFO] [stderr] Checking duct v0.13.7 [INFO] [stderr] Compiling ucd-trie v0.1.6 [INFO] [stderr] Checking shell-escape v0.1.5 [INFO] [stderr] Checking rayon v1.10.0 [INFO] [stderr] Compiling phf v0.11.2 [INFO] [stderr] Compiling indexmap v1.9.3 [INFO] [stderr] Checking unic-common v0.9.0 [INFO] [stderr] Checking same-file v1.0.6 [INFO] [stderr] Checking unic-char-range v0.9.0 [INFO] [stderr] Checking unic-ucd-version v0.9.0 [INFO] [stderr] Checking walkdir v2.5.0 [INFO] [stderr] Checking unic-char-property v0.9.0 [INFO] [stderr] Checking base64 v0.20.0 [INFO] [stderr] Checking fixedbitset v0.4.2 [INFO] [stderr] Checking iana-time-zone v0.1.60 [INFO] [stderr] Checking hashbrown v0.12.3 [INFO] [stderr] Checking unic-ucd-segment v0.9.0 [INFO] [stderr] Checking str_indices v0.4.3 [INFO] [stderr] Checking chrono v0.4.37 [INFO] [stderr] Checking deunicode v1.4.3 [INFO] [stderr] Checking smallvec v1.13.2 [INFO] [stderr] Checking minimal-lexical v0.2.1 [INFO] [stderr] Checking bitflags v1.3.2 [INFO] [stderr] Checking slug v0.1.5 [INFO] [stderr] Checking humansize v2.1.3 [INFO] [stderr] Checking quick-error v2.0.1 [INFO] [stderr] Checking unic-segment v0.9.0 [INFO] [stderr] Checking xmlparser v0.13.6 [INFO] [stderr] Checking ropey v1.6.1 [INFO] [stderr] Checking percent-encoding v2.3.1 [INFO] [stderr] Checking uom v0.33.0 [INFO] [stderr] Checking nom v7.1.3 [INFO] [stderr] Checking roxmltree v0.18.1 [INFO] [stderr] Checking tempfile v3.10.1 [INFO] [stderr] Compiling nalgebra-macros v0.1.0 [INFO] [stderr] Compiling serde_derive v1.0.197 [INFO] [stderr] Compiling thiserror-impl v1.0.58 [INFO] [stderr] Compiling clap_derive v4.5.4 [INFO] [stderr] Checking bstr v1.9.1 [INFO] [stderr] Checking regex v1.10.4 [INFO] [stderr] Checking env_logger v0.10.2 [INFO] [stderr] Checking globset v0.4.14 [INFO] [stderr] Checking grep-searcher v0.1.13 [INFO] [stderr] Checking grep-regex v0.1.12 [INFO] [stderr] Compiling thiserror v1.0.58 [INFO] [stderr] Compiling pest v2.7.9 [INFO] [stderr] Checking grep-cli v0.1.10 [INFO] [stderr] Checking ignore v0.4.22 [INFO] [stderr] Compiling parse-zoneinfo v0.3.0 [INFO] [stderr] Checking clap v4.5.4 [INFO] [stderr] Checking globwalk v0.8.1 [INFO] [stderr] Compiling lazy-regex-proc_macros v2.4.1 [INFO] [stderr] Compiling pest_meta v2.7.9 [INFO] [stderr] Checking serde v1.0.197 [INFO] [stderr] Compiling pest_generator v2.7.9 [INFO] [stderr] Checking lazy-regex v2.5.0 [INFO] [stderr] Compiling pest_derive v2.7.9 [INFO] [stderr] Checking rand_core v0.6.4 [INFO] [stderr] Checking toml_datetime v0.6.5 [INFO] [stderr] Checking serde_spanned v0.6.5 [INFO] [stderr] Checking num-complex v0.4.5 [INFO] [stderr] Checking petgraph v0.6.4 [INFO] [stderr] Checking envy v0.4.2 [INFO] [stderr] Checking bimap v0.6.3 [INFO] [stderr] Checking minijinja v1.0.16 [INFO] [stderr] Checking toml_edit v0.19.15 [INFO] [stderr] Checking rand_chacha v0.3.1 [INFO] [stderr] Checking simba v0.7.3 [INFO] [stderr] Checking rand v0.8.5 [INFO] [stderr] Checking grep-printer v0.2.1 [INFO] [stderr] Checking grep-printer v0.1.7 [INFO] [stderr] Checking handlebars v4.0.1 [INFO] [stderr] Checking grep v0.2.13 [INFO] [stderr] Checking ordered-float v3.9.2 [INFO] [stderr] Checking rand_distr v0.4.3 [INFO] [stderr] Checking grep v0.3.1 [INFO] [stderr] Checking grep-reader v0.1.3 [INFO] [stderr] Checking toml v0.7.8 [INFO] [stderr] Checking extxyz v0.2.0 [INFO] [stderr] Checking gchemol-graph v0.1.6 [INFO] [stderr] Checking gchemol-gut v0.4.4 [INFO] [stderr] Compiling phf_generator v0.11.2 [INFO] [stderr] Checking gchemol-parser v0.4.6 [INFO] [stderr] Compiling phf_codegen v0.11.2 [INFO] [stderr] Compiling chrono-tz-build v0.2.1 [INFO] [stderr] Compiling chrono-tz v0.8.6 [INFO] [stderr] Checking nalgebra v0.31.4 [INFO] [stderr] Checking tera v1.19.1 [INFO] [stderr] Checking vecfx v0.1.6 [INFO] [stderr] Checking octree v0.1.0 [INFO] [stderr] Checking gchemol-lattice v0.1.2 [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 v0.1.11 [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::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: 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: 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: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: 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> { [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: 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> { [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: 5 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 4 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 25.54s [INFO] running `Command { std: "docker" "inspect" "fdd8834515a1c7056eae8b9419008797b4cf6a98587da09ded3fabc09e94f4dc", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "fdd8834515a1c7056eae8b9419008797b4cf6a98587da09ded3fabc09e94f4dc", kill_on_drop: false }` [INFO] [stdout] fdd8834515a1c7056eae8b9419008797b4cf6a98587da09ded3fabc09e94f4dc [INFO] checking spdkit-surface-0.1.1 against try#36dbcaee1a55543dfc181be52a69d99ff46ff62f for pr-122960-3 [INFO] extracting crate spdkit-surface 0.1.1 into /workspace/builds/worker-4-tc2/source [INFO] validating manifest of crates.io crate spdkit-surface 0.1.1 on toolchain 36dbcaee1a55543dfc181be52a69d99ff46ff62f [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+36dbcaee1a55543dfc181be52a69d99ff46ff62f" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [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-4-tc2/source/Cargo.toml [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+36dbcaee1a55543dfc181be52a69d99ff46ff62f" "generate-lockfile" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+36dbcaee1a55543dfc181be52a69d99ff46ff62f" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+36dbcaee1a55543dfc181be52a69d99ff46ff62f" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 6ed1f5b6efdaca272643718022095e08136a866d9f2c3414f49951e2adc37e89 [INFO] running `Command { std: "docker" "start" "-a" "6ed1f5b6efdaca272643718022095e08136a866d9f2c3414f49951e2adc37e89", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "6ed1f5b6efdaca272643718022095e08136a866d9f2c3414f49951e2adc37e89", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "6ed1f5b6efdaca272643718022095e08136a866d9f2c3414f49951e2adc37e89", kill_on_drop: false }` [INFO] [stdout] 6ed1f5b6efdaca272643718022095e08136a866d9f2c3414f49951e2adc37e89 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+36dbcaee1a55543dfc181be52a69d99ff46ff62f" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] c1e33d31ef0b368e5f932d34491e27c88bbc25e88fdd6b0a41bd4a60ad4d490b [INFO] running `Command { std: "docker" "start" "-a" "c1e33d31ef0b368e5f932d34491e27c88bbc25e88fdd6b0a41bd4a60ad4d490b", kill_on_drop: false }` [INFO] [stderr] Copying to /tmp/fixit [INFO] [stderr] Running `cargo fix --edition` [INFO] [stderr] Compiling libc v0.2.153 [INFO] [stderr] Checking memchr v2.7.2 [INFO] [stderr] Compiling autocfg v1.2.0 [INFO] [stderr] Checking cfg-if v1.0.0 [INFO] [stderr] Checking regex-syntax v0.8.3 [INFO] [stderr] Checking log v0.4.21 [INFO] [stderr] Compiling libm v0.2.8 [INFO] [stderr] Compiling serde_json v1.0.115 [INFO] [stderr] Compiling crossbeam-utils v0.8.19 [INFO] [stderr] Checking ryu 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[stderr] Compiling chrono-tz-build v0.2.1 [INFO] [stderr] Compiling chrono-tz v0.8.6 [INFO] [stderr] Checking nalgebra v0.31.4 [INFO] [stderr] Checking tera v1.19.1 [INFO] [stderr] Checking vecfx v0.1.6 [INFO] [stderr] Checking octree v0.1.0 [INFO] [stderr] Checking gchemol-lattice v0.1.2 [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 v0.1.11 [INFO] [stderr] Checking gchemol v0.1.7 [INFO] [stderr] Checking spdkit-surface v0.1.1 (/tmp/fixit) [INFO] [stderr] Migrating src/lib.rs from 2021 edition to 2024 [INFO] [stderr] Fixed src/layers.rs (1 fix) [INFO] [stdout] warning: use of deprecated method `gchemol::Atom::label`: use get_label instead [INFO] [stdout] --> src/layers.rs:16:33 [INFO] [stdout] | [INFO] [stdout] 16 | 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:27:32 [INFO] [stdout] | [INFO] [stdout] 27 | 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> { [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: 3 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Fixed src/lib.rs (1 fix) [INFO] [stdout] warning: use of deprecated method `gchemol::Atom::label`: use get_label instead [INFO] [stdout] --> src/layers.rs:16:33 [INFO] [stdout] | [INFO] [stdout] 16 | 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:27:32 [INFO] [stdout] | [INFO] [stdout] 27 | 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> { [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: 3 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 28.20s [INFO] [stderr] Running `cargo check` to verify 2024 [INFO] [stderr] Checking spdkit-surface v0.1.1 (/tmp/fixit) [INFO] [stdout] warning: use of deprecated method `gchemol::Atom::label`: use get_label instead [INFO] [stdout] --> src/layers.rs:16:33 [INFO] [stdout] | [INFO] [stdout] 16 | 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:27:32 [INFO] [stdout] | [INFO] [stdout] 27 | 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> { [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: 3 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no function or associated item named `from_file` found for struct `gchemol::Molecule` in the current scope [INFO] [stdout] --> src/probe.rs:100:25 [INFO] [stdout] | [INFO] [stdout] 100 | let mol = Molecule::from_file(file)?; [INFO] [stdout] | ^^^^^^^^^ function or associated item not found in `Molecule` [INFO] [stdout] | [INFO] [stdout] note: if you're trying to build a new `gchemol::Molecule` consider using one of the following associated functions: [INFO] [stdout] gchemol_core::data::::from_database [INFO] [stdout] gchemol::Molecule::new [INFO] [stdout] gchemol::Molecule::from_atoms [INFO] [stdout] gchemol::Molecule::from_graph [INFO] [stdout] gchemol::Molecule::from_graph_raw [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-6f17d22bba15001f/gchemol-core-0.1.7/src/data.rs:264:5 [INFO] [stdout] | [INFO] [stdout] 264 | pub fn from_database(name: &str) -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] ::: /opt/rustwide/cargo-home/registry/src/index.crates.io-6f17d22bba15001f/gchemol-core-0.1.7/src/molecule.rs:77:5 [INFO] [stdout] | [INFO] [stdout] 77 | pub fn new(name: &str) -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 86 | / pub fn from_atoms(atoms: T) -> Self [INFO] [stdout] 87 | | where [INFO] [stdout] 88 | | T: IntoIterator, [INFO] [stdout] 89 | | T::Item: Into, [INFO] [stdout] | |____________________________^ [INFO] [stdout] ... [INFO] [stdout] 100 | pub fn from_graph(graph: MolGraph) -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 105 | pub fn from_graph_raw(graph: MolGraph, atoms: impl IntoIterator) -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] = help: items from traits can only be used if the trait is in scope [INFO] [stdout] help: trait `FromFile` which provides `from_file` is implemented but not in scope; perhaps you want to import it [INFO] [stdout] | [INFO] [stdout] 2 + use gchemol::prelude::FromFile; [INFO] [stdout] | [INFO] [stdout] help: there is a method `to_file` with a similar name [INFO] [stdout] | [INFO] [stdout] 100 | let mol = Molecule::to_file(file)?; [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:16:33 [INFO] [stdout] | [INFO] [stdout] 16 | 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:27:32 [INFO] [stdout] | [INFO] [stdout] 27 | mol.atoms().map(|(_, a)| a.label().parse().unwrap()).collect() [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no function or associated item named `from_file` found for struct `gchemol::Molecule` in the current scope [INFO] [stdout] --> src/layers.rs:80:23 [INFO] [stdout] | [INFO] [stdout] 80 | let m = Molecule::from_file(f)?; [INFO] [stdout] | ^^^^^^^^^ function or associated item not found in `Molecule` [INFO] [stdout] | [INFO] [stdout] note: if you're trying to build a new `gchemol::Molecule` consider using one of the following associated functions: [INFO] [stdout] gchemol_core::data::::from_database [INFO] [stdout] gchemol::Molecule::new [INFO] [stdout] gchemol::Molecule::from_atoms [INFO] [stdout] gchemol::Molecule::from_graph [INFO] [stdout] gchemol::Molecule::from_graph_raw [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-6f17d22bba15001f/gchemol-core-0.1.7/src/data.rs:264:5 [INFO] [stdout] | [INFO] [stdout] 264 | pub fn from_database(name: &str) -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] ::: /opt/rustwide/cargo-home/registry/src/index.crates.io-6f17d22bba15001f/gchemol-core-0.1.7/src/molecule.rs:77:5 [INFO] [stdout] | [INFO] [stdout] 77 | pub fn new(name: &str) -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 86 | / pub fn from_atoms(atoms: T) -> Self [INFO] [stdout] 87 | | where [INFO] [stdout] 88 | | T: IntoIterator, [INFO] [stdout] 89 | | T::Item: Into, [INFO] [stdout] | |____________________________^ [INFO] [stdout] ... [INFO] [stdout] 100 | pub fn from_graph(graph: MolGraph) -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 105 | pub fn from_graph_raw(graph: MolGraph, atoms: impl IntoIterator) -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] = help: items from traits can only be used if the trait is in scope [INFO] [stdout] help: trait `FromFile` which provides `from_file` is implemented but not in scope; perhaps you want to import it [INFO] [stdout] | [INFO] [stdout] 2 + use gchemol::prelude::FromFile; [INFO] [stdout] | [INFO] [stdout] help: there is a method `to_file` with a similar name [INFO] [stdout] | [INFO] [stdout] 80 | let m = Molecule::to_file(f)?; [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> { [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] error: aborting due to 2 previous errors; 3 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0599`. [INFO] [stdout] [INFO] [stderr] error: could not compile `spdkit-surface` (lib test) due to 3 previous errors; 3 warnings emitted [INFO] [stderr] error: failed to check after updating to 2024 [INFO] [stderr] [INFO] [stderr] Caused by: [INFO] [stderr] process didn't exit successfully: `cargo check --frozen --all --all-targets --message-format=json` (exit status: 101) [INFO] running `Command { std: "docker" "inspect" "c1e33d31ef0b368e5f932d34491e27c88bbc25e88fdd6b0a41bd4a60ad4d490b", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "c1e33d31ef0b368e5f932d34491e27c88bbc25e88fdd6b0a41bd4a60ad4d490b", kill_on_drop: false }` [INFO] [stdout] c1e33d31ef0b368e5f932d34491e27c88bbc25e88fdd6b0a41bd4a60ad4d490b