[INFO] fetching crate spdkit-surface 0.1.1... [INFO] checking spdkit-surface-0.1.1 against try#ccf408f4326a858c00dd845a64a86b16f360a801 for pr-129466-2 [INFO] extracting crate spdkit-surface 0.1.1 into /workspace/builds/worker-0-tc2/source [INFO] validating manifest of crates.io crate spdkit-surface 0.1.1 on toolchain ccf408f4326a858c00dd845a64a86b16f360a801 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ccf408f4326a858c00dd845a64a86b16f360a801" "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-0-tc2/source/Cargo.toml [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ccf408f4326a858c00dd845a64a86b16f360a801" "generate-lockfile" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Locking 209 packages to latest compatible versions [INFO] [stderr] Adding base64 v0.20.0 (available: v0.22.1) [INFO] [stderr] Adding chrono-tz v0.9.0 (available: v0.10.0) [INFO] [stderr] Adding chrono-tz-build v0.3.0 (available: v0.4.0) [INFO] [stderr] Adding env_logger v0.10.2 (available: v0.11.5) [INFO] [stderr] Adding fixedbitset v0.4.2 (available: v0.5.7) [INFO] [stderr] Adding gchemol-parser v0.4.6 (available: v0.5.1) [INFO] [stderr] Adding generic-array v0.14.7 (available: v1.1.0) [INFO] [stderr] Adding grep v0.2.13 (available: v0.3.2) [INFO] [stderr] Adding grep-printer v0.1.7 (available: v0.2.2) [INFO] [stderr] Adding handlebars v4.0.1 (available: v4.5.0) [INFO] [stderr] Adding hashbrown v0.12.3 (available: v0.14.5) [INFO] [stderr] Adding indexmap v1.9.3 (available: v2.5.0) [INFO] [stderr] Adding itertools v0.10.5 (available: v0.13.0) [INFO] 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(available: v0.58.0) [INFO] [stderr] Adding windows-sys v0.52.0 (available: v0.59.0) [INFO] [stderr] Adding winnow v0.5.40 (available: v0.6.20) [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ccf408f4326a858c00dd845a64a86b16f360a801" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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:ceb6ea022f8a89cebbe621bb4987e73a935bd40dfbb726f832cfff4742a5b95a" "/opt/rustwide/cargo-home/bin/cargo" "+ccf408f4326a858c00dd845a64a86b16f360a801" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 239ee0344add0624193eac9e4d0c6d793969cf3cc14eec803423289bddd0b7c8 [INFO] running `Command { std: "docker" "start" "-a" "239ee0344add0624193eac9e4d0c6d793969cf3cc14eec803423289bddd0b7c8", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "239ee0344add0624193eac9e4d0c6d793969cf3cc14eec803423289bddd0b7c8", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "239ee0344add0624193eac9e4d0c6d793969cf3cc14eec803423289bddd0b7c8", kill_on_drop: false }` [INFO] [stdout] 239ee0344add0624193eac9e4d0c6d793969cf3cc14eec803423289bddd0b7c8 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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:ceb6ea022f8a89cebbe621bb4987e73a935bd40dfbb726f832cfff4742a5b95a" "/opt/rustwide/cargo-home/bin/cargo" "+ccf408f4326a858c00dd845a64a86b16f360a801" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] be6846a1de49c0eb1caa06b331bbdfd380fe14d25d1d1dcfa28cf2c54ddb4f23 [INFO] running `Command { std: "docker" "start" "-a" "be6846a1de49c0eb1caa06b331bbdfd380fe14d25d1d1dcfa28cf2c54ddb4f23", kill_on_drop: false }` [INFO] [stderr] Copying to /tmp/fixit [INFO] [stderr] Running `cargo fix --edition` [INFO] [stderr] Migrating Cargo.toml from 2021 edition to 2024 [INFO] [stderr] Compiling libc v0.2.159 [INFO] [stderr] Checking aho-corasick v1.1.3 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Checking byteorder v1.5.0 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Checking bytemuck v1.18.0 [INFO] [stderr] Compiling syn v2.0.77 [INFO] [stderr] Checking grep-matcher v0.1.7 [INFO] [stderr] Compiling matrixmultiply v0.3.9 [INFO] [stderr] Checking winnow v0.5.40 [INFO] [stderr] Compiling phf_shared v0.11.2 [INFO] [stderr] Checking encoding_rs_io v0.1.7 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Checking clap_builder v4.5.18 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[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 v0.2.2 [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 grep v0.3.2 [INFO] [stderr] Checking grep-reader v0.1.3 [INFO] [stderr] Checking extxyz v0.2.0 [INFO] [stderr] Checking ordered-float v3.9.2 [INFO] [stderr] Checking rand_distr v0.4.3 [INFO] [stderr] Checking toml v0.7.8 [INFO] [stderr] Compiling phf_generator v0.11.2 [INFO] [stderr] Checking gchemol-graph v0.1.6 [INFO] [stderr] Compiling phf_codegen v0.11.2 [INFO] [stderr] Compiling chrono-tz-build v0.3.0 [INFO] [stderr] Checking gchemol-gut v0.4.4 [INFO] [stderr] Compiling chrono-tz v0.9.0 [INFO] [stderr] Checking gchemol-parser v0.4.6 [INFO] [stderr] Checking nalgebra v0.31.4 [INFO] [stderr] Checking tera v1.20.0 [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] [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] [stderr] Fixed src/layers.rs (3 fixes) [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] 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] [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: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 28.84s [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:81:23 [INFO] [stdout] | [INFO] [stdout] 81 | 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] 81 | 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" "be6846a1de49c0eb1caa06b331bbdfd380fe14d25d1d1dcfa28cf2c54ddb4f23", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "be6846a1de49c0eb1caa06b331bbdfd380fe14d25d1d1dcfa28cf2c54ddb4f23", kill_on_drop: false }` [INFO] [stdout] be6846a1de49c0eb1caa06b331bbdfd380fe14d25d1d1dcfa28cf2c54ddb4f23