[INFO] fetching crate pdbrust 0.7.0... [INFO] testing pdbrust-0.7.0 against master#562dee4820c458d823175268e41601d4c060588a for pr-154210-1 [INFO] extracting crate pdbrust 0.7.0 into /workspace/builds/worker-3-tc1/source [INFO] started tweaking crates.io crate pdbrust 0.7.0 [INFO] removed 0 missing examples [INFO] removed 0 missing tests [INFO] finished tweaking crates.io crate pdbrust 0.7.0 [INFO] tweaked toml for crates.io crate pdbrust 0.7.0 written to /workspace/builds/worker-3-tc1/source/Cargo.toml [INFO] validating manifest of crates.io crate pdbrust 0.7.0 on toolchain 562dee4820c458d823175268e41601d4c060588a [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+562dee4820c458d823175268e41601d4c060588a" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate crates.io crate pdbrust 0.7.0 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" "+562dee4820c458d823175268e41601d4c060588a" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded once_cell v1.21.1 [INFO] [stderr] Downloaded codecov v0.4.0 [INFO] [stderr] Downloaded hermit-abi v0.5.0 [INFO] [stderr] Downloaded wide v0.7.32 [INFO] [stderr] Downloaded half v2.5.0 [INFO] [stderr] Downloaded matrixmultiply v0.3.9 [INFO] [stderr] Downloaded bytemuck v1.22.0 [INFO] [stderr] Downloaded clap v4.5.32 [INFO] [stderr] Downloaded flate2 v1.1.5 [INFO] [stderr] Downloaded zerocopy-derive v0.8.24 [INFO] [stderr] Downloaded cc v1.2.17 [INFO] [stderr] Downloaded h2 v0.3.26 [INFO] [stderr] Downloaded clap_builder v4.5.32 [INFO] [stderr] Downloaded zerocopy v0.8.24 [INFO] [stderr] Downloaded rustix v1.0.3 [INFO] [stderr] Downloaded linux-raw-sys v0.9.3 [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" 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"770eb8775b7b472e08bf34bc65a081bce9ecbe7000d21f6a7607590029882269", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "770eb8775b7b472e08bf34bc65a081bce9ecbe7000d21f6a7607590029882269", kill_on_drop: false }` [INFO] [stdout] 770eb8775b7b472e08bf34bc65a081bce9ecbe7000d21f6a7607590029882269 [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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+562dee4820c458d823175268e41601d4c060588a" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 382772500cf0b1d78cc86c31e0a548c65026caa06d2a15ab7a7360c51706b73e [INFO] running `Command { std: "docker" "start" "-a" "382772500cf0b1d78cc86c31e0a548c65026caa06d2a15ab7a7360c51706b73e", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.94 [INFO] [stderr] Compiling itertools v0.12.1 [INFO] [stderr] Compiling quote v1.0.40 [INFO] [stderr] Compiling syn v2.0.100 [INFO] [stderr] Compiling thiserror-impl v1.0.69 [INFO] [stderr] Compiling thiserror v1.0.69 [INFO] [stderr] Compiling pdbrust v0.7.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 6.92s [INFO] running `Command { std: "docker" "inspect" "382772500cf0b1d78cc86c31e0a548c65026caa06d2a15ab7a7360c51706b73e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "382772500cf0b1d78cc86c31e0a548c65026caa06d2a15ab7a7360c51706b73e", kill_on_drop: false }` [INFO] [stdout] 382772500cf0b1d78cc86c31e0a548c65026caa06d2a15ab7a7360c51706b73e [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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+562dee4820c458d823175268e41601d4c060588a" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 09f3a2ed25a8b8012c16eca35f4032a3cff3bb93b72801b7b6f683fb619055da [INFO] running `Command { std: "docker" "start" "-a" "09f3a2ed25a8b8012c16eca35f4032a3cff3bb93b72801b7b6f683fb619055da", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.171 [INFO] [stderr] Compiling autocfg v1.4.0 [INFO] [stderr] Compiling stable_deref_trait v1.2.0 [INFO] [stderr] Compiling once_cell v1.21.1 [INFO] [stderr] Compiling writeable v0.5.5 [INFO] [stderr] Compiling bitflags v2.9.0 [INFO] [stderr] Compiling litemap v0.7.5 [INFO] [stderr] Compiling cc 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[stderr] Compiling tokio-util v0.7.14 [INFO] [stderr] Compiling zerovec-derive v0.10.3 [INFO] [stderr] Compiling displaydoc v0.2.5 [INFO] [stderr] Compiling icu_provider_macros v1.5.0 [INFO] [stderr] Compiling serde_derive v1.0.219 [INFO] [stderr] Compiling openssl-macros v0.1.1 [INFO] [stderr] Compiling thiserror-impl v1.0.69 [INFO] [stderr] Compiling h2 v0.3.26 [INFO] [stderr] Compiling zerofrom-derive v0.1.6 [INFO] [stderr] Compiling yoke-derive v0.7.5 [INFO] [stderr] Compiling thiserror v1.0.69 [INFO] [stderr] Compiling pdbrust v0.7.0 (/opt/rustwide/workdir) [INFO] [stderr] Compiling zerofrom v0.1.6 [INFO] [stderr] Compiling yoke v0.7.5 [INFO] [stderr] Compiling zerovec v0.10.4 [INFO] [stderr] Compiling tinystr v0.7.6 [INFO] [stderr] Compiling icu_collections v1.5.0 [INFO] [stderr] Compiling icu_locid v1.5.0 [INFO] [stderr] Compiling icu_provider v1.5.0 [INFO] [stderr] Compiling icu_locid_transform v1.5.0 [INFO] [stderr] Compiling hyper v0.14.32 [INFO] [stderr] Compiling tokio-native-tls v0.3.1 [INFO] [stderr] Compiling icu_properties v1.5.1 [INFO] [stderr] Compiling serde_urlencoded v0.7.1 [INFO] [stderr] Compiling ciborium v0.2.2 [INFO] [stderr] Compiling hyper-tls v0.5.0 [INFO] [stderr] Compiling icu_normalizer v1.5.0 [INFO] [stderr] Compiling tinytemplate v1.2.1 [INFO] [stderr] Compiling idna_adapter v1.2.0 [INFO] [stderr] Compiling idna v1.0.3 [INFO] [stderr] Compiling criterion v0.5.1 [INFO] [stderr] Compiling url v2.5.4 [INFO] [stderr] Compiling reqwest v0.11.27 [INFO] [stderr] Compiling codecov v0.4.0 [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:25:29 [INFO] [stdout] | [INFO] [stdout] 25 | let chain_a = structure.select("chain A")?; [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:29:30 [INFO] [stdout] | [INFO] [stdout] 29 | let ca_atoms = structure.select("name CA")?; [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:33:34 [INFO] [stdout] | [INFO] [stdout] 33 | let met_residues = structure.select("resname MET")?; [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:37:26 [INFO] [stdout] | [INFO] [stdout] 37 | let res1 = structure.select("resid 1")?; [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:41:31 [INFO] [stdout] | [INFO] [stdout] 41 | let res_range = structure.select("resid 1:10")?; [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:45:31 [INFO] [stdout] | [INFO] [stdout] 45 | let nitrogens = structure.select("element N")?; [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:54:30 [INFO] [stdout] | [INFO] [stdout] 54 | let backbone = structure.select("backbone")?; [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:57:29 [INFO] [stdout] | [INFO] [stdout] 57 | let protein = structure.select("protein")?; [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:60:31 [INFO] [stdout] | [INFO] [stdout] 60 | let all_atoms = structure.select("all")?; [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `pdbrust::summary` [INFO] [stdout] --> examples/batch_processing.rs:15:14 [INFO] [stdout] | [INFO] [stdout] 15 | use pdbrust::summary::{StructureSummary, batch_summarize, summaries_to_csv}; [INFO] [stdout] | ^^^^^^^ could not find `summary` in `pdbrust` [INFO] [stdout] | [INFO] [stdout] note: found an item that was configured out [INFO] [stdout] --> src/lib.rs:308:9 [INFO] [stdout] | [INFO] [stdout] 307 | #[cfg(feature = "summary")] [INFO] [stdout] | ------------------- the item is gated behind the `summary` feature [INFO] [stdout] 308 | pub mod summary; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:70:32 [INFO] [stdout] | [INFO] [stdout] 70 | let chain_a_ca = structure.select("chain A and name CA")?; [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:74:32 [INFO] [stdout] | [INFO] [stdout] 74 | let met_or_gln = structure.select("resname MET or resname GLN")?; [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:81:34 [INFO] [stdout] | [INFO] [stdout] 81 | let not_hydrogen = structure.select("not hydrogen")?; [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved import `pdbrust::rcsb` [INFO] [stdout] --> examples/async_download_demo.rs:13:14 [INFO] [stdout] | [INFO] [stdout] 13 | use pdbrust::rcsb::{ [INFO] [stdout] | ^^^^ could not find `rcsb` in `pdbrust` [INFO] [stdout] | [INFO] [stdout] note: found an item that was configured out [INFO] [stdout] --> src/lib.rs:311:9 [INFO] [stdout] | [INFO] [stdout] 310 | #[cfg(feature = "rcsb")] [INFO] [stdout] | ---------------- the item is gated behind the `rcsb` feature [INFO] [stdout] 311 | pub mod rcsb; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0433]: cannot find module or crate `tokio` in this scope [INFO] [stdout] --> examples/async_download_demo.rs:19:3 [INFO] [stdout] | [INFO] [stdout] 19 | #[tokio::main] [INFO] [stdout] | ^^^^^ use of unresolved module or unlinked crate `tokio` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:85:30 [INFO] [stdout] | [INFO] [stdout] 85 | let complex1 = structure.select("(resid 1 or resid 2) and name CA")?; [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:97:33 [INFO] [stdout] | [INFO] [stdout] 97 | let low_bfactor = structure.select("bfactor < 20.0")?; [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:100:36 [INFO] [stdout] | [INFO] [stdout] 100 | let high_occupancy = structure.select("occupancy >= 0.5")?; [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:110:30 [INFO] [stdout] | [INFO] [stdout] 110 | let complex2 = structure.select("chain A and backbone and bfactor < 30.0")?; [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:117:29 [INFO] [stdout] | [INFO] [stdout] 117 | let termini = structure.select("(resid 1:10 or resid 67:76) and name CA")?; [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `is_predicted` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/validate_new_files.rs:62:34 [INFO] [stdout] | [INFO] [stdout] 62 | let is_predicted = structure.is_predicted(); [INFO] [stdout] | ^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `plddt_mean` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/validate_new_files.rs:72:32 [INFO] [stdout] | [INFO] [stdout] 72 | let plddt_mean = structure.plddt_mean(); [INFO] [stdout] | ^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:124:33 [INFO] [stdout] | [INFO] [stdout] 124 | let heavy_atoms = structure.select("protein and not hydrogen")?; [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `keep_only_chain` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/filtering_demo.rs:29:29 [INFO] [stdout] | [INFO] [stdout] 29 | let chain_a = structure.keep_only_chain("A"); [INFO] [stdout] | ^^^^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `keep_only_ca` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/filtering_demo.rs:36:29 [INFO] [stdout] | [INFO] [stdout] 36 | let ca_only = structure.keep_only_ca(); [INFO] [stdout] | ^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:137:35 [INFO] [stdout] | [INFO] [stdout] 137 | let ca_via_select = structure.select("name CA")?.get_num_atoms(); [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `keep_only_backbone` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/filtering_demo.rs:40:30 [INFO] [stdout] | [INFO] [stdout] 40 | let backbone = structure.keep_only_backbone(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `get_ca_coords` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/filtering_demo.rs:47:31 [INFO] [stdout] | [INFO] [stdout] 47 | let ca_coords = structure.get_ca_coords(None); [INFO] [stdout] | ^^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `get_ca_coords` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/filtering_demo.rs:51:39 [INFO] [stdout] | [INFO] [stdout] 51 | let chain_a_ca_coords = structure.get_ca_coords(Some("A")); [INFO] [stdout] | ^^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `per_residue_plddt` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/validate_new_files.rs:82:33 [INFO] [stdout] | [INFO] [stdout] 82 | let per_residue = structure.per_residue_plddt(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `remove_ligands` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/filtering_demo.rs:58:32 [INFO] [stdout] | [INFO] [stdout] 58 | let no_ligands = structure.remove_ligands(); [INFO] [stdout] | ^^^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `remove_hydrogens` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/filtering_demo.rs:66:34 [INFO] [stdout] | [INFO] [stdout] 66 | let no_hydrogens = structure.remove_hydrogens(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `keep_only_ca` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:138:35 [INFO] [stdout] | [INFO] [stdout] 138 | let ca_via_method = structure.keep_only_ca().get_num_atoms(); [INFO] [stdout] | ^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `remove_ligands` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/filtering_demo.rs:78:10 [INFO] [stdout] | [INFO] [stdout] 77 | let cleaned = structure [INFO] [stdout] | ___________________- [INFO] [stdout] 78 | | .remove_ligands() [INFO] [stdout] | | -^^^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] | |_________| [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `remove_ligands` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/filtering_demo.rs:87:29 [INFO] [stdout] | [INFO] [stdout] 87 | let ca_repr = structure.remove_ligands().keep_only_ca(); [INFO] [stdout] | ^^^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `get_centroid` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/filtering_demo.rs:100:32 [INFO] [stdout] | [INFO] [stdout] 100 | let (cx, cy, cz) = mutable.get_centroid(); [INFO] [stdout] | ^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `center_structure` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/filtering_demo.rs:104:13 [INFO] [stdout] | [INFO] [stdout] 104 | mutable.center_structure(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:147:35 [INFO] [stdout] | [INFO] [stdout] 147 | let bb_via_select = structure.select("backbone")?.get_num_atoms(); [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `get_centroid` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/filtering_demo.rs:105:32 [INFO] [stdout] | [INFO] [stdout] 105 | let (cx, cy, cz) = mutable.get_centroid(); [INFO] [stdout] | ^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `keep_only_backbone` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:148:35 [INFO] [stdout] | [INFO] [stdout] 148 | let bb_via_method = structure.keep_only_backbone().get_num_atoms(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `renumber_atoms` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/filtering_demo.rs:109:13 [INFO] [stdout] | [INFO] [stdout] 109 | mutable.renumber_atoms(); [INFO] [stdout] | ^^^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `select` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:157:38 [INFO] [stdout] | [INFO] [stdout] 157 | let chain_via_select = structure.select("chain A")?.get_num_atoms(); [INFO] [stdout] | ^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `keep_only_chain` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:158:38 [INFO] [stdout] | [INFO] [stdout] 158 | let chain_via_method = structure.keep_only_chain("A").get_num_atoms(); [INFO] [stdout] | ^^^^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `normalize_chain_ids` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/filtering_demo.rs:118:17 [INFO] [stdout] | [INFO] [stdout] 118 | multi_chain.normalize_chain_ids(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] help: there is a method `get_chain_ids` with a similar name [INFO] [stdout] | [INFO] [stdout] 118 - multi_chain.normalize_chain_ids(); [INFO] [stdout] 118 + multi_chain.get_chain_ids(); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no function or associated item named `validate_selection` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:173:34 [INFO] [stdout] | [INFO] [stdout] 173 | match pdbrust::PdbStructure::validate_selection("chain A and name CA") { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ function or associated item not found in `PdbStructure` [INFO] [stdout] | [INFO] [stdout] note: if you're trying to build a new `PdbStructure` consider using one of the following associated functions: [INFO] [stdout] PdbStructure::new [INFO] [stdout] PdbStructure::from_file [INFO] [stdout] --> src/core/pdb.rs:98:5 [INFO] [stdout] | [INFO] [stdout] 98 | pub fn new() -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 126 | pub fn from_file>(path: P) -> Result { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `low_confidence_regions` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/validate_new_files.rs:92:30 [INFO] [stdout] | [INFO] [stdout] 92 | let low_conf = structure.low_confidence_regions(70.0); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no function or associated item named `validate_selection` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:179:34 [INFO] [stdout] | [INFO] [stdout] 179 | match pdbrust::PdbStructure::validate_selection("") { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ function or associated item not found in `PdbStructure` [INFO] [stdout] | [INFO] [stdout] note: if you're trying to build a new `PdbStructure` consider using one of the following associated functions: [INFO] [stdout] PdbStructure::new [INFO] [stdout] PdbStructure::from_file [INFO] [stdout] --> src/core/pdb.rs:98:5 [INFO] [stdout] | [INFO] [stdout] 98 | pub fn new() -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 126 | pub fn from_file>(path: P) -> Result { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `reindex_residues` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/filtering_demo.rs:123:15 [INFO] [stdout] | [INFO] [stdout] 123 | reindexed.reindex_residues(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] help: there is a method `get_residues` with a similar name [INFO] [stdout] | [INFO] [stdout] 123 - reindexed.reindex_residues(); [INFO] [stdout] 123 + reindexed.get_residues(); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0599`. [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `high_confidence_regions` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/validate_new_files.rs:93:31 [INFO] [stdout] | [INFO] [stdout] 93 | let high_conf = structure.high_confidence_regions(90.0); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no function or associated item named `validate_selection` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:185:34 [INFO] [stdout] | [INFO] [stdout] 185 | match pdbrust::PdbStructure::validate_selection("(chain A and name CA") { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ function or associated item not found in `PdbStructure` [INFO] [stdout] | [INFO] [stdout] note: if you're trying to build a new `PdbStructure` consider using one of the following associated functions: [INFO] [stdout] PdbStructure::new [INFO] [stdout] PdbStructure::from_file [INFO] [stdout] --> src/core/pdb.rs:98:5 [INFO] [stdout] | [INFO] [stdout] 98 | pub fn new() -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 126 | pub fn from_file>(path: P) -> Result { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: could not compile `pdbrust` (example "filtering_demo") due to 15 previous errors [INFO] [stderr] warning: build failed, waiting for other jobs to finish... [INFO] [stdout] error[E0599]: no function or associated item named `validate_selection` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/selection_demo.rs:191:34 [INFO] [stdout] | [INFO] [stdout] 191 | match pdbrust::PdbStructure::validate_selection("invalid_keyword") { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ function or associated item not found in `PdbStructure` [INFO] [stdout] | [INFO] [stdout] note: if you're trying to build a new `PdbStructure` consider using one of the following associated functions: [INFO] [stdout] PdbStructure::new [INFO] [stdout] PdbStructure::from_file [INFO] [stdout] --> src/core/pdb.rs:98:5 [INFO] [stdout] | [INFO] [stdout] 98 | pub fn new() -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 126 | pub fn from_file>(path: P) -> Result { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `plddt_distribution` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/validate_new_files.rs:102:59 [INFO] [stdout] | [INFO] [stdout] 102 | let (very_high, confident, low, very_low) = structure.plddt_distribution(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0599`. [INFO] [stdout] [INFO] [stdout] error[E0752]: `main` function is not allowed to be `async` [INFO] [stdout] --> examples/async_download_demo.rs:20:1 [INFO] [stdout] | [INFO] [stdout] 20 | async fn main() -> Result<(), Box> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ `main` function is not allowed to be `async` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `binding_site` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/validate_new_files.rs:142:35 [INFO] [stdout] | [INFO] [stdout] 142 | if let Some(site) = structure.binding_site("MK1", 5.0) { [INFO] [stdout] | ^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `ligand_interactions` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/validate_new_files.rs:164:38 [INFO] [stdout] | [INFO] [stdout] 164 | if let Some(profile) = structure.ligand_interactions("MK1") { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0432, E0433, E0752. [INFO] [stdout] [INFO] [stdout] For more information about an error, try `rustc --explain E0432`. [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `all_ligand_interactions` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/validate_new_files.rs:202:29 [INFO] [stdout] | [INFO] [stdout] 202 | let all_lig = structure.all_ligand_interactions(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: could not compile `pdbrust` (example "selection_demo") due to 28 previous errors [INFO] [stdout] error[E0599]: no method named `has_multiple_models` found for struct `PdbStructure` in the current scope [INFO] [stdout] --> examples/validate_new_files.rs:290:34 [INFO] [stdout] | [INFO] [stdout] 290 | let has_multiple = structure.has_multiple_models(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ method not found in `PdbStructure` [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: could not compile `pdbrust` (example "async_download_demo") due to 3 previous errors [INFO] [stdout] For more information about this error, try `rustc --explain E0432`. [INFO] [stdout] [INFO] [stderr] error: could not compile `pdbrust` (example "batch_processing") due to 1 previous error [INFO] [stdout] For more information about this error, try `rustc --explain E0599`. [INFO] [stdout] [INFO] [stderr] error: could not compile `pdbrust` (example "validate_new_files") due to 10 previous errors [INFO] running `Command { std: "docker" "inspect" "09f3a2ed25a8b8012c16eca35f4032a3cff3bb93b72801b7b6f683fb619055da", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "09f3a2ed25a8b8012c16eca35f4032a3cff3bb93b72801b7b6f683fb619055da", kill_on_drop: false }` [INFO] [stdout] 09f3a2ed25a8b8012c16eca35f4032a3cff3bb93b72801b7b6f683fb619055da