[INFO] fetching crate gchemol-geometry 0.0.39...
[INFO] checking gchemol-geometry-0.0.39 against try#a7a572ce3edd6d476191fbfe92c9c1986e009b34 for pr-87190-3
[INFO] extracting crate gchemol-geometry 0.0.39 into /workspace/builds/worker-5/source
[INFO] validating manifest of crates.io crate gchemol-geometry 0.0.39 on toolchain a7a572ce3edd6d476191fbfe92c9c1986e009b34
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking crates.io crate gchemol-geometry 0.0.39
[INFO] finished tweaking crates.io crate gchemol-geometry 0.0.39
[INFO] tweaked toml for crates.io crate gchemol-geometry 0.0.39 written to /workspace/builds/worker-5/source/Cargo.toml
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update", kill_on_drop: false }`
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/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@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] c494bfd7258330c4c9b451d3d2eb3f2712a795809f079691f2159b318f47d605
[INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
[INFO] running `Command { std: "docker" "start" "-a" "c494bfd7258330c4c9b451d3d2eb3f2712a795809f079691f2159b318f47d605", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "c494bfd7258330c4c9b451d3d2eb3f2712a795809f079691f2159b318f47d605", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "c494bfd7258330c4c9b451d3d2eb3f2712a795809f079691f2159b318f47d605", kill_on_drop: false }`
[INFO] [stdout] c494bfd7258330c4c9b451d3d2eb3f2712a795809f079691f2159b318f47d605
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/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" "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@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
[INFO] [stdout] 6b5acf95fd85d3c411f78765667c2ffee4217a6e3c14eff7f87fbea992b2618b
[INFO] running `Command { std: "docker" "start" "-a" "6b5acf95fd85d3c411f78765667c2ffee4217a6e3c14eff7f87fbea992b2618b", kill_on_drop: false }`
[INFO] [stderr] Copying to /tmp/fixit
[INFO] [stderr] Running `cargo fix --edition`
[INFO] [stderr] note: Switching to Edition 2021 will enable the use of the version 2 feature resolver in Cargo.
[INFO] [stderr] This may cause some dependencies to be built with fewer features enabled than previously.
[INFO] [stderr] More information about the resolver changes may be found at https://doc.rust-lang.org/nightly/edition-guide/rust-2021/default-cargo-resolver.html
[INFO] [stderr] When building the following dependencies, the given features will no longer be used:
[INFO] [stderr] 
[INFO] [stderr]   approx v0.3.2: default, std
[INFO] [stderr] 
[INFO] [stderr]    Compiling libm v0.2.1
[INFO] [stderr]     Checking ppv-lite86 v0.2.10
[INFO] [stderr]     Checking remove_dir_all v0.5.3
[INFO] [stderr]    Compiling num-traits v0.2.14
[INFO] [stderr]    Compiling num-complex v0.2.4
[INFO] [stderr]    Compiling num-integer v0.1.44
[INFO] [stderr]    Compiling num-rational v0.2.4
[INFO] [stderr]     Checking getrandom v0.1.16
[INFO] [stderr]     Checking getrandom v0.2.3
[INFO] [stderr]     Checking generic-array v0.13.3
[INFO] [stderr]     Checking gchemol-gut v0.1.7
[INFO] [stderr]     Checking rand_core v0.5.1
[INFO] [stderr]     Checking rand_core v0.6.3
[INFO] [stderr]     Checking rand_chacha v0.2.2
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]     Checking rand v0.7.3
[INFO] [stderr]     Checking rand v0.8.4
[INFO] [stderr]     Checking tempfile v3.2.0
[INFO] [stderr]     Checking approx v0.3.2
[INFO] [stderr]     Checking rand_distr v0.2.2
[INFO] [stderr]     Checking alga v0.9.3
[INFO] [stderr]     Checking nalgebra v0.20.0
[INFO] [stderr]     Checking vecfx v0.1.2
[INFO] [stderr]     Checking gchemol-geometry v0.0.39 (/tmp/fixit)
[INFO] [stderr]    Migrating src/lib.rs from 2018 edition to 2021
[INFO] [stderr]        Fixed src/random.rs (1 fix)
[INFO] [stdout] error[E0425]: cannot find function `euclidean_distance` in this scope
[INFO] [stdout]    --> src/random.rs:146:22
[INFO] [stdout]     |
[INFO] [stdout] 146 |             let d1 = euclidean_distance(points[i], points[j]);
[INFO] [stdout]     |                      ^^^^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this function
[INFO] [stdout]     |
[INFO] [stdout] 4   | use crate::base::euclidean_distance;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function `euclidean_distance` in this scope
[INFO] [stdout]    --> src/random.rs:147:22
[INFO] [stdout]     |
[INFO] [stdout] 147 |             let d2 = euclidean_distance(rpoints[i], rpoints[j]);
[INFO] [stdout]     |                      ^^^^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this function
[INFO] [stdout]     |
[INFO] [stdout] 4   | use crate::base::euclidean_distance;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `prepare_test_data`
[INFO] [stdout]    --> src/alignment/qcprot.rs:460:15
[INFO] [stdout]     |
[INFO] [stdout] 460 | pub(crate) fn prepare_test_data() -> (Vec<[f64; 3]>, Vec<[f64; 3]>, Vec<f64>) {
[INFO] [stdout]     |               ^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `euclidean_distance`
[INFO] [stdout]   --> src/base.rs:13:8
[INFO] [stdout]    |
[INFO] [stdout] 13 | pub fn euclidean_distance(p1: [f64; 3], p2: [f64; 3]) -> f64 {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `weighted_center_of_geometry`
[INFO] [stdout]   --> src/base.rs:24:8
[INFO] [stdout]    |
[INFO] [stdout] 24 | pub fn weighted_center_of_geometry(positions: &[[f64; 3]], weights: &[f64]) -> Result<Vector3f> {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type alias is never used: `Point3D`
[INFO] [stdout]   --> src/random.rs:17:1
[INFO] [stdout]    |
[INFO] [stdout] 17 | type Point3D = [f64; 3];
[INFO] [stdout]    | ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type alias is never used: `Points`
[INFO] [stdout]   --> src/random.rs:18:1
[INFO] [stdout]    |
[INFO] [stdout] 18 | type Points = Vec<Point3D>;
[INFO] [stdout]    | ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `rand_point_within_sphere`
[INFO] [stdout]   --> src/random.rs:24:8
[INFO] [stdout]    |
[INFO] [stdout] 24 | pub fn rand_point_within_sphere(radius: f64) -> Point3D {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `rand_point_on_sphere`
[INFO] [stdout]   --> src/random.rs:49:8
[INFO] [stdout]    |
[INFO] [stdout] 49 | pub fn rand_point_on_sphere(radius: f64) -> Point3D {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `rand_points_within_sphere`
[INFO] [stdout]   --> src/random.rs:76:8
[INFO] [stdout]    |
[INFO] [stdout] 76 | pub fn rand_points_within_sphere(radius: f64, npts: usize) -> Points {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `rand_rotate`
[INFO] [stdout]    --> src/random.rs:102:8
[INFO] [stdout]     |
[INFO] [stdout] 102 | pub fn rand_rotate(points: &Points) -> Points {
[INFO] [stdout]     |        ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type alias is never used: `Point3`
[INFO] [stdout]   --> src/transform.rs:15:1
[INFO] [stdout]    |
[INFO] [stdout] 15 | type Point3 = [f64; 3];
[INFO] [stdout]    | ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type alias is never used: `Points`
[INFO] [stdout]   --> src/transform.rs:16:1
[INFO] [stdout]    |
[INFO] [stdout] 16 | type Points = Vec<Point3>;
[INFO] [stdout]    | ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `translate`
[INFO] [stdout]   --> src/transform.rs:19:8
[INFO] [stdout]    |
[INFO] [stdout] 19 | pub fn translate(points: &mut Points, loc: Point3) {
[INFO] [stdout]    |        ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `close_contact`
[INFO] [stdout]   --> src/transform.rs:28:8
[INFO] [stdout]    |
[INFO] [stdout] 28 | pub fn close_contact(points: &Points) -> bool {
[INFO] [stdout]    |        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `get_distance_matrix`
[INFO] [stdout]   --> src/transform.rs:50:8
[INFO] [stdout]    |
[INFO] [stdout] 50 | pub fn get_distance_matrix(points: &[Point3]) -> Vec<Vec<f64>> {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `rotate_about_x_axis`
[INFO] [stdout]   --> src/transform.rs:68:8
[INFO] [stdout]    |
[INFO] [stdout] 68 | pub fn rotate_about_x_axis(points: &Points, angle: f64, center: Point3) -> Points {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `mirror_invert`
[INFO] [stdout]   --> src/transform.rs:84:8
[INFO] [stdout]    |
[INFO] [stdout] 84 | pub fn mirror_invert(positions: &[[f64; 3]]) -> Vector3fVec {
[INFO] [stdout]    |        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `point_invert`
[INFO] [stdout]   --> src/transform.rs:91:8
[INFO] [stdout]    |
[INFO] [stdout] 91 | pub fn point_invert(positions: &[[f64; 3]]) -> Vector3fVec {
[INFO] [stdout]    |        ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 17 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 2 previous errors
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0425`.
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `gchemol-geometry` due to 3 previous errors
[INFO] [stderr] error: failed to migrate to next edition
[INFO] [stderr] 
[INFO] [stderr] Caused by:
[INFO] [stderr]   process didn't exit successfully: `cargo fix --edition --allow-no-vcs --allow-dirty --frozen --all --all-targets --message-format=json` (exit status: 101)
[INFO] running `Command { std: "docker" "inspect" "6b5acf95fd85d3c411f78765667c2ffee4217a6e3c14eff7f87fbea992b2618b", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "6b5acf95fd85d3c411f78765667c2ffee4217a6e3c14eff7f87fbea992b2618b", kill_on_drop: false }`
[INFO] [stdout] 6b5acf95fd85d3c411f78765667c2ffee4217a6e3c14eff7f87fbea992b2618b