[INFO] fetching crate gchemol-geometry 0.1.1...
[INFO] checking gchemol-geometry-0.1.1 against master#3139ff09e9d07f7700f8d15ed25a231e29c43627 for pr-121848-3
[INFO] extracting crate gchemol-geometry 0.1.1 into /workspace/builds/worker-2-tc1/source
[INFO] validating manifest of crates.io crate gchemol-geometry 0.1.1 on toolchain 3139ff09e9d07f7700f8d15ed25a231e29c43627
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+3139ff09e9d07f7700f8d15ed25a231e29c43627" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking crates.io crate gchemol-geometry 0.1.1
[INFO] finished tweaking crates.io crate gchemol-geometry 0.1.1
[INFO] tweaked toml for crates.io crate gchemol-geometry 0.1.1 written to /workspace/builds/worker-2-tc1/source/Cargo.toml
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+3139ff09e9d07f7700f8d15ed25a231e29c43627" "generate-lockfile" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
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[INFO] [stdout] 8bacccaf4e42d5441241a6ecc3b5c1686c1ef7e1605d7f6604c9ade40d03cc13
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[INFO] [stdout] warning: unused import: `vecfx::*`
[INFO] [stdout]  --> src/alignment/quaternion.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use vecfx::*;
[INFO] [stdout]   |     ^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::base::euclidean_distance`
[INFO] [stdout]   --> src/random.rs:10:5
[INFO] [stdout]    |
[INFO] [stdout] 10 | use crate::base::euclidean_distance;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `alignment::Alignment`: use Superpose instead
[INFO] [stdout]   --> src/alignment.rs:97:10
[INFO] [stdout]    |
[INFO] [stdout] 97 | impl<'a> Alignment<'a> {
[INFO] [stdout]    |          ^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(deprecated)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `vecfx::*`
[INFO] [stdout]  --> src/alignment/quaternion.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use vecfx::*;
[INFO] [stdout]   |     ^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `alignment::Alignment`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:100:9
[INFO] [stdout]     |
[INFO] [stdout] 100 |         Alignment {
[INFO] [stdout]     |         ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::f64::consts::PI`
[INFO] [stdout]    --> src/traits.rs:133:9
[INFO] [stdout]     |
[INFO] [stdout] 133 |     use std::f64::consts::PI;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `alignment::Alignment`: use Superpose instead
[INFO] [stdout]   --> src/alignment.rs:97:10
[INFO] [stdout]    |
[INFO] [stdout] 97 | impl<'a> Alignment<'a> {
[INFO] [stdout]    |          ^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(deprecated)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `alignment::Alignment`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:100:9
[INFO] [stdout]     |
[INFO] [stdout] 100 |         Alignment {
[INFO] [stdout]     |         ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `alignment::Alignment::positions`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:101:13
[INFO] [stdout]     |
[INFO] [stdout] 101 |             positions,
[INFO] [stdout]     |             ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `alignment::Alignment::algorithm`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:102:13
[INFO] [stdout]     |
[INFO] [stdout] 102 |             algorithm: SuperpositionAlgo::default(),
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `alignment::Alignment::positions`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:114:20
[INFO] [stdout]     |
[INFO] [stdout] 114 |         let npts = self.positions.len();
[INFO] [stdout]     |                    ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `alignment::Alignment::positions`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:127:28
[INFO] [stdout]     |
[INFO] [stdout] 127 |             let dx = wi * (self.positions[i][0] - reference[i][0]);
[INFO] [stdout]     |                            ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `alignment::Alignment::positions`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:128:28
[INFO] [stdout]     |
[INFO] [stdout] 128 |             let dy = wi * (self.positions[i][1] - reference[i][1]);
[INFO] [stdout]     |                            ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `alignment::Alignment::positions`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:129:28
[INFO] [stdout]     |
[INFO] [stdout] 129 |             let dz = wi * (self.positions[i][2] - reference[i][2]);
[INFO] [stdout]     |                            ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `alignment::Alignment::algorithm`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:147:40
[INFO] [stdout]     |
[INFO] [stdout] 147 |         let (rmsd, trans, rot) = match self.algorithm {
[INFO] [stdout]     |                                        ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `alignment::Alignment::positions`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:148:94
[INFO] [stdout]     |
[INFO] [stdout] 148 |             SuperpositionAlgo::QCP => self::qcprot::calc_rmsd_rotational_matrix(&reference, &self.positions, weights),
[INFO] [stdout]     |                                                                                              ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `alignment::Alignment::positions`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:149:105
[INFO] [stdout]     |
[INFO] [stdout] 149 |             SuperpositionAlgo::Quaternion => self::quaternion::calc_rmsd_rotational_matrix(&reference, &self.positions, weights),
[INFO] [stdout]     |                                                                                                         ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `alignment::Alignment::positions`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:101:13
[INFO] [stdout]     |
[INFO] [stdout] 101 |             positions,
[INFO] [stdout]     |             ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `alignment::Alignment::algorithm`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:102:13
[INFO] [stdout]     |
[INFO] [stdout] 102 |             algorithm: SuperpositionAlgo::default(),
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `alignment::Alignment::positions`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:114:20
[INFO] [stdout]     |
[INFO] [stdout] 114 |         let npts = self.positions.len();
[INFO] [stdout]     |                    ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `alignment::Alignment::positions`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:127:28
[INFO] [stdout]     |
[INFO] [stdout] 127 |             let dx = wi * (self.positions[i][0] - reference[i][0]);
[INFO] [stdout]     |                            ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `alignment::Alignment::positions`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:128:28
[INFO] [stdout]     |
[INFO] [stdout] 128 |             let dy = wi * (self.positions[i][1] - reference[i][1]);
[INFO] [stdout]     |                            ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `alignment::Alignment::positions`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:129:28
[INFO] [stdout]     |
[INFO] [stdout] 129 |             let dz = wi * (self.positions[i][2] - reference[i][2]);
[INFO] [stdout]     |                            ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `alignment::Alignment::algorithm`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:147:40
[INFO] [stdout]     |
[INFO] [stdout] 147 |         let (rmsd, trans, rot) = match self.algorithm {
[INFO] [stdout]     |                                        ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `alignment::Alignment::positions`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:148:94
[INFO] [stdout]     |
[INFO] [stdout] 148 |             SuperpositionAlgo::QCP => self::qcprot::calc_rmsd_rotational_matrix(&reference, &self.positions, weights),
[INFO] [stdout]     |                                                                                              ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `alignment::Alignment::positions`: use Superpose instead
[INFO] [stdout]    --> src/alignment.rs:149:105
[INFO] [stdout]     |
[INFO] [stdout] 149 |             SuperpositionAlgo::Quaternion => self::quaternion::calc_rmsd_rotational_matrix(&reference, &self.positions, weights),
[INFO] [stdout]     |                                                                                                         ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/alignment/quaternion.rs:30:9
[INFO] [stdout]    |
[INFO] [stdout] 30 |     for mut v in vectors_ref.iter_mut() {
[INFO] [stdout]    |         ----^
[INFO] [stdout]    |         |
[INFO] [stdout]    |         help: remove this `mut`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_mut)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/alignment/quaternion.rs:33:9
[INFO] [stdout]    |
[INFO] [stdout] 33 |     for mut v in vectors_can.iter_mut() {
[INFO] [stdout]    |         ----^
[INFO] [stdout]    |         |
[INFO] [stdout]    |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `trans`
[INFO] [stdout]    --> src/alignment/qcprot.rs:487:16
[INFO] [stdout]     |
[INFO] [stdout] 487 |     let (rmsd, trans, rot) = calc_rmsd_rotational_matrix(&mut frag_a, &mut frag_b, Some(&weights));
[INFO] [stdout]     |                ^^^^^ help: if this is intentional, prefix it with an underscore: `_trans`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/alignment/quaternion.rs:30:9
[INFO] [stdout]    |
[INFO] [stdout] 30 |     for mut v in vectors_ref.iter_mut() {
[INFO] [stdout]    |         ----^
[INFO] [stdout]    |         |
[INFO] [stdout]    |         help: remove this `mut`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_mut)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/alignment/quaternion.rs:33:9
[INFO] [stdout]    |
[INFO] [stdout] 33 |     for mut v in vectors_can.iter_mut() {
[INFO] [stdout]    |         ----^
[INFO] [stdout]    |         |
[INFO] [stdout]    |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `prepare_test_data` is never used
[INFO] [stdout]    --> src/alignment/qcprot.rs:456:15
[INFO] [stdout]     |
[INFO] [stdout] 456 | 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 `translate` is never used
[INFO] [stdout]   --> src/transform.rs:14:8
[INFO] [stdout]    |
[INFO] [stdout] 14 | pub fn translate(points: &mut Points, loc: Coord3) {
[INFO] [stdout]    |        ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_distance_matrix` is never used
[INFO] [stdout]   --> src/transform.rs:23:8
[INFO] [stdout]    |
[INFO] [stdout] 23 | pub fn get_distance_matrix(points: &[Coord3]) -> Vec<Vec<f64>> {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `mirror_invert` is never used
[INFO] [stdout]   --> src/transform.rs:57:8
[INFO] [stdout]    |
[INFO] [stdout] 57 | pub fn mirror_invert(positions: &[[f64; 3]]) -> Vector3fVec {
[INFO] [stdout]    |        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `point_invert` is never used
[INFO] [stdout]   --> src/transform.rs:64:8
[INFO] [stdout]    |
[INFO] [stdout] 64 | pub fn point_invert(positions: &[[f64; 3]]) -> Vector3fVec {
[INFO] [stdout]    |        ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `t`
[INFO] [stdout]    --> src/alignment.rs:302:9
[INFO] [stdout]     |
[INFO] [stdout] 302 |     let t = Vector3f::from([0.423160235, 0.2715202, 0.0]);
[INFO] [stdout]     |         ^ help: if this is intentional, prefix it with an underscore: `_t`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 20 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `translate` is never used
[INFO] [stdout]   --> src/transform.rs:14:8
[INFO] [stdout]    |
[INFO] [stdout] 14 | pub fn translate(points: &mut Points, loc: Coord3) {
[INFO] [stdout]    |        ^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_distance_matrix` is never used
[INFO] [stdout]   --> src/transform.rs:23:8
[INFO] [stdout]    |
[INFO] [stdout] 23 | pub fn get_distance_matrix(points: &[Coord3]) -> Vec<Vec<f64>> {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `mirror_invert` is never used
[INFO] [stdout]   --> src/transform.rs:57:8
[INFO] [stdout]    |
[INFO] [stdout] 57 | pub fn mirror_invert(positions: &[[f64; 3]]) -> Vector3fVec {
[INFO] [stdout]    |        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `point_invert` is never used
[INFO] [stdout]   --> src/transform.rs:64:8
[INFO] [stdout]    |
[INFO] [stdout] 64 | pub fn point_invert(positions: &[[f64; 3]]) -> Vector3fVec {
[INFO] [stdout]    |        ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 21 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 11.10s
[INFO] running `Command { std: "docker" "inspect" "8bacccaf4e42d5441241a6ecc3b5c1686c1ef7e1605d7f6604c9ade40d03cc13", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "8bacccaf4e42d5441241a6ecc3b5c1686c1ef7e1605d7f6604c9ade40d03cc13", kill_on_drop: false }`
[INFO] [stdout] 8bacccaf4e42d5441241a6ecc3b5c1686c1ef7e1605d7f6604c9ade40d03cc13
