[INFO] updating cached repository StephanHeijl/global-supertrees
[INFO] running `"git" "fetch" "--all"`
[INFO] [stdout] Fetching origin
[INFO] [stderr] From git://github.com/StephanHeijl/global-supertrees
[INFO] [stderr]  * branch            HEAD       -> FETCH_HEAD
[INFO] running `"git" "clone" "work/cache/sources/gh/StephanHeijl/global-supertrees" "work/ex/clippy-test-run/sources/stable/gh/StephanHeijl/global-supertrees"`
[INFO] [stderr] Cloning into 'work/ex/clippy-test-run/sources/stable/gh/StephanHeijl/global-supertrees'...
[INFO] [stderr] done.
[INFO] running `"git" "clone" "work/cache/sources/gh/StephanHeijl/global-supertrees" "work/ex/clippy-test-run/sources/stable+rustflags=-Dclippy%3A%3Ainto_iter_on_array/gh/StephanHeijl/global-supertrees"`
[INFO] [stderr] Cloning into 'work/ex/clippy-test-run/sources/stable+rustflags=-Dclippy%3A%3Ainto_iter_on_array/gh/StephanHeijl/global-supertrees'...
[INFO] [stderr] done.
[INFO] running `"git" "rev-parse" "HEAD"`
[INFO] [stdout] 6daceb7fd6152ba353f43af41e100f638990185a
[INFO] sha for GitHub repo StephanHeijl/global-supertrees: 6daceb7fd6152ba353f43af41e100f638990185a
[INFO] validating manifest of StephanHeijl/global-supertrees on toolchain stable
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+stable" "read-manifest" "--manifest-path" "Cargo.toml"`
[INFO] validating manifest of StephanHeijl/global-supertrees on toolchain stable+rustflags=-Dclippy::into_iter_on_array
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+stable" "read-manifest" "--manifest-path" "Cargo.toml"`
[INFO] started frobbing StephanHeijl/global-supertrees
[INFO] finished frobbing StephanHeijl/global-supertrees
[INFO] frobbed toml for StephanHeijl/global-supertrees written to work/ex/clippy-test-run/sources/stable/gh/StephanHeijl/global-supertrees/Cargo.toml
[INFO] started frobbing StephanHeijl/global-supertrees
[INFO] finished frobbing StephanHeijl/global-supertrees
[INFO] frobbed toml for StephanHeijl/global-supertrees written to work/ex/clippy-test-run/sources/stable+rustflags=-Dclippy%3A%3Ainto_iter_on_array/gh/StephanHeijl/global-supertrees/Cargo.toml
[INFO] crate StephanHeijl/global-supertrees has a lockfile. skipping
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+stable" "fetch" "--locked" "--manifest-path" "Cargo.toml"`
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+stable" "fetch" "--locked" "--manifest-path" "Cargo.toml"`
[INFO] linting StephanHeijl/global-supertrees against stable for clippy-test-run
[INFO] running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/clippy-test-run/worker-7/stable:/opt/crater/target:rw,Z" "-v" "/mnt/big/crater/work/ex/clippy-test-run/sources/stable/gh/StephanHeijl/global-supertrees:/opt/crater/workdir:ro,Z" "-v" "/mnt/big/crater/work/local/cargo-home:/opt/crater/cargo-home:ro,Z" "-v" "/mnt/big/crater/work/local/rustup-home:/opt/crater/rustup-home:ro,Z" "-e" "USER_ID=1000" "-e" "SOURCE_DIR=/opt/crater/workdir" "-e" "MAP_USER_ID=1000" "-e" "CARGO_TARGET_DIR=/opt/crater/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/crater/cargo-home" "-e" "RUSTUP_HOME=/opt/crater/rustup-home" "-w" "/opt/crater/workdir" "-m" "1536M" "--network" "none" "rustops/crates-build-env" "/opt/crater/cargo-home/bin/cargo" "+stable" "clippy" "--frozen" "--all" "--all-targets"`
[INFO] [stdout] b3d911d70bb51a84f5f02c79ac8f4b167314e9e2cdfeccff09bdb85a24f39847
[INFO] running `"docker" "start" "-a" "b3d911d70bb51a84f5f02c79ac8f4b167314e9e2cdfeccff09bdb85a24f39847"`
[INFO] [stderr]     Checking itertools v0.7.8
[INFO] [stderr]     Checking ndarray v0.11.2
[INFO] [stderr]     Checking newick v0.1.0 (/opt/crater/workdir)
[INFO] [stderr] warning: redundant field names in struct initialization
[INFO] [stderr]    --> src/tree.rs:234:13
[INFO] [stderr]     |
[INFO] [stderr] 234 |             leaves: leaves,
[INFO] [stderr]     |             ^^^^^^^^^^^^^^ help: replace it with: `leaves`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::redundant_field_names)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_field_names
[INFO] [stderr] 
[INFO] [stderr] warning: redundant field names in struct initialization
[INFO] [stderr]    --> src/tree.rs:235:13
[INFO] [stderr]     |
[INFO] [stderr] 235 |             branches: branches,
[INFO] [stderr]     |             ^^^^^^^^^^^^^^^^^^ help: replace it with: `branches`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_field_names
[INFO] [stderr] 
[INFO] [stderr] warning: redundant field names in struct initialization
[INFO] [stderr]    --> src/tree.rs:236:13
[INFO] [stderr]     |
[INFO] [stderr] 236 |             leaf_distances: leaf_distances,
[INFO] [stderr]     |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: replace it with: `leaf_distances`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_field_names
[INFO] [stderr] 
[INFO] [stderr] warning: redundant field names in struct initialization
[INFO] [stderr]    --> src/tree.rs:237:13
[INFO] [stderr]     |
[INFO] [stderr] 237 |             branch_distances: branch_distances,
[INFO] [stderr]     |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: replace it with: `branch_distances`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_field_names
[INFO] [stderr] 
[INFO] [stderr] warning: redundant field names in struct initialization
[INFO] [stderr]    --> src/tree.rs:239:13
[INFO] [stderr]     |
[INFO] [stderr] 239 |             branch_number: branch_number,
[INFO] [stderr]     |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: replace it with: `branch_number`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_field_names
[INFO] [stderr] 
[INFO] [stderr] warning: redundant field names in struct initialization
[INFO] [stderr]    --> src/tree.rs:234:13
[INFO] [stderr]     |
[INFO] [stderr] 234 |             leaves: leaves,
[INFO] [stderr]     |             ^^^^^^^^^^^^^^ help: replace it with: `leaves`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::redundant_field_names)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_field_names
[INFO] [stderr] 
[INFO] [stderr] warning: redundant field names in struct initialization
[INFO] [stderr]    --> src/tree.rs:235:13
[INFO] [stderr]     |
[INFO] [stderr] 235 |             branches: branches,
[INFO] [stderr]     |             ^^^^^^^^^^^^^^^^^^ help: replace it with: `branches`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_field_names
[INFO] [stderr] 
[INFO] [stderr] warning: redundant field names in struct initialization
[INFO] [stderr]    --> src/tree.rs:236:13
[INFO] [stderr]     |
[INFO] [stderr] 236 |             leaf_distances: leaf_distances,
[INFO] [stderr]     |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: replace it with: `leaf_distances`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_field_names
[INFO] [stderr] 
[INFO] [stderr] warning: redundant field names in struct initialization
[INFO] [stderr]    --> src/tree.rs:237:13
[INFO] [stderr]     |
[INFO] [stderr] 237 |             branch_distances: branch_distances,
[INFO] [stderr]     |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: replace it with: `branch_distances`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_field_names
[INFO] [stderr] 
[INFO] [stderr] warning: redundant field names in struct initialization
[INFO] [stderr]    --> src/tree.rs:239:13
[INFO] [stderr]     |
[INFO] [stderr] 239 |             branch_number: branch_number,
[INFO] [stderr]     |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: replace it with: `branch_number`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_field_names
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/tree.rs:39:9
[INFO] [stderr]    |
[INFO] [stderr] 39 |         return leaves_self == leaves_other;
[INFO] [stderr]    |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `leaves_self == leaves_other`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::needless_return)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree.rs:124:9
[INFO] [stderr]     |
[INFO] [stderr] 124 |         return Some(current_branch_idx);
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `Some(current_branch_idx)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: returning the result of a let binding from a block. Consider returning the expression directly.
[INFO] [stderr]    --> src/tree.rs:131:9
[INFO] [stderr]     |
[INFO] [stderr] 131 |         children
[INFO] [stderr]     |         ^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::let_and_return)] on by default
[INFO] [stderr] note: this expression can be directly returned
[INFO] [stderr]    --> src/tree.rs:130:24
[INFO] [stderr]     |
[INFO] [stderr] 130 |         let children = self.build_depth_first_path();
[INFO] [stderr]     |                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#let_and_return
[INFO] [stderr] 
[INFO] [stderr] warning: returning the result of a let binding from a block. Consider returning the expression directly.
[INFO] [stderr]    --> src/tree.rs:138:9
[INFO] [stderr]     |
[INFO] [stderr] 138 |         snapshot_children
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr] note: this expression can be directly returned
[INFO] [stderr]    --> src/tree.rs:137:33
[INFO] [stderr]     |
[INFO] [stderr] 137 |         let snapshot_children = children.iter().map(| x | (x.0.clone(), *x.1) ).collect();
[INFO] [stderr]     |                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#let_and_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree.rs:242:9
[INFO] [stderr]     |
[INFO] [stderr] 242 |         return (tree, c);
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `(tree, c)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: this `else { if .. }` block can be collapsed
[INFO] [stderr]    --> src/tree.rs:222:20
[INFO] [stderr]     |
[INFO] [stderr] 222 |               } else {
[INFO] [stderr]     |  ____________________^
[INFO] [stderr] 223 | |                 if read_mode == "LEAF" {
[INFO] [stderr] 224 | |                     current_leaf.push(chr);
[INFO] [stderr] 225 | |                 } else if read_mode == "DIST" {
[INFO] [stderr] ...   |
[INFO] [stderr] 229 | |                 }
[INFO] [stderr] 230 | |             }
[INFO] [stderr]     | |_____________^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::collapsible_if)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#collapsible_if
[INFO] [stderr] help: try
[INFO] [stderr]     |
[INFO] [stderr] 222 |             } else if read_mode == "LEAF" {
[INFO] [stderr] 223 |     current_leaf.push(chr);
[INFO] [stderr] 224 | } else if read_mode == "DIST" {
[INFO] [stderr] 225 |     current_distance.push(chr);
[INFO] [stderr] 226 | } else if read_mode == "BDON" {
[INFO] [stderr] 227 |     continue; // Ignore edge values.
[INFO] [stderr]   ...
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree.rs:247:9
[INFO] [stderr]     |
[INFO] [stderr] 247 |         return Tree::parse_tree_from_string(tree_string, 0, 0).0;
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `Tree::parse_tree_from_string(tree_string, 0, 0).0`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree.rs:286:9
[INFO] [stderr]     |
[INFO] [stderr] 286 | /         return Tree {
[INFO] [stderr] 287 | |             leaves,
[INFO] [stderr] 288 | |             branches,
[INFO] [stderr] 289 | |             leaf_distances,
[INFO] [stderr] ...   |
[INFO] [stderr] 292 | |             branch_number: 0,
[INFO] [stderr] 293 | |         };
[INFO] [stderr]     | |__________^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] help: remove `return` as shown
[INFO] [stderr]     |
[INFO] [stderr] 286 |         Tree {
[INFO] [stderr] 287 |             leaves,
[INFO] [stderr] 288 |             branches,
[INFO] [stderr] 289 |             leaf_distances,
[INFO] [stderr] 290 |             branch_distances,
[INFO] [stderr] 291 |             levels_from_root: 0,
[INFO] [stderr]   ...
[INFO] [stderr] 
[INFO] [stderr] warning: returning the result of a let binding from a block. Consider returning the expression directly.
[INFO] [stderr]    --> src/tree.rs:373:9
[INFO] [stderr]     |
[INFO] [stderr] 373 |         distance_matrix
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr] note: this expression can be directly returned
[INFO] [stderr]    --> src/tree.rs:372:13
[INFO] [stderr]     |
[INFO] [stderr] 372 |             TreeDistanceMatrix::new(leaf_distance_matrix, identity_matrix, leaf_map);
[INFO] [stderr]     |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#let_and_return
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `ndarray::prelude::*`
[INFO] [stderr]  --> src/graph_tree.rs:1:5
[INFO] [stderr]   |
[INFO] [stderr] 1 | use ndarray::prelude::*;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: #[warn(unused_imports)] on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::collections::HashMap`
[INFO] [stderr]  --> src/graph_tree.rs:2:5
[INFO] [stderr]   |
[INFO] [stderr] 2 | use std::collections::HashMap;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `tree_distance_matrix::*`
[INFO] [stderr]  --> src/graph_tree.rs:4:5
[INFO] [stderr]   |
[INFO] [stderr] 4 | use tree_distance_matrix::*;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `Incoming`
[INFO] [stderr]  --> src/graph_tree.rs:7:23
[INFO] [stderr]   |
[INFO] [stderr] 7 | use petgraph::{Graph, Incoming};
[INFO] [stderr]   |                       ^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/graph_tree.rs:34:9
[INFO] [stderr]    |
[INFO] [stderr] 34 |         return children;
[INFO] [stderr]    |         ^^^^^^^^^^^^^^^^ help: remove `return` as shown: `children`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/graph_tree.rs:126:9
[INFO] [stderr]     |
[INFO] [stderr] 126 |         return (graph, c)
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `(graph, c)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: this `else { if .. }` block can be collapsed
[INFO] [stderr]    --> src/graph_tree.rs:111:20
[INFO] [stderr]     |
[INFO] [stderr] 111 |               } else {
[INFO] [stderr]     |  ____________________^
[INFO] [stderr] 112 | |                 if read_mode == "LEAF" {
[INFO] [stderr] 113 | |                     current_leaf.push(chr);
[INFO] [stderr] 114 | |                 } else if read_mode == "DIST" {
[INFO] [stderr] ...   |
[INFO] [stderr] 118 | |                 }
[INFO] [stderr] 119 | |             }
[INFO] [stderr]     | |_____________^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#collapsible_if
[INFO] [stderr] help: try
[INFO] [stderr]     |
[INFO] [stderr] 111 |             } else if read_mode == "LEAF" {
[INFO] [stderr] 112 |     current_leaf.push(chr);
[INFO] [stderr] 113 | } else if read_mode == "DIST" {
[INFO] [stderr] 114 |     current_distance.push(chr);
[INFO] [stderr] 115 | } else if read_mode == "BDON" {
[INFO] [stderr] 116 |     continue; // Ignore edge values.
[INFO] [stderr]   ...
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/tree_distance_matrix.rs:60:9
[INFO] [stderr]    |
[INFO] [stderr] 60 |         return new_distances;
[INFO] [stderr]    |         ^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `new_distances`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/tree_distance_matrix.rs:76:9
[INFO] [stderr]    |
[INFO] [stderr] 76 |         return (d_fu, d_gu);
[INFO] [stderr]    |         ^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `(d_fu, d_gu)`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/tree_distance_matrix.rs:95:9
[INFO] [stderr]    |
[INFO] [stderr] 95 |         return idx;
[INFO] [stderr]    |         ^^^^^^^^^^^ help: remove `return` as shown: `idx`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_distance_matrix.rs:188:9
[INFO] [stderr]     |
[INFO] [stderr] 188 |         return result_tree;
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `result_tree`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_distance_matrix.rs:193:9
[INFO] [stderr]     |
[INFO] [stderr] 193 |         return self.get_distance_ref(&leaf_one, &leaf_two);
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `self.get_distance_ref(&leaf_one, &leaf_two)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_distance_matrix.rs:214:9
[INFO] [stderr]     |
[INFO] [stderr] 214 |         return Some(self.distance_matrix[[x, y]]);
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `Some(self.distance_matrix[[x, y]])`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_distance_matrix.rs:260:9
[INFO] [stderr]     |
[INFO] [stderr] 260 |         return csv;
[INFO] [stderr]     |         ^^^^^^^^^^^ help: remove `return` as shown: `csv`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_distance_matrix.rs:265:9
[INFO] [stderr]     |
[INFO] [stderr] 265 |         return self.distance_matrix.shape();
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `self.distance_matrix.shape()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_distance_matrix.rs:283:9
[INFO] [stderr]     |
[INFO] [stderr] 283 |         return 0;
[INFO] [stderr]     |         ^^^^^^^^^ help: remove `return` as shown: `0`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: immediately dereferencing a reference
[INFO] [stderr]    --> src/tree_distance_matrix.rs:288:76
[INFO] [stderr]     |
[INFO] [stderr] 288 |         let p1 = TreeDistanceMatrix::find_first_zero(identity_matrix.slice(s![l1, ..]));
[INFO] [stderr]     |                                                                            ^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::deref_addrof)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#deref_addrof
[INFO] [stderr]     = note: this error originates in a macro outside of the current crate (in Nightly builds, run with -Z external-macro-backtrace for more info)
[INFO] [stderr] 
[INFO] [stderr] warning: immediately dereferencing a reference
[INFO] [stderr]    --> src/tree_distance_matrix.rs:289:76
[INFO] [stderr]     |
[INFO] [stderr] 289 |         let p2 = TreeDistanceMatrix::find_first_zero(identity_matrix.slice(s![l2, ..]));
[INFO] [stderr]     |                                                                            ^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#deref_addrof
[INFO] [stderr]     = note: this error originates in a macro outside of the current crate (in Nightly builds, run with -Z external-macro-backtrace for more info)
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_distance_matrix.rs:315:9
[INFO] [stderr]     |
[INFO] [stderr] 315 |         return 0;
[INFO] [stderr]     |         ^^^^^^^^^ help: remove `return` as shown: `0`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: immediately dereferencing a reference
[INFO] [stderr]    --> src/tree_distance_matrix.rs:303:46
[INFO] [stderr]     |
[INFO] [stderr] 303 |         let id_row_1 = identity_matrix.slice(s![l1, ..]);
[INFO] [stderr]     |                                              ^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#deref_addrof
[INFO] [stderr]     = note: this error originates in a macro outside of the current crate (in Nightly builds, run with -Z external-macro-backtrace for more info)
[INFO] [stderr] 
[INFO] [stderr] warning: immediately dereferencing a reference
[INFO] [stderr]    --> src/tree_distance_matrix.rs:304:46
[INFO] [stderr]     |
[INFO] [stderr] 304 |         let id_row_2 = identity_matrix.slice(s![l2, ..]);
[INFO] [stderr]     |                                              ^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#deref_addrof
[INFO] [stderr]     = note: this error originates in a macro outside of the current crate (in Nightly builds, run with -Z external-macro-backtrace for more info)
[INFO] [stderr] 
[INFO] [stderr] warning: immediately dereferencing a reference
[INFO] [stderr]    --> src/tree_distance_matrix.rs:411:31
[INFO] [stderr]     |
[INFO] [stderr] 411 |         distance_matrix.slice(s![..n_leaves, ..n_leaves]).to_owned()
[INFO] [stderr]     |                               ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#deref_addrof
[INFO] [stderr]     = note: this error originates in a macro outside of the current crate (in Nightly builds, run with -Z external-macro-backtrace for more info)
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_distance_matrix.rs:474:9
[INFO] [stderr]     |
[INFO] [stderr] 474 |         return TreeDistanceMatrix::new_from_matrix_and_leaves(ndm, leaves.to_vec());
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `TreeDistanceMatrix::new_from_matrix_and_leaves(ndm, leaves.to_vec())`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_distance_matrix.rs:514:9
[INFO] [stderr]     |
[INFO] [stderr] 514 | /         return TreeDistanceMatrix {
[INFO] [stderr] 515 | |             leaf_map,
[INFO] [stderr] 516 | |             leaf_map_inv,
[INFO] [stderr] 517 | |             distance_matrix,
[INFO] [stderr] 518 | |         };
[INFO] [stderr]     | |__________^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] help: remove `return` as shown
[INFO] [stderr]     |
[INFO] [stderr] 514 |         TreeDistanceMatrix {
[INFO] [stderr] 515 |             leaf_map,
[INFO] [stderr] 516 |             leaf_map_inv,
[INFO] [stderr] 517 |             distance_matrix,
[INFO] [stderr] 518 |         }
[INFO] [stderr]     |
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::collections::HashMap`
[INFO] [stderr]  --> src/tree_merging.rs:3:5
[INFO] [stderr]   |
[INFO] [stderr] 3 | use std::collections::HashMap;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/tree_merging.rs:34:5
[INFO] [stderr]    |
[INFO] [stderr] 34 |     return tree.traverse_children().len();
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `tree.traverse_children().len()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded unit return type
[INFO] [stderr]   --> src/tree_merging.rs:37:42
[INFO] [stderr]    |
[INFO] [stderr] 37 | fn sibling_merging(mut trees: Vec<Tree>) -> () {
[INFO] [stderr]    |                                          ^^^^^ help: remove the `-> ()`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::unused_unit)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unused_unit
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_merging.rs:126:5
[INFO] [stderr]     |
[INFO] [stderr] 126 | /     return TreeDistanceMatrix::new_from_matrix_and_leaves(
[INFO] [stderr] 127 | |         average_matrix,
[INFO] [stderr] 128 | |         all_leaves.iter().map(|l| l.clone()).collect(),
[INFO] [stderr] 129 | |     );
[INFO] [stderr]     | |______^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] help: remove `return` as shown
[INFO] [stderr]     |
[INFO] [stderr] 126 |     TreeDistanceMatrix::new_from_matrix_and_leaves(
[INFO] [stderr] 127 |         average_matrix,
[INFO] [stderr] 128 |         all_leaves.iter().map(|l| l.clone()).collect(),
[INFO] [stderr] 129 |     )
[INFO] [stderr]     |
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/utils.rs:20:5
[INFO] [stderr]    |
[INFO] [stderr] 20 |     return hm.keys().cloned().collect();
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `hm.keys().cloned().collect()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/utils.rs:30:5
[INFO] [stderr]    |
[INFO] [stderr] 30 |     return set;
[INFO] [stderr]    |     ^^^^^^^^^^^ help: remove `return` as shown: `set`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: module has the same name as its containing module
[INFO] [stderr]    --> src/tests.rs:2:1
[INFO] [stderr]     |
[INFO] [stderr] 2   | / mod tests {
[INFO] [stderr] 3   | |     use ndarray::prelude::*;
[INFO] [stderr] 4   | |     use tree;
[INFO] [stderr] 5   | |     use tree_distance_matrix;
[INFO] [stderr] ...   |
[INFO] [stderr] 189 | |     }
[INFO] [stderr] 190 | | }
[INFO] [stderr]     | |_^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::module_inception)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#module_inception
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/tree.rs:39:9
[INFO] [stderr]    |
[INFO] [stderr] 39 |         return leaves_self == leaves_other;
[INFO] [stderr]    |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `leaves_self == leaves_other`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::needless_return)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree.rs:124:9
[INFO] [stderr]     |
[INFO] [stderr] 124 |         return Some(current_branch_idx);
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `Some(current_branch_idx)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: returning the result of a let binding from a block. Consider returning the expression directly.
[INFO] [stderr]    --> src/tree.rs:131:9
[INFO] [stderr]     |
[INFO] [stderr] 131 |         children
[INFO] [stderr]     |         ^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::let_and_return)] on by default
[INFO] [stderr] note: this expression can be directly returned
[INFO] [stderr]    --> src/tree.rs:130:24
[INFO] [stderr]     |
[INFO] [stderr] 130 |         let children = self.build_depth_first_path();
[INFO] [stderr]     |                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#let_and_return
[INFO] [stderr] 
[INFO] [stderr] warning: returning the result of a let binding from a block. Consider returning the expression directly.
[INFO] [stderr]    --> src/tree.rs:138:9
[INFO] [stderr]     |
[INFO] [stderr] 138 |         snapshot_children
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr] note: this expression can be directly returned
[INFO] [stderr]    --> src/tree.rs:137:33
[INFO] [stderr]     |
[INFO] [stderr] 137 |         let snapshot_children = children.iter().map(| x | (x.0.clone(), *x.1) ).collect();
[INFO] [stderr]     |                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#let_and_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree.rs:242:9
[INFO] [stderr]     |
[INFO] [stderr] 242 |         return (tree, c);
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `(tree, c)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: this `else { if .. }` block can be collapsed
[INFO] [stderr]    --> src/tree.rs:222:20
[INFO] [stderr]     |
[INFO] [stderr] 222 |               } else {
[INFO] [stderr]     |  ____________________^
[INFO] [stderr] 223 | |                 if read_mode == "LEAF" {
[INFO] [stderr] 224 | |                     current_leaf.push(chr);
[INFO] [stderr] 225 | |                 } else if read_mode == "DIST" {
[INFO] [stderr] ...   |
[INFO] [stderr] 229 | |                 }
[INFO] [stderr] 230 | |             }
[INFO] [stderr]     | |_____________^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::collapsible_if)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#collapsible_if
[INFO] [stderr] help: try
[INFO] [stderr]     |
[INFO] [stderr] 222 |             } else if read_mode == "LEAF" {
[INFO] [stderr] 223 |     current_leaf.push(chr);
[INFO] [stderr] 224 | } else if read_mode == "DIST" {
[INFO] [stderr] 225 |     current_distance.push(chr);
[INFO] [stderr] 226 | } else if read_mode == "BDON" {
[INFO] [stderr] 227 |     continue; // Ignore edge values.
[INFO] [stderr]   ...
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree.rs:247:9
[INFO] [stderr]     |
[INFO] [stderr] 247 |         return Tree::parse_tree_from_string(tree_string, 0, 0).0;
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `Tree::parse_tree_from_string(tree_string, 0, 0).0`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree.rs:286:9
[INFO] [stderr]     |
[INFO] [stderr] 286 | /         return Tree {
[INFO] [stderr] 287 | |             leaves,
[INFO] [stderr] 288 | |             branches,
[INFO] [stderr] 289 | |             leaf_distances,
[INFO] [stderr] ...   |
[INFO] [stderr] 292 | |             branch_number: 0,
[INFO] [stderr] 293 | |         };
[INFO] [stderr]     | |__________^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] help: remove `return` as shown
[INFO] [stderr]     |
[INFO] [stderr] 286 |         Tree {
[INFO] [stderr] 287 |             leaves,
[INFO] [stderr] 288 |             branches,
[INFO] [stderr] 289 |             leaf_distances,
[INFO] [stderr] 290 |             branch_distances,
[INFO] [stderr] 291 |             levels_from_root: 0,
[INFO] [stderr]   ...
[INFO] [stderr] 
[INFO] [stderr] warning: returning the result of a let binding from a block. Consider returning the expression directly.
[INFO] [stderr]    --> src/tree.rs:373:9
[INFO] [stderr]     |
[INFO] [stderr] 373 |         distance_matrix
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr] note: this expression can be directly returned
[INFO] [stderr]    --> src/tree.rs:372:13
[INFO] [stderr]     |
[INFO] [stderr] 372 |             TreeDistanceMatrix::new(leaf_distance_matrix, identity_matrix, leaf_map);
[INFO] [stderr]     |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#let_and_return
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `ndarray::prelude::*`
[INFO] [stderr]  --> src/graph_tree.rs:1:5
[INFO] [stderr]   |
[INFO] [stderr] 1 | use ndarray::prelude::*;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: #[warn(unused_imports)] on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::collections::HashMap`
[INFO] [stderr]  --> src/graph_tree.rs:2:5
[INFO] [stderr]   |
[INFO] [stderr] 2 | use std::collections::HashMap;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `tree_distance_matrix::*`
[INFO] [stderr]  --> src/graph_tree.rs:4:5
[INFO] [stderr]   |
[INFO] [stderr] 4 | use tree_distance_matrix::*;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `Incoming`
[INFO] [stderr]  --> src/graph_tree.rs:7:23
[INFO] [stderr]   |
[INFO] [stderr] 7 | use petgraph::{Graph, Incoming};
[INFO] [stderr]   |                       ^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/graph_tree.rs:34:9
[INFO] [stderr]    |
[INFO] [stderr] 34 |         return children;
[INFO] [stderr]    |         ^^^^^^^^^^^^^^^^ help: remove `return` as shown: `children`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/graph_tree.rs:126:9
[INFO] [stderr]     |
[INFO] [stderr] 126 |         return (graph, c)
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `(graph, c)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: this `else { if .. }` block can be collapsed
[INFO] [stderr]    --> src/graph_tree.rs:111:20
[INFO] [stderr]     |
[INFO] [stderr] 111 |               } else {
[INFO] [stderr]     |  ____________________^
[INFO] [stderr] 112 | |                 if read_mode == "LEAF" {
[INFO] [stderr] 113 | |                     current_leaf.push(chr);
[INFO] [stderr] 114 | |                 } else if read_mode == "DIST" {
[INFO] [stderr] ...   |
[INFO] [stderr] 118 | |                 }
[INFO] [stderr] 119 | |             }
[INFO] [stderr]     | |_____________^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#collapsible_if
[INFO] [stderr] help: try
[INFO] [stderr]     |
[INFO] [stderr] 111 |             } else if read_mode == "LEAF" {
[INFO] [stderr] 112 |     current_leaf.push(chr);
[INFO] [stderr] 113 | } else if read_mode == "DIST" {
[INFO] [stderr] 114 |     current_distance.push(chr);
[INFO] [stderr] 115 | } else if read_mode == "BDON" {
[INFO] [stderr] 116 |     continue; // Ignore edge values.
[INFO] [stderr]   ...
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/tree_distance_matrix.rs:60:9
[INFO] [stderr]    |
[INFO] [stderr] 60 |         return new_distances;
[INFO] [stderr]    |         ^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `new_distances`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/tree_distance_matrix.rs:76:9
[INFO] [stderr]    |
[INFO] [stderr] 76 |         return (d_fu, d_gu);
[INFO] [stderr]    |         ^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `(d_fu, d_gu)`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/tree_distance_matrix.rs:95:9
[INFO] [stderr]    |
[INFO] [stderr] 95 |         return idx;
[INFO] [stderr]    |         ^^^^^^^^^^^ help: remove `return` as shown: `idx`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_distance_matrix.rs:188:9
[INFO] [stderr]     |
[INFO] [stderr] 188 |         return result_tree;
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `result_tree`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_distance_matrix.rs:193:9
[INFO] [stderr]     |
[INFO] [stderr] 193 |         return self.get_distance_ref(&leaf_one, &leaf_two);
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `self.get_distance_ref(&leaf_one, &leaf_two)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_distance_matrix.rs:214:9
[INFO] [stderr]     |
[INFO] [stderr] 214 |         return Some(self.distance_matrix[[x, y]]);
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `Some(self.distance_matrix[[x, y]])`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_distance_matrix.rs:260:9
[INFO] [stderr]     |
[INFO] [stderr] 260 |         return csv;
[INFO] [stderr]     |         ^^^^^^^^^^^ help: remove `return` as shown: `csv`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_distance_matrix.rs:265:9
[INFO] [stderr]     |
[INFO] [stderr] 265 |         return self.distance_matrix.shape();
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `self.distance_matrix.shape()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_distance_matrix.rs:283:9
[INFO] [stderr]     |
[INFO] [stderr] 283 |         return 0;
[INFO] [stderr]     |         ^^^^^^^^^ help: remove `return` as shown: `0`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: immediately dereferencing a reference
[INFO] [stderr]    --> src/tree_distance_matrix.rs:288:76
[INFO] [stderr]     |
[INFO] [stderr] 288 |         let p1 = TreeDistanceMatrix::find_first_zero(identity_matrix.slice(s![l1, ..]));
[INFO] [stderr]     |                                                                            ^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::deref_addrof)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#deref_addrof
[INFO] [stderr]     = note: this error originates in a macro outside of the current crate (in Nightly builds, run with -Z external-macro-backtrace for more info)
[INFO] [stderr] 
[INFO] [stderr] warning: immediately dereferencing a reference
[INFO] [stderr]    --> src/tree_distance_matrix.rs:289:76
[INFO] [stderr]     |
[INFO] [stderr] 289 |         let p2 = TreeDistanceMatrix::find_first_zero(identity_matrix.slice(s![l2, ..]));
[INFO] [stderr]     |                                                                            ^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#deref_addrof
[INFO] [stderr]     = note: this error originates in a macro outside of the current crate (in Nightly builds, run with -Z external-macro-backtrace for more info)
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_distance_matrix.rs:315:9
[INFO] [stderr]     |
[INFO] [stderr] 315 |         return 0;
[INFO] [stderr]     |         ^^^^^^^^^ help: remove `return` as shown: `0`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: immediately dereferencing a reference
[INFO] [stderr]    --> src/tree_distance_matrix.rs:303:46
[INFO] [stderr]     |
[INFO] [stderr] 303 |         let id_row_1 = identity_matrix.slice(s![l1, ..]);
[INFO] [stderr]     |                                              ^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#deref_addrof
[INFO] [stderr]     = note: this error originates in a macro outside of the current crate (in Nightly builds, run with -Z external-macro-backtrace for more info)
[INFO] [stderr] 
[INFO] [stderr] warning: immediately dereferencing a reference
[INFO] [stderr]    --> src/tree_distance_matrix.rs:304:46
[INFO] [stderr]     |
[INFO] [stderr] 304 |         let id_row_2 = identity_matrix.slice(s![l2, ..]);
[INFO] [stderr]     |                                              ^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#deref_addrof
[INFO] [stderr]     = note: this error originates in a macro outside of the current crate (in Nightly builds, run with -Z external-macro-backtrace for more info)
[INFO] [stderr] 
[INFO] [stderr] warning: immediately dereferencing a reference
[INFO] [stderr]    --> src/tree_distance_matrix.rs:411:31
[INFO] [stderr]     |
[INFO] [stderr] 411 |         distance_matrix.slice(s![..n_leaves, ..n_leaves]).to_owned()
[INFO] [stderr]     |                               ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#deref_addrof
[INFO] [stderr]     = note: this error originates in a macro outside of the current crate (in Nightly builds, run with -Z external-macro-backtrace for more info)
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_distance_matrix.rs:474:9
[INFO] [stderr]     |
[INFO] [stderr] 474 |         return TreeDistanceMatrix::new_from_matrix_and_leaves(ndm, leaves.to_vec());
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `TreeDistanceMatrix::new_from_matrix_and_leaves(ndm, leaves.to_vec())`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_distance_matrix.rs:514:9
[INFO] [stderr]     |
[INFO] [stderr] 514 | /         return TreeDistanceMatrix {
[INFO] [stderr] 515 | |             leaf_map,
[INFO] [stderr] 516 | |             leaf_map_inv,
[INFO] [stderr] 517 | |             distance_matrix,
[INFO] [stderr] 518 | |         };
[INFO] [stderr]     | |__________^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] help: remove `return` as shown
[INFO] [stderr]     |
[INFO] [stderr] 514 |         TreeDistanceMatrix {
[INFO] [stderr] 515 |             leaf_map,
[INFO] [stderr] 516 |             leaf_map_inv,
[INFO] [stderr] 517 |             distance_matrix,
[INFO] [stderr] 518 |         }
[INFO] [stderr]     |
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::collections::HashMap`
[INFO] [stderr]  --> src/tree_merging.rs:3:5
[INFO] [stderr]   |
[INFO] [stderr] 3 | use std::collections::HashMap;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/tree_merging.rs:34:5
[INFO] [stderr]    |
[INFO] [stderr] 34 |     return tree.traverse_children().len();
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `tree.traverse_children().len()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded unit return type
[INFO] [stderr]   --> src/tree_merging.rs:37:42
[INFO] [stderr]    |
[INFO] [stderr] 37 | fn sibling_merging(mut trees: Vec<Tree>) -> () {
[INFO] [stderr]    |                                          ^^^^^ help: remove the `-> ()`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::unused_unit)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unused_unit
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/tree_merging.rs:126:5
[INFO] [stderr]     |
[INFO] [stderr] 126 | /     return TreeDistanceMatrix::new_from_matrix_and_leaves(
[INFO] [stderr] 127 | |         average_matrix,
[INFO] [stderr] 128 | |         all_leaves.iter().map(|l| l.clone()).collect(),
[INFO] [stderr] 129 | |     );
[INFO] [stderr]     | |______^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] help: remove `return` as shown
[INFO] [stderr]     |
[INFO] [stderr] 126 |     TreeDistanceMatrix::new_from_matrix_and_leaves(
[INFO] [stderr] 127 |         average_matrix,
[INFO] [stderr] 128 |         all_leaves.iter().map(|l| l.clone()).collect(),
[INFO] [stderr] 129 |     )
[INFO] [stderr]     |
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/utils.rs:20:5
[INFO] [stderr]    |
[INFO] [stderr] 20 |     return hm.keys().cloned().collect();
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `hm.keys().cloned().collect()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/utils.rs:30:5
[INFO] [stderr]    |
[INFO] [stderr] 30 |     return set;
[INFO] [stderr]    |     ^^^^^^^^^^^ help: remove `return` as shown: `set`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `graph`
[INFO] [stderr]   --> src/graph_tree.rs:62:22
[INFO] [stderr]    |
[INFO] [stderr] 62 |                 let (graph, new_skip) = Tree::parse_tree_from_string(
[INFO] [stderr]    |                      ^^^^^ help: consider using `_graph` instead
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(unused_variables)] on by default
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]   --> src/tree_merging.rs:21:9
[INFO] [stderr]    |
[INFO] [stderr] 21 |     let mut new_trees: Vec<Tree> = tree_leafs
[INFO] [stderr]    |         ----^^^^^^^^^
[INFO] [stderr]    |         |
[INFO] [stderr]    |         help: remove this `mut`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(unused_mut)] on by default
[INFO] [stderr] 
[INFO] [stderr] warning: method is never used: `perform_operation_on_branch`
[INFO] [stderr]    --> src/tree.rs:106:5
[INFO] [stderr]     |
[INFO] [stderr] 106 |     pub fn perform_operation_on_branch<F : FnMut(&mut Tree) >(&mut self, target_branch_idx : usize, mut current_branch_idx : usize, op : &mut F) -> Option<usize> {
[INFO] [stderr]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(dead_code)] on by default
[INFO] [stderr] 
[INFO] [stderr] warning: method is never used: `add_root_levels`
[INFO] [stderr]    --> src/tree.rs:250:5
[INFO] [stderr]     |
[INFO] [stderr] 250 |     pub fn add_root_levels(&mut self, depth: usize) {
[INFO] [stderr]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: method is never used: `traverse_children`
[INFO] [stderr]   --> src/graph_tree.rs:17:5
[INFO] [stderr]    |
[INFO] [stderr] 17 |     pub fn traverse_children(&self) -> Vec<Vec<String>> {
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: method is never used: `calculate_q_matrix`
[INFO] [stderr]   --> src/tree_distance_matrix.rs:18:5
[INFO] [stderr]    |
[INFO] [stderr] 18 |     pub fn calculate_q_matrix(dm: &Array2<f32>) -> Array2<f32> {
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: method is never used: `calculate_pair_distance_matrix`
[INFO] [stderr]   --> src/tree_distance_matrix.rs:32:5
[INFO] [stderr]    |
[INFO] [stderr] 32 |     pub fn calculate_pair_distance_matrix(i: usize, j: usize, dm: &Array2<f32>) -> Array2<f32> {
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: method is never used: `calculate_new_leaf_distances`
[INFO] [stderr]   --> src/tree_distance_matrix.rs:63:5
[INFO] [stderr]    |
[INFO] [stderr] 63 |     pub fn calculate_new_leaf_distances(f: usize, g: usize, dm: &Array2<f32>) -> (f32, f32) {
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: method is never used: `find_min_matrix_ne`
[INFO] [stderr]   --> src/tree_distance_matrix.rs:79:5
[INFO] [stderr]    |
[INFO] [stderr] 79 |     pub fn find_min_matrix_ne(matrix: Array2<f32>) -> [usize; 2] {
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: method is never used: `neighbour_joining`
[INFO] [stderr]   --> src/tree_distance_matrix.rs:98:5
[INFO] [stderr]    |
[INFO] [stderr] 98 |     pub fn neighbour_joining(&self) -> Tree {
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: method is never used: `get_partial_distance_matrix`
[INFO] [stderr]    --> src/tree_distance_matrix.rs:450:5
[INFO] [stderr]     |
[INFO] [stderr] 450 |     pub fn get_partial_distance_matrix(&self, leaves: &Vec<String>) -> TreeDistanceMatrix {
[INFO] [stderr]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: method is never used: `new_from_matrix_and_leaves`
[INFO] [stderr]    --> src/tree_distance_matrix.rs:502:5
[INFO] [stderr]     |
[INFO] [stderr] 502 | /     pub fn new_from_matrix_and_leaves(
[INFO] [stderr] 503 | |         distance_matrix: Array2<f32>,
[INFO] [stderr] 504 | |         leaves: Vec<String>,
[INFO] [stderr] 505 | |     ) -> TreeDistanceMatrix {
[INFO] [stderr] ...   |
[INFO] [stderr] 518 | |         };
[INFO] [stderr] 519 | |     }
[INFO] [stderr]     | |_____^
[INFO] [stderr] 
[INFO] [stderr] warning: function is never used: `merge_trees`
[INFO] [stderr]   --> src/tree_merging.rs:10:1
[INFO] [stderr]    |
[INFO] [stderr] 10 | pub fn merge_trees(trees: Vec<Tree>) {
[INFO] [stderr]    | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function is never used: `get_tree_size`
[INFO] [stderr]   --> src/tree_merging.rs:33:1
[INFO] [stderr]    |
[INFO] [stderr] 33 | fn get_tree_size(tree: &Tree) -> usize {
[INFO] [stderr]    | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function is never used: `sibling_merging`
[INFO] [stderr]   --> src/tree_merging.rs:37:1
[INFO] [stderr]    |
[INFO] [stderr] 37 | fn sibling_merging(mut trees: Vec<Tree>) -> () {
[INFO] [stderr]    | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function is never used: `merge_distance_matrices`
[INFO] [stderr]   --> src/tree_merging.rs:96:1
[INFO] [stderr]    |
[INFO] [stderr] 96 | fn merge_distance_matrices(dms: Vec<TreeDistanceMatrix>) -> TreeDistanceMatrix {
[INFO] [stderr]    | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function is never used: `keys_vec`
[INFO] [stderr]   --> src/utils.rs:17:1
[INFO] [stderr]    |
[INFO] [stderr] 17 | / pub fn keys_vec<T: std::cmp::Eq + std::hash::Hash + std::clone::Clone, V>(
[INFO] [stderr] 18 | |     hm: &HashMap<T, V>,
[INFO] [stderr] 19 | | ) -> Vec<T> {
[INFO] [stderr] 20 | |     return hm.keys().cloned().collect();
[INFO] [stderr] 21 | | }
[INFO] [stderr]    | |_^
[INFO] [stderr] 
[INFO] [stderr] warning: function is never used: `vec_to_set`
[INFO] [stderr]   --> src/utils.rs:23:1
[INFO] [stderr]    |
[INFO] [stderr] 23 | / pub fn vec_to_set<T: std::cmp::Eq + std::hash::Hash + std::clone::Clone>(
[INFO] [stderr] 24 | |     vector: &Vec<T>,
[INFO] [stderr] 25 | | ) -> HashSet<T> {
[INFO] [stderr] 26 | |     let mut set: HashSet<T> = HashSet::new();
[INFO] [stderr] ...  |
[INFO] [stderr] 30 | |     return set;
[INFO] [stderr] 31 | | }
[INFO] [stderr]    | |_^
[INFO] [stderr] 
[INFO] [stderr] warning: You are using an explicit closure for cloning elements
[INFO] [stderr]   --> src/tree.rs:47:23
[INFO] [stderr]    |
[INFO] [stderr] 47 |             branches: self.branches.iter().map( | b | b.clone() ).collect(),
[INFO] [stderr]    |                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: Consider calling the dedicated `cloned` method: `self.branches.iter().cloned()`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::map_clone)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#map_clone
[INFO] [stderr] 
[INFO] [stderr] warning: You are using an explicit closure for cloning elements
[INFO] [stderr]   --> src/tree.rs:48:29
[INFO] [stderr]    |
[INFO] [stderr] 48 |             leaf_distances: self.leaf_distances.iter().map( | ld | *ld ).collect(),
[INFO] [stderr]    |                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: Consider calling the dedicated `cloned` method: `self.leaf_distances.iter().cloned()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#map_clone
[INFO] [stderr] 
[INFO] [stderr] warning: You are using an explicit closure for cloning elements
[INFO] [stderr]   --> src/tree.rs:49:31
[INFO] [stderr]    |
[INFO] [stderr] 49 |             branch_distances: self.branch_distances.iter().map( | bd | *bd ).collect(),
[INFO] [stderr]    |                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: Consider calling the dedicated `cloned` method: `self.branch_distances.iter().cloned()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#map_clone
[INFO] [stderr] 
[INFO] [stderr] warning: use of `expect` followed by a function call
[INFO] [stderr]   --> src/tree.rs:92:64
[INFO] [stderr]    |
[INFO] [stderr] 92 |               let branch_distance = self.branch_distances.get(b).expect(&format!(
[INFO] [stderr]    |  ________________________________________________________________^
[INFO] [stderr] 93 | |                 "Branch state is invalid: Branch distance for branch {} missing",
[INFO] [stderr] 94 | |                 b
[INFO] [stderr] 95 | |             ));
[INFO] [stderr]    | |______________^ help: try this: `unwrap_or_else(|| panic!("Branch state is invalid: Branch distance for branch {} missing", b))`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::expect_fun_call)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#expect_fun_call
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]   --> src/tree.rs:98:16
[INFO] [stderr]    |
[INFO] [stderr] 98 |             if branch.branches.len() > 0 {
[INFO] [stderr]    |                ^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!branch.branches.is_empty()`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::len_zero)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/tree.rs:115:16
[INFO] [stderr]     |
[INFO] [stderr] 115 |             if branch.branches.len() > 0 {
[INFO] [stderr]     |                ^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!branch.branches.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/tree.rs:184:24
[INFO] [stderr]     |
[INFO] [stderr] 184 |                     if current_leaf.len() > 0 {
[INFO] [stderr]     |                        ^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!current_leaf.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/tree.rs:203:24
[INFO] [stderr]     |
[INFO] [stderr] 203 |                     if current_leaf.len() > 0 {
[INFO] [stderr]     |                        ^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!current_leaf.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/tree.rs:264:12
[INFO] [stderr]     |
[INFO] [stderr] 264 |         if (leaf_distances.len() > 0) & (leaf_distances.len() != leaves.len()) {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!leaf_distances.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/tree.rs:268:12
[INFO] [stderr]     |
[INFO] [stderr] 268 |         if (branch_distances.len() > 0) & (branch_distances.len() != branches.len()) {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!branch_distances.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/tree.rs:272:12
[INFO] [stderr]     |
[INFO] [stderr] 272 |         if leaf_distances.len() == 0 {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `leaf_distances.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/tree.rs:279:12
[INFO] [stderr]     |
[INFO] [stderr] 279 |         if branch_distances.len() == 0 {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `branch_distances.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: an inclusive range would be more readable
[INFO] [stderr]    --> src/tree.rs:354:47
[INFO] [stderr]     |
[INFO] [stderr] 354 |                         accumulated_distances[0..l + 1].iter().sum();
[INFO] [stderr]     |                                               ^^^^^^^^ help: use: `0..=l`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::range_plus_one)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#range_plus_one
[INFO] [stderr] 
[INFO] [stderr] warning: identical conversion
[INFO] [stderr]   --> src/graph_tree.rs:56:39
[INFO] [stderr]    |
[INFO] [stderr] 56 |                 let node_count_name = String::from(format!(">>{}", graph.node_count()));
[INFO] [stderr]    |                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider removing `String::from()`: `format!(">>{}", graph.node_count())`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::identity_conversion)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#identity_conversion
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]   --> src/graph_tree.rs:71:24
[INFO] [stderr]    |
[INFO] [stderr] 71 |                     if current_leaf.len() > 0 {
[INFO] [stderr]    |                        ^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!current_leaf.is_empty()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]   --> src/graph_tree.rs:91:24
[INFO] [stderr]    |
[INFO] [stderr] 91 |                     if current_leaf.len() > 0 {
[INFO] [stderr]    |                        ^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!current_leaf.is_empty()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: called `.get().unwrap()` on a Vec. Using `[]` is more clear and more concise
[INFO] [stderr]    --> src/tree_distance_matrix.rs:145:29
[INFO] [stderr]     |
[INFO] [stderr] 145 |                 leaves.push(leaf_map_inv_vec.get(lowest_pair[0]).unwrap().1.clone());
[INFO] [stderr]     |                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try this: `leaf_map_inv_vec[lowest_pair[0]]`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::get_unwrap)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#get_unwrap
[INFO] [stderr] 
[INFO] [stderr] warning: called `.get().unwrap()` on a Vec. Using `[]` is more clear and more concise
[INFO] [stderr]    --> src/tree_distance_matrix.rs:155:29
[INFO] [stderr]     |
[INFO] [stderr] 155 |                 leaves.push(leaf_map_inv_vec.get(lowest_pair[1]).unwrap().1.clone());
[INFO] [stderr]     |                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try this: `leaf_map_inv_vec[lowest_pair[1]]`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#get_unwrap
[INFO] [stderr] 
[INFO] [stderr] warning: You are using an explicit closure for cloning elements
[INFO] [stderr]    --> src/tree_distance_matrix.rs:172:41
[INFO] [stderr]     |
[INFO] [stderr] 172 |             let tree_keys: Vec<usize> = trees.keys().map(|x| *x).collect();
[INFO] [stderr]     |                                         ^^^^^^^^^^^^^^^^^^^^^^^^ help: Consider calling the dedicated `cloned` method: `trees.keys().cloned()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#map_clone
[INFO] [stderr] 
[INFO] [stderr] warning: You are using an explicit closure for cloning elements
[INFO] [stderr]    --> src/tree_distance_matrix.rs:185:37
[INFO] [stderr]     |
[INFO] [stderr] 185 |         let tree_keys: Vec<usize> = trees.keys().map(|x| *x).collect();
[INFO] [stderr]     |                                     ^^^^^^^^^^^^^^^^^^^^^^^^ help: Consider calling the dedicated `cloned` method: `trees.keys().cloned()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#map_clone
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]    --> src/tree_distance_matrix.rs:197:46
[INFO] [stderr]     |
[INFO] [stderr] 197 |     pub fn get_distance_ref(&self, leaf_one: &String, leaf_two: &String) -> Option<f32> {
[INFO] [stderr]     |                                              ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::ptr_arg)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]    --> src/tree_distance_matrix.rs:197:65
[INFO] [stderr]     |
[INFO] [stderr] 197 |     pub fn get_distance_ref(&self, leaf_one: &String, leaf_two: &String) -> Option<f32> {
[INFO] [stderr]     |                                                                 ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: taken reference of right operand
[INFO] [stderr]    --> src/tree_distance_matrix.rs:226:16
[INFO] [stderr]     |
[INFO] [stderr] 226 |             if key > &max_key {
[INFO] [stderr]     |                ^^^^^^--------
[INFO] [stderr]     |                      |
[INFO] [stderr]     |                      help: use the right value directly: `max_key`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::op_ref)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#op_ref
[INFO] [stderr] 
[INFO] [stderr] warning: an inclusive range would be more readable
[INFO] [stderr]    --> src/tree_distance_matrix.rs:233:18
[INFO] [stderr]     |
[INFO] [stderr] 233 |         for l in 0..max_key + 1 {
[INFO] [stderr]     |                  ^^^^^^^^^^^^^^ help: use: `0..=max_key`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#range_plus_one
[INFO] [stderr] 
[INFO] [stderr] warning: you seem to be trying to use match for destructuring a single pattern. Consider using `if let`
[INFO] [stderr]    --> src/tree_distance_matrix.rs:234:13
[INFO] [stderr]     |
[INFO] [stderr] 234 | /             match self.leaf_map_inv.get(&l) {
[INFO] [stderr] 235 | |                 Some(name) => {
[INFO] [stderr] 236 | |                     csv.push_str(name);
[INFO] [stderr] 237 | |                     leaves.push(name.to_string());
[INFO] [stderr] ...   |
[INFO] [stderr] 242 | |                 None => {}
[INFO] [stderr] 243 | |             }
[INFO] [stderr]     | |_____________^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::single_match)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#single_match
[INFO] [stderr] help: try this
[INFO] [stderr]     |
[INFO] [stderr] 234 |             if let Some(name) = self.leaf_map_inv.get(&l) {
[INFO] [stderr] 235 |     csv.push_str(name);
[INFO] [stderr] 236 |     leaves.push(name.to_string());
[INFO] [stderr] 237 |     if l < max_key {
[INFO] [stderr] 238 |         csv.push(delim);
[INFO] [stderr] 239 |     }
[INFO] [stderr]   ...
[INFO] [stderr] 
[INFO] [stderr] warning: the variable `v` is used as a loop counter. Consider using `for (v, item) in row.enumerate()` or similar iterators
[INFO] [stderr]    --> src/tree_distance_matrix.rs:251:24
[INFO] [stderr]     |
[INFO] [stderr] 251 |             for val in row {
[INFO] [stderr]     |                        ^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::explicit_counter_loop)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#explicit_counter_loop
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]    --> src/tree_distance_matrix.rs:450:55
[INFO] [stderr]     |
[INFO] [stderr] 450 |     pub fn get_partial_distance_matrix(&self, leaves: &Vec<String>) -> TreeDistanceMatrix {
[INFO] [stderr]     |                                                       ^^^^^^^^^^^^ help: change this to: `&[String]`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]   --> src/tree_merging.rs:64:24
[INFO] [stderr]    |
[INFO] [stderr] 64 |                     if overlapping_leaves.len() == 0 {
[INFO] [stderr]    |                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `overlapping_leaves.is_empty()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]   --> src/tree_merging.rs:68:24
[INFO] [stderr]    |
[INFO] [stderr] 68 |                     if new_leaves.len() == 0 {
[INFO] [stderr]    |                        ^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `new_leaves.is_empty()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: you seem to be trying to use match for destructuring a single pattern. Consider using `if let`
[INFO] [stderr]    --> src/tree_merging.rs:113:17
[INFO] [stderr]     |
[INFO] [stderr] 113 | /                 match dist {
[INFO] [stderr] 114 | |                     Some(d) => {
[INFO] [stderr] 115 | |                         overlapping_distance_matrix[[x, y]] = d;
[INFO] [stderr] 116 | |                         count_matrix[[x, y]] += 1.0
[INFO] [stderr] 117 | |                     }
[INFO] [stderr] 118 | |                     None => {}
[INFO] [stderr] 119 | |                 }
[INFO] [stderr]     | |_________________^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#single_match
[INFO] [stderr] help: try this
[INFO] [stderr]     |
[INFO] [stderr] 113 |                 if let Some(d) = dist {
[INFO] [stderr] 114 |     overlapping_distance_matrix[[x, y]] = d;
[INFO] [stderr] 115 |     count_matrix[[x, y]] += 1.0
[INFO] [stderr] 116 | }
[INFO] [stderr]     |
[INFO] [stderr] 
[INFO] [stderr] warning: You are using an explicit closure for cloning elements
[INFO] [stderr]    --> src/tree_merging.rs:128:9
[INFO] [stderr]     |
[INFO] [stderr] 128 |         all_leaves.iter().map(|l| l.clone()).collect(),
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: Consider calling the dedicated `cloned` method: `all_leaves.iter().cloned()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#map_clone
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]   --> src/utils.rs:24:13
[INFO] [stderr]    |
[INFO] [stderr] 24 |     vector: &Vec<T>,
[INFO] [stderr]    |             ^^^^^^^ help: change this to: `&[T]`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: identical conversion
[INFO] [stderr]   --> src/main.rs:27:43
[INFO] [stderr]    |
[INFO] [stderr] 27 |     let tree_file = utils::load_tree_file(String::from(fname));
[INFO] [stderr]    |                                           ^^^^^^^^^^^^^^^^^^^ help: consider removing `String::from()`: `fname`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#identity_conversion
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `graph`
[INFO] [stderr]   --> src/graph_tree.rs:62:22
[INFO] [stderr]    |
[INFO] [stderr] 62 |                 let (graph, new_skip) = Tree::parse_tree_from_string(
[INFO] [stderr]    |                      ^^^^^ help: consider using `_graph` instead
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(unused_variables)] on by default
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]   --> src/tree_merging.rs:21:9
[INFO] [stderr]    |
[INFO] [stderr] 21 |     let mut new_trees: Vec<Tree> = tree_leafs
[INFO] [stderr]    |         ----^^^^^^^^^
[INFO] [stderr]    |         |
[INFO] [stderr]    |         help: remove this `mut`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(unused_mut)] on by default
[INFO] [stderr] 
[INFO] [stderr] warning: single-character string constant used as pattern
[INFO] [stderr]   --> src/tests.rs:40:36
[INFO] [stderr]    |
[INFO] [stderr] 40 |         assert!(tree_file.contains("("));
[INFO] [stderr]    |                                    ^^^ help: try using a char instead: `'('`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::single_char_pattern)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#single_char_pattern
[INFO] [stderr] 
[INFO] [stderr] warning: You are using an explicit closure for cloning elements
[INFO] [stderr]   --> src/tree.rs:47:23
[INFO] [stderr]    |
[INFO] [stderr] 47 |             branches: self.branches.iter().map( | b | b.clone() ).collect(),
[INFO] [stderr]    |                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: Consider calling the dedicated `cloned` method: `self.branches.iter().cloned()`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::map_clone)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#map_clone
[INFO] [stderr] 
[INFO] [stderr] warning: You are using an explicit closure for cloning elements
[INFO] [stderr]   --> src/tree.rs:48:29
[INFO] [stderr]    |
[INFO] [stderr] 48 |             leaf_distances: self.leaf_distances.iter().map( | ld | *ld ).collect(),
[INFO] [stderr]    |                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: Consider calling the dedicated `cloned` method: `self.leaf_distances.iter().cloned()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#map_clone
[INFO] [stderr] 
[INFO] [stderr] warning: You are using an explicit closure for cloning elements
[INFO] [stderr]   --> src/tree.rs:49:31
[INFO] [stderr]    |
[INFO] [stderr] 49 |             branch_distances: self.branch_distances.iter().map( | bd | *bd ).collect(),
[INFO] [stderr]    |                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: Consider calling the dedicated `cloned` method: `self.branch_distances.iter().cloned()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#map_clone
[INFO] [stderr] 
[INFO] [stderr] warning: use of `expect` followed by a function call
[INFO] [stderr]   --> src/tree.rs:92:64
[INFO] [stderr]    |
[INFO] [stderr] 92 |               let branch_distance = self.branch_distances.get(b).expect(&format!(
[INFO] [stderr]    |  ________________________________________________________________^
[INFO] [stderr] 93 | |                 "Branch state is invalid: Branch distance for branch {} missing",
[INFO] [stderr] 94 | |                 b
[INFO] [stderr] 95 | |             ));
[INFO] [stderr]    | |______________^ help: try this: `unwrap_or_else(|| panic!("Branch state is invalid: Branch distance for branch {} missing", b))`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::expect_fun_call)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#expect_fun_call
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]   --> src/tree.rs:98:16
[INFO] [stderr]    |
[INFO] [stderr] 98 |             if branch.branches.len() > 0 {
[INFO] [stderr]    |                ^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!branch.branches.is_empty()`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::len_zero)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/tree.rs:115:16
[INFO] [stderr]     |
[INFO] [stderr] 115 |             if branch.branches.len() > 0 {
[INFO] [stderr]     |                ^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!branch.branches.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/tree.rs:184:24
[INFO] [stderr]     |
[INFO] [stderr] 184 |                     if current_leaf.len() > 0 {
[INFO] [stderr]     |                        ^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!current_leaf.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/tree.rs:203:24
[INFO] [stderr]     |
[INFO] [stderr] 203 |                     if current_leaf.len() > 0 {
[INFO] [stderr]     |                        ^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!current_leaf.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/tree.rs:264:12
[INFO] [stderr]     |
[INFO] [stderr] 264 |         if (leaf_distances.len() > 0) & (leaf_distances.len() != leaves.len()) {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!leaf_distances.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/tree.rs:268:12
[INFO] [stderr]     |
[INFO] [stderr] 268 |         if (branch_distances.len() > 0) & (branch_distances.len() != branches.len()) {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!branch_distances.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/tree.rs:272:12
[INFO] [stderr]     |
[INFO] [stderr] 272 |         if leaf_distances.len() == 0 {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `leaf_distances.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/tree.rs:279:12
[INFO] [stderr]     |
[INFO] [stderr] 279 |         if branch_distances.len() == 0 {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `branch_distances.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: an inclusive range would be more readable
[INFO] [stderr]    --> src/tree.rs:354:47
[INFO] [stderr]     |
[INFO] [stderr] 354 |                         accumulated_distances[0..l + 1].iter().sum();
[INFO] [stderr]     |                                               ^^^^^^^^ help: use: `0..=l`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::range_plus_one)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#range_plus_one
[INFO] [stderr] 
[INFO] [stderr] warning: identical conversion
[INFO] [stderr]   --> src/graph_tree.rs:56:39
[INFO] [stderr]    |
[INFO] [stderr] 56 |                 let node_count_name = String::from(format!(">>{}", graph.node_count()));
[INFO] [stderr]    |                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider removing `String::from()`: `format!(">>{}", graph.node_count())`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::identity_conversion)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#identity_conversion
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]   --> src/graph_tree.rs:71:24
[INFO] [stderr]    |
[INFO] [stderr] 71 |                     if current_leaf.len() > 0 {
[INFO] [stderr]    |                        ^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!current_leaf.is_empty()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]   --> src/graph_tree.rs:91:24
[INFO] [stderr]    |
[INFO] [stderr] 91 |                     if current_leaf.len() > 0 {
[INFO] [stderr]    |                        ^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!current_leaf.is_empty()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: called `.get().unwrap()` on a Vec. Using `[]` is more clear and more concise
[INFO] [stderr]    --> src/tree_distance_matrix.rs:145:29
[INFO] [stderr]     |
[INFO] [stderr] 145 |                 leaves.push(leaf_map_inv_vec.get(lowest_pair[0]).unwrap().1.clone());
[INFO] [stderr]     |                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try this: `leaf_map_inv_vec[lowest_pair[0]]`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::get_unwrap)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#get_unwrap
[INFO] [stderr] 
[INFO] [stderr] warning: called `.get().unwrap()` on a Vec. Using `[]` is more clear and more concise
[INFO] [stderr]    --> src/tree_distance_matrix.rs:155:29
[INFO] [stderr]     |
[INFO] [stderr] 155 |                 leaves.push(leaf_map_inv_vec.get(lowest_pair[1]).unwrap().1.clone());
[INFO] [stderr]     |                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try this: `leaf_map_inv_vec[lowest_pair[1]]`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#get_unwrap
[INFO] [stderr] 
[INFO] [stderr] warning: You are using an explicit closure for cloning elements
[INFO] [stderr]    --> src/tree_distance_matrix.rs:172:41
[INFO] [stderr]     |
[INFO] [stderr] 172 |             let tree_keys: Vec<usize> = trees.keys().map(|x| *x).collect();
[INFO] [stderr]     |                                         ^^^^^^^^^^^^^^^^^^^^^^^^ help: Consider calling the dedicated `cloned` method: `trees.keys().cloned()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#map_clone
[INFO] [stderr] 
[INFO] [stderr] warning: You are using an explicit closure for cloning elements
[INFO] [stderr]    --> src/tree_distance_matrix.rs:185:37
[INFO] [stderr]     |
[INFO] [stderr] 185 |         let tree_keys: Vec<usize> = trees.keys().map(|x| *x).collect();
[INFO] [stderr]     |                                     ^^^^^^^^^^^^^^^^^^^^^^^^ help: Consider calling the dedicated `cloned` method: `trees.keys().cloned()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#map_clone
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]    --> src/tree_distance_matrix.rs:197:46
[INFO] [stderr]     |
[INFO] [stderr] 197 |     pub fn get_distance_ref(&self, leaf_one: &String, leaf_two: &String) -> Option<f32> {
[INFO] [stderr]     |                                              ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::ptr_arg)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]    --> src/tree_distance_matrix.rs:197:65
[INFO] [stderr]     |
[INFO] [stderr] 197 |     pub fn get_distance_ref(&self, leaf_one: &String, leaf_two: &String) -> Option<f32> {
[INFO] [stderr]     |                                                                 ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: taken reference of right operand
[INFO] [stderr]    --> src/tree_distance_matrix.rs:226:16
[INFO] [stderr]     |
[INFO] [stderr] 226 |             if key > &max_key {
[INFO] [stderr]     |                ^^^^^^--------
[INFO] [stderr]     |                      |
[INFO] [stderr]     |                      help: use the right value directly: `max_key`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::op_ref)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#op_ref
[INFO] [stderr] 
[INFO] [stderr] warning: an inclusive range would be more readable
[INFO] [stderr]    --> src/tree_distance_matrix.rs:233:18
[INFO] [stderr]     |
[INFO] [stderr] 233 |         for l in 0..max_key + 1 {
[INFO] [stderr]     |                  ^^^^^^^^^^^^^^ help: use: `0..=max_key`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#range_plus_one
[INFO] [stderr] 
[INFO] [stderr] warning: you seem to be trying to use match for destructuring a single pattern. Consider using `if let`
[INFO] [stderr]    --> src/tree_distance_matrix.rs:234:13
[INFO] [stderr]     |
[INFO] [stderr] 234 | /             match self.leaf_map_inv.get(&l) {
[INFO] [stderr] 235 | |                 Some(name) => {
[INFO] [stderr] 236 | |                     csv.push_str(name);
[INFO] [stderr] 237 | |                     leaves.push(name.to_string());
[INFO] [stderr] ...   |
[INFO] [stderr] 242 | |                 None => {}
[INFO] [stderr] 243 | |             }
[INFO] [stderr]     | |_____________^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::single_match)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#single_match
[INFO] [stderr] help: try this
[INFO] [stderr]     |
[INFO] [stderr] 234 |             if let Some(name) = self.leaf_map_inv.get(&l) {
[INFO] [stderr] 235 |     csv.push_str(name);
[INFO] [stderr] 236 |     leaves.push(name.to_string());
[INFO] [stderr] 237 |     if l < max_key {
[INFO] [stderr] 238 |         csv.push(delim);
[INFO] [stderr] 239 |     }
[INFO] [stderr]   ...
[INFO] [stderr] 
[INFO] [stderr] warning: the variable `v` is used as a loop counter. Consider using `for (v, item) in row.enumerate()` or similar iterators
[INFO] [stderr]    --> src/tree_distance_matrix.rs:251:24
[INFO] [stderr]     |
[INFO] [stderr] 251 |             for val in row {
[INFO] [stderr]     |                        ^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::explicit_counter_loop)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#explicit_counter_loop
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]    --> src/tree_distance_matrix.rs:450:55
[INFO] [stderr]     |
[INFO] [stderr] 450 |     pub fn get_partial_distance_matrix(&self, leaves: &Vec<String>) -> TreeDistanceMatrix {
[INFO] [stderr]     |                                                       ^^^^^^^^^^^^ help: change this to: `&[String]`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]   --> src/tree_merging.rs:64:24
[INFO] [stderr]    |
[INFO] [stderr] 64 |                     if overlapping_leaves.len() == 0 {
[INFO] [stderr]    |                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `overlapping_leaves.is_empty()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]   --> src/tree_merging.rs:68:24
[INFO] [stderr]    |
[INFO] [stderr] 68 |                     if new_leaves.len() == 0 {
[INFO] [stderr]    |                        ^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `new_leaves.is_empty()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: you seem to be trying to use match for destructuring a single pattern. Consider using `if let`
[INFO] [stderr]    --> src/tree_merging.rs:113:17
[INFO] [stderr]     |
[INFO] [stderr] 113 | /                 match dist {
[INFO] [stderr] 114 | |                     Some(d) => {
[INFO] [stderr] 115 | |                         overlapping_distance_matrix[[x, y]] = d;
[INFO] [stderr] 116 | |                         count_matrix[[x, y]] += 1.0
[INFO] [stderr] 117 | |                     }
[INFO] [stderr] 118 | |                     None => {}
[INFO] [stderr] 119 | |                 }
[INFO] [stderr]     | |_________________^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#single_match
[INFO] [stderr] help: try this
[INFO] [stderr]     |
[INFO] [stderr] 113 |                 if let Some(d) = dist {
[INFO] [stderr] 114 |     overlapping_distance_matrix[[x, y]] = d;
[INFO] [stderr] 115 |     count_matrix[[x, y]] += 1.0
[INFO] [stderr] 116 | }
[INFO] [stderr]     |
[INFO] [stderr] 
[INFO] [stderr] warning: You are using an explicit closure for cloning elements
[INFO] [stderr]    --> src/tree_merging.rs:128:9
[INFO] [stderr]     |
[INFO] [stderr] 128 |         all_leaves.iter().map(|l| l.clone()).collect(),
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: Consider calling the dedicated `cloned` method: `all_leaves.iter().cloned()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#map_clone
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]   --> src/utils.rs:24:13
[INFO] [stderr]    |
[INFO] [stderr] 24 |     vector: &Vec<T>,
[INFO] [stderr]    |             ^^^^^^^ help: change this to: `&[T]`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: identical conversion
[INFO] [stderr]   --> src/main.rs:27:43
[INFO] [stderr]    |
[INFO] [stderr] 27 |     let tree_file = utils::load_tree_file(String::from(fname));
[INFO] [stderr]    |                                           ^^^^^^^^^^^^^^^^^^^ help: consider removing `String::from()`: `fname`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#identity_conversion
[INFO] [stderr] 
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 12.14s
[INFO] running `"docker" "inspect" "b3d911d70bb51a84f5f02c79ac8f4b167314e9e2cdfeccff09bdb85a24f39847"`
[INFO] running `"docker" "rm" "-f" "b3d911d70bb51a84f5f02c79ac8f4b167314e9e2cdfeccff09bdb85a24f39847"`
[INFO] [stdout] b3d911d70bb51a84f5f02c79ac8f4b167314e9e2cdfeccff09bdb85a24f39847