[INFO] fetching crate lorikeet-genome 0.8.2...
[INFO] documenting lorikeet-genome-0.8.2 against 1.99.0-beta.1 for beta-rustdoc-1.99-1
[INFO] extracting crate lorikeet-genome 0.8.2 into /workspace/builds/worker-5-tc2/source
[INFO] started tweaking crates.io crate lorikeet-genome 0.8.2
[INFO] finished tweaking crates.io crate lorikeet-genome 0.8.2
[INFO] tweaked toml for crates.io crate lorikeet-genome 0.8.2 written to /workspace/builds/worker-5-tc2/source/Cargo.toml
[INFO] validating manifest of crates.io crate lorikeet-genome 0.8.2 on toolchain 1.99.0-beta.1
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.99.0-beta.1" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate lorikeet-genome 0.8.2 already has a lockfile, it will not be regenerated
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.99.0-beta.1" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr] warning: Cargo.toml: `panic` setting is ignored for `bench` profile
[INFO] [stderr] warning: Cargo.toml: `panic` setting is ignored for `test` profile
[INFO] [stderr] warning: `lorikeet-genome` (manifest) generated 2 warnings
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-m" "1610612736" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:a670955b218de27f2233287a1a3574f813d7f1e57e0ee2514f4dc7311f730a9d" "sleep" "infinity", kill_on_drop: false }`
[INFO] [stdout] 186569ca435cebfd606c1134982a4b1bf480211c6d5a791267668e9d6765588a
[INFO] running `Command { std: "docker" "start" "186569ca435cebfd606c1134982a4b1bf480211c6d5a791267668e9d6765588a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "186569ca435cebfd606c1134982a4b1bf480211c6d5a791267668e9d6765588a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-w" "/opt/rustwide/workdir" "--user" "0:0" "186569ca435cebfd606c1134982a4b1bf480211c6d5a791267668e9d6765588a" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.1" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "186569ca435cebfd606c1134982a4b1bf480211c6d5a791267668e9d6765588a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-w" "/opt/rustwide/workdir" "--user" "0:0" "186569ca435cebfd606c1134982a4b1bf480211c6d5a791267668e9d6765588a" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.1" "doc" "--frozen" "--no-deps" "--document-private-items" "--message-format=json", kill_on_drop: false }`
[INFO] [stderr] warning: Cargo.toml: `panic` setting is ignored for `bench` profile
[INFO] [stderr] warning: Cargo.toml: `panic` setting is ignored for `test` profile
[INFO] [stderr] warning: `lorikeet-genome` (manifest) generated 2 warnings
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[INFO] [stderr]  Documenting lorikeet-genome v0.8.2 (/opt/rustwide/workdir)
[INFO] [stderr]     Checking lorikeet-genome v0.8.2 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unnecessary parentheses around closure body
[INFO] [stdout]    --> src/assembly/assembly_based_caller_utils.rs:646:25
[INFO] [stdout]     |
[INFO] [stdout] 646 |             .filter(|v| (include_spanning_event || v.loc.get_start() == loc))
[INFO] [stdout]     |                         ^                                                  ^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_parens)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] help: remove these parentheses
[INFO] [stdout]     |
[INFO] [stdout] 646 -             .filter(|v| (include_spanning_event || v.loc.get_start() == loc))
[INFO] [stdout] 646 +             .filter(|v| include_spanning_event || v.loc.get_start() == loc)
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition name: `assert_no_panic`
[INFO] [stdout]   --> src/utils/natural_log_utils.rs:51:26
[INFO] [stdout]    |
[INFO] [stdout] 51 |     #[cfg_attr(all(test, assert_no_panic), no_panic::no_panic)]
[INFO] [stdout]    |                          ^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: expected names are: `docsrs`, `feature`, and `test` and 34 more
[INFO] [stdout]    = help: consider using a Cargo feature instead
[INFO] [stdout]    = help: or consider adding in `Cargo.toml` the `check-cfg` lint config for the lint:
[INFO] [stdout]             [lints.rust]
[INFO] [stdout]             unexpected_cfgs = { level = "warn", check-cfg = ['cfg(assert_no_panic)'] }
[INFO] [stdout]    = help: or consider adding `println!("cargo::rustc-check-cfg=cfg(assert_no_panic)");` to the top of the `build.rs`
[INFO] [stdout]    = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout]    = note: `#[warn(unexpected_cfgs)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unnecessary parentheses around closure body
[INFO] [stdout]    --> src/assembly/assembly_based_caller_utils.rs:646:25
[INFO] [stdout]     |
[INFO] [stdout] 646 |             .filter(|v| (include_spanning_event || v.loc.get_start() == loc))
[INFO] [stdout]     |                         ^                                                  ^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_parens)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] help: remove these parentheses
[INFO] [stdout]     |
[INFO] [stdout] 646 -             .filter(|v| (include_spanning_event || v.loc.get_start() == loc))
[INFO] [stdout] 646 +             .filter(|v| include_spanning_event || v.loc.get_start() == loc)
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition name: `assert_no_panic`
[INFO] [stdout]   --> src/utils/natural_log_utils.rs:51:26
[INFO] [stdout]    |
[INFO] [stdout] 51 |     #[cfg_attr(all(test, assert_no_panic), no_panic::no_panic)]
[INFO] [stdout]    |                          ^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: expected names are: `docsrs`, `feature`, and `test` and 34 more
[INFO] [stdout]    = help: consider using a Cargo feature instead
[INFO] [stdout]    = help: or consider adding in `Cargo.toml` the `check-cfg` lint config for the lint:
[INFO] [stdout]             [lints.rust]
[INFO] [stdout]             unexpected_cfgs = { level = "warn", check-cfg = ['cfg(assert_no_panic)'] }
[INFO] [stdout]    = help: or consider adding `println!("cargo::rustc-check-cfg=cfg(assert_no_panic)");` to the top of the `build.rs`
[INFO] [stdout]    = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout]    = note: `#[warn(unexpected_cfgs)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f32::MAX`: replaced by the `MAX` associated constant on `f32`
[INFO] [stdout]    --> src/activity_profile/activity_profile.rs:589:35
[INFO] [stdout]     |
[INFO] [stdout] 589 |         let mut min_p = std::f32::MAX;
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(deprecated)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NEG_INFINITY`: replaced by the `NEG_INFINITY` associated constant on `f64`
[INFO] [stdout]    --> src/assembly/assembly_based_caller_utils.rs:936:23
[INFO] [stdout]     |
[INFO] [stdout] 936 |             std::f64::NEG_INFINITY
[INFO] [stdout]     |                       ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::u64::MAX`: replaced by the `MAX` associated constant on this type
[INFO] [stdout]    --> src/assembly/assembly_region.rs:489:43
[INFO] [stdout]     |
[INFO] [stdout] 489 |                     .unwrap_or(&std::u64::MAX) as usize
[INFO] [stdout]     |                                           ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::i32::MAX`: replaced by the `MAX` associated constant on this type
[INFO] [stdout]   --> src/genotype/genotype_likelihoods.rs:24:39
[INFO] [stdout]    |
[INFO] [stdout] 24 |     pub const MAX_PL: i32 = std::i32::MAX;
[INFO] [stdout]    |                                       ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NEG_INFINITY`: replaced by the `NEG_INFINITY` associated constant on `f64`
[INFO] [stdout]   --> src/genotype/genotype_likelihoods.rs:73:49
[INFO] [stdout]    |
[INFO] [stdout] 73 |         let mut adjust = OrderedFloat(std::f64::NEG_INFINITY);
[INFO] [stdout]    |                                                 ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NEG_INFINITY`: replaced by the `NEG_INFINITY` associated constant on `f64`
[INFO] [stdout]   --> src/genotype/genotype_likelihoods.rs:88:34
[INFO] [stdout]    |
[INFO] [stdout] 88 |         let mut qual = std::f64::NEG_INFINITY;
[INFO] [stdout]    |                                  ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NAN`: replaced by the `NAN` associated constant on `f64`
[INFO] [stdout]    --> src/genotype/genotyping_engine.rs:260:29
[INFO] [stdout]     |
[INFO] [stdout] 260 |             .fold(std::f64::NAN, |a, b| {
[INFO] [stdout]     |                             ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NAN`: replaced by the `NAN` associated constant on `f64`
[INFO] [stdout]    --> src/genotype/genotyping_engine.rs:278:31
[INFO] [stdout]     |
[INFO] [stdout] 278 |             None => std::f64::NAN,
[INFO] [stdout]     |                               ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::INFINITY`: replaced by the `INFINITY` associated constant on `f64`
[INFO] [stdout]    --> src/graphs/adaptive_chain_pruner.rs:102:42
[INFO] [stdout]     |
[INFO] [stdout] 102 |             OrderedFloat::from(std::f64::INFINITY),
[INFO] [stdout]     |                                          ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::usize::MAX`: replaced by the `MAX` associated constant on this type
[INFO] [stdout]   --> src/graphs/seq_graph.rs:47:53
[INFO] [stdout]    |
[INFO] [stdout] 47 |         self.simplify_graph_with_cycles(std::usize::MAX, name)
[INFO] [stdout]    |                                                     ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::usize::MAX`: replaced by the `MAX` associated constant on this type
[INFO] [stdout]    --> src/graphs/shared_vertex_sequence_splitter.rs:448:35
[INFO] [stdout]     |
[INFO] [stdout] 448 |         let mut min = std::usize::MAX;
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::MIN`: replaced by the `MIN` associated constant on `f64`
[INFO] [stdout]   --> src/haplotype/haplotype.rs:45:43
[INFO] [stdout]    |
[INFO] [stdout] 45 |             score: OrderedFloat(std::f64::MIN),
[INFO] [stdout]    |                                           ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::MIN`: replaced by the `MIN` associated constant on `f64`
[INFO] [stdout]    --> src/haplotype/haplotype.rs:324:43
[INFO] [stdout]     |
[INFO] [stdout] 324 |             score: OrderedFloat(std::f64::MIN),
[INFO] [stdout]     |                                           ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::INFINITY`: replaced by the `INFINITY` associated constant on `f64`
[INFO] [stdout]    --> src/model/allele_frequency_calculator.rs:222:62
[INFO] [stdout]     |
[INFO] [stdout] 222 |         let mut allele_counts_maximum_difference = std::f64::INFINITY;
[INFO] [stdout]     |                                                              ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NAN`: replaced by the `NAN` associated constant on `f64`
[INFO] [stdout]    --> src/model/allele_frequency_calculator.rs:233:42
[INFO] [stdout]     |
[INFO] [stdout] 233 |                     .unwrap_or(std::f64::NAN);
[INFO] [stdout]     |                                          ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NEG_INFINITY`: replaced by the `NEG_INFINITY` associated constant on `f64`
[INFO] [stdout]    --> src/model/allele_frequency_calculator.rs:417:64
[INFO] [stdout]     |
[INFO] [stdout] 417 |         let log10_result = Rc::new(RefCell::new(vec![std::f64::NEG_INFINITY; num_alleles]));
[INFO] [stdout]     |                                                                ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NAN`: replaced by the `NAN` associated constant on `f64`
[INFO] [stdout]  --> src/model/allele_likelihoods.rs:5:15
[INFO] [stdout]   |
[INFO] [stdout] 5 | use std::f64::NAN;
[INFO] [stdout]   |               ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NAN`: replaced by the `NAN` associated constant on `f64`
[INFO] [stdout]    --> src/model/allele_likelihoods.rs:610:29
[INFO] [stdout]     |
[INFO] [stdout] 610 | ...                   NAN
[INFO] [stdout]     |                       ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NEG_INFINITY`: replaced by the `NEG_INFINITY` associated constant on `f64`
[INFO] [stdout]    --> src/model/allele_subsetting_utils.rs:205:46
[INFO] [stdout]     |
[INFO] [stdout] 205 |             let mut new_log10_gq = std::f64::NEG_INFINITY;
[INFO] [stdout]     |                                              ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NEG_INFINITY`: replaced by the `NEG_INFINITY` associated constant on `f64`
[INFO] [stdout]    --> src/model/allele_subsetting_utils.rs:250:42
[INFO] [stdout]     |
[INFO] [stdout] 250 |             if new_log10_gq != std::f64::NEG_INFINITY {
[INFO] [stdout]     |                                          ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::i32::MIN`: replaced by the `MIN` associated constant on this type
[INFO] [stdout]    --> src/model/variant_context.rs:454:47
[INFO] [stdout]     |
[INFO] [stdout] 454 |         let mut current_max_depth = std::i32::MIN;
[INFO] [stdout]     |                                               ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::i32::MIN`: replaced by the `MIN` associated constant on this type
[INFO] [stdout]    --> src/model/variant_context.rs:486:47
[INFO] [stdout]     |
[INFO] [stdout] 486 |         let mut current_max_depth = std::i32::MIN;
[INFO] [stdout]     |                                               ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::u8::MAX`: replaced by the `MAX` associated constant on this type
[INFO] [stdout]  --> src/read_threading/multi_debruijn_vertex.rs:9:69
[INFO] [stdout]   |
[INFO] [stdout] 9 |     static ref suffices_as_byte_array: Vec<Vec<u8>> = (0..=std::u8::MAX)
[INFO] [stdout]   |                                                                     ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::usize::MAX`: replaced by the `MAX` associated constant on this type
[INFO] [stdout]    --> src/read_threading/read_threading_assembler.rs:145:25
[INFO] [stdout]     |
[INFO] [stdout] 145 |             std::usize::MAX,
[INFO] [stdout]     |                         ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::usize::MAX`: replaced by the `MAX` associated constant on this type
[INFO] [stdout]    --> src/read_threading/read_threading_assembler.rs:169:25
[INFO] [stdout]     |
[INFO] [stdout] 169 |             std::usize::MAX,
[INFO] [stdout]     |                         ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::usize::MAX`: replaced by the `MAX` associated constant on this type
[INFO] [stdout]    --> src/read_threading/read_threading_assembler.rs:988:25
[INFO] [stdout]     |
[INFO] [stdout] 988 |             std::usize::MAX,
[INFO] [stdout]     |                         ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::usize::MIN`: replaced by the `MIN` associated constant on this type
[INFO] [stdout]   --> src/reads/read_utils.rs:17:68
[INFO] [stdout]    |
[INFO] [stdout] 17 |     pub const CANNOT_COMPUTE_ADAPTOR_BOUNDARY: usize = std::usize::MIN;
[INFO] [stdout]    |                                                                    ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::i32::MIN`: replaced by the `MIN` associated constant on this type
[INFO] [stdout]    --> src/smith_waterman/smith_waterman_aligner.rs:139:40
[INFO] [stdout]     |
[INFO] [stdout] 139 |         let low_init_value = std::i32::MIN / 2;
[INFO] [stdout]     |                                        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::i32::MIN`: replaced by the `MIN` associated constant on this type
[INFO] [stdout]    --> src/smith_waterman/smith_waterman_aligner.rs:285:39
[INFO] [stdout]     |
[INFO] [stdout] 285 |         let mut max_score = std::i32::MIN; // sw scores are allowed to be negative
[INFO] [stdout]     |                                       ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::EPSILON`: replaced by the `EPSILON` associated constant on `f64`
[INFO] [stdout]   --> src/test_utils/variant_context_test_utils.rs:33:33
[INFO] [stdout]    |
[INFO] [stdout] 33 |             epsilon = std::f64::EPSILON,
[INFO] [stdout]    |                                 ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NAN`: replaced by the `NAN` associated constant on `f64`
[INFO] [stdout]   --> src/utils/math_utils.rs:52:35
[INFO] [stdout]    |
[INFO] [stdout] 52 |             .unwrap_or(&std::f64::NAN);
[INFO] [stdout]    |                                   ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NEG_INFINITY`: replaced by the `NEG_INFINITY` associated constant on `f64`
[INFO] [stdout]    --> src/utils/math_utils.rs:163:30
[INFO] [stdout]     |
[INFO] [stdout] 163 |             return std::f64::NEG_INFINITY;
[INFO] [stdout]     |                              ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NEG_INFINITY`: replaced by the `NEG_INFINITY` associated constant on `f64`
[INFO] [stdout]    --> src/utils/math_utils.rs:170:35
[INFO] [stdout]     |
[INFO] [stdout] 170 |         if max_value == std::f64::NEG_INFINITY {
[INFO] [stdout]     |                                   ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NEG_INFINITY`: replaced by the `NEG_INFINITY` associated constant on `f64`
[INFO] [stdout]    --> src/utils/math_utils.rs:179:73
[INFO] [stdout]     |
[INFO] [stdout] 179 |                     *index != max_element_index && **value != std::f64::NEG_INFINITY
[INFO] [stdout]     |                                                                         ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::INFINITY`: replaced by the `INFINITY` associated constant on `f64`
[INFO] [stdout]    --> src/utils/math_utils.rs:187:53
[INFO] [stdout]     |
[INFO] [stdout] 187 |         if sum_tot.is_nan() || sum_tot == std::f64::INFINITY {
[INFO] [stdout]     |                                                     ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NAN`: replaced by the `NAN` associated constant on `f64`
[INFO] [stdout]    --> src/utils/math_utils.rs:236:35
[INFO] [stdout]     |
[INFO] [stdout] 236 |             .unwrap_or(&std::f64::NAN);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NAN`: replaced by the `NAN` associated constant on `f64`
[INFO] [stdout]    --> src/utils/math_utils.rs:261:35
[INFO] [stdout]     |
[INFO] [stdout] 261 |             .unwrap_or(&std::f64::NAN);
[INFO] [stdout]     |                                   ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NAN`: replaced by the `NAN` associated constant on `f64`
[INFO] [stdout]    --> src/utils/math_utils.rs:304:30
[INFO] [stdout]     |
[INFO] [stdout] 304 |             return std::f64::NAN;
[INFO] [stdout]     |                              ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NEG_INFINITY`: replaced by the `NEG_INFINITY` associated constant on `f64`
[INFO] [stdout]    --> src/utils/math_utils.rs:307:30
[INFO] [stdout]     |
[INFO] [stdout] 307 |             return std::f64::NEG_INFINITY;
[INFO] [stdout]     |                              ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NEG_INFINITY`: replaced by the `NEG_INFINITY` associated constant on `f64`
[INFO] [stdout]    --> src/utils/math_utils.rs:318:34
[INFO] [stdout]     |
[INFO] [stdout] 318 |         } else if a == std::f64::NEG_INFINITY {
[INFO] [stdout]     |                                  ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NEG_INFINITY`: replaced by the `NEG_INFINITY` associated constant on `f64`
[INFO] [stdout]    --> src/utils/math_utils.rs:350:30
[INFO] [stdout]     |
[INFO] [stdout] 350 |             return std::f64::NEG_INFINITY;
[INFO] [stdout]     |                              ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NEG_INFINITY`: replaced by the `NEG_INFINITY` associated constant on `f64`
[INFO] [stdout]    --> src/utils/math_utils.rs:357:60
[INFO] [stdout]     |
[INFO] [stdout] 357 |             if i == max_element_index || val == &std::f64::NEG_INFINITY {
[INFO] [stdout]     |                                                            ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NAN`: replaced by the `NAN` associated constant on `f64`
[INFO] [stdout]   --> src/utils/natural_log_utils.rs:38:30
[INFO] [stdout]    |
[INFO] [stdout] 38 |             return std::f64::NAN;
[INFO] [stdout]    |                              ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::NEG_INFINITY`: replaced by the `NEG_INFINITY` associated constant on `f64`
[INFO] [stdout]   --> src/utils/natural_log_utils.rs:41:30
[INFO] [stdout]    |
[INFO] [stdout] 41 |             return std::f64::NEG_INFINITY;
[INFO] [stdout]    |                              ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::MIN`: replaced by the `MIN` associated constant on `f64`
[INFO] [stdout]  --> src/utils/quality_utils.rs:8:56
[INFO] [stdout]   |
[INFO] [stdout] 8 |     static ref MIN_LOG10_SCALED_QUAL: f64 = (std::f64::MIN).log10();
[INFO] [stdout]   |                                                        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `std::f64::MAX`: replaced by the `MAX` associated constant on `f64`
[INFO] [stdout]   --> src/utils/quality_utils.rs:56:28
[INFO] [stdout]    |
[INFO] [stdout] 56 |             0 => std::f64::MAX,
[INFO] [stdout]    |                            ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unknown disambiguator `0,{`
[INFO] [stdout]    --> src/genotype/genotype_allele_counts.rs:548:117
[INFO] [stdout]     |
[INFO] [stdout] 548 |      *   If negative, the absolute value can be used to determine where would be that index inserted within {@code [0,{@link #disti...
[INFO] [stdout]     |                                                                                                                     ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: see https://doc.rust-lang.org/beta/rustdoc/write-documentation/linking-to-items-by-name.html#namespaces-and-disambiguators for more info about disambiguators
[INFO] [stdout]     = note: `#[warn(rustdoc::broken_intra_doc_links)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `from,to`
[INFO] [stdout]    --> src/genotype/genotype_allele_counts.rs:592:61
[INFO] [stdout]     |
[INFO] [stdout] 592 |      *  the potential insertion point (within the interval [from,to]) as {@code -result - 1}
[INFO] [stdout]     |                                                             ^^^^^^^ no item named `from,to` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `0,1,2,1`
[INFO] [stdout]    --> src/genotype/genotype_allele_counts.rs:694:48
[INFO] [stdout]     |
[INFO] [stdout] 694 |      * is 4 and {@code sortedAlleleCounts} is [0,1,2,1] then alleles 0 and 2 are present, each with a count of 1, while
[INFO] [stdout]     |                                                ^^^^^^^ no item named `0,1,2,1` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `r`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculator.rs:363:53
[INFO] [stdout]     |
[INFO] [stdout] 363 |      * @param readLikelihoodsByGenotypeIndex <i>[g][r]</i> likelihoods for each genotype <i>g</i> and <i>r</i>.
[INFO] [stdout]     |                                                     ^ no item named `r` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `f`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculator.rs:390:57
[INFO] [stdout]     |
[INFO] [stdout] 390 |      * @param readLikelihoodComponentsByAlleleCount [a][f][r] likelihood stratified by allele <i>a</i>, frequency in genotype <i>f<...
[INFO] [stdout]     |                                                         ^ no item named `f` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `r`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculator.rs:390:60
[INFO] [stdout]     |
[INFO] [stdout] 390 |      * @param readLikelihoodComponentsByAlleleCount [a][f][r] likelihood stratified by allele <i>a</i>, frequency in genotype <i>f<...
[INFO] [stdout]     |                                                            ^ no item named `r` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `a`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:120:41
[INFO] [stdout]     |
[INFO] [stdout] 120 |      * Thus the value a position <i>[p][a]</i> indicates how many genotypes of ploidy <i>p</i> there are before the first
[INFO] [stdout]     |                                         ^ no item named `a` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `A`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:124:12
[INFO] [stdout]     |
[INFO] [stdout] 124 |      * [3][A] == [3][0] == 0 as the first genotype AAA contains A.
[INFO] [stdout]     |            ^ no item named `A` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `0`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:124:22
[INFO] [stdout]     |
[INFO] [stdout] 124 |      * [3][A] == [3][0] == 0 as the first genotype AAA contains A.
[INFO] [stdout]     |                      ^ no item named `0` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `C`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:125:12
[INFO] [stdout]     |
[INFO] [stdout] 125 |      * [3][C] == [3][2] == 4 as the first genotype that contains C, AAC follows: AAA AAB ABB BBB
[INFO] [stdout]     |            ^ no item named `C` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `2`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:125:22
[INFO] [stdout]     |
[INFO] [stdout] 125 |      * [3][C] == [3][2] == 4 as the first genotype that contains C, AAC follows: AAA AAB ABB BBB
[INFO] [stdout]     |                      ^ no item named `2` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `D`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:126:12
[INFO] [stdout]     |
[INFO] [stdout] 126 |      * [4][D] == [4][3] == 14  as the first genotype that contains D, AAAD follows: AAAA AAAB AABB ABBB BBBB AAAC
[INFO] [stdout]     |            ^ no item named `D` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `3`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:126:22
[INFO] [stdout]     |
[INFO] [stdout] 126 |      * [4][D] == [4][3] == 14  as the first genotype that contains D, AAAD follows: AAAA AAAB AABB ABBB BBBB AAAC
[INFO] [stdout]     |                      ^ no item named `3` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `a`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:136:18
[INFO] [stdout]     |
[INFO] [stdout] 136 |      * Offset[p][a] := Offset[p-1][a] + Offset[p][a-1] when a > 0, p > 0
[INFO] [stdout]     |                  ^ no item named `a` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `a`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:136:36
[INFO] [stdout]     |
[INFO] [stdout] 136 |      * Offset[p][a] := Offset[p-1][a] + Offset[p][a-1] when a > 0, p > 0
[INFO] [stdout]     |                                    ^ no item named `a` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `a-1`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:136:51
[INFO] [stdout]     |
[INFO] [stdout] 136 |      * Offset[p][a] := Offset[p-1][a] + Offset[p][a-1] when a > 0, p > 0
[INFO] [stdout]     |                                                   ^^^ no item named `a-1` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `1`
[INFO] [stdout]   --> src/graphs/low_weight_chain_pruner.rs:10:12
[INFO] [stdout]    |
[INFO] [stdout] 10 |  * For A -[1]> B -[1]> C -[1]> D would be removed with pruneFactor 2
[INFO] [stdout]    |            ^ no item named `1` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `1`
[INFO] [stdout]   --> src/graphs/low_weight_chain_pruner.rs:10:20
[INFO] [stdout]    |
[INFO] [stdout] 10 |  * For A -[1]> B -[1]> C -[1]> D would be removed with pruneFactor 2
[INFO] [stdout]    |                    ^ no item named `1` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `1`
[INFO] [stdout]   --> src/graphs/low_weight_chain_pruner.rs:10:28
[INFO] [stdout]    |
[INFO] [stdout] 10 |  * For A -[1]> B -[1]> C -[1]> D would be removed with pruneFactor 2
[INFO] [stdout]    |                            ^ no item named `1` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `1`
[INFO] [stdout]   --> src/graphs/low_weight_chain_pruner.rs:11:12
[INFO] [stdout]    |
[INFO] [stdout] 11 |  * but A -[1]> B -[2]> C -[1]> D would not be because the linear chain includes an edge with weight >= 2
[INFO] [stdout]    |            ^ no item named `1` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `2`
[INFO] [stdout]   --> src/graphs/low_weight_chain_pruner.rs:11:20
[INFO] [stdout]    |
[INFO] [stdout] 11 |  * but A -[1]> B -[2]> C -[1]> D would not be because the linear chain includes an edge with weight >= 2
[INFO] [stdout]    |                    ^ no item named `2` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `1`
[INFO] [stdout]   --> src/graphs/low_weight_chain_pruner.rs:11:28
[INFO] [stdout]    |
[INFO] [stdout] 11 |  * but A -[1]> B -[2]> C -[1]> D would not be because the linear chain includes an edge with weight >= 2
[INFO] [stdout]    |                            ^ no item named `1` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `7`
[INFO] [stdout]    --> src/model/allele_subsetting_utils.rs:300:38
[INFO] [stdout]     |
[INFO] [stdout] 300 |      * to new PL indices i.e. result[7] = old PL index of genotype containing same alleles as the new genotype with PL index 7.
[INFO] [stdout]     |                                      ^ no item named `7` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `r`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm.rs:214:84
[INFO] [stdout]     |
[INFO] [stdout] 214 |      * @param logLikelihoods where to store the log likelihoods where position [a][r] is reserved for the log likelihood of {@code ...
[INFO] [stdout]     |                                                                                    ^ no item named `r` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `r`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm.rs:214:138
[INFO] [stdout]     |
[INFO] [stdout] 214 | ...s reserved for the log likelihood of {@code reads[r]}
[INFO] [stdout]     |                                                      ^ no item named `r` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `a`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm.rs:215:50
[INFO] [stdout]     |
[INFO] [stdout] 215 |      *             conditional to {@code alleles[a]}.
[INFO] [stdout]     |                                                  ^ no item named `a` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `0`
[INFO] [stdout]    --> src/reads/alignment_utils.rs:752:112
[INFO] [stdout]     |
[INFO] [stdout] 752 |      * @param basesStartOnRef where does the bases array start w.r.t. the reference start?  For example, bases[0] of
[INFO] [stdout]     |                                                                                                                ^ no item named `0` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `AaCcGgTt`
[INFO] [stdout]   --> src/utils/base_utils.rs:65:21
[INFO] [stdout]    |
[INFO] [stdout] 65 |      * @param base [AaCcGgTt]
[INFO] [stdout]    |                     ^^^^^^^^ no item named `AaCcGgTt` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `A`
[INFO] [stdout]   --> src/utils/utils.rs:53:18
[INFO] [stdout]    |
[INFO] [stdout] 53 |  * if N = 1 => [[A], [B], [C]]
[INFO] [stdout]    |                  ^ no item named `A` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `B`
[INFO] [stdout]   --> src/utils/utils.rs:53:23
[INFO] [stdout]    |
[INFO] [stdout] 53 |  * if N = 1 => [[A], [B], [C]]
[INFO] [stdout]    |                       ^ no item named `B` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `C`
[INFO] [stdout]   --> src/utils/utils.rs:53:28
[INFO] [stdout]    |
[INFO] [stdout] 53 |  * if N = 1 => [[A], [B], [C]]
[INFO] [stdout]    |                            ^ no item named `C` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `1,2,3,4,5`
[INFO] [stdout]    --> src/activity_profile/activity_profile.rs:303:9
[INFO] [stdout]     |
[INFO] [stdout] 303 |      * [1,2,3,4,5] but not [1,2,3,5].
[INFO] [stdout]     |         ^^^^^^^^^ no item named `1,2,3,4,5` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `1,2,3,5`
[INFO] [stdout]    --> src/activity_profile/activity_profile.rs:303:29
[INFO] [stdout]     |
[INFO] [stdout] 303 |      * [1,2,3,4,5] but not [1,2,3,5].
[INFO] [stdout]     |                             ^^^^^^^ no item named `1,2,3,5` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/ani_calculator/ani_calculator.rs:15:26
[INFO] [stdout]    |
[INFO] [stdout] 15 | /// Defined by InStrain: https://www.nature.com/articles/s41587-020-00797-0?proof=t%3B#Sec9
[INFO] [stdout]    |                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout]    = note: `#[warn(rustdoc::bare_urls)]` on by default
[INFO] [stdout] help: use an automatic link instead
[INFO] [stdout]    |
[INFO] [stdout] 15 | /// Defined by InStrain: <https://www.nature.com/articles/s41587-020-00797-0?proof=t%3B#Sec9>
[INFO] [stdout]    |                          +                                                                  +
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `p`
[INFO] [stdout]   --> src/annotator/tandem_repeat.rs:11:4
[INFO] [stdout]    |
[INFO] [stdout] 11 |  * <p>A tandem repeat unit is composed of one or more nucleotides that are repeated multiple times in series. Repetitive sequences a...
[INFO] [stdout]    |    ^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(rustdoc::invalid_html_tags)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]   --> src/assembly/assembly_region_trimmer.rs:13:4
[INFO] [stdout]    |
[INFO] [stdout] 13 |  * <p/>
[INFO] [stdout]    |    ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/assembly/assembly_region_trimmer.rs:273:9
[INFO] [stdout]     |
[INFO] [stdout] 273 |      *  <p/>
[INFO] [stdout]     |         ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/assembly/assembly_result_set.rs:274:8
[INFO] [stdout]     |
[INFO] [stdout] 274 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unopened HTML tag `p`
[INFO] [stdout]   --> src/genotype/genotype_allele_counts.rs:20:123
[INFO] [stdout]    |
[INFO] [stdout] 20 |  * Collection of allele counts for a genotype. It encompasses what alleles are present in the genotype and in what number.</p>
[INFO] [stdout]    |                                                                                                                           ^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculator.rs:102:88
[INFO] [stdout]     |
[INFO] [stdout] 102 |      * calculation request calling {@link #ensureReadCapacity(int) ensureReadCapacity}.<p/>
[INFO] [stdout]     |                                                                                        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `p`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculator.rs:101:8
[INFO] [stdout]     |
[INFO] [stdout] 101 |      * <p>This figure is increased dynamically as per the
[INFO] [stdout]     |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `li`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculator.rs:241:13
[INFO] [stdout]     |
[INFO] [stdout] 241 |      *      <li>or it contains any negatives,
[INFO] [stdout]     |             ^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `T`
[INFO] [stdout]    --> src/graphs/base_graph.rs:885:15
[INFO] [stdout]     |
[INFO] [stdout] 885 |      * @param <T> the type of the nodes in those graphs
[INFO] [stdout]     |               ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unopened HTML tag `ul`
[INFO] [stdout]   --> src/graphs/graph_based_k_best_haplotype_finder.rs:35:8
[INFO] [stdout]    |
[INFO] [stdout] 32 |      * @throws IllegalArgumentException if <ul>
[INFO] [stdout]    |                                            ---- does not match this unclosed tag
[INFO] [stdout] ...
[INFO] [stdout] 35 |      * </ul>
[INFO] [stdout]    |        -^^^^
[INFO] [stdout]    |        |
[INFO] [stdout]    |        this unopened tag
[INFO] [stdout]    |        because the Markdown paragraph ends here
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/graphs/graph_based_k_best_haplotype_finder.rs:62:55
[INFO] [stdout]    |
[INFO] [stdout] 62 |      * Implement Dijkstra's algorithm as described in https://en.wikipedia.org/wiki/K_shortest_path_routing
[INFO] [stdout]    |                                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] help: use an automatic link instead
[INFO] [stdout]    |
[INFO] [stdout] 62 |      * Implement Dijkstra's algorithm as described in <https://en.wikipedia.org/wiki/K_shortest_path_routing>
[INFO] [stdout]    |                                                       +                                                     +
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `A`
[INFO] [stdout]   --> src/model/allele_likelihoods.rs:25:11
[INFO] [stdout]    |
[INFO] [stdout] 25 |  * @param <A> the type of the allele the likelihood makes reference to.
[INFO] [stdout]    |           ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `usize`
[INFO] [stdout]    --> src/model/allele_likelihoods.rs:204:28
[INFO] [stdout]     |
[INFO] [stdout] 204 |      * @return never Option<usize>.
[INFO] [stdout]     |                            ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout] help: try marking as source code
[INFO] [stdout]     |
[INFO] [stdout] 204 |      * @return never `Option<usize>`.
[INFO] [stdout]     |                      +             +
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `A`
[INFO] [stdout]   --> src/model/allele_list.rs:59:15
[INFO] [stdout]    |
[INFO] [stdout] 59 |      * @param <A> the allele class.
[INFO] [stdout]    |               ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> src/model/variant_context_utils.rs:370:49
[INFO] [stdout]     |
[INFO] [stdout] 370 |      * For more information on this method see: http://www.thedistractionnetwork.com/programmer-problem/
[INFO] [stdout]     |                                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] help: use an automatic link instead
[INFO] [stdout]     |
[INFO] [stdout] 370 |      * For more information on this method see: <http://www.thedistractionnetwork.com/programmer-problem/>
[INFO] [stdout]     |                                                 +                                                        +
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]   --> src/pair_hmm/pair_hmm_model.rs:29:8
[INFO] [stdout]    |
[INFO] [stdout] 29 |      * <p/>
[INFO] [stdout]    |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]   --> src/pair_hmm/pair_hmm_model.rs:31:8
[INFO] [stdout]    |
[INFO] [stdout] 31 |      * <p/>
[INFO] [stdout]    |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]   --> src/pair_hmm/pair_hmm_model.rs:38:8
[INFO] [stdout]    |
[INFO] [stdout] 38 |      * <p/>
[INFO] [stdout]    |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]   --> src/pair_hmm/pair_hmm_model.rs:40:8
[INFO] [stdout]    |
[INFO] [stdout] 40 |      * <p/>
[INFO] [stdout]    |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm_model.rs:180:8
[INFO] [stdout]     |
[INFO] [stdout] 180 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm_model.rs:183:8
[INFO] [stdout]     |
[INFO] [stdout] 183 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm_model.rs:237:8
[INFO] [stdout]     |
[INFO] [stdout] 237 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm_model.rs:240:8
[INFO] [stdout]     |
[INFO] [stdout] 240 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm_model.rs:347:8
[INFO] [stdout]     |
[INFO] [stdout] 347 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm_model.rs:350:8
[INFO] [stdout]     |
[INFO] [stdout] 350 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm_model.rs:401:8
[INFO] [stdout]     |
[INFO] [stdout] 401 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm_model.rs:404:8
[INFO] [stdout]     |
[INFO] [stdout] 404 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm_model.rs:430:8
[INFO] [stdout]     |
[INFO] [stdout] 430 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/reads/alignment_utils.rs:407:8
[INFO] [stdout]     |
[INFO] [stdout] 407 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/reads/bird_tool_reads.rs:206:8
[INFO] [stdout]     |
[INFO] [stdout] 206 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `p`
[INFO] [stdout]    --> src/reads/clipping_op.rs:184:8
[INFO] [stdout]     |
[INFO] [stdout] 184 |      * <p>
[INFO] [stdout]     |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `p`
[INFO] [stdout]    --> src/reads/clipping_op.rs:188:8
[INFO] [stdout]     |
[INFO] [stdout] 188 |      * <p>
[INFO] [stdout]     |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `p`
[INFO] [stdout]    --> src/reads/clipping_op.rs:192:8
[INFO] [stdout]     |
[INFO] [stdout] 192 |      * <p>
[INFO] [stdout]     |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `p`
[INFO] [stdout]    --> src/reads/clipping_op.rs:194:8
[INFO] [stdout]     |
[INFO] [stdout] 194 |      * <p>
[INFO] [stdout]     |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `File`
[INFO] [stdout]   --> src/reference/reference_reader.rs:13:48
[INFO] [stdout]    |
[INFO] [stdout] 13 | * indexed_reader represents the #[IndexedReader<File>]
[INFO] [stdout]    |                                                ^^^^^^
[INFO] [stdout]    |
[INFO] [stdout] help: try marking as source code
[INFO] [stdout]    |
[INFO] [stdout] 13 | * indexed_reader represents the #[`IndexedReader<File>`]
[INFO] [stdout]    |                                   +                   +
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]   --> src/test_utils/allele_list_unit_tester.rs:32:8
[INFO] [stdout]    |
[INFO] [stdout] 32 |      * <p/>
[INFO] [stdout]    |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `p`
[INFO] [stdout]   --> src/test_utils/random_dna.rs:34:8
[INFO] [stdout]    |
[INFO] [stdout] 34 |      * <p>
[INFO] [stdout]    |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `p`
[INFO] [stdout]   --> src/test_utils/random_dna.rs:42:8
[INFO] [stdout]    |
[INFO] [stdout] 42 |      * <p>
[INFO] [stdout]    |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `p`
[INFO] [stdout]   --> src/test_utils/read_clipper_test_utils.rs:77:8
[INFO] [stdout]    |
[INFO] [stdout] 77 |      * <p>
[INFO] [stdout]    |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> src/utils/math_utils.rs:421:12
[INFO] [stdout]     |
[INFO] [stdout] 421 |      * See http://www.nezumi.demon.co.uk/consult/logx.htm
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] help: use an automatic link instead
[INFO] [stdout]     |
[INFO] [stdout] 421 |      * See <http://www.nezumi.demon.co.uk/consult/logx.htm>
[INFO] [stdout]     |            +                                              +
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: hiding a lifetime that's elided elsewhere is confusing
[INFO] [stdout]   --> src/bam_parsing/bam_generator.rs:27:15
[INFO] [stdout]    |
[INFO] [stdout] 27 |     fn pileup(&mut self) -> Option<bam::pileup::Pileups<bam::Reader>>;
[INFO] [stdout]    |               ^^^^^^^^^            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ the same lifetime is hidden here
[INFO] [stdout]    |               |
[INFO] [stdout]    |               the lifetime is elided here
[INFO] [stdout]    |
[INFO] [stdout]    = help: the same lifetime is referred to in inconsistent ways, making the signature confusing
[INFO] [stdout]    = note: `#[warn(mismatched_lifetime_syntaxes)]` on by default
[INFO] [stdout] help: use `'_` for type paths
[INFO] [stdout]    |
[INFO] [stdout] 27 |     fn pileup(&mut self) -> Option<bam::pileup::Pileups<'_, bam::Reader>>;
[INFO] [stdout]    |                                                         +++
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: hiding a lifetime that's elided elsewhere is confusing
[INFO] [stdout]   --> src/bam_parsing/bam_generator.rs:60:15
[INFO] [stdout]    |
[INFO] [stdout] 60 |     fn pileup(&mut self) -> Option<bam::pileup::Pileups<bam::IndexedReader>>;
[INFO] [stdout]    |               ^^^^^^^^^            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ the same lifetime is hidden here
[INFO] [stdout]    |               |
[INFO] [stdout]    |               the lifetime is elided here
[INFO] [stdout]    |
[INFO] [stdout]    = help: the same lifetime is referred to in inconsistent ways, making the signature confusing
[INFO] [stdout] help: use `'_` for type paths
[INFO] [stdout]    |
[INFO] [stdout] 60 |     fn pileup(&mut self) -> Option<bam::pileup::Pileups<'_, bam::IndexedReader>>;
[INFO] [stdout]    |                                                         +++
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: hiding a lifetime that's elided elsewhere is confusing
[INFO] [stdout]    --> src/bam_parsing/bam_generator.rs:116:15
[INFO] [stdout]     |
[INFO] [stdout] 116 |     fn pileup(&mut self) -> Option<bam::pileup::Pileups<bam::Reader>> {
[INFO] [stdout]     |               ^^^^^^^^^            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ the same lifetime is hidden here
[INFO] [stdout]     |               |
[INFO] [stdout]     |               the lifetime is elided here
[INFO] [stdout]     |
[INFO] [stdout]     = help: the same lifetime is referred to in inconsistent ways, making the signature confusing
[INFO] [stdout] help: use `'_` for type paths
[INFO] [stdout]     |
[INFO] [stdout] 116 |     fn pileup(&mut self) -> Option<bam::pileup::Pileups<'_, bam::Reader>> {
[INFO] [stdout]     |                                                         +++
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: hiding a lifetime that's elided elsewhere is confusing
[INFO] [stdout]    --> src/bam_parsing/bam_generator.rs:182:15
[INFO] [stdout]     |
[INFO] [stdout] 182 |     fn pileup(&mut self) -> Option<bam::pileup::Pileups<bam::IndexedReader>> {
[INFO] [stdout]     |               ^^^^^^^^^            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ the same lifetime is hidden here
[INFO] [stdout]     |               |
[INFO] [stdout]     |               the lifetime is elided here
[INFO] [stdout]     |
[INFO] [stdout]     = help: the same lifetime is referred to in inconsistent ways, making the signature confusing
[INFO] [stdout] help: use `'_` for type paths
[INFO] [stdout]     |
[INFO] [stdout] 182 |     fn pileup(&mut self) -> Option<bam::pileup::Pileups<'_, bam::IndexedReader>> {
[INFO] [stdout]     |                                                         +++
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: hiding a lifetime that's elided elsewhere is confusing
[INFO] [stdout]    --> src/bam_parsing/bam_generator.rs:356:15
[INFO] [stdout]     |
[INFO] [stdout] 356 |     fn pileup(&mut self) -> Option<bam::pileup::Pileups<bam::Reader>> {
[INFO] [stdout]     |               ^^^^^^^^^            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ the same lifetime is hidden here
[INFO] [stdout]     |               |
[INFO] [stdout]     |               the lifetime is elided here
[INFO] [stdout]     |
[INFO] [stdout]     = help: the same lifetime is referred to in inconsistent ways, making the signature confusing
[INFO] [stdout] help: use `'_` for type paths
[INFO] [stdout]     |
[INFO] [stdout] 356 |     fn pileup(&mut self) -> Option<bam::pileup::Pileups<'_, bam::Reader>> {
[INFO] [stdout]     |                                                         +++
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: hiding a lifetime that's elided elsewhere is confusing
[INFO] [stdout]    --> src/bam_parsing/bam_generator.rs:627:15
[INFO] [stdout]     |
[INFO] [stdout] 627 |     fn pileup(&mut self) -> Option<bam::pileup::Pileups<bam::Reader>> {
[INFO] [stdout]     |               ^^^^^^^^^            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ the same lifetime is hidden here
[INFO] [stdout]     |               |
[INFO] [stdout]     |               the lifetime is elided here
[INFO] [stdout]     |
[INFO] [stdout]     = help: the same lifetime is referred to in inconsistent ways, making the signature confusing
[INFO] [stdout] help: use `'_` for type paths
[INFO] [stdout]     |
[INFO] [stdout] 627 |     fn pileup(&mut self) -> Option<bam::pileup::Pileups<'_, bam::Reader>> {
[INFO] [stdout]     |                                                         +++
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: hiding a lifetime that's elided elsewhere is confusing
[INFO] [stdout]    --> src/bam_parsing/bam_generator.rs:797:15
[INFO] [stdout]     |
[INFO] [stdout] 797 |     fn pileup(&mut self) -> Option<bam::pileup::Pileups<bam::Reader>> {
[INFO] [stdout]     |               ^^^^^^^^^            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ the same lifetime is hidden here
[INFO] [stdout]     |               |
[INFO] [stdout]     |               the lifetime is elided here
[INFO] [stdout]     |
[INFO] [stdout]     = help: the same lifetime is referred to in inconsistent ways, making the signature confusing
[INFO] [stdout] help: use `'_` for type paths
[INFO] [stdout]     |
[INFO] [stdout] 797 |     fn pileup(&mut self) -> Option<bam::pileup::Pileups<'_, bam::Reader>> {
[INFO] [stdout]     |                                                         +++
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: hiding a lifetime that's elided elsewhere is confusing
[INFO] [stdout]     --> src/bam_parsing/bam_generator.rs:1128:15
[INFO] [stdout]      |
[INFO] [stdout] 1128 |     fn pileup(&mut self) -> Option<bam::pileup::Pileups<bam::Reader>> {
[INFO] [stdout]      |               ^^^^^^^^^            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ the same lifetime is hidden here
[INFO] [stdout]      |               |
[INFO] [stdout]      |               the lifetime is elided here
[INFO] [stdout]      |
[INFO] [stdout]      = help: the same lifetime is referred to in inconsistent ways, making the signature confusing
[INFO] [stdout] help: use `'_` for type paths
[INFO] [stdout]      |
[INFO] [stdout] 1128 |     fn pileup(&mut self) -> Option<bam::pileup::Pileups<'_, bam::Reader>> {
[INFO] [stdout]      |                                                         +++
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: hiding a lifetime that's elided elsewhere is confusing
[INFO] [stdout]    --> src/bam_parsing/filter.rs:225:19
[INFO] [stdout]     |
[INFO] [stdout] 225 |     pub fn pileup(&mut self) -> bam::pileup::Pileups<bam::Reader> {
[INFO] [stdout]     |                   ^^^^^^^^^     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ the same lifetime is hidden here
[INFO] [stdout]     |                   |
[INFO] [stdout]     |                   the lifetime is elided here
[INFO] [stdout]     |
[INFO] [stdout]     = help: the same lifetime is referred to in inconsistent ways, making the signature confusing
[INFO] [stdout] help: use `'_` for type paths
[INFO] [stdout]     |
[INFO] [stdout] 225 |     pub fn pileup(&mut self) -> bam::pileup::Pileups<'_, bam::Reader> {
[INFO] [stdout]     |                                                      +++
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: hiding a lifetime that's named elsewhere is confusing
[INFO] [stdout]    --> src/read_threading/abstract_read_threading_graph.rs:594:10
[INFO] [stdout]     |
[INFO] [stdout] 589 |         sequence: &'a [u8],
[INFO] [stdout]     |                    -- the lifetime is named here
[INFO] [stdout] ...
[INFO] [stdout] 594 |     ) -> SequenceForKmers {
[INFO] [stdout]     |          ^^^^^^^^^^^^^^^^ the same lifetime is hidden here
[INFO] [stdout]     |
[INFO] [stdout]     = help: the same lifetime is referred to in inconsistent ways, making the signature confusing
[INFO] [stdout] help: consistently use `'a`
[INFO] [stdout]     |
[INFO] [stdout] 594 |     ) -> SequenceForKmers<'a> {
[INFO] [stdout]     |                          ++++
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 09s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: partitions v0.2.4
[INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 2`
[INFO] [stderr]    Generated /opt/rustwide/target/doc/lorikeet_genome/index.html and 1 other file
[INFO] running `Command { std: "docker" "inspect" "186569ca435cebfd606c1134982a4b1bf480211c6d5a791267668e9d6765588a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-e" "DOCS_RS=1" "-e" "RUSTC_BOOTSTRAP=1" "-w" "/opt/rustwide/workdir" "--user" "0:0" "186569ca435cebfd606c1134982a4b1bf480211c6d5a791267668e9d6765588a" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.1" "rustdoc" "--lib" "-Zrustdoc-map" "--config" "build.rustdocflags=[\"--cfg\", \"docsrs\", \"-Z\", \"unstable-options\", \"--document-private-items\"]" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stderr] warning: Cargo.toml: `panic` setting is ignored for `bench` profile
[INFO] [stderr] warning: Cargo.toml: `panic` setting is ignored for `test` profile
[INFO] [stderr] warning: `lorikeet-genome` (manifest) generated 2 warnings
[INFO] [stderr]  Documenting lorikeet-genome v0.8.2 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unnecessary parentheses around closure body
[INFO] [stdout]    --> src/assembly/assembly_based_caller_utils.rs:646:25
[INFO] [stdout]     |
[INFO] [stdout] 646 |             .filter(|v| (include_spanning_event || v.loc.get_start() == loc))
[INFO] [stdout]     |                         ^                                                  ^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_parens)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] help: remove these parentheses
[INFO] [stdout]     |
[INFO] [stdout] 646 -             .filter(|v| (include_spanning_event || v.loc.get_start() == loc))
[INFO] [stdout] 646 +             .filter(|v| include_spanning_event || v.loc.get_start() == loc)
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition name: `assert_no_panic`
[INFO] [stdout]   --> src/utils/natural_log_utils.rs:51:26
[INFO] [stdout]    |
[INFO] [stdout] 51 |     #[cfg_attr(all(test, assert_no_panic), no_panic::no_panic)]
[INFO] [stdout]    |                          ^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: expected names are: `docsrs`, `feature`, and `test` and 34 more
[INFO] [stdout]    = help: consider using a Cargo feature instead
[INFO] [stdout]    = help: or consider adding in `Cargo.toml` the `check-cfg` lint config for the lint:
[INFO] [stdout]             [lints.rust]
[INFO] [stdout]             unexpected_cfgs = { level = "warn", check-cfg = ['cfg(assert_no_panic)'] }
[INFO] [stdout]    = help: or consider adding `println!("cargo::rustc-check-cfg=cfg(assert_no_panic)");` to the top of the `build.rs`
[INFO] [stdout]    = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout]    = note: `#[warn(unexpected_cfgs)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unknown disambiguator `0,{`
[INFO] [stdout]    --> src/genotype/genotype_allele_counts.rs:548:117
[INFO] [stdout]     |
[INFO] [stdout] 548 |      *   If negative, the absolute value can be used to determine where would be that index inserted within {@code [0,{@link #disti...
[INFO] [stdout]     |                                                                                                                     ^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: see https://doc.rust-lang.org/beta/rustdoc/write-documentation/linking-to-items-by-name.html#namespaces-and-disambiguators for more info about disambiguators
[INFO] [stdout]     = note: `#[warn(rustdoc::broken_intra_doc_links)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `0,1,2,1`
[INFO] [stdout]    --> src/genotype/genotype_allele_counts.rs:694:48
[INFO] [stdout]     |
[INFO] [stdout] 694 |      * is 4 and {@code sortedAlleleCounts} is [0,1,2,1] then alleles 0 and 2 are present, each with a count of 1, while
[INFO] [stdout]     |                                                ^^^^^^^ no item named `0,1,2,1` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `a`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:120:41
[INFO] [stdout]     |
[INFO] [stdout] 120 |      * Thus the value a position <i>[p][a]</i> indicates how many genotypes of ploidy <i>p</i> there are before the first
[INFO] [stdout]     |                                         ^ no item named `a` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `A`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:124:12
[INFO] [stdout]     |
[INFO] [stdout] 124 |      * [3][A] == [3][0] == 0 as the first genotype AAA contains A.
[INFO] [stdout]     |            ^ no item named `A` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `0`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:124:22
[INFO] [stdout]     |
[INFO] [stdout] 124 |      * [3][A] == [3][0] == 0 as the first genotype AAA contains A.
[INFO] [stdout]     |                      ^ no item named `0` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `C`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:125:12
[INFO] [stdout]     |
[INFO] [stdout] 125 |      * [3][C] == [3][2] == 4 as the first genotype that contains C, AAC follows: AAA AAB ABB BBB
[INFO] [stdout]     |            ^ no item named `C` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `2`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:125:22
[INFO] [stdout]     |
[INFO] [stdout] 125 |      * [3][C] == [3][2] == 4 as the first genotype that contains C, AAC follows: AAA AAB ABB BBB
[INFO] [stdout]     |                      ^ no item named `2` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `D`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:126:12
[INFO] [stdout]     |
[INFO] [stdout] 126 |      * [4][D] == [4][3] == 14  as the first genotype that contains D, AAAD follows: AAAA AAAB AABB ABBB BBBB AAAC
[INFO] [stdout]     |            ^ no item named `D` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `3`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:126:22
[INFO] [stdout]     |
[INFO] [stdout] 126 |      * [4][D] == [4][3] == 14  as the first genotype that contains D, AAAD follows: AAAA AAAB AABB ABBB BBBB AAAC
[INFO] [stdout]     |                      ^ no item named `3` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `a`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:136:18
[INFO] [stdout]     |
[INFO] [stdout] 136 |      * Offset[p][a] := Offset[p-1][a] + Offset[p][a-1] when a > 0, p > 0
[INFO] [stdout]     |                  ^ no item named `a` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `a`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:136:36
[INFO] [stdout]     |
[INFO] [stdout] 136 |      * Offset[p][a] := Offset[p-1][a] + Offset[p][a-1] when a > 0, p > 0
[INFO] [stdout]     |                                    ^ no item named `a` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `a-1`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculators.rs:136:51
[INFO] [stdout]     |
[INFO] [stdout] 136 |      * Offset[p][a] := Offset[p-1][a] + Offset[p][a-1] when a > 0, p > 0
[INFO] [stdout]     |                                                   ^^^ no item named `a-1` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `1`
[INFO] [stdout]   --> src/graphs/low_weight_chain_pruner.rs:10:12
[INFO] [stdout]    |
[INFO] [stdout] 10 |  * For A -[1]> B -[1]> C -[1]> D would be removed with pruneFactor 2
[INFO] [stdout]    |            ^ no item named `1` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `1`
[INFO] [stdout]   --> src/graphs/low_weight_chain_pruner.rs:10:20
[INFO] [stdout]    |
[INFO] [stdout] 10 |  * For A -[1]> B -[1]> C -[1]> D would be removed with pruneFactor 2
[INFO] [stdout]    |                    ^ no item named `1` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `1`
[INFO] [stdout]   --> src/graphs/low_weight_chain_pruner.rs:10:28
[INFO] [stdout]    |
[INFO] [stdout] 10 |  * For A -[1]> B -[1]> C -[1]> D would be removed with pruneFactor 2
[INFO] [stdout]    |                            ^ no item named `1` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `1`
[INFO] [stdout]   --> src/graphs/low_weight_chain_pruner.rs:11:12
[INFO] [stdout]    |
[INFO] [stdout] 11 |  * but A -[1]> B -[2]> C -[1]> D would not be because the linear chain includes an edge with weight >= 2
[INFO] [stdout]    |            ^ no item named `1` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `2`
[INFO] [stdout]   --> src/graphs/low_weight_chain_pruner.rs:11:20
[INFO] [stdout]    |
[INFO] [stdout] 11 |  * but A -[1]> B -[2]> C -[1]> D would not be because the linear chain includes an edge with weight >= 2
[INFO] [stdout]    |                    ^ no item named `2` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `1`
[INFO] [stdout]   --> src/graphs/low_weight_chain_pruner.rs:11:28
[INFO] [stdout]    |
[INFO] [stdout] 11 |  * but A -[1]> B -[2]> C -[1]> D would not be because the linear chain includes an edge with weight >= 2
[INFO] [stdout]    |                            ^ no item named `1` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `7`
[INFO] [stdout]    --> src/model/allele_subsetting_utils.rs:300:38
[INFO] [stdout]     |
[INFO] [stdout] 300 |      * to new PL indices i.e. result[7] = old PL index of genotype containing same alleles as the new genotype with PL index 7.
[INFO] [stdout]     |                                      ^ no item named `7` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `r`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm.rs:214:84
[INFO] [stdout]     |
[INFO] [stdout] 214 |      * @param logLikelihoods where to store the log likelihoods where position [a][r] is reserved for the log likelihood of {@code ...
[INFO] [stdout]     |                                                                                    ^ no item named `r` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `r`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm.rs:214:138
[INFO] [stdout]     |
[INFO] [stdout] 214 | ...s reserved for the log likelihood of {@code reads[r]}
[INFO] [stdout]     |                                                      ^ no item named `r` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `a`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm.rs:215:50
[INFO] [stdout]     |
[INFO] [stdout] 215 |      *             conditional to {@code alleles[a]}.
[INFO] [stdout]     |                                                  ^ no item named `a` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `0`
[INFO] [stdout]    --> src/reads/alignment_utils.rs:752:112
[INFO] [stdout]     |
[INFO] [stdout] 752 |      * @param basesStartOnRef where does the bases array start w.r.t. the reference start?  For example, bases[0] of
[INFO] [stdout]     |                                                                                                                ^ no item named `0` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `AaCcGgTt`
[INFO] [stdout]   --> src/utils/base_utils.rs:65:21
[INFO] [stdout]    |
[INFO] [stdout] 65 |      * @param base [AaCcGgTt]
[INFO] [stdout]    |                     ^^^^^^^^ no item named `AaCcGgTt` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `A`
[INFO] [stdout]   --> src/utils/utils.rs:53:18
[INFO] [stdout]    |
[INFO] [stdout] 53 |  * if N = 1 => [[A], [B], [C]]
[INFO] [stdout]    |                  ^ no item named `A` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `B`
[INFO] [stdout]   --> src/utils/utils.rs:53:23
[INFO] [stdout]    |
[INFO] [stdout] 53 |  * if N = 1 => [[A], [B], [C]]
[INFO] [stdout]    |                       ^ no item named `B` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `C`
[INFO] [stdout]   --> src/utils/utils.rs:53:28
[INFO] [stdout]    |
[INFO] [stdout] 53 |  * if N = 1 => [[A], [B], [C]]
[INFO] [stdout]    |                            ^ no item named `C` in scope
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `1,2,3,4,5`
[INFO] [stdout]    --> src/activity_profile/activity_profile.rs:303:9
[INFO] [stdout]     |
[INFO] [stdout] 303 |      * [1,2,3,4,5] but not [1,2,3,5].
[INFO] [stdout]     |         ^^^^^^^^^ no item named `1,2,3,4,5` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `1,2,3,5`
[INFO] [stdout]    --> src/activity_profile/activity_profile.rs:303:29
[INFO] [stdout]     |
[INFO] [stdout] 303 |      * [1,2,3,4,5] but not [1,2,3,5].
[INFO] [stdout]     |                             ^^^^^^^ no item named `1,2,3,5` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/ani_calculator/ani_calculator.rs:15:26
[INFO] [stdout]    |
[INFO] [stdout] 15 | /// Defined by InStrain: https://www.nature.com/articles/s41587-020-00797-0?proof=t%3B#Sec9
[INFO] [stdout]    |                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout]    = note: `#[warn(rustdoc::bare_urls)]` on by default
[INFO] [stdout] help: use an automatic link instead
[INFO] [stdout]    |
[INFO] [stdout] 15 | /// Defined by InStrain: <https://www.nature.com/articles/s41587-020-00797-0?proof=t%3B#Sec9>
[INFO] [stdout]    |                          +                                                                  +
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `p`
[INFO] [stdout]   --> src/annotator/tandem_repeat.rs:11:4
[INFO] [stdout]    |
[INFO] [stdout] 11 |  * <p>A tandem repeat unit is composed of one or more nucleotides that are repeated multiple times in series. Repetitive sequences a...
[INFO] [stdout]    |    ^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(rustdoc::invalid_html_tags)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]   --> src/assembly/assembly_region_trimmer.rs:13:4
[INFO] [stdout]    |
[INFO] [stdout] 13 |  * <p/>
[INFO] [stdout]    |    ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/assembly/assembly_region_trimmer.rs:273:9
[INFO] [stdout]     |
[INFO] [stdout] 273 |      *  <p/>
[INFO] [stdout]     |         ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/assembly/assembly_result_set.rs:274:8
[INFO] [stdout]     |
[INFO] [stdout] 274 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unopened HTML tag `p`
[INFO] [stdout]   --> src/genotype/genotype_allele_counts.rs:20:123
[INFO] [stdout]    |
[INFO] [stdout] 20 |  * Collection of allele counts for a genotype. It encompasses what alleles are present in the genotype and in what number.</p>
[INFO] [stdout]    |                                                                                                                           ^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculator.rs:102:88
[INFO] [stdout]     |
[INFO] [stdout] 102 |      * calculation request calling {@link #ensureReadCapacity(int) ensureReadCapacity}.<p/>
[INFO] [stdout]     |                                                                                        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `p`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculator.rs:101:8
[INFO] [stdout]     |
[INFO] [stdout] 101 |      * <p>This figure is increased dynamically as per the
[INFO] [stdout]     |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `li`
[INFO] [stdout]    --> src/genotype/genotype_likelihood_calculator.rs:241:13
[INFO] [stdout]     |
[INFO] [stdout] 241 |      *      <li>or it contains any negatives,
[INFO] [stdout]     |             ^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `T`
[INFO] [stdout]    --> src/graphs/base_graph.rs:885:15
[INFO] [stdout]     |
[INFO] [stdout] 885 |      * @param <T> the type of the nodes in those graphs
[INFO] [stdout]     |               ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unopened HTML tag `ul`
[INFO] [stdout]   --> src/graphs/graph_based_k_best_haplotype_finder.rs:35:8
[INFO] [stdout]    |
[INFO] [stdout] 32 |      * @throws IllegalArgumentException if <ul>
[INFO] [stdout]    |                                            ---- does not match this unclosed tag
[INFO] [stdout] ...
[INFO] [stdout] 35 |      * </ul>
[INFO] [stdout]    |        -^^^^
[INFO] [stdout]    |        |
[INFO] [stdout]    |        this unopened tag
[INFO] [stdout]    |        because the Markdown paragraph ends here
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/graphs/graph_based_k_best_haplotype_finder.rs:62:55
[INFO] [stdout]    |
[INFO] [stdout] 62 |      * Implement Dijkstra's algorithm as described in https://en.wikipedia.org/wiki/K_shortest_path_routing
[INFO] [stdout]    |                                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] help: use an automatic link instead
[INFO] [stdout]    |
[INFO] [stdout] 62 |      * Implement Dijkstra's algorithm as described in <https://en.wikipedia.org/wiki/K_shortest_path_routing>
[INFO] [stdout]    |                                                       +                                                     +
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `A`
[INFO] [stdout]   --> src/model/allele_likelihoods.rs:25:11
[INFO] [stdout]    |
[INFO] [stdout] 25 |  * @param <A> the type of the allele the likelihood makes reference to.
[INFO] [stdout]    |           ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `usize`
[INFO] [stdout]    --> src/model/allele_likelihoods.rs:204:28
[INFO] [stdout]     |
[INFO] [stdout] 204 |      * @return never Option<usize>.
[INFO] [stdout]     |                            ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout] help: try marking as source code
[INFO] [stdout]     |
[INFO] [stdout] 204 |      * @return never `Option<usize>`.
[INFO] [stdout]     |                      +             +
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `A`
[INFO] [stdout]   --> src/model/allele_list.rs:59:15
[INFO] [stdout]    |
[INFO] [stdout] 59 |      * @param <A> the allele class.
[INFO] [stdout]    |               ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> src/model/variant_context_utils.rs:370:49
[INFO] [stdout]     |
[INFO] [stdout] 370 |      * For more information on this method see: http://www.thedistractionnetwork.com/programmer-problem/
[INFO] [stdout]     |                                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] help: use an automatic link instead
[INFO] [stdout]     |
[INFO] [stdout] 370 |      * For more information on this method see: <http://www.thedistractionnetwork.com/programmer-problem/>
[INFO] [stdout]     |                                                 +                                                        +
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]   --> src/pair_hmm/pair_hmm_model.rs:29:8
[INFO] [stdout]    |
[INFO] [stdout] 29 |      * <p/>
[INFO] [stdout]    |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]   --> src/pair_hmm/pair_hmm_model.rs:31:8
[INFO] [stdout]    |
[INFO] [stdout] 31 |      * <p/>
[INFO] [stdout]    |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]   --> src/pair_hmm/pair_hmm_model.rs:38:8
[INFO] [stdout]    |
[INFO] [stdout] 38 |      * <p/>
[INFO] [stdout]    |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]   --> src/pair_hmm/pair_hmm_model.rs:40:8
[INFO] [stdout]    |
[INFO] [stdout] 40 |      * <p/>
[INFO] [stdout]    |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm_model.rs:180:8
[INFO] [stdout]     |
[INFO] [stdout] 180 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm_model.rs:183:8
[INFO] [stdout]     |
[INFO] [stdout] 183 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm_model.rs:237:8
[INFO] [stdout]     |
[INFO] [stdout] 237 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm_model.rs:240:8
[INFO] [stdout]     |
[INFO] [stdout] 240 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm_model.rs:347:8
[INFO] [stdout]     |
[INFO] [stdout] 347 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm_model.rs:350:8
[INFO] [stdout]     |
[INFO] [stdout] 350 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm_model.rs:401:8
[INFO] [stdout]     |
[INFO] [stdout] 401 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm_model.rs:404:8
[INFO] [stdout]     |
[INFO] [stdout] 404 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/pair_hmm/pair_hmm_model.rs:430:8
[INFO] [stdout]     |
[INFO] [stdout] 430 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/reads/alignment_utils.rs:407:8
[INFO] [stdout]     |
[INFO] [stdout] 407 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]    --> src/reads/bird_tool_reads.rs:206:8
[INFO] [stdout]     |
[INFO] [stdout] 206 |      * <p/>
[INFO] [stdout]     |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `File`
[INFO] [stdout]   --> src/reference/reference_reader.rs:13:48
[INFO] [stdout]    |
[INFO] [stdout] 13 | * indexed_reader represents the #[IndexedReader<File>]
[INFO] [stdout]    |                                                ^^^^^^
[INFO] [stdout]    |
[INFO] [stdout] help: try marking as source code
[INFO] [stdout]    |
[INFO] [stdout] 13 | * indexed_reader represents the #[`IndexedReader<File>`]
[INFO] [stdout]    |                                   +                   +
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: invalid self-closing HTML tag `p`
[INFO] [stdout]   --> src/test_utils/allele_list_unit_tester.rs:32:8
[INFO] [stdout]    |
[INFO] [stdout] 32 |      * <p/>
[INFO] [stdout]    |        ^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `p`
[INFO] [stdout]   --> src/test_utils/random_dna.rs:34:8
[INFO] [stdout]    |
[INFO] [stdout] 34 |      * <p>
[INFO] [stdout]    |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `p`
[INFO] [stdout]   --> src/test_utils/random_dna.rs:42:8
[INFO] [stdout]    |
[INFO] [stdout] 42 |      * <p>
[INFO] [stdout]    |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unclosed HTML tag `p`
[INFO] [stdout]   --> src/test_utils/read_clipper_test_utils.rs:77:8
[INFO] [stdout]    |
[INFO] [stdout] 77 |      * <p>
[INFO] [stdout]    |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> src/utils/math_utils.rs:421:12
[INFO] [stdout]     |
[INFO] [stdout] 421 |      * See http://www.nezumi.demon.co.uk/consult/logx.htm
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] help: use an automatic link instead
[INFO] [stdout]     |
[INFO] [stdout] 421 |      * See <http://www.nezumi.demon.co.uk/consult/logx.htm>
[INFO] [stdout]     |            +                                              +
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 2.72s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: partitions v0.2.4
[INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 2`
[INFO] [stderr]    Generated /opt/rustwide/target/doc/lorikeet_genome/index.html
[INFO] running `Command { std: "docker" "inspect" "186569ca435cebfd606c1134982a4b1bf480211c6d5a791267668e9d6765588a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "186569ca435cebfd606c1134982a4b1bf480211c6d5a791267668e9d6765588a", kill_on_drop: false }`
[INFO] [stdout] 186569ca435cebfd606c1134982a4b1bf480211c6d5a791267668e9d6765588a
