[INFO] fetching crate bio 1.1.0...
[INFO] documenting bio-1.1.0 against 1.69.0 for beta-1.70-rustdoc-1
[INFO] extracting crate bio 1.1.0 into /workspace/builds/worker-7-tc1/source
[INFO] validating manifest of crates.io crate bio 1.1.0 on toolchain 1.69.0
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.69.0" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking crates.io crate bio 1.1.0
[INFO] finished tweaking crates.io crate bio 1.1.0
[INFO] tweaked toml for crates.io crate bio 1.1.0 written to /workspace/builds/worker-7-tc1/source/Cargo.toml
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" __CARGO_TEST_CHANNEL_OVERRIDE_DO_NOT_USE_THIS="nightly" "/workspace/cargo-home/bin/cargo" "+1.69.0" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.69.0" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded newtype_derive v0.1.6
[INFO] [stderr]   Downloaded triple_accel v0.4.0
[INFO] [stderr]   Downloaded semver v0.1.20
[INFO] [stderr]   Downloaded nalgebra v0.29.0
[INFO] [stderr]   Downloaded bio-types v0.13.0
[INFO] [stderr]   Downloaded enum-map-derive v0.6.0
[INFO] [stderr]   Downloaded custom_derive v0.1.7
[INFO] [stderr]   Downloaded enum-map v1.1.1
[INFO] [stderr]   Downloaded itertools-num v0.1.3
[INFO] [stderr]   Downloaded simba v0.6.0
[INFO] [stderr]   Downloaded wide v0.7.8
[INFO] [stderr]   Downloaded statrs v0.16.0
[INFO] [stderr]   Downloaded rustc_version v0.1.7
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:5ff2268d62e97bff2cde7d5815dd6ed5b47097566f13b8d0ca110b04b60e07ed" "/opt/rustwide/cargo-home/bin/cargo" "+1.69.0" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 4f6b919c77d7367b4d39a277df337b41ab61e3f0c469c13e218d12845230d877
[INFO] running `Command { std: "docker" "start" "-a" "4f6b919c77d7367b4d39a277df337b41ab61e3f0c469c13e218d12845230d877", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "4f6b919c77d7367b4d39a277df337b41ab61e3f0c469c13e218d12845230d877", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "4f6b919c77d7367b4d39a277df337b41ab61e3f0c469c13e218d12845230d877", kill_on_drop: false }`
[INFO] [stdout] 4f6b919c77d7367b4d39a277df337b41ab61e3f0c469c13e218d12845230d877
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:5ff2268d62e97bff2cde7d5815dd6ed5b47097566f13b8d0ca110b04b60e07ed" "/opt/rustwide/cargo-home/bin/cargo" "+1.69.0" "doc" "--frozen" "--no-deps" "--document-private-items" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 007d046837bae61c6e2f3d87416cae7150d826cdf6590eaaf9c0eac5ffded26a
[INFO] running `Command { std: "docker" "start" "-a" "007d046837bae61c6e2f3d87416cae7150d826cdf6590eaaf9c0eac5ffded26a", kill_on_drop: false }`
[INFO] [stderr]    Compiling libm v0.2.6
[INFO] [stderr]    Compiling num-traits v0.2.15
[INFO] [stderr]    Compiling num-integer v0.1.45
[INFO] [stderr]    Compiling matrixmultiply v0.3.5
[INFO] [stderr]    Compiling paste v1.0.12
[INFO] [stderr]     Checking bytemuck v1.13.1
[INFO] [stderr]    Compiling num-rational v0.4.1
[INFO] [stderr]     Checking rawpointer v0.2.1
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]    Compiling feature-probe v0.1.1
[INFO] [stderr]    Compiling serde_derive v1.0.160
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]    Compiling heck v0.4.1
[INFO] [stderr]     Checking csv-core v0.1.10
[INFO] [stderr]     Checking fixedbitset v0.4.2
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]     Checking safe_arch v0.6.0
[INFO] [stderr]     Checking petgraph v0.6.3
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling bv v0.11.1
[INFO] [stderr]     Checking bytecount v0.6.3
[INFO] [stderr]     Checking strum v0.24.1
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking wide v0.7.8
[INFO] [stderr]     Checking num-complex v0.4.3
[INFO] [stderr]     Checking approx v0.5.1
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking ordered-float v3.7.0
[INFO] [stderr]     Checking simba v0.6.0
[INFO] [stderr]     Checking ndarray v0.15.6
[INFO] [stderr]     Checking serde v1.0.160
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]    Compiling nalgebra-macros v0.1.0
[INFO] [stderr]    Compiling strum_macros v0.24.3
[INFO] [stderr]    Compiling enum-map-derive v0.6.0
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]    Compiling getset v0.1.2
[INFO] [stderr]     Checking enum-map v1.1.1
[INFO] [stderr]     Checking bio-types v0.13.0
[INFO] [stderr]     Checking multimap v0.8.3
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking csv v1.2.1
[INFO] [stderr]     Checking nalgebra v0.29.0
[INFO] [stderr]     Checking statrs v0.16.0
[INFO] [stderr]  Documenting bio v1.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unclosed HTML tag `usize`
[INFO] [stdout]    --> src/alignment/pairwise/banded.rs:326:51
[INFO] [stdout]     |
[INFO] [stdout] 326 |     /// the specified number of mismatches (Option<usize>)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(rustdoc::invalid_html_tags)]` on by default
[INFO] [stdout] help: try marking as source code
[INFO] [stdout]     |
[INFO] [stdout] 326 |     /// the specified number of mismatches (`Option<usize>`)
[INFO] [stdout]     |                                             +             +
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/alignment/poa.rs:17:5
[INFO] [stdout]    |
[INFO] [stdout] 17 | //! https://github.com/ljdursi/poapy
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/ljdursi/poapy>`
[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] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/alignment/sparse.rs:51:17
[INFO] [stdout]    |
[INFO] [stdout] 51 | /// Paper here :https://arxiv.org/abs/1407.2407.  Original implementation here:
[INFO] [stdout]    |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://arxiv.org/abs/1407.2407.>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/alignment/sparse.rs:52:5
[INFO] [stdout]    |
[INFO] [stdout] 52 | /// https://github.com/fpavetic/lcskpp
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/fpavetic/lcskpp>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]  --> src/data_structures/bit_tree.rs:8:35
[INFO] [stdout]   |
[INFO] [stdout] 8 | //! Implementation outlined here: https://www.topcoder.com/community/data-science/data-science-tutorials/binary-indexed-trees/
[INFO] [stdout]   |                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://www.topcoder.com/community/data-science/data-science-tutorials/binary-indexed-trees/>`
[INFO] [stdout]   |
[INFO] [stdout]   = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]  --> src/data_structures/interval_tree/array_backed_interval_tree.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | //! https://github.com/lh3/cgranges / https://github.com/lh3/cgranges/blob/master/cpp/IITree.h
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/lh3/cgranges>`
[INFO] [stdout]   |
[INFO] [stdout]   = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]  --> src/data_structures/interval_tree/array_backed_interval_tree.rs:4:39
[INFO] [stdout]   |
[INFO] [stdout] 4 | //! https://github.com/lh3/cgranges / https://github.com/lh3/cgranges/blob/master/cpp/IITree.h
[INFO] [stdout]   |                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/lh3/cgranges/blob/master/cpp/IITree.h>`
[INFO] [stdout]   |
[INFO] [stdout]   = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> src/data_structures/suffix_array.rs:223:5
[INFO] [stdout]     |
[INFO] [stdout] 223 | /// http://ls11-www.cs.tu-dortmund.de/people/rahmann/algoseq.pdf
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://ls11-www.cs.tu-dortmund.de/people/rahmann/algoseq.pdf>`
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> src/io/bed.rs:121:6
[INFO] [stdout]     |
[INFO] [stdout] 121 | /// (http://bedtools.readthedocs.org/en/latest/content/general-usage.html)
[INFO] [stdout]     |      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://bedtools.readthedocs.org/en/latest/content/general-usage.html>`
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/pattern_matching/mod.rs:18:102
[INFO] [stdout]    |
[INFO] [stdout] 18 | //! Another library that provides heavily optimized routines for string search primitives is memchr: https://crates.io/crates/memchr
[INFO] [stdout]    |                                                                                                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://crates.io/crates/memchr>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/pattern_matching/pssm/dnamotif.rs:31:9
[INFO] [stdout]    |
[INFO] [stdout] 31 |     /// https://github.com/rust-lang/rust/issues/42863
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/rust-lang/rust/issues/42863>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/pattern_matching/pssm/protmotif.rs:31:9
[INFO] [stdout]    |
[INFO] [stdout] 31 |     /// https://github.com/rust-lang/rust/issues/42863
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/rust-lang/rust/issues/42863>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> src/pattern_matching/pssm/mod.rs:231:11
[INFO] [stdout]     |
[INFO] [stdout] 231 |     ///   https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169193/
[INFO] [stdout]     |           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169193/>`
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> src/pattern_matching/pssm/mod.rs:280:12
[INFO] [stdout]     |
[INFO] [stdout] 280 |     ///    https://en.wikipedia.org/wiki/Sequence_logo#Logo_creation
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://en.wikipedia.org/wiki/Sequence_logo#Logo_creation>`
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]  --> src/stats/pairhmm/mod.rs:3:45
[INFO] [stdout]   |
[INFO] [stdout] 3 | //! Current Topics in Genome Analysis 2008. http://doi.org/10.1017/CBO9780511790492.
[INFO] [stdout]   |                                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://doi.org/10.1017/CBO9780511790492.>`
[INFO] [stdout]   |
[INFO] [stdout]   = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> src/stats/pairhmm/homopolypairhmm.rs:215:45
[INFO] [stdout]     |
[INFO] [stdout] 215 | /// Current Topics in Genome Analysis 2008. http://doi.org/10.1017/CBO9780511790492.
[INFO] [stdout]     |                                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://doi.org/10.1017/CBO9780511790492.>`
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/stats/pairhmm/pairhmm.rs:46:45
[INFO] [stdout]    |
[INFO] [stdout] 46 | /// Current Topics in Genome Analysis 2008. http://doi.org/10.1017/CBO9780511790492.
[INFO] [stdout]    |                                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://doi.org/10.1017/CBO9780511790492.>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/stats/probs/mod.rs:35:5
[INFO] [stdout]    |
[INFO] [stdout] 35 | /// http://cran.r-project.org/web/packages/Rmpfr/vignettes/log1mexp-note.pdf.
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://cran.r-project.org/web/packages/Rmpfr/vignettes/log1mexp-note.pdf.>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/utils/fastexp.rs:32:9
[INFO] [stdout]    |
[INFO] [stdout] 32 |     /// https://eldorado.tu-dortmund.de/bitstream/2003/36203/1/Dissertation_Kopczynski.pdf
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://eldorado.tu-dortmund.de/bitstream/2003/36203/1/Dissertation_Kopczynski.pdf>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 19 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 15.51s
[INFO] running `Command { std: "docker" "inspect" "007d046837bae61c6e2f3d87416cae7150d826cdf6590eaaf9c0eac5ffded26a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "007d046837bae61c6e2f3d87416cae7150d826cdf6590eaaf9c0eac5ffded26a", kill_on_drop: false }`
[INFO] [stdout] 007d046837bae61c6e2f3d87416cae7150d826cdf6590eaaf9c0eac5ffded26a
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-e" "DOCS_RS=1" "-e" "RUSTC_BOOTSTRAP=1" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:5ff2268d62e97bff2cde7d5815dd6ed5b47097566f13b8d0ca110b04b60e07ed" "/opt/rustwide/cargo-home/bin/cargo" "+1.69.0" "rustdoc" "--lib" "-Zrustdoc-map" "-Z" "unstable-options" "--config" "build.rustdocflags=[\"-Z\", \"unstable-options\", \"--document-private-items\"]" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 0d66394e369cbd482e6a0140c1b42ce399d4ada42d89756ced7c77b204a3d0dc
[INFO] running `Command { std: "docker" "start" "-a" "0d66394e369cbd482e6a0140c1b42ce399d4ada42d89756ced7c77b204a3d0dc", kill_on_drop: false }`
[INFO] [stderr]  Documenting bio v1.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unclosed HTML tag `usize`
[INFO] [stdout]    --> src/alignment/pairwise/banded.rs:326:51
[INFO] [stdout]     |
[INFO] [stdout] 326 |     /// the specified number of mismatches (Option<usize>)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(rustdoc::invalid_html_tags)]` on by default
[INFO] [stdout] help: try marking as source code
[INFO] [stdout]     |
[INFO] [stdout] 326 |     /// the specified number of mismatches (`Option<usize>`)
[INFO] [stdout]     |                                             +             +
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/alignment/poa.rs:17:5
[INFO] [stdout]    |
[INFO] [stdout] 17 | //! https://github.com/ljdursi/poapy
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/ljdursi/poapy>`
[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] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/alignment/sparse.rs:51:17
[INFO] [stdout]    |
[INFO] [stdout] 51 | /// Paper here :https://arxiv.org/abs/1407.2407.  Original implementation here:
[INFO] [stdout]    |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://arxiv.org/abs/1407.2407.>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/alignment/sparse.rs:52:5
[INFO] [stdout]    |
[INFO] [stdout] 52 | /// https://github.com/fpavetic/lcskpp
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/fpavetic/lcskpp>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]  --> src/data_structures/bit_tree.rs:8:35
[INFO] [stdout]   |
[INFO] [stdout] 8 | //! Implementation outlined here: https://www.topcoder.com/community/data-science/data-science-tutorials/binary-indexed-trees/
[INFO] [stdout]   |                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://www.topcoder.com/community/data-science/data-science-tutorials/binary-indexed-trees/>`
[INFO] [stdout]   |
[INFO] [stdout]   = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]  --> src/data_structures/interval_tree/array_backed_interval_tree.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | //! https://github.com/lh3/cgranges / https://github.com/lh3/cgranges/blob/master/cpp/IITree.h
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/lh3/cgranges>`
[INFO] [stdout]   |
[INFO] [stdout]   = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]  --> src/data_structures/interval_tree/array_backed_interval_tree.rs:4:39
[INFO] [stdout]   |
[INFO] [stdout] 4 | //! https://github.com/lh3/cgranges / https://github.com/lh3/cgranges/blob/master/cpp/IITree.h
[INFO] [stdout]   |                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/lh3/cgranges/blob/master/cpp/IITree.h>`
[INFO] [stdout]   |
[INFO] [stdout]   = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> src/data_structures/suffix_array.rs:223:5
[INFO] [stdout]     |
[INFO] [stdout] 223 | /// http://ls11-www.cs.tu-dortmund.de/people/rahmann/algoseq.pdf
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://ls11-www.cs.tu-dortmund.de/people/rahmann/algoseq.pdf>`
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> src/io/bed.rs:121:6
[INFO] [stdout]     |
[INFO] [stdout] 121 | /// (http://bedtools.readthedocs.org/en/latest/content/general-usage.html)
[INFO] [stdout]     |      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://bedtools.readthedocs.org/en/latest/content/general-usage.html>`
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/pattern_matching/mod.rs:18:102
[INFO] [stdout]    |
[INFO] [stdout] 18 | //! Another library that provides heavily optimized routines for string search primitives is memchr: https://crates.io/crates/memchr
[INFO] [stdout]    |                                                                                                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://crates.io/crates/memchr>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/pattern_matching/pssm/dnamotif.rs:31:9
[INFO] [stdout]    |
[INFO] [stdout] 31 |     /// https://github.com/rust-lang/rust/issues/42863
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/rust-lang/rust/issues/42863>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/pattern_matching/pssm/protmotif.rs:31:9
[INFO] [stdout]    |
[INFO] [stdout] 31 |     /// https://github.com/rust-lang/rust/issues/42863
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/rust-lang/rust/issues/42863>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> src/pattern_matching/pssm/mod.rs:231:11
[INFO] [stdout]     |
[INFO] [stdout] 231 |     ///   https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169193/
[INFO] [stdout]     |           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169193/>`
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> src/pattern_matching/pssm/mod.rs:280:12
[INFO] [stdout]     |
[INFO] [stdout] 280 |     ///    https://en.wikipedia.org/wiki/Sequence_logo#Logo_creation
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://en.wikipedia.org/wiki/Sequence_logo#Logo_creation>`
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]  --> src/stats/pairhmm/mod.rs:3:45
[INFO] [stdout]   |
[INFO] [stdout] 3 | //! Current Topics in Genome Analysis 2008. http://doi.org/10.1017/CBO9780511790492.
[INFO] [stdout]   |                                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://doi.org/10.1017/CBO9780511790492.>`
[INFO] [stdout]   |
[INFO] [stdout]   = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> src/stats/pairhmm/homopolypairhmm.rs:215:45
[INFO] [stdout]     |
[INFO] [stdout] 215 | /// Current Topics in Genome Analysis 2008. http://doi.org/10.1017/CBO9780511790492.
[INFO] [stdout]     |                                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://doi.org/10.1017/CBO9780511790492.>`
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/stats/pairhmm/pairhmm.rs:46:45
[INFO] [stdout]    |
[INFO] [stdout] 46 | /// Current Topics in Genome Analysis 2008. http://doi.org/10.1017/CBO9780511790492.
[INFO] [stdout]    |                                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://doi.org/10.1017/CBO9780511790492.>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/utils/fastexp.rs:32:9
[INFO] [stdout]    |
[INFO] [stdout] 32 |     /// https://eldorado.tu-dortmund.de/bitstream/2003/36203/1/Dissertation_Kopczynski.pdf
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://eldorado.tu-dortmund.de/bitstream/2003/36203/1/Dissertation_Kopczynski.pdf>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 18 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 2.37s
[INFO] running `Command { std: "docker" "inspect" "0d66394e369cbd482e6a0140c1b42ce399d4ada42d89756ced7c77b204a3d0dc", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "0d66394e369cbd482e6a0140c1b42ce399d4ada42d89756ced7c77b204a3d0dc", kill_on_drop: false }`
[INFO] [stdout] 0d66394e369cbd482e6a0140c1b42ce399d4ada42d89756ced7c77b204a3d0dc
