[INFO] fetching crate bio 0.37.0...
[INFO] documenting bio-0.37.0 against 1.54.0 for beta-1.55-rustdoc-1
[INFO] extracting crate bio 0.37.0 into /workspace/builds/worker-62/source
[INFO] validating manifest of crates.io crate bio 0.37.0 on toolchain 1.54.0
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.54.0" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking crates.io crate bio 0.37.0
[INFO] finished tweaking crates.io crate bio 0.37.0
[INFO] tweaked toml for crates.io crate bio 0.37.0 written to /workspace/builds/worker-62/source/Cargo.toml
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.54.0" "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: "/workspace/cargo-home/bin/cargo" "+1.54.0" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded packed_simd_2 v0.3.5
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-62/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-62/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+1.54.0" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] af10f4e88b8d2d43c9aa125e81ddd0329393c4a381d6cc91b247723fb744e495
[INFO] running `Command { std: "docker" "start" "-a" "af10f4e88b8d2d43c9aa125e81ddd0329393c4a381d6cc91b247723fb744e495", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "af10f4e88b8d2d43c9aa125e81ddd0329393c4a381d6cc91b247723fb744e495", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "af10f4e88b8d2d43c9aa125e81ddd0329393c4a381d6cc91b247723fb744e495", kill_on_drop: false }`
[INFO] [stdout] af10f4e88b8d2d43c9aa125e81ddd0329393c4a381d6cc91b247723fb744e495
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-62/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-62/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" "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@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+1.54.0" "doc" "--frozen" "--no-deps" "--document-private-items" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 02177ff79ad0b68678bf97e207956aff5990afce5423e7bad96f8f45639acc71
[INFO] running `Command { std: "docker" "start" "-a" "02177ff79ad0b68678bf97e207956aff5990afce5423e7bad96f8f45639acc71", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]    Compiling syn v1.0.74
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling paste v1.0.5
[INFO] [stderr]    Compiling feature-probe v0.1.1
[INFO] [stderr]     Checking regex-automata v0.1.10
[INFO] [stderr]    Compiling ndarray v0.14.0
[INFO] [stderr]     Checking array-macro v1.0.5
[INFO] [stderr]     Checking bit-vec v0.6.3
[INFO] [stderr]    Compiling bio v0.37.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Checking fixedbitset v0.2.0
[INFO] [stderr]     Checking bytecount v0.6.2
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking strum v0.20.0
[INFO] [stderr]    Compiling num-traits v0.2.14
[INFO] [stderr]    Compiling num-integer v0.1.44
[INFO] [stderr]    Compiling num-rational v0.3.2
[INFO] [stderr]    Compiling heck v0.3.3
[INFO] [stderr]     Checking matrixmultiply v0.3.1
[INFO] [stderr]     Checking itertools v0.9.0
[INFO] [stderr]     Checking csv-core v0.1.10
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling bv v0.11.1
[INFO] [stderr]     Checking petgraph v0.5.1
[INFO] [stderr]     Checking bit-set v0.5.2
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking num-complex v0.3.1
[INFO] [stderr]     Checking approx v0.4.0
[INFO] [stderr]     Checking rand_distr v0.4.1
[INFO] [stderr]     Checking approx v0.3.2
[INFO] [stderr]     Checking ordered-float v1.1.1
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking simba v0.4.0
[INFO] [stderr]    Compiling serde_derive v1.0.127
[INFO] [stderr]    Compiling thiserror-impl v1.0.26
[INFO] [stderr]    Compiling enum-map-derive v0.4.6
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]    Compiling strum_macros v0.20.1
[INFO] [stderr]    Compiling getset v0.0.9
[INFO] [stderr]     Checking enum-map v0.6.4
[INFO] [stderr]     Checking thiserror v1.0.26
[INFO] [stderr]     Checking bio-types v0.12.0
[INFO] [stderr]     Checking serde v1.0.127
[INFO] [stderr]     Checking nalgebra v0.26.2
[INFO] [stderr]     Checking bstr v0.2.16
[INFO] [stderr]     Checking multimap v0.8.3
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking csv v1.1.6
[INFO] [stderr]     Checking statrs v0.14.0
[INFO] [stderr]  Documenting bio v0.37.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/alignment/poa.rs:15:5
[INFO] [stdout]    |
[INFO] [stdout] 15 | //! https://github.com/ljdursi/poapy
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/ljdursi/poapy>`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(rustdoc::bare_urls)]` on by default
[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: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:181:5
[INFO] [stdout]     |
[INFO] [stdout] 181 | /// 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:120:6
[INFO] [stdout]     |
[INFO] [stdout] 120 | /// (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:18:79
[INFO] [stdout]    |
[INFO] [stdout] 18 | //! Another fast pattern matching algorithm is available in the twoway crate: https://crates.io/crates/twoway
[INFO] [stdout]    |                                                                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://crates.io/crates/twoway>`
[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:170:45
[INFO] [stdout]     |
[INFO] [stdout] 170 | /// 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:33:5
[INFO] [stdout]    |
[INFO] [stdout] 33 | /// 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: 18 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 45.44s
[INFO] running `Command { std: "docker" "inspect" "02177ff79ad0b68678bf97e207956aff5990afce5423e7bad96f8f45639acc71", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "02177ff79ad0b68678bf97e207956aff5990afce5423e7bad96f8f45639acc71", kill_on_drop: false }`
[INFO] [stdout] 02177ff79ad0b68678bf97e207956aff5990afce5423e7bad96f8f45639acc71
