[INFO] fetching crate varlociraptor 5.8.0...
[INFO] documenting varlociraptor-5.8.0 against master#c04832643d70479988a3ad9d92b63d9bc95e9c6d for pr-107291
[INFO] extracting crate varlociraptor 5.8.0 into /workspace/builds/worker-2-tc1/source
[INFO] validating manifest of crates.io crate varlociraptor 5.8.0 on toolchain c04832643d70479988a3ad9d92b63d9bc95e9c6d
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+c04832643d70479988a3ad9d92b63d9bc95e9c6d" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking crates.io crate varlociraptor 5.8.0
[INFO] finished tweaking crates.io crate varlociraptor 5.8.0
[INFO] tweaked toml for crates.io crate varlociraptor 5.8.0 written to /workspace/builds/worker-2-tc1/source/Cargo.toml
[INFO] crate crates.io crate varlociraptor 5.8.0 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" "+c04832643d70479988a3ad9d92b63d9bc95e9c6d" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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@sha256:542af8c9c691278ea8427c9f55ce1005b509eeebcbbcbc893145cd6832507671" "/opt/rustwide/cargo-home/bin/cargo" "+c04832643d70479988a3ad9d92b63d9bc95e9c6d" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 8c74df19989704170ccf83ba2c0b09308584ef28dc474c2bcd7eb4f53713456a
[INFO] running `Command { std: "docker" "start" "-a" "8c74df19989704170ccf83ba2c0b09308584ef28dc474c2bcd7eb4f53713456a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "8c74df19989704170ccf83ba2c0b09308584ef28dc474c2bcd7eb4f53713456a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "8c74df19989704170ccf83ba2c0b09308584ef28dc474c2bcd7eb4f53713456a", kill_on_drop: false }`
[INFO] [stdout] 8c74df19989704170ccf83ba2c0b09308584ef28dc474c2bcd7eb4f53713456a
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-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@sha256:542af8c9c691278ea8427c9f55ce1005b509eeebcbbcbc893145cd6832507671" "/opt/rustwide/cargo-home/bin/cargo" "+c04832643d70479988a3ad9d92b63d9bc95e9c6d" "doc" "--frozen" "--no-deps" "--document-private-items" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 9bc805e03eae432236f3d628eebd3273030d21286c3100e131c05f6d24bb8a9a
[INFO] running `Command { std: "docker" "start" "-a" "9bc805e03eae432236f3d628eebd3273030d21286c3100e131c05f6d24bb8a9a", kill_on_drop: false }`
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[INFO] [stderr]     Checking futures v0.3.25
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]     Checking ndarray v0.15.6
[INFO] [stderr]     Checking ordered-float v3.4.0
[INFO] [stderr]     Checking itertools-num v0.1.3
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[INFO] [stderr]     Checking instant v0.1.12
[INFO] [stderr]     Checking async_once v0.2.6
[INFO] [stderr]     Checking untrusted v0.7.1
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]     Checking bytecount v0.6.3
[INFO] [stderr]     Checking spin v0.5.2
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[INFO] [stderr]     Checking time-core v0.1.0
[INFO] [stderr]     Checking strum v0.23.0
[INFO] [stderr]     Checking fastrand v1.8.0
[INFO] [stderr]     Checking remove_dir_all v0.5.3
[INFO] [stderr]     Checking smallvec v1.10.0
[INFO] [stderr]     Checking time v0.3.17
[INFO] [stderr]     Checking tempfile v3.3.0
[INFO] [stderr]     Checking rusty-machine v0.5.4
[INFO] [stderr]     Checking boolean_expression v0.4.4
[INFO] [stderr]     Checking progress-logger v0.3.1
[INFO] [stderr]     Checking GSL v6.0.0
[INFO] [stderr]     Checking fern v0.6.1
[INFO] [stderr]     Checking counter v0.5.7
[INFO] [stderr]     Checking lru v0.7.8
[INFO] [stderr]     Checking uuid v0.8.2
[INFO] [stderr]     Checking data-encoding v2.3.2
[INFO] [stderr]     Checking auto_ops v0.3.0
[INFO] [stderr]     Checking lru_time_cache v0.11.11
[INFO] [stderr]    Compiling derefable v0.1.0
[INFO] [stderr]    Compiling thiserror-impl v1.0.37
[INFO] [stderr]    Compiling darling_macro v0.14.2
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]    Compiling nalgebra-macros v0.1.0
[INFO] [stderr]    Compiling strum_macros v0.24.3
[INFO] [stderr]    Compiling darling_macro v0.13.4
[INFO] [stderr]    Compiling enum-map-derive v0.6.0
[INFO] [stderr]    Compiling tokio-macros v1.8.2
[INFO] [stderr]    Compiling structopt-derive v0.4.18
[INFO] [stderr]     Checking enum-map v1.1.1
[INFO] [stderr]    Compiling darling v0.14.2
[INFO] [stderr]     Checking nalgebra v0.29.0
[INFO] [stderr]    Compiling derive_builder_core v0.12.0
[INFO] [stderr]    Compiling getset v0.1.2
[INFO] [stderr]    Compiling darling v0.13.4
[INFO] [stderr]    Compiling cached_proc_macro v0.15.0
[INFO] [stderr]    Compiling typed-builder v0.9.1
[INFO] [stderr]    Compiling shrinkwraprs v0.3.0
[INFO] [stderr]    Compiling strum_macros v0.23.1
[INFO] [stderr]     Checking pest v2.5.1
[INFO] [stderr]    Compiling derive_builder_macro v0.12.0
[INFO] [stderr]     Checking cached v0.41.0
[INFO] [stderr]    Compiling pest_meta v2.5.1
[INFO] [stderr]     Checking derive_builder v0.12.0
[INFO] [stderr]    Compiling pest_generator v2.5.1
[INFO] [stderr]    Compiling pest_derive v2.5.1
[INFO] [stderr]    Compiling toml v0.5.9
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking bstr v0.2.15
[INFO] [stderr]     Checking bio-types v0.13.0
[INFO] [stderr]     Checking multimap v0.8.3
[INFO] [stderr]     Checking clap v2.34.0
[INFO] [stderr]     Checking ordered-float v1.1.1
[INFO] [stderr]     Checking bincode v1.3.3
[INFO] [stderr]     Checking half v1.8.2
[INFO] [stderr]     Checking serde_yaml v0.8.26
[INFO] [stderr]     Checking statrs v0.16.0
[INFO] [stderr]     Checking csv v1.1.6
[INFO] [stderr]     Checking eval v0.4.3
[INFO] [stderr]     Checking askama_shared v0.12.2
[INFO] [stderr]     Checking bio v1.1.0
[INFO] [stderr]     Checking structopt v0.3.26
[INFO] [stderr]    Compiling askama_derive v0.11.2
[INFO] [stderr]     Checking askama v0.11.1
[INFO] [stderr]     Checking rust-htslib v0.40.2
[INFO] [stderr]     Checking jemallocator v0.3.2
[INFO] [stderr]  Documenting varlociraptor v5.8.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> src/grammar/mod.rs:390:24
[INFO] [stdout]     |
[INFO] [stdout] 390 | /// * mnvs: 0.001 (see https://www.nature.com/articles/s41467-019-12438-5)
[INFO] [stdout]     |                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://www.nature.com/articles/s41467-019-12438-5>`
[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/grammar/mod.rs:391:27
[INFO] [stdout]     |
[INFO] [stdout] 391 | /// * indels: 0.0125 (see https://gatk.broadinstitute.org/hc/en-us/articles/360036826431-HaplotypeCaller, reduction in heterozygosity)
[INFO] [stdout]     |                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://gatk.broadinstitute.org/hc/en-us/articles/360036826431-HaplotypeCaller>`
[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/grammar/mod.rs:392:76
[INFO] [stdout]     |
[INFO] [stdout] 392 | /// * svs: 0.001 (predicted several hundred times less frequent that SNVs: https://doi.org/10.1038/s41588-018-0107-y)
[INFO] [stdout]     |                                                                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://doi.org/10.1038/s41588-018-0107-y>`
[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/mod.rs:613:16
[INFO] [stdout]     |
[INFO] [stdout] 613 | /// Taken from https://stackoverflow.com/a/60498499/7070491
[INFO] [stdout]     |                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://stackoverflow.com/a/60498499/7070491>`
[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/variants/sampling_bias/fragments.rs:163:17
[INFO] [stdout]     |
[INFO] [stdout] 163 | /// as shown in http://www.milefoot.com/math/stat/pdfc-normaldisc.htm
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://www.milefoot.com/math/stat/pdfc-normaldisc.htm>`
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 5 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 58.66s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: fs_extra v1.2.0
[INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1`
[INFO] running `Command { std: "docker" "inspect" "9bc805e03eae432236f3d628eebd3273030d21286c3100e131c05f6d24bb8a9a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "9bc805e03eae432236f3d628eebd3273030d21286c3100e131c05f6d24bb8a9a", kill_on_drop: false }`
[INFO] [stdout] 9bc805e03eae432236f3d628eebd3273030d21286c3100e131c05f6d24bb8a9a
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "RUSTC_BOOTSTRAP=1" "-e" "DOCS_RS=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@sha256:542af8c9c691278ea8427c9f55ce1005b509eeebcbbcbc893145cd6832507671" "/opt/rustwide/cargo-home/bin/cargo" "+c04832643d70479988a3ad9d92b63d9bc95e9c6d" "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] ab939a6c545abd0d8a7ae6ccc45753a86e69a1aa109963e9c87cdd08a80f1656
[INFO] running `Command { std: "docker" "start" "-a" "ab939a6c545abd0d8a7ae6ccc45753a86e69a1aa109963e9c87cdd08a80f1656", kill_on_drop: false }`
[INFO] [stderr]  Documenting varlociraptor v5.8.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 3.28s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: fs_extra v1.2.0
[INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 2`
[INFO] running `Command { std: "docker" "inspect" "ab939a6c545abd0d8a7ae6ccc45753a86e69a1aa109963e9c87cdd08a80f1656", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "ab939a6c545abd0d8a7ae6ccc45753a86e69a1aa109963e9c87cdd08a80f1656", kill_on_drop: false }`
[INFO] [stdout] ab939a6c545abd0d8a7ae6ccc45753a86e69a1aa109963e9c87cdd08a80f1656