[INFO] fetching crate bio 0.32.0...
[INFO] documenting bio-0.32.0 against beta-2020-10-09 for beta-1.48-rustdoc-1
[INFO] extracting crate bio 0.32.0 into /workspace/builds/worker-13/source
[INFO] validating manifest of crates.io crate bio 0.32.0 on toolchain beta-2020-10-09
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2020-10-09" "read-manifest" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] started tweaking crates.io crate bio 0.32.0
[INFO] finished tweaking crates.io crate bio 0.32.0
[INFO] tweaked toml for crates.io crate bio 0.32.0 written to /workspace/builds/worker-13/source/Cargo.toml
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2020-10-09" "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" "+beta-2020-10-09" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded proptest v0.10.1
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-13/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-13/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" "rustops/crates-build-env@sha256:d92eaeed33fa75130ca1ee6c8a01d1ffb62bac859dfdfb3450e3e5d1c0146529" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2020-10-09" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] c98fc37d7cd9eb7bd0a4151aec04dd5c80cb35976a0688228fcfb088ee03a08c
[INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
[INFO] running `Command { std: "docker" "start" "-a" "c98fc37d7cd9eb7bd0a4151aec04dd5c80cb35976a0688228fcfb088ee03a08c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "c98fc37d7cd9eb7bd0a4151aec04dd5c80cb35976a0688228fcfb088ee03a08c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "c98fc37d7cd9eb7bd0a4151aec04dd5c80cb35976a0688228fcfb088ee03a08c", kill_on_drop: false }`
[INFO] [stdout] c98fc37d7cd9eb7bd0a4151aec04dd5c80cb35976a0688228fcfb088ee03a08c
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-13/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-13/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" "rustops/crates-build-env@sha256:d92eaeed33fa75130ca1ee6c8a01d1ffb62bac859dfdfb3450e3e5d1c0146529" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2020-10-09" "doc" "--frozen" "--no-deps" "--document-private-items" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] dfe4cebb1691743b74f0f05c8a561576894262ad10cc3807cf6742d4b1df7940
[INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
[INFO] running `Command { std: "docker" "start" "-a" "dfe4cebb1691743b74f0f05c8a561576894262ad10cc3807cf6742d4b1df7940", kill_on_drop: false }`
[INFO] [stderr]    Compiling syn v1.0.45
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling feature-probe v0.1.1
[INFO] [stderr]    Compiling doc-comment v0.3.3
[INFO] [stderr]    Compiling ndarray v0.13.1
[INFO] [stderr]     Checking fixedbitset v0.2.0
[INFO] [stderr]     Checking array-macro v1.0.5
[INFO] [stderr]    Compiling bio v0.32.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Checking bytecount v0.6.0
[INFO] [stderr]     Checking triple_accel v0.3.4
[INFO] [stderr]     Checking strum v0.18.0
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]    Compiling num-complex v0.2.4
[INFO] [stderr]     Checking itertools v0.9.0
[INFO] [stderr]     Checking ordered-float v1.1.0
[INFO] [stderr]     Checking approx v0.3.2
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking statrs v0.12.0
[INFO] [stderr]     Checking petgraph v0.5.1
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling bv v0.11.1
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling serde_derive v1.0.117
[INFO] [stderr]    Compiling enum-map-derive v0.4.3
[INFO] [stderr]    Compiling snafu-derive v0.6.9
[INFO] [stderr]    Compiling derive-new v0.5.8
[INFO] [stderr]    Compiling getset v0.0.9
[INFO] [stderr]    Compiling strum_macros v0.18.0
[INFO] [stderr]     Checking enum-map v0.6.3
[INFO] [stderr]     Checking snafu v0.6.9
[INFO] [stderr]     Checking serde v1.0.117
[INFO] [stderr]     Checking bstr v0.2.14
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking bio-types v0.7.0
[INFO] [stderr]     Checking multimap v0.8.2
[INFO] [stderr]     Checking csv v1.1.3
[INFO] [stderr]  Documenting bio v0.32.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unresolved link to `i`
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:399:42
[INFO] [stdout]     |
[INFO] [stdout] 399 | /// M(i,j) is the best score such that x[i] and y[j] ends in a match
[INFO] [stdout]     |                                          ^ the module `pairwise` contains no item named `i`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(broken_intra_doc_links)]` on by default
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `j`
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:399:51
[INFO] [stdout]     |
[INFO] [stdout] 399 | /// M(i,j) is the best score such that x[i] and y[j] ends in a match
[INFO] [stdout]     |                                                   ^ the module `pairwise` contains no item named `j`
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `i`
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:403:42
[INFO] [stdout]     |
[INFO] [stdout] 403 | /// I(i,j) is the best score such that x[i] is aligned with a gap
[INFO] [stdout]     |                                          ^ the module `pairwise` contains no item named `i`
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `j`
[INFO] [stdout]    --> src/alignment/pairwise/mod.rs:408:42
[INFO] [stdout]     |
[INFO] [stdout] 408 | /// D(i,j) is the best score such that y[j] is aligned with a gap
[INFO] [stdout]     |                                          ^ the module `pairwise` contains no item named `j`
[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/pattern_matching/horspool.rs:23:27
[INFO] [stdout]    |
[INFO] [stdout] 23 | //! 2. shift phase: let l[a] be the rightmost position of a in
[INFO] [stdout]    |                           ^ the module `horspool` contains no item named `a`
[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/pattern_matching/horspool.rs:25:14
[INFO] [stdout]    |
[INFO] [stdout] 25 | //!    let l[a] be -1. Shift the window by m - 1 - l[a]. I.e.
[INFO] [stdout]    |              ^ the module `horspool` contains no item named `a`
[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/pattern_matching/horspool.rs:25:54
[INFO] [stdout]    |
[INFO] [stdout] 25 | //!    let l[a] be -1. Shift the window by m - 1 - l[a]. I.e.
[INFO] [stdout]    |                                                      ^ the module `horspool` contains no item named `a`
[INFO] [stdout]    |
[INFO] [stdout]    = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `i`
[INFO] [stdout]    --> src/stats/pairhmm/mod.rs:112:37
[INFO] [stdout]     |
[INFO] [stdout] 112 |     /// Emission probability for (x[i], y[j]).
[INFO] [stdout]     |                                     ^ the module `pairhmm` contains no item named `i`
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `j`
[INFO] [stdout]    --> src/stats/pairhmm/mod.rs:112:43
[INFO] [stdout]     |
[INFO] [stdout] 112 |     /// Emission probability for (x[i], y[j]).
[INFO] [stdout]     |                                           ^ the module `pairhmm` contains no item named `j`
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `i`
[INFO] [stdout]    --> src/stats/pairhmm/mod.rs:117:37
[INFO] [stdout]     |
[INFO] [stdout] 117 |     /// Emission probability for (x[i], -).
[INFO] [stdout]     |                                     ^ the module `pairhmm` contains no item named `i`
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `j`
[INFO] [stdout]    --> src/stats/pairhmm/mod.rs:120:40
[INFO] [stdout]     |
[INFO] [stdout] 120 |     /// Emission probability for (-, y[j]).
[INFO] [stdout]     |                                        ^ the module `pairhmm` contains no item named `j`
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `i`
[INFO] [stdout]    --> src/stats/pairhmm/mod.rs:159:35
[INFO] [stdout]     |
[INFO] [stdout] 159 |     /// Probability to start at x[i]. This can be left unchanged if you use `free_start_gap_x` and
[INFO] [stdout]     |                                   ^ the module `pairhmm` contains no item named `i`
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 12 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 56.14s
[INFO] running `Command { std: "docker" "inspect" "dfe4cebb1691743b74f0f05c8a561576894262ad10cc3807cf6742d4b1df7940", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "dfe4cebb1691743b74f0f05c8a561576894262ad10cc3807cf6742d4b1df7940", kill_on_drop: false }`
[INFO] [stdout] dfe4cebb1691743b74f0f05c8a561576894262ad10cc3807cf6742d4b1df7940
