[INFO] fetching crate bio 0.31.0... [INFO] documenting bio-0.31.0 against master#394e1b40d264aa6928811919c1124fa248e7d802 for pr-73566 [INFO] extracting crate bio 0.31.0 into /workspace/builds/worker-6/source [INFO] validating manifest of crates.io crate bio 0.31.0 on toolchain 394e1b40d264aa6928811919c1124fa248e7d802 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+394e1b40d264aa6928811919c1124fa248e7d802" "read-manifest" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] started tweaking crates.io crate bio 0.31.0 [INFO] finished tweaking crates.io crate bio 0.31.0 [INFO] tweaked toml for crates.io crate bio 0.31.0 written to /workspace/builds/worker-6/source/Cargo.toml [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+394e1b40d264aa6928811919c1124fa248e7d802" "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" "+394e1b40d264aa6928811919c1124fa248e7d802" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/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" "MAP_USER_ID=0" "-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" "--network" "none" "rustops/crates-build-env@sha256:819119df93c0f5eca3f29186f14981ef29945a311854d7222af07488600a2584" "/opt/rustwide/cargo-home/bin/cargo" "+394e1b40d264aa6928811919c1124fa248e7d802" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] fb32eb271777dc8d36b8295c65a4537d27713d5379eee2128af59710c54e938d [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" "fb32eb271777dc8d36b8295c65a4537d27713d5379eee2128af59710c54e938d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "fb32eb271777dc8d36b8295c65a4537d27713d5379eee2128af59710c54e938d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "fb32eb271777dc8d36b8295c65a4537d27713d5379eee2128af59710c54e938d", kill_on_drop: false }` [INFO] [stdout] fb32eb271777dc8d36b8295c65a4537d27713d5379eee2128af59710c54e938d [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/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" "MAP_USER_ID=0" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-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" "--network" "none" "rustops/crates-build-env@sha256:819119df93c0f5eca3f29186f14981ef29945a311854d7222af07488600a2584" "/opt/rustwide/cargo-home/bin/cargo" "+394e1b40d264aa6928811919c1124fa248e7d802" "doc" "--frozen" "--no-deps" "--document-private-items" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 91bb180dfcaa0f17b87ccb3c30b0797c2d207222bfe822ccf13648b8c2414b9c [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" "91bb180dfcaa0f17b87ccb3c30b0797c2d207222bfe822ccf13648b8c2414b9c", kill_on_drop: false }` [INFO] [stderr] Compiling autocfg v1.0.0 [INFO] [stderr] Compiling memchr v2.3.3 [INFO] [stderr] Compiling libc v0.2.71 [INFO] [stderr] Compiling getrandom v0.1.14 [INFO] [stderr] Compiling byteorder v1.3.4 [INFO] [stderr] Checking lazy_static v1.4.0 [INFO] [stderr] Checking cfg-if v0.1.10 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Checking ppv-lite86 v0.2.8 [INFO] [stderr] Compiling doc-comment v0.3.3 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Compiling ndarray v0.13.1 [INFO] [stderr] Checking ordermap v0.3.5 [INFO] [stderr] Checking bit-vec v0.6.2 [INFO] [stderr] Checking fixedbitset v0.1.9 [INFO] [stderr] Checking either v1.5.3 [INFO] [stderr] Compiling bio v0.31.0 (/opt/rustwide/workdir) [INFO] [stderr] Checking fnv v1.0.7 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking bytecount v0.6.0 [INFO] [stderr] Checking strum v0.18.0 [INFO] [stderr] Checking matrixmultiply v0.2.3 [INFO] [stderr] Checking thread_local v1.0.1 [INFO] [stderr] Checking itertools v0.9.0 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Checking bit-set v0.5.2 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Compiling syn v1.0.33 [INFO] [stderr] Checking petgraph v0.4.13 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling num-traits v0.2.12 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling num-integer v0.1.43 [INFO] [stderr] Checking aho-corasick v0.7.13 [INFO] [stderr] Checking csv-core v0.1.10 [INFO] [stderr] Checking regex-automata v0.1.9 [INFO] [stderr] Checking fxhash v0.2.1 [INFO] [stderr] Checking rand_core v0.5.1 [INFO] [stderr] Checking rand_chacha v0.2.2 [INFO] [stderr] Checking rand v0.7.3 [INFO] [stderr] Checking regex v1.3.9 [INFO] [stderr] Checking itertools-num v0.1.3 [INFO] [stderr] Checking ordered-float v1.1.0 [INFO] [stderr] Checking approx v0.3.2 [INFO] [stderr] Checking statrs v0.12.0 [INFO] [stderr] Compiling serde_derive v1.0.114 [INFO] [stderr] Compiling derive-new v0.5.8 [INFO] [stderr] Compiling snafu-derive v0.6.8 [INFO] [stderr] Compiling getset v0.0.9 [INFO] [stderr] Compiling strum_macros v0.18.0 [INFO] [stderr] Checking snafu v0.6.8 [INFO] [stderr] Checking serde v1.0.114 [INFO] [stderr] Checking bstr v0.2.13 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking multimap v0.6.0 [INFO] [stderr] Checking bio-types v0.6.0 [INFO] [stderr] Checking csv v1.1.3 [INFO] [stderr] Documenting bio v0.31.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: `[i]` cannot be resolved, ignoring it. [INFO] [stdout] --> src/alignment/pairwise/mod.rs:367:42 [INFO] [stdout] | [INFO] [stdout] 367 | /// M(i,j) is the best score such that x[i] and y[j] ends in a match [INFO] [stdout] | ^ cannot be resolved, ignoring [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(intra_doc_link_resolution_failure)]` on by default [INFO] [stdout] = help: to escape `[` and `]` characters, just add '\' before them like `\[` or `\]` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: `[j]` cannot be resolved, ignoring it. [INFO] [stdout] --> src/alignment/pairwise/mod.rs:367:51 [INFO] [stdout] | [INFO] [stdout] 367 | /// M(i,j) is the best score such that x[i] and y[j] ends in a match [INFO] [stdout] | ^ cannot be resolved, ignoring [INFO] [stdout] | [INFO] [stdout] = help: to escape `[` and `]` characters, just add '\' before them like `\[` or `\]` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: `[i]` cannot be resolved, ignoring it. [INFO] [stdout] --> src/alignment/pairwise/mod.rs:371:42 [INFO] [stdout] | [INFO] [stdout] 371 | /// I(i,j) is the best score such that x[i] is aligned with a gap [INFO] [stdout] | ^ cannot be resolved, ignoring [INFO] [stdout] | [INFO] [stdout] = help: to escape `[` and `]` characters, just add '\' before them like `\[` or `\]` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: `[j]` cannot be resolved, ignoring it. [INFO] [stdout] --> src/alignment/pairwise/mod.rs:376:42 [INFO] [stdout] | [INFO] [stdout] 376 | /// D(i,j) is the best score such that y[j] is aligned with a gap [INFO] [stdout] | ^ cannot be resolved, ignoring [INFO] [stdout] | [INFO] [stdout] = help: to escape `[` and `]` characters, just add '\' before them like `\[` or `\]` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: `[a]` cannot be resolved, ignoring it. [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] | ^ cannot be resolved, ignoring [INFO] [stdout] | [INFO] [stdout] = help: to escape `[` and `]` characters, just add '\' before them like `\[` or `\]` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: `[a]` cannot be resolved, ignoring it. [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] | ^ cannot be resolved, ignoring [INFO] [stdout] | [INFO] [stdout] = help: to escape `[` and `]` characters, just add '\' before them like `\[` or `\]` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: `[a]` cannot be resolved, ignoring it. [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] | ^ cannot be resolved, ignoring [INFO] [stdout] | [INFO] [stdout] = help: to escape `[` and `]` characters, just add '\' before them like `\[` or `\]` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: `[i]` cannot be resolved, ignoring it. [INFO] [stdout] --> src/stats/pairhmm.rs:37:35 [INFO] [stdout] | [INFO] [stdout] 37 | /// Probability to start at x[i]. This can be left unchanged if you use `free_start_gap_x` and [INFO] [stdout] | ^ cannot be resolved, ignoring [INFO] [stdout] | [INFO] [stdout] = help: to escape `[` and `]` characters, just add '\' before them like `\[` or `\]` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: `[i]` cannot be resolved, ignoring it. [INFO] [stdout] --> src/stats/pairhmm.rs:80:37 [INFO] [stdout] | [INFO] [stdout] 80 | /// Emission probability for (x[i], y[j]). [INFO] [stdout] | ^ cannot be resolved, ignoring [INFO] [stdout] | [INFO] [stdout] = help: to escape `[` and `]` characters, just add '\' before them like `\[` or `\]` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: `[j]` cannot be resolved, ignoring it. [INFO] [stdout] --> src/stats/pairhmm.rs:80:43 [INFO] [stdout] | [INFO] [stdout] 80 | /// Emission probability for (x[i], y[j]). [INFO] [stdout] | ^ cannot be resolved, ignoring [INFO] [stdout] | [INFO] [stdout] = help: to escape `[` and `]` characters, just add '\' before them like `\[` or `\]` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: `[i]` cannot be resolved, ignoring it. [INFO] [stdout] --> src/stats/pairhmm.rs:85:37 [INFO] [stdout] | [INFO] [stdout] 85 | /// Emission probability for (x[i], -). [INFO] [stdout] | ^ cannot be resolved, ignoring [INFO] [stdout] | [INFO] [stdout] = help: to escape `[` and `]` characters, just add '\' before them like `\[` or `\]` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: `[j]` cannot be resolved, ignoring it. [INFO] [stdout] --> src/stats/pairhmm.rs:88:40 [INFO] [stdout] | [INFO] [stdout] 88 | /// Emission probability for (-, y[j]). [INFO] [stdout] | ^ cannot be resolved, ignoring [INFO] [stdout] | [INFO] [stdout] = help: to escape `[` and `]` characters, just 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 1m 12s [INFO] running `Command { std: "docker" "inspect" "91bb180dfcaa0f17b87ccb3c30b0797c2d207222bfe822ccf13648b8c2414b9c", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "91bb180dfcaa0f17b87ccb3c30b0797c2d207222bfe822ccf13648b8c2414b9c", kill_on_drop: false }` [INFO] [stdout] 91bb180dfcaa0f17b87ccb3c30b0797c2d207222bfe822ccf13648b8c2414b9c