[INFO] cloning repository https://github.com/hillst/bamreadfilt
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/hillst/bamreadfilt" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fhillst%2Fbamreadfilt", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fhillst%2Fbamreadfilt'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 451c40cb7beb3c32eb64c42ed165b16126358e7d
[INFO] documenting hillst/bamreadfilt against beta-2020-08-29 for beta-1.47-rustdoc-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fhillst%2Fbamreadfilt" "/workspace/builds/worker-11/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-11/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/hillst/bamreadfilt on toolchain beta-2020-08-29
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2020-08-29" "read-manifest" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/hillst/bamreadfilt
[INFO] finished tweaking git repo https://github.com/hillst/bamreadfilt
[INFO] tweaked toml for git repo https://github.com/hillst/bamreadfilt written to /workspace/builds/worker-11/source/Cargo.toml
[INFO] crate git repo https://github.com/hillst/bamreadfilt already has a lockfile, it will not be regenerated
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2020-08-29" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded fs-utils v1.1.4
[INFO] [stderr]   Downloaded ieee754 v0.2.6
[INFO] [stderr]   Downloaded rust-htslib v0.16.0
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/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-2020-08-29" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] edc1d21de06fdf1e7f966ccb70e036e60e3ba061f06d2f5541b69f6eaa937226
[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" "edc1d21de06fdf1e7f966ccb70e036e60e3ba061f06d2f5541b69f6eaa937226", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "edc1d21de06fdf1e7f966ccb70e036e60e3ba061f06d2f5541b69f6eaa937226", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "edc1d21de06fdf1e7f966ccb70e036e60e3ba061f06d2f5541b69f6eaa937226", kill_on_drop: false }`
[INFO] [stdout] edc1d21de06fdf1e7f966ccb70e036e60e3ba061f06d2f5541b69f6eaa937226
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/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-2020-08-29" "doc" "--frozen" "--no-deps" "--document-private-items" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 11e7f8bc67fc10014eae357db2b95eba069855dc3800011b48955e1b36ee85be
[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" "11e7f8bc67fc10014eae357db2b95eba069855dc3800011b48955e1b36ee85be", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]    Compiling libc v0.2.71
[INFO] [stderr]    Compiling glob v0.2.11
[INFO] [stderr]    Compiling ucd-util v0.1.8
[INFO] [stderr]    Compiling libloading v0.4.3
[INFO] [stderr]    Compiling utf8-ranges v1.0.4
[INFO] [stderr]    Compiling unicode-width v0.1.8
[INFO] [stderr]    Compiling bindgen v0.32.3
[INFO] [stderr]     Checking tinyvec v0.3.3
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking argparse v0.2.2
[INFO] [stderr]    Compiling thread_local v0.3.6
[INFO] [stderr]    Compiling proc-macro2 v0.2.3
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]     Checking itertools v0.6.5
[INFO] [stderr]    Compiling memchr v2.3.3
[INFO] [stderr]    Compiling regex-syntax v0.5.6
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling log v0.3.9
[INFO] [stderr]    Compiling textwrap v0.11.0
[INFO] [stderr]    Compiling aho-corasick v0.6.10
[INFO] [stderr]     Checking unicode-normalization v0.1.13
[INFO] [stderr]    Compiling quote v0.4.2
[INFO] [stderr]    Compiling clang-sys v0.21.2
[INFO] [stderr]     Checking rand v0.4.6
[INFO] [stderr]    Compiling memchr v1.0.2
[INFO] [stderr]    Compiling atty v0.2.14
[INFO] [stderr]    Compiling which v1.0.5
[INFO] [stderr]    Compiling clap v2.33.1
[INFO] [stderr]     Checking idna v0.1.5
[INFO] [stderr]    Compiling nom v3.2.1
[INFO] [stderr]     Checking url v1.7.2
[INFO] [stderr]    Compiling cexpr v0.2.3
[INFO] [stderr]    Compiling regex v0.2.11
[INFO] [stderr]    Compiling env_logger v0.4.3
[INFO] [stderr]    Compiling rust-htslib v0.16.0
[INFO] [stderr]     Checking bamreadfilt v0.1.1 (/opt/rustwide/workdir)
[INFO] [stderr]  Documenting bamreadfilt v0.1.1 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused imports: `StoreFalse`, `StoreOption`
[INFO] [stdout]  --> src/lib.rs:5:50
[INFO] [stdout]   |
[INFO] [stdout] 5 | use argparse::{ArgumentParser, StoreTrue, Store, StoreFalse, StoreOption};
[INFO] [stdout]   |                                                  ^^^^^^^^^^  ^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::collections::HashSet`
[INFO] [stdout]  --> src/lib.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use std::collections::HashSet;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fs::File`
[INFO] [stdout]   --> src/lib.rs:10:5
[INFO] [stdout]    |
[INFO] [stdout] 10 | use std::fs::File;
[INFO] [stdout]    |     ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `fetched`
[INFO] [stdout]    --> src/lib.rs:213:13
[INFO] [stdout]     |
[INFO] [stdout] 213 |         let fetched = match bam_reader.fetch(vcf_head.chrm, vcf_head.pos, vcf_head.pos + 1){
[INFO] [stdout]     |             ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_fetched`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `fetched`
[INFO] [stdout]    --> src/lib.rs:237:21
[INFO] [stdout]     |
[INFO] [stdout] 237 |                 let fetched = match self._bam.fetch(rid, entry.pos(), entry.pos() + 1){
[INFO] [stdout]     |                     ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_fetched`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `vcf`
[INFO] [stdout]    --> src/lib.rs:352:64
[INFO] [stdout]     |
[INFO] [stdout] 352 |     pub fn collect_stats_stream(&mut self, item: &bam::Record, vcf: &VCFRecord, pir: usize) {
[INFO] [stdout]     |                                                                ^^^ help: if this is intentional, prefix it with an underscore: `_vcf`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variant is never constructed: `BamRecord`
[INFO] [stdout]    --> src/lib.rs:432:5
[INFO] [stdout]     |
[INFO] [stdout] 432 |     BamRecord(bam::Record),
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated function is never used: `iter`
[INFO] [stdout]    --> src/lib.rs:480:8
[INFO] [stdout]     |
[INFO] [stdout] 480 |     fn iter(&self) -> std::collections::hash_set::Iter<UniqueRead> {
[INFO] [stdout]     |        ^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated function is never used: `len`
[INFO] [stdout]    --> src/lib.rs:484:8
[INFO] [stdout]     |
[INFO] [stdout] 484 |     fn len(&self) -> usize {
[INFO] [stdout]     |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated function is never used: `max`
[INFO] [stdout]    --> src/lib.rs:488:8
[INFO] [stdout]     |
[INFO] [stdout] 488 |     fn max(&self) -> Option<&UniqueRead> {
[INFO] [stdout]     |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated function is never used: `min`
[INFO] [stdout]    --> src/lib.rs:492:8
[INFO] [stdout]     |
[INFO] [stdout] 492 |     fn min(&self) -> Option<&UniqueRead> {
[INFO] [stdout]     |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 11 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 2m 05s
[INFO] running `Command { std: "docker" "inspect" "11e7f8bc67fc10014eae357db2b95eba069855dc3800011b48955e1b36ee85be", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "11e7f8bc67fc10014eae357db2b95eba069855dc3800011b48955e1b36ee85be", kill_on_drop: false }`
[INFO] [stdout] 11e7f8bc67fc10014eae357db2b95eba069855dc3800011b48955e1b36ee85be