[INFO] cloning repository https://github.com/clinico-omics/omics-tools
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/clinico-omics/omics-tools" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fclinico-omics%2Fomics-tools", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fclinico-omics%2Fomics-tools'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 7383ef18607940b0e210b7272dd9646a360af70b
[INFO] checking clinico-omics/omics-tools against master#9fa580b1175018b0a276b0bc68f9827a106f7260 for pr-82565
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fclinico-omics%2Fomics-tools" "/workspace/builds/worker-3/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-3/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/clinico-omics/omics-tools on toolchain 9fa580b1175018b0a276b0bc68f9827a106f7260
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+9fa580b1175018b0a276b0bc68f9827a106f7260" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/clinico-omics/omics-tools
[INFO] finished tweaking git repo https://github.com/clinico-omics/omics-tools
[INFO] tweaked toml for git repo https://github.com/clinico-omics/omics-tools written to /workspace/builds/worker-3/source/Cargo.toml
[INFO] crate git repo https://github.com/clinico-omics/omics-tools already has a lockfile, it will not be regenerated
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+9fa580b1175018b0a276b0bc68f9827a106f7260" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3/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:f2f6bcd4b43ebee4e173f653a26493129bdb64017c85f916b780ca7fbdbaa79d" "/opt/rustwide/cargo-home/bin/cargo" "+9fa580b1175018b0a276b0bc68f9827a106f7260" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
[INFO] [stdout] 07a2ecb5305f09a8908075fe789a2e7789bf6b57d9f258cc461959072a01bceb
[INFO] running `Command { std: "docker" "start" "-a" "07a2ecb5305f09a8908075fe789a2e7789bf6b57d9f258cc461959072a01bceb", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "07a2ecb5305f09a8908075fe789a2e7789bf6b57d9f258cc461959072a01bceb", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "07a2ecb5305f09a8908075fe789a2e7789bf6b57d9f258cc461959072a01bceb", kill_on_drop: false }`
[INFO] [stdout] 07a2ecb5305f09a8908075fe789a2e7789bf6b57d9f258cc461959072a01bceb
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3/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" "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:f2f6bcd4b43ebee4e173f653a26493129bdb64017c85f916b780ca7fbdbaa79d" "/opt/rustwide/cargo-home/bin/cargo" "+9fa580b1175018b0a276b0bc68f9827a106f7260" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
[INFO] [stdout] df6d9ec598e462854d9cc6516dfaa863b92c056f67c41ecb366e3ecc9d836f04
[INFO] running `Command { std: "docker" "start" "-a" "df6d9ec598e462854d9cc6516dfaa863b92c056f67c41ecb366e3ecc9d836f04", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.77
[INFO] [stderr]    Compiling proc-macro2 v1.0.21
[INFO] [stderr]    Compiling syn v1.0.40
[INFO] [stderr]    Compiling version_check v0.9.2
[INFO] [stderr]     Checking cfg-if v0.1.10
[INFO] [stderr]    Compiling maybe-uninit v2.0.0
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]    Compiling lexical-core v0.7.4
[INFO] [stderr]     Checking scopeguard v1.1.0
[INFO] [stderr]    Compiling failure_derive v0.1.8
[INFO] [stderr]     Checking matches v0.1.8
[INFO] [stderr]    Compiling glob v0.3.0
[INFO] [stderr]     Checking gimli v0.23.0
[INFO] [stderr]    Compiling serde v1.0.116
[INFO] [stderr]    Compiling rayon-core v1.8.0
[INFO] [stderr]    Compiling serde_derive v1.0.116
[INFO] [stderr]     Checking rustc-demangle v0.1.18
[INFO] [stderr]     Checking void v1.0.2
[INFO] [stderr]     Checking arrayvec v0.5.2
[INFO] [stderr]     Checking regex-syntax v0.6.18
[INFO] [stderr]     Checking object v0.22.0
[INFO] [stderr]     Checking unicode-width v0.1.8
[INFO] [stderr]     Checking ansi_term v0.11.0
[INFO] [stderr]     Checking percent-encoding v2.1.0
[INFO] [stderr]     Checking lazy_static v0.2.11
[INFO] [stderr]     Checking smallvec v1.6.1
[INFO] [stderr]     Checking fallible-iterator v0.2.0
[INFO] [stderr]     Checking either v1.6.0
[INFO] [stderr]     Checking fallible-streaming-iterator v0.1.9
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]    Compiling crossbeam-utils v0.7.2
[INFO] [stderr]    Compiling miniz_oxide v0.4.3
[INFO] [stderr]    Compiling memoffset v0.5.5
[INFO] [stderr]    Compiling num-traits v0.2.12
[INFO] [stderr]    Compiling crossbeam-epoch v0.8.2
[INFO] [stderr]    Compiling num-integer v0.1.43
[INFO] [stderr]    Compiling rayon v1.4.0
[INFO] [stderr]     Checking thread_local v1.0.1
[INFO] [stderr]    Compiling libsqlite3-sys v0.20.1
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]     Checking unicode-bidi v0.3.4
[INFO] [stderr]     Checking unreachable v1.0.0
[INFO] [stderr]     Checking hashbrown v0.9.1
[INFO] [stderr]     Checking textwrap v0.11.0
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]    Compiling nom v5.1.2
[INFO] [stderr]     Checking crc32fast v1.2.1
[INFO] [stderr]     Checking log v0.4.11
[INFO] [stderr]     Checking thread_local v0.3.4
[INFO] [stderr]     Checking aho-corasick v0.7.13
[INFO] [stderr]     Checking idna v0.2.0
[INFO] [stderr]     Checking hashlink v0.6.0
[INFO] [stderr]     Checking crossbeam-channel v0.4.4
[INFO] [stderr]    Compiling quote v1.0.7
[INFO] [stderr]     Checking rusqlite v0.24.2
[INFO] [stderr]     Checking url v2.1.1
[INFO] [stderr]     Checking atty v0.2.11
[INFO] [stderr]     Checking num_cpus v1.13.0
[INFO] [stderr]     Checking time v0.1.44
[INFO] [stderr]     Checking flate2 v1.0.19
[INFO] [stderr]     Checking crossbeam-deque v0.7.3
[INFO] [stderr]    Compiling jobserver v0.1.21
[INFO] [stderr]     Checking clap v2.33.3
[INFO] [stderr]     Checking chrono v0.4.15
[INFO] [stderr]    Compiling cc v1.0.59
[INFO] [stderr]     Checking regex v1.3.9
[INFO] [stderr]     Checking addr2line v0.14.1
[INFO] [stderr]     Checking backtrace v0.3.55
[INFO] [stderr]    Compiling openssl-src v111.10.2+1.1.1g
[INFO] [stderr]     Checking stderrlog v0.4.3
[INFO] [stderr]    Compiling libz-sys v1.1.2
[INFO] [stderr]    Compiling openssl-sys v0.9.58
[INFO] [stderr]    Compiling bzip2-sys v0.1.9+1.0.8
[INFO] [stderr]    Compiling lzma-sys v0.1.16
[INFO] [stderr]    Compiling curl-sys v0.4.36+curl-7.71.1
[INFO] [stderr]    Compiling hts-sys v1.10.3
[INFO] [stderr]    Compiling synstructure v0.12.4
[INFO] [stderr]    Compiling derive-new v0.5.8
[INFO] [stderr]    Compiling thiserror-impl v1.0.20
[INFO] [stderr]    Compiling structopt-derive v0.4.10
[INFO] [stderr]     Checking failure v0.1.8
[INFO] [stderr]     Checking vcf v0.5.0
[INFO] [stderr]     Checking thiserror v1.0.20
[INFO] [stderr]     Checking structopt v0.3.17
[INFO] [stderr]     Checking bio-types v0.7.0
[INFO] [stderr]     Checking rust-htslib v0.32.0
[INFO] [stderr]     Checking omics-tools v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: function is never used: `infer_format_schema`
[INFO] [stdout]    --> src/vcf/convertor.rs:103:4
[INFO] [stdout]     |
[INFO] [stdout] 103 | fn infer_format_schema<R: BufRead>(reader: &VCFReader<R>) -> HashMap<String, String> {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `f64_into_vec_u8`
[INFO] [stdout]    --> src/vcf/convertor.rs:156:4
[INFO] [stdout]     |
[INFO] [stdout] 156 | fn f64_into_vec_u8(value: std::option::Option<f64>) -> Vec<u8> {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `infer_format_schema`
[INFO] [stdout]    --> src/vcf/convertor.rs:103:4
[INFO] [stdout]     |
[INFO] [stdout] 103 | fn infer_format_schema<R: BufRead>(reader: &VCFReader<R>) -> HashMap<String, String> {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function is never used: `f64_into_vec_u8`
[INFO] [stdout]    --> src/vcf/convertor.rs:156:4
[INFO] [stdout]     |
[INFO] [stdout] 156 | fn f64_into_vec_u8(value: std::option::Option<f64>) -> Vec<u8> {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 2 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 2 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused `#[macro_use]` import
[INFO] [stdout]  --> src/bin/vcf-util.rs:1:1
[INFO] [stdout]   |
[INFO] [stdout] 1 | #[macro_use]
[INFO] [stdout]   | ^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused `#[macro_use]` import
[INFO] [stdout]  --> src/bin/vcf-util.rs:4:1
[INFO] [stdout]   |
[INFO] [stdout] 4 | #[macro_use]
[INFO] [stdout]   | ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused `#[macro_use]` import
[INFO] [stdout]  --> src/bin/vcf-util.rs:1:1
[INFO] [stdout]   |
[INFO] [stdout] 1 | #[macro_use]
[INFO] [stdout]   | ^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused `#[macro_use]` import
[INFO] [stdout]  --> src/bin/vcf-util.rs:4:1
[INFO] [stdout]   |
[INFO] [stdout] 4 | #[macro_use]
[INFO] [stdout]   | ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused `#[macro_use]` import
[INFO] [stdout]  --> src/bin/bam-util.rs:1:1
[INFO] [stdout]   |
[INFO] [stdout] 1 | #[macro_use]
[INFO] [stdout]   | ^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused `#[macro_use]` import
[INFO] [stdout]  --> src/bin/bam-util.rs:4:1
[INFO] [stdout]   |
[INFO] [stdout] 4 | #[macro_use]
[INFO] [stdout]   | ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused `#[macro_use]` import
[INFO] [stdout]  --> src/bin/bam-util.rs:1:1
[INFO] [stdout]   |
[INFO] [stdout] 1 | #[macro_use]
[INFO] [stdout]   | ^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused `#[macro_use]` import
[INFO] [stdout]  --> src/bin/bam-util.rs:4:1
[INFO] [stdout]   |
[INFO] [stdout] 4 | #[macro_use]
[INFO] [stdout]   | ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 2 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 2 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 2 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 2 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 3m 48s
[INFO] running `Command { std: "docker" "inspect" "df6d9ec598e462854d9cc6516dfaa863b92c056f67c41ecb366e3ecc9d836f04", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "df6d9ec598e462854d9cc6516dfaa863b92c056f67c41ecb366e3ecc9d836f04", kill_on_drop: false }`
[INFO] [stdout] df6d9ec598e462854d9cc6516dfaa863b92c056f67c41ecb366e3ecc9d836f04