[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] 225d596d6872b010a31f9f8703e5294decfa73ef
[INFO] checking clinico-omics/omics-tools/225d596d6872b010a31f9f8703e5294decfa73ef against master#ff0b4b6091a75ad840035a991426c8bc9fbd93bb for pr-117673
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fclinico-omics%2Fomics-tools" "/workspace/builds/worker-2-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-2-tc1/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/clinico-omics/omics-tools on toolchain ff0b4b6091a75ad840035a991426c8bc9fbd93bb
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ff0b4b6091a75ad840035a991426c8bc9fbd93bb" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] removed /workspace/builds/worker-2-tc1/source/.cargo/config.toml
[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-2-tc1/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: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ff0b4b6091a75ad840035a991426c8bc9fbd93bb" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr] warning: profiles for the non root package will be ignored, specify profiles at the workspace root:
[INFO] [stderr] package:   /workspace/builds/worker-2-tc1/source/bam-util/Cargo.toml
[INFO] [stderr] workspace: /workspace/builds/worker-2-tc1/source/Cargo.toml
[INFO] [stderr] warning: profiles for the non root package will be ignored, specify profiles at the workspace root:
[INFO] [stderr] package:   /workspace/builds/worker-2-tc1/source/vcf-util/Cargo.toml
[INFO] [stderr] workspace: /workspace/builds/worker-2-tc1/source/Cargo.toml
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded fs-utils v1.1.4
[INFO] [stderr]   Downloaded structopt v0.3.21
[INFO] [stderr]   Downloaded newtype_derive v0.1.6
[INFO] [stderr]   Downloaded structopt-derive v0.4.14
[INFO] [stderr]   Downloaded hashlink v0.6.0
[INFO] [stderr]   Downloaded stderrlog v0.4.3
[INFO] [stderr]   Downloaded rusqlite v0.24.2
[INFO] [stderr]   Downloaded lzma-sys v0.1.17
[INFO] [stderr]   Downloaded libsqlite3-sys v0.20.1
[INFO] [stderr]   Downloaded curl-sys v0.4.43+curl-7.76.0
[INFO] [stderr]   Downloaded vcf v0.5.0
[INFO] [stderr]   Downloaded bio-types v0.11.0
[INFO] [stderr]   Downloaded derefable v0.1.0
[INFO] [stderr]   Downloaded cloudflare-zlib-sys v0.2.0
[INFO] [stderr]   Downloaded rust-htslib v0.35.2
[INFO] [stderr]   Downloaded hts-sys v1.11.1-fix1
[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@sha256:0c7e0e8312ad82a1bed3696438480b7da990d348377d3754e1cd95b06a8a36c7" "/opt/rustwide/cargo-home/bin/cargo" "+ff0b4b6091a75ad840035a991426c8bc9fbd93bb" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 7aee717c535ad6a0f96c66b5d703945ef2cf55ce9ee6f9b44a4925b5654bbf46
[INFO] running `Command { std: "docker" "start" "-a" "7aee717c535ad6a0f96c66b5d703945ef2cf55ce9ee6f9b44a4925b5654bbf46", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "7aee717c535ad6a0f96c66b5d703945ef2cf55ce9ee6f9b44a4925b5654bbf46", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "7aee717c535ad6a0f96c66b5d703945ef2cf55ce9ee6f9b44a4925b5654bbf46", kill_on_drop: false }`
[INFO] [stdout] 7aee717c535ad6a0f96c66b5d703945ef2cf55ce9ee6f9b44a4925b5654bbf46
[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@sha256:0c7e0e8312ad82a1bed3696438480b7da990d348377d3754e1cd95b06a8a36c7" "/opt/rustwide/cargo-home/bin/cargo" "+ff0b4b6091a75ad840035a991426c8bc9fbd93bb" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 37a852f48efddd58c3fed39b28759e64cd767a4e3f08fd36d73cab1decc0cf15
[INFO] running `Command { std: "docker" "start" "-a" "37a852f48efddd58c3fed39b28759e64cd767a4e3f08fd36d73cab1decc0cf15", kill_on_drop: false }`
[INFO] [stderr] warning: profiles for the non root package will be ignored, specify profiles at the workspace root:
[INFO] [stderr] package:   /opt/rustwide/workdir/bam-util/Cargo.toml
[INFO] [stderr] workspace: /opt/rustwide/workdir/Cargo.toml
[INFO] [stderr] warning: profiles for the non root package will be ignored, specify profiles at the workspace root:
[INFO] [stderr] package:   /opt/rustwide/workdir/vcf-util/Cargo.toml
[INFO] [stderr] workspace: /opt/rustwide/workdir/Cargo.toml
[INFO] [stderr]    Compiling libc v0.2.94
[INFO] [stderr]    Compiling autocfg v1.0.1
[INFO] [stderr]    Compiling pkg-config v0.3.19
[INFO] [stderr]    Compiling proc-macro2 v1.0.26
[INFO] [stderr]    Compiling unicode-xid v0.2.2
[INFO] [stderr]    Compiling syn v1.0.72
[INFO] [stderr]    Compiling version_check v0.9.3
[INFO] [stderr]    Compiling memchr v2.4.0
[INFO] [stderr]    Compiling unicode-segmentation v1.7.1
[INFO] [stderr]    Compiling log v0.4.14
[INFO] [stderr]     Checking void v1.0.2
[INFO] [stderr]     Checking unicode-width v0.1.8
[INFO] [stderr]     Checking regex-syntax v0.6.25
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]    Compiling proc-macro2 v0.4.30
[INFO] [stderr]     Checking ansi_term v0.11.0
[INFO] [stderr]     Checking unreachable v1.0.0
[INFO] [stderr]     Checking textwrap v0.11.0
[INFO] [stderr]     Checking strsim v0.8.0
[INFO] [stderr]     Checking lazy_static v0.2.11
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]     Checking thread_local v0.3.4
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]     Checking termcolor v1.1.2
[INFO] [stderr]     Checking tinyvec_macros v0.1.0
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]     Checking tinyvec v1.2.0
[INFO] [stderr]    Compiling glob v0.3.0
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]    Compiling heck v0.3.2
[INFO] [stderr]    Compiling num-traits v0.2.14
[INFO] [stderr]    Compiling num-integer v0.1.44
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]    Compiling miniz_oxide v0.4.4
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]     Checking exitcode v1.1.2
[INFO] [stderr]     Checking gimli v0.24.0
[INFO] [stderr]    Compiling syn v0.15.44
[INFO] [stderr]    Compiling lexical-core v0.7.6
[INFO] [stderr]    Compiling failure_derive v0.1.8
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling nom v5.1.2
[INFO] [stderr]     Checking unicode-bidi v0.3.5
[INFO] [stderr]     Checking aho-corasick v0.7.18
[INFO] [stderr]    Compiling quote v1.0.9
[INFO] [stderr]    Compiling quote v0.6.13
[INFO] [stderr]    Compiling jobserver v0.1.22
[INFO] [stderr]     Checking object v0.24.0
[INFO] [stderr]    Compiling crc32fast v1.2.1
[INFO] [stderr]     Checking percent-encoding v2.1.0
[INFO] [stderr]     Checking ahash v0.4.7
[INFO] [stderr]     Checking atty v0.2.11
[INFO] [stderr]     Checking time v0.1.44
[INFO] [stderr]     Checking clap v2.33.3
[INFO] [stderr]    Compiling cc v1.0.67
[INFO] [stderr]     Checking unicode-normalization v0.1.17
[INFO] [stderr]     Checking arrayvec v0.5.2
[INFO] [stderr]     Checking rustc-demangle v0.1.19
[INFO] [stderr]     Checking hashbrown v0.9.1
[INFO] [stderr]     Checking form_urlencoded v1.0.1
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]     Checking smallvec v1.6.1
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking fallible-streaming-iterator v0.1.9
[INFO] [stderr]     Checking fallible-iterator v0.2.0
[INFO] [stderr]    Compiling openssl-src v111.15.0+1.1.1k
[INFO] [stderr]     Checking hashlink v0.6.0
[INFO] [stderr]     Checking chrono v0.4.19
[INFO] [stderr]     Checking regex v1.5.4
[INFO] [stderr]    Compiling libz-sys v1.1.3
[INFO] [stderr]    Compiling openssl-sys v0.9.63
[INFO] [stderr]    Compiling curl-sys v0.4.43+curl-7.76.0
[INFO] [stderr]    Compiling lzma-sys v0.1.17
[INFO] [stderr]    Compiling bzip2-sys v0.1.10+1.0.8
[INFO] [stderr]    Compiling backtrace v0.3.59
[INFO] [stderr]    Compiling libsqlite3-sys v0.20.1
[INFO] [stderr]    Compiling hts-sys v1.11.1-fix1
[INFO] [stderr]    Compiling cloudflare-zlib-sys v0.2.0
[INFO] [stderr]     Checking idna v0.2.3
[INFO] [stderr]     Checking stderrlog v0.4.3
[INFO] [stderr]     Checking addr2line v0.15.1
[INFO] [stderr]     Checking url v2.2.2
[INFO] [stderr]     Checking flate2 v1.0.20
[INFO] [stderr]    Compiling derefable v0.1.0
[INFO] [stderr]    Compiling synstructure v0.12.4
[INFO] [stderr]    Compiling structopt-derive v0.4.14
[INFO] [stderr]    Compiling thiserror-impl v1.0.24
[INFO] [stderr]    Compiling strum_macros v0.20.1
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]     Checking thiserror v1.0.24
[INFO] [stderr]     Checking structopt v0.3.21
[INFO] [stderr]     Checking failure v0.1.8
[INFO] [stderr]     Checking vcf v0.5.0
[INFO] [stderr]     Checking bio-types v0.11.0
[INFO] [stderr]     Checking rusqlite v0.24.2
[INFO] [stderr]     Checking vcf-util v0.1.0 (/opt/rustwide/workdir/vcf-util)
[INFO] [stdout] warning: function `infer_format_schema` is never used
[INFO] [stdout]    --> vcf-util/src/vcf/convertor.rs:106:4
[INFO] [stdout]     |
[INFO] [stdout] 106 | 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 `f64_into_vec_u8` is never used
[INFO] [stdout]    --> vcf-util/src/vcf/convertor.rs:159:4
[INFO] [stdout]     |
[INFO] [stdout] 159 | 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: unused `#[macro_use]` import
[INFO] [stdout]  --> vcf-util/src/main.rs:2:1
[INFO] [stdout]   |
[INFO] [stdout] 2 | #[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]  --> vcf-util/src/main.rs:5:1
[INFO] [stdout]   |
[INFO] [stdout] 5 | #[macro_use]
[INFO] [stdout]   | ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 2 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused `#[macro_use]` import
[INFO] [stdout]  --> vcf-util/src/main.rs:2:1
[INFO] [stdout]   |
[INFO] [stdout] 2 | #[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]  --> vcf-util/src/main.rs:5:1
[INFO] [stdout]   |
[INFO] [stdout] 5 | #[macro_use]
[INFO] [stdout]   | ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 2 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `infer_format_schema` is never used
[INFO] [stdout]    --> vcf-util/src/vcf/convertor.rs:106:4
[INFO] [stdout]     |
[INFO] [stdout] 106 | 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 `f64_into_vec_u8` is never used
[INFO] [stdout]    --> vcf-util/src/vcf/convertor.rs:159:4
[INFO] [stdout]     |
[INFO] [stdout] 159 | 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] [stderr]     Checking rust-htslib v0.35.2
[INFO] [stderr]     Checking bam-util v0.1.0 (/opt/rustwide/workdir/bam-util)
[INFO] [stdout] warning: unused `#[macro_use]` import
[INFO] [stdout]  --> bam-util/src/main.rs:2:1
[INFO] [stdout]   |
[INFO] [stdout] 2 | #[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]  --> bam-util/src/main.rs:5:1
[INFO] [stdout]   |
[INFO] [stdout] 5 | #[macro_use]
[INFO] [stdout]   | ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused `#[macro_use]` import
[INFO] [stdout]  --> bam-util/src/main.rs:2:1
[INFO] [stdout]   |
[INFO] [stdout] 2 | #[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]  --> bam-util/src/main.rs:5:1
[INFO] [stdout]   |
[INFO] [stdout] 5 | #[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] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 17.23s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nom v5.1.2
[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" "37a852f48efddd58c3fed39b28759e64cd767a4e3f08fd36d73cab1decc0cf15", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "37a852f48efddd58c3fed39b28759e64cd767a4e3f08fd36d73cab1decc0cf15", kill_on_drop: false }`
[INFO] [stdout] 37a852f48efddd58c3fed39b28759e64cd767a4e3f08fd36d73cab1decc0cf15