[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] documenting clinico-omics/omics-tools against beta-2022-05-20 for beta-1.62-rustdoc-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fclinico-omics%2Fomics-tools" "/workspace/builds/worker-37/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-37/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/clinico-omics/omics-tools on toolchain beta-2022-05-20
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2022-05-20" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] removed /workspace/builds/worker-37/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-37/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" "+beta-2022-05-20" "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-37/source/bam-util/Cargo.toml
[INFO] [stderr] workspace: /workspace/builds/worker-37/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-37/source/vcf-util/Cargo.toml
[INFO] [stderr] workspace: /workspace/builds/worker-37/source/Cargo.toml
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-37/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-37/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:d190cb871061d98bc6d0581d85cb2ecb09a0f8a142ba5463de30be9999fc3251" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2022-05-20" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 2954e45b7f3ceccf27675ece265f380f6f56eac0f78783b32baed8d3d86b65a1
[INFO] running `Command { std: "docker" "start" "-a" "2954e45b7f3ceccf27675ece265f380f6f56eac0f78783b32baed8d3d86b65a1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "2954e45b7f3ceccf27675ece265f380f6f56eac0f78783b32baed8d3d86b65a1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "2954e45b7f3ceccf27675ece265f380f6f56eac0f78783b32baed8d3d86b65a1", kill_on_drop: false }`
[INFO] [stdout] 2954e45b7f3ceccf27675ece265f380f6f56eac0f78783b32baed8d3d86b65a1
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-37/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-37/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" "ghcr.io/rust-lang/crates-build-env/linux@sha256:d190cb871061d98bc6d0581d85cb2ecb09a0f8a142ba5463de30be9999fc3251" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2022-05-20" "doc" "--frozen" "--no-deps" "--document-private-items" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] beb03c76413bc8595dee013b23ba598d7294efe59957f00f47250f00764b2524
[INFO] running `Command { std: "docker" "start" "-a" "beb03c76413bc8595dee013b23ba598d7294efe59957f00f47250f00764b2524", 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]     Blocking waiting for file lock on package cache
[INFO] [stderr] warning: output filename collision.
[INFO] [stderr] The bin target `bam-util` in package `bam-util v0.1.0 (/opt/rustwide/workdir/bam-util)` has the same output filename as the lib target `bam_util` in package `bam-util v0.1.0 (/opt/rustwide/workdir/bam-util)`.
[INFO] [stderr] Colliding filename is: /opt/rustwide/target/doc/bam_util/index.html
[INFO] [stderr] The output filenames should be unique.
[INFO] [stderr] This is a known bug where multiple crates with the same name use
[INFO] [stderr] the same path; see <https://github.com/rust-lang/cargo/issues/6313>.
[INFO] [stderr] If this looks unexpected, it may be a bug in Cargo. Please file a bug report at
[INFO] [stderr] https://github.com/rust-lang/cargo/issues/ with as much information as you
[INFO] [stderr] can provide.
[INFO] [stderr] cargo 1.62.0-beta.2 (3f052d8ee 2022-05-12) running on `x86_64-unknown-linux-gnu` target `x86_64-unknown-linux-gnu`
[INFO] [stderr] First unit: Unit { pkg: Package { id: PackageId { name: "bam-util", version: "0.1.0", source: "/opt/rustwide/workdir/bam-util" }, ..: ".." }, target: TargetInner { name: "bam-util", doc: true, ..: with_path("/opt/rustwide/workdir/bam-util/src/main.rs", Edition2018) }, profile: Profile { incremental: false, ..: default_dev() }, kind: Host, mode: Doc { deps: false }, features: [], artifact: false, is_std: false, dep_hash: 15676540475813126195 }
[INFO] [stderr] Second unit: Unit { pkg: Package { id: PackageId { name: "bam-util", version: "0.1.0", source: "/opt/rustwide/workdir/bam-util" }, ..: ".." }, target: TargetInner { ..: lib_target("bam_util", ["cdylib", "staticlib", "rlib"], "/opt/rustwide/workdir/bam-util/src/lib.rs", Edition2018) }, profile: Profile { incremental: false, ..: default_dev() }, kind: Host, mode: Doc { deps: false }, features: [], artifact: false, is_std: false, dep_hash: 15807271091155671459 }
[INFO] [stderr] warning: output filename collision.
[INFO] [stderr] The bin target `vcf-util` in package `vcf-util v0.1.0 (/opt/rustwide/workdir/vcf-util)` has the same output filename as the lib target `vcf_util` in package `vcf-util v0.1.0 (/opt/rustwide/workdir/vcf-util)`.
[INFO] [stderr] Colliding filename is: /opt/rustwide/target/doc/vcf_util/index.html
[INFO] [stderr] The output filenames should be unique.
[INFO] [stderr] This is a known bug where multiple crates with the same name use
[INFO] [stderr] the same path; see <https://github.com/rust-lang/cargo/issues/6313>.
[INFO] [stderr] If this looks unexpected, it may be a bug in Cargo. Please file a bug report at
[INFO] [stderr] https://github.com/rust-lang/cargo/issues/ with as much information as you
[INFO] [stderr] can provide.
[INFO] [stderr] cargo 1.62.0-beta.2 (3f052d8ee 2022-05-12) running on `x86_64-unknown-linux-gnu` target `x86_64-unknown-linux-gnu`
[INFO] [stderr] First unit: Unit { pkg: Package { id: PackageId { name: "vcf-util", version: "0.1.0", source: "/opt/rustwide/workdir/vcf-util" }, ..: ".." }, target: TargetInner { name: "vcf-util", doc: true, ..: with_path("/opt/rustwide/workdir/vcf-util/src/main.rs", Edition2018) }, profile: Profile { incremental: false, ..: default_dev() }, kind: Host, mode: Doc { deps: false }, features: [], artifact: false, is_std: false, dep_hash: 1620597551403836360 }
[INFO] [stderr] Second unit: Unit { pkg: Package { id: PackageId { name: "vcf-util", version: "0.1.0", source: "/opt/rustwide/workdir/vcf-util" }, ..: ".." }, target: TargetInner { ..: lib_target("vcf_util", ["cdylib", "staticlib", "rlib"], "/opt/rustwide/workdir/vcf-util/src/lib.rs", Edition2018) }, profile: Profile { incremental: false, ..: default_dev() }, kind: Host, mode: Doc { deps: false }, features: [], artifact: false, is_std: false, dep_hash: 3041998646694977681 }
[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 syn v1.0.72
[INFO] [stderr]    Compiling memchr v2.4.0
[INFO] [stderr]    Compiling bitflags v1.2.1
[INFO] [stderr]    Compiling unicode-segmentation v1.7.1
[INFO] [stderr]     Checking unicode-width v0.1.8
[INFO] [stderr]    Compiling log v0.4.14
[INFO] [stderr]    Compiling proc-macro2 v0.4.30
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]     Checking lazy_static v0.2.11
[INFO] [stderr]     Checking matches v0.1.8
[INFO] [stderr]     Checking ansi_term v0.11.0
[INFO] [stderr]    Compiling unicode-xid v0.1.0
[INFO] [stderr]    Compiling glob v0.3.0
[INFO] [stderr]     Checking termcolor v1.1.2
[INFO] [stderr]     Checking gimli v0.24.0
[INFO] [stderr]    Compiling syn v0.15.44
[INFO] [stderr]     Checking exitcode v1.1.2
[INFO] [stderr]     Checking ahash v0.4.7
[INFO] [stderr]     Checking rustc-demangle v0.1.19
[INFO] [stderr]    Compiling crc32fast v1.2.1
[INFO] [stderr]     Checking object v0.24.0
[INFO] [stderr]     Checking smallvec v1.6.1
[INFO] [stderr]     Checking fallible-streaming-iterator v0.1.9
[INFO] [stderr]     Checking fallible-iterator v0.2.0
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]    Compiling libc v0.2.94
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]     Checking unreachable v1.0.0
[INFO] [stderr]     Checking tinyvec v1.2.0
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling failure_derive v0.1.8
[INFO] [stderr]    Compiling lexical-core v0.7.6
[INFO] [stderr]    Compiling nom v5.1.2
[INFO] [stderr]     Checking atty v0.2.11
[INFO] [stderr]     Checking time v0.1.44
[INFO] [stderr]     Checking unicode-bidi v0.3.5
[INFO] [stderr]     Checking form_urlencoded v1.0.1
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]     Checking textwrap v0.11.0
[INFO] [stderr]    Compiling heck v0.3.2
[INFO] [stderr]     Checking hashbrown v0.9.1
[INFO] [stderr]    Compiling num-traits v0.2.14
[INFO] [stderr]    Compiling num-integer v0.1.44
[INFO] [stderr]    Compiling miniz_oxide v0.4.4
[INFO] [stderr]     Checking thread_local v0.3.4
[INFO] [stderr]    Compiling jobserver v0.1.22
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling cc v1.0.67
[INFO] [stderr]     Checking clap v2.33.3
[INFO] [stderr]     Checking unicode-normalization v0.1.17
[INFO] [stderr]    Compiling quote v0.6.13
[INFO] [stderr]     Checking aho-corasick v0.7.18
[INFO] [stderr]     Checking hashlink v0.6.0
[INFO] [stderr]    Compiling quote v1.0.9
[INFO] [stderr]     Checking regex v1.5.4
[INFO] [stderr]    Compiling openssl-src v111.15.0+1.1.1k
[INFO] [stderr]     Checking idna v0.2.3
[INFO] [stderr]     Checking chrono v0.4.19
[INFO] [stderr]     Checking addr2line v0.15.1
[INFO] [stderr]    Compiling libz-sys v1.1.3
[INFO] [stderr]    Compiling openssl-sys v0.9.63
[INFO] [stderr]    Compiling lzma-sys v0.1.17
[INFO] [stderr]    Compiling bzip2-sys v0.1.10+1.0.8
[INFO] [stderr]    Compiling curl-sys v0.4.43+curl-7.76.0
[INFO] [stderr]    Compiling backtrace v0.3.59
[INFO] [stderr]    Compiling libsqlite3-sys v0.20.1
[INFO] [stderr]    Compiling cloudflare-zlib-sys v0.2.0
[INFO] [stderr]    Compiling hts-sys v1.11.1-fix1
[INFO] [stderr]     Checking stderrlog v0.4.3
[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 rusqlite v0.24.2
[INFO] [stderr]     Checking failure v0.1.8
[INFO] [stderr]     Checking vcf v0.5.0
[INFO] [stderr]     Checking thiserror v1.0.24
[INFO] [stderr]     Checking structopt v0.3.21
[INFO] [stderr]     Checking bio-types v0.11.0
[INFO] [stderr]  Documenting vcf-util v0.1.0 (/opt/rustwide/workdir/vcf-util)
[INFO] [stderr]     Checking vcf-util v0.1.0 (/opt/rustwide/workdir/vcf-util)
[INFO] [stdout] warning: function is never used: `infer_format_schema`
[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 is never used: `f64_into_vec_u8`
[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] [stderr]  Documenting bam-util v0.1.0 (/opt/rustwide/workdir/bam-util)
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 1m 26s
[INFO] running `Command { std: "docker" "inspect" "beb03c76413bc8595dee013b23ba598d7294efe59957f00f47250f00764b2524", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "beb03c76413bc8595dee013b23ba598d7294efe59957f00f47250f00764b2524", kill_on_drop: false }`
[INFO] [stdout] beb03c76413bc8595dee013b23ba598d7294efe59957f00f47250f00764b2524
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-37/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-37/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=warn" "-e" "RUSTC_BOOTSTRAP=1" "-e" "DOCS_RS=1" "-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:d190cb871061d98bc6d0581d85cb2ecb09a0f8a142ba5463de30be9999fc3251" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2022-05-20" "rustdoc" "--lib" "-Zrustdoc-map" "--frozen" "--message-format=json" "--" "-Z" "unstable-options" "--document-private-items", kill_on_drop: false }`
[INFO] [stdout] 1b654f48dbb70c7449806b07601177b7771b3753028d684b783fb42d24a929d4
[INFO] running `Command { std: "docker" "start" "-a" "1b654f48dbb70c7449806b07601177b7771b3753028d684b783fb42d24a929d4", 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] error: manifest path `/opt/rustwide/workdir/Cargo.toml` is a virtual manifest, but this command requires running against an actual package in this workspace
[INFO] running `Command { std: "docker" "inspect" "1b654f48dbb70c7449806b07601177b7771b3753028d684b783fb42d24a929d4", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "1b654f48dbb70c7449806b07601177b7771b3753028d684b783fb42d24a929d4", kill_on_drop: false }`
[INFO] [stdout] 1b654f48dbb70c7449806b07601177b7771b3753028d684b783fb42d24a929d4