[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] testing clinico-omics/omics-tools/225d596d6872b010a31f9f8703e5294decfa73ef against master#b03b3a7ec92682be2917540b679478d41c95a30c for pr-137122-1 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fclinico-omics%2Fomics-tools" "/workspace/builds/worker-7-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-7-tc1/source'... [INFO] [stderr] done. [INFO] removed /workspace/builds/worker-7-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-7-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/clinico-omics/omics-tools on toolchain b03b3a7ec92682be2917540b679478d41c95a30c [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+b03b3a7ec92682be2917540b679478d41c95a30c" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [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" "+b03b3a7ec92682be2917540b679478d41c95a30c" "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-7-tc1/source/bam-util/Cargo.toml [INFO] [stderr] workspace: /workspace/builds/worker-7-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-7-tc1/source/vcf-util/Cargo.toml [INFO] [stderr] workspace: /workspace/builds/worker-7-tc1/source/Cargo.toml [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded bio-types v0.11.0 [INFO] [stderr] Downloaded derefable v0.1.0 [INFO] [stderr] Downloaded vcf v0.5.0 [INFO] [stderr] Downloaded rust-htslib v0.35.2 [INFO] [stderr] Downloaded cloudflare-zlib-sys v0.2.0 [INFO] [stderr] Downloaded lzma-sys v0.1.17 [INFO] [stderr] Downloaded hts-sys v1.11.1-fix1 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+b03b3a7ec92682be2917540b679478d41c95a30c" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 7c2783a8a3bf36d344a944943188e812ad232eb0cd7335e162bdb3000e311fd2 [INFO] running `Command { std: "docker" "start" "-a" "7c2783a8a3bf36d344a944943188e812ad232eb0cd7335e162bdb3000e311fd2", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "7c2783a8a3bf36d344a944943188e812ad232eb0cd7335e162bdb3000e311fd2", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "7c2783a8a3bf36d344a944943188e812ad232eb0cd7335e162bdb3000e311fd2", kill_on_drop: false }` [INFO] [stdout] 7c2783a8a3bf36d344a944943188e812ad232eb0cd7335e162bdb3000e311fd2 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+b03b3a7ec92682be2917540b679478d41c95a30c" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] a8019d41a23aef47a76aa4cb9cee94e7156e8e001d45c622a6f9ff7127f024a5 [INFO] running `Command { std: "docker" "start" "-a" "a8019d41a23aef47a76aa4cb9cee94e7156e8e001d45c622a6f9ff7127f024a5", 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 pkg-config v0.3.19 [INFO] [stderr] Compiling autocfg v1.0.1 [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 cfg-if v1.0.0 [INFO] [stderr] Compiling bitflags v1.2.1 [INFO] [stderr] Compiling unicode-segmentation v1.7.1 [INFO] [stderr] Compiling lazy_static v1.4.0 [INFO] [stderr] Compiling proc-macro2 v0.4.30 [INFO] [stderr] Compiling log v0.4.14 [INFO] [stderr] Compiling unicode-xid v0.1.0 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling unicode-width v0.1.8 [INFO] [stderr] Compiling tinyvec_macros v0.1.0 [INFO] [stderr] Compiling ryu v1.0.5 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling regex-syntax v0.6.25 [INFO] [stderr] Compiling void v1.0.2 [INFO] [stderr] Compiling matches v0.1.8 [INFO] [stderr] Compiling unreachable v1.0.0 [INFO] [stderr] Compiling heck v0.3.2 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Compiling textwrap v0.11.0 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling tinyvec v1.2.0 [INFO] [stderr] Compiling lazy_static v0.2.11 [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] Compiling strsim v0.8.0 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling failure_derive v0.1.8 [INFO] [stderr] Compiling adler v1.0.2 [INFO] [stderr] Compiling lexical-core v0.7.6 [INFO] [stderr] Compiling glob v0.3.0 [INFO] [stderr] Compiling gimli v0.24.0 [INFO] [stderr] Compiling syn v0.15.44 [INFO] [stderr] Compiling ansi_term v0.11.0 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling aho-corasick v0.7.18 [INFO] [stderr] Compiling quote v1.0.9 [INFO] [stderr] Compiling jobserver v0.1.22 [INFO] [stderr] Compiling atty v0.2.11 [INFO] [stderr] Compiling time v0.1.44 [INFO] [stderr] Compiling clap v2.33.3 [INFO] [stderr] Compiling quote v0.6.13 [INFO] [stderr] Compiling thread_local v0.3.4 [INFO] [stderr] Compiling cc v1.0.67 [INFO] [stderr] Compiling unicode-normalization v0.1.17 [INFO] [stderr] Compiling unicode-bidi v0.3.5 [INFO] [stderr] Compiling nom v5.1.2 [INFO] [stderr] Compiling termcolor v1.1.2 [INFO] [stderr] Compiling rustc-demangle v0.1.19 [INFO] [stderr] Compiling object v0.24.0 [INFO] [stderr] Compiling crc32fast v1.2.1 [INFO] [stderr] Compiling ahash v0.4.7 [INFO] [stderr] Compiling arrayvec v0.5.2 [INFO] [stderr] Compiling static_assertions v1.1.0 [INFO] [stderr] Compiling percent-encoding v2.1.0 [INFO] [stderr] Compiling openssl-src v111.15.0+1.1.1k [INFO] [stderr] Compiling form_urlencoded v1.0.1 [INFO] [stderr] Compiling hashbrown v0.9.1 [INFO] [stderr] Compiling chrono v0.4.19 [INFO] [stderr] Compiling exitcode v1.1.2 [INFO] [stderr] Compiling idna v0.2.3 [INFO] [stderr] Compiling smallvec v1.6.1 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling regex v1.5.4 [INFO] [stderr] Compiling hashlink v0.6.0 [INFO] [stderr] Compiling fallible-streaming-iterator v0.1.9 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling fallible-iterator v0.2.0 [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 bzip2-sys v0.1.10+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.17 [INFO] [stderr] Compiling backtrace v0.3.59 [INFO] [stderr] Compiling hts-sys v1.11.1-fix1 [INFO] [stderr] Compiling libsqlite3-sys v0.20.1 [INFO] [stderr] Compiling addr2line v0.15.1 [INFO] [stderr] Compiling cloudflare-zlib-sys v0.2.0 [INFO] [stderr] Compiling url v2.2.2 [INFO] [stderr] Compiling stderrlog v0.4.3 [INFO] [stderr] Compiling derefable v0.1.0 [INFO] [stderr] Compiling synstructure v0.12.4 [INFO] [stderr] Compiling flate2 v1.0.20 [INFO] [stderr] Compiling thiserror-impl v1.0.24 [INFO] [stderr] Compiling structopt-derive v0.4.14 [INFO] [stderr] Compiling strum_macros v0.20.1 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling failure v0.1.8 [INFO] [stderr] Compiling vcf v0.5.0 [INFO] [stderr] Compiling thiserror v1.0.24 [INFO] [stderr] Compiling bio-types v0.11.0 [INFO] [stderr] Compiling structopt v0.3.21 [INFO] [stderr] Compiling rusqlite v0.24.2 [INFO] [stderr] Compiling 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(reader: &VCFReader) -> HashMap { [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) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [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] [stderr] Compiling rust-htslib v0.35.2 [INFO] [stderr] Compiling 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] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 07s [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" "a8019d41a23aef47a76aa4cb9cee94e7156e8e001d45c622a6f9ff7127f024a5", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "a8019d41a23aef47a76aa4cb9cee94e7156e8e001d45c622a6f9ff7127f024a5", kill_on_drop: false }` [INFO] [stdout] a8019d41a23aef47a76aa4cb9cee94e7156e8e001d45c622a6f9ff7127f024a5 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+b03b3a7ec92682be2917540b679478d41c95a30c" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 2a95265949227478eb7c14e39e6b3296d61cbe030e791dc723a048b3c61d55fd [INFO] running `Command { std: "docker" "start" "-a" "2a95265949227478eb7c14e39e6b3296d61cbe030e791dc723a048b3c61d55fd", 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] [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(reader: &VCFReader) -> HashMap { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Compiling vcf-util v0.1.0 (/opt/rustwide/workdir/vcf-util) [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) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Compiling bam-util v0.1.0 (/opt/rustwide/workdir/bam-util) [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: 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: 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(reader: &VCFReader) -> HashMap { [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) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.45s [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" "2a95265949227478eb7c14e39e6b3296d61cbe030e791dc723a048b3c61d55fd", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "2a95265949227478eb7c14e39e6b3296d61cbe030e791dc723a048b3c61d55fd", kill_on_drop: false }` [INFO] [stdout] 2a95265949227478eb7c14e39e6b3296d61cbe030e791dc723a048b3c61d55fd [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+b03b3a7ec92682be2917540b679478d41c95a30c" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] f719aa19273b53bd6df09e6a2730f6e418076177b05d19a6fde6994f5b020384 [INFO] running `Command { std: "docker" "start" "-a" "f719aa19273b53bd6df09e6a2730f6e418076177b05d19a6fde6994f5b020384", 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] warning: function `infer_format_schema` is never used [INFO] [stderr] --> vcf-util/src/vcf/convertor.rs:106:4 [INFO] [stderr] | [INFO] [stderr] 106 | fn infer_format_schema(reader: &VCFReader) -> HashMap { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` on by default [INFO] [stderr] [INFO] [stderr] warning: function `f64_into_vec_u8` is never used [INFO] [stderr] --> vcf-util/src/vcf/convertor.rs:159:4 [INFO] [stderr] | [INFO] [stderr] 159 | fn f64_into_vec_u8(value: std::option::Option) -> Vec { [INFO] [stderr] | ^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: `vcf-util` (lib) generated 2 warnings [INFO] [stderr] warning: `vcf-util` (lib test) generated 2 warnings (2 duplicates) [INFO] [stderr] warning: unused `#[macro_use]` import [INFO] [stderr] --> vcf-util/src/main.rs:2:1 [INFO] [stderr] | [INFO] [stderr] 2 | #[macro_use] [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_imports)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused `#[macro_use]` import [INFO] [stderr] --> vcf-util/src/main.rs:5:1 [INFO] [stderr] | [INFO] [stderr] 5 | #[macro_use] [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused `#[macro_use]` import [INFO] [stderr] --> bam-util/src/main.rs:2:1 [INFO] [stderr] | [INFO] [stderr] 2 | #[macro_use] [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_imports)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused `#[macro_use]` import [INFO] [stderr] --> bam-util/src/main.rs:5:1 [INFO] [stderr] | [INFO] [stderr] 5 | #[macro_use] [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: `vcf-util` (bin "vcf-util" test) generated 2 warnings [INFO] [stderr] warning: `bam-util` (bin "bam-util" test) generated 2 warnings [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.16s [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] [stderr] Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/bam_util-27ea689921a2c561) [INFO] [stderr] Running unittests src/main.rs (/opt/rustwide/target/debug/deps/bam_util-8d8990ed63bea1ad) [INFO] [stdout] [INFO] [stdout] running 0 tests [INFO] [stdout] [INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] running 0 tests [INFO] [stdout] [INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] [stderr] Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/vcf_util-17bf0603b22a0018) [INFO] [stdout] [INFO] [stderr] Running unittests src/main.rs (/opt/rustwide/target/debug/deps/vcf_util-92719d3db388725d) [INFO] [stdout] running 0 tests [INFO] [stdout] [INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] running 0 tests [INFO] [stdout] [INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] [stderr] Doc-tests bam_util [INFO] [stdout] [INFO] [stdout] running 1 test [INFO] [stdout] test bam-util/src/bam/cigar.rs - bam::cigar::remove_whitespace (line 21) ... FAILED [INFO] [stdout] [INFO] [stdout] failures: [INFO] [stdout] [INFO] [stdout] ---- bam-util/src/bam/cigar.rs - bam::cigar::remove_whitespace (line 21) stdout ---- [INFO] [stdout] error[E0425]: cannot find function `remove_whitespace` in this scope [INFO] [stdout] --> bam-util/src/bam/cigar.rs:22:15 [INFO] [stdout] | [INFO] [stdout] 3 | let removed = remove_whitespace(" each(S) && all(M)"); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ not found in this scope [INFO] [stdout] | [INFO] [stdout] help: consider importing this function [INFO] [stdout] | [INFO] [stdout] 2 + use bam_util::bam::cigar::remove_whitespace; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0425`. [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] [INFO] [stdout] failures: [INFO] [stdout] bam-util/src/bam/cigar.rs - bam::cigar::remove_whitespace (line 21) [INFO] [stdout] [INFO] [stdout] test result: FAILED. 0 passed; 1 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.07s [INFO] [stdout] [INFO] [stderr] error: doctest failed, to rerun pass `-p bam-util --doc` [INFO] running `Command { std: "docker" "inspect" "f719aa19273b53bd6df09e6a2730f6e418076177b05d19a6fde6994f5b020384", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f719aa19273b53bd6df09e6a2730f6e418076177b05d19a6fde6994f5b020384", kill_on_drop: false }` [INFO] [stdout] f719aa19273b53bd6df09e6a2730f6e418076177b05d19a6fde6994f5b020384