[INFO] cloning repository https://github.com/clinico-omics/preqc-pack [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/preqc-pack" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fclinico-omics%2Fpreqc-pack", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fclinico-omics%2Fpreqc-pack'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] f699d7eaf7c4d13f444f531cfca35ee766155e7b [INFO] testing clinico-omics/preqc-pack against 1.59.0 for beta-1.60-1 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fclinico-omics%2Fpreqc-pack" "/workspace/builds/worker-60/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-60/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/clinico-omics/preqc-pack on toolchain 1.59.0 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.59.0" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/clinico-omics/preqc-pack [INFO] finished tweaking git repo https://github.com/clinico-omics/preqc-pack [INFO] tweaked toml for git repo https://github.com/clinico-omics/preqc-pack written to /workspace/builds/worker-60/source/Cargo.toml [INFO] crate git repo https://github.com/clinico-omics/preqc-pack already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.59.0" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded stderrlog v0.4.3 [INFO] [stderr] Downloaded seq_io v0.3.1 [INFO] [stderr] Downloaded bio-types v0.10.0 [INFO] [stderr] Downloaded openssl-src v111.13.0+1.1.1i [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-60/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-60/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@sha256:0cd99ca24d8e8c98e67c542213511d985b8778b5bdcbb160e038429496686047" "/opt/rustwide/cargo-home/bin/cargo" "+1.59.0" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 096684a72fd30bd569246701845f1536480344deee86a85f1f149aace708b5ff [INFO] running `Command { std: "docker" "start" "-a" "096684a72fd30bd569246701845f1536480344deee86a85f1f149aace708b5ff", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "096684a72fd30bd569246701845f1536480344deee86a85f1f149aace708b5ff", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "096684a72fd30bd569246701845f1536480344deee86a85f1f149aace708b5ff", kill_on_drop: false }` [INFO] [stdout] 096684a72fd30bd569246701845f1536480344deee86a85f1f149aace708b5ff [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-60/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-60/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" "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@sha256:0cd99ca24d8e8c98e67c542213511d985b8778b5bdcbb160e038429496686047" "/opt/rustwide/cargo-home/bin/cargo" "+1.59.0" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 63be1a03aa77ba180a19bf143c772aebf0cbf2143782fe2bb6b3cc8c9f5f6276 [INFO] running `Command { std: "docker" "start" "-a" "63be1a03aa77ba180a19bf143c772aebf0cbf2143782fe2bb6b3cc8c9f5f6276", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Compiling libc v0.2.82 [INFO] [stderr] Compiling autocfg v1.0.1 [INFO] [stderr] Compiling pkg-config v0.3.19 [INFO] [stderr] Compiling proc-macro2 v1.0.24 [INFO] [stderr] Compiling unicode-xid v0.2.1 [INFO] [stderr] Compiling version_check v0.9.2 [INFO] [stderr] Compiling syn v1.0.58 [INFO] [stderr] Compiling memchr v2.3.4 [INFO] [stderr] Compiling typenum v1.12.0 [INFO] [stderr] Compiling const_fn v0.4.5 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling scopeguard v1.1.0 [INFO] [stderr] Compiling unicode-segmentation v1.7.1 [INFO] [stderr] Compiling matches v0.1.8 [INFO] [stderr] Compiling serde_derive v1.0.119 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling tinyvec_macros v0.1.0 [INFO] [stderr] Compiling rayon-core v1.9.0 [INFO] [stderr] Compiling bitflags v1.2.1 [INFO] [stderr] Compiling serde v1.0.119 [INFO] [stderr] Compiling glob v0.3.0 [INFO] [stderr] Compiling crc32fast v1.2.1 [INFO] [stderr] Compiling log v0.4.13 [INFO] [stderr] Compiling percent-encoding v2.1.0 [INFO] [stderr] Compiling regex-syntax v0.6.22 [INFO] [stderr] Compiling void v1.0.2 [INFO] [stderr] Compiling cfg-if v0.1.10 [INFO] [stderr] Compiling strsim v0.8.0 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling serde_json v1.0.61 [INFO] [stderr] Compiling ansi_term v0.11.0 [INFO] [stderr] Compiling lazy_static v0.2.11 [INFO] [stderr] Compiling opaque-debug v0.3.0 [INFO] [stderr] Compiling safemem v0.3.3 [INFO] [stderr] Compiling subtle v2.4.0 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling scoped_threadpool v0.1.9 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling either v1.6.1 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling itoa v0.4.7 [INFO] [stderr] Compiling exitcode v1.1.2 [INFO] [stderr] Compiling thread_local v1.1.0 [INFO] [stderr] Compiling textwrap v0.11.0 [INFO] [stderr] Compiling crossbeam-utils v0.8.1 [INFO] [stderr] Compiling memoffset v0.6.1 [INFO] [stderr] Compiling num-traits v0.2.14 [INFO] [stderr] Compiling num-integer v0.1.44 [INFO] [stderr] Compiling rayon v1.5.0 [INFO] [stderr] Compiling generic-array v0.14.4 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Compiling tinyvec v1.1.0 [INFO] [stderr] Compiling unreachable v1.0.0 [INFO] [stderr] Compiling unicode-bidi v0.3.4 [INFO] [stderr] Compiling form_urlencoded v1.0.0 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling heck v0.3.2 [INFO] [stderr] Compiling thread_local v0.3.4 [INFO] [stderr] Compiling unicode-normalization v0.1.16 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling idna v0.2.0 [INFO] [stderr] Compiling aho-corasick v0.7.15 [INFO] [stderr] Compiling buf_redux v0.8.4 [INFO] [stderr] Compiling quote v1.0.8 [INFO] [stderr] Compiling url v2.2.0 [INFO] [stderr] Compiling jobserver v0.1.21 [INFO] [stderr] Compiling atty v0.2.11 [INFO] [stderr] Compiling num_cpus v1.13.0 [INFO] [stderr] Compiling time v0.1.44 [INFO] [stderr] Compiling clap v2.33.3 [INFO] [stderr] Compiling cc v1.0.66 [INFO] [stderr] Compiling digest v0.9.0 [INFO] [stderr] Compiling block-buffer v0.9.0 [INFO] [stderr] Compiling crypto-mac v0.8.0 [INFO] [stderr] Compiling regex v1.4.3 [INFO] [stderr] Compiling md-5 v0.9.1 [INFO] [stderr] Compiling blake2 v0.9.1 [INFO] [stderr] Compiling crossbeam-epoch v0.9.1 [INFO] [stderr] Compiling crossbeam-channel v0.5.0 [INFO] [stderr] Compiling crossbeam-queue v0.3.1 [INFO] [stderr] Compiling cmake v0.1.45 [INFO] [stderr] Compiling openssl-src v111.13.0+1.1.1i [INFO] [stderr] Compiling bzip2-sys v0.1.9+1.0.8 [INFO] [stderr] Compiling curl-sys v0.4.39+curl-7.74.0 [INFO] [stderr] Compiling lzma-sys v0.1.17 [INFO] [stderr] Compiling hts-sys v1.10.3 [INFO] [stderr] Compiling openssl-sys v0.9.60 [INFO] [stderr] Compiling libz-sys v1.1.2 [INFO] [stderr] Compiling crossbeam-deque v0.8.0 [INFO] [stderr] Compiling chrono v0.4.19 [INFO] [stderr] Compiling crossbeam v0.8.0 [INFO] [stderr] Compiling flate2 v1.0.20 [INFO] [stderr] Compiling stderrlog v0.4.3 [INFO] [stderr] Compiling thiserror-impl v1.0.23 [INFO] [stderr] Compiling strum_macros v0.20.1 [INFO] [stderr] Compiling derive-new v0.5.8 [INFO] [stderr] Compiling structopt-derive v0.4.14 [INFO] [stderr] Compiling thiserror v1.0.23 [INFO] [stderr] Compiling bio-types v0.10.0 [INFO] [stderr] Compiling structopt v0.3.21 [INFO] [stderr] Compiling seq_io v0.3.1 [INFO] [stderr] Compiling rust-htslib v0.32.0 [INFO] [stderr] Compiling preqc-pack v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused `#[macro_use]` import [INFO] [stdout] --> src/bin/preqc-pack.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/preqc-pack.rs:5:1 [INFO] [stdout] | [INFO] [stdout] 5 | #[macro_use] [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `is_fastq_file` [INFO] [stdout] --> src/bin/cmd/merge.rs:24:4 [INFO] [stdout] | [INFO] [stdout] 24 | fn is_fastq_file(filepath: &str) -> bool { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `is_fastq_gz_file` [INFO] [stdout] --> src/bin/cmd/merge.rs:33:4 [INFO] [stdout] | [INFO] [stdout] 33 | fn is_fastq_gz_file(filepath: &str) -> bool { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 4 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 2m 41s [INFO] running `Command { std: "docker" "inspect" "63be1a03aa77ba180a19bf143c772aebf0cbf2143782fe2bb6b3cc8c9f5f6276", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "63be1a03aa77ba180a19bf143c772aebf0cbf2143782fe2bb6b3cc8c9f5f6276", kill_on_drop: false }` [INFO] [stdout] 63be1a03aa77ba180a19bf143c772aebf0cbf2143782fe2bb6b3cc8c9f5f6276 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-60/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-60/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" "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@sha256:0cd99ca24d8e8c98e67c542213511d985b8778b5bdcbb160e038429496686047" "/opt/rustwide/cargo-home/bin/cargo" "+1.59.0" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 602a5b32152207333e11c66c603296d9bb306cb171c4aebce3f8ca86c03254d2 [INFO] running `Command { std: "docker" "start" "-a" "602a5b32152207333e11c66c603296d9bb306cb171c4aebce3f8ca86c03254d2", kill_on_drop: false }` [INFO] [stderr] Compiling preqc-pack v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused `#[macro_use]` import [INFO] [stdout] --> src/bin/preqc-pack.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/preqc-pack.rs:5:1 [INFO] [stdout] | [INFO] [stdout] 5 | #[macro_use] [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `is_fastq_file` [INFO] [stdout] --> src/bin/cmd/merge.rs:24:4 [INFO] [stdout] | [INFO] [stdout] 24 | fn is_fastq_file(filepath: &str) -> bool { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `is_fastq_gz_file` [INFO] [stdout] --> src/bin/cmd/merge.rs:33:4 [INFO] [stdout] | [INFO] [stdout] 33 | fn is_fastq_gz_file(filepath: &str) -> bool { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 4 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished test [unoptimized + debuginfo] target(s) in 1.80s [INFO] running `Command { std: "docker" "inspect" "602a5b32152207333e11c66c603296d9bb306cb171c4aebce3f8ca86c03254d2", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "602a5b32152207333e11c66c603296d9bb306cb171c4aebce3f8ca86c03254d2", kill_on_drop: false }` [INFO] [stdout] 602a5b32152207333e11c66c603296d9bb306cb171c4aebce3f8ca86c03254d2 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-60/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-60/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" "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@sha256:0cd99ca24d8e8c98e67c542213511d985b8778b5bdcbb160e038429496686047" "/opt/rustwide/cargo-home/bin/cargo" "+1.59.0" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] fb9e2d9faef5920fb80074a42e6fbc789e99cc54e9209462c1e0ca1399869099 [INFO] running `Command { std: "docker" "start" "-a" "fb9e2d9faef5920fb80074a42e6fbc789e99cc54e9209462c1e0ca1399869099", kill_on_drop: false }` [INFO] [stderr] warning: unused `#[macro_use]` import [INFO] [stderr] --> src/bin/preqc-pack.rs:1:1 [INFO] [stderr] | [INFO] [stderr] 1 | #[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] --> src/bin/preqc-pack.rs:5:1 [INFO] [stderr] | [INFO] [stderr] 5 | #[macro_use] [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function is never used: `is_fastq_file` [INFO] [stderr] --> src/bin/cmd/merge.rs:24:4 [INFO] [stderr] | [INFO] [stderr] 24 | fn is_fastq_file(filepath: &str) -> bool { [INFO] [stderr] | ^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` on by default [INFO] [stderr] [INFO] [stderr] warning: function is never used: `is_fastq_gz_file` [INFO] [stderr] --> src/bin/cmd/merge.rs:33:4 [INFO] [stderr] | [INFO] [stderr] 33 | fn is_fastq_gz_file(filepath: &str) -> bool { [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: `preqc-pack` (bin "preqc-pack" test) generated 4 warnings [INFO] [stderr] Finished test [unoptimized + debuginfo] target(s) in 0.12s [INFO] [stderr] Running unittests (/opt/rustwide/target/debug/deps/preqc_pack-eef0d49ff8e998db) [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 (/opt/rustwide/target/debug/deps/preqc_pack-9a76e81a7994b333) [INFO] [stdout] [INFO] [stderr] Doc-tests preqc-pack [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] running `Command { std: "docker" "inspect" "fb9e2d9faef5920fb80074a42e6fbc789e99cc54e9209462c1e0ca1399869099", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "fb9e2d9faef5920fb80074a42e6fbc789e99cc54e9209462c1e0ca1399869099", kill_on_drop: false }` [INFO] [stdout] fb9e2d9faef5920fb80074a42e6fbc789e99cc54e9209462c1e0ca1399869099