[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] checking clinico-omics/preqc-pack against try#a7a572ce3edd6d476191fbfe92c9c1986e009b34 for pr-87190-3 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fclinico-omics%2Fpreqc-pack" "/workspace/builds/worker-117/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-117/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/clinico-omics/preqc-pack on toolchain a7a572ce3edd6d476191fbfe92c9c1986e009b34 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "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-117/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" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "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 crossbeam v0.8.0 [INFO] [stderr] Downloaded serde v1.0.119 [INFO] [stderr] Downloaded serde_derive v1.0.119 [INFO] [stderr] Downloaded memoffset v0.6.1 [INFO] [stderr] Downloaded crossbeam-queue v0.3.1 [INFO] [stderr] Downloaded openssl-sys v0.9.60 [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded libc v0.2.82 [INFO] [stderr] Downloaded bio-types v0.10.0 [INFO] [stderr] Downloaded exitcode v1.1.2 [INFO] [stderr] Downloaded custom_derive v0.1.7 [INFO] [stderr] Downloaded derive-new v0.5.8 [INFO] [stderr] Downloaded crossbeam-epoch v0.9.1 [INFO] [stderr] Downloaded linear-map v1.2.0 [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded rust-htslib v0.32.0 [INFO] [stderr] Downloaded stderrlog v0.4.3 [INFO] [stderr] Downloaded syn v1.0.58 [INFO] [stderr] Downloaded seq_io v0.3.1 [INFO] [stderr] Downloaded bzip2-sys v0.1.9+1.0.8 [INFO] [stderr] Downloaded libz-sys v1.1.2 [INFO] [stderr] Downloaded lzma-sys v0.1.17 [INFO] [stderr] Downloaded hts-sys v1.10.3 [INFO] [stderr] Downloaded curl-sys v0.4.39+curl-7.74.0 [INFO] [stderr] Downloaded openssl-src v111.13.0+1.1.1i [INFO] [stderr] Downloaded serde_json v1.0.61 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-117/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-117/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@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 12d63b6a8135b68da18de1dbd92a0bc85556784f80a4cab1b81b7a491dea6428 [INFO] running `Command { std: "docker" "start" "-a" "12d63b6a8135b68da18de1dbd92a0bc85556784f80a4cab1b81b7a491dea6428", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "12d63b6a8135b68da18de1dbd92a0bc85556784f80a4cab1b81b7a491dea6428", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "12d63b6a8135b68da18de1dbd92a0bc85556784f80a4cab1b81b7a491dea6428", kill_on_drop: false }` [INFO] [stdout] 12d63b6a8135b68da18de1dbd92a0bc85556784f80a4cab1b81b7a491dea6428 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-117/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-117/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" "ghcr.io/rust-lang/crates-build-env/linux@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] ff40566ee3dd87429b932ec9a7b3ed6c9d02e72446e8b1906a3cbe420dccea8e [INFO] running `Command { std: "docker" "start" "-a" "ff40566ee3dd87429b932ec9a7b3ed6c9d02e72446e8b1906a3cbe420dccea8e", kill_on_drop: false }` [INFO] [stderr] Copying to /tmp/fixit [INFO] [stderr] Running `cargo fix --edition` [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 unicode-xid v0.2.1 [INFO] [stderr] Compiling version_check v0.9.2 [INFO] [stderr] Compiling syn v1.0.58 [INFO] [stderr] Checking lazy_static v1.4.0 [INFO] [stderr] Checking cfg-if v1.0.0 [INFO] [stderr] Compiling typenum v1.12.0 [INFO] [stderr] Compiling const_fn v0.4.5 [INFO] [stderr] Compiling unicode-segmentation v1.7.1 [INFO] [stderr] Checking scopeguard v1.1.0 [INFO] [stderr] Compiling serde_derive v1.0.119 [INFO] [stderr] Checking matches v0.1.8 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Checking tinyvec_macros v0.1.0 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling glob v0.3.0 [INFO] [stderr] Compiling rayon-core v1.9.0 [INFO] 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v0.1.7 [INFO] [stderr] Checking exitcode v1.1.2 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling proc-macro2 v1.0.24 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Checking unreachable v1.0.0 [INFO] [stderr] Checking thread_local v1.1.0 [INFO] [stderr] Checking tinyvec v1.1.0 [INFO] [stderr] Checking unicode-bidi v0.3.4 [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] Checking buf_redux v0.8.4 [INFO] [stderr] Checking textwrap v0.11.0 [INFO] [stderr] Checking form_urlencoded v1.0.0 [INFO] [stderr] Checking thread_local v0.3.4 [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 heck v0.3.2 [INFO] [stderr] Compiling quote v1.0.8 [INFO] 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Checking url v2.2.0 [INFO] [stderr] Compiling libz-sys v1.1.2 [INFO] [stderr] Compiling openssl-sys v0.9.60 [INFO] [stderr] Compiling bzip2-sys v0.1.9+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.17 [INFO] [stderr] Compiling curl-sys v0.4.39+curl-7.74.0 [INFO] [stderr] Compiling hts-sys v1.10.3 [INFO] [stderr] Checking stderrlog v0.4.3 [INFO] [stderr] Checking flate2 v1.0.20 [INFO] [stderr] Compiling derive-new v0.5.8 [INFO] [stderr] Compiling thiserror-impl v1.0.23 [INFO] [stderr] Compiling strum_macros v0.20.1 [INFO] [stderr] Compiling structopt-derive v0.4.14 [INFO] [stderr] Checking thiserror v1.0.23 [INFO] [stderr] Checking structopt v0.3.21 [INFO] [stderr] Checking bio-types v0.10.0 [INFO] [stderr] Checking seq_io v0.3.1 [INFO] [stderr] Checking rust-htslib v0.32.0 [INFO] [stderr] Checking preqc-pack v0.1.0 (/tmp/fixit) [INFO] [stderr] Migrating src/lib.rs from 2018 edition to 2021 [INFO] [stderr] Migrating src/bin/preqc-pack.rs from 2018 edition to 2021 [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] [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 52.89s [INFO] [stderr] Running `cargo check` to verify 2021 [INFO] [stderr] Checking preqc-pack v0.1.0 (/tmp/fixit) [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: 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] [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 1.01s [INFO] running `Command { std: "docker" "inspect" "ff40566ee3dd87429b932ec9a7b3ed6c9d02e72446e8b1906a3cbe420dccea8e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "ff40566ee3dd87429b932ec9a7b3ed6c9d02e72446e8b1906a3cbe420dccea8e", kill_on_drop: false }` [INFO] [stdout] ff40566ee3dd87429b932ec9a7b3ed6c9d02e72446e8b1906a3cbe420dccea8e