[INFO] fetching crate omics-tools 0.1.0... [INFO] testing omics-tools-0.1.0 against master#62efba8a050c64249dab942951bb28f710208bc8 for pr-90799 [INFO] extracting crate omics-tools 0.1.0 into /workspace/builds/worker-1/source [INFO] validating manifest of crates.io crate omics-tools 0.1.0 on toolchain 62efba8a050c64249dab942951bb28f710208bc8 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+62efba8a050c64249dab942951bb28f710208bc8" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking crates.io crate omics-tools 0.1.0 [INFO] finished tweaking crates.io crate omics-tools 0.1.0 [INFO] tweaked toml for crates.io crate omics-tools 0.1.0 written to /workspace/builds/worker-1/source/Cargo.toml [INFO] crate crates.io crate omics-tools 0.1.0 already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+62efba8a050c64249dab942951bb28f710208bc8" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded semver v0.1.20 [INFO] [stderr] Downloaded rustc_version v0.1.7 [INFO] [stderr] Downloaded linear-map v1.2.0 [INFO] [stderr] Downloaded termion v1.5.5 [INFO] [stderr] Downloaded derive-new v0.5.8 [INFO] [stderr] Downloaded either v1.6.0 [INFO] [stderr] Downloaded memoffset v0.5.5 [INFO] [stderr] Downloaded atty v0.2.11 [INFO] [stderr] Downloaded redox_termios v0.1.1 [INFO] [stderr] Downloaded exitcode v1.1.2 [INFO] [stderr] Downloaded structopt-derive v0.4.10 [INFO] [stderr] Downloaded rayon-core v1.8.0 [INFO] [stderr] Downloaded custom_derive v0.1.7 [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded thiserror-impl v1.0.20 [INFO] [stderr] Downloaded thiserror v1.0.20 [INFO] [stderr] Downloaded thread_local v0.3.4 [INFO] [stderr] Downloaded numtoa v0.1.0 [INFO] [stderr] Downloaded bio-types v0.7.0 [INFO] [stderr] Downloaded jobserver v0.1.21 [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded structopt v0.3.17 [INFO] [stderr] Downloaded rayon v1.4.0 [INFO] [stderr] Downloaded syn v1.0.40 [INFO] [stderr] Downloaded lzma-sys v0.1.16 [INFO] [stderr] Downloaded stderrlog v0.4.3 [INFO] [stderr] Downloaded curl-sys v0.4.36+curl-7.71.1 [INFO] [stderr] Downloaded openssl-src v111.10.2+1.1.1g [INFO] [stderr] Downloaded rust-htslib v0.32.0 [INFO] [stderr] Downloaded hts-sys v1.10.3 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/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:e8397a04204aaf8b9f284182a6f9e27a3c2e67044d0943b4415b160bfc957681" "/opt/rustwide/cargo-home/bin/cargo" "+62efba8a050c64249dab942951bb28f710208bc8" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 8257dc7eebf4416c3f5c25c25b327ef11a9f0d8b53ef62140765552491e73893 [INFO] running `Command { std: "docker" "start" "-a" "8257dc7eebf4416c3f5c25c25b327ef11a9f0d8b53ef62140765552491e73893", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "8257dc7eebf4416c3f5c25c25b327ef11a9f0d8b53ef62140765552491e73893", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "8257dc7eebf4416c3f5c25c25b327ef11a9f0d8b53ef62140765552491e73893", kill_on_drop: false }` [INFO] [stdout] 8257dc7eebf4416c3f5c25c25b327ef11a9f0d8b53ef62140765552491e73893 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/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:e8397a04204aaf8b9f284182a6f9e27a3c2e67044d0943b4415b160bfc957681" "/opt/rustwide/cargo-home/bin/cargo" "+62efba8a050c64249dab942951bb28f710208bc8" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] a213e8b327aeccd9fc1a504facee687cdcfa0ed1f4929f3fd09cdda170e9d36b [INFO] running `Command { std: "docker" "start" "-a" "a213e8b327aeccd9fc1a504facee687cdcfa0ed1f4929f3fd09cdda170e9d36b", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.77 [INFO] [stderr] Compiling autocfg v1.0.1 [INFO] [stderr] Compiling pkg-config v0.3.18 [INFO] [stderr] Compiling proc-macro2 v1.0.21 [INFO] [stderr] Compiling unicode-xid v0.2.1 [INFO] [stderr] Compiling syn v1.0.40 [INFO] [stderr] Compiling version_check v0.9.2 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling tinyvec v0.3.4 [INFO] [stderr] Compiling glob v0.3.0 [INFO] [stderr] Compiling bitflags v1.2.1 [INFO] [stderr] Compiling serde v1.0.116 [INFO] [stderr] Compiling rayon-core v1.8.0 [INFO] [stderr] Compiling matches v0.1.8 [INFO] [stderr] Compiling serde_derive v1.0.116 [INFO] [stderr] Compiling unicode-width v0.1.8 [INFO] [stderr] Compiling regex-syntax v0.6.18 [INFO] [stderr] Compiling log v0.4.11 [INFO] [stderr] Compiling strsim v0.8.0 [INFO] [stderr] Compiling ansi_term v0.11.0 [INFO] [stderr] Compiling lazy_static v0.2.11 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling either v1.6.0 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling termcolor v1.1.0 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling exitcode v1.1.2 [INFO] [stderr] Compiling thread_local v1.0.1 [INFO] [stderr] Compiling unreachable v1.0.0 [INFO] [stderr] Compiling unicode-bidi v0.3.4 [INFO] [stderr] Compiling aho-corasick v0.7.13 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling unicode-normalization v0.1.13 [INFO] [stderr] Compiling textwrap v0.11.0 [INFO] [stderr] Compiling thread_local v0.3.4 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Compiling crossbeam-utils v0.7.2 [INFO] [stderr] Compiling memoffset v0.5.5 [INFO] [stderr] Compiling num-traits v0.2.12 [INFO] [stderr] Compiling crossbeam-epoch v0.8.2 [INFO] [stderr] Compiling num-integer v0.1.43 [INFO] [stderr] Compiling rayon v1.4.0 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling quote v1.0.7 [INFO] [stderr] Compiling idna v0.2.0 [INFO] [stderr] Compiling jobserver v0.1.21 [INFO] [stderr] Compiling atty v0.2.11 [INFO] [stderr] Compiling time v0.1.44 [INFO] [stderr] Compiling num_cpus v1.13.0 [INFO] [stderr] Compiling clap v2.33.3 [INFO] [stderr] Compiling crossbeam-channel v0.4.4 [INFO] [stderr] Compiling cc v1.0.59 [INFO] [stderr] Compiling url v2.1.1 [INFO] [stderr] Compiling crossbeam-deque v0.7.3 [INFO] [stderr] Compiling openssl-src v111.10.2+1.1.1g [INFO] [stderr] Compiling chrono v0.4.15 [INFO] [stderr] Compiling libz-sys v1.1.2 [INFO] [stderr] Compiling openssl-sys v0.9.58 [INFO] [stderr] Compiling curl-sys v0.4.36+curl-7.71.1 [INFO] [stderr] Compiling bzip2-sys v0.1.9+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.16 [INFO] [stderr] Compiling hts-sys v1.10.3 [INFO] [stderr] Compiling regex v1.3.9 [INFO] [stderr] Compiling stderrlog v0.4.3 [INFO] [stderr] Compiling thiserror-impl v1.0.20 [INFO] [stderr] Compiling derive-new v0.5.8 [INFO] [stderr] Compiling structopt-derive v0.4.10 [INFO] [stderr] Compiling thiserror v1.0.20 [INFO] [stderr] Compiling structopt v0.3.17 [INFO] [stderr] Compiling bio-types v0.7.0 [INFO] [stderr] Compiling rust-htslib v0.32.0 [INFO] [stderr] Compiling omics-tools v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused `#[macro_use]` import [INFO] [stdout] --> src/bin/bam-util.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: field is never read: `quiet` [INFO] [stdout] --> src/bin/bam-util.rs:15:3 [INFO] [stdout] | [INFO] [stdout] 15 | quiet: bool, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `verbose` [INFO] [stdout] --> src/bin/bam-util.rs:16:3 [INFO] [stdout] | [INFO] [stdout] 16 | verbose: usize, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `ts` [INFO] [stdout] --> src/bin/bam-util.rs:17:3 [INFO] [stdout] | [INFO] [stdout] 17 | ts: Option, [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 29.97s [INFO] running `Command { std: "docker" "inspect" "a213e8b327aeccd9fc1a504facee687cdcfa0ed1f4929f3fd09cdda170e9d36b", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "a213e8b327aeccd9fc1a504facee687cdcfa0ed1f4929f3fd09cdda170e9d36b", kill_on_drop: false }` [INFO] [stdout] a213e8b327aeccd9fc1a504facee687cdcfa0ed1f4929f3fd09cdda170e9d36b [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/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:e8397a04204aaf8b9f284182a6f9e27a3c2e67044d0943b4415b160bfc957681" "/opt/rustwide/cargo-home/bin/cargo" "+62efba8a050c64249dab942951bb28f710208bc8" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 5f5b074b2b19944e98fcf3899c2386f0c16b257c53d11401fc56e03cbf8a20cc [INFO] running `Command { std: "docker" "start" "-a" "5f5b074b2b19944e98fcf3899c2386f0c16b257c53d11401fc56e03cbf8a20cc", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Compiling omics-tools v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused `#[macro_use]` import [INFO] [stdout] --> src/bin/bam-util.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: field is never read: `quiet` [INFO] [stdout] --> src/bin/bam-util.rs:15:3 [INFO] [stdout] | [INFO] [stdout] 15 | quiet: bool, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `verbose` [INFO] [stdout] --> src/bin/bam-util.rs:16:3 [INFO] [stdout] | [INFO] [stdout] 16 | verbose: usize, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `ts` [INFO] [stdout] --> src/bin/bam-util.rs:17:3 [INFO] [stdout] | [INFO] [stdout] 17 | ts: Option, [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 2.77s [INFO] running `Command { std: "docker" "inspect" "5f5b074b2b19944e98fcf3899c2386f0c16b257c53d11401fc56e03cbf8a20cc", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "5f5b074b2b19944e98fcf3899c2386f0c16b257c53d11401fc56e03cbf8a20cc", kill_on_drop: false }` [INFO] [stdout] 5f5b074b2b19944e98fcf3899c2386f0c16b257c53d11401fc56e03cbf8a20cc [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/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:e8397a04204aaf8b9f284182a6f9e27a3c2e67044d0943b4415b160bfc957681" "/opt/rustwide/cargo-home/bin/cargo" "+62efba8a050c64249dab942951bb28f710208bc8" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] a340f7157458d52b641ce1a41ebabfaa99cc5b890223f25c890dc780cdf3a599 [INFO] running `Command { std: "docker" "start" "-a" "a340f7157458d52b641ce1a41ebabfaa99cc5b890223f25c890dc780cdf3a599", kill_on_drop: false }` [INFO] [stderr] warning: unused `#[macro_use]` import [INFO] [stderr] --> src/bin/bam-util.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: field is never read: `quiet` [INFO] [stderr] --> src/bin/bam-util.rs:15:3 [INFO] [stderr] | [INFO] [stderr] 15 | quiet: bool, [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` on by default [INFO] [stderr] [INFO] [stderr] warning: field is never read: `verbose` [INFO] [stderr] --> src/bin/bam-util.rs:16:3 [INFO] [stderr] | [INFO] [stderr] 16 | verbose: usize, [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: field is never read: `ts` [INFO] [stderr] --> src/bin/bam-util.rs:17:3 [INFO] [stderr] | [INFO] [stderr] 17 | ts: Option, [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: `omics-tools` (bin "bam-util" test) generated 4 warnings [INFO] [stderr] Finished test [unoptimized + debuginfo] target(s) in 0.25s [INFO] [stderr] Running unittests (/opt/rustwide/target/debug/deps/omics_tools-5feddf2d3b2e636b) [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 (/opt/rustwide/target/debug/deps/bam_util-bc1ded65b9bae40a) [INFO] [stderr] Doc-tests omics-tools [INFO] [stdout] [INFO] [stdout] running 1 test [INFO] [stdout] test src/bam/cigar.rs - bam::cigar::remove_whitespace (line 21) ... FAILED [INFO] [stdout] [INFO] [stdout] failures: [INFO] [stdout] [INFO] [stdout] ---- 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] --> 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 omics_tools::bam::cigar::remove_whitespace; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] error: aborting due to 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] 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 0.21s [INFO] [stdout] [INFO] [stderr] error: test failed, to rerun pass '--doc' [INFO] running `Command { std: "docker" "inspect" "a340f7157458d52b641ce1a41ebabfaa99cc5b890223f25c890dc780cdf3a599", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "a340f7157458d52b641ce1a41ebabfaa99cc5b890223f25c890dc780cdf3a599", kill_on_drop: false }` [INFO] [stdout] a340f7157458d52b641ce1a41ebabfaa99cc5b890223f25c890dc780cdf3a599