[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] 96f423d5c14ff72193b09d0de4711f0ab48de373 [INFO] checking clinico-omics/preqc-pack against master#506512391b1a75ae450d36c9420978402a91abcc for pr-125384 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fclinico-omics%2Fpreqc-pack" "/workspace/builds/worker-3-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-3-tc1/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/clinico-omics/preqc-pack on toolchain 506512391b1a75ae450d36c9420978402a91abcc [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+506512391b1a75ae450d36c9420978402a91abcc" "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-3-tc1/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: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+506512391b1a75ae450d36c9420978402a91abcc" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating git repository `https://github.com/yjcyxky/rust-bwa` [INFO] [stderr] Updating git submodule `https://github.com/10XGenomics/bwa.git` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded redox_termios v0.1.2 [INFO] [stderr] Downloaded termion v1.5.6 [INFO] [stderr] Downloaded numtoa v0.1.0 [INFO] [stderr] Downloaded stderrlog v0.5.4 [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded random v0.12.2 [INFO] [stderr] Downloaded cxxbridge-flags v1.0.79 [INFO] [stderr] Downloaded cxxbridge-macro v1.0.79 [INFO] [stderr] Downloaded exitcode v1.1.2 [INFO] [stderr] Downloaded anyhow v1.0.65 [INFO] [stderr] Downloaded bio-types v0.13.0 [INFO] [stderr] Downloaded syn v1.0.102 [INFO] [stderr] Downloaded custom_derive v0.1.7 [INFO] [stderr] Downloaded rust-htslib v0.40.2 [INFO] [stderr] Downloaded futures v0.3.24 [INFO] [stderr] Downloaded serde_json v1.0.86 [INFO] [stderr] Downloaded cxx v1.0.79 [INFO] [stderr] Downloaded derive-new v0.5.9 [INFO] [stderr] Downloaded ieee754 v0.2.6 [INFO] [stderr] Downloaded serde_bytes v0.11.7 [INFO] [stderr] Downloaded cmake v0.1.49 [INFO] [stderr] Downloaded futures-macro v0.3.24 [INFO] [stderr] Downloaded futures-sink v0.3.24 [INFO] [stderr] Downloaded md-5 v0.9.1 [INFO] [stderr] Downloaded special v0.9.0 [INFO] [stderr] Downloaded probability v0.19.1 [INFO] [stderr] Downloaded cxx-build v1.0.79 [INFO] [stderr] Downloaded hts-sys v2.0.3 [INFO] [stderr] Downloaded fastq v0.6.0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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:beeedbb442662e57d416641ecc3200b38e573c25b057896194468d05594dd835" "/opt/rustwide/cargo-home/bin/cargo" "+506512391b1a75ae450d36c9420978402a91abcc" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 5321e914f607cf4e9d8d3ce7dd2fbb9c1d0b9df038e6b2335912c97f0b9b15a8 [INFO] running `Command { std: "docker" "start" "-a" "5321e914f607cf4e9d8d3ce7dd2fbb9c1d0b9df038e6b2335912c97f0b9b15a8", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "5321e914f607cf4e9d8d3ce7dd2fbb9c1d0b9df038e6b2335912c97f0b9b15a8", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "5321e914f607cf4e9d8d3ce7dd2fbb9c1d0b9df038e6b2335912c97f0b9b15a8", kill_on_drop: false }` [INFO] [stdout] 5321e914f607cf4e9d8d3ce7dd2fbb9c1d0b9df038e6b2335912c97f0b9b15a8 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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=allow" "-e" "RUSTDOCFLAGS=--cap-lints=allow" "-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:beeedbb442662e57d416641ecc3200b38e573c25b057896194468d05594dd835" "/opt/rustwide/cargo-home/bin/cargo" "+506512391b1a75ae450d36c9420978402a91abcc" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 93bb65552f5667f036396ffaec403fbab7fb175642a61134ed4f3b4124a03bc6 [INFO] running `Command { std: "docker" "start" "-a" "93bb65552f5667f036396ffaec403fbab7fb175642a61134ed4f3b4124a03bc6", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.135 [INFO] [stderr] Compiling proc-macro2 v1.0.47 [INFO] [stderr] Compiling syn v1.0.102 [INFO] [stderr] Compiling serde v1.0.145 [INFO] [stderr] Compiling rustversion v1.0.9 [INFO] [stderr] Compiling generic-array v0.14.6 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling futures-channel v0.3.24 [INFO] [stderr] Compiling glob v0.3.0 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling num-integer v0.1.45 [INFO] [stderr] Compiling libm v0.2.5 [INFO] [stderr] Checking futures-sink v0.3.24 [INFO] [stderr] Compiling futures-util v0.3.24 [INFO] [stderr] Checking idna v0.3.0 [INFO] [stderr] Checking futures-io v0.3.24 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Checking textwrap v0.11.0 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Checking iana-time-zone v0.1.51 [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Checking subtle v2.4.1 [INFO] [stderr] Compiling anyhow v1.0.65 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Compiling serde_json v1.0.86 [INFO] [stderr] Checking thread_local v1.1.4 [INFO] [stderr] Checking random v0.12.2 [INFO] [stderr] Checking exitcode v1.1.2 [INFO] [stdout] error[E0422]: cannot find struct, variant or union type `LineColumn` in crate `proc_macro` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-6f17d22bba15001f/proc-macro2-1.0.47/src/wrapper.rs:479:33 [INFO] [stdout] | [INFO] [stdout] 479 | let proc_macro::LineColumn { line, column } = s.start(); [INFO] [stdout] | ^^^^^^^^^^ not found in `proc_macro` [INFO] [stdout] | [INFO] [stdout] help: consider importing one of these items [INFO] [stdout] | [INFO] [stdout] 1 + use crate::LineColumn; [INFO] [stdout] | [INFO] [stdout] 1 + use crate::fallback::LineColumn; [INFO] [stdout] | [INFO] [stdout] help: if you import `LineColumn`, refer to it directly [INFO] [stdout] | [INFO] [stdout] 479 - let proc_macro::LineColumn { line, column } = s.start(); [INFO] [stdout] 479 + let LineColumn { line, column } = s.start(); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0422]: cannot find struct, variant or union type `LineColumn` in crate `proc_macro` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-6f17d22bba15001f/proc-macro2-1.0.47/src/wrapper.rs:496:33 [INFO] [stdout] | [INFO] [stdout] 496 | let proc_macro::LineColumn { line, column } = s.end(); [INFO] [stdout] | ^^^^^^^^^^ not found in `proc_macro` [INFO] [stdout] | [INFO] [stdout] help: consider importing one of these items [INFO] [stdout] | [INFO] [stdout] 1 + use crate::LineColumn; [INFO] [stdout] | [INFO] [stdout] 1 + use crate::fallback::LineColumn; [INFO] [stdout] | [INFO] [stdout] help: if you import `LineColumn`, refer to it directly [INFO] [stdout] | [INFO] [stdout] 496 - let proc_macro::LineColumn { line, column } = s.end(); [INFO] [stdout] 496 + let LineColumn { line, column } = s.end(); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0635]: unknown feature `proc_macro_span_shrink` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-6f17d22bba15001f/proc-macro2-1.0.47/src/lib.rs:92:30 [INFO] [stdout] | [INFO] [stdout] 92 | feature(proc_macro_span, proc_macro_span_shrink) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Checking url v2.3.1 [INFO] [stderr] Checking digest v0.9.0 [INFO] [stderr] Checking block-buffer v0.9.0 [INFO] [stderr] Checking crypto-mac v0.8.0 [INFO] [stderr] Checking chrono v0.4.22 [INFO] [stderr] Checking blake2 v0.9.2 [INFO] [stderr] Checking md-5 v0.9.1 [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0422, E0635. [INFO] [stdout] [INFO] [stdout] For more information about an error, try `rustc --explain E0422`. [INFO] [stdout] [INFO] [stderr] error: could not compile `proc-macro2` (lib) due to 4 previous errors [INFO] [stderr] warning: build failed, waiting for other jobs to finish... [INFO] running `Command { std: "docker" "inspect" "93bb65552f5667f036396ffaec403fbab7fb175642a61134ed4f3b4124a03bc6", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "93bb65552f5667f036396ffaec403fbab7fb175642a61134ed4f3b4124a03bc6", kill_on_drop: false }` [INFO] [stdout] 93bb65552f5667f036396ffaec403fbab7fb175642a61134ed4f3b4124a03bc6 [INFO] checking clinico-omics/preqc-pack against try#dae34b759e282c069aa28752564694effd121a63 for pr-125384 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fclinico-omics%2Fpreqc-pack" "/workspace/builds/worker-3-tc2/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-3-tc2/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/clinico-omics/preqc-pack on toolchain dae34b759e282c069aa28752564694effd121a63 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+dae34b759e282c069aa28752564694effd121a63" "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-3-tc2/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: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+dae34b759e282c069aa28752564694effd121a63" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/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:beeedbb442662e57d416641ecc3200b38e573c25b057896194468d05594dd835" "/opt/rustwide/cargo-home/bin/cargo" "+dae34b759e282c069aa28752564694effd121a63" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] aee44624a9b2cad9af3f64bfd007a3e4214fdac5f58064ea9a015e1e95c97a53 [INFO] running `Command { std: "docker" "start" "-a" "aee44624a9b2cad9af3f64bfd007a3e4214fdac5f58064ea9a015e1e95c97a53", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "aee44624a9b2cad9af3f64bfd007a3e4214fdac5f58064ea9a015e1e95c97a53", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "aee44624a9b2cad9af3f64bfd007a3e4214fdac5f58064ea9a015e1e95c97a53", kill_on_drop: false }` [INFO] [stdout] aee44624a9b2cad9af3f64bfd007a3e4214fdac5f58064ea9a015e1e95c97a53 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/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=allow" "-e" "RUSTDOCFLAGS=--cap-lints=allow" "-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:beeedbb442662e57d416641ecc3200b38e573c25b057896194468d05594dd835" "/opt/rustwide/cargo-home/bin/cargo" "+dae34b759e282c069aa28752564694effd121a63" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] a38a27e3b892520df510a537e8b370aedfcc8ccd13a0f4f167e9f950bc783298 [INFO] running `Command { std: "docker" "start" "-a" "a38a27e3b892520df510a537e8b370aedfcc8ccd13a0f4f167e9f950bc783298", kill_on_drop: false }` [INFO] [stderr] Copying to /tmp/fixit [INFO] [stderr] skipping non-2021 edition `2018` [INFO] running `Command { std: "docker" "inspect" "a38a27e3b892520df510a537e8b370aedfcc8ccd13a0f4f167e9f950bc783298", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "a38a27e3b892520df510a537e8b370aedfcc8ccd13a0f4f167e9f950bc783298", kill_on_drop: false }` [INFO] [stdout] a38a27e3b892520df510a537e8b370aedfcc8ccd13a0f4f167e9f950bc783298