[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] testing clinico-omics/preqc-pack against master#cdb45c87e2cd43495379f7e867e3cc15dcee9f93 for pr-145838-1 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fclinico-omics%2Fpreqc-pack" "/workspace/builds/worker-1-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-1-tc1/source'... [INFO] [stderr] done. [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-1-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/clinico-omics/preqc-pack on toolchain cdb45c87e2cd43495379f7e867e3cc15dcee9f93 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+cdb45c87e2cd43495379f7e867e3cc15dcee9f93" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [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" "+cdb45c87e2cd43495379f7e867e3cc15dcee9f93" "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 atty v0.2.11 [INFO] [stderr] Downloaded unicode-ident v1.0.5 [INFO] [stderr] Downloaded random v0.12.2 [INFO] [stderr] Downloaded thread_local v1.1.4 [INFO] [stderr] Downloaded futures-macro v0.3.24 [INFO] [stderr] Downloaded bio-types v0.13.0 [INFO] [stderr] Downloaded serde_derive v1.0.145 [INFO] [stderr] Downloaded proc-macro2 v1.0.47 [INFO] [stderr] Downloaded serde_bytes v0.11.7 [INFO] [stderr] Downloaded anyhow v1.0.65 [INFO] [stderr] Downloaded thiserror-impl v1.0.37 [INFO] [stderr] Downloaded derive-new v0.5.9 [INFO] [stderr] Downloaded rustversion v1.0.9 [INFO] [stderr] Downloaded rust-htslib v0.40.2 [INFO] [stderr] Downloaded futures-util v0.3.24 [INFO] [stderr] Downloaded serde v1.0.145 [INFO] [stderr] Downloaded lz4-sys v1.9.4 [INFO] [stderr] Downloaded js-sys v0.3.60 [INFO] [stderr] Downloaded wasm-bindgen v0.2.83 [INFO] [stderr] Downloaded flate2 v1.0.24 [INFO] [stderr] Downloaded special v0.9.0 [INFO] [stderr] Downloaded wasm-bindgen-macro v0.2.83 [INFO] [stderr] Downloaded ieee754 v0.2.6 [INFO] [stderr] Downloaded miniz_oxide v0.5.4 [INFO] [stderr] Downloaded libm v0.2.5 [INFO] [stderr] Downloaded serde_json v1.0.86 [INFO] [stderr] Downloaded futures-executor v0.3.24 [INFO] [stderr] Downloaded ryu v1.0.11 [INFO] [stderr] Downloaded cxx v1.0.79 [INFO] [stderr] Downloaded iana-time-zone v0.1.51 [INFO] [stderr] Downloaded bumpalo v3.11.0 [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded futures-io v0.3.24 [INFO] [stderr] Downloaded itoa v1.0.4 [INFO] [stderr] Downloaded link-cplusplus v1.0.7 [INFO] [stderr] Downloaded cxx-build v1.0.79 [INFO] [stderr] Downloaded wasm-bindgen-macro-support v0.2.83 [INFO] [stderr] Downloaded exitcode v1.1.2 [INFO] [stderr] Downloaded futures-core v0.3.24 [INFO] [stderr] Downloaded generic-array v0.14.6 [INFO] [stderr] Downloaded md-5 v0.9.1 [INFO] [stderr] Downloaded probability v0.19.1 [INFO] [stderr] Downloaded chrono v0.4.22 [INFO] [stderr] Downloaded jobserver v0.1.25 [INFO] [stderr] Downloaded scratch v1.0.2 [INFO] [stderr] Downloaded iana-time-zone-haiku v0.1.1 [INFO] [stderr] Downloaded wasm-bindgen-backend v0.2.83 [INFO] [stderr] Downloaded wasm-bindgen-shared v0.2.83 [INFO] [stderr] Downloaded libc v0.2.135 [INFO] [stderr] Downloaded blake2 v0.9.2 [INFO] [stderr] Downloaded custom_derive v0.1.7 [INFO] [stderr] Downloaded semver v0.1.20 [INFO] [stderr] Downloaded libz-sys v1.1.8 [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded cmake v0.1.49 [INFO] [stderr] Downloaded fastq v0.6.0 [INFO] [stderr] Downloaded futures-sink v0.3.24 [INFO] [stderr] Downloaded slab v0.4.7 [INFO] [stderr] Downloaded futures v0.3.24 [INFO] [stderr] Downloaded core-foundation-sys v0.8.3 [INFO] [stderr] Downloaded cxxbridge-macro v1.0.79 [INFO] [stderr] Downloaded once_cell v1.15.0 [INFO] [stderr] Downloaded thiserror v1.0.37 [INFO] [stderr] Downloaded cxxbridge-flags v1.0.79 [INFO] [stderr] Downloaded unicode-segmentation v1.10.0 [INFO] [stderr] Downloaded syn v1.0.102 [INFO] [stderr] Downloaded linear-map v1.2.0 [INFO] [stderr] Downloaded rustc_version v0.1.7 [INFO] [stderr] Downloaded lz4 v1.24.0 [INFO] [stderr] Downloaded futures-channel v0.3.24 [INFO] [stderr] Downloaded futures-task v0.3.24 [INFO] [stderr] Downloaded stderrlog v0.5.4 [INFO] [stderr] Downloaded quote v1.0.21 [INFO] [stderr] Downloaded hts-sys v2.0.3 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+cdb45c87e2cd43495379f7e867e3cc15dcee9f93" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] a26bd3332eabb79d35e28a5c13cfd7b3d134aefccfb7e3bdd517baebfd532ee5 [INFO] running `Command { std: "docker" "start" "-a" "a26bd3332eabb79d35e28a5c13cfd7b3d134aefccfb7e3bdd517baebfd532ee5", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "a26bd3332eabb79d35e28a5c13cfd7b3d134aefccfb7e3bdd517baebfd532ee5", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "a26bd3332eabb79d35e28a5c13cfd7b3d134aefccfb7e3bdd517baebfd532ee5", kill_on_drop: false }` [INFO] [stdout] a26bd3332eabb79d35e28a5c13cfd7b3d134aefccfb7e3bdd517baebfd532ee5 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+cdb45c87e2cd43495379f7e867e3cc15dcee9f93" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 359447afed73a7b139545c3e2c8198a1d5cfa3d920f7c5822fc04ba94f741f51 [INFO] running `Command { std: "docker" "start" "-a" "359447afed73a7b139545c3e2c8198a1d5cfa3d920f7c5822fc04ba94f741f51", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.135 [INFO] [stderr] Compiling proc-macro2 v1.0.47 [INFO] [stderr] Compiling unicode-ident v1.0.5 [INFO] [stderr] Compiling quote v1.0.21 [INFO] [stderr] Compiling syn v1.0.102 [INFO] [stderr] Compiling memchr v2.5.0 [INFO] [stderr] Compiling pkg-config v0.3.25 [INFO] [stderr] Compiling serde_derive v1.0.145 [INFO] [stderr] Compiling generic-array v0.14.6 [INFO] [stderr] Compiling serde v1.0.145 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling semver v0.1.20 [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-1949cf8c6b5b557f/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 structs [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-1949cf8c6b5b557f/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 structs [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-1949cf8c6b5b557f/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] Compiling futures-core v0.3.24 [INFO] [stderr] Compiling rustversion v1.0.9 [INFO] [stderr] Compiling tinyvec v1.6.0 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling rustc_version v0.1.7 [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 3 previous errors [INFO] [stderr] warning: build failed, waiting for other jobs to finish... [INFO] running `Command { std: "docker" "inspect" "359447afed73a7b139545c3e2c8198a1d5cfa3d920f7c5822fc04ba94f741f51", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "359447afed73a7b139545c3e2c8198a1d5cfa3d920f7c5822fc04ba94f741f51", kill_on_drop: false }` [INFO] [stdout] 359447afed73a7b139545c3e2c8198a1d5cfa3d920f7c5822fc04ba94f741f51