[INFO] cloning repository https://github.com/ARU-life-sciences/gffplot
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/ARU-life-sciences/gffplot" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FARU-life-sciences%2Fgffplot", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FARU-life-sciences%2Fgffplot'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 13a36a9f87fc3eb8bf6fabef34482f5c348bc4fc
[INFO] documenting ARU-life-sciences/gffplot against beta-2025-10-28 for beta-1.92-rustdoc-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FARU-life-sciences%2Fgffplot" "/workspace/builds/worker-6-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-6-tc2/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/ARU-life-sciences/gffplot
[INFO] finished tweaking git repo https://github.com/ARU-life-sciences/gffplot
[INFO] tweaked toml for git repo https://github.com/ARU-life-sciences/gffplot written to /workspace/builds/worker-6-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/ARU-life-sciences/gffplot on toolchain beta-2025-10-28
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+beta-2025-10-28" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/ARU-life-sciences/gffplot 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" "+beta-2025-10-28" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-10-28" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 695ed32ed97797709d49c05dacd2200259d4880cadea9d62a7bfae26707d283a
[INFO] running `Command { std: "docker" "start" "-a" "695ed32ed97797709d49c05dacd2200259d4880cadea9d62a7bfae26707d283a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "695ed32ed97797709d49c05dacd2200259d4880cadea9d62a7bfae26707d283a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "695ed32ed97797709d49c05dacd2200259d4880cadea9d62a7bfae26707d283a", kill_on_drop: false }`
[INFO] [stdout] 695ed32ed97797709d49c05dacd2200259d4880cadea9d62a7bfae26707d283a
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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=warn" "-e" "RUSTDOCFLAGS=--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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-10-28" "doc" "--frozen" "--no-deps" "--document-private-items" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] f9e4512024888c0ea3627f5108c62796c785b5d515efff12852d74a556906f26
[INFO] running `Command { std: "docker" "start" "-a" "f9e4512024888c0ea3627f5108c62796c785b5d515efff12852d74a556906f26", kill_on_drop: false }`
[INFO] [stderr]    Compiling proc-macro2 v1.0.93
[INFO] [stderr]    Compiling unicode-ident v1.0.16
[INFO] [stderr]    Compiling libm v0.2.11
[INFO] [stderr]    Compiling libc v0.2.169
[INFO] [stderr]     Checking byteorder v1.5.0
[INFO] [stderr]    Compiling serde v1.0.217
[INFO] [stderr]     Checking bytemuck v1.21.0
[INFO] [stderr]    Compiling paste v1.0.15
[INFO] [stderr]    Compiling getrandom v0.3.1
[INFO] [stderr]    Compiling rustversion v1.0.19
[INFO] [stderr]    Compiling zerocopy v0.8.18
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling matrixmultiply v0.3.9
[INFO] [stderr]     Checking aho-corasick v1.1.3
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]     Checking safe_arch v0.7.4
[INFO] [stderr]    Compiling anyhow v1.0.95
[INFO] [stderr]     Checking indexmap v2.7.1
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]     Checking csv-core v0.1.12
[INFO] [stderr]     Checking bit-vec v0.8.0
[INFO] [stderr]     Checking either v1.13.0
[INFO] [stderr]     Checking fixedbitset v0.4.2
[INFO] [stderr]     Checking wide v0.7.32
[INFO] [stderr]     Checking clap_builder v4.5.29
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking bit-set v0.8.0
[INFO] [stderr]     Checking strum v0.26.3
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking bytecount v0.6.8
[INFO] [stderr]     Checking editdistancek v1.0.2
[INFO] [stderr]     Checking itertools v0.13.0
[INFO] [stderr]     Checking getrandom v0.2.15
[INFO] [stderr]     Checking num-integer v0.1.46
[INFO] [stderr]     Checking num-complex v0.4.6
[INFO] [stderr]     Checking approx v0.5.1
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking ordered-float v4.6.0
[INFO] [stderr]    Compiling quote v1.0.38
[INFO] [stderr]     Checking petgraph v0.6.5
[INFO] [stderr]     Checking rand_core v0.6.4
[INFO] [stderr]    Compiling syn v2.0.98
[INFO] [stderr]     Checking num-rational v0.4.2
[INFO] [stderr]     Checking ndarray v0.16.1
[INFO] [stderr]     Checking regex-automata v0.4.9
[INFO] [stderr]     Checking simba v0.8.1
[INFO] [stderr]     Checking rand_core v0.9.1
[INFO] [stderr]     Checking clap v4.5.29
[INFO] [stderr]     Checking regex v1.11.1
[INFO] [stderr]    Compiling calmio_filters v0.1.0
[INFO] [stderr]     Checking calm_io v0.1.1
[INFO] [stderr]    Compiling zerocopy-derive v0.7.35
[INFO] [stderr]    Compiling serde_derive v1.0.217
[INFO] [stderr]    Compiling nalgebra-macros v0.2.2
[INFO] [stderr]    Compiling thiserror-impl v1.0.69
[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]    Compiling enum-map-derive v0.17.0
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]     Checking enum-map v2.7.3
[INFO] [stderr]     Checking zerocopy v0.7.35
[INFO] [stderr]     Checking ppv-lite86 v0.2.20
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[INFO] [stderr]     Checking bio-types v1.0.4
[INFO] [stderr]     Checking rand_chacha v0.3.1
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[INFO] [stderr]     Checking nalgebra v0.32.6
[INFO] [stderr]     Checking multimap v0.10.0
[INFO] [stderr]     Checking csv v1.3.1
[INFO] [stderr]     Checking bv v0.11.1
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking statrs v0.17.1
[INFO] [stderr]     Checking bio v2.0.3
[INFO] [stderr]  Documenting gffplot v0.1.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 38.99s
[INFO] [stderr]    Generated /opt/rustwide/target/doc/gffplot/index.html
[INFO] running `Command { std: "docker" "inspect" "f9e4512024888c0ea3627f5108c62796c785b5d515efff12852d74a556906f26", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "f9e4512024888c0ea3627f5108c62796c785b5d515efff12852d74a556906f26", kill_on_drop: false }`
[INFO] [stdout] f9e4512024888c0ea3627f5108c62796c785b5d515efff12852d74a556906f26
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-e" "DOCS_RS=1" "-e" "RUSTC_BOOTSTRAP=1" "-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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-10-28" "rustdoc" "--lib" "-Zrustdoc-map" "--config" "build.rustdocflags=[\"--cfg\", \"docsrs\", \"-Z\", \"unstable-options\", \"--document-private-items\"]" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] ea5733fdf366d1a84d16366a787d72b7221a79be3bbffb59c539b5f035b7af59
[INFO] running `Command { std: "docker" "start" "-a" "ea5733fdf366d1a84d16366a787d72b7221a79be3bbffb59c539b5f035b7af59", kill_on_drop: false }`
[INFO] [stderr]    Compiling proc-macro2 v1.0.93
[INFO] [stderr]    Compiling thiserror v1.0.69
[INFO] [stderr]    Compiling anyhow v1.0.95
[INFO] [stdout] error[E0412]: cannot find type `SourceFile` in crate `proc_macro`
[INFO] [stdout]    --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/proc-macro2-1.0.93/src/wrapper.rs:366:26
[INFO] [stdout]     |
[INFO] [stdout] 366 |     Compiler(proc_macro::SourceFile),
[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::SourceFile;
[INFO] [stdout]     |
[INFO] [stdout]   1 + use crate::fallback::SourceFile;
[INFO] [stdout]     |
[INFO] [stdout] help: if you import `SourceFile`, refer to it directly
[INFO] [stdout]     |
[INFO] [stdout] 366 -     Compiler(proc_macro::SourceFile),
[INFO] [stdout] 366 +     Compiler(SourceFile),
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0412]: cannot find type `SourceFile` in crate `proc_macro`
[INFO] [stdout]    --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/proc-macro2-1.0.93/src/wrapper.rs:372:32
[INFO] [stdout]     |
[INFO] [stdout] 372 |     fn nightly(sf: proc_macro::SourceFile) -> Self {
[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::SourceFile;
[INFO] [stdout]     |
[INFO] [stdout]   1 + use crate::fallback::SourceFile;
[INFO] [stdout]     |
[INFO] [stdout] help: if you import `SourceFile`, refer to it directly
[INFO] [stdout]     |
[INFO] [stdout] 372 -     fn nightly(sf: proc_macro::SourceFile) -> Self {
[INFO] [stdout] 372 +     fn nightly(sf: SourceFile) -> Self {
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `source_file` found for reference `&proc_macro::Span` in the current scope
[INFO] [stdout]    --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/proc-macro2-1.0.93/src/wrapper.rs:462:56
[INFO] [stdout]     |
[INFO] [stdout] 462 |             Span::Compiler(s) => SourceFile::nightly(s.source_file()),
[INFO] [stdout]     |                                                        ^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout] help: there is a method `source` with a similar name
[INFO] [stdout]     |
[INFO] [stdout] 462 -             Span::Compiler(s) => SourceFile::nightly(s.source_file()),
[INFO] [stdout] 462 +             Span::Compiler(s) => SourceFile::nightly(s.source()),
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0412, E0599.
[INFO] [stdout] 
[INFO] [stdout] For more information about an error, try `rustc --explain E0412`.
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `proc-macro2` (lib) due to 3 previous errors
[INFO] running `Command { std: "docker" "inspect" "ea5733fdf366d1a84d16366a787d72b7221a79be3bbffb59c539b5f035b7af59", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "ea5733fdf366d1a84d16366a787d72b7221a79be3bbffb59c539b5f035b7af59", kill_on_drop: false }`
[INFO] [stdout] ea5733fdf366d1a84d16366a787d72b7221a79be3bbffb59c539b5f035b7af59
