[INFO] cloning repository https://github.com/Benoitdw/kmer_count
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/Benoitdw/kmer_count" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FBenoitdw%2Fkmer_count", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FBenoitdw%2Fkmer_count'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 143a0b4fbfdd791dbdba84c98f524c302490a588
[INFO] documenting Benoitdw/kmer_count 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%2FBenoitdw%2Fkmer_count" "/workspace/builds/worker-7-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-7-tc2/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/Benoitdw/kmer_count
[INFO] finished tweaking git repo https://github.com/Benoitdw/kmer_count
[INFO] tweaked toml for git repo https://github.com/Benoitdw/kmer_count written to /workspace/builds/worker-7-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/Benoitdw/kmer_count 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/Benoitdw/kmer_count 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-7-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-10-28" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] e0fdf4e7e063e93e705b83b702c0fa01aef79cce77205cb4c74e97a9b7aea7c0
[INFO] running `Command { std: "docker" "start" "-a" "e0fdf4e7e063e93e705b83b702c0fa01aef79cce77205cb4c74e97a9b7aea7c0", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "e0fdf4e7e063e93e705b83b702c0fa01aef79cce77205cb4c74e97a9b7aea7c0", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "e0fdf4e7e063e93e705b83b702c0fa01aef79cce77205cb4c74e97a9b7aea7c0", kill_on_drop: false }`
[INFO] [stdout] e0fdf4e7e063e93e705b83b702c0fa01aef79cce77205cb4c74e97a9b7aea7c0
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/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] d80f6d516e9162a8a7f868d7008c17ed76819f5fa6b132f98273e4460788515c
[INFO] running `Command { std: "docker" "start" "-a" "d80f6d516e9162a8a7f868d7008c17ed76819f5fa6b132f98273e4460788515c", kill_on_drop: false }`
[INFO] [stderr]    Compiling syn v2.0.87
[INFO] [stderr]    Compiling libm v0.2.11
[INFO] [stderr]    Compiling libc v0.2.164
[INFO] [stderr]    Compiling serde v1.0.215
[INFO] [stderr]    Compiling matrixmultiply v0.3.9
[INFO] [stderr]    Compiling rustversion v1.0.18
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]     Checking aho-corasick v1.1.3
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]     Checking anstyle-parse v0.2.6
[INFO] [stderr]    Compiling proc-macro-error-attr2 v2.0.0
[INFO] [stderr]     Checking colorchoice v1.0.3
[INFO] [stderr]     Checking anstyle v1.0.10
[INFO] [stderr]     Checking anstyle-query v1.1.2
[INFO] [stderr]    Compiling anyhow v1.0.93
[INFO] [stderr]     Checking csv-core v0.1.11
[INFO] [stderr]     Checking clap_lex v0.7.3
[INFO] [stderr]     Checking bit-vec v0.6.3
[INFO] [stderr]     Checking itertools v0.10.5
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]     Checking anstream v0.6.18
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking strum v0.23.0
[INFO] [stderr]     Checking bytecount v0.6.8
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking bit-set v0.5.3
[INFO] [stderr]     Checking clap_builder v4.5.21
[INFO] [stderr]     Checking num-traits v0.2.19
[INFO] [stderr]     Checking getrandom v0.2.15
[INFO] [stderr]     Checking regex-automata v0.4.9
[INFO] [stderr]     Checking rand_core v0.6.4
[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 ordered-float v2.10.1
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking num-rational v0.4.2
[INFO] [stderr]     Checking simba v0.5.1
[INFO] [stderr]     Checking ndarray v0.15.6
[INFO] [stderr]     Checking regex v1.11.1
[INFO] [stderr]    Compiling proc-macro-error2 v2.0.1
[INFO] [stderr]    Compiling zerocopy-derive v0.7.35
[INFO] [stderr]    Compiling serde_derive v1.0.215
[INFO] [stderr]    Compiling thiserror-impl v1.0.69
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]    Compiling clap_derive v4.5.18
[INFO] [stderr]    Compiling getset v0.1.3
[INFO] [stderr]    Compiling nalgebra-macros v0.1.0
[INFO] [stderr]    Compiling enum-map-derive v0.6.0
[INFO] [stderr]    Compiling strum_macros v0.23.1
[INFO] [stderr]     Checking enum-map v1.1.1
[INFO] [stderr]     Checking zerocopy v0.7.35
[INFO] [stderr]     Checking thiserror v1.0.69
[INFO] [stderr]     Checking bio-types v1.0.4
[INFO] [stderr]     Checking clap v4.5.21
[INFO] [stderr]     Checking ppv-lite86 v0.2.20
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]     Checking rand v0.8.5
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking nalgebra v0.27.1
[INFO] [stderr]     Checking bv v0.11.1
[INFO] [stderr]     Checking multimap v0.8.3
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking csv v1.3.1
[INFO] [stderr]     Checking statrs v0.15.0
[INFO] [stderr]     Checking bio v0.42.0
[INFO] [stderr]  Documenting count_kmer v0.1.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 35.91s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nalgebra v0.27.1
[INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 5`
[INFO] [stderr]    Generated /opt/rustwide/target/doc/count_kmer/index.html
[INFO] running `Command { std: "docker" "inspect" "d80f6d516e9162a8a7f868d7008c17ed76819f5fa6b132f98273e4460788515c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "d80f6d516e9162a8a7f868d7008c17ed76819f5fa6b132f98273e4460788515c", kill_on_drop: false }`
[INFO] [stdout] d80f6d516e9162a8a7f868d7008c17ed76819f5fa6b132f98273e4460788515c
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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" "RUSTC_BOOTSTRAP=1" "-e" "DOCS_RS=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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/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] cdc228fb879a56234b4109ab1c1ac2e6cafcc2fc3cdb163b8252a1bcbb08dae0
[INFO] running `Command { std: "docker" "start" "-a" "cdc228fb879a56234b4109ab1c1ac2e6cafcc2fc3cdb163b8252a1bcbb08dae0", kill_on_drop: false }`
[INFO] [stderr]    Compiling proc-macro2 v1.0.89
[INFO] [stderr]    Compiling thiserror v1.0.69
[INFO] [stderr]    Compiling anyhow v1.0.93
[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-macro2-1.0.89/src/wrapper.rs:365:26
[INFO] [stdout]     |
[INFO] [stdout] 365 |     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] 365 -     Compiler(proc_macro::SourceFile),
[INFO] [stdout] 365 +     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-macro2-1.0.89/src/wrapper.rs:371:32
[INFO] [stdout]     |
[INFO] [stdout] 371 |     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] 371 -     fn nightly(sf: proc_macro::SourceFile) -> Self {
[INFO] [stdout] 371 +     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-macro2-1.0.89/src/wrapper.rs:461:56
[INFO] [stdout]     |
[INFO] [stdout] 461 |             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] 461 -             Span::Compiler(s) => SourceFile::nightly(s.source_file()),
[INFO] [stdout] 461 +             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" "cdc228fb879a56234b4109ab1c1ac2e6cafcc2fc3cdb163b8252a1bcbb08dae0", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "cdc228fb879a56234b4109ab1c1ac2e6cafcc2fc3cdb163b8252a1bcbb08dae0", kill_on_drop: false }`
[INFO] [stdout] cdc228fb879a56234b4109ab1c1ac2e6cafcc2fc3cdb163b8252a1bcbb08dae0
