[INFO] cloning repository https://github.com/davidlougheed/strkit_rust_ext
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/davidlougheed/strkit_rust_ext" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fdavidlougheed%2Fstrkit_rust_ext", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fdavidlougheed%2Fstrkit_rust_ext'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 9a792b64aff31d44073dcf6c8214beafc404c5df
[INFO] checking davidlougheed/strkit_rust_ext against try#78c81ee3917a99dcff6e2e6822800f0492c415c3 for pr-148967
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fdavidlougheed%2Fstrkit_rust_ext" "/workspace/builds/worker-3-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-3-tc2/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/davidlougheed/strkit_rust_ext
[INFO] finished tweaking git repo https://github.com/davidlougheed/strkit_rust_ext
[INFO] tweaked toml for git repo https://github.com/davidlougheed/strkit_rust_ext written to /workspace/builds/worker-3-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/davidlougheed/strkit_rust_ext on toolchain 78c81ee3917a99dcff6e2e6822800f0492c415c3
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+78c81ee3917a99dcff6e2e6822800f0492c415c3" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/davidlougheed/strkit_rust_ext 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" "+78c81ee3917a99dcff6e2e6822800f0492c415c3" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded derive-new v0.6.0
[INFO] [stderr]   Downloaded derive-new v0.7.0
[INFO] [stderr]   Downloaded editdistancek v1.0.2
[INFO] [stderr]   Downloaded itertools-num v0.1.3
[INFO] [stderr]   Downloaded simba v0.9.0
[INFO] [stderr]   Downloaded triple_accel v0.4.0
[INFO] [stderr]   Downloaded rust-lapper v1.2.0
[INFO] [stderr]   Downloaded numpy v0.25.0
[INFO] [stderr]   Downloaded libdeflate-sys v1.24.0
[INFO] [stderr]   Downloaded python3-dll-a v0.2.14
[INFO] [stderr]   Downloaded statrs v0.18.0
[INFO] [stderr]   Downloaded bio v2.2.0
[INFO] [stderr]   Downloaded rust-htslib v0.50.0
[INFO] [stderr]   Downloaded parasail-rs v0.8.1
[INFO] [stderr]   Downloaded bio-types v1.0.4
[INFO] [stderr]   Downloaded nalgebra v0.33.2
[INFO] [stderr]   Downloaded hts-sys v2.2.0
[INFO] [stderr]   Downloaded libparasail-sys v0.1.12
[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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+78c81ee3917a99dcff6e2e6822800f0492c415c3" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] dfe5d122578f5198be9e37ccb486ab9783c23e293fcc628622f6dc084d526252
[INFO] running `Command { std: "docker" "start" "-a" "dfe5d122578f5198be9e37ccb486ab9783c23e293fcc628622f6dc084d526252", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "dfe5d122578f5198be9e37ccb486ab9783c23e293fcc628622f6dc084d526252", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "dfe5d122578f5198be9e37ccb486ab9783c23e293fcc628622f6dc084d526252", kill_on_drop: false }`
[INFO] [stdout] dfe5d122578f5198be9e37ccb486ab9783c23e293fcc628622f6dc084d526252
[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=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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+78c81ee3917a99dcff6e2e6822800f0492c415c3" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 0b2e61483b0a08aa2f6c613d26e1c5a16664d084485f691b86a2fce53aeab1be
[INFO] running `Command { std: "docker" "start" "-a" "0b2e61483b0a08aa2f6c613d26e1c5a16664d084485f691b86a2fce53aeab1be", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.175
[INFO] [stderr]    Compiling target-lexicon v0.13.2
[INFO] [stderr]    Compiling libm v0.2.15
[INFO] [stderr]    Compiling python3-dll-a v0.2.14
[INFO] [stderr]    Compiling glob v0.3.3
[INFO] [stderr]    Compiling rustix v0.38.44
[INFO] [stderr]    Compiling prettyplease v0.2.37
[INFO] [stderr]    Compiling memchr v2.7.5
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling either v1.15.0
[INFO] [stderr]    Compiling linux-raw-sys v0.4.15
[INFO] [stderr]    Compiling bitflags v2.9.3
[INFO] [stderr]    Compiling regex-syntax v0.8.6
[INFO] [stderr]    Compiling syn v2.0.106
[INFO] [stderr]    Compiling bindgen v0.69.5
[INFO] [stderr]    Compiling home v0.5.11
[INFO] [stderr]    Compiling serde v1.0.219
[INFO] [stderr]    Compiling lazy_static v1.5.0
[INFO] [stderr]     Checking ppv-lite86 v0.2.21
[INFO] [stderr]    Compiling matrixmultiply v0.3.10
[INFO] [stderr]     Checking bytemuck v1.23.2
[INFO] [stderr]     Checking aho-corasick v1.1.3
[INFO] [stderr]    Compiling itertools v0.12.1
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]     Checking smallvec v1.15.1
[INFO] [stderr]    Compiling thiserror v2.0.16
[INFO] [stderr]    Compiling nom v7.1.3
[INFO] [stderr]    Compiling clang-sys v1.8.1
[INFO] [stderr]     Checking safe_arch v0.7.4
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]    Compiling memoffset v0.9.1
[INFO] [stderr]     Checking getrandom v0.2.16
[INFO] [stderr]    Compiling pyo3-build-config v0.25.1
[INFO] [stderr]     Checking getrandom v0.3.3
[INFO] [stderr]     Checking rand_core v0.6.4
[INFO] [stderr]     Checking rand_core v0.9.3
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]     Checking percent-encoding v2.3.2
[INFO] [stderr]     Checking hashbrown v0.15.5
[INFO] [stderr]     Checking form_urlencoded v1.2.2
[INFO] [stderr]     Checking csv-core v0.1.12
[INFO] [stderr]    Compiling indoc v2.0.6
[INFO] [stderr]     Checking rand_chacha v0.9.0
[INFO] [stderr]    Compiling jobserver v0.1.34
[INFO] [stderr]     Checking wide v0.7.33
[INFO] [stderr]     Checking rand v0.8.5
[INFO] [stderr]    Compiling regex-automata v0.4.13
[INFO] [stderr]    Compiling cc v1.2.34
[INFO] [stderr]     Checking indexmap v2.11.0
[INFO] [stderr]    Compiling virtue v0.0.18
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking bit-vec v0.8.0
[INFO] [stderr]     Checking unindent v0.2.4
[INFO] [stderr]     Checking fixedbitset v0.5.7
[INFO] [stderr]     Checking rand v0.9.2
[INFO] [stderr]     Checking bit-set v0.8.0
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking rustc-hash v2.1.1
[INFO] [stderr]     Checking petgraph v0.7.1
[INFO] [stderr]     Checking editdistancek v1.0.2
[INFO] [stderr]     Checking bytecount v0.6.9
[INFO] [stderr]    Compiling cmake v0.1.54
[INFO] [stderr]    Compiling cexpr v0.6.0
[INFO] [stderr]     Checking num-complex v0.4.6
[INFO] [stderr]     Checking num-integer v0.1.46
[INFO] [stderr]     Checking approx v0.5.1
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]    Compiling pyo3-ffi v0.25.1
[INFO] [stderr]    Compiling pyo3-macros-backend v0.25.1
[INFO] [stderr]     Checking num-rational v0.4.2
[INFO] [stderr]    Compiling pyo3 v0.25.1
[INFO] [stderr]    Compiling numpy v0.25.0
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking ordered-float v5.0.0
[INFO] [stderr]    Compiling bincode_derive v2.0.1
[INFO] [stderr]     Checking unty v0.0.4
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]     Checking rust-lapper v1.2.0
[INFO] [stderr]     Checking simba v0.9.0
[INFO] [stderr]     Checking ndarray v0.16.1
[INFO] [stderr]    Compiling which v4.4.2
[INFO] [stderr]    Compiling libdeflate-sys v1.24.0
[INFO] [stderr]    Compiling lzma-sys v0.1.20
[INFO] [stderr]    Compiling bzip2-sys v0.1.13+1.0.8
[INFO] [stderr]    Compiling libz-sys v1.1.22
[INFO] [stderr]    Compiling regex v1.12.2
[INFO] [stderr]    Compiling synstructure v0.13.2
[INFO] [stderr]    Compiling zerovec-derive v0.11.1
[INFO] [stderr]    Compiling displaydoc v0.2.5
[INFO] [stderr]    Compiling serde_derive v1.0.219
[INFO] [stderr]    Compiling thiserror-impl v1.0.69
[INFO] [stderr]    Compiling thiserror-impl v2.0.16
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]    Compiling derive_more-impl v2.0.1
[INFO] [stderr]    Compiling enum-map-derive v0.17.0
[INFO] [stderr]    Compiling derive-new v0.7.0
[INFO] [stderr]    Compiling zerofrom-derive v0.1.6
[INFO] [stderr]    Compiling yoke-derive v0.8.0
[INFO] [stderr]     Checking enum-map v2.7.3
[INFO] [stderr]     Checking derive_more v2.0.1
[INFO] [stderr]     Checking thiserror v1.0.69
[INFO] [stderr]     Checking bio-types v1.0.4
[INFO] [stderr]     Checking zerofrom v0.1.6
[INFO] [stderr]     Checking yoke v0.8.0
[INFO] [stderr]     Checking zerovec v0.11.4
[INFO] [stderr]     Checking zerotrie v0.2.2
[INFO] [stderr]     Checking nalgebra v0.33.2
[INFO] [stderr]     Checking tinystr v0.8.1
[INFO] [stderr]     Checking potential_utf v0.1.2
[INFO] [stderr]     Checking icu_collections v2.0.0
[INFO] [stderr]     Checking icu_locale_core v2.0.0
[INFO] [stderr]    Compiling pyo3-macros v0.25.1
[INFO] [stderr]     Checking icu_provider v2.0.0
[INFO] [stderr]     Checking icu_properties v2.0.1
[INFO] [stderr]     Checking icu_normalizer v2.0.0
[INFO] [stderr]     Checking multimap v0.10.1
[INFO] [stderr]     Checking bv v0.11.1
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking csv v1.3.1
[INFO] [stderr]     Checking bincode v2.0.1
[INFO] [stderr]     Checking idna_adapter v1.2.1
[INFO] [stderr]     Checking idna v1.1.0
[INFO] [stderr]     Checking url v2.5.7
[INFO] [stderr]    Compiling hts-sys v2.2.0
[INFO] [stderr]    Compiling libparasail-sys v0.1.12
[INFO] [stderr]     Checking statrs v0.18.0
[INFO] [stderr]     Checking bio v2.2.0
[INFO] [stderr]     Checking rust-htslib v0.50.0
[INFO] [stderr]     Checking parasail-rs v0.8.1
[INFO] [stderr]     Checking strkit_rust_ext v0.24.2 (/opt/rustwide/workdir)
[INFO] [stdout] error[E0425]: cannot find function `starts_with_chr` in this scope
[INFO] [stdout]    --> src/strkit/reads.rs:229:71
[INFO] [stdout]     |
[INFO] [stdout] 229 |             let any_contig_name_has_chr = contig_names.iter().any(|c| starts_with_chr(c));
[INFO] [stdout]     |                                                                       ^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this function
[INFO] [stdout]     |
[INFO] [stdout]   1 + use crate::utils::starts_with_chr;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function `starts_with_chr` in this scope
[INFO] [stdout]    --> src/strkit/reads.rs:229:71
[INFO] [stdout]     |
[INFO] [stdout] 229 |             let any_contig_name_has_chr = contig_names.iter().any(|c| starts_with_chr(c));
[INFO] [stdout]     |                                                                       ^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this function
[INFO] [stdout]     |
[INFO] [stdout]   1 + use crate::utils::starts_with_chr;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0412]: cannot find type `STRkitLocusBlock` in this scope
[INFO] [stdout]    --> src/strkit/reads.rs:254:23
[INFO] [stdout]     |
[INFO] [stdout] 254 |         locus_block: &STRkitLocusBlock,
[INFO] [stdout]     |                       ^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/strkit/locus.rs:20:1
[INFO] [stdout]     |
[INFO] [stdout]  20 | pub struct STRkitLocus {
[INFO] [stdout]     | ---------------------- similarly named struct `STRkitLocus` defined here
[INFO] [stdout]     |
[INFO] [stdout] help: a struct with a similar name exists
[INFO] [stdout]     |
[INFO] [stdout] 254 -         locus_block: &STRkitLocusBlock,
[INFO] [stdout] 254 +         locus_block: &STRkitLocus,
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]     |
[INFO] [stdout]   1 + use crate::locus::STRkitLocusBlock;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0412]: cannot find type `STRkitLocusBlock` in this scope
[INFO] [stdout]    --> src/strkit/reads.rs:254:23
[INFO] [stdout]     |
[INFO] [stdout] 254 |         locus_block: &STRkitLocusBlock,
[INFO] [stdout]     |                       ^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/strkit/locus.rs:20:1
[INFO] [stdout]     |
[INFO] [stdout]  20 | pub struct STRkitLocus {
[INFO] [stdout]     | ---------------------- similarly named struct `STRkitLocus` defined here
[INFO] [stdout]     |
[INFO] [stdout] help: a struct with a similar name exists
[INFO] [stdout]     |
[INFO] [stdout] 254 -         locus_block: &STRkitLocusBlock,
[INFO] [stdout] 254 +         locus_block: &STRkitLocus,
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]     |
[INFO] [stdout]   1 + use crate::locus::STRkitLocusBlock;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function `normalize_contig` in this scope
[INFO] [stdout]    --> src/strkit/reads.rs:258:27
[INFO] [stdout]     |
[INFO] [stdout] 258 |         let contig_norm = normalize_contig(&locus_block.loci[0].contig, self.any_contig_name_has_chr); // TODO: hash map
[INFO] [stdout]     |                           ^^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this function
[INFO] [stdout]     |
[INFO] [stdout]   1 + use crate::utils::normalize_contig;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0425]: cannot find function `normalize_contig` in this scope
[INFO] [stdout]    --> src/strkit/reads.rs:258:27
[INFO] [stdout]     |
[INFO] [stdout] 258 |         let contig_norm = normalize_contig(&locus_block.loci[0].contig, self.any_contig_name_has_chr); // TODO: hash map
[INFO] [stdout]     |                           ^^^^^^^^^^^^^^^^ not found in this scope
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this function
[INFO] [stdout]     |
[INFO] [stdout]   1 + use crate::utils::normalize_contig;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `pyo3::pybacked::PyBackedStr`
[INFO] [stdout]  --> src/strkit/snvs.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use pyo3::pybacked::PyBackedStr;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `pyo3::pybacked::PyBackedStr`
[INFO] [stdout]  --> src/strkit/snvs.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use pyo3::pybacked::PyBackedStr;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0412, E0425.
[INFO] [stdout] 
[INFO] [stdout] For more information about an error, try `rustc --explain E0412`.
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `strkit_rust_ext` (lib) due to 3 previous errors; 1 warning emitted
[INFO] [stderr] warning: build failed, waiting for other jobs to finish...
[INFO] [stdout] Some errors have detailed explanations: E0412, E0425.
[INFO] [stdout] 
[INFO] [stdout] For more information about an error, try `rustc --explain E0412`.
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `strkit_rust_ext` (lib test) due to 3 previous errors; 1 warning emitted
[INFO] running `Command { std: "docker" "inspect" "0b2e61483b0a08aa2f6c613d26e1c5a16664d084485f691b86a2fce53aeab1be", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "0b2e61483b0a08aa2f6c613d26e1c5a16664d084485f691b86a2fce53aeab1be", kill_on_drop: false }`
[INFO] [stdout] 0b2e61483b0a08aa2f6c613d26e1c5a16664d084485f691b86a2fce53aeab1be
