[INFO] cloning repository https://github.com/kgori/pb_genotyper
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/kgori/pb_genotyper" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkgori%2Fpb_genotyper", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkgori%2Fpb_genotyper'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] d75384c05ee2c52725cc73fc3b717f492af69c01
[INFO] checking kgori/pb_genotyper against master#1f12b9b0fdbe735968ac002792a720f0ba4faca6 for crater-rollup-uwu
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkgori%2Fpb_genotyper" "/workspace/builds/worker-0-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc1/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/kgori/pb_genotyper on toolchain 1f12b9b0fdbe735968ac002792a720f0ba4faca6
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1f12b9b0fdbe735968ac002792a720f0ba4faca6" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/kgori/pb_genotyper
[INFO] finished tweaking git repo https://github.com/kgori/pb_genotyper
[INFO] tweaked toml for git repo https://github.com/kgori/pb_genotyper written to /workspace/builds/worker-0-tc1/source/Cargo.toml
[INFO] crate git repo https://github.com/kgori/pb_genotyper 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" "+1f12b9b0fdbe735968ac002792a720f0ba4faca6" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded url v2.5.0
[INFO] [stderr]   Downloaded newtype_derive v0.1.6
[INFO] [stderr]   Downloaded fs-utils v1.1.4
[INFO] [stderr]   Downloaded is_terminal_polyfill v1.70.0
[INFO] [stderr]   Downloaded itertools-num v0.1.3
[INFO] [stderr]   Downloaded linear-map v1.2.0
[INFO] [stderr]   Downloaded derive-new v0.5.9
[INFO] [stderr]   Downloaded thiserror-impl v1.0.59
[INFO] [stderr]   Downloaded anstyle-parse v0.2.4
[INFO] [stderr]   Downloaded strum v0.25.0
[INFO] [stderr]   Downloaded anstyle-wincon v3.0.3
[INFO] [stderr]   Downloaded num-complex v0.4.5
[INFO] [stderr]   Downloaded strum_macros v0.25.3
[INFO] [stderr]   Downloaded bytecount v0.6.8
[INFO] [stderr]   Downloaded matrixmultiply v0.3.8
[INFO] [stderr]   Downloaded rand_distr v0.4.3
[INFO] [stderr]   Downloaded safe_arch v0.7.1
[INFO] [stderr]   Downloaded cc v1.0.95
[INFO] [stderr]   Downloaded rust-htslib v0.46.0
[INFO] [stderr]   Downloaded statrs v0.16.0
[INFO] [stderr]   Downloaded clap_builder v4.5.7
[INFO] [stderr]   Downloaded syn v2.0.60
[INFO] [stderr]   Downloaded wide v0.7.16
[INFO] [stderr]   Downloaded bio v1.6.0
[INFO] [stderr]   Downloaded serde_derive v1.0.198
[INFO] [stderr]   Downloaded serde v1.0.198
[INFO] [stderr]   Downloaded ndarray v0.15.6
[INFO] [stderr]   Downloaded simba v0.6.0
[INFO] [stderr]   Downloaded triple_accel v0.4.0
[INFO] [stderr]   Downloaded colorchoice v1.0.1
[INFO] [stderr]   Downloaded nalgebra v0.29.0
[INFO] [stderr]   Downloaded anstream v0.6.14
[INFO] [stderr]   Downloaded clap_lex v0.7.1
[INFO] [stderr]   Downloaded clap_derive v4.5.5
[INFO] [stderr]   Downloaded clap v4.5.7
[INFO] [stderr]   Downloaded custom_derive v0.1.7
[INFO] [stderr]   Downloaded proc-macro2 v1.0.81
[INFO] [stderr]   Downloaded editdistancek v1.0.2
[INFO] [stderr]   Downloaded enum-map-derive v0.17.0
[INFO] [stderr]   Downloaded enum-map v2.7.3
[INFO] [stderr]   Downloaded multimap v0.9.1
[INFO] [stderr]   Downloaded ordered-float v3.9.2
[INFO] [stderr]   Downloaded anstyle-query v1.1.0
[INFO] [stderr]   Downloaded bzip2-sys v0.1.11+1.0.8
[INFO] [stderr]   Downloaded anstyle v1.0.7
[INFO] [stderr]   Downloaded bio-types v1.0.1
[INFO] [stderr]   Downloaded ieee754 v0.2.6
[INFO] [stderr]   Downloaded thiserror v1.0.59
[INFO] [stderr]   Downloaded hts-sys v2.1.1
[INFO] [stderr]   Downloaded libz-sys v1.1.16
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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@sha256:923055f121b5182466d55868a8b05e67af8ba4a3a3f6bad814e953ca3cd3ac2a" "/opt/rustwide/cargo-home/bin/cargo" "+1f12b9b0fdbe735968ac002792a720f0ba4faca6" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 1397084062bb9c20cebe43d9008bc3538599e3fe07f7e9ce914eaa70d2b78edd
[INFO] running `Command { std: "docker" "start" "-a" "1397084062bb9c20cebe43d9008bc3538599e3fe07f7e9ce914eaa70d2b78edd", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "1397084062bb9c20cebe43d9008bc3538599e3fe07f7e9ce914eaa70d2b78edd", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "1397084062bb9c20cebe43d9008bc3538599e3fe07f7e9ce914eaa70d2b78edd", kill_on_drop: false }`
[INFO] [stdout] 1397084062bb9c20cebe43d9008bc3538599e3fe07f7e9ce914eaa70d2b78edd
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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@sha256:923055f121b5182466d55868a8b05e67af8ba4a3a3f6bad814e953ca3cd3ac2a" "/opt/rustwide/cargo-home/bin/cargo" "+1f12b9b0fdbe735968ac002792a720f0ba4faca6" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] cdedfbe16d12297449752f08c09ac66c7c5c41bfb32db62b8859eeb294cce134
[INFO] running `Command { std: "docker" "start" "-a" "cdedfbe16d12297449752f08c09ac66c7c5c41bfb32db62b8859eeb294cce134", kill_on_drop: false }`
[INFO] [stderr]    Compiling proc-macro2 v1.0.81
[INFO] [stderr]    Compiling autocfg v1.2.0
[INFO] [stderr]    Compiling once_cell v1.19.0
[INFO] [stderr]    Compiling libm v0.2.8
[INFO] [stderr]    Compiling pkg-config v0.3.30
[INFO] [stderr]     Checking memchr v2.7.2
[INFO] [stderr]    Compiling serde v1.0.198
[INFO] [stderr]    Compiling paste v1.0.14
[INFO] [stderr]    Compiling rustversion v1.0.15
[INFO] [stderr]     Checking bytemuck v1.15.0
[INFO] [stderr]    Compiling libc v0.2.153
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]    Compiling vcpkg v0.2.15
[INFO] [stderr]     Checking getrandom v0.2.14
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]    Compiling thiserror v1.0.59
[INFO] [stderr]     Checking regex-syntax v0.8.3
[INFO] [stderr]    Compiling typenum v1.17.0
[INFO] [stderr]     Checking safe_arch v0.7.1
[INFO] [stderr]     Checking rawpointer v0.2.1
[INFO] [stderr]     Checking rand_core v0.6.4
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling feature-probe v0.1.1
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]    Compiling num-traits v0.2.18
[INFO] [stderr]    Compiling matrixmultiply v0.3.8
[INFO] [stderr]    Compiling num-rational v0.4.1
[INFO] [stderr]     Checking utf8parse v0.2.2
[INFO] [stderr]     Checking aho-corasick v1.1.3
[INFO] [stderr]     Checking anstyle-parse v0.2.4
[INFO] [stderr]     Checking rand v0.8.5
[INFO] [stderr]     Checking wide v0.7.16
[INFO] [stderr]    Compiling bv v0.11.1
[INFO] [stderr]     Checking unicode-normalization v0.1.23
[INFO] [stderr]     Checking anstyle-query v1.1.0
[INFO] [stderr]     Checking anstyle v1.0.7
[INFO] [stderr]    Compiling quote v1.0.36
[INFO] [stderr]    Compiling jobserver v0.1.31
[INFO] [stderr]    Compiling anyhow v1.0.82
[INFO] [stderr]    Compiling crc32fast v1.4.0
[INFO] [stderr]     Checking colorchoice v1.0.1
[INFO] [stderr]     Checking unicode-bidi v0.3.15
[INFO] [stderr]     Checking is_terminal_polyfill v1.70.0
[INFO] [stderr]    Compiling syn v2.0.60
[INFO] [stderr]     Checking byteorder v1.5.0
[INFO] [stderr]    Compiling cc v1.0.95
[INFO] [stderr]     Checking indexmap v2.2.6
[INFO] [stderr]     Checking anstream v0.6.14
[INFO] [stderr]     Checking csv-core v0.1.11
[INFO] [stderr]     Checking either v1.11.0
[INFO] [stderr]     Checking bit-vec v0.6.3
[INFO] [stderr]     Checking clap_lex v0.7.1
[INFO] [stderr]     Checking idna v0.5.0
[INFO] [stderr]    Compiling heck v0.5.0
[INFO] [stderr]     Checking strsim v0.11.1
[INFO] [stderr]     Checking itoa v1.0.11
[INFO] [stderr]     Checking fixedbitset v0.4.2
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking bit-set v0.5.3
[INFO] [stderr]     Checking itertools v0.11.0
[INFO] [stderr]     Checking miniz_oxide v0.7.2
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]     Checking clap_builder v4.5.7
[INFO] [stderr]     Checking bytecount v0.6.8
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]     Checking editdistancek v1.0.2
[INFO] [stderr]     Checking strum v0.25.0
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking url v2.5.0
[INFO] [stderr]     Checking petgraph v0.6.4
[INFO] [stderr]    Compiling cmake v0.1.50
[INFO] [stderr]     Checking flate2 v1.0.28
[INFO] [stderr]     Checking num-complex v0.4.5
[INFO] [stderr]     Checking num-integer v0.1.46
[INFO] [stderr]     Checking regex-automata v0.4.6
[INFO] [stderr]     Checking approx v0.5.1
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking ordered-float v3.9.2
[INFO] [stderr]    Compiling bzip2-sys v0.1.11+1.0.8
[INFO] [stderr]    Compiling lzma-sys v0.1.20
[INFO] [stderr]    Compiling hts-sys v2.1.1
[INFO] [stderr]    Compiling libz-sys v1.1.16
[INFO] [stderr]     Checking simba v0.6.0
[INFO] [stderr]     Checking ndarray v0.15.6
[INFO] [stderr]    Compiling nalgebra-macros v0.1.0
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]     Checking regex v1.10.4
[INFO] [stderr]    Compiling serde_derive v1.0.198
[INFO] [stderr]    Compiling thiserror-impl v1.0.59
[INFO] [stderr]    Compiling strum_macros v0.25.3
[INFO] [stderr]    Compiling enum-map-derive v0.17.0
[INFO] [stderr]    Compiling clap_derive v4.5.5
[INFO] [stderr]     Checking enum-map v2.7.3
[INFO] [stderr]     Checking bio-types v1.0.1
[INFO] [stderr]     Checking clap v4.5.7
[INFO] [stderr]     Checking rust-htslib v0.46.0
[INFO] [stderr]     Checking nalgebra v0.29.0
[INFO] [stderr]     Checking multimap v0.9.1
[INFO] [stderr]     Checking csv v1.3.0
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking statrs v0.16.0
[INFO] [stderr]     Checking bio v1.6.0
[INFO] [stderr]     Checking pb_genotyper v0.1.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 18.87s
[INFO] running `Command { std: "docker" "inspect" "cdedfbe16d12297449752f08c09ac66c7c5c41bfb32db62b8859eeb294cce134", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "cdedfbe16d12297449752f08c09ac66c7c5c41bfb32db62b8859eeb294cce134", kill_on_drop: false }`
[INFO] [stdout] cdedfbe16d12297449752f08c09ac66c7c5c41bfb32db62b8859eeb294cce134