[INFO] cloning repository https://github.com/8051Enthusiast/biodiff
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/8051Enthusiast/biodiff" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2F8051Enthusiast%2Fbiodiff", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2F8051Enthusiast%2Fbiodiff'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 7df6377aa2d260e7bb754f51f0c2f9bc601fc768
[INFO] checking 8051Enthusiast/biodiff against master#779e19d8baa3e3625bd4fc5c85cbb2ad47b43155 for pr-147589-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2F8051Enthusiast%2Fbiodiff" "/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/8051Enthusiast/biodiff
[INFO] finished tweaking git repo https://github.com/8051Enthusiast/biodiff
[INFO] tweaked toml for git repo https://github.com/8051Enthusiast/biodiff written to /workspace/builds/worker-1-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/8051Enthusiast/biodiff on toolchain 779e19d8baa3e3625bd4fc5c85cbb2ad47b43155
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+779e19d8baa3e3625bd4fc5c85cbb2ad47b43155" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/8051Enthusiast/biodiff 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" "+779e19d8baa3e3625bd4fc5c85cbb2ad47b43155" "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 trycmd v0.15.1
[INFO] [stderr]   Downloaded windows-targets v0.52.4
[INFO] [stderr]   Downloaded itertools-num v0.1.3
[INFO] [stderr]   Downloaded triple_accel v0.4.0
[INFO] [stderr]   Downloaded enumset_derive v0.8.1
[INFO] [stderr]   Downloaded num-complex v0.4.5
[INFO] [stderr]   Downloaded editdistancek v1.0.2
[INFO] [stderr]   Downloaded derive-new v0.5.9
[INFO] [stderr]   Downloaded bio-types v1.0.1
[INFO] [stderr]   Downloaded ordered-float v3.9.2
[INFO] [stderr]   Downloaded semver v0.1.20
[INFO] [stderr]   Downloaded num v0.4.1
[INFO] [stderr]   Downloaded cursive v0.20.0
[INFO] [stderr]   Downloaded matrixmultiply v0.3.8
[INFO] [stderr]   Downloaded wide v0.7.15
[INFO] [stderr]   Downloaded cc v1.0.92
[INFO] [stderr]   Downloaded time v0.3.35
[INFO] [stderr]   Downloaded cursive_core v0.3.7
[INFO] [stderr]   Downloaded statrs v0.16.0
[INFO] [stderr]   Downloaded bio v1.6.0
[INFO] [stderr]   Downloaded serde_json v1.0.115
[INFO] [stderr]   Downloaded crossterm v0.25.0
[INFO] [stderr]   Downloaded safe_arch v0.7.1
[INFO] [stderr]   Downloaded similar v2.5.0
[INFO] [stderr]   Downloaded anstream v0.6.13
[INFO] [stderr]   Downloaded ndarray v0.15.6
[INFO] [stderr]   Downloaded nalgebra v0.29.0
[INFO] [stderr]   Downloaded rustc_version v0.1.7
[INFO] [stderr]   Downloaded rustix v0.38.32
[INFO] [stderr]   Downloaded simba v0.6.0
[INFO] [stderr]   Downloaded windows_x86_64_gnullvm v0.52.4
[INFO] [stderr]   Downloaded owning_ref v0.4.1
[INFO] [stderr]   Downloaded windows_aarch64_gnullvm v0.52.4
[INFO] [stderr]   Downloaded thiserror-impl v1.0.58
[INFO] [stderr]   Downloaded either v1.10.0
[INFO] [stderr]   Downloaded os_pipe v1.1.5
[INFO] [stderr]   Downloaded enumset v1.1.3
[INFO] [stderr]   Downloaded thiserror v1.0.58
[INFO] [stderr]   Downloaded bytecount v0.6.7
[INFO] [stderr]   Downloaded multimap v0.9.1
[INFO] [stderr]   Downloaded cursive_buffered_backend v0.6.1
[INFO] [stderr]   Downloaded primal-check v0.3.3
[INFO] [stderr]   Downloaded content_inspector v0.2.4
[INFO] [stderr]   Downloaded snapbox-macros v0.3.8
[INFO] [stderr]   Downloaded snapbox v0.5.9
[INFO] [stderr]   Downloaded newtype_derive v0.1.6
[INFO] [stderr]   Downloaded nalgebra-macros v0.1.0
[INFO] [stderr]   Downloaded windows_x86_64_msvc v0.52.4
[INFO] [stderr]   Downloaded humantime-serde v1.1.1
[INFO] [stderr]   Downloaded windows_aarch64_msvc v0.52.4
[INFO] [stderr]   Downloaded dunce v1.0.4
[INFO] [stderr]   Downloaded windows_i686_gnu v0.52.4
[INFO] [stderr]   Downloaded windows_x86_64_gnu v0.52.4
[INFO] [stderr]   Downloaded windows_i686_msvc v0.52.4
[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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+779e19d8baa3e3625bd4fc5c85cbb2ad47b43155" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 4b11da0716d2e8681a1fd147ae619cc42c0c34834eb626f9a23ac3bb2b8ac0b3
[INFO] running `Command { std: "docker" "start" "-a" "4b11da0716d2e8681a1fd147ae619cc42c0c34834eb626f9a23ac3bb2b8ac0b3", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "4b11da0716d2e8681a1fd147ae619cc42c0c34834eb626f9a23ac3bb2b8ac0b3", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "4b11da0716d2e8681a1fd147ae619cc42c0c34834eb626f9a23ac3bb2b8ac0b3", kill_on_drop: false }`
[INFO] [stdout] 4b11da0716d2e8681a1fd147ae619cc42c0c34834eb626f9a23ac3bb2b8ac0b3
[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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+779e19d8baa3e3625bd4fc5c85cbb2ad47b43155" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] e4723ddbf3666b8db8d5696502950e3340c9bc2055cf613cc61ae2f72f4ae3fc
[INFO] running `Command { std: "docker" "start" "-a" "e4723ddbf3666b8db8d5696502950e3340c9bc2055cf613cc61ae2f72f4ae3fc", kill_on_drop: false }`
[INFO] [stderr]    Compiling proc-macro2 v1.0.79
[INFO] [stderr]    Compiling libm v0.2.8
[INFO] [stderr]     Checking memchr v2.7.2
[INFO] [stderr]    Compiling serde v1.0.197
[INFO] [stderr]    Compiling num-traits v0.2.18
[INFO] [stderr]    Compiling num-rational v0.4.1
[INFO] [stderr]    Compiling matrixmultiply v0.3.8
[INFO] [stderr]     Checking bytemuck v1.15.0
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]     Checking rawpointer v0.2.1
[INFO] [stderr]     Checking hashbrown v0.14.3
[INFO] [stderr]    Compiling cc v1.0.92
[INFO] [stderr]     Checking utf8parse v0.2.1
[INFO] [stderr]     Checking getrandom v0.2.14
[INFO] [stderr]     Checking colorchoice v1.0.0
[INFO] [stderr]    Compiling thiserror v1.0.58
[INFO] [stderr]     Checking log v0.4.21
[INFO] [stderr]     Checking anstyle-parse v0.2.3
[INFO] [stderr]     Checking either v1.10.0
[INFO] [stderr]     Checking rand_core v0.6.4
[INFO] [stderr]     Checking safe_arch v0.7.1
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]     Checking anstyle-query v1.0.2
[INFO] [stderr]    Compiling ahash v0.8.11
[INFO] [stderr]    Compiling lock_api v0.4.11
[INFO] [stderr]     Checking anstream v0.6.13
[INFO] [stderr]    Compiling parking_lot_core v0.9.9
[INFO] [stderr]     Checking deranged v0.3.11
[INFO] [stderr]     Checking signal-hook-registry v1.4.1
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]     Checking aho-corasick v1.1.3
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking indexmap v2.2.6
[INFO] [stderr]     Checking csv-core v0.1.11
[INFO] [stderr]     Checking wide v0.7.15
[INFO] [stderr]     Checking fixedbitset v0.4.2
[INFO] [stderr]     Checking num_threads v0.1.7
[INFO] [stderr]     Checking once_cell v1.19.0
[INFO] [stderr]     Checking rand v0.8.5
[INFO] [stderr]     Checking bit-vec v0.6.3
[INFO] [stderr]     Checking signal-hook v0.3.17
[INFO] [stderr]     Checking owning_ref v0.4.1
[INFO] [stderr]    Compiling quote v1.0.36
[INFO] [stderr]    Compiling cmake v0.1.50
[INFO] [stderr]     Checking bit-set v0.5.3
[INFO] [stderr]    Compiling syn v2.0.58
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]     Checking itertools v0.11.0
[INFO] [stderr]     Checking mio v0.8.11
[INFO] [stderr]     Checking crossbeam-channel v0.5.12
[INFO] [stderr]    Compiling rustfft v6.2.0
[INFO] [stderr]     Checking unicode-segmentation v1.11.0
[INFO] [stderr]    Compiling rustix v0.38.32
[INFO] [stderr]     Checking bytecount v0.6.7
[INFO] [stderr]     Checking xi-unicode v0.3.0
[INFO] [stderr]     Checking time v0.3.35
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]     Checking petgraph v0.6.4
[INFO] [stderr]     Checking strum v0.25.0
[INFO] [stderr]     Checking unicode-width v0.1.11
[INFO] [stderr]     Checking editdistancek v1.0.2
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking signal-hook-mio v0.2.3
[INFO] [stderr]     Checking regex-automata v0.4.6
[INFO] [stderr]     Checking parking_lot v0.12.1
[INFO] [stderr]     Checking bitflags v2.5.0
[INFO] [stderr]    Compiling serde_json v1.0.115
[INFO] [stderr]     Checking option-ext v0.2.0
[INFO] [stderr]     Checking num-integer v0.1.46
[INFO] [stderr]     Checking num-complex v0.4.5
[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]    Compiling biodiff-wfa2-sys v2.3.5 (/opt/rustwide/workdir/biodiff-wfa2-sys)
[INFO] [stderr]     Checking ordered-float v3.9.2
[INFO] [stderr]     Checking linux-raw-sys v0.4.13
[INFO] [stderr]     Checking num-iter v0.1.44
[INFO] [stderr]     Checking primal-check v0.3.3
[INFO] [stderr]     Checking transpose v0.2.3
[INFO] [stderr]     Checking crossterm v0.25.0
[INFO] [stderr]     Checking dirs-sys v0.4.1
[INFO] [stderr]     Checking simba v0.6.0
[INFO] [stderr]     Checking ndarray v0.15.6
[INFO] [stderr]     Checking clap_builder v4.5.2
[INFO] [stderr] error: failed to run custom build command for `biodiff-wfa2-sys v2.3.5 (/opt/rustwide/workdir/biodiff-wfa2-sys)`
[INFO] [stderr] note: To improve backtraces for build dependencies, set the CARGO_PROFILE_DEV_BUILD_OVERRIDE_DEBUG=true environment variable to enable debug information generation.
[INFO] [stderr] 
[INFO] [stderr] Caused by:
[INFO] [stderr]   process didn't exit successfully: `/opt/rustwide/target/debug/build/biodiff-wfa2-sys-ff247aa61a8cf85c/build-script-build` (exit status: 1)
[INFO] [stderr]   --- stderr
[INFO] [stderr]   The WFA2 submodule is not present. Please run `git submodule update --init` to fetch it.
[INFO] [stderr] warning: build failed, waiting for other jobs to finish...
[INFO] running `Command { std: "docker" "inspect" "e4723ddbf3666b8db8d5696502950e3340c9bc2055cf613cc61ae2f72f4ae3fc", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "e4723ddbf3666b8db8d5696502950e3340c9bc2055cf613cc61ae2f72f4ae3fc", kill_on_drop: false }`
[INFO] [stdout] e4723ddbf3666b8db8d5696502950e3340c9bc2055cf613cc61ae2f72f4ae3fc
