[INFO] fetching crate phylodm 3.0.0...
[INFO] checking phylodm-3.0.0 against master#506512391b1a75ae450d36c9420978402a91abcc for pr-125384
[INFO] extracting crate phylodm 3.0.0 into /workspace/builds/worker-1-tc1/source
[INFO] validating manifest of crates.io crate phylodm 3.0.0 on toolchain 506512391b1a75ae450d36c9420978402a91abcc
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+506512391b1a75ae450d36c9420978402a91abcc" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] removed /workspace/builds/worker-1-tc1/source/.cargo/config
[INFO] started tweaking crates.io crate phylodm 3.0.0
[INFO] finished tweaking crates.io crate phylodm 3.0.0
[INFO] tweaked toml for crates.io crate phylodm 3.0.0 written to /workspace/builds/worker-1-tc1/source/Cargo.toml
[INFO] crate crates.io crate phylodm 3.0.0 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" "+506512391b1a75ae450d36c9420978402a91abcc" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded pyo3-macros-backend v0.19.0
[INFO] [stderr]   Downloaded numpy v0.19.0
[INFO] [stderr]   Downloaded random_color v0.5.1
[INFO] [stderr]   Downloaded pyo3-build-config v0.19.0
[INFO] [stderr]   Downloaded pyo3-macros v0.19.0
[INFO] [stderr]   Downloaded roxmltree v0.14.1
[INFO] [stderr]   Downloaded target-lexicon v0.12.7
[INFO] [stderr]   Downloaded getopt v1.1.3
[INFO] [stderr]   Downloaded pyo3-ffi v0.19.0
[INFO] [stderr]   Downloaded pyo3 v0.19.0
[INFO] [stderr]   Downloaded light_phylogeny v2.1.5
[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:beeedbb442662e57d416641ecc3200b38e573c25b057896194468d05594dd835" "/opt/rustwide/cargo-home/bin/cargo" "+506512391b1a75ae450d36c9420978402a91abcc" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] e15fa81c9007e7485c6fd3912f2b43f75134bbda483565cb24e43d67b9bcc5f2
[INFO] running `Command { std: "docker" "start" "-a" "e15fa81c9007e7485c6fd3912f2b43f75134bbda483565cb24e43d67b9bcc5f2", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "e15fa81c9007e7485c6fd3912f2b43f75134bbda483565cb24e43d67b9bcc5f2", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "e15fa81c9007e7485c6fd3912f2b43f75134bbda483565cb24e43d67b9bcc5f2", kill_on_drop: false }`
[INFO] [stdout] e15fa81c9007e7485c6fd3912f2b43f75134bbda483565cb24e43d67b9bcc5f2
[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=allow" "-e" "RUSTDOCFLAGS=--cap-lints=allow" "-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:beeedbb442662e57d416641ecc3200b38e573c25b057896194468d05594dd835" "/opt/rustwide/cargo-home/bin/cargo" "+506512391b1a75ae450d36c9420978402a91abcc" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 4d3088a31a694be179bbf1de9421bdde75be1e387215e0d75047cdded1f35c32
[INFO] running `Command { std: "docker" "start" "-a" "4d3088a31a694be179bbf1de9421bdde75be1e387215e0d75047cdded1f35c32", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.146
[INFO] [stderr]    Compiling proc-macro2 v1.0.60
[INFO] [stderr]    Compiling unicode-ident v1.0.9
[INFO] [stderr]    Compiling quote v1.0.28
[INFO] [stderr]    Compiling unicode-segmentation v1.10.1
[INFO] [stderr]     Checking unicode-width v0.1.10
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking strsim v0.8.0
[INFO] [stderr]     Checking regex-syntax v0.7.2
[INFO] [stderr]    Compiling num-traits v0.2.15
[INFO] [stderr]    Compiling matrixmultiply v0.3.7
[INFO] [stderr]    Compiling num-integer v0.1.45
[INFO] [stderr]     Checking aho-corasick v1.0.2
[INFO] [stderr]     Checking xmlparser v0.13.5
[INFO] [stderr]     Checking termcolor v1.2.0
[INFO] [stderr]     Checking log v0.4.19
[INFO] [stderr]     Checking textwrap v0.11.0
[INFO] [stderr]     Checking svg v0.13.1
[INFO] [stderr]     Checking getopt v1.1.3
[INFO] [stderr]     Checking either v1.8.1
[INFO] [stderr]    Compiling convert_case v0.4.0
[INFO] [stderr]     Checking itertools v0.10.5
[INFO] [stderr]    Compiling heck v0.3.3
[INFO] [stderr]     Checking roxmltree v0.14.1
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]     Checking regex v1.8.4
[INFO] [stderr]     Checking getrandom v0.1.16
[INFO] [stderr]     Checking atty v0.2.14
[INFO] [stderr]     Checking num-complex v0.4.3
[INFO] [stderr]     Checking clap v2.34.0
[INFO] [stderr]     Checking rand_core v0.5.1
[INFO] [stderr]     Checking rand_pcg v0.2.1
[INFO] [stderr]     Checking rand_chacha v0.2.2
[INFO] [stderr]     Checking rand v0.7.3
[INFO] [stderr]     Checking ndarray v0.15.6
[INFO] [stderr]     Checking env_logger v0.8.4
[INFO] [stderr]     Checking random_color v0.5.1
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]    Compiling structopt-derive v0.4.18
[INFO] [stderr]    Compiling derive_more v0.99.17
[INFO] [stderr]     Checking structopt v0.3.26
[INFO] [stderr]     Checking light_phylogeny v2.1.5
[INFO] [stderr]     Checking phylodm v3.0.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 5.02s
[INFO] running `Command { std: "docker" "inspect" "4d3088a31a694be179bbf1de9421bdde75be1e387215e0d75047cdded1f35c32", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "4d3088a31a694be179bbf1de9421bdde75be1e387215e0d75047cdded1f35c32", kill_on_drop: false }`
[INFO] [stdout] 4d3088a31a694be179bbf1de9421bdde75be1e387215e0d75047cdded1f35c32
[INFO] checking phylodm-3.0.0 against try#dae34b759e282c069aa28752564694effd121a63 for pr-125384
[INFO] extracting crate phylodm 3.0.0 into /workspace/builds/worker-1-tc2/source
[INFO] validating manifest of crates.io crate phylodm 3.0.0 on toolchain dae34b759e282c069aa28752564694effd121a63
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+dae34b759e282c069aa28752564694effd121a63" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] removed /workspace/builds/worker-1-tc2/source/.cargo/config
[INFO] started tweaking crates.io crate phylodm 3.0.0
[INFO] finished tweaking crates.io crate phylodm 3.0.0
[INFO] tweaked toml for crates.io crate phylodm 3.0.0 written to /workspace/builds/worker-1-tc2/source/Cargo.toml
[INFO] crate crates.io crate phylodm 3.0.0 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" "+dae34b759e282c069aa28752564694effd121a63" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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:beeedbb442662e57d416641ecc3200b38e573c25b057896194468d05594dd835" "/opt/rustwide/cargo-home/bin/cargo" "+dae34b759e282c069aa28752564694effd121a63" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 9a857d937244ee2c0609f580d1b59cb1d7675db0a93cae2f2bc9ee088f701530
[INFO] running `Command { std: "docker" "start" "-a" "9a857d937244ee2c0609f580d1b59cb1d7675db0a93cae2f2bc9ee088f701530", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "9a857d937244ee2c0609f580d1b59cb1d7675db0a93cae2f2bc9ee088f701530", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "9a857d937244ee2c0609f580d1b59cb1d7675db0a93cae2f2bc9ee088f701530", kill_on_drop: false }`
[INFO] [stdout] 9a857d937244ee2c0609f580d1b59cb1d7675db0a93cae2f2bc9ee088f701530
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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=allow" "-e" "RUSTDOCFLAGS=--cap-lints=allow" "-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:beeedbb442662e57d416641ecc3200b38e573c25b057896194468d05594dd835" "/opt/rustwide/cargo-home/bin/cargo" "+dae34b759e282c069aa28752564694effd121a63" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 0f0233224811d29f5a78d0d3dd9a5741c4ee6c931a4fd7c8c75d1f845cd299a5
[INFO] running `Command { std: "docker" "start" "-a" "0f0233224811d29f5a78d0d3dd9a5741c4ee6c931a4fd7c8c75d1f845cd299a5", kill_on_drop: false }`
[INFO] [stderr] Copying to /tmp/fixit
[INFO] [stderr] Running `cargo fix --edition`
[INFO] [stderr]    Migrating Cargo.toml from 2021 edition to 2024
[INFO] [stderr]        Fixed Cargo.toml (2 fixes)
[INFO] [stderr]    Compiling libc v0.2.146
[INFO] [stderr]    Compiling proc-macro2 v1.0.60
[INFO] [stderr]    Compiling unicode-ident v1.0.9
[INFO] [stderr]    Compiling quote v1.0.28
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]     Checking unicode-width v0.1.10
[INFO] [stderr]    Compiling unicode-segmentation v1.10.1
[INFO] [stderr]     Checking strsim v0.8.0
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]    Compiling num-traits v0.2.15
[INFO] [stderr]    Compiling matrixmultiply v0.3.7
[INFO] [stderr]    Compiling num-integer v0.1.45
[INFO] [stderr]     Checking regex-syntax v0.7.2
[INFO] [stderr]     Checking aho-corasick v1.0.2
[INFO] [stderr]     Checking xmlparser v0.13.5
[INFO] [stderr]     Checking termcolor v1.2.0
[INFO] [stderr]     Checking textwrap v0.11.0
[INFO] [stderr]     Checking rawpointer v0.2.1
[INFO] [stderr]     Checking log v0.4.19
[INFO] [stderr]     Checking svg v0.13.1
[INFO] [stderr]     Checking either v1.8.1
[INFO] [stderr]    Compiling convert_case v0.4.0
[INFO] [stderr]     Checking getopt v1.1.3
[INFO] [stderr]     Checking itertools v0.10.5
[INFO] [stderr]     Checking roxmltree v0.14.1
[INFO] [stderr]    Compiling heck v0.3.3
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]     Checking getrandom v0.1.16
[INFO] [stderr]     Checking atty v0.2.14
[INFO] [stderr]     Checking clap v2.34.0
[INFO] [stderr]     Checking regex v1.8.4
[INFO] [stderr]     Checking rand_core v0.5.1
[INFO] [stderr]     Checking num-complex v0.4.3
[INFO] [stderr]     Checking rand_pcg v0.2.1
[INFO] [stderr]     Checking rand_chacha v0.2.2
[INFO] [stderr]     Checking rand v0.7.3
[INFO] [stderr]     Checking ndarray v0.15.6
[INFO] [stderr]     Checking env_logger v0.8.4
[INFO] [stderr]     Checking random_color v0.5.1
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]    Compiling structopt-derive v0.4.18
[INFO] [stderr]    Compiling derive_more v0.99.17
[INFO] [stderr]     Checking structopt v0.3.26
[INFO] [stderr]     Checking light_phylogeny v2.1.5
[INFO] [stderr]     Checking phylodm v3.0.0 (/tmp/fixit)
[INFO] [stderr]    Migrating src/lib.rs from 2021 edition to 2024
[INFO] [stderr]    Migrating tests/tree.rs from 2021 edition to 2024
[INFO] [stderr]    Migrating src/main.rs from 2021 edition to 2024
[INFO] [stderr]    Migrating tests/util.rs from 2021 edition to 2024
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 4.58s
[INFO] [stderr] Running `cargo check` to verify 2024
[INFO] [stderr] error: failed to parse manifest at `/tmp/fixit/Cargo.toml`
[INFO] [stderr] 
[INFO] [stderr] Caused by:
[INFO] [stderr]   feature `python` includes `pyo3` which is neither a dependency nor another feature
[INFO] [stderr] error: failed to check after updating to 2024
[INFO] [stderr] 
[INFO] [stderr] Caused by:
[INFO] [stderr]   process didn't exit successfully: `cargo check --frozen --all --all-targets --message-format=json` (exit status: 101)
[INFO] running `Command { std: "docker" "inspect" "0f0233224811d29f5a78d0d3dd9a5741c4ee6c931a4fd7c8c75d1f845cd299a5", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "0f0233224811d29f5a78d0d3dd9a5741c4ee6c931a4fd7c8c75d1f845cd299a5", kill_on_drop: false }`
[INFO] [stdout] 0f0233224811d29f5a78d0d3dd9a5741c4ee6c931a4fd7c8c75d1f845cd299a5