[INFO] cloning repository https://github.com/rejuve-bio/fastVEP
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/rejuve-bio/fastVEP" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Frejuve-bio%2FfastVEP", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Frejuve-bio%2FfastVEP'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 477db1d571e25a9f3f6a2225a5fe8ac04fa720b1
[INFO] checking rejuve-bio/fastVEP against 5c543b0b8c73c7b72bc8284ced4fb22ead15734d for pr-160186
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Frejuve-bio%2FfastVEP" "/workspace/builds/worker-3-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-3-tc1/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/rejuve-bio/fastVEP
[INFO] finished tweaking git repo https://github.com/rejuve-bio/fastVEP
[INFO] tweaked toml for git repo https://github.com/rejuve-bio/fastVEP written to /workspace/builds/worker-3-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/rejuve-bio/fastVEP on toolchain 5c543b0b8c73c7b72bc8284ced4fb22ead15734d
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+5c543b0b8c73c7b72bc8284ced4fb22ead15734d" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/rejuve-bio/fastVEP 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" "+5c543b0b8c73c7b72bc8284ced4fb22ead15734d" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr] warning: unused workspace dependency `crossbeam`
[INFO] [stderr]   --> Cargo.toml:14:1
[INFO] [stderr]    |
[INFO] [stderr] 14 | crossbeam = "0.8"
[INFO] [stderr]    | ^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `cargo::unused_workspace_dependencies` is set to `warn` by default
[INFO] [stderr] help: consider removing the workspace dependency `crossbeam`
[INFO] [stderr] warning: unused field `description` in `workspace.package`
[INFO] [stderr]   --> Cargo.toml:74:1
[INFO] [stderr]    |
[INFO] [stderr] 74 | description = "A high-performance variant effect predictor with clinical database integration, written in Rust"
[INFO] [stderr]    | ^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `cargo::unused_workspace_package_fields` is set to `warn` by default
[INFO] [stderr] help: consider removing the field `workspace.package.description`
[INFO] [stderr] warning: workspace (manifest) generated 2 warnings
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded cc v1.2.59
[INFO] [stderr]   Downloaded noodles-tabix v0.61.0
[INFO] [stderr]   Downloaded lru v0.12.5
[INFO] [stderr]   Downloaded env_logger v0.11.10
[INFO] [stderr]   Downloaded noodles-core v0.19.0
[INFO] [stderr]   Downloaded noodles-csi v0.55.0
[INFO] [stderr]   Downloaded portable-atomic-util v0.2.6
[INFO] [stderr]   Downloaded noodles-bgzf v0.46.0
[INFO] [stderr]   Downloaded jiff-static v0.2.23
[INFO] [stderr]   Downloaded env_filter v1.0.1
[INFO] [stderr]   Downloaded zlib-rs v0.6.3
[INFO] [stderr]   Downloaded bstr v1.12.1
[INFO] [stderr]   Downloaded libc v0.2.184
[INFO] [stderr]   Downloaded jiff v0.2.23
[INFO] [stderr]   Downloaded tokio v1.51.1
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,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" "-m" "1610612736" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:77db811e55d90add9212f6832c23229e3de5f1c1f9905e8cb07319ea15df73ac" "sleep" "infinity", kill_on_drop: false }`
[INFO] [stdout] 4decba8a1b62e85a245b669e839b41bac532eaa51a9698783e1733c77a0c98be
[INFO] running `Command { std: "docker" "start" "4decba8a1b62e85a245b669e839b41bac532eaa51a9698783e1733c77a0c98be", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "4decba8a1b62e85a245b669e839b41bac532eaa51a9698783e1733c77a0c98be", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-w" "/opt/rustwide/workdir" "--user" "0:0" "4decba8a1b62e85a245b669e839b41bac532eaa51a9698783e1733c77a0c98be" "/opt/rustwide/cargo-home/bin/cargo" "+5c543b0b8c73c7b72bc8284ced4fb22ead15734d" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "4decba8a1b62e85a245b669e839b41bac532eaa51a9698783e1733c77a0c98be", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-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" "-w" "/opt/rustwide/workdir" "--user" "0:0" "4decba8a1b62e85a245b669e839b41bac532eaa51a9698783e1733c77a0c98be" "/opt/rustwide/cargo-home/bin/cargo" "+5c543b0b8c73c7b72bc8284ced4fb22ead15734d" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stderr] warning: unused workspace dependency `crossbeam`
[INFO] [stderr]   --> Cargo.toml:14:1
[INFO] [stderr]    |
[INFO] [stderr] 14 | crossbeam = "0.8"
[INFO] [stderr]    | ^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `cargo::unused_workspace_dependencies` is set to `warn` by default
[INFO] [stderr] help: consider removing the workspace dependency `crossbeam`
[INFO] [stderr] warning: unused field `description` in `workspace.package`
[INFO] [stderr]   --> Cargo.toml:74:1
[INFO] [stderr]    |
[INFO] [stderr] 74 | description = "A high-performance variant effect predictor with clinical database integration, written in Rust"
[INFO] [stderr]    | ^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `cargo::unused_workspace_package_fields` is set to `warn` by default
[INFO] [stderr] help: consider removing the field `workspace.package.description`
[INFO] [stderr] warning: workspace (manifest) generated 2 warnings
[INFO] [stderr]    Compiling syn v2.0.117
[INFO] [stderr]    Compiling serde_core v1.0.228
[INFO] [stderr]    Compiling serde v1.0.228
[INFO] [stderr]    Compiling libc v0.2.184
[INFO] [stderr]     Checking log v0.4.29
[INFO] [stderr]     Checking hashbrown v0.16.1
[INFO] [stderr]     Checking simd-adler32 v0.3.9
[INFO] [stderr]     Checking zlib-rs v0.6.3
[INFO] [stderr]     Checking tracing-core v0.1.36
[INFO] [stderr]     Checking crossbeam-channel v0.5.15
[INFO] [stderr]     Checking bstr v1.12.1
[INFO] [stderr]    Compiling zstd-safe v7.2.4
[INFO] [stderr]     Checking bit-vec v0.9.1
[INFO] [stderr]     Checking aho-corasick v1.1.4
[INFO] [stderr]     Checking bumpalo v3.20.2
[INFO] [stderr]     Checking foldhash v0.1.5
[INFO] [stderr]     Checking regex-syntax v0.8.10
[INFO] [stderr]     Checking toml_write v0.1.2
[INFO] [stderr]    Compiling zip v2.4.2
[INFO] [stderr]     Checking winnow v0.7.15
[INFO] [stderr]     Checking hashbrown v0.15.5
[INFO] [stderr]     Checking bitflags v2.11.0
[INFO] [stderr]     Checking miniz_oxide v0.8.9
[INFO] [stderr]     Checking zopfli v0.8.3
[INFO] [stderr]     Checking either v1.15.0
[INFO] [stderr]     Checking rayon v1.11.0
[INFO] [stderr]     Checking clap_builder v4.6.0
[INFO] [stderr]    Compiling rustix v1.1.4
[INFO] [stderr]     Checking noodles-core v0.19.0
[INFO] [stderr]     Checking linux-raw-sys v0.12.1
[INFO] [stderr]     Checking jiff v0.2.23
[INFO] [stderr]     Checking indexmap v2.13.0
[INFO] [stderr]     Checking futures-task v0.3.32
[INFO] [stderr]     Checking sync_wrapper v1.0.2
[INFO] [stderr]     Checking slab v0.4.12
[INFO] [stderr]     Checking sharded-slab v0.1.7
[INFO] [stderr]     Checking futures-util v0.3.32
[INFO] [stderr]     Checking lru v0.12.5
[INFO] [stderr]     Checking tracing-log v0.2.0
[INFO] [stderr]     Checking thread_local v1.1.9
[INFO] [stderr]     Checking nu-ansi-term v0.50.3
[INFO] [stderr]     Checking flate2 v1.1.9
[INFO] [stderr]     Checking regex-automata v0.4.14
[INFO] [stderr]     Checking memmap2 v0.9.10
[INFO] [stderr]     Checking errno v0.3.14
[INFO] [stderr]     Checking socket2 v0.6.3
[INFO] [stderr]    Compiling jobserver v0.1.34
[INFO] [stderr]     Checking mio v1.2.0
[INFO] [stderr]     Checking getrandom v0.4.2
[INFO] [stderr]     Checking signal-hook-registry v1.4.8
[INFO] [stderr]     Checking noodles-bgzf v0.46.0
[INFO] [stderr]    Compiling cc v1.2.59
[INFO] [stderr]     Checking noodles-csi v0.55.0
[INFO] [stderr]     Checking noodles-tabix v0.61.0
[INFO] [stderr]     Checking tempfile v3.27.0
[INFO] [stderr]     Checking serde_json v1.0.149
[INFO] [stderr]     Checking serde_path_to_error v0.1.20
[INFO] [stderr]    Compiling zstd-sys v2.0.16+zstd.1.5.7
[INFO] [stderr]     Checking regex v1.12.3
[INFO] [stderr]     Checking matchers v0.2.0
[INFO] [stderr]     Checking env_filter v1.0.1
[INFO] [stderr]     Checking env_logger v0.11.10
[INFO] [stderr]    Compiling serde_derive v1.0.228
[INFO] [stderr]    Compiling thiserror-impl v2.0.18
[INFO] [stderr]    Compiling tracing-attributes v0.1.31
[INFO] [stderr]    Compiling displaydoc v0.2.5
[INFO] [stderr]    Compiling tokio-macros v2.7.0
[INFO] [stderr]    Compiling clap_derive v4.6.0
[INFO] [stderr]     Checking tokio v1.51.1
[INFO] [stderr]     Checking thiserror v2.0.18
[INFO] [stderr]     Checking tracing v0.1.44
[INFO] [stderr]     Checking axum-core v0.5.6
[INFO] [stderr]     Checking tracing-subscriber v0.3.23
[INFO] [stderr]     Checking tower-http v0.6.8
[INFO] [stderr]     Checking clap v4.6.0
[INFO] [stderr]     Checking fastvep-core v0.1.0 (/opt/rustwide/workdir/crates/fastvep-core)
[INFO] [stderr]     Checking bincode v1.3.3
[INFO] [stderr]     Checking toml_datetime v0.6.11
[INFO] [stderr]     Checking serde_spanned v0.6.9
[INFO] [stderr]     Checking serde_urlencoded v0.7.1
[INFO] [stderr]     Checking toml_edit v0.22.27
[INFO] [stderr]     Checking fastvep-genome v0.1.0 (/opt/rustwide/workdir/crates/fastvep-genome)
[INFO] [stderr]     Checking fastvep-filter v0.1.0 (/opt/rustwide/workdir/crates/fastvep-filter)
[INFO] [stderr]     Checking fastvep-io v0.1.0 (/opt/rustwide/workdir/crates/fastvep-io)
[INFO] [stderr]     Checking fastvep-hgvs v0.1.0 (/opt/rustwide/workdir/crates/fastvep-hgvs)
[INFO] [stderr]     Checking fastvep-consequence v0.1.0 (/opt/rustwide/workdir/crates/fastvep-consequence)
[INFO] [stderr]     Checking zstd v0.13.3
[INFO] [stderr]     Checking fastvep-cache v0.1.0 (/opt/rustwide/workdir/crates/fastvep-cache)
[INFO] [stderr]     Checking hyper v1.9.0
[INFO] [stderr]     Checking tokio-util v0.7.18
[INFO] [stderr]     Checking fastvep-sa v0.1.0 (/opt/rustwide/workdir/crates/fastvep-sa)
[INFO] [stderr]     Checking tower v0.5.3
[INFO] [stderr]     Checking hyper-util v0.1.20
[INFO] [stderr]     Checking toml v0.8.23
[INFO] [stderr]     Checking axum v0.8.8
[INFO] [stderr]     Checking fastvep-classification v0.1.0 (/opt/rustwide/workdir/crates/fastvep-classification)
[INFO] [stdout] warning: value assigned to `hom_points` is never read
[INFO] [stdout]    --> crates/fastvep-classification/src/criteria/pathogenic_moderate.rs:366:13
[INFO] [stdout]     |
[INFO] [stdout] 366 |             hom_points += pts;
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout]     = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `hom_points` is never read
[INFO] [stdout]    --> crates/fastvep-classification/src/criteria/pathogenic_moderate.rs:366:13
[INFO] [stdout]     |
[INFO] [stdout] 366 |             hom_points += pts;
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout]     = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Checking fastvep-annotate v0.1.0 (/opt/rustwide/workdir/crates/fastvep-annotate)
[INFO] [stderr]     Checking fastvep-cli v0.1.0 (/opt/rustwide/workdir/crates/fastvep-cli)
[INFO] [stderr]     Checking fastvep-web v0.1.0 (/opt/rustwide/workdir/crates/fastvep-web)
[INFO] [stderr] warning: unused dependency `serde_json`
[INFO] [stderr]   --> crates/fastvep-cache/Cargo.toml:13:1
[INFO] [stderr]    |
[INFO] [stderr] 13 | serde_json = { workspace = true }
[INFO] [stderr]    | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `cargo::unused_dependencies` is set to `warn` by default
[INFO] [stderr] help: consider removing the dependency on `serde_json`
[INFO] [stderr] warning: `fastvep-cache` (manifest) generated 1 warning
[INFO] [stderr] warning: unused dependency `log`
[INFO] [stderr]   --> crates/fastvep-classification/Cargo.toml:13:1
[INFO] [stderr]    |
[INFO] [stderr] 13 | log = { workspace = true }
[INFO] [stderr]    | ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `cargo::unused_dependencies` is set to `warn` by default
[INFO] [stderr] help: consider removing the dependency on `log`
[INFO] [stderr] warning: `fastvep-classification` (manifest) generated 1 warning
[INFO] [stderr] warning: unused dependency `log`
[INFO] [stderr]   --> crates/fastvep-consequence/Cargo.toml:11:1
[INFO] [stderr]    |
[INFO] [stderr] 11 | log = { workspace = true }
[INFO] [stderr]    | ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `cargo::unused_dependencies` is set to `warn` by default
[INFO] [stderr] help: consider removing the dependency on `log`
[INFO] [stderr] warning: `fastvep-consequence` (manifest) generated 1 warning
[INFO] [stderr] warning: unused dependency `thiserror`
[INFO] [stderr]   --> crates/fastvep-core/Cargo.toml:10:1
[INFO] [stderr]    |
[INFO] [stderr] 10 | thiserror = { workspace = true }
[INFO] [stderr]    | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `cargo::unused_dependencies` is set to `warn` by default
[INFO] [stderr] help: consider removing the dependency on `thiserror`
[INFO] [stderr] warning: `fastvep-core` (manifest) generated 1 warning
[INFO] [stderr] warning: unused dependency `fastvep-core`
[INFO] [stderr]  --> crates/fastvep-filter/Cargo.toml:9:1
[INFO] [stderr]   |
[INFO] [stderr] 9 | fastvep-core = { workspace = true }
[INFO] [stderr]   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: `cargo::unused_dependencies` is set to `warn` by default
[INFO] [stderr] help: consider removing the dependency on `fastvep-core`
[INFO] [stderr] warning: `fastvep-filter` (manifest) generated 1 warning
[INFO] [stderr] warning: unused dependency `fastvep-genome`
[INFO] [stderr]   --> crates/fastvep-io/Cargo.toml:10:1
[INFO] [stderr]    |
[INFO] [stderr] 10 | fastvep-genome = { workspace = true }
[INFO] [stderr]    | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `cargo::unused_dependencies` is set to `warn` by default
[INFO] [stderr] help: consider removing the dependency on `fastvep-genome`
[INFO] [stderr] help: to still use for development builds, move to `dev-dependencies`
[INFO] [stderr] warning: unused dependency `log`
[INFO] [stderr]   --> crates/fastvep-io/Cargo.toml:14:1
[INFO] [stderr]    |
[INFO] [stderr] 14 | log = { workspace = true }
[INFO] [stderr]    | ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr] help: consider removing the dependency on `log`
[INFO] [stderr] warning: `fastvep-io` (manifest) generated 2 warnings
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 57.17s
[INFO] running `Command { std: "docker" "inspect" "4decba8a1b62e85a245b669e839b41bac532eaa51a9698783e1733c77a0c98be", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "4decba8a1b62e85a245b669e839b41bac532eaa51a9698783e1733c77a0c98be", kill_on_drop: false }`
[INFO] [stdout] 4decba8a1b62e85a245b669e839b41bac532eaa51a9698783e1733c77a0c98be
