[INFO] cloning repository https://github.com/IMTMarburg/mbf_bam [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/IMTMarburg/mbf_bam" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FIMTMarburg%2Fmbf_bam", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FIMTMarburg%2Fmbf_bam'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 906a4ccff4ac21ca2ed097e42c89b1df983bae0e [INFO] building IMTMarburg/mbf_bam against master#c7f6aa2869acdbf014d094c6e427e554e160b6db for pr-146237-2 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FIMTMarburg%2Fmbf_bam" "/workspace/builds/worker-4-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-4-tc1/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/IMTMarburg/mbf_bam [INFO] finished tweaking git repo https://github.com/IMTMarburg/mbf_bam [INFO] tweaked toml for git repo https://github.com/IMTMarburg/mbf_bam written to /workspace/builds/worker-4-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/IMTMarburg/mbf_bam on toolchain c7f6aa2869acdbf014d094c6e427e554e160b6db [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+c7f6aa2869acdbf014d094c6e427e554e160b6db" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/IMTMarburg/mbf_bam 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" "+c7f6aa2869acdbf014d094c6e427e554e160b6db" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded linear-map v1.2.0 [INFO] [stderr] Downloaded semver v0.1.20 [INFO] [stderr] Downloaded custom_derive v0.1.7 [INFO] [stderr] Downloaded proc-macro2 v1.0.88 [INFO] [stderr] Downloaded enum-map v2.7.3 [INFO] [stderr] Downloaded enum-map-derive v0.17.0 [INFO] [stderr] Downloaded editdistancek v1.0.2 [INFO] [stderr] Downloaded multimap v0.10.0 [INFO] [stderr] Downloaded portable-atomic-util v0.2.2 [INFO] [stderr] Downloaded triple_accel v0.4.0 [INFO] [stderr] Downloaded pyo3-ffi v0.20.3 [INFO] [stderr] Downloaded pyo3-build-config v0.20.3 [INFO] [stderr] Downloaded statrs v0.17.1 [INFO] [stderr] Downloaded rust-htslib v0.46.0 [INFO] [stderr] Downloaded pyo3-macros-backend v0.20.3 [INFO] [stderr] Downloaded failure v0.1.8 [INFO] [stderr] Downloaded bio v2.0.3 [INFO] [stderr] Downloaded pyo3-macros v0.20.3 [INFO] [stderr] Downloaded unindent v0.2.3 [INFO] [stderr] Downloaded ex v0.1.3 [INFO] [stderr] Downloaded ndarray v0.16.1 [INFO] [stderr] Downloaded derive-new v0.6.0 [INFO] [stderr] Downloaded bio-types v1.0.4 [INFO] [stderr] Downloaded ordered-float v4.4.0 [INFO] [stderr] Downloaded itertools-num v0.1.3 [INFO] [stderr] Downloaded failure_derive v0.1.8 [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded rustc_version v0.1.7 [INFO] [stderr] Downloaded libc v0.2.160 [INFO] [stderr] Downloaded libz-sys v1.1.20 [INFO] [stderr] Downloaded pyo3 v0.20.3 [INFO] [stderr] Downloaded curl-sys v0.4.77+curl-8.10.1 [INFO] [stderr] Downloaded hts-sys v2.1.4 [INFO] [stderr] Downloaded openssl-src v300.3.2+3.3.2 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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" "+c7f6aa2869acdbf014d094c6e427e554e160b6db" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 47739d31553ebb0e0e6605300c357fb1fb6eb2604c57cf6af7df51b71e8479ef [INFO] running `Command { std: "docker" "start" "-a" "47739d31553ebb0e0e6605300c357fb1fb6eb2604c57cf6af7df51b71e8479ef", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "47739d31553ebb0e0e6605300c357fb1fb6eb2604c57cf6af7df51b71e8479ef", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "47739d31553ebb0e0e6605300c357fb1fb6eb2604c57cf6af7df51b71e8479ef", kill_on_drop: false }` [INFO] [stdout] 47739d31553ebb0e0e6605300c357fb1fb6eb2604c57cf6af7df51b71e8479ef [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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" "+c7f6aa2869acdbf014d094c6e427e554e160b6db" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] f40e3018a1783cec4a9d02f15d908f6f6b78bdc53934f4fb80a1536fa0a22c02 [INFO] running `Command { std: "docker" "start" "-a" "f40e3018a1783cec4a9d02f15d908f6f6b78bdc53934f4fb80a1536fa0a22c02", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.160 [INFO] [stderr] Compiling proc-macro2 v1.0.88 [INFO] [stderr] Compiling libm v0.2.8 [INFO] [stderr] Compiling target-lexicon v0.12.16 [INFO] [stderr] Compiling once_cell v1.20.2 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling matrixmultiply v0.3.9 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling bytemuck v1.19.0 [INFO] [stderr] Compiling aho-corasick v1.1.3 [INFO] [stderr] Compiling thiserror v1.0.64 [INFO] [stderr] Compiling 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serde_derive v1.0.210 [INFO] [stderr] Compiling thiserror-impl v1.0.64 [INFO] [stderr] Compiling derive-new v0.6.0 [INFO] [stderr] Compiling nalgebra-macros v0.2.2 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling enum-map-derive v0.17.0 [INFO] [stderr] Compiling enum-map v2.7.3 [INFO] [stderr] Compiling zerocopy v0.7.35 [INFO] [stderr] Compiling pyo3-macros v0.20.3 [INFO] [stderr] Compiling ppv-lite86 v0.2.20 [INFO] [stderr] Compiling bio-types v1.0.4 [INFO] [stderr] Compiling rand_chacha v0.3.1 [INFO] [stderr] Compiling rand v0.8.5 [INFO] [stderr] Compiling rand_distr v0.4.3 [INFO] [stderr] Compiling serde v1.0.210 [INFO] [stderr] Compiling nalgebra v0.32.6 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling csv v1.3.0 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Compiling multimap v0.10.0 [INFO] [stderr] Compiling statrs v0.17.1 [INFO] [stderr] Compiling bio v2.0.3 [INFO] [stderr] Compiling rust-htslib v0.46.0 [INFO] [stderr] Compiling mbf_bam v0.6.1 (/opt/rustwide/workdir) [INFO] [stdout] warning: unnecessary parentheses around closure body [INFO] [stdout] --> src/count_reads/by_barcode.rs:95:25 [INFO] [stdout] | [INFO] [stdout] 95 | flat.sort_by(|a, b| (a.1.cmp(&b.1))); [INFO] [stdout] | ^ ^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_parens)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] help: remove these parentheses [INFO] [stdout] | [INFO] [stdout] 95 - flat.sort_by(|a, b| (a.1.cmp(&b.1))); [INFO] [stdout] 95 + flat.sort_by(|a, b| a.1.cmp(&b.1)); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stdout] --> src/lib.rs:20:17 [INFO] [stdout] | [INFO] [stdout] 20 | #[derive(Debug, Fail, Clone)] [INFO] [stdout] | ^--- [INFO] [stdout] | | [INFO] [stdout] | `Fail` is not local [INFO] [stdout] | move the `impl` block outside of this constant `_DERIVE_failure_Fail_FOR_BamError` [INFO] [stdout] 21 | pub enum BamError { [INFO] [stdout] | -------- `BamError` is not local [INFO] [stdout] | [INFO] [stdout] = note: the derive macro `Fail` defines the non-local `impl`, and may need to be changed [INFO] [stdout] = note: the derive macro `Fail` may come from an old version of the `failure_derive` crate, try updating your dependency with `cargo update -p failure_derive` [INFO] [stdout] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stdout] = note: items in an anonymous const item (`const _: () = { ... }`) are treated as in the same scope as the anonymous const's declaration for the purpose of this lint [INFO] [stdout] = note: `#[warn(non_local_definitions)]` on by default [INFO] [stdout] = note: this warning originates in the derive macro `Fail` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stdout] --> src/lib.rs:20:17 [INFO] [stdout] | [INFO] [stdout] 20 | #[derive(Debug, Fail, Clone)] [INFO] [stdout] | ^--- [INFO] [stdout] | | [INFO] [stdout] | `Display` is not local [INFO] [stdout] | move the `impl` block outside of this constant `_DERIVE_failure_core_fmt_Display_FOR_BamError` [INFO] [stdout] 21 | pub enum BamError { [INFO] [stdout] | -------- `BamError` is not local [INFO] [stdout] | [INFO] [stdout] = note: the derive macro `Fail` defines the non-local `impl`, and may need to be changed [INFO] [stdout] = note: the derive macro `Fail` may come from an old version of the `failure_derive` crate, try updating your dependency with `cargo update -p failure_derive` [INFO] [stdout] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stdout] = note: items in an anonymous const item (`const _: () = { ... }`) are treated as in the same scope as the anonymous const's declaration for the purpose of this lint [INFO] [stdout] = note: this warning originates in the derive macro `Fail` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: hiding a lifetime that's elided elsewhere is confusing [INFO] [stdout] --> src/count_reads/chunked_genome.rs:45:17 [INFO] [stdout] | [INFO] [stdout] 45 | pub fn iter(&self) -> ChunkedGenomeIterator { [INFO] [stdout] | ^^^^^ ^^^^^^^^^^^^^^^^^^^^^ the same lifetime is hidden here [INFO] [stdout] | | [INFO] [stdout] | the lifetime is elided here [INFO] [stdout] | [INFO] [stdout] = help: the same lifetime is referred to in inconsistent ways, making the signature confusing [INFO] [stdout] = note: `#[warn(mismatched_lifetime_syntaxes)]` on by default [INFO] [stdout] help: use `'_` for type paths [INFO] [stdout] | [INFO] [stdout] 45 | pub fn iter(&self) -> ChunkedGenomeIterator<'_> { [INFO] [stdout] | ++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 3m 26s [INFO] running `Command { std: "docker" "inspect" "f40e3018a1783cec4a9d02f15d908f6f6b78bdc53934f4fb80a1536fa0a22c02", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f40e3018a1783cec4a9d02f15d908f6f6b78bdc53934f4fb80a1536fa0a22c02", kill_on_drop: false }` [INFO] [stdout] f40e3018a1783cec4a9d02f15d908f6f6b78bdc53934f4fb80a1536fa0a22c02 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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" "+c7f6aa2869acdbf014d094c6e427e554e160b6db" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 0eb1248e6c1fc5a67a08d007baf024797fea4c3a06fb823d3160130ef83ad866 [INFO] running `Command { std: "docker" "start" "-a" "0eb1248e6c1fc5a67a08d007baf024797fea4c3a06fb823d3160130ef83ad866", kill_on_drop: false }` [INFO] [stderr] Compiling pyo3-build-config v0.20.3 [INFO] [stderr] Compiling rustix v0.38.37 [INFO] [stderr] Compiling bitflags v2.6.0 [INFO] [stderr] Compiling linux-raw-sys v0.4.14 [INFO] [stderr] Compiling fastrand v2.1.1 [INFO] [stderr] Compiling pyo3-macros-backend v0.20.3 [INFO] [stderr] Compiling pyo3-ffi v0.20.3 [INFO] [stderr] Compiling pyo3 v0.20.3 [INFO] [stderr] Compiling tempfile v3.13.0 [INFO] [stderr] Compiling pyo3-macros v0.20.3 [INFO] [stderr] Compiling mbf_bam v0.6.1 (/opt/rustwide/workdir) [INFO] [stdout] warning: unnecessary parentheses around closure body [INFO] [stdout] --> src/count_reads/by_barcode.rs:95:25 [INFO] [stdout] | [INFO] [stdout] 95 | flat.sort_by(|a, b| (a.1.cmp(&b.1))); [INFO] [stdout] | ^ ^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_parens)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] help: remove these parentheses [INFO] [stdout] | [INFO] [stdout] 95 - flat.sort_by(|a, b| (a.1.cmp(&b.1))); [INFO] [stdout] 95 + flat.sort_by(|a, b| a.1.cmp(&b.1)); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stdout] --> src/lib.rs:20:17 [INFO] [stdout] | [INFO] [stdout] 20 | #[derive(Debug, Fail, Clone)] [INFO] [stdout] | ^--- [INFO] [stdout] | | [INFO] [stdout] | `Fail` is not local [INFO] [stdout] | move the `impl` block outside of this constant `_DERIVE_failure_Fail_FOR_BamError` [INFO] [stdout] 21 | pub enum BamError { [INFO] [stdout] | -------- `BamError` is not local [INFO] [stdout] | [INFO] [stdout] = note: the derive macro `Fail` defines the non-local `impl`, and may need to be changed [INFO] [stdout] = note: the derive macro `Fail` may come from an old version of the `failure_derive` crate, try updating your dependency with `cargo update -p failure_derive` [INFO] [stdout] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stdout] = note: items in an anonymous const item (`const _: () = { ... }`) are treated as in the same scope as the anonymous const's declaration for the purpose of this lint [INFO] [stdout] = note: `#[warn(non_local_definitions)]` on by default [INFO] [stdout] = note: this warning originates in the derive macro `Fail` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stdout] --> src/lib.rs:20:17 [INFO] [stdout] | [INFO] [stdout] 20 | #[derive(Debug, Fail, Clone)] [INFO] [stdout] | ^--- [INFO] [stdout] | | [INFO] [stdout] | `Display` is not local [INFO] [stdout] | move the `impl` block outside of this constant `_DERIVE_failure_core_fmt_Display_FOR_BamError` [INFO] [stdout] 21 | pub enum BamError { [INFO] [stdout] | -------- `BamError` is not local [INFO] [stdout] | [INFO] [stdout] = note: the derive macro `Fail` defines the non-local `impl`, and may need to be changed [INFO] [stdout] = note: the derive macro `Fail` may come from an old version of the `failure_derive` crate, try updating your dependency with `cargo update -p failure_derive` [INFO] [stdout] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stdout] = note: items in an anonymous const item (`const _: () = { ... }`) are treated as in the same scope as the anonymous const's declaration for the purpose of this lint [INFO] [stdout] = note: this warning originates in the derive macro `Fail` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: hiding a lifetime that's elided elsewhere is confusing [INFO] [stdout] --> src/count_reads/chunked_genome.rs:45:17 [INFO] [stdout] | [INFO] [stdout] 45 | pub fn iter(&self) -> ChunkedGenomeIterator { [INFO] [stdout] | ^^^^^ ^^^^^^^^^^^^^^^^^^^^^ the same lifetime is hidden here [INFO] [stdout] | | [INFO] [stdout] | the lifetime is elided here [INFO] [stdout] | [INFO] [stdout] = help: the same lifetime is referred to in inconsistent ways, making the signature confusing [INFO] [stdout] = note: `#[warn(mismatched_lifetime_syntaxes)]` on by default [INFO] [stdout] help: use `'_` for type paths [INFO] [stdout] | [INFO] [stdout] 45 | pub fn iter(&self) -> ChunkedGenomeIterator<'_> { [INFO] [stdout] | ++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 14.20s [INFO] running `Command { std: "docker" "inspect" "0eb1248e6c1fc5a67a08d007baf024797fea4c3a06fb823d3160130ef83ad866", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "0eb1248e6c1fc5a67a08d007baf024797fea4c3a06fb823d3160130ef83ad866", kill_on_drop: false }` [INFO] [stdout] 0eb1248e6c1fc5a67a08d007baf024797fea4c3a06fb823d3160130ef83ad866