[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#ad85bc524b1ad696e42061ad8338d382dffbdbe5 for pr-146237-1 [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 ad85bc524b1ad696e42061ad8338d382dffbdbe5 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "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" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded unindent v0.2.3 [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded derive-new v0.5.9 [INFO] [stderr] Downloaded bio-types v1.0.4 [INFO] [stderr] Downloaded nalgebra-macros v0.2.2 [INFO] [stderr] Downloaded cc v1.1.30 [INFO] [stderr] Downloaded editdistancek v1.0.2 [INFO] [stderr] Downloaded csv-core v0.1.11 [INFO] [stderr] Downloaded enum-map-derive v0.17.0 [INFO] [stderr] Downloaded simba v0.8.1 [INFO] [stderr] Downloaded pyo3-ffi v0.20.3 [INFO] [stderr] Downloaded rust-htslib v0.46.0 [INFO] [stderr] Downloaded bytemuck v1.19.0 [INFO] [stderr] Downloaded wide v0.7.28 [INFO] [stderr] Downloaded statrs v0.17.1 [INFO] [stderr] Downloaded triple_accel v0.4.0 [INFO] [stderr] Downloaded pyo3-macros-backend v0.20.3 [INFO] [stderr] Downloaded pyo3-build-config v0.20.3 [INFO] [stderr] Downloaded ex v0.1.3 [INFO] [stderr] Downloaded enum-map v2.7.3 [INFO] [stderr] Downloaded matrixmultiply v0.3.9 [INFO] [stderr] Downloaded rand_distr v0.4.3 [INFO] 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"/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" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 1d941ae1734963ff1a3dc66349cafe75ac7ddeb605b235b92c535cca619689ca [INFO] running `Command { std: "docker" "start" "-a" "1d941ae1734963ff1a3dc66349cafe75ac7ddeb605b235b92c535cca619689ca", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "1d941ae1734963ff1a3dc66349cafe75ac7ddeb605b235b92c535cca619689ca", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "1d941ae1734963ff1a3dc66349cafe75ac7ddeb605b235b92c535cca619689ca", kill_on_drop: false }` [INFO] [stdout] 1d941ae1734963ff1a3dc66349cafe75ac7ddeb605b235b92c535cca619689ca [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" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 0853d3d39a8ca8d26ced36f59ca9b2b27188ecccf3e15a3bde9b3a02597644db [INFO] running `Command { std: "docker" "start" "-a" "0853d3d39a8ca8d26ced36f59ca9b2b27188ecccf3e15a3bde9b3a02597644db", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.160 [INFO] [stderr] Compiling proc-macro2 v1.0.88 [INFO] [stderr] Compiling pkg-config v0.3.31 [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 serde v1.0.210 [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 crossbeam-utils v0.8.20 [INFO] [stderr] 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Compiling rand_core v0.6.4 [INFO] [stderr] Compiling cc v1.1.30 [INFO] [stderr] Compiling num-rational v0.4.2 [INFO] [stderr] Compiling ndarray v0.16.1 [INFO] [stderr] Compiling parking_lot v0.12.3 [INFO] [stderr] Compiling ordered-float v4.4.0 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling rayon v1.10.0 [INFO] [stderr] Compiling simba v0.8.1 [INFO] [stderr] Compiling pyo3-ffi v0.20.3 [INFO] [stderr] Compiling pyo3 v0.20.3 [INFO] [stderr] Compiling regex v1.11.0 [INFO] [stderr] Compiling openssl-src v300.3.2+3.3.2 [INFO] [stderr] Compiling cmake v0.1.51 [INFO] [stderr] Compiling openssl-sys v0.9.104 [INFO] [stderr] Compiling libz-sys v1.1.20 [INFO] [stderr] Compiling bzip2-sys v0.1.11+1.0.8 [INFO] [stderr] Compiling curl-sys v0.4.77+curl-8.10.1 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling hts-sys v2.1.4 [INFO] [stderr] Compiling synstructure v0.12.6 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling backtrace v0.3.74 [INFO] [stderr] Compiling pyo3-macros-backend v0.20.3 [INFO] [stderr] Compiling zerocopy-derive v0.7.35 [INFO] [stderr] Compiling serde_derive v1.0.210 [INFO] [stderr] Compiling thiserror-impl v1.0.64 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling derive-new v0.6.0 [INFO] [stderr] Compiling nalgebra-macros v0.2.2 [INFO] [stderr] Compiling enum-map-derive v0.17.0 [INFO] [stderr] Compiling failure v0.1.8 [INFO] [stderr] Compiling enum-map v2.7.3 [INFO] [stderr] Compiling zerocopy v0.7.35 [INFO] [stderr] Compiling thiserror v1.0.64 [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 pyo3-macros v0.20.3 [INFO] [stderr] Compiling rand_distr v0.4.3 [INFO] [stderr] Compiling nalgebra v0.32.6 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling multimap v0.10.0 [INFO] [stderr] Compiling csv v1.3.0 [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 29s [INFO] running `Command { std: "docker" "inspect" "0853d3d39a8ca8d26ced36f59ca9b2b27188ecccf3e15a3bde9b3a02597644db", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "0853d3d39a8ca8d26ced36f59ca9b2b27188ecccf3e15a3bde9b3a02597644db", kill_on_drop: false }` [INFO] [stdout] 0853d3d39a8ca8d26ced36f59ca9b2b27188ecccf3e15a3bde9b3a02597644db [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" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 788362e784c1acb93b4313468418b45e4b3284a799087a7a1af3385b1f0b1373 [INFO] running `Command { std: "docker" "start" "-a" "788362e784c1acb93b4313468418b45e4b3284a799087a7a1af3385b1f0b1373", kill_on_drop: false }` [INFO] [stderr] Compiling pyo3-build-config v0.20.3 [INFO] [stderr] Compiling rustix v0.38.37 [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 12.92s [INFO] running `Command { std: "docker" "inspect" "788362e784c1acb93b4313468418b45e4b3284a799087a7a1af3385b1f0b1373", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "788362e784c1acb93b4313468418b45e4b3284a799087a7a1af3385b1f0b1373", kill_on_drop: false }` [INFO] [stdout] 788362e784c1acb93b4313468418b45e4b3284a799087a7a1af3385b1f0b1373