[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] checking IMTMarburg/mbf_bam against 5c543b0b8c73c7b72bc8284ced4fb22ead15734d for pr-160186 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FIMTMarburg%2Fmbf_bam" "/workspace/builds/worker-6-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-6-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-6-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/IMTMarburg/mbf_bam 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/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" "+5c543b0b8c73c7b72bc8284ced4fb22ead15734d" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded thiserror-impl v1.0.64 [INFO] [stderr] Downloaded derive-new v0.5.9 [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded ex v0.1.3 [INFO] [stderr] Downloaded failure_derive v0.1.8 [INFO] [stderr] Downloaded custom_derive v0.1.7 [INFO] [stderr] Downloaded thiserror v1.0.64 [INFO] [stderr] Downloaded rustc_version v0.1.7 [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded ieee754 v0.2.6 [INFO] [stderr] Downloaded cmake v0.1.51 [INFO] [stderr] Downloaded derive-new v0.6.0 [INFO] [stderr] Downloaded portable-atomic-util v0.2.2 [INFO] [stderr] Downloaded itertools-num v0.1.3 [INFO] [stderr] Downloaded rustversion v1.0.18 [INFO] [stderr] Downloaded unindent v0.2.3 [INFO] [stderr] Downloaded triple_accel v0.4.0 [INFO] [stderr] Downloaded bytemuck v1.19.0 [INFO] [stderr] Downloaded multimap v0.10.0 [INFO] [stderr] Downloaded editdistancek v1.0.2 [INFO] [stderr] Downloaded proc-macro2 v1.0.88 [INFO] [stderr] Downloaded semver 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"/var/lib/crater-agent-workspace/builds/worker-6-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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] 86792499435da34b39c1c118d4dd7481224e4b9c09c46e05057500b1ab59aea2 [INFO] running `Command { std: "docker" "start" "86792499435da34b39c1c118d4dd7481224e4b9c09c46e05057500b1ab59aea2", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "86792499435da34b39c1c118d4dd7481224e4b9c09c46e05057500b1ab59aea2", 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" "86792499435da34b39c1c118d4dd7481224e4b9c09c46e05057500b1ab59aea2" "/opt/rustwide/cargo-home/bin/cargo" "+5c543b0b8c73c7b72bc8284ced4fb22ead15734d" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "86792499435da34b39c1c118d4dd7481224e4b9c09c46e05057500b1ab59aea2", 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" "86792499435da34b39c1c118d4dd7481224e4b9c09c46e05057500b1ab59aea2" "/opt/rustwide/cargo-home/bin/cargo" "+5c543b0b8c73c7b72bc8284ced4fb22ead15734d" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.160 [INFO] [stderr] Compiling proc-macro2 v1.0.88 [INFO] [stderr] Compiling unicode-ident v1.0.13 [INFO] [stderr] Compiling libm v0.2.8 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling target-lexicon v0.12.16 [INFO] [stderr] Checking memchr v2.7.4 [INFO] [stderr] Compiling once_cell v1.20.2 [INFO] [stderr] Compiling serde v1.0.210 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Compiling matrixmultiply v0.3.9 [INFO] [stderr] Compiling crossbeam-utils v0.8.20 [INFO] [stderr] Compiling rustversion v1.0.18 [INFO] [stderr] Checking bytemuck v1.19.0 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling quote v1.0.37 [INFO] [stderr] Checking safe_arch v0.7.2 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling pyo3-build-config v0.20.3 [INFO] [stderr] Checking aho-corasick v1.1.3 [INFO] [stderr] Compiling syn v2.0.79 [INFO] [stderr] Compiling thiserror v1.0.64 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Checking tinyvec v1.8.0 [INFO] [stderr] Checking getrandom v0.2.15 [INFO] [stderr] Checking rand_core v0.6.4 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Checking num-complex v0.4.6 [INFO] [stderr] Checking num-integer v0.1.46 [INFO] [stderr] Checking approx v0.5.1 [INFO] [stderr] Compiling jobserver v0.1.32 [INFO] [stderr] Checking regex-automata v0.4.8 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling cc v1.1.30 [INFO] [stderr] Checking wide v0.7.28 [INFO] [stderr] Compiling pyo3-ffi v0.20.3 [INFO] [stderr] Compiling glob v0.3.1 [INFO] [stderr] Checking miniz_oxide v0.8.0 [INFO] [stderr] Checking crossbeam-epoch v0.9.18 [INFO] [stderr] Checking unicode-normalization v0.1.24 [INFO] [stderr] Checking num-rational v0.4.2 [INFO] [stderr] 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Compiling pyo3-macros v0.20.3 [INFO] [stderr] Checking enum-map v2.7.3 [INFO] [stderr] Checking rayon-core v1.12.1 [INFO] [stderr] Checking nalgebra v0.32.6 [INFO] [stderr] Checking url v2.5.2 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Checking bio-types v1.0.4 [INFO] [stderr] Checking parking_lot v0.12.3 [INFO] [stderr] Checking itertools v0.13.0 [INFO] [stderr] Checking ndarray v0.16.1 [INFO] [stderr] Checking ordered-float v4.4.0 [INFO] [stderr] Checking itertools-num v0.1.3 [INFO] [stderr] Checking fxhash v0.2.1 [INFO] [stderr] Checking bytecount v0.6.8 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Checking unindent v0.2.3 [INFO] [stderr] Compiling indoc v2.0.5 [INFO] [stderr] Checking strum v0.26.3 [INFO] [stderr] Checking bitflags v2.6.0 [INFO] [stderr] Checking linux-raw-sys v0.4.14 [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Checking triple_accel v0.4.0 [INFO] [stderr] Checking editdistancek v1.0.2 [INFO] [stderr] Checking ex v0.1.3 [INFO] [stderr] Checking flate2 v1.0.34 [INFO] [stderr] Checking failure v0.1.8 [INFO] [stderr] Checking rayon v1.10.0 [INFO] [stderr] Checking fastrand v2.1.1 [INFO] [stderr] Checking bv v0.11.1 [INFO] [stderr] Checking csv v1.3.0 [INFO] [stderr] Checking multimap v0.10.0 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking tempfile v3.13.0 [INFO] [stderr] Checking statrs v0.17.1 [INFO] [stderr] Checking bio v2.0.3 [INFO] [stderr] Checking rust-htslib v0.46.0 [INFO] [stderr] Checking 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: 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: use of deprecated constant `std::u32::MAX`: replaced by the `MAX` associated constant on this type [INFO] [stdout] --> src/count_reads/introns.rs:48:31 [INFO] [stdout] | [INFO] [stdout] 48 | .entry((std::u32::MAX, std::u32::MAX - intron_count)) [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(deprecated)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated constant `std::u32::MAX`: replaced by the `MAX` associated constant on this type [INFO] [stdout] --> src/count_reads/introns.rs:48:46 [INFO] [stdout] | [INFO] [stdout] 48 | .entry((std::u32::MAX, std::u32::MAX - intron_count)) [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated constant `std::u32::MAX`: replaced by the `MAX` associated constant on this type [INFO] [stdout] --> src/count_reads/introns.rs:48:31 [INFO] [stdout] | [INFO] [stdout] 48 | .entry((std::u32::MAX, std::u32::MAX - intron_count)) [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(deprecated)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated constant `std::u32::MAX`: replaced by the `MAX` associated constant on this type [INFO] [stdout] --> src/count_reads/introns.rs:48:46 [INFO] [stdout] | [INFO] [stdout] 48 | .entry((std::u32::MAX, std::u32::MAX - intron_count)) [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] [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 6m 53s [INFO] running `Command { std: "docker" "inspect" "86792499435da34b39c1c118d4dd7481224e4b9c09c46e05057500b1ab59aea2", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "86792499435da34b39c1c118d4dd7481224e4b9c09c46e05057500b1ab59aea2", kill_on_drop: false }` [INFO] [stdout] 86792499435da34b39c1c118d4dd7481224e4b9c09c46e05057500b1ab59aea2