[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] testing IMTMarburg/mbf_bam against master#733b47ea4b1b86216f14ef56e49440c33933f230+rustflags=-Copt-level=3 for pr-138759 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FIMTMarburg%2Fmbf_bam" "/workspace/builds/worker-7-tc2/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-7-tc2/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-7-tc2/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/IMTMarburg/mbf_bam on toolchain 733b47ea4b1b86216f14ef56e49440c33933f230 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+733b47ea4b1b86216f14ef56e49440c33933f230" "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" "+733b47ea4b1b86216f14ef56e49440c33933f230" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+733b47ea4b1b86216f14ef56e49440c33933f230" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] fb4440bd1b83b717c173fac4660dc68bbdb852bb24a91007355ef9d83ea814e3 [INFO] running `Command { std: "docker" "start" "-a" "fb4440bd1b83b717c173fac4660dc68bbdb852bb24a91007355ef9d83ea814e3", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "fb4440bd1b83b717c173fac4660dc68bbdb852bb24a91007355ef9d83ea814e3", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "fb4440bd1b83b717c173fac4660dc68bbdb852bb24a91007355ef9d83ea814e3", kill_on_drop: false }` [INFO] [stdout] fb4440bd1b83b717c173fac4660dc68bbdb852bb24a91007355ef9d83ea814e3 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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=forbid -Copt-level=3" "-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" "+733b47ea4b1b86216f14ef56e49440c33933f230" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 162aa6e6f7564f08d43721999dbc78d8753da08afaebb22ee05681f1c14acffd [INFO] running `Command { std: "docker" "start" "-a" "162aa6e6f7564f08d43721999dbc78d8753da08afaebb22ee05681f1c14acffd", 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] Compiling byteorder v1.5.0 [INFO] [stderr] Compiling once_cell v1.20.2 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Compiling serde v1.0.210 [INFO] [stderr] Compiling matrixmultiply v0.3.9 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling rustversion v1.0.18 [INFO] [stderr] Compiling bytemuck v1.19.0 [INFO] [stderr] Compiling aho-corasick v1.1.3 [INFO] [stderr] Compiling safe_arch v0.7.2 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling quote v1.0.37 [INFO] [stderr] Compiling syn v2.0.79 [INFO] [stderr] Compiling num-integer v0.1.46 [INFO] [stderr] Compiling num-complex v0.4.6 [INFO] [stderr] Compiling jobserver v0.1.32 [INFO] [stderr] Compiling cc v1.1.30 [INFO] [stderr] Compiling pyo3-build-config v0.20.3 [INFO] [stderr] Compiling getrandom v0.2.15 [INFO] [stderr] Compiling rand_core v0.6.4 [INFO] [stderr] Compiling rawpointer v0.2.1 [INFO] [stderr] Compiling thiserror v1.0.64 [INFO] [stderr] Compiling regex-automata v0.4.8 [INFO] [stderr] Compiling approx v0.5.1 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling cmake v0.1.51 [INFO] [stderr] Compiling openssl-src v300.3.2+3.3.2 [INFO] [stderr] Compiling wide v0.7.28 [INFO] [stderr] Compiling pyo3-ffi v0.20.3 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling glob v0.3.1 [INFO] [stderr] Compiling miniz_oxide v0.8.0 [INFO] [stderr] Compiling simba v0.8.1 [INFO] [stderr] Compiling regex v1.11.0 [INFO] [stderr] Compiling libz-sys v1.1.20 [INFO] [stderr] Compiling openssl-sys v0.9.104 [INFO] [stderr] Compiling curl-sys v0.4.77+curl-8.10.1 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling bzip2-sys v0.1.11+1.0.8 [INFO] [stderr] Compiling hts-sys v2.1.4 [INFO] [stderr] Compiling unicode-normalization v0.1.24 [INFO] [stderr] Compiling num-rational v0.4.2 [INFO] [stderr] Compiling unicode-bidi v0.3.17 [INFO] [stderr] Compiling smallvec v1.13.2 [INFO] [stderr] Compiling portable-atomic v1.9.0 [INFO] [stderr] Compiling either v1.13.0 [INFO] [stderr] Compiling hashbrown v0.15.0 [INFO] [stderr] Compiling anyhow v1.0.89 [INFO] [stderr] Compiling unicode-xid v0.2.6 [INFO] [stderr] Compiling failure_derive v0.1.8 [INFO] [stderr] Compiling gimli v0.31.1 [INFO] [stderr] Compiling synstructure v0.12.6 [INFO] [stderr] Compiling pyo3-macros-backend v0.20.3 [INFO] [stderr] Compiling indexmap v2.6.0 [INFO] [stderr] Compiling parking_lot_core v0.9.10 [INFO] [stderr] Compiling idna v0.5.0 [INFO] [stderr] Compiling addr2line v0.24.2 [INFO] [stderr] Compiling pyo3 v0.20.3 [INFO] [stderr] Compiling csv-core v0.1.11 [INFO] [stderr] Compiling object v0.36.5 [INFO] [stderr] Compiling fixedbitset v0.4.2 [INFO] [stderr] Compiling bit-vec v0.8.0 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling bit-set v0.8.0 [INFO] [stderr] Compiling petgraph v0.6.5 [INFO] [stderr] Compiling url v2.5.2 [INFO] [stderr] Compiling parking_lot v0.12.3 [INFO] [stderr] Compiling itertools v0.13.0 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling ndarray v0.16.1 [INFO] [stderr] Compiling backtrace v0.3.74 [INFO] [stderr] Compiling ordered-float v4.4.0 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling fxhash v0.2.1 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling editdistancek v1.0.2 [INFO] [stderr] Compiling strum v0.26.3 [INFO] [stderr] Compiling bytecount v0.6.8 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling triple_accel v0.4.0 [INFO] [stderr] Compiling indoc v2.0.5 [INFO] [stderr] Compiling unindent v0.2.3 [INFO] [stderr] Compiling flate2 v1.0.34 [INFO] [stderr] Compiling failure v0.1.8 [INFO] [stderr] Compiling rayon v1.10.0 [INFO] [stderr] Compiling ex v0.1.3 [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 derive-new v0.6.0 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling nalgebra-macros v0.2.2 [INFO] [stderr] Compiling zerocopy v0.7.35 [INFO] [stderr] Compiling enum-map-derive v0.17.0 [INFO] [stderr] Compiling ppv-lite86 v0.2.20 [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 enum-map v2.7.3 [INFO] [stderr] Compiling bio-types v1.0.4 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Compiling multimap v0.10.0 [INFO] [stderr] Compiling vec_map v0.8.2 [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: 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: lifetime flowing from input to output with different syntax can be confusing [INFO] [stdout] --> src/count_reads/chunked_genome.rs:45:17 [INFO] [stdout] | [INFO] [stdout] 45 | pub fn iter(&self) -> ChunkedGenomeIterator { [INFO] [stdout] | ^^^^^ --------------------- the lifetime gets resolved as `'_` [INFO] [stdout] | | [INFO] [stdout] | this lifetime flows to the output [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(mismatched_lifetime_syntaxes)]` on by default [INFO] [stdout] help: one option is to remove the lifetime for references and use the anonymous lifetime for 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 11m 02s [INFO] running `Command { std: "docker" "inspect" "162aa6e6f7564f08d43721999dbc78d8753da08afaebb22ee05681f1c14acffd", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "162aa6e6f7564f08d43721999dbc78d8753da08afaebb22ee05681f1c14acffd", kill_on_drop: false }` [INFO] [stdout] 162aa6e6f7564f08d43721999dbc78d8753da08afaebb22ee05681f1c14acffd [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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=forbid -Copt-level=3" "-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" "+733b47ea4b1b86216f14ef56e49440c33933f230" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 0e4e562508b1e3e4abc1b74d3cc7878b27c49be43f95258769b3188d68da257d [INFO] running `Command { std: "docker" "start" "-a" "0e4e562508b1e3e4abc1b74d3cc7878b27c49be43f95258769b3188d68da257d", kill_on_drop: false }` [INFO] [stderr] Compiling once_cell v1.20.2 [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-build-config v0.20.3 [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: 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: lifetime flowing from input to output with different syntax can be confusing [INFO] [stdout] --> src/count_reads/chunked_genome.rs:45:17 [INFO] [stdout] | [INFO] [stdout] 45 | pub fn iter(&self) -> ChunkedGenomeIterator { [INFO] [stdout] | ^^^^^ --------------------- the lifetime gets resolved as `'_` [INFO] [stdout] | | [INFO] [stdout] | this lifetime flows to the output [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(mismatched_lifetime_syntaxes)]` on by default [INFO] [stdout] help: one option is to remove the lifetime for references and use the anonymous lifetime for 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 1m 10s [INFO] running `Command { std: "docker" "inspect" "0e4e562508b1e3e4abc1b74d3cc7878b27c49be43f95258769b3188d68da257d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "0e4e562508b1e3e4abc1b74d3cc7878b27c49be43f95258769b3188d68da257d", kill_on_drop: false }` [INFO] [stdout] 0e4e562508b1e3e4abc1b74d3cc7878b27c49be43f95258769b3188d68da257d [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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=forbid -Copt-level=3" "-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" "+733b47ea4b1b86216f14ef56e49440c33933f230" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] 73b2a838c49119796ca957954b893a440fdd36b304ef55b8b7073207fa8b1de0 [INFO] running `Command { std: "docker" "start" "-a" "73b2a838c49119796ca957954b893a440fdd36b304ef55b8b7073207fa8b1de0", kill_on_drop: false }` [INFO] [stdout] [INFO] [stdout] running 6 tests [INFO] [stdout] test bam_ext::tests::test_introns ... ok [INFO] [stdout] test bam_ext::tests::spliced_reads ... ok [INFO] [stdout] test bam_manipulation::tests::test_filter_and_rename ... ok [INFO] [stderr] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stderr] --> src/lib.rs:20:17 [INFO] [stderr] | [INFO] [stderr] 20 | #[derive(Debug, Fail, Clone)] [INFO] [stderr] | ^--- [INFO] [stderr] | | [INFO] [stderr] | `Fail` is not local [INFO] [stderr] | move the `impl` block outside of this constant `_DERIVE_failure_Fail_FOR_BamError` [INFO] [stderr] 21 | pub enum BamError { [INFO] [stderr] | -------- `BamError` is not local [INFO] [stderr] | [INFO] [stderr] = note: the derive macro `Fail` defines the non-local `impl`, and may need to be changed [INFO] [stderr] = 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] [stderr] = 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] [stderr] = 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] [stderr] = note: `#[warn(non_local_definitions)]` on by default [INFO] [stderr] = note: this warning originates in the derive macro `Fail` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stderr] [INFO] [stderr] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stderr] --> src/lib.rs:20:17 [INFO] [stderr] | [INFO] [stderr] 20 | #[derive(Debug, Fail, Clone)] [INFO] [stderr] | ^--- [INFO] [stderr] | | [INFO] [stderr] | `Display` is not local [INFO] [stderr] | move the `impl` block outside of this constant `_DERIVE_failure_core_fmt_Display_FOR_BamError` [INFO] [stderr] 21 | pub enum BamError { [INFO] [stderr] | -------- `BamError` is not local [INFO] [stderr] | [INFO] [stderr] = note: the derive macro `Fail` defines the non-local `impl`, and may need to be changed [INFO] [stderr] = 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] [stderr] = 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] [stderr] = 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] [stderr] = note: this warning originates in the derive macro `Fail` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stderr] [INFO] [stderr] warning: lifetime flowing from input to output with different syntax can be confusing [INFO] [stderr] --> src/count_reads/chunked_genome.rs:45:17 [INFO] [stderr] | [INFO] [stderr] 45 | pub fn iter(&self) -> ChunkedGenomeIterator { [INFO] [stderr] | ^^^^^ --------------------- the lifetime gets resolved as `'_` [INFO] [stderr] | | [INFO] [stderr] | this lifetime flows to the output [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(mismatched_lifetime_syntaxes)]` on by default [INFO] [stderr] help: one option is to remove the lifetime for references and use the anonymous lifetime for paths [INFO] [stderr] | [INFO] [stderr] 45 | pub fn iter(&self) -> ChunkedGenomeIterator<'_> { [INFO] [stderr] | ++++ [INFO] [stderr] [INFO] [stderr] warning: `mbf_bam` (lib test) generated 3 warnings [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.17s [INFO] [stderr] Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/mbf_bam-0169cb99273afaca) [INFO] [stderr] [E::hts_open_format] Failed to open file "test.bam" : Read-only file system [INFO] [stdout] test bam_manipulation::tests::test_filter_and_rename_none ... ok [INFO] [stdout] test bam_manipulation::tests::test_filter_and_rename_noop ... ok [INFO] [stdout] test bam_manipulation::tests::test_filter_and_rename2 ... FAILED [INFO] [stdout] [INFO] [stdout] failures: [INFO] [stdout] [INFO] [stdout] ---- bam_manipulation::tests::test_filter_and_rename2 stdout ---- [INFO] [stdout] [src/bam_manipulation.rs:172:5] &new_header.clone().to_hashmap() = { [INFO] [stdout] "HD": [ [INFO] [stdout] { [INFO] [stdout] "VN": "1.0", [INFO] [stdout] }, [INFO] [stdout] ], [INFO] [stdout] "PG": [ [INFO] [stdout] { [INFO] [stdout] "ID": "P1", [INFO] [stdout] "VN": "1.0", [INFO] [stdout] }, [INFO] [stdout] { [INFO] [stdout] "ID": "P2", [INFO] [stdout] "VN": "1.1", [INFO] [stdout] }, [INFO] [stdout] { [INFO] [stdout] "ID": "mbf_bam.filter_and_rename_references", [INFO] [stdout] }, [INFO] [stdout] ], [INFO] [stdout] "SQ": [ [INFO] [stdout] { [INFO] [stdout] "SN": "2", [INFO] [stdout] "LN": "1584", [INFO] [stdout] }, [INFO] [stdout] ], [INFO] [stdout] "RG": [ [INFO] [stdout] { [INFO] [stdout] "ID": "L1", [INFO] [stdout] "PU": "SC_1_10", [INFO] [stdout] "LB": "SC_1", [INFO] [stdout] "SM": "NA12891", [INFO] [stdout] "CN": "name:with:colon", [INFO] [stdout] }, [INFO] [stdout] { [INFO] [stdout] "ID": "L2", [INFO] [stdout] "PU": "SC_2_12", [INFO] [stdout] "LB": "SC_2", [INFO] [stdout] "SM": "NA12891", [INFO] [stdout] "CN": "name:with:colon", [INFO] [stdout] }, [INFO] [stdout] ], [INFO] [stdout] } [INFO] [stdout] [INFO] [stdout] thread 'bam_manipulation::tests::test_filter_and_rename2' panicked at src/bam_manipulation.rs:338:92: [INFO] [stdout] called `Result::unwrap()` on an `Err` value: UnknownError { msg: "BamOpen { target: \"test.bam\" }" } [INFO] [stdout] stack backtrace: [INFO] [stdout] 0: 0x56867dfea122 - std::backtrace_rs::backtrace::libunwind::trace::h73a647620bf1c49d [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/../../backtrace/src/backtrace/libunwind.rs:117:9 [INFO] [stdout] 1: 0x56867dfea122 - std::backtrace_rs::backtrace::trace_unsynchronized::hd4d513ed96cb3cb1 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/../../backtrace/src/backtrace/mod.rs:66:14 [INFO] [stdout] 2: 0x56867dfea122 - std::sys::backtrace::_print_fmt::h61bb95f7476aafa5 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/sys/backtrace.rs:66:9 [INFO] [stdout] 3: 0x56867dfea122 - ::fmt::ha2e7e3a01df69042 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/sys/backtrace.rs:39:26 [INFO] [stdout] 4: 0x56867e010623 - core::fmt::rt::Argument::fmt::hf14163372f0f9a76 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/core/src/fmt/rt.rs:173:76 [INFO] [stdout] 5: 0x56867e010623 - core::fmt::write::h7cb8f63788cd01d2 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/core/src/fmt/mod.rs:1465:25 [INFO] [stdout] 6: 0x56867dfe6e63 - std::io::default_write_fmt::h9ed739ccee8a150c [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/io/mod.rs:639:11 [INFO] [stdout] 7: 0x56867dfe6e63 - std::io::Write::write_fmt::h1c0a32da913b32f1 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/io/mod.rs:1954:13 [INFO] [stdout] 8: 0x56867dfe9f72 - std::sys::backtrace::BacktraceLock::print::h3ec4d7883eb25e61 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/sys/backtrace.rs:42:9 [INFO] [stdout] 9: 0x56867dfeb73c - std::panicking::default_hook::{{closure}}::h29548987efd832cb [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/panicking.rs:300:27 [INFO] [stdout] 10: 0x56867dfeb592 - std::panicking::default_hook::ha25170a15c643514 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/panicking.rs:324:9 [INFO] [stdout] 11: 0x56867da65514 - as core::ops::function::Fn>::call::h562adeecbf43c420 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/alloc/src/boxed.rs:1985:9 [INFO] [stdout] 12: 0x56867da65514 - test::test_main_with_exit_callback::{{closure}}::h97dd2a879d27e0e4 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/test/src/lib.rs:145:21 [INFO] [stdout] 13: 0x56867dfec21b - as core::ops::function::Fn>::call::h7e85cbdbda26fdb7 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/alloc/src/boxed.rs:1985:9 [INFO] [stdout] 14: 0x56867dfec21b - std::panicking::rust_panic_with_hook::h0d81afcd829aa24b [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/panicking.rs:841:13 [INFO] [stdout] 15: 0x56867dfebeea - std::panicking::begin_panic_handler::{{closure}}::hc84a33f1202346cf [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/panicking.rs:706:13 [INFO] [stdout] 16: 0x56867dfea619 - std::sys::backtrace::__rust_end_short_backtrace::h373067a14f6c59aa [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/sys/backtrace.rs:168:18 [INFO] [stdout] 17: 0x56867dfebb7d - __rustc[beb0385846a06d21]::rust_begin_unwind [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/panicking.rs:697:5 [INFO] [stdout] 18: 0x56867e00ee60 - core::panicking::panic_fmt::ha33fa2ae772efba9 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/core/src/panicking.rs:75:14 [INFO] [stdout] 19: 0x56867e00f206 - core::result::unwrap_failed::hfbbd3c78a73fea3d [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/core/src/result.rs:1761:5 [INFO] [stdout] 20: 0x56867da297e8 - core::result::Result::unwrap::h2dbdbcd6ccf4b4dc [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/core/src/result.rs:1167:23 [INFO] [stdout] 21: 0x56867da297e8 - mbf_bam::bam_manipulation::tests::test_filter_and_rename2::hc7dbddacf390d179 [INFO] [stdout] at /opt/rustwide/workdir/src/bam_manipulation.rs:338:92 [INFO] [stdout] 22: 0x56867da25529 - mbf_bam::bam_manipulation::tests::test_filter_and_rename2::{{closure}}::h3159e6972f3b00c0 [INFO] [stdout] at /opt/rustwide/workdir/src/bam_manipulation.rs:324:33 [INFO] [stdout] 23: 0x56867da25529 - core::ops::function::FnOnce::call_once::h18fa803ea55179c1 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 24: 0x56867da6ac4b - core::ops::function::FnOnce::call_once::hf84b9c3d864a6959 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 25: 0x56867da6ac4b - test::__rust_begin_short_backtrace::h5724e31441c16fcb [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/test/src/lib.rs:648:18 [INFO] [stdout] 26: 0x56867da69e8e - test::run_test_in_process::{{closure}}::hbc28c9aa91793d7d [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/test/src/lib.rs:671:74 [INFO] [stdout] 27: 0x56867da69e8e - as core::ops::function::FnOnce<()>>::call_once::hc17b0e238c0f8f3e [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/core/src/panic/unwind_safe.rs:272:9 [INFO] [stdout] 28: 0x56867da69e8e - std::panicking::catch_unwind::do_call::hcdbce0d6dd6c83ce [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/panicking.rs:589:40 [INFO] [stdout] 29: 0x56867da69e8e - std::panicking::catch_unwind::h9477967ceea044e8 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/panicking.rs:552:19 [INFO] [stdout] 30: 0x56867da69e8e - std::panic::catch_unwind::h616a2e249da12e16 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/panic.rs:359:14 [INFO] [stdout] 31: 0x56867da69e8e - test::run_test_in_process::h2758deb0f2e54430 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/test/src/lib.rs:671:27 [INFO] [stdout] 32: 0x56867da69e8e - test::run_test::{{closure}}::habe5cd2564b18aaa [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/test/src/lib.rs:592:43 [INFO] [stdout] 33: 0x56867da2da34 - test::run_test::{{closure}}::h9a0a6928f1a15421 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/test/src/lib.rs:622:41 [INFO] [stdout] 34: 0x56867da2da34 - std::sys::backtrace::__rust_begin_short_backtrace::hd68b5332434a22ca [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/sys/backtrace.rs:152:18 [INFO] [stdout] 35: 0x56867da313da - std::thread::Builder::spawn_unchecked_::{{closure}}::{{closure}}::h264ddcc3098eacae [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/thread/mod.rs:559:17 [INFO] [stdout] 36: 0x56867da313da - as core::ops::function::FnOnce<()>>::call_once::h9fa39489749d6f3c [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/core/src/panic/unwind_safe.rs:272:9 [INFO] [stdout] 37: 0x56867da313da - std::panicking::catch_unwind::do_call::hb9a1944b9f85100f [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/panicking.rs:589:40 [INFO] [stdout] 38: 0x56867da313da - std::panicking::catch_unwind::h0c6f100786c0dad8 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/panicking.rs:552:19 [INFO] [stdout] 39: 0x56867da313da - std::panic::catch_unwind::hf6084e2723385823 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/panic.rs:359:14 [INFO] [stdout] 40: 0x56867da313da - std::thread::Builder::spawn_unchecked_::{{closure}}::hf0af58ce658143ad [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/thread/mod.rs:557:30 [INFO] [stdout] 41: 0x56867da313da - core::ops::function::FnOnce::call_once{{vtable.shim}}::h88a14f9b2e79f9de [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/core/src/ops/function.rs:250:5 [INFO] [stdout] 42: 0x56867dfef207 - as core::ops::function::FnOnce>::call_once::hf31256ba38644b65 [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/alloc/src/boxed.rs:1971:9 [INFO] [stdout] 43: 0x56867dfef207 - as core::ops::function::FnOnce>::call_once::h100ad77f3448041b [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/alloc/src/boxed.rs:1971:9 [INFO] [stdout] 44: 0x56867dfef207 - std::sys::pal::unix::thread::Thread::new::thread_start::h1a22ded422ce395b [INFO] [stdout] at /rustc/733b47ea4b1b86216f14ef56e49440c33933f230/library/std/src/sys/pal/unix/thread.rs:97:17 [INFO] [stdout] 45: 0x7a4b1ba1aaa4 - [INFO] [stdout] 46: 0x7a4b1baa7a34 - clone [INFO] [stdout] 47: 0x0 - [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] failures: [INFO] [stdout] bam_manipulation::tests::test_filter_and_rename2 [INFO] [stdout] [INFO] [stdout] test result: FAILED. 5 passed; 1 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.22s [INFO] [stdout] [INFO] [stderr] error: test failed, to rerun pass `--lib` [INFO] running `Command { std: "docker" "inspect" "73b2a838c49119796ca957954b893a440fdd36b304ef55b8b7073207fa8b1de0", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "73b2a838c49119796ca957954b893a440fdd36b304ef55b8b7073207fa8b1de0", kill_on_drop: false }` [INFO] [stdout] 73b2a838c49119796ca957954b893a440fdd36b304ef55b8b7073207fa8b1de0