[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] e6b45525494fed999d3e0b7f4f49b73603d1ab60
[INFO] checking IMTMarburg/mbf_bam against master#385fa9d845dd326c6bbfd58c22244215e431948a for absurd-question-mark-desugar
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FIMTMarburg%2Fmbf_bam" "/workspace/builds/worker-5-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-5-tc1/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/IMTMarburg/mbf_bam on toolchain 385fa9d845dd326c6bbfd58c22244215e431948a
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+385fa9d845dd326c6bbfd58c22244215e431948a" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[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-5-tc1/source/Cargo.toml
[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" "+385fa9d845dd326c6bbfd58c22244215e431948a" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded smallvec v0.6.9
[INFO] [stderr]   Downloaded thiserror-impl v1.0.21
[INFO] [stderr]   Downloaded thiserror v1.0.21
[INFO] [stderr]   Downloaded rustc_version v0.1.7
[INFO] [stderr]   Downloaded newtype_derive v0.1.6
[INFO] [stderr]   Downloaded url v2.1.1
[INFO] [stderr]   Downloaded serde_derive v1.0.90
[INFO] [stderr]   Downloaded bit-vec v0.5.1
[INFO] [stderr]   Downloaded either v1.5.2
[INFO] [stderr]   Downloaded syn v2.0.53
[INFO] [stderr]   Downloaded backtrace-sys v0.1.28
[INFO] [stderr]   Downloaded lzma-sys v0.1.17
[INFO] [stderr]   Downloaded crossbeam-deque v0.8.0
[INFO] [stderr]   Downloaded bio-types v1.0.1
[INFO] [stderr]   Downloaded fs-utils v1.1.0
[INFO] [stderr]   Downloaded ieee754 v0.2.6
[INFO] [stderr]   Downloaded bit-set v0.5.1
[INFO] [stderr]   Downloaded array-macro v1.0.5
[INFO] [stderr]   Downloaded enum-map-derive v0.4.6
[INFO] [stderr]   Downloaded enum-map v0.6.4
[INFO] [stderr]   Downloaded itertools-num v0.1.3
[INFO] [stderr]   Downloaded rand_distr v0.4.1
[INFO] [stderr]   Downloaded statrs v0.14.0
[INFO] [stderr]   Downloaded triple_accel v0.3.4
[INFO] [stderr]   Downloaded serde v1.0.90
[INFO] [stderr]   Downloaded bio v0.37.1
[INFO] [stderr]   Downloaded ex v0.1.3
[INFO] [stderr]   Downloaded backtrace v0.3.15
[INFO] [stderr]   Downloaded libz-sys v1.1.15
[INFO] [stderr]   Downloaded quote v0.6.12
[INFO] [stderr]   Downloaded syn v0.15.30
[INFO] [stderr]   Downloaded synstructure v0.10.1
[INFO] [stderr]   Downloaded adler32 v1.0.4
[INFO] [stderr]   Downloaded miniz_oxide v0.3.5
[INFO] [stderr]   Downloaded hts-sys v2.1.1
[INFO] [stderr]   Downloaded flate2 v1.0.13
[INFO] [stderr]   Downloaded openssl-src v111.12.0+1.1.1h
[INFO] [stderr]   Downloaded lock_api v0.4.1
[INFO] [stderr]   Downloaded derive-new v0.5.8
[INFO] [stderr]   Downloaded quick-error v1.2.2
[INFO] [stderr]   Downloaded openssl-sys v0.9.65
[INFO] [stderr]   Downloaded semver v0.1.20
[INFO] [stderr]   Downloaded rustc-demangle v0.1.13
[INFO] [stderr]   Downloaded unicode-normalization v0.1.8
[INFO] [stderr]   Downloaded rust-htslib v0.46.0
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+385fa9d845dd326c6bbfd58c22244215e431948a" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 7f52b1408b74a68d6920fd44912ae104dc365e44e366130acae25d8e0a44d356
[INFO] running `Command { std: "docker" "start" "-a" "7f52b1408b74a68d6920fd44912ae104dc365e44e366130acae25d8e0a44d356", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "7f52b1408b74a68d6920fd44912ae104dc365e44e366130acae25d8e0a44d356", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "7f52b1408b74a68d6920fd44912ae104dc365e44e366130acae25d8e0a44d356", kill_on_drop: false }`
[INFO] [stdout] 7f52b1408b74a68d6920fd44912ae104dc365e44e366130acae25d8e0a44d356
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+385fa9d845dd326c6bbfd58c22244215e431948a" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 3f4d9fc410e3d1e3d632dfc06190ad0e173333b6397ec2ad891360eaadb51c21
[INFO] running `Command { std: "docker" "start" "-a" "3f4d9fc410e3d1e3d632dfc06190ad0e173333b6397ec2ad891360eaadb51c21", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.153
[INFO] [stderr]    Compiling proc-macro2 v1.0.79
[INFO] [stderr]    Compiling pkg-config v0.3.14
[INFO] [stderr]    Compiling libm v0.2.1
[INFO] [stderr]    Compiling num-traits v0.2.14
[INFO] [stderr]    Compiling proc-macro2 v0.4.27
[INFO] [stderr]    Compiling unicode-xid v0.1.0
[INFO] [stderr]    Compiling target-lexicon v0.12.14
[INFO] [stderr]    Compiling syn v0.15.30
[INFO] [stderr]    Compiling syn v1.0.73
[INFO] [stderr]    Compiling unicode-xid v0.2.0
[INFO] [stderr]     Checking memchr v2.7.2
[INFO] [stderr]    Compiling quote v0.6.12
[INFO] [stderr]    Compiling pyo3-build-config v0.20.3
[INFO] [stderr]    Compiling quote v1.0.35
[INFO] [stderr]     Checking cfg-if v0.1.10
[INFO] [stderr]    Compiling vcpkg v0.2.15
[INFO] [stderr]    Compiling serde v1.0.90
[INFO] [stderr]    Compiling num-integer v0.1.44
[INFO] [stderr]    Compiling matrixmultiply v0.3.8
[INFO] [stderr]     Checking ppv-lite86 v0.2.10
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]     Checking getrandom v0.2.3
[INFO] [stderr]    Compiling jobserver v0.1.28
[INFO] [stderr]     Checking rand_core v0.6.3
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling cc v1.0.90
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]     Checking aho-corasick v1.1.3
[INFO] [stderr]    Compiling num-rational v0.3.2
[INFO] [stderr]    Compiling typenum v1.13.0
[INFO] [stderr]    Compiling byteorder v1.3.1
[INFO] [stderr]     Checking rawpointer v0.2.1
[INFO] [stderr]    Compiling unicode-segmentation v1.8.0
[INFO] [stderr]    Compiling crossbeam-epoch v0.9.5
[INFO] [stderr]     Checking regex-syntax v0.8.3
[INFO] [stderr]    Compiling quick-error v1.2.2
[INFO] [stderr]    Compiling cmake v0.1.50
[INFO] [stderr]    Compiling openssl-src v111.12.0+1.1.1h
[INFO] [stderr]    Compiling fs-utils v1.1.0
[INFO] [stderr]    Compiling heck v0.3.3
[INFO] [stderr]    Compiling pyo3-ffi v0.20.3
[INFO] [stderr]     Checking rand v0.8.4
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking approx v0.4.0
[INFO] [stderr]     Checking num-complex v0.3.1
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]    Compiling rayon-core v1.9.1
[INFO] [stderr]    Compiling paste v1.0.5
[INFO] [stderr]    Compiling glob v0.3.0
[INFO] [stderr]    Compiling libz-sys v1.1.15
[INFO] [stderr]    Compiling openssl-sys v0.9.65
[INFO] [stderr]    Compiling curl-sys v0.4.72+curl-8.6.0
[INFO] [stderr]    Compiling bzip2-sys v0.1.9+1.0.8
[INFO] [stderr]    Compiling serde_derive v1.0.90
[INFO] [stderr]    Compiling lzma-sys v0.1.17
[INFO] [stderr]    Compiling backtrace-sys v0.1.28
[INFO] [stderr]     Checking regex-automata v0.4.6
[INFO] [stderr]    Compiling thiserror-impl v1.0.21
[INFO] [stderr]     Checking matches v0.1.8
[INFO] [stderr]    Compiling feature-probe v0.1.1
[INFO] [stderr]    Compiling autocfg v0.1.2
[INFO] [stderr]     Checking smallvec v0.6.9
[INFO] [stderr]    Compiling backtrace v0.3.15
[INFO] [stderr]     Checking unicode-normalization v0.1.8
[INFO] [stderr]    Compiling bv v0.11.1
[INFO] [stderr]     Checking unicode-bidi v0.3.4
[INFO] [stderr]    Compiling derive-new v0.5.8
[INFO] [stderr]     Checking thiserror v1.0.21
[INFO] [stderr]    Compiling strum_macros v0.20.1
[INFO] [stderr]     Checking simba v0.4.0
[INFO] [stderr]     Checking regex v1.10.4
[INFO] [stderr]    Compiling hts-sys v2.1.1
[INFO] [stderr]     Checking rand_distr v0.4.1
[INFO] [stderr]     Checking instant v0.1.7
[INFO] [stderr]    Compiling syn v2.0.53
[INFO] [stderr]    Compiling memoffset v0.9.0
[INFO] [stderr]     Checking either v1.5.2
[INFO] [stderr]    Compiling crc32fast v1.2.0
[INFO] [stderr]    Compiling anyhow v1.0.42
[INFO] [stderr]    Compiling failure_derive v0.1.5
[INFO] [stderr]     Checking smallvec v1.4.2
[INFO] [stderr]    Compiling portable-atomic v1.6.0
[INFO] [stderr]     Checking regex-automata v0.1.10
[INFO] [stderr]     Checking parking_lot_core v0.8.0
[INFO] [stderr]     Checking bio-types v1.0.1
[INFO] [stderr]     Checking crossbeam-deque v0.8.0
[INFO] [stderr]     Checking idna v0.2.0
[INFO] [stderr]    Compiling enum-map-derive v0.4.6
[INFO] [stderr]    Compiling synstructure v0.10.1
[INFO] [stderr]    Compiling pyo3 v0.20.3
[INFO] [stderr]     Checking crossbeam-channel v0.5.1
[INFO] [stderr]     Checking num_cpus v1.10.0
[INFO] [stderr]     Checking num-complex v0.4.5
[INFO] [stderr]     Checking lock_api v0.4.1
[INFO] [stderr]     Checking csv-core v0.1.10
[INFO] [stderr]    Compiling rayon v1.5.1
[INFO] [stderr]     Checking fixedbitset v0.2.0
[INFO] [stderr]    Compiling rustix v0.38.32
[INFO] [stderr]     Checking rustc-demangle v0.1.13
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]    Compiling bio v0.37.1
[INFO] [stderr]     Checking bit-vec v0.5.1
[INFO] [stderr]     Checking itoa v0.4.3
[INFO] [stderr]     Checking adler32 v1.0.4
[INFO] [stderr]     Checking array-macro v1.0.5
[INFO] [stderr]     Checking enum-map v0.6.4
[INFO] [stderr]     Checking miniz_oxide v0.3.5
[INFO] [stderr]     Checking bit-set v0.5.1
[INFO] [stderr]     Checking url v2.1.1
[INFO] [stderr]     Checking petgraph v0.5.1
[INFO] [stderr]     Checking ndarray v0.15.6
[INFO] [stderr]     Checking parking_lot v0.11.0
[INFO] [stderr]    Compiling getset v0.1.2
[INFO] [stderr]     Checking bstr v0.2.15
[INFO] [stderr]    Compiling pyo3-macros-backend v0.20.3
[INFO] [stderr]     Checking csv v1.1.6
[INFO] [stderr]     Checking vec_map v0.8.1
[INFO] [stderr]     Checking multimap v0.8.3
[INFO] [stderr]     Checking nalgebra v0.26.2
[INFO] [stderr]     Checking itertools v0.9.0
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking ordered-float v1.1.1
[INFO] [stderr]     Checking unindent v0.2.3
[INFO] [stderr]     Checking strum v0.20.0
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking bitflags v2.5.0
[INFO] [stderr]     Checking linux-raw-sys v0.4.13
[INFO] [stderr]     Checking triple_accel v0.3.4
[INFO] [stderr]     Checking bytecount v0.6.2
[INFO] [stderr]    Compiling indoc v2.0.4
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]     Checking ex v0.1.3
[INFO] [stderr]     Checking flate2 v1.0.13
[INFO] [stderr]     Checking failure v0.1.5
[INFO] [stderr]     Checking fastrand v2.0.1
[INFO] [stderr]    Compiling pyo3-macros v0.20.3
[INFO] [stderr]     Checking tempfile v3.10.1
[INFO] [stderr]     Checking statrs v0.14.0
[INFO] [stderr]     Checking rust-htslib v0.46.0
[INFO] [stderr]     Checking mbf_bam v0.5.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: the item `PyErr` is imported redundantly
[INFO] [stdout]   --> src/lib.rs:11:24
[INFO] [stdout]    |
[INFO] [stdout] 8  | use pyo3::prelude::*;
[INFO] [stdout]    |     ---------------- the item `PyErr` is already imported here
[INFO] [stdout] ...
[INFO] [stdout] 11 | use pyo3::{exceptions, PyErr, PyResult};
[INFO] [stdout]    |                        ^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: the item `PyResult` is imported redundantly
[INFO] [stdout]   --> src/lib.rs:11:31
[INFO] [stdout]    |
[INFO] [stdout] 8  | use pyo3::prelude::*;
[INFO] [stdout]    |     ---------------- the item `PyResult` is already imported here
[INFO] [stdout] ...
[INFO] [stdout] 11 | use pyo3::{exceptions, PyErr, PyResult};
[INFO] [stdout]    |                               ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: the item `PyAny` is imported redundantly
[INFO] [stdout]   --> src/count_reads/mod.rs:15:19
[INFO] [stdout]    |
[INFO] [stdout] 14 | use pyo3::prelude::*;
[INFO] [stdout]    |     ---------------- the item `PyAny` is already imported here
[INFO] [stdout] 15 | use pyo3::types::{PyAny, PyList, PyTuple};
[INFO] [stdout]    |                   ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: the item `PyErr` is imported redundantly
[INFO] [stdout]   --> src/lib.rs:11:24
[INFO] [stdout]    |
[INFO] [stdout] 8  | use pyo3::prelude::*;
[INFO] [stdout]    |     ---------------- the item `PyErr` is already imported here
[INFO] [stdout] ...
[INFO] [stdout] 11 | use pyo3::{exceptions, PyErr, PyResult};
[INFO] [stdout]    |                        ^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: the item `PyResult` is imported redundantly
[INFO] [stdout]   --> src/lib.rs:11:31
[INFO] [stdout]    |
[INFO] [stdout] 8  | use pyo3::prelude::*;
[INFO] [stdout]    |     ---------------- the item `PyResult` is already imported here
[INFO] [stdout] ...
[INFO] [stdout] 11 | use pyo3::{exceptions, PyErr, PyResult};
[INFO] [stdout]    |                               ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: the item `PyAny` is imported redundantly
[INFO] [stdout]   --> src/count_reads/mod.rs:15:19
[INFO] [stdout]    |
[INFO] [stdout] 14 | use pyo3::prelude::*;
[INFO] [stdout]    |     ---------------- the item `PyAny` is already imported here
[INFO] [stdout] 15 | use pyo3::types::{PyAny, PyList, PyTuple};
[INFO] [stdout]    |                   ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 3 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 3 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 3m 54s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nalgebra v0.26.2
[INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 2`
[INFO] running `Command { std: "docker" "inspect" "3f4d9fc410e3d1e3d632dfc06190ad0e173333b6397ec2ad891360eaadb51c21", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "3f4d9fc410e3d1e3d632dfc06190ad0e173333b6397ec2ad891360eaadb51c21", kill_on_drop: false }`
[INFO] [stdout] 3f4d9fc410e3d1e3d632dfc06190ad0e173333b6397ec2ad891360eaadb51c21
[INFO] checking IMTMarburg/mbf_bam against try#645bb72776a6a56a1a8f52631a44bd082b2ba509 for absurd-question-mark-desugar
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FIMTMarburg%2Fmbf_bam" "/workspace/builds/worker-5-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-5-tc2/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/IMTMarburg/mbf_bam on toolchain 645bb72776a6a56a1a8f52631a44bd082b2ba509
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+645bb72776a6a56a1a8f52631a44bd082b2ba509" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[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-5-tc2/source/Cargo.toml
[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" "+645bb72776a6a56a1a8f52631a44bd082b2ba509" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+645bb72776a6a56a1a8f52631a44bd082b2ba509" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 17f80d1e21974344dc35f29f35c95c1db5042056a9908896b843b0297fe86bcd
[INFO] running `Command { std: "docker" "start" "-a" "17f80d1e21974344dc35f29f35c95c1db5042056a9908896b843b0297fe86bcd", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "17f80d1e21974344dc35f29f35c95c1db5042056a9908896b843b0297fe86bcd", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "17f80d1e21974344dc35f29f35c95c1db5042056a9908896b843b0297fe86bcd", kill_on_drop: false }`
[INFO] [stdout] 17f80d1e21974344dc35f29f35c95c1db5042056a9908896b843b0297fe86bcd
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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" "-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+645bb72776a6a56a1a8f52631a44bd082b2ba509" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 319b1e446017f3eca823508aaa176fc9f84edfdd386294d206801d8c143b4383
[INFO] running `Command { std: "docker" "start" "-a" "319b1e446017f3eca823508aaa176fc9f84edfdd386294d206801d8c143b4383", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.153
[INFO] [stderr]    Compiling proc-macro2 v1.0.79
[INFO] [stderr]    Compiling pkg-config v0.3.14
[INFO] [stderr]    Compiling libm v0.2.1
[INFO] [stderr]    Compiling num-traits v0.2.14
[INFO] [stderr]    Compiling proc-macro2 v0.4.27
[INFO] [stderr]    Compiling unicode-xid v0.1.0
[INFO] [stderr]    Compiling syn v0.15.30
[INFO] [stderr]    Compiling syn v1.0.73
[INFO] [stderr]    Compiling target-lexicon v0.12.14
[INFO] [stderr]    Compiling unicode-xid v0.2.0
[INFO] [stderr]    Compiling once_cell v1.8.0
[INFO] [stderr]     Checking memchr v2.7.2
[INFO] [stderr]    Compiling serde v1.0.90
[INFO] [stderr]    Compiling quote v0.6.12
[INFO] [stderr]    Compiling quote v1.0.35
[INFO] [stderr]    Compiling pyo3-build-config v0.20.3
[INFO] [stderr]    Compiling vcpkg v0.2.15
[INFO] [stderr]     Checking cfg-if v0.1.10
[INFO] [stderr]    Compiling num-integer v0.1.44
[INFO] [stderr]     Checking scopeguard v1.1.0
[INFO] [stderr]    Compiling crossbeam-utils v0.8.5
[INFO] [stderr]    Compiling matrixmultiply v0.3.8
[INFO] [stderr]    Compiling memoffset v0.6.4
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]     Checking ppv-lite86 v0.2.10
[INFO] [stderr]     Checking getrandom v0.2.3
[INFO] [stderr]     Checking rand_core v0.6.3
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]    Compiling jobserver v0.1.28
[INFO] [stderr]     Checking aho-corasick v1.1.3
[INFO] [stderr]    Compiling num-rational v0.3.2
[INFO] [stderr]    Compiling unicode-segmentation v1.8.0
[INFO] [stderr]    Compiling typenum v1.13.0
[INFO] [stderr]    Compiling cc v1.0.90
[INFO] [stderr]    Compiling crossbeam-epoch v0.9.5
[INFO] [stderr]    Compiling byteorder v1.3.1
[INFO] [stderr]    Compiling quick-error v1.2.2
[INFO] [stderr]     Checking rawpointer v0.2.1
[INFO] [stderr]     Checking regex-syntax v0.8.3
[INFO] [stderr]    Compiling fs-utils v1.1.0
[INFO] [stderr]    Compiling openssl-src v111.12.0+1.1.1h
[INFO] [stderr]    Compiling cmake v0.1.50
[INFO] [stderr]    Compiling heck v0.3.3
[INFO] [stderr]    Compiling pyo3-ffi v0.20.3
[INFO] [stderr]     Checking rand v0.8.4
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]     Checking num-complex v0.3.1
[INFO] [stderr]     Checking approx v0.4.0
[INFO] [stderr]    Compiling indexmap v1.7.0
[INFO] [stderr]    Compiling autocfg v0.1.2
[INFO] [stderr]    Compiling openssl-sys v0.9.65
[INFO] [stderr]    Compiling libz-sys v1.1.15
[INFO] [stderr]    Compiling bzip2-sys v0.1.9+1.0.8
[INFO] [stderr]    Compiling curl-sys v0.4.72+curl-8.6.0
[INFO] [stderr]    Compiling lzma-sys v0.1.17
[INFO] [stderr]    Compiling serde_derive v1.0.90
[INFO] [stderr]    Compiling backtrace-sys v0.1.28
[INFO] [stderr]    Compiling thiserror-impl v1.0.21
[INFO] [stderr]     Checking regex-automata v0.4.6
[INFO] [stderr]     Checking matches v0.1.8
[INFO] [stderr]    Compiling ryu v1.0.5
[INFO] [stderr]    Compiling feature-probe v0.1.1
[INFO] [stderr]     Checking smallvec v0.6.9
[INFO] [stderr]    Compiling rayon-core v1.9.1
[INFO] [stderr]    Compiling glob v0.3.0
[INFO] [stderr]    Compiling paste v1.0.5
[INFO] [stderr]    Compiling hts-sys v2.1.1
[INFO] [stderr]     Checking thiserror v1.0.21
[INFO] [stderr]     Checking simba v0.4.0
[INFO] [stderr]     Checking unicode-normalization v0.1.8
[INFO] [stderr]    Compiling bv v0.11.1
[INFO] [stderr]     Checking unicode-bidi v0.3.4
[INFO] [stderr]    Compiling derive-new v0.5.8
[INFO] [stderr]    Compiling strum_macros v0.20.1
[INFO] [stderr]    Compiling backtrace v0.3.15
[INFO] [stderr]     Checking regex v1.10.4
[INFO] [stderr]     Checking rand_distr v0.4.1
[INFO] [stderr]     Checking instant v0.1.7
[INFO] [stderr]    Compiling syn v2.0.53
[INFO] [stderr]    Compiling memoffset v0.9.0
[INFO] [stderr]    Compiling crc32fast v1.2.0
[INFO] [stderr]     Checking smallvec v1.4.2
[INFO] [stderr]     Checking either v1.5.2
[INFO] [stderr]     Checking regex-automata v0.1.10
[INFO] [stderr]    Compiling anyhow v1.0.42
[INFO] [stderr]    Compiling portable-atomic v1.6.0
[INFO] [stderr]     Checking hashbrown v0.11.2
[INFO] [stderr]    Compiling failure_derive v0.1.5
[INFO] [stderr]     Checking bio-types v1.0.1
[INFO] [stderr]     Checking parking_lot_core v0.8.0
[INFO] [stderr]     Checking crossbeam-deque v0.8.0
[INFO] [stderr]     Checking idna v0.2.0
[INFO] [stderr]    Compiling enum-map-derive v0.4.6
[INFO] [stderr]    Compiling synstructure v0.10.1
[INFO] [stderr]    Compiling pyo3 v0.20.3
[INFO] [stderr]     Checking crossbeam-channel v0.5.1
[INFO] [stderr]     Checking num_cpus v1.10.0
[INFO] [stderr]     Checking lock_api v0.4.1
[INFO] [stderr]     Checking num-complex v0.4.5
[INFO] [stderr]     Checking csv-core v0.1.10
[INFO] [stderr]    Compiling rayon v1.5.1
[INFO] [stderr]     Checking rustc-demangle v0.1.13
[INFO] [stderr]     Checking bit-vec v0.5.1
[INFO] [stderr]     Checking array-macro v1.0.5
[INFO] [stderr]     Checking itoa v0.4.3
[INFO] [stderr]    Compiling bio v0.37.1
[INFO] [stderr]    Compiling rustix v0.38.32
[INFO] [stderr]     Checking percent-encoding v2.1.0
[INFO] [stderr]     Checking fixedbitset v0.2.0
[INFO] [stderr]     Checking adler32 v1.0.4
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking miniz_oxide v0.3.5
[INFO] [stderr]     Checking petgraph v0.5.1
[INFO] [stderr]     Checking url v2.1.1
[INFO] [stderr]    Compiling pyo3-macros-backend v0.20.3
[INFO] [stderr]     Checking ndarray v0.15.6
[INFO] [stderr]     Checking bit-set v0.5.1
[INFO] [stderr]     Checking enum-map v0.6.4
[INFO] [stderr]     Checking nalgebra v0.26.2
[INFO] [stderr]     Checking bstr v0.2.15
[INFO] [stderr]     Checking vec_map v0.8.1
[INFO] [stderr]     Checking csv v1.1.6
[INFO] [stderr]     Checking multimap v0.8.3
[INFO] [stderr]     Checking parking_lot v0.11.0
[INFO] [stderr]    Compiling getset v0.1.2
[INFO] [stderr]     Checking itertools v0.9.0
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]     Checking ordered-float v1.1.1
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking linux-raw-sys v0.4.13
[INFO] [stderr]    Compiling indoc v2.0.4
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]     Checking triple_accel v0.3.4
[INFO] [stderr]     Checking unindent v0.2.3
[INFO] [stderr]     Checking strum v0.20.0
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking bytecount v0.6.2
[INFO] [stderr]     Checking bitflags v2.5.0
[INFO] [stderr]     Checking ex v0.1.3
[INFO] [stderr]     Checking flate2 v1.0.13
[INFO] [stderr]     Checking failure v0.1.5
[INFO] [stderr]     Checking fastrand v2.0.1
[INFO] [stderr]    Compiling pyo3-macros v0.20.3
[INFO] [stderr]     Checking tempfile v3.10.1
[INFO] [stderr]     Checking statrs v0.14.0
[INFO] [stderr]     Checking rust-htslib v0.46.0
[INFO] [stderr]     Checking mbf_bam v0.5.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: the item `PyErr` is imported redundantly
[INFO] [stdout]   --> src/lib.rs:11:24
[INFO] [stdout]    |
[INFO] [stdout] 8  | use pyo3::prelude::*;
[INFO] [stdout]    |     ---------------- the item `PyErr` is already imported here
[INFO] [stdout] ...
[INFO] [stdout] 11 | use pyo3::{exceptions, PyErr, PyResult};
[INFO] [stdout]    |                        ^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: the item `PyResult` is imported redundantly
[INFO] [stdout]   --> src/lib.rs:11:31
[INFO] [stdout]    |
[INFO] [stdout] 8  | use pyo3::prelude::*;
[INFO] [stdout]    |     ---------------- the item `PyResult` is already imported here
[INFO] [stdout] ...
[INFO] [stdout] 11 | use pyo3::{exceptions, PyErr, PyResult};
[INFO] [stdout]    |                               ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: the item `PyAny` is imported redundantly
[INFO] [stdout]   --> src/count_reads/mod.rs:15:19
[INFO] [stdout]    |
[INFO] [stdout] 14 | use pyo3::prelude::*;
[INFO] [stdout]    |     ---------------- the item `PyAny` is already imported here
[INFO] [stdout] 15 | use pyo3::types::{PyAny, PyList, PyTuple};
[INFO] [stdout]    |                   ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: the item `PyErr` is imported redundantly
[INFO] [stdout]   --> src/lib.rs:11:24
[INFO] [stdout]    |
[INFO] [stdout] 8  | use pyo3::prelude::*;
[INFO] [stdout]    |     ---------------- the item `PyErr` is already imported here
[INFO] [stdout] ...
[INFO] [stdout] 11 | use pyo3::{exceptions, PyErr, PyResult};
[INFO] [stdout]    |                        ^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: the item `PyResult` is imported redundantly
[INFO] [stdout]   --> src/lib.rs:11:31
[INFO] [stdout]    |
[INFO] [stdout] 8  | use pyo3::prelude::*;
[INFO] [stdout]    |     ---------------- the item `PyResult` is already imported here
[INFO] [stdout] ...
[INFO] [stdout] 11 | use pyo3::{exceptions, PyErr, PyResult};
[INFO] [stdout]    |                               ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: the item `PyAny` is imported redundantly
[INFO] [stdout]   --> src/count_reads/mod.rs:15:19
[INFO] [stdout]    |
[INFO] [stdout] 14 | use pyo3::prelude::*;
[INFO] [stdout]    |     ---------------- the item `PyAny` is already imported here
[INFO] [stdout] 15 | use pyo3::types::{PyAny, PyList, PyTuple};
[INFO] [stdout]    |                   ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 3 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 3 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 3m 50s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nalgebra v0.26.2
[INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1`
[INFO] running `Command { std: "docker" "inspect" "319b1e446017f3eca823508aaa176fc9f84edfdd386294d206801d8c143b4383", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "319b1e446017f3eca823508aaa176fc9f84edfdd386294d206801d8c143b4383", kill_on_drop: false }`
[INFO] [stdout] 319b1e446017f3eca823508aaa176fc9f84edfdd386294d206801d8c143b4383