[INFO] cloning repository https://github.com/ormorni/bio_utils
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/ormorni/bio_utils" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Formorni%2Fbio_utils", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Formorni%2Fbio_utils'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] c41f1e42db2a238633814bed7e64f05c652fe7fa
[INFO] checking ormorni/bio_utils against master#3139ff09e9d07f7700f8d15ed25a231e29c43627 for pr-121848-3
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Formorni%2Fbio_utils" "/workspace/builds/worker-3-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-3-tc1/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/ormorni/bio_utils on toolchain 3139ff09e9d07f7700f8d15ed25a231e29c43627
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+3139ff09e9d07f7700f8d15ed25a231e29c43627" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/ormorni/bio_utils
[INFO] finished tweaking git repo https://github.com/ormorni/bio_utils
[INFO] tweaked toml for git repo https://github.com/ormorni/bio_utils written to /workspace/builds/worker-3-tc1/source/Cargo.toml
[INFO] crate git repo https://github.com/ormorni/bio_utils 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" "+3139ff09e9d07f7700f8d15ed25a231e29c43627" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded rustfft v6.0.1
[INFO] [stderr]   Downloaded realfft v3.0.1
[INFO] [stderr]   Downloaded primal-check v0.3.2
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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@sha256:923055f121b5182466d55868a8b05e67af8ba4a3a3f6bad814e953ca3cd3ac2a" "/opt/rustwide/cargo-home/bin/cargo" "+3139ff09e9d07f7700f8d15ed25a231e29c43627" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] d97a432a98b761387248b1a3cc617c76f8eec8f5340f5098cd2ca6577b1cb4cb
[INFO] running `Command { std: "docker" "start" "-a" "d97a432a98b761387248b1a3cc617c76f8eec8f5340f5098cd2ca6577b1cb4cb", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "d97a432a98b761387248b1a3cc617c76f8eec8f5340f5098cd2ca6577b1cb4cb", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "d97a432a98b761387248b1a3cc617c76f8eec8f5340f5098cd2ca6577b1cb4cb", kill_on_drop: false }`
[INFO] [stdout] d97a432a98b761387248b1a3cc617c76f8eec8f5340f5098cd2ca6577b1cb4cb
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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@sha256:923055f121b5182466d55868a8b05e67af8ba4a3a3f6bad814e953ca3cd3ac2a" "/opt/rustwide/cargo-home/bin/cargo" "+3139ff09e9d07f7700f8d15ed25a231e29c43627" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 5524b091013992ef09f07edc3b07598a7b80bd741b901fb8424a59fd717e31a0
[INFO] running `Command { std: "docker" "start" "-a" "5524b091013992ef09f07edc3b07598a7b80bd741b901fb8424a59fd717e31a0", kill_on_drop: false }`
[INFO] [stderr]    Compiling autocfg v1.1.0
[INFO] [stderr]    Compiling libm v0.2.5
[INFO] [stderr]     Checking cfg-if v1.0.0
[INFO] [stderr]    Compiling libc v0.2.132
[INFO] [stderr]    Compiling crossbeam-utils v0.8.11
[INFO] [stderr]    Compiling proc-macro2 v1.0.43
[INFO] [stderr]     Checking once_cell v1.14.0
[INFO] [stderr]    Compiling quote v1.0.21
[INFO] [stderr]    Compiling unicode-ident v1.0.4
[INFO] [stderr]     Checking scopeguard v1.1.0
[INFO] [stderr]    Compiling syn v1.0.99
[INFO] [stderr]     Checking bytemuck v1.12.1
[INFO] [stderr]    Compiling rayon-core v1.9.3
[INFO] [stderr]    Compiling memchr v2.5.0
[INFO] [stderr]     Checking safe_arch v0.6.0
[INFO] [stderr]    Compiling num-traits v0.2.15
[INFO] [stderr]    Compiling num-integer v0.1.45
[INFO] [stderr]    Compiling memoffset v0.6.5
[INFO] [stderr]    Compiling crossbeam-epoch v0.9.10
[INFO] [stderr]    Compiling num-rational v0.4.1
[INFO] [stderr]     Checking strength_reduce v0.2.3
[INFO] [stderr]     Checking ppv-lite86 v0.2.16
[INFO] [stderr]    Compiling typenum v1.15.0
[INFO] [stderr]     Checking wide v0.7.4
[INFO] [stderr]     Checking getrandom v0.2.7
[INFO] [stderr]     Checking num_cpus v1.13.1
[INFO] [stderr]     Checking rand_core v0.6.4
[INFO] [stderr]     Checking crossbeam-deque v0.8.2
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]     Checking crossbeam-channel v0.5.6
[INFO] [stderr]    Compiling rayon v1.5.3
[INFO] [stderr]    Compiling paste v1.0.9
[INFO] [stderr]     Checking either v1.8.0
[INFO] [stderr]     Checking rawpointer v0.2.1
[INFO] [stderr]     Checking matrixmultiply v0.3.2
[INFO] [stderr]     Checking aho-corasick v0.7.19
[INFO] [stderr]     Checking num-complex v0.4.2
[INFO] [stderr]     Checking approx v0.5.1
[INFO] [stderr]     Checking primal-check v0.3.2
[INFO] [stderr]     Checking transpose v0.2.1
[INFO] [stderr]     Checking rand v0.8.5
[INFO] [stderr]     Checking byteorder v1.4.3
[INFO] [stderr]     Checking regex-syntax v0.6.27
[INFO] [stderr]     Checking rustfft v6.0.1
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]     Checking itertools v0.10.4
[INFO] [stderr]     Checking uuid v1.1.2
[INFO] [stderr]     Checking simba v0.7.2
[INFO] [stderr]     Checking lazy_static v1.4.0
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking regex v1.6.0
[INFO] [stderr]    Compiling nalgebra-macros v0.1.0
[INFO] [stderr]     Checking realfft v3.0.1
[INFO] [stderr]     Checking nalgebra v0.31.1
[INFO] [stderr]     Checking bio_utils v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `Lines`
[INFO] [stdout]  --> src/alignment/parsers.rs:2:64
[INFO] [stdout]   |
[INFO] [stdout] 2 | use std::io::{BufRead, BufReader, BufWriter, Error, ErrorKind, Lines, Read, Write};
[INFO] [stdout]   |                                                                ^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Float`
[INFO] [stdout]  --> src/distributions/conv.rs:3:27
[INFO] [stdout]   |
[INFO] [stdout] 3 | use realfft::num_traits::{Float, FromPrimitive, Zero};
[INFO] [stdout]   |                           ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Lines`
[INFO] [stdout]  --> src/alignment/parsers.rs:2:64
[INFO] [stdout]   |
[INFO] [stdout] 2 | use std::io::{BufRead, BufReader, BufWriter, Error, ErrorKind, Lines, Read, Write};
[INFO] [stdout]   |                                                                ^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Float`
[INFO] [stdout]  --> src/distributions/conv.rs:3:27
[INFO] [stdout]   |
[INFO] [stdout] 3 | use realfft::num_traits::{Float, FromPrimitive, Zero};
[INFO] [stdout]   |                           ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `name_length`
[INFO] [stdout]   --> src/alignment/parsers.rs:86:17
[INFO] [stdout]    |
[INFO] [stdout] 86 |             let name_length = reader.read_until(b'\n', &mut self.buf).unwrap();
[INFO] [stdout]    |                 ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_name_length`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: enum `FastaIterState` is never used
[INFO] [stdout]   --> src/alignment/parsers.rs:43:6
[INFO] [stdout]    |
[INFO] [stdout] 43 | enum FastaIterState {
[INFO] [stdout]    |      ^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `name_length`
[INFO] [stdout]   --> src/alignment/parsers.rs:86:17
[INFO] [stdout]    |
[INFO] [stdout] 86 |             let name_length = reader.read_until(b'\n', &mut self.buf).unwrap();
[INFO] [stdout]    |                 ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_name_length`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: enum `FastaIterState` is never used
[INFO] [stdout]   --> src/alignment/parsers.rs:43:6
[INFO] [stdout]    |
[INFO] [stdout] 43 | enum FastaIterState {
[INFO] [stdout]    |      ^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 4 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 4 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [optimized + debuginfo] target(s) in 9.37s
[INFO] running `Command { std: "docker" "inspect" "5524b091013992ef09f07edc3b07598a7b80bd741b901fb8424a59fd717e31a0", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "5524b091013992ef09f07edc3b07598a7b80bd741b901fb8424a59fd717e31a0", kill_on_drop: false }`
[INFO] [stdout] 5524b091013992ef09f07edc3b07598a7b80bd741b901fb8424a59fd717e31a0
[INFO] checking ormorni/bio_utils against try#a2cff3b7a9661c90ec0d581d3f3a69bb97c11138 for pr-121848-3
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Formorni%2Fbio_utils" "/workspace/builds/worker-3-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-3-tc2/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/ormorni/bio_utils on toolchain a2cff3b7a9661c90ec0d581d3f3a69bb97c11138
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+a2cff3b7a9661c90ec0d581d3f3a69bb97c11138" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/ormorni/bio_utils
[INFO] finished tweaking git repo https://github.com/ormorni/bio_utils
[INFO] tweaked toml for git repo https://github.com/ormorni/bio_utils written to /workspace/builds/worker-3-tc2/source/Cargo.toml
[INFO] crate git repo https://github.com/ormorni/bio_utils 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" "+a2cff3b7a9661c90ec0d581d3f3a69bb97c11138" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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@sha256:923055f121b5182466d55868a8b05e67af8ba4a3a3f6bad814e953ca3cd3ac2a" "/opt/rustwide/cargo-home/bin/cargo" "+a2cff3b7a9661c90ec0d581d3f3a69bb97c11138" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 612ad83398cc748630bbe5ec7063367fd950ede379fffd91768e09f9c8ca76d7
[INFO] running `Command { std: "docker" "start" "-a" "612ad83398cc748630bbe5ec7063367fd950ede379fffd91768e09f9c8ca76d7", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "612ad83398cc748630bbe5ec7063367fd950ede379fffd91768e09f9c8ca76d7", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "612ad83398cc748630bbe5ec7063367fd950ede379fffd91768e09f9c8ca76d7", kill_on_drop: false }`
[INFO] [stdout] 612ad83398cc748630bbe5ec7063367fd950ede379fffd91768e09f9c8ca76d7
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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@sha256:923055f121b5182466d55868a8b05e67af8ba4a3a3f6bad814e953ca3cd3ac2a" "/opt/rustwide/cargo-home/bin/cargo" "+a2cff3b7a9661c90ec0d581d3f3a69bb97c11138" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 21952f745344a831315ccf472723b36d7025ef5d7897f7a201b43c66ca444e04
[INFO] running `Command { std: "docker" "start" "-a" "21952f745344a831315ccf472723b36d7025ef5d7897f7a201b43c66ca444e04", kill_on_drop: false }`
[INFO] [stderr]    Compiling autocfg v1.1.0
[INFO] [stderr]    Compiling libm v0.2.5
[INFO] [stderr]     Checking cfg-if v1.0.0
[INFO] [stderr]    Compiling libc v0.2.132
[INFO] [stderr]    Compiling crossbeam-utils v0.8.11
[INFO] [stderr]    Compiling proc-macro2 v1.0.43
[INFO] [stderr]     Checking once_cell v1.14.0
[INFO] [stderr]    Compiling unicode-ident v1.0.4
[INFO] [stderr]    Compiling quote v1.0.21
[INFO] [stderr]    Compiling rayon-core v1.9.3
[INFO] [stderr]    Compiling syn v1.0.99
[INFO] [stderr]     Checking scopeguard v1.1.0
[INFO] [stderr]    Compiling memchr v2.5.0
[INFO] [stderr]     Checking bytemuck v1.12.1
[INFO] [stderr]    Compiling num-traits v0.2.15
[INFO] [stderr]    Compiling num-integer v0.1.45
[INFO] [stderr]    Compiling memoffset v0.6.5
[INFO] [stderr]    Compiling crossbeam-epoch v0.9.10
[INFO] [stderr]     Checking safe_arch v0.6.0
[INFO] [stderr]    Compiling num-rational v0.4.1
[INFO] [stderr]     Checking ppv-lite86 v0.2.16
[INFO] [stderr]     Checking strength_reduce v0.2.3
[INFO] [stderr]    Compiling typenum v1.15.0
[INFO] [stderr]     Checking wide v0.7.4
[INFO] [stderr]     Checking getrandom v0.2.7
[INFO] [stderr]     Checking crossbeam-deque v0.8.2
[INFO] [stderr]     Checking num_cpus v1.13.1
[INFO] [stderr]     Checking rand_core v0.6.4
[INFO] [stderr]     Checking crossbeam-channel v0.5.6
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]    Compiling rayon v1.5.3
[INFO] [stderr]     Checking either v1.8.0
[INFO] [stderr]    Compiling paste v1.0.9
[INFO] [stderr]     Checking rawpointer v0.2.1
[INFO] [stderr]     Checking matrixmultiply v0.3.2
[INFO] [stderr]     Checking rand v0.8.5
[INFO] [stderr]     Checking aho-corasick v0.7.19
[INFO] [stderr]     Checking num-complex v0.4.2
[INFO] [stderr]     Checking approx v0.5.1
[INFO] [stderr]     Checking transpose v0.2.1
[INFO] [stderr]     Checking primal-check v0.3.2
[INFO] [stderr]     Checking rustfft v6.0.1
[INFO] [stderr]     Checking regex-syntax v0.6.27
[INFO] [stderr]     Checking byteorder v1.4.3
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]     Checking itertools v0.10.4
[INFO] [stderr]     Checking simba v0.7.2
[INFO] [stderr]     Checking uuid v1.1.2
[INFO] [stderr]     Checking lazy_static v1.4.0
[INFO] [stderr]     Checking regex v1.6.0
[INFO] [stderr]    Compiling nalgebra-macros v0.1.0
[INFO] [stderr]     Checking realfft v3.0.1
[INFO] [stderr]     Checking nalgebra v0.31.1
[ERROR] error running command: no output for 300 seconds
[INFO] running `Command { std: "docker" "inspect" "21952f745344a831315ccf472723b36d7025ef5d7897f7a201b43c66ca444e04", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "21952f745344a831315ccf472723b36d7025ef5d7897f7a201b43c66ca444e04", kill_on_drop: false }`
[INFO] [stdout] 21952f745344a831315ccf472723b36d7025ef5d7897f7a201b43c66ca444e04
