[INFO] cloning repository https://github.com/informationsea/sequencetoolkit
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/informationsea/sequencetoolkit" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Finformationsea%2Fsequencetoolkit", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Finformationsea%2Fsequencetoolkit'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] d3244698b3dad669577b81f0d3c912fc76e14d25
[INFO] checking informationsea/sequencetoolkit against master#8007b506ac5da629f223b755f5a5391edd5f6d01 for pr-88041
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Finformationsea%2Fsequencetoolkit" "/workspace/builds/worker-2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-2/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/informationsea/sequencetoolkit on toolchain 8007b506ac5da629f223b755f5a5391edd5f6d01
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+8007b506ac5da629f223b755f5a5391edd5f6d01" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/informationsea/sequencetoolkit
[INFO] finished tweaking git repo https://github.com/informationsea/sequencetoolkit
[INFO] tweaked toml for git repo https://github.com/informationsea/sequencetoolkit written to /workspace/builds/worker-2/source/Cargo.toml
[INFO] crate git repo https://github.com/informationsea/sequencetoolkit already has a lockfile, it will not be regenerated
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+8007b506ac5da629f223b755f5a5391edd5f6d01" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2/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@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+8007b506ac5da629f223b755f5a5391edd5f6d01" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
[INFO] [stdout] ab8f041ee418e308bb0d09d04eb615f7a623fc28749eb3cb4a59fb4de577322c
[INFO] running `Command { std: "docker" "start" "-a" "ab8f041ee418e308bb0d09d04eb615f7a623fc28749eb3cb4a59fb4de577322c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "ab8f041ee418e308bb0d09d04eb615f7a623fc28749eb3cb4a59fb4de577322c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "ab8f041ee418e308bb0d09d04eb615f7a623fc28749eb3cb4a59fb4de577322c", kill_on_drop: false }`
[INFO] [stdout] ab8f041ee418e308bb0d09d04eb615f7a623fc28749eb3cb4a59fb4de577322c
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2/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" "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@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+8007b506ac5da629f223b755f5a5391edd5f6d01" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 254795cc27b4c8ee48da40f39b5068682cb7d2312b38e989b9f76d7078586cee
[INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
[INFO] running `Command { std: "docker" "start" "-a" "254795cc27b4c8ee48da40f39b5068682cb7d2312b38e989b9f76d7078586cee", kill_on_drop: false }`
[INFO] [stderr]    Compiling proc-macro2 v1.0.27
[INFO] [stderr]    Compiling autocfg v1.0.1
[INFO] [stderr]    Compiling serde_derive v1.0.126
[INFO] [stderr]    Compiling serde v1.0.126
[INFO] [stderr]     Checking cfg-if v1.0.0
[INFO] [stderr]    Compiling ryu v1.0.5
[INFO] [stderr]    Compiling bitflags v1.2.1
[INFO] [stderr]    Compiling glob v0.3.0
[INFO] [stderr]     Checking lazy_static v1.4.0
[INFO] [stderr]    Compiling log v0.4.14
[INFO] [stderr]    Compiling pkg-config v0.3.19
[INFO] [stderr]     Checking regex-automata v0.1.10
[INFO] [stderr]     Checking unicode-width v0.1.8
[INFO] [stderr]     Checking regex-syntax v0.6.25
[INFO] [stderr]     Checking ansi_term v0.11.0
[INFO] [stderr]     Checking strsim v0.8.0
[INFO] [stderr]     Checking alloc-no-stdlib v2.0.1
[INFO] [stderr]    Compiling doc-comment v0.3.3
[INFO] [stderr]     Checking ppv-lite86 v0.2.10
[INFO] [stderr]    Compiling snap v1.0.5
[INFO] [stderr]     Checking fixedbitset v0.2.0
[INFO] [stderr]     Checking array-macro v1.0.5
[INFO] [stderr]    Compiling bindgen v0.58.1
[INFO] [stderr]    Compiling shlex v1.0.0
[INFO] [stderr]    Compiling serde_json v1.0.64
[INFO] [stderr]    Compiling nom v5.1.2
[INFO] [stderr]    Compiling libloading v0.7.0
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]     Checking humantime v1.3.0
[INFO] [stderr]     Checking textwrap v0.11.0
[INFO] [stderr]     Checking alloc-stdlib v0.2.1
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]     Checking itertools v0.9.0
[INFO] [stderr]    Compiling libc v0.2.98
[INFO] [stderr]     Checking crc32fast v1.2.1
[INFO] [stderr]     Checking getrandom v0.1.16
[INFO] [stderr]     Checking object v0.25.3
[INFO] [stderr]    Compiling miniz_oxide v0.4.4
[INFO] [stderr]    Compiling num-traits v0.2.14
[INFO] [stderr]    Compiling num-complex v0.2.4
[INFO] [stderr]    Compiling indexmap v1.7.0
[INFO] [stderr]    Compiling num-integer v0.1.44
[INFO] [stderr]     Checking brotli-decompressor v2.3.1
[INFO] [stderr]    Compiling clang-sys v1.2.0
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking rand_core v0.5.1
[INFO] [stderr]    Compiling lexical-core v0.7.6
[INFO] [stderr]    Compiling jobserver v0.1.22
[INFO] [stderr]    Compiling atty v0.2.14
[INFO] [stderr]    Compiling which v3.1.1
[INFO] [stderr]     Checking rand_chacha v0.2.2
[INFO] [stderr]    Compiling env_logger v0.8.4
[INFO] [stderr]    Compiling quote v1.0.9
[INFO] [stderr]    Compiling cc v1.0.68
[INFO] [stderr]     Checking flate2 v1.0.20
[INFO] [stderr]     Checking rand v0.7.3
[INFO] [stderr]    Compiling syn v1.0.73
[INFO] [stderr]     Checking petgraph v0.5.1
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking ordered-float v1.1.1
[INFO] [stderr]     Checking approx v0.3.2
[INFO] [stderr]     Checking regex v1.5.4
[INFO] [stderr]     Checking brotli v3.3.0
[INFO] [stderr]    Compiling backtrace v0.3.60
[INFO] [stderr]    Compiling zstd-sys v1.4.18+zstd.1.4.7
[INFO] [stderr]    Compiling bzip2-sys v0.1.11+1.0.8
[INFO] [stderr]    Compiling lzma-sys v0.1.17
[INFO] [stderr]    Compiling lz4-sys v1.9.2
[INFO] [stderr]     Checking statrs v0.12.0
[INFO] [stderr]     Checking ndarray v0.13.1
[INFO] [stderr]     Checking env_logger v0.7.1
[INFO] [stderr]     Checking xz2 v0.1.6
[INFO] [stderr]     Checking pretty_env_logger v0.4.0
[INFO] [stderr]     Checking bzip2 v0.3.3
[INFO] [stderr]    Compiling cexpr v0.4.0
[INFO] [stderr]    Compiling synstructure v0.12.4
[INFO] [stderr]     Checking lz4 v1.23.2
[INFO] [stderr]    Compiling failure_derive v0.1.8
[INFO] [stderr]    Compiling thiserror-impl v1.0.26
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]    Compiling strum_macros v0.20.1
[INFO] [stderr]    Compiling snafu-derive v0.6.10
[INFO] [stderr]    Compiling enum-map-derive v0.4.6
[INFO] [stderr]    Compiling strum_macros v0.18.0
[INFO] [stderr]    Compiling getset v0.0.9
[INFO] [stderr]     Checking enum-map v0.6.4
[INFO] [stderr]     Checking failure v0.1.8
[INFO] [stderr]     Checking vcf v0.5.0
[INFO] [stderr]     Checking thiserror v1.0.26
[INFO] [stderr]     Checking snafu v0.6.10
[INFO] [stderr]     Checking bio-types v0.11.0
[INFO] [stderr]     Checking bstr v0.2.16
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking multimap v0.8.3
[INFO] [stderr]     Checking bv v0.11.1
[INFO] [stderr]     Checking bio-types v0.7.0
[INFO] [stderr]     Checking bincode v1.3.3
[INFO] [stderr]     Checking clap v2.33.3
[INFO] [stderr]     Checking csv v1.1.6
[INFO] [stderr]     Checking bio v0.32.0
[INFO] [stderr]     Checking sequencetoolkit_common v0.1.0 (/opt/rustwide/workdir/sequencetoolkit_common)
[INFO] [stderr]     Checking fastqutils v0.1.0 (/opt/rustwide/workdir/fastqutils)
[INFO] [stderr]    Compiling zstd-safe v2.0.6+zstd.1.4.7
[INFO] [stderr]     Checking zstd v0.5.4+zstd.1.4.7
[INFO] [stderr]     Checking autocompress v0.1.0
[INFO] [stderr]     Checking bedutils v0.1.0 (/opt/rustwide/workdir/bedutils)
[INFO] [stderr]     Checking geneannot v0.1.0 (/opt/rustwide/workdir/geneannot)
[INFO] [stderr]    Compiling libxlsxwriter-sys v1.0.6
[INFO] [stderr]     Checking xlsxwriter v0.3.4
[INFO] [stderr]     Checking vcfutils v0.1.0 (/opt/rustwide/workdir/vcfutils)
[INFO] [stderr]     Checking sequencetoolkit v0.2.1 (/opt/rustwide/workdir/sequencetoolkit)
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 2m 40s
[INFO] running `Command { std: "docker" "inspect" "254795cc27b4c8ee48da40f39b5068682cb7d2312b38e989b9f76d7078586cee", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "254795cc27b4c8ee48da40f39b5068682cb7d2312b38e989b9f76d7078586cee", kill_on_drop: false }`
[INFO] [stdout] 254795cc27b4c8ee48da40f39b5068682cb7d2312b38e989b9f76d7078586cee