[INFO] cloning repository https://github.com/kgori/vcf_to_fasta
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/kgori/vcf_to_fasta" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkgori%2Fvcf_to_fasta", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkgori%2Fvcf_to_fasta'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 82e538c05372ef757d308b68af1f270623da97e9
[INFO] checking kgori/vcf_to_fasta against master#bca37a20bd376ce3fd138e7cdee7fe704e0f8814 for pr-139493-3
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkgori%2Fvcf_to_fasta" "/workspace/builds/worker-1-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-1-tc1/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/kgori/vcf_to_fasta
[INFO] finished tweaking git repo https://github.com/kgori/vcf_to_fasta
[INFO] tweaked toml for git repo https://github.com/kgori/vcf_to_fasta written to /workspace/builds/worker-1-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/kgori/vcf_to_fasta on toolchain bca37a20bd376ce3fd138e7cdee7fe704e0f8814
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+bca37a20bd376ce3fd138e7cdee7fe704e0f8814" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/kgori/vcf_to_fasta 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" "+bca37a20bd376ce3fd138e7cdee7fe704e0f8814" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded triple_accel v0.4.0
[INFO] [stderr]   Downloaded bio-types v0.12.1
[INFO] [stderr]   Downloaded enum-map-derive v0.6.0
[INFO] [stderr]   Downloaded enum-map v1.1.1
[INFO] [stderr]   Downloaded simba v0.5.1
[INFO] [stderr]   Downloaded matrixmultiply v0.3.2
[INFO] [stderr]   Downloaded rust-htslib v0.38.2
[INFO] [stderr]   Downloaded statrs v0.15.0
[INFO] [stderr]   Downloaded bio v0.40.0
[INFO] [stderr]   Downloaded ndarray v0.15.4
[INFO] [stderr]   Downloaded nalgebra v0.27.1
[INFO] [stderr]   Downloaded lzma-sys v0.1.17
[INFO] [stderr]   Downloaded libz-sys v1.1.5
[INFO] [stderr]   Downloaded curl-sys v0.4.53+curl-7.82.0
[INFO] [stderr]   Downloaded hts-sys v2.0.2
[INFO] [stderr]   Downloaded openssl-src v111.18.0+1.1.1n
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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:aa71247004a7fa38d13ec170f48f06cdedf5bc50b2a8645e56ed7e992e6fa513" "/opt/rustwide/cargo-home/bin/cargo" "+bca37a20bd376ce3fd138e7cdee7fe704e0f8814" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 7ddc36738d153a849c807a324219444272de987e27d60564469207aff5c4923e
[INFO] running `Command { std: "docker" "start" "-a" "7ddc36738d153a849c807a324219444272de987e27d60564469207aff5c4923e", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "7ddc36738d153a849c807a324219444272de987e27d60564469207aff5c4923e", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "7ddc36738d153a849c807a324219444272de987e27d60564469207aff5c4923e", kill_on_drop: false }`
[INFO] [stdout] 7ddc36738d153a849c807a324219444272de987e27d60564469207aff5c4923e
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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:aa71247004a7fa38d13ec170f48f06cdedf5bc50b2a8645e56ed7e992e6fa513" "/opt/rustwide/cargo-home/bin/cargo" "+bca37a20bd376ce3fd138e7cdee7fe704e0f8814" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] f9e53d97257e35a9fe16d410c0a84cce3590f401f1719cb7b14a8c12c88a7391
[INFO] running `Command { std: "docker" "start" "-a" "f9e53d97257e35a9fe16d410c0a84cce3590f401f1719cb7b14a8c12c88a7391", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.121
[INFO] [stderr]    Compiling syn v1.0.90
[INFO] [stderr]    Compiling libm v0.2.2
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling num-traits v0.2.14
[INFO] [stderr]    Compiling num-integer v0.1.44
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]    Compiling quote v1.0.17
[INFO] [stderr]     Checking matrixmultiply v0.3.2
[INFO] [stderr]    Compiling anyhow v1.0.56
[INFO] [stderr]     Checking fixedbitset v0.4.1
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking strum v0.23.0
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]     Checking bytecount v0.6.2
[INFO] [stderr]     Checking petgraph v0.6.0
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling jobserver v0.1.24
[INFO] [stderr]     Checking getrandom v0.2.6
[INFO] [stderr]     Checking atty v0.2.14
[INFO] [stderr]    Compiling cc v1.0.73
[INFO] [stderr]     Checking rand_core v0.6.3
[INFO] [stderr]    Compiling cmake v0.1.48
[INFO] [stderr]    Compiling openssl-src v111.18.0+1.1.1n
[INFO] [stderr]    Compiling bzip2-sys v0.1.11+1.0.8
[INFO] [stderr]    Compiling openssl-sys v0.9.72
[INFO] [stderr]    Compiling lzma-sys v0.1.17
[INFO] [stderr]    Compiling curl-sys v0.4.53+curl-7.82.0
[INFO] [stderr]    Compiling hts-sys v2.0.2
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]     Checking rand v0.8.5
[INFO] [stderr]    Compiling libz-sys v1.1.5
[INFO] [stderr]     Checking num-complex v0.4.0
[INFO] [stderr]     Checking approx v0.5.1
[INFO] [stderr]     Checking ordered-float v1.1.1
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking num-rational v0.4.0
[INFO] [stderr]     Checking simba v0.5.1
[INFO] [stderr]     Checking ndarray v0.15.4
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]    Compiling serde_derive v1.0.136
[INFO] [stderr]    Compiling thiserror-impl v1.0.30
[INFO] [stderr]    Compiling strum_macros v0.23.1
[INFO] [stderr]    Compiling nalgebra-macros v0.1.0
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]    Compiling enum-map-derive v0.6.0
[INFO] [stderr]    Compiling getset v0.1.2
[INFO] [stderr]    Compiling clap_derive v3.1.4
[INFO] [stderr]     Checking enum-map v1.1.1
[INFO] [stderr]     Checking nalgebra v0.27.1
[INFO] [stderr]     Checking thiserror v1.0.30
[INFO] [stderr]     Checking bio-types v0.12.1
[INFO] [stderr]     Checking clap v3.1.6
[INFO] [stderr]     Checking serde v1.0.136
[INFO] [stderr]     Checking bstr v0.2.17
[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 csv v1.1.6
[INFO] [stderr]     Checking statrs v0.15.0
[INFO] [stderr]     Checking bio v0.40.0
[INFO] [stderr]     Checking rust-htslib v0.38.2
[INFO] [stderr]     Checking vcf_to_fasta v0.1.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 44s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nalgebra v0.27.1
[INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 19`
[INFO] running `Command { std: "docker" "inspect" "f9e53d97257e35a9fe16d410c0a84cce3590f401f1719cb7b14a8c12c88a7391", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "f9e53d97257e35a9fe16d410c0a84cce3590f401f1719cb7b14a8c12c88a7391", kill_on_drop: false }`
[INFO] [stdout] f9e53d97257e35a9fe16d410c0a84cce3590f401f1719cb7b14a8c12c88a7391
