[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] testing kgori/vcf_to_fasta against 1.90.0 for beta-1.91-3
[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 1.90.0
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.90.0" "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" "+1.90.0" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded derive-new v0.5.9
[INFO] [stderr]   Downloaded fs-utils v1.1.4
[INFO] [stderr]   Downloaded linear-map v1.2.0
[INFO] [stderr]   Downloaded cmake v0.1.48
[INFO] [stderr]   Downloaded enum-map-derive v0.6.0
[INFO] [stderr]   Downloaded bit-set v0.5.2
[INFO] [stderr]   Downloaded getset v0.1.2
[INFO] [stderr]   Downloaded strum v0.23.0
[INFO] [stderr]   Downloaded enum-map v1.1.1
[INFO] [stderr]   Downloaded paste v1.0.7
[INFO] [stderr]   Downloaded num-rational v0.4.0
[INFO] [stderr]   Downloaded anyhow v1.0.56
[INFO] [stderr]   Downloaded matrixmultiply v0.3.2
[INFO] [stderr]   Downloaded rust-htslib v0.38.2
[INFO] [stderr]   Downloaded num-complex v0.4.0
[INFO] [stderr]   Downloaded libm v0.2.2
[INFO] [stderr]   Downloaded statrs v0.15.0
[INFO] [stderr]   Downloaded triple_accel v0.4.0
[INFO] [stderr]   Downloaded bio v0.40.0
[INFO] [stderr]   Downloaded strum_macros v0.23.1
[INFO] [stderr]   Downloaded bio-types v0.12.1
[INFO] [stderr]   Downloaded itertools-num v0.1.3
[INFO] [stderr]   Downloaded ndarray v0.15.4
[INFO] [stderr]   Downloaded libz-sys v1.1.5
[INFO] [stderr]   Downloaded curl-sys v0.4.53+curl-7.82.0
[INFO] [stderr]   Downloaded openssl-src v111.18.0+1.1.1n
[INFO] [stderr]   Downloaded hts-sys v2.0.2
[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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+1.90.0" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 29228d508000e37812c696540a64967c14cb6092ba795128a325a745d8157354
[INFO] running `Command { std: "docker" "start" "-a" "29228d508000e37812c696540a64967c14cb6092ba795128a325a745d8157354", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "29228d508000e37812c696540a64967c14cb6092ba795128a325a745d8157354", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "29228d508000e37812c696540a64967c14cb6092ba795128a325a745d8157354", kill_on_drop: false }`
[INFO] [stdout] 29228d508000e37812c696540a64967c14cb6092ba795128a325a745d8157354
[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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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" "+1.90.0" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 53a86b36a25cba1794aecf6a0a7a56cf6955f869e0d05cf62f61b9f71b6d2de1
[INFO] running `Command { std: "docker" "start" "-a" "53a86b36a25cba1794aecf6a0a7a56cf6955f869e0d05cf62f61b9f71b6d2de1", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.121
[INFO] [stderr]    Compiling autocfg v1.1.0
[INFO] [stderr]    Compiling proc-macro2 v1.0.36
[INFO] [stderr]    Compiling unicode-xid v0.2.2
[INFO] [stderr]    Compiling syn v1.0.90
[INFO] [stderr]    Compiling pkg-config v0.3.24
[INFO] [stderr]    Compiling libm v0.2.2
[INFO] [stderr]    Compiling memchr v2.4.1
[INFO] [stderr]    Compiling serde_derive v1.0.136
[INFO] [stderr]    Compiling serde v1.0.136
[INFO] [stderr]    Compiling lazy_static v1.4.0
[INFO] [stderr]    Compiling ppv-lite86 v0.2.16
[INFO] [stderr]    Compiling rustversion v1.0.6
[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 quote v1.0.17
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling num-rational v0.4.0
[INFO] [stderr]    Compiling indexmap v1.8.0
[INFO] [stderr]    Compiling unicode-segmentation v1.9.0
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]    Compiling rawpointer v0.2.1
[INFO] [stderr]    Compiling tinyvec_macros v0.1.0
[INFO] [stderr]    Compiling typenum v1.15.0
[INFO] [stderr]    Compiling matrixmultiply v0.3.2
[INFO] [stderr]    Compiling tinyvec v1.5.1
[INFO] [stderr]    Compiling jobserver v0.1.24
[INFO] [stderr]    Compiling getrandom v0.2.6
[INFO] [stderr]    Compiling heck v0.3.3
[INFO] [stderr]    Compiling rand_core v0.6.3
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]    Compiling cc v1.0.73
[INFO] [stderr]    Compiling rand_chacha v0.3.1
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling aho-corasick v0.7.18
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[INFO] [stderr]    Compiling rand v0.8.5
[INFO] [stderr]    Compiling openssl-src v111.18.0+1.1.1n
[INFO] [stderr]    Compiling cmake v0.1.48
[INFO] [stderr]    Compiling approx v0.5.1
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[INFO] [stderr]    Compiling lzma-sys v0.1.17
[INFO] [stderr]    Compiling bzip2-sys v0.1.11+1.0.8
[INFO] [stderr]    Compiling curl-sys v0.4.53+curl-7.82.0
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[INFO] [stderr]    Compiling rand_distr v0.4.3
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[INFO] [stderr]    Compiling bv v0.11.1
[INFO] [stderr]    Compiling unicode-normalization v0.1.19
[INFO] [stderr]    Compiling simba v0.5.1
[INFO] [stderr]    Compiling unicode-bidi v0.3.7
[INFO] [stderr]    Compiling byteorder v1.4.3
[INFO] [stderr]    Compiling percent-encoding v2.1.0
[INFO] [stderr]    Compiling regex v1.5.5
[INFO] [stderr]    Compiling regex-automata v0.1.10
[INFO] [stderr]    Compiling anyhow v1.0.56
[INFO] [stderr]    Compiling idna v0.2.3
[INFO] [stderr]    Compiling form_urlencoded v1.0.1
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]    Compiling csv-core v0.1.10
[INFO] [stderr]    Compiling custom_derive v0.1.7
[INFO] [stderr]    Compiling fixedbitset v0.4.1
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[INFO] [stderr]    Compiling itoa v0.4.8
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[INFO] [stderr]    Compiling either v1.6.1
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[INFO] [stderr]    Compiling itertools v0.10.3
[INFO] [stderr]    Compiling petgraph v0.6.0
[INFO] [stderr]    Compiling url v2.2.2
[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 thiserror v1.0.30
[INFO] [stderr]    Compiling enum-map-derive v0.6.0
[INFO] [stderr]    Compiling clap_derive v3.1.4
[INFO] [stderr]    Compiling enum-map v1.1.1
[INFO] [stderr]    Compiling getset v0.1.2
[INFO] [stderr]    Compiling fxhash v0.2.1
[INFO] [stderr]    Compiling bio-types v0.12.1
[INFO] [stderr]    Compiling nalgebra v0.27.1
[INFO] [stderr]    Compiling ndarray v0.15.4
[INFO] [stderr]    Compiling itertools-num v0.1.3
[INFO] [stderr]    Compiling ordered-float v1.1.1
[INFO] [stderr]    Compiling atty v0.2.14
[INFO] [stderr]    Compiling os_str_bytes v6.0.0
[INFO] [stderr]    Compiling triple_accel v0.4.0
[INFO] [stderr]    Compiling strum v0.23.0
[INFO] [stderr]    Compiling bytecount v0.6.2
[INFO] [stderr]    Compiling linear-map v1.2.0
[INFO] [stderr]    Compiling textwrap v0.15.0
[INFO] [stderr]    Compiling ieee754 v0.2.6
[INFO] [stderr]    Compiling clap v3.1.6
[INFO] [stderr]    Compiling bstr v0.2.17
[INFO] [stderr]    Compiling vec_map v0.8.2
[INFO] [stderr]    Compiling multimap v0.8.3
[INFO] [stderr]    Compiling csv v1.1.6
[INFO] [stderr]    Compiling statrs v0.15.0
[INFO] [stderr]    Compiling bio v0.40.0
[INFO] [stderr]    Compiling rust-htslib v0.38.2
[INFO] [stderr]    Compiling vcf_to_fasta v0.1.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 4m 05s
[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 1`
[INFO] running `Command { std: "docker" "inspect" "53a86b36a25cba1794aecf6a0a7a56cf6955f869e0d05cf62f61b9f71b6d2de1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "53a86b36a25cba1794aecf6a0a7a56cf6955f869e0d05cf62f61b9f71b6d2de1", kill_on_drop: false }`
[INFO] [stdout] 53a86b36a25cba1794aecf6a0a7a56cf6955f869e0d05cf62f61b9f71b6d2de1
[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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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" "+1.90.0" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] a204f2460ee3e75324991ab9aad4c31d2cd7f22becfcccb42ce899b4d5a1c3f2
[INFO] running `Command { std: "docker" "start" "-a" "a204f2460ee3e75324991ab9aad4c31d2cd7f22becfcccb42ce899b4d5a1c3f2", kill_on_drop: false }`
[INFO] [stderr]    Compiling vcf_to_fasta v0.1.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.72s
[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 1`
[INFO] running `Command { std: "docker" "inspect" "a204f2460ee3e75324991ab9aad4c31d2cd7f22becfcccb42ce899b4d5a1c3f2", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "a204f2460ee3e75324991ab9aad4c31d2cd7f22becfcccb42ce899b4d5a1c3f2", kill_on_drop: false }`
[INFO] [stdout] a204f2460ee3e75324991ab9aad4c31d2cd7f22becfcccb42ce899b4d5a1c3f2
[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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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" "+1.90.0" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] fb4d00b968a3bc1ba606f56f43b0027a6765697108a829faf2c904b20eb63e7c
[INFO] running `Command { std: "docker" "start" "-a" "fb4d00b968a3bc1ba606f56f43b0027a6765697108a829faf2c904b20eb63e7c", kill_on_drop: false }`
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.16s
[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 1`
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/vcf_to_fasta-55beaddf7c456f30)
[INFO] [stdout] 
[INFO] [stdout] running 0 tests
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "fb4d00b968a3bc1ba606f56f43b0027a6765697108a829faf2c904b20eb63e7c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "fb4d00b968a3bc1ba606f56f43b0027a6765697108a829faf2c904b20eb63e7c", kill_on_drop: false }`
[INFO] [stdout] fb4d00b968a3bc1ba606f56f43b0027a6765697108a829faf2c904b20eb63e7c