[INFO] cloning repository https://github.com/ban-m/kiley [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/ban-m/kiley" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fban-m%2Fkiley", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fban-m%2Fkiley'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 823976103f0dde17e28c5bc6044fe598cf788a30 [INFO] testing ban-m/kiley/823976103f0dde17e28c5bc6044fe598cf788a30 against master#67da586efe13aa66eef576ba095e1875ba65fd20 for pr-112849 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fban-m%2Fkiley" "/workspace/builds/worker-6-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-6-tc1/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/ban-m/kiley on toolchain 67da586efe13aa66eef576ba095e1875ba65fd20 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+67da586efe13aa66eef576ba095e1875ba65fd20" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/ban-m/kiley [INFO] finished tweaking git repo https://github.com/ban-m/kiley [INFO] tweaked toml for git repo https://github.com/ban-m/kiley written to /workspace/builds/worker-6-tc1/source/Cargo.toml [INFO] crate git repo https://github.com/ban-m/kiley 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" "+67da586efe13aa66eef576ba095e1875ba65fd20" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating git repository `https://github.com/ban-m/bio_utils.git` [INFO] [stderr] Updating git repository `https://github.com/ban-m/edlib-sys.git` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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:a420fdec406141845121210faa381f8029b0be6d4170deff7c4445a424f67918" "/opt/rustwide/cargo-home/bin/cargo" "+67da586efe13aa66eef576ba095e1875ba65fd20" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 64586c6ec5d36c64df1ea48b3b3867bcb2b491838ad37d93b1c064b74dbfd3d1 [INFO] running `Command { std: "docker" "start" "-a" "64586c6ec5d36c64df1ea48b3b3867bcb2b491838ad37d93b1c064b74dbfd3d1", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "64586c6ec5d36c64df1ea48b3b3867bcb2b491838ad37d93b1c064b74dbfd3d1", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "64586c6ec5d36c64df1ea48b3b3867bcb2b491838ad37d93b1c064b74dbfd3d1", kill_on_drop: false }` [INFO] [stdout] 64586c6ec5d36c64df1ea48b3b3867bcb2b491838ad37d93b1c064b74dbfd3d1 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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:a420fdec406141845121210faa381f8029b0be6d4170deff7c4445a424f67918" "/opt/rustwide/cargo-home/bin/cargo" "+67da586efe13aa66eef576ba095e1875ba65fd20" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] fe6e660c8bcfd9f9f079e1d4a8e8eb837ed8f1ef2e240b34ea44f158045a7ee2 [INFO] running `Command { std: "docker" "start" "-a" "fe6e660c8bcfd9f9f079e1d4a8e8eb837ed8f1ef2e240b34ea44f158045a7ee2", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.134 [INFO] [stderr] Compiling crossbeam-utils v0.8.12 [INFO] [stderr] Compiling proc-macro2 v1.0.46 [INFO] [stderr] Compiling unicode-ident v1.0.4 [INFO] [stderr] Compiling syn v1.0.101 [INFO] [stderr] Compiling rayon-core v1.9.3 [INFO] [stderr] Compiling serde_derive v1.0.145 [INFO] [stderr] Compiling serde v1.0.145 [INFO] [stderr] Compiling log v0.4.17 [INFO] [stderr] Compiling ppv-lite86 v0.2.16 [INFO] [stderr] Compiling regex-syntax v0.6.27 [INFO] [stderr] Compiling memoffset v0.6.5 [INFO] [stderr] Compiling crossbeam-epoch v0.9.11 [INFO] [stderr] Compiling rayon v1.5.3 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling termcolor v1.1.3 [INFO] [stderr] Compiling either v1.8.0 [INFO] [stderr] Compiling ansi_term v0.12.1 [INFO] [stderr] Compiling strsim v0.8.0 [INFO] [stderr] Compiling humantime v2.1.0 [INFO] [stderr] Compiling bytecount v0.6.3 [INFO] [stderr] Compiling crossbeam-channel v0.5.6 [INFO] [stderr] Compiling quote v1.0.21 [INFO] [stderr] Compiling crossbeam-deque v0.8.2 [INFO] [stderr] Compiling getrandom v0.2.7 [INFO] [stderr] Compiling jobserver v0.1.25 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling num_cpus v1.13.1 [INFO] [stderr] Compiling clap v2.34.0 [INFO] [stderr] Compiling rand_core v0.6.4 [INFO] [stderr] Compiling cc v1.0.73 [INFO] [stderr] Compiling rand_chacha v0.3.1 [INFO] [stderr] Compiling rand_xoshiro v0.6.0 [INFO] [stderr] Compiling regex v1.6.0 [INFO] [stderr] Compiling rand v0.8.5 [INFO] [stderr] Compiling edlib_sys v0.2.0 (https://github.com/ban-m/edlib-sys.git?branch=master#7ab12d04) [INFO] [stderr] Compiling env_logger v0.9.1 [INFO] [stderr] Compiling bio_utils v0.3.0 (https://github.com/ban-m/bio_utils.git#dc32ea1d) [INFO] [stderr] Compiling kiley v0.3.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 13.74s [INFO] running `Command { std: "docker" "inspect" "fe6e660c8bcfd9f9f079e1d4a8e8eb837ed8f1ef2e240b34ea44f158045a7ee2", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "fe6e660c8bcfd9f9f079e1d4a8e8eb837ed8f1ef2e240b34ea44f158045a7ee2", kill_on_drop: false }` [INFO] [stdout] fe6e660c8bcfd9f9f079e1d4a8e8eb837ed8f1ef2e240b34ea44f158045a7ee2 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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:a420fdec406141845121210faa381f8029b0be6d4170deff7c4445a424f67918" "/opt/rustwide/cargo-home/bin/cargo" "+67da586efe13aa66eef576ba095e1875ba65fd20" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 91b449167b6870f34c81cf5f3301c9565555f9759f150182945783e2cb41bc76 [INFO] running `Command { std: "docker" "start" "-a" "91b449167b6870f34c81cf5f3301c9565555f9759f150182945783e2cb41bc76", kill_on_drop: false }` [INFO] [stderr] Compiling kiley v0.3.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished test [unoptimized + debuginfo] target(s) in 6.87s [INFO] running `Command { std: "docker" "inspect" "91b449167b6870f34c81cf5f3301c9565555f9759f150182945783e2cb41bc76", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "91b449167b6870f34c81cf5f3301c9565555f9759f150182945783e2cb41bc76", kill_on_drop: false }` [INFO] [stdout] 91b449167b6870f34c81cf5f3301c9565555f9759f150182945783e2cb41bc76 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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:a420fdec406141845121210faa381f8029b0be6d4170deff7c4445a424f67918" "/opt/rustwide/cargo-home/bin/cargo" "+67da586efe13aa66eef576ba095e1875ba65fd20" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] 7d5a533067df39394da55aa81753822dfd7a33d02e5fede87341f052ca4b056a [INFO] running `Command { std: "docker" "start" "-a" "7d5a533067df39394da55aa81753822dfd7a33d02e5fede87341f052ca4b056a", kill_on_drop: false }` [INFO] [stderr] Finished test [unoptimized + debuginfo] target(s) in 0.07s [INFO] [stdout] [INFO] [stderr] Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/kiley-968fbede8459f9e4) [INFO] [stdout] running 42 tests [INFO] [stdout] test bialignment::test::edit_dist_check ... ok [INFO] [stdout] test bialignment::test::edit_dist_ops_check ... ok [INFO] [stdout] test bialignment::test::global_affine_check ... ok [INFO] [stdout] test bialignment::test::edit_dist_fast_check_short ... ok [INFO] [stdout] test hmm::full::test::align ... ok [INFO] [stdout] test bialignment::guided::test::edit_dist_check_iden ... ok [INFO] [stdout] test hmm::full::test::forward ... ok [INFO] [stdout] test hmm::guided::tests::align ... ok [INFO] [stdout] test hmm::guided::tests::likelihood2 ... ok [INFO] [stdout] test bialignment::guided::test::edit_dist_check ... ok [INFO] [stdout] test bialignment::guided::test::global_check ... ok [INFO] [stdout] test bialignment::guided::test::overlap_check ... ok [INFO] [stdout] test hmm::guided::tests::likelihood ... ok [INFO] [stdout] test hmm::guided::tests::update_aln_path_test ... ok [INFO] [stdout] test hmm::guided_antidiagonal::test::align ... ok [INFO] [stdout] test bialignment::guided::test::infix_check ... ok [INFO] [stdout] test bialignment::banded::tests::banded_naive_check ... ok [INFO] [stdout] test bialignment::test::naive_edit_dist_modification_check ... ok [INFO] [stdout] test bialignment::banded::tests::global_affine_banded_check ... ok [INFO] [stdout] test hmm::guided_antidiagonal::test::lk_post_test ... ok [INFO] [stdout] test hmm::guided_antidiagonal::test::align_test ... ok [INFO] [stdout] test bialignment::banded::tests::edit_dist_modification_check has been running for over 60 seconds [INFO] [stdout] test bialignment::guided::test::modification_table_check has been running for over 60 seconds [INFO] [stdout] test bialignment::guided::test::polish_test has been running for over 60 seconds [INFO] [stdout] test bialignment::test::edit_dist_fast_check has been running for over 60 seconds [INFO] [stdout] test bialignment::test::edit_dist_fast_check_sim has been running for over 60 seconds [INFO] [stdout] test bialignment::test::edit_dist_post_check has been running for over 60 seconds [INFO] [stdout] test hmm::full::test::modification_table_test has been running for over 60 seconds [INFO] [stdout] test hmm::guided::tests::modification_table has been running for over 60 seconds [INFO] [stdout] test hmm::guided::tests::modification_table2 has been running for over 60 seconds [INFO] [stdout] test hmm::guided::tests::polish_long_insertion has been running for over 60 seconds [INFO] [stdout] test hmm::guided::tests::polish_test has been running for over 60 seconds [INFO] [stdout] test hmm::guided_antidiagonal::test::fit_test has been running for over 60 seconds [INFO] [stdout] test hmm::guided_antidiagonal::test::lk_post has been running for over 60 seconds [INFO] [stdout] test hmm::guided_antidiagonal::test::fit_test ... ok [INFO] [stdout] test hmm::guided_antidiagonal::test::lk_pre has been running for over 60 seconds [INFO] [stdout] test hmm::guided_antidiagonal::test::lk_post ... ok [INFO] [stdout] test hmm::tests::align ... ok [INFO] [stdout] test hmm::tests::hmm_full_guided ... ok [INFO] [stdout] test op::tests::take_skip ... ok [INFO] [stdout] test hmm::guided_antidiagonal::test::lk_test has been running for over 60 seconds [INFO] [stdout] test padseq::tests::padseq ... ok [INFO] [stdout] test hmm::guided_antidiagonal::test::lk_test ... ok [INFO] [stdout] test hmm::guided_antidiagonal::test::modification_table_test has been running for over 60 seconds [INFO] [stdout] test hmm::full::test::modification_table_test ... ok [INFO] [stdout] test hmm::guided_antidiagonal::test::lk_pre ... ok [INFO] [stdout] test hmm::guided_antidiagonal::test::polish has been running for over 60 seconds [INFO] [stdout] test bialignment::guided::test::polish_test ... ok [INFO] [stdout] test bialignment::test::edit_dist_fast_check_sim ... ok [INFO] [stdout] test bialignment::banded::tests::edit_dist_modification_check ... ok [INFO] [stdout] test bialignment::test::edit_dist_fast_check ... ok [INFO] [stdout] test hmm::guided_antidiagonal::test::modification_table_test ... ok [INFO] [stdout] test bialignment::test::edit_dist_post_check ... ok [INFO] [stdout] test hmm::guided::tests::modification_table ... ok [INFO] [stdout] test bialignment::guided::test::modification_table_check ... ok [INFO] [stdout] test hmm::guided::tests::polish_test ... ok [INFO] [stdout] test hmm::guided::tests::polish_long_insertion ... ok [INFO] [stdout] test hmm::guided_antidiagonal::test::polish ... ok [ERROR] error running command: command timed out after 900 seconds [INFO] running `Command { std: "docker" "inspect" "7d5a533067df39394da55aa81753822dfd7a33d02e5fede87341f052ca4b056a", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "7d5a533067df39394da55aa81753822dfd7a33d02e5fede87341f052ca4b056a", kill_on_drop: false }` [INFO] [stdout] 7d5a533067df39394da55aa81753822dfd7a33d02e5fede87341f052ca4b056a