[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] f4e9c0d11d8218d561f91d68117a3827a3d5a8b4 [INFO] testing ban-m/kiley/f4e9c0d11d8218d561f91d68117a3827a3d5a8b4 against master#ad85bc524b1ad696e42061ad8338d382dffbdbe5 for pr-146237 [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] 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] validating manifest of git repo https://github.com/ban-m/kiley on toolchain ad85bc524b1ad696e42061ad8338d382dffbdbe5 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [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" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [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] [stderr] Blocking waiting for file lock on package cache [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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 5bb6da1d932a7a587666c27c4da5cdb639423709821f24d0511c2562c852bcef [INFO] running `Command { std: "docker" "start" "-a" "5bb6da1d932a7a587666c27c4da5cdb639423709821f24d0511c2562c852bcef", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "5bb6da1d932a7a587666c27c4da5cdb639423709821f24d0511c2562c852bcef", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "5bb6da1d932a7a587666c27c4da5cdb639423709821f24d0511c2562c852bcef", kill_on_drop: false }` [INFO] [stdout] 5bb6da1d932a7a587666c27c4da5cdb639423709821f24d0511c2562c852bcef [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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] fcfaff28d6d170d5682a4bc62baf82358a3aa27c4bad933dcb9d872f3148570b [INFO] running `Command { std: "docker" "start" "-a" "fcfaff28d6d170d5682a4bc62baf82358a3aa27c4bad933dcb9d872f3148570b", kill_on_drop: false }` [INFO] [stderr] Compiling regex-syntax v0.8.4 [INFO] [stderr] Compiling anstyle v1.0.8 [INFO] [stderr] Compiling colorchoice v1.0.2 [INFO] [stderr] Compiling anstyle-query v1.1.1 [INFO] [stderr] Compiling anstyle-parse v0.2.5 [INFO] [stderr] Compiling serde v1.0.204 [INFO] [stderr] Compiling bytecount v0.6.8 [INFO] [stderr] Compiling either v1.13.0 [INFO] [stderr] Compiling jobserver v0.1.32 [INFO] [stderr] Compiling getrandom v0.2.15 [INFO] [stderr] Compiling syn v2.0.72 [INFO] [stderr] Compiling anstream v0.6.15 [INFO] [stderr] Compiling cc v1.1.7 [INFO] [stderr] Compiling rand_core v0.6.4 [INFO] [stderr] Compiling rayon v1.10.0 [INFO] [stderr] Compiling rand_xoshiro v0.6.0 [INFO] [stderr] Compiling regex-automata v0.4.7 [INFO] [stderr] Compiling edlib_sys v0.2.0 (https://github.com/ban-m/edlib-sys.git?branch=master#ef696f3f) [INFO] [stderr] Compiling zerocopy-derive v0.7.35 [INFO] [stderr] Compiling serde_derive v1.0.204 [INFO] [stderr] Compiling zerocopy v0.7.35 [INFO] [stderr] Compiling ppv-lite86 v0.2.20 [INFO] [stderr] Compiling rand_chacha v0.3.1 [INFO] [stderr] Compiling rand v0.8.5 [INFO] [stderr] Compiling regex v1.10.6 [INFO] [stderr] Compiling env_filter v0.1.2 [INFO] [stderr] Compiling env_logger v0.11.5 [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` profile [unoptimized + debuginfo] target(s) in 22.61s [INFO] running `Command { std: "docker" "inspect" "fcfaff28d6d170d5682a4bc62baf82358a3aa27c4bad933dcb9d872f3148570b", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "fcfaff28d6d170d5682a4bc62baf82358a3aa27c4bad933dcb9d872f3148570b", kill_on_drop: false }` [INFO] [stdout] fcfaff28d6d170d5682a4bc62baf82358a3aa27c4bad933dcb9d872f3148570b [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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 82143111c7632954a921dd01f2a0e33f5f7de6c1e26b7b94b406ccc728216753 [INFO] running `Command { std: "docker" "start" "-a" "82143111c7632954a921dd01f2a0e33f5f7de6c1e26b7b94b406ccc728216753", kill_on_drop: false }` [INFO] [stderr] Compiling kiley v0.3.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 4.64s [INFO] running `Command { std: "docker" "inspect" "82143111c7632954a921dd01f2a0e33f5f7de6c1e26b7b94b406ccc728216753", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "82143111c7632954a921dd01f2a0e33f5f7de6c1e26b7b94b406ccc728216753", kill_on_drop: false }` [INFO] [stdout] 82143111c7632954a921dd01f2a0e33f5f7de6c1e26b7b94b406ccc728216753 [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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] ab81a4467cf534a447875aa7a0aaa5701d70f579e86271bf060051175aec4e2a [INFO] running `Command { std: "docker" "start" "-a" "ab81a4467cf534a447875aa7a0aaa5701d70f579e86271bf060051175aec4e2a", kill_on_drop: false }` [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.07s [INFO] [stderr] Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/kiley-48d334cf0b367c88) [INFO] [stdout] [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 hmm::guided::tests::likelihood ... ok [INFO] [stdout] test bialignment::guided::test::infix_check ... ok [INFO] [stdout] test bialignment::guided::test::global_check ... 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::overlap_check ... ok [INFO] [stdout] test bialignment::test::naive_edit_dist_modification_check ... ok [INFO] [stdout] test bialignment::banded::tests::banded_naive_check ... ok [INFO] [stdout] test bialignment::banded::tests::global_affine_banded_check ... 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::align_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_test ... ok [INFO] [stdout] test hmm::guided_antidiagonal::test::lk_post has been running for over 60 seconds [INFO] [stdout] test hmm::guided_antidiagonal::test::lk_pre has been running for over 60 seconds [INFO] [stdout] test hmm::guided_antidiagonal::test::align_test ... ok [INFO] [stdout] test hmm::guided_antidiagonal::test::lk_test has been running for over 60 seconds [INFO] [stdout] test hmm::guided_antidiagonal::test::lk_post ... ok [INFO] [stdout] test hmm::guided_antidiagonal::test::fit_test ... 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 padseq::tests::padseq ... ok [INFO] [stdout] test hmm::guided_antidiagonal::test::modification_table_test has been running for over 60 seconds [INFO] [stdout] test hmm::guided_antidiagonal::test::lk_test ... ok [INFO] [stdout] test hmm::guided_antidiagonal::test::polish has been running for over 60 seconds [INFO] [stdout] test hmm::guided_antidiagonal::test::lk_pre ... ok [INFO] [stdout] test hmm::full::test::modification_table_test ... ok [INFO] [stdout] test bialignment::guided::test::polish_test ... ok [INFO] [stdout] test bialignment::banded::tests::edit_dist_modification_check ... ok [INFO] [stdout] test bialignment::test::edit_dist_fast_check_sim ... 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 [ERROR] error running command: command timed out after 900 seconds [INFO] running `Command { std: "docker" "inspect" "ab81a4467cf534a447875aa7a0aaa5701d70f579e86271bf060051175aec4e2a", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "ab81a4467cf534a447875aa7a0aaa5701d70f579e86271bf060051175aec4e2a", kill_on_drop: false }` [INFO] [stdout] ab81a4467cf534a447875aa7a0aaa5701d70f579e86271bf060051175aec4e2a