[INFO] cloning repository https://github.com/mbhall88/psdm [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/mbhall88/psdm" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fmbhall88%2Fpsdm", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fmbhall88%2Fpsdm'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 14dc193d59b6a886ea56532c2d68f8f614aebbd3 [INFO] testing mbhall88/psdm against 1.60.0 for beta-1.61-1 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fmbhall88%2Fpsdm" "/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/mbhall88/psdm on toolchain 1.60.0 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.60.0" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/mbhall88/psdm [INFO] finished tweaking git repo https://github.com/mbhall88/psdm [INFO] tweaked toml for git repo https://github.com/mbhall88/psdm written to /workspace/builds/worker-2/source/Cargo.toml [INFO] crate git repo https://github.com/mbhall88/psdm already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.60.0" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded termtree v0.2.3 [INFO] [stderr] Downloaded predicates v2.0.3 [INFO] [stderr] Downloaded predicates-tree v1.0.4 [INFO] [stderr] Downloaded assert_cmd v2.0.2 [INFO] [stderr] Downloaded matrixmultiply v0.3.1 [INFO] [stderr] Downloaded ndarray v0.15.3 [INFO] [stderr] Downloaded noodles-core v0.2.3 [INFO] [stderr] Downloaded noodles-fasta v0.3.1 [INFO] [stderr] Downloaded noodles-bgzf v0.4.0 [INFO] [stderr] Downloaded noodles-sam v0.6.0 [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:eaef2f80f755933c374d2ae5edccceec0c1312ceb8a4e0b6404e8ab76561e1e5" "/opt/rustwide/cargo-home/bin/cargo" "+1.60.0" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 4241156128a4d6fbdacbd850932b4e5223515ad8345856a8f359404b97777d1f [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" "4241156128a4d6fbdacbd850932b4e5223515ad8345856a8f359404b97777d1f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "4241156128a4d6fbdacbd850932b4e5223515ad8345856a8f359404b97777d1f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "4241156128a4d6fbdacbd850932b4e5223515ad8345856a8f359404b97777d1f", kill_on_drop: false }` [INFO] [stdout] 4241156128a4d6fbdacbd850932b4e5223515ad8345856a8f359404b97777d1f [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=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:eaef2f80f755933c374d2ae5edccceec0c1312ceb8a4e0b6404e8ab76561e1e5" "/opt/rustwide/cargo-home/bin/cargo" "+1.60.0" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 476b0b121509fe3b16a80097b5852dac4c5e997ee96cc6dd0197e11562e03281 [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" "476b0b121509fe3b16a80097b5852dac4c5e997ee96cc6dd0197e11562e03281", kill_on_drop: false }` [INFO] [stderr] Compiling syn v1.0.81 [INFO] [stderr] Compiling num-traits v0.2.14 [INFO] [stderr] Compiling bzip2-sys v0.1.11+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.17 [INFO] [stderr] Compiling matrixmultiply v0.3.1 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling terminal_size v0.1.17 [INFO] [stderr] Compiling flate2 v1.0.22 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Compiling crossbeam-deque v0.8.1 [INFO] [stderr] Compiling regex v1.5.4 [INFO] [stderr] Compiling clap v2.33.3 [INFO] [stderr] Compiling console v0.15.0 [INFO] [stderr] Compiling rayon-core v1.9.1 [INFO] [stderr] Compiling noodles-bgzf v0.4.0 [INFO] [stderr] Compiling noodles-sam v0.6.0 [INFO] [stderr] Compiling xz2 v0.1.6 [INFO] [stderr] Compiling rayon v1.5.1 [INFO] [stderr] Compiling bzip2 v0.4.3 [INFO] [stderr] Compiling env_logger v0.9.0 [INFO] [stderr] Compiling num-integer v0.1.44 [INFO] [stderr] Compiling num-complex v0.4.0 [INFO] [stderr] Compiling noodles-core v0.2.3 [INFO] [stderr] Compiling ndarray v0.15.3 [INFO] [stderr] Compiling noodles-fasta v0.3.1 [INFO] [stderr] Compiling indicatif v0.16.2 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Compiling thiserror-impl v1.0.30 [INFO] [stderr] Compiling structopt-derive v0.4.18 [INFO] [stderr] Compiling thiserror v1.0.30 [INFO] [stderr] Compiling bgzip v0.2.1 [INFO] [stderr] Compiling structopt v0.3.25 [INFO] [stderr] Compiling niffler v2.3.2 [INFO] [stderr] Compiling psdm v0.1.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 1m 16s [INFO] running `Command { std: "docker" "inspect" "476b0b121509fe3b16a80097b5852dac4c5e997ee96cc6dd0197e11562e03281", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "476b0b121509fe3b16a80097b5852dac4c5e997ee96cc6dd0197e11562e03281", kill_on_drop: false }` [INFO] [stdout] 476b0b121509fe3b16a80097b5852dac4c5e997ee96cc6dd0197e11562e03281 [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=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:eaef2f80f755933c374d2ae5edccceec0c1312ceb8a4e0b6404e8ab76561e1e5" "/opt/rustwide/cargo-home/bin/cargo" "+1.60.0" "test" "--frozen" "--no-run" "--message-format=json", 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] 15a2286d265f33bedd29f4392d2b089475ecd1e0a21c29c22764002c3aa41ce6 [INFO] running `Command { std: "docker" "start" "-a" "15a2286d265f33bedd29f4392d2b089475ecd1e0a21c29c22764002c3aa41ce6", kill_on_drop: false }` [INFO] [stderr] Compiling termtree v0.2.3 [INFO] [stderr] Compiling predicates v2.0.3 [INFO] [stderr] Compiling bstr v0.2.17 [INFO] [stderr] Compiling wait-timeout v0.2.0 [INFO] [stderr] Compiling predicates-tree v1.0.4 [INFO] [stderr] Compiling assert_cmd v2.0.2 [INFO] [stderr] Compiling psdm v0.1.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished test [unoptimized + debuginfo] target(s) in 13.10s [INFO] running `Command { std: "docker" "inspect" "15a2286d265f33bedd29f4392d2b089475ecd1e0a21c29c22764002c3aa41ce6", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "15a2286d265f33bedd29f4392d2b089475ecd1e0a21c29c22764002c3aa41ce6", kill_on_drop: false }` [INFO] [stdout] 15a2286d265f33bedd29f4392d2b089475ecd1e0a21c29c22764002c3aa41ce6 [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=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:eaef2f80f755933c374d2ae5edccceec0c1312ceb8a4e0b6404e8ab76561e1e5" "/opt/rustwide/cargo-home/bin/cargo" "+1.60.0" "test" "--frozen", 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] 56de08bdf808ae80a87e670904bb95661435b7d610377e36077be61ecba5f97e [INFO] running `Command { std: "docker" "start" "-a" "56de08bdf808ae80a87e670904bb95661435b7d610377e36077be61ecba5f97e", kill_on_drop: false }` [INFO] [stderr] Finished test [unoptimized + debuginfo] target(s) in 0.17s [INFO] [stderr] Running unittests (/opt/rustwide/target/debug/deps/psdm-377da916ec0106e4) [INFO] [stdout] [INFO] [stdout] running 15 tests [INFO] [stdout] test tests::alignments_all_have_same_length ... ok [INFO] [stdout] test tests::alignments_do_not_have_same_length_as_starting_seqlen ... ok [INFO] [stdout] test tests::argsort_on_empty ... ok [INFO] [stdout] test tests::argsort_with_str ... ok [INFO] [stdout] test tests::sort_by_index ... ok [INFO] [stdout] test tests::test_hamming_distance ... ok [INFO] [stdout] test tests::transform_ignore_case ... ok [INFO] [stdout] test tests::transform_ignore_chars ... ok [INFO] [stdout] test tests::transform_ignore_chars_case_insensitive ... ok [INFO] [stdout] test tests::transform_preserve_case ... ok [INFO] [stdout] test tests::argsort ... ok [INFO] [stdout] test tests::parse_chars ... ok [INFO] [stdout] test tests::transform_ignore_chars_case_sensitive ... ok [INFO] [stdout] test tests::alignments_sorted_by_id ... ok [INFO] [stdout] test tests::alignments_do_not_all_have_same_length ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 15 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.02s [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Running unittests (/opt/rustwide/target/debug/deps/psdm-72163d55f8cbdfdf) [INFO] [stdout] running 2 tests [INFO] [stdout] test tests::check_path_exists_it_doesnt ... ok [INFO] [stderr] Running tests/main.rs (/opt/rustwide/target/debug/deps/main-1d5f44d7d02e785e) [INFO] [stdout] test tests::check_path_it_does ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 2 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] running 15 tests [INFO] [stdout] test alignment_files_do_not_have_same_length ... ok [INFO] [stdout] test intra_alignment_with_defaults_long_form ... ok [INFO] [stdout] test intra_alignment_with_ignore_case_ignore_no_characters ... ok [INFO] [stdout] test inter_alignment_with_tab_delim ... ok [INFO] [stdout] test input_file_does_not_exist ... ok [INFO] [stdout] test intra_alignment_with_ignore_case_ignore_characters ... ok [INFO] [stdout] test alignment_seqs_do_not_have_same_length ... ok [INFO] [stdout] test inter_alignment_in_long_form_sorted ... ok [INFO] [stdout] test intra_alignment_with_ignore_case_ignore_characters_sorted ... ok [INFO] [stdout] test intra_alignment_with_defaults_long_form_sorted ... ok [INFO] [stdout] test trying_to_create_output_in_nonexistent_dir ... ok [INFO] [stdout] test alignment_is_not_fasta ... ok [INFO] [stdout] test intra_alignment_with_defaults ... ok [INFO] [stdout] test more_than_two_input_files_fails ... ok [INFO] [stderr] Doc-tests psdm [INFO] [stdout] test intra_alignment_with_use_case_ignore_characters ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 15 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.14s [INFO] [stdout] [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" "56de08bdf808ae80a87e670904bb95661435b7d610377e36077be61ecba5f97e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "56de08bdf808ae80a87e670904bb95661435b7d610377e36077be61ecba5f97e", kill_on_drop: false }` [INFO] [stdout] 56de08bdf808ae80a87e670904bb95661435b7d610377e36077be61ecba5f97e