[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 beta-2022-02-22 for beta-1.60-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fmbhall88%2Fpsdm" "/workspace/builds/worker-5/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-5/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/mbhall88/psdm on toolchain beta-2022-02-22
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2022-02-22" "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-5/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" "+beta-2022-02-22" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded termtree v0.2.3
[INFO] [stderr]   Downloaded predicates-tree v1.0.4
[INFO] [stderr]   Downloaded noodles-sam v0.6.0
[INFO] [stderr]   Downloaded noodles-bgzf v0.4.0
[INFO] [stderr]   Downloaded predicates v2.0.3
[INFO] [stderr]   Downloaded noodles-fasta v0.3.1
[INFO] [stderr]   Downloaded noodles-core v0.2.3
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/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@sha256:0cd99ca24d8e8c98e67c542213511d985b8778b5bdcbb160e038429496686047" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2022-02-22" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 39da4e86cd32a22e502c83d9e5e80019ad5c867e5ac84f5d643f0cea8727a206
[INFO] running `Command { std: "docker" "start" "-a" "39da4e86cd32a22e502c83d9e5e80019ad5c867e5ac84f5d643f0cea8727a206", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "39da4e86cd32a22e502c83d9e5e80019ad5c867e5ac84f5d643f0cea8727a206", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "39da4e86cd32a22e502c83d9e5e80019ad5c867e5ac84f5d643f0cea8727a206", kill_on_drop: false }`
[INFO] [stdout] 39da4e86cd32a22e502c83d9e5e80019ad5c867e5ac84f5d643f0cea8727a206
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/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@sha256:0cd99ca24d8e8c98e67c542213511d985b8778b5bdcbb160e038429496686047" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2022-02-22" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 336c5c4ff85c7cb27352ca41f803334f1a3a1e62c8a2bdbbbf9b3ee804a4ef25
[INFO] running `Command { std: "docker" "start" "-a" "336c5c4ff85c7cb27352ca41f803334f1a3a1e62c8a2bdbbbf9b3ee804a4ef25", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]    Compiling libc v0.2.105
[INFO] [stderr]    Compiling syn v1.0.81
[INFO] [stderr]    Compiling cc v1.0.71
[INFO] [stderr]    Compiling pkg-config v0.3.22
[INFO] [stderr]    Compiling adler v1.0.2
[INFO] [stderr]    Compiling crossbeam-epoch v0.9.5
[INFO] [stderr]    Compiling rayon-core v1.9.1
[INFO] [stderr]    Compiling regex-syntax v0.6.25
[INFO] [stderr]    Compiling unicode-width v0.1.9
[INFO] [stderr]    Compiling once_cell v1.8.0
[INFO] [stderr]    Compiling anyhow v1.0.44
[INFO] [stderr]    Compiling rawpointer v0.2.1
[INFO] [stderr]    Compiling number_prefix v0.4.0
[INFO] [stderr]    Compiling miniz_oxide v0.4.4
[INFO] [stderr]    Compiling num-traits v0.2.14
[INFO] [stderr]    Compiling rayon v1.5.1
[INFO] [stderr]    Compiling num-integer v0.1.44
[INFO] [stderr]    Compiling crossbeam-utils v0.8.5
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]    Compiling itertools v0.10.1
[INFO] [stderr]    Compiling memoffset v0.6.4
[INFO] [stderr]    Compiling indexmap v1.7.0
[INFO] [stderr]    Compiling textwrap v0.11.0
[INFO] [stderr]    Compiling matrixmultiply v0.3.1
[INFO] [stderr]    Compiling crossbeam-channel v0.5.1
[INFO] [stderr]    Compiling crossbeam-deque v0.8.1
[INFO] [stderr]    Compiling lzma-sys v0.1.17
[INFO] [stderr]    Compiling bzip2-sys v0.1.11+1.0.8
[INFO] [stderr]    Compiling flate2 v1.0.22
[INFO] [stderr]    Compiling num_cpus v1.13.0
[INFO] [stderr]    Compiling atty v0.2.14
[INFO] [stderr]    Compiling terminal_size v0.1.17
[INFO] [stderr]    Compiling clap v2.33.3
[INFO] [stderr]    Compiling console v0.15.0
[INFO] [stderr]    Compiling regex v1.5.4
[INFO] [stderr]    Compiling noodles-bgzf v0.4.0
[INFO] [stderr]    Compiling num-complex v0.4.0
[INFO] [stderr]    Compiling xz2 v0.1.6
[INFO] [stderr]    Compiling noodles-sam v0.6.0
[INFO] [stderr]    Compiling ndarray v0.15.3
[INFO] [stderr]    Compiling bzip2 v0.4.3
[INFO] [stderr]    Compiling env_logger v0.9.0
[INFO] [stderr]    Compiling noodles-core v0.2.3
[INFO] [stderr]    Compiling noodles-fasta v0.3.1
[INFO] [stderr]    Compiling indicatif v0.16.2
[INFO] [stderr]    Compiling thiserror-impl v1.0.30
[INFO] [stderr]    Compiling structopt-derive v0.4.18
[INFO] [stderr]    Compiling structopt v0.3.25
[INFO] [stderr]    Compiling thiserror v1.0.30
[INFO] [stderr]    Compiling bgzip v0.2.1
[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 19.99s
[INFO] running `Command { std: "docker" "inspect" "336c5c4ff85c7cb27352ca41f803334f1a3a1e62c8a2bdbbbf9b3ee804a4ef25", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "336c5c4ff85c7cb27352ca41f803334f1a3a1e62c8a2bdbbbf9b3ee804a4ef25", kill_on_drop: false }`
[INFO] [stdout] 336c5c4ff85c7cb27352ca41f803334f1a3a1e62c8a2bdbbbf9b3ee804a4ef25
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/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@sha256:0cd99ca24d8e8c98e67c542213511d985b8778b5bdcbb160e038429496686047" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2022-02-22" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 40d2c78c7344c3065a9867f7deaad16105505e7fe3e48fd677063e5d555bc190
[INFO] running `Command { std: "docker" "start" "-a" "40d2c78c7344c3065a9867f7deaad16105505e7fe3e48fd677063e5d555bc190", kill_on_drop: false }`
[INFO] [stderr]    Compiling doc-comment v0.3.3
[INFO] [stderr]    Compiling predicates-core v1.0.2
[INFO] [stderr]    Compiling difflib v0.4.0
[INFO] [stderr]    Compiling termtree v0.2.3
[INFO] [stderr]    Compiling regex-automata v0.1.10
[INFO] [stderr]    Compiling getrandom v0.2.3
[INFO] [stderr]    Compiling wait-timeout v0.2.0
[INFO] [stderr]    Compiling predicates-tree v1.0.4
[INFO] [stderr]    Compiling rand_core v0.6.3
[INFO] [stderr]    Compiling predicates v2.0.3
[INFO] [stderr]    Compiling bstr v0.2.17
[INFO] [stderr]    Compiling rand_chacha v0.3.1
[INFO] [stderr]    Compiling rand v0.8.4
[INFO] [stderr]    Compiling assert_cmd v2.0.2
[INFO] [stderr]    Compiling tempfile v3.2.0
[INFO] [stderr]    Compiling psdm v0.1.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished test [unoptimized + debuginfo] target(s) in 6.69s
[INFO] running `Command { std: "docker" "inspect" "40d2c78c7344c3065a9867f7deaad16105505e7fe3e48fd677063e5d555bc190", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "40d2c78c7344c3065a9867f7deaad16105505e7fe3e48fd677063e5d555bc190", kill_on_drop: false }`
[INFO] [stdout] 40d2c78c7344c3065a9867f7deaad16105505e7fe3e48fd677063e5d555bc190
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/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@sha256:0cd99ca24d8e8c98e67c542213511d985b8778b5bdcbb160e038429496686047" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2022-02-22" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] e54f5a3035bf7dbb0d8a7b1f8fd1075af5c4d5fa986339abb0db357bd1cd3931
[INFO] running `Command { std: "docker" "start" "-a" "e54f5a3035bf7dbb0d8a7b1f8fd1075af5c4d5fa986339abb0db357bd1cd3931", kill_on_drop: false }`
[INFO] [stdout] 
[INFO] [stderr]     Finished test [unoptimized + debuginfo] target(s) in 0.10s
[INFO] [stdout] running 15 tests
[INFO] [stderr]      Running unittests (/opt/rustwide/target/debug/deps/psdm-48ea956370be0b06)
[INFO] [stdout] test tests::alignments_do_not_all_have_same_length ... ok
[INFO] [stdout] test tests::alignments_do_not_have_same_length_as_starting_seqlen ... ok
[INFO] [stdout] test tests::alignments_sorted_by_id ... ok
[INFO] [stdout] test tests::argsort_with_str ... ok
[INFO] [stdout] test tests::transform_ignore_case ... ok
[INFO] [stdout] test tests::transform_ignore_chars_case_insensitive ... ok
[INFO] [stdout] test tests::transform_ignore_chars_case_sensitive ... ok
[INFO] [stdout] test tests::parse_chars ... ok
[INFO] [stdout] test tests::argsort ... ok
[INFO] [stdout] test tests::sort_by_index ... ok
[INFO] [stdout] test tests::transform_ignore_chars ... ok
[INFO] [stdout] test tests::test_hamming_distance ... ok
[INFO] [stderr]      Running unittests (/opt/rustwide/target/debug/deps/psdm-b5b00aface3897a2)
[INFO] [stdout] test tests::alignments_all_have_same_length ... ok
[INFO] [stdout] test tests::argsort_on_empty ... ok
[INFO] [stdout] test tests::transform_preserve_case ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 15 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.03s
[INFO] [stdout] 
[INFO] [stdout] 
[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-d4278c9daf3a2e47)
[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 inter_alignment_with_tab_delim ... ok
[INFO] [stdout] test input_file_does_not_exist ... ok
[INFO] [stdout] test alignment_seqs_do_not_have_same_length ... ok
[INFO] [stdout] test alignment_files_do_not_have_same_length ... ok
[INFO] [stdout] test intra_alignment_with_defaults_long_form ... ok
[INFO] [stdout] test inter_alignment_in_long_form_sorted ... ok
[INFO] [stdout] test alignment_is_not_fasta ... 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 intra_alignment_with_defaults ... ok
[INFO] [stdout] test more_than_two_input_files_fails ... ok
[INFO] [stdout] test intra_alignment_with_use_case_ignore_characters ... ok
[INFO] [stderr]    Doc-tests psdm
[INFO] [stdout] test intra_alignment_with_ignore_case_ignore_no_characters ... ok
[INFO] [stdout] test intra_alignment_with_ignore_case_ignore_characters_sorted ... ok
[INFO] [stdout] test intra_alignment_with_ignore_case_ignore_characters ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 15 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.07s
[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" "e54f5a3035bf7dbb0d8a7b1f8fd1075af5c4d5fa986339abb0db357bd1cd3931", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "e54f5a3035bf7dbb0d8a7b1f8fd1075af5c4d5fa986339abb0db357bd1cd3931", kill_on_drop: false }`
[INFO] [stdout] e54f5a3035bf7dbb0d8a7b1f8fd1075af5c4d5fa986339abb0db357bd1cd3931