[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] d12fabdb6fe103b494d5767e31bdb67d4c8d2604
[INFO] testing mbhall88/psdm against try#8de4c7234dd9b97c9d76b58671343fdbbc9a433e+target=x86_64-unknown-linux-musl for musl_upgrade_1_2_5_with_libc_patch_0
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fmbhall88%2Fpsdm" "/workspace/builds/worker-0-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc1/source'...
[INFO] [stderr] done.
[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-0-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/mbhall88/psdm on toolchain 8de4c7234dd9b97c9d76b58671343fdbbc9a433e
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/mbhall88/psdm 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" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded noodles-bgzf v0.31.0
[INFO] [stderr]   Downloaded noodles-core v0.15.0
[INFO] [stderr]   Downloaded predicates v2.0.3
[INFO] [stderr]   Downloaded bgzip v0.2.1
[INFO] [stderr]   Downloaded niffler v2.3.2
[INFO] [stderr]   Downloaded noodles-fasta v0.40.0
[INFO] [stderr]   Downloaded ndarray v0.15.3
[INFO] [stderr]   Downloaded serde v1.0.185
[INFO] [stderr]   Downloaded bstr v1.9.1
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 49467562b651873f201b466a746384028038ca7dcb5c35b5c648a41730f14c9c
[INFO] running `Command { std: "docker" "start" "-a" "49467562b651873f201b466a746384028038ca7dcb5c35b5c648a41730f14c9c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "49467562b651873f201b466a746384028038ca7dcb5c35b5c648a41730f14c9c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "49467562b651873f201b466a746384028038ca7dcb5c35b5c648a41730f14c9c", kill_on_drop: false }`
[INFO] [stdout] 49467562b651873f201b466a746384028038ca7dcb5c35b5c648a41730f14c9c
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "build" "--frozen" "--message-format=json" "--target" "x86_64-unknown-linux-musl", kill_on_drop: false }`
[INFO] [stdout] d96d464e940109d41bdd094ba10c68a1272ec15001a531f61a1831c48fae974c
[INFO] running `Command { std: "docker" "start" "-a" "d96d464e940109d41bdd094ba10c68a1272ec15001a531f61a1831c48fae974c", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.105
[INFO] [stderr]    Compiling syn v1.0.81
[INFO] [stderr]    Compiling pkg-config v0.3.22
[INFO] [stderr]    Compiling cc v1.0.71
[INFO] [stderr]    Compiling miniz_oxide v0.4.4
[INFO] [stderr]    Compiling crc32fast v1.2.1
[INFO] [stderr]    Compiling memoffset v0.6.4
[INFO] [stderr]    Compiling num-traits v0.2.14
[INFO] [stderr]    Compiling crossbeam-epoch v0.9.5
[INFO] [stderr]    Compiling aho-corasick v0.7.18
[INFO] [stderr]    Compiling indexmap v1.7.0
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]    Compiling anstyle-parse v0.2.4
[INFO] [stderr]    Compiling crossbeam-channel v0.5.13
[INFO] [stderr]    Compiling bstr v1.9.1
[INFO] [stderr]    Compiling anstyle-query v1.1.0
[INFO] [stderr]    Compiling either v1.6.1
[INFO] [stderr]    Compiling os_str_bytes v6.1.0
[INFO] [stderr]    Compiling is_terminal_polyfill v1.70.0
[INFO] [stderr]    Compiling colorchoice v1.0.1
[INFO] [stderr]    Compiling log v0.4.21
[INFO] [stderr]    Compiling anstyle v1.0.7
[INFO] [stderr]    Compiling rawpointer v0.2.1
[INFO] [stderr]    Compiling matrixmultiply v0.3.1
[INFO] [stderr]    Compiling anstream v0.6.14
[INFO] [stderr]    Compiling clap_lex v0.2.0
[INFO] [stderr]    Compiling anyhow v1.0.44
[INFO] [stderr]    Compiling termcolor v1.1.2
[INFO] [stderr]    Compiling itertools v0.13.0
[INFO] [stderr]    Compiling crossbeam-deque v0.8.1
[INFO] [stderr]    Compiling noodles-core v0.15.0
[INFO] [stderr]    Compiling flate2 v1.0.22
[INFO] [stderr]    Compiling atty v0.2.14
[INFO] [stderr]    Compiling rayon-core v1.12.1
[INFO] [stderr]    Compiling regex v1.5.4
[INFO] [stderr]    Compiling num-integer v0.1.44
[INFO] [stderr]    Compiling num-complex v0.4.0
[INFO] [stderr]    Compiling noodles-bgzf v0.31.0
[INFO] [stderr]    Compiling lzma-sys v0.1.17
[INFO] [stderr]    Compiling bzip2-sys v0.1.11+1.0.8
[INFO] [stderr]    Compiling rayon v1.10.0
[INFO] [stderr]    Compiling noodles-fasta v0.40.0
[INFO] [stderr]    Compiling ndarray v0.15.3
[INFO] [stderr]    Compiling env_filter v0.1.0
[INFO] [stderr]    Compiling env_logger v0.11.3
[INFO] [stderr]    Compiling bzip2 v0.4.3
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]    Compiling thiserror-impl v1.0.30
[INFO] [stderr]    Compiling clap_derive v3.1.18
[INFO] [stderr]    Compiling thiserror v1.0.30
[INFO] [stderr]    Compiling bgzip v0.2.1
[INFO] [stderr]    Compiling clap v3.1.18
[INFO] [stderr]    Compiling xz2 v0.1.6
[INFO] [stderr]    Compiling niffler v2.3.2
[INFO] [stderr]    Compiling psdm v0.3.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 12.25s
[INFO] running `Command { std: "docker" "inspect" "d96d464e940109d41bdd094ba10c68a1272ec15001a531f61a1831c48fae974c", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "d96d464e940109d41bdd094ba10c68a1272ec15001a531f61a1831c48fae974c", kill_on_drop: false }`
[INFO] [stdout] d96d464e940109d41bdd094ba10c68a1272ec15001a531f61a1831c48fae974c
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "test" "--frozen" "--no-run" "--message-format=json" "--target" "x86_64-unknown-linux-musl", kill_on_drop: false }`
[INFO] [stdout] ff70fafb328c6afed40da67f3cd82d14aa517de93add61594ec0ac2355d513c9
[INFO] running `Command { std: "docker" "start" "-a" "ff70fafb328c6afed40da67f3cd82d14aa517de93add61594ec0ac2355d513c9", kill_on_drop: false }`
[INFO] [stderr]    Compiling getrandom v0.2.3
[INFO] [stderr]    Compiling predicates-core v1.0.2
[INFO] [stderr]    Compiling doc-comment v0.3.3
[INFO] [stderr]    Compiling itertools v0.10.1
[INFO] [stderr]    Compiling termtree v0.2.3
[INFO] [stderr]    Compiling difflib v0.4.0
[INFO] [stderr]    Compiling regex-automata v0.1.10
[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 bstr v0.2.17
[INFO] [stderr]    Compiling rand_chacha v0.3.1
[INFO] [stderr]    Compiling rand v0.8.4
[INFO] [stderr]    Compiling tempfile v3.2.0
[INFO] [stderr]    Compiling predicates v2.0.3
[INFO] [stderr]    Compiling assert_cmd v2.0.2
[INFO] [stderr]    Compiling psdm v0.3.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 2.23s
[INFO] running `Command { std: "docker" "inspect" "ff70fafb328c6afed40da67f3cd82d14aa517de93add61594ec0ac2355d513c9", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "ff70fafb328c6afed40da67f3cd82d14aa517de93add61594ec0ac2355d513c9", kill_on_drop: false }`
[INFO] [stdout] ff70fafb328c6afed40da67f3cd82d14aa517de93add61594ec0ac2355d513c9
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "test" "--frozen" "--target" "x86_64-unknown-linux-musl", kill_on_drop: false }`
[INFO] [stdout] a60f388a3ae5724db15ed331fad2e0a4af9e77f249c363bb5b55da756dbb5fdb
[INFO] running `Command { std: "docker" "start" "-a" "a60f388a3ae5724db15ed331fad2e0a4af9e77f249c363bb5b55da756dbb5fdb", kill_on_drop: false }`
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.06s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/x86_64-unknown-linux-musl/debug/deps/psdm-29d61db2769c83fe)
[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::alignments_do_not_all_have_same_length ... ok
[INFO] [stdout] test tests::alignments_sorted_by_id ... ok
[INFO] [stdout] test tests::argsort ... ok
[INFO] [stdout] test tests::argsort_on_empty ... ok
[INFO] [stdout] test tests::argsort_with_str ... ok
[INFO] [stdout] test tests::parse_chars ... 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_ignore_chars_case_sensitive ... 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 0.00s
[INFO] [stdout] 
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/x86_64-unknown-linux-musl/debug/deps/psdm-dfa73d2228a62d15)
[INFO] [stdout] 
[INFO] [stdout] running 2 tests
[INFO] [stdout] test tests::check_path_exists_it_doesnt ... ok
[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 0.00s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/main.rs (/opt/rustwide/target/x86_64-unknown-linux-musl/debug/deps/main-2c0af81faf963b68)
[INFO] [stdout] 
[INFO] [stdout] running 15 tests
[INFO] [stdout] test input_file_does_not_exist ... ok
[INFO] [stdout] test alignment_is_not_fasta ... ok
[INFO] [stdout] test intra_alignment_with_defaults ... ok
[INFO] [stdout] test intra_alignment_with_defaults_long_form_sorted ... ok
[INFO] [stdout] test inter_alignment_with_tab_delim ... ok
[INFO] [stdout] test inter_alignment_in_long_form_sorted ... ok
[INFO] [stdout] test intra_alignment_with_ignore_case_ignore_characters ... 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 alignment_seqs_do_not_have_same_length ... ok
[INFO] [stdout] test intra_alignment_with_ignore_case_ignore_characters_sorted ... ok
[INFO] [stdout] test more_than_two_input_files_fails ... ok
[INFO] [stdout] test alignment_files_do_not_have_same_length ... ok
[INFO] [stdout] test trying_to_create_output_in_nonexistent_dir ... ok
[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 0.02s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "a60f388a3ae5724db15ed331fad2e0a4af9e77f249c363bb5b55da756dbb5fdb", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "a60f388a3ae5724db15ed331fad2e0a4af9e77f249c363bb5b55da756dbb5fdb", kill_on_drop: false }`
[INFO] [stdout] a60f388a3ae5724db15ed331fad2e0a4af9e77f249c363bb5b55da756dbb5fdb