[INFO] cloning repository https://github.com/justicengom/psdm
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/justicengom/psdm" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fjusticengom%2Fpsdm", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fjusticengom%2Fpsdm'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 763e48a5e4dc2603f2c353bf07e547cff96f35cc
[INFO] testing justicengom/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%2Fjusticengom%2Fpsdm" "/workspace/builds/worker-7-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-7-tc1/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/justicengom/psdm
[INFO] finished tweaking git repo https://github.com/justicengom/psdm
[INFO] tweaked toml for git repo https://github.com/justicengom/psdm written to /workspace/builds/worker-7-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/justicengom/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/justicengom/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]     Blocking waiting for file lock on package cache
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded bzip2 v0.4.3
[INFO] [stderr]   Downloaded noodles-fasta v0.3.1
[INFO] [stderr]   Downloaded bgzip v0.2.1
[INFO] [stderr]   Downloaded niffler v2.3.2
[INFO] [stderr]   Downloaded xz2 v0.1.6
[INFO] [stderr]   Downloaded noodles-core v0.2.3
[INFO] [stderr]   Downloaded noodles-bgzf v0.4.0
[INFO] [stderr]   Downloaded clap_lex v0.2.0
[INFO] [stderr]   Downloaded anyhow v1.0.44
[INFO] [stderr]   Downloaded matrixmultiply v0.3.1
[INFO] [stderr]   Downloaded num-complex v0.4.0
[INFO] [stderr]   Downloaded noodles-sam v0.6.0
[INFO] [stderr]   Downloaded ndarray v0.15.3
[INFO] [stderr]   Downloaded lzma-sys v0.1.17
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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] 90ab0b8ecccc2c7e3675a4fa4b9b0b66763198f7c62b47b01e077c78b3b7c857
[INFO] running `Command { std: "docker" "start" "-a" "90ab0b8ecccc2c7e3675a4fa4b9b0b66763198f7c62b47b01e077c78b3b7c857", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "90ab0b8ecccc2c7e3675a4fa4b9b0b66763198f7c62b47b01e077c78b3b7c857", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "90ab0b8ecccc2c7e3675a4fa4b9b0b66763198f7c62b47b01e077c78b3b7c857", kill_on_drop: false }`
[INFO] [stdout] 90ab0b8ecccc2c7e3675a4fa4b9b0b66763198f7c62b47b01e077c78b3b7c857
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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] cdeadf99faa30968f13f0beaca31beabd26b3ceb3e987409e1c08843066ad327
[INFO] running `Command { std: "docker" "start" "-a" "cdeadf99faa30968f13f0beaca31beabd26b3ceb3e987409e1c08843066ad327", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.105
[INFO] [stderr]    Compiling proc-macro2 v1.0.32
[INFO] [stderr]    Compiling unicode-xid v0.2.2
[INFO] [stderr]    Compiling miniz_oxide v0.4.4
[INFO] [stderr]    Compiling cc v1.0.71
[INFO] [stderr]    Compiling pkg-config v0.3.22
[INFO] [stderr]    Compiling crc32fast v1.2.1
[INFO] [stderr]    Compiling syn v1.0.81
[INFO] [stderr]    Compiling version_check v0.9.4
[INFO] [stderr]    Compiling crossbeam-utils v0.8.5
[INFO] [stderr]    Compiling adler v1.0.2
[INFO] [stderr]    Compiling memoffset v0.6.4
[INFO] [stderr]    Compiling memchr v2.4.1
[INFO] [stderr]    Compiling indexmap v1.7.0
[INFO] [stderr]    Compiling crossbeam-epoch v0.9.5
[INFO] [stderr]    Compiling num-traits v0.2.14
[INFO] [stderr]    Compiling rayon-core v1.9.1
[INFO] [stderr]    Compiling hashbrown v0.11.2
[INFO] [stderr]    Compiling bitflags v1.3.2
[INFO] [stderr]    Compiling byteorder v1.4.3
[INFO] [stderr]    Compiling rayon v1.5.1
[INFO] [stderr]    Compiling num-integer v0.1.44
[INFO] [stderr]    Compiling crossbeam-channel v0.5.1
[INFO] [stderr]    Compiling either v1.6.1
[INFO] [stderr]    Compiling regex-syntax v0.6.25
[INFO] [stderr]    Compiling log v0.4.14
[INFO] [stderr]    Compiling heck v0.4.0
[INFO] [stderr]    Compiling anyhow v1.0.44
[INFO] [stderr]    Compiling termcolor v1.1.2
[INFO] [stderr]    Compiling os_str_bytes v6.1.0
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]    Compiling aho-corasick v0.7.18
[INFO] [stderr]    Compiling crossbeam-deque v0.8.1
[INFO] [stderr]    Compiling once_cell v1.8.0
[INFO] [stderr]    Compiling rawpointer v0.2.1
[INFO] [stderr]    Compiling clap_lex v0.2.0
[INFO] [stderr]    Compiling matrixmultiply v0.3.1
[INFO] [stderr]    Compiling quote v1.0.10
[INFO] [stderr]    Compiling humantime v2.1.0
[INFO] [stderr]    Compiling strsim v0.10.0
[INFO] [stderr]    Compiling number_prefix v0.4.0
[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 console v0.15.0
[INFO] [stderr]    Compiling num-complex v0.4.0
[INFO] [stderr]    Compiling textwrap v0.15.0
[INFO] [stderr]    Compiling itertools v0.10.1
[INFO] [stderr]    Compiling noodles-bgzf v0.4.0
[INFO] [stderr]    Compiling regex v1.5.4
[INFO] [stderr]    Compiling ndarray v0.15.3
[INFO] [stderr]    Compiling noodles-sam v0.6.0
[INFO] [stderr]    Compiling bzip2-sys v0.1.11+1.0.8
[INFO] [stderr]    Compiling lzma-sys v0.1.17
[INFO] [stderr]    Compiling env_logger v0.9.0
[INFO] [stderr]    Compiling noodles-core v0.2.3
[INFO] [stderr]    Compiling bzip2 v0.4.3
[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 clap_derive v3.1.18
[INFO] [stderr]    Compiling xz2 v0.1.6
[INFO] [stderr]    Compiling thiserror v1.0.30
[INFO] [stderr]    Compiling bgzip v0.2.1
[INFO] [stderr]    Compiling niffler v2.3.2
[INFO] [stderr]    Compiling clap v3.1.18
[INFO] [stderr]    Compiling psdm v0.2.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 26.94s
[INFO] running `Command { std: "docker" "inspect" "cdeadf99faa30968f13f0beaca31beabd26b3ceb3e987409e1c08843066ad327", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "cdeadf99faa30968f13f0beaca31beabd26b3ceb3e987409e1c08843066ad327", kill_on_drop: false }`
[INFO] [stdout] cdeadf99faa30968f13f0beaca31beabd26b3ceb3e987409e1c08843066ad327
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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] be228a3c3982ff295d462e48a168b2f5b2d11c012d831e85caedfc82a0e3d2c2
[INFO] running `Command { std: "docker" "start" "-a" "be228a3c3982ff295d462e48a168b2f5b2d11c012d831e85caedfc82a0e3d2c2", 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 ppv-lite86 v0.2.15
[INFO] [stderr]    Compiling termtree v0.2.3
[INFO] [stderr]    Compiling regex-automata v0.1.10
[INFO] [stderr]    Compiling difflib v0.4.0
[INFO] [stderr]    Compiling wait-timeout v0.2.0
[INFO] [stderr]    Compiling remove_dir_all v0.5.3
[INFO] [stderr]    Compiling predicates-tree v1.0.4
[INFO] [stderr]    Compiling bstr v0.2.17
[INFO] [stderr]    Compiling rand_core v0.6.3
[INFO] [stderr]    Compiling predicates v2.0.3
[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 v0.2.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 5.55s
[INFO] running `Command { std: "docker" "inspect" "be228a3c3982ff295d462e48a168b2f5b2d11c012d831e85caedfc82a0e3d2c2", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "be228a3c3982ff295d462e48a168b2f5b2d11c012d831e85caedfc82a0e3d2c2", kill_on_drop: false }`
[INFO] [stdout] be228a3c3982ff295d462e48a168b2f5b2d11c012d831e85caedfc82a0e3d2c2
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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] a22f4de218f6c58ecdb713e417454e5071335bb63da731d1d9695a6b1f754a95
[INFO] running `Command { std: "docker" "start" "-a" "a22f4de218f6c58ecdb713e417454e5071335bb63da731d1d9695a6b1f754a95", kill_on_drop: false }`
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.21s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/x86_64-unknown-linux-musl/debug/deps/psdm-f9d71eb08ca32926)
[INFO] [stdout] 
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/x86_64-unknown-linux-musl/debug/deps/psdm-8e7ad0306aea673b)
[INFO] [stdout] running 15 tests
[INFO] [stderr]      Running tests/main.rs (/opt/rustwide/target/x86_64-unknown-linux-musl/debug/deps/main-e02107ae6ee05620)
[INFO] [stdout] test tests::alignments_all_have_same_length ... ok
[INFO] [stdout] test tests::alignments_sorted_by_id ... ok
[INFO] [stdout] test tests::argsort_on_empty ... ok
[INFO] [stdout] test tests::alignments_do_not_have_same_length_as_starting_seqlen ... ok
[INFO] [stdout] test tests::argsort ... ok
[INFO] [stdout] test tests::alignments_do_not_all_have_same_length ... 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] [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] [stdout] 
[INFO] [stdout] running 15 tests
[INFO] [stdout] test alignment_is_not_fasta ... ok
[INFO] [stdout] test intra_alignment_with_ignore_case_ignore_characters_sorted ... ok
[INFO] [stdout] test intra_alignment_with_ignore_case_ignore_no_characters ... ok
[INFO] [stdout] test intra_alignment_with_defaults_long_form ... ok
[INFO] [stdout] test inter_alignment_with_tab_delim ... 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_defaults_long_form_sorted ... ok
[INFO] [stdout] test more_than_two_input_files_fails ... ok
[INFO] [stdout] test input_file_does_not_exist ... ok
[INFO] [stdout] test intra_alignment_with_use_case_ignore_characters ... ok
[INFO] [stdout] test alignment_files_do_not_have_same_length ... ok
[INFO] [stdout] test intra_alignment_with_defaults ... ok
[INFO] [stdout] test trying_to_create_output_in_nonexistent_dir ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 15 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.05s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "a22f4de218f6c58ecdb713e417454e5071335bb63da731d1d9695a6b1f754a95", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "a22f4de218f6c58ecdb713e417454e5071335bb63da731d1d9695a6b1f754a95", kill_on_drop: false }`
[INFO] [stdout] a22f4de218f6c58ecdb713e417454e5071335bb63da731d1d9695a6b1f754a95