[INFO] cloning repository https://github.com/Adoni5/readfish-tools [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/Adoni5/readfish-tools" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FAdoni5%2Freadfish-tools", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FAdoni5%2Freadfish-tools'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 65e2b67ce81834e429cc46aea86166036fa2971a [INFO] testing Adoni5/readfish-tools against beta-2025-04-13 for beta-1.87-1 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FAdoni5%2Freadfish-tools" "/workspace/builds/worker-7-tc2/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-7-tc2/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/Adoni5/readfish-tools on toolchain beta-2025-04-13 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+beta-2025-04-13" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/Adoni5/readfish-tools [INFO] finished tweaking git repo https://github.com/Adoni5/readfish-tools [INFO] tweaked toml for git repo https://github.com/Adoni5/readfish-tools written to /workspace/builds/worker-7-tc2/source/Cargo.toml [INFO] crate git repo https://github.com/Adoni5/readfish-tools 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" "+beta-2025-04-13" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/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:b0b074c097205a61b89e8ad263052f976b2b332c4dc5f02aef1fe52501660d6e" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-04-13" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] f91c3c73b41234485465445884e8fc7c9f0491292dc26f630d63f8acece672e4 [INFO] running `Command { std: "docker" "start" "-a" "f91c3c73b41234485465445884e8fc7c9f0491292dc26f630d63f8acece672e4", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "f91c3c73b41234485465445884e8fc7c9f0491292dc26f630d63f8acece672e4", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f91c3c73b41234485465445884e8fc7c9f0491292dc26f630d63f8acece672e4", kill_on_drop: false }` [INFO] [stdout] f91c3c73b41234485465445884e8fc7c9f0491292dc26f630d63f8acece672e4 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/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" "RUSTDOCFLAGS=--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:b0b074c097205a61b89e8ad263052f976b2b332c4dc5f02aef1fe52501660d6e" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-04-13" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 2ed17cc830d3d03d86c137db58d5ccdc69f95aa489adbbbb1f6b6997ead0d1f5 [INFO] running `Command { std: "docker" "start" "-a" "2ed17cc830d3d03d86c137db58d5ccdc69f95aa489adbbbb1f6b6997ead0d1f5", kill_on_drop: false }` [INFO] [stderr] Compiling autocfg v1.1.0 [INFO] [stderr] Compiling proc-macro2 v1.0.64 [INFO] [stderr] Compiling quote v1.0.29 [INFO] [stderr] Compiling unicode-ident v1.0.10 [INFO] [stderr] Compiling libc v0.2.147 [INFO] [stderr] Compiling cfg-if v1.0.0 [INFO] [stderr] Compiling target-lexicon v0.12.10 [INFO] [stderr] Compiling cc v1.0.79 [INFO] [stderr] Compiling scopeguard v1.1.0 [INFO] [stderr] Compiling serde v1.0.171 [INFO] [stderr] Compiling memchr v2.5.0 [INFO] [stderr] Compiling once_cell v1.18.0 [INFO] [stderr] Compiling crossbeam-utils v0.8.16 [INFO] [stderr] Compiling pkg-config v0.3.27 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Compiling vcpkg v0.2.15 [INFO] [stderr] Compiling futures-core v0.3.28 [INFO] [stderr] Compiling crc32fast v1.3.2 [INFO] [stderr] Compiling parking_lot_core v0.9.8 [INFO] [stderr] Compiling rustix v0.38.4 [INFO] [stderr] Compiling smallvec v1.11.0 [INFO] [stderr] Compiling rayon-core v1.11.0 [INFO] [stderr] Compiling bitflags v2.3.3 [INFO] [stderr] Compiling adler v1.0.2 [INFO] [stderr] Compiling itoa v1.0.8 [INFO] [stderr] Compiling linux-raw-sys v0.4.3 [INFO] [stderr] Compiling equivalent v1.0.1 [INFO] [stderr] Compiling hashbrown v0.14.0 [INFO] [stderr] Compiling thiserror v1.0.43 [INFO] [stderr] Compiling miniz_oxide v0.7.1 [INFO] [stderr] Compiling cmake v0.1.50 [INFO] [stderr] Compiling aho-corasick v1.0.2 [INFO] [stderr] Compiling csv-core v0.1.10 [INFO] [stderr] Compiling indexmap v2.0.0 [INFO] [stderr] Compiling syn v2.0.25 [INFO] [stderr] Compiling memoffset v0.9.0 [INFO] [stderr] Compiling pyo3-build-config v0.19.1 [INFO] [stderr] Compiling lock_api v0.4.10 [INFO] [stderr] Compiling num-traits v0.2.15 [INFO] [stderr] Compiling crossbeam-epoch v0.9.15 [INFO] [stderr] Compiling num_cpus v1.16.0 [INFO] [stderr] Compiling getrandom v0.2.10 [INFO] [stderr] Compiling dirs-sys-next v0.1.2 [INFO] [stderr] Compiling num-integer v0.1.45 [INFO] [stderr] Compiling matrixmultiply v0.3.7 [INFO] [stderr] Compiling dirs-next v2.0.0 [INFO] [stderr] Compiling crossbeam-deque v0.8.3 [INFO] [stderr] Compiling nanorand v0.7.0 [INFO] [stderr] Compiling spin v0.9.8 [INFO] [stderr] Compiling crossbeam-channel v0.5.8 [INFO] [stderr] Compiling regex-syntax v0.7.4 [INFO] [stderr] Compiling ryu v1.0.14 [INFO] [stderr] Compiling either v1.8.1 [INFO] [stderr] Compiling rawpointer v0.2.1 [INFO] [stderr] Compiling futures-sink v0.3.28 [INFO] [stderr] Compiling winnow v0.4.9 [INFO] [stderr] Compiling parking_lot v0.12.1 [INFO] [stderr] Compiling num-complex v0.4.3 [INFO] [stderr] Compiling term v0.7.0 [INFO] [stderr] Compiling core_affinity v0.8.0 [INFO] [stderr] Compiling is-terminal v0.4.9 [INFO] [stderr] Compiling indoc v1.0.9 [INFO] [stderr] Compiling encode_unicode v1.0.0 [INFO] [stderr] Compiling unicode-width v0.1.10 [INFO] [stderr] Compiling byteorder v1.4.3 [INFO] [stderr] Compiling bytes v1.4.0 [INFO] [stderr] Compiling lazy_static v1.4.0 [INFO] [stderr] Compiling arrayvec v0.7.4 [INFO] [stderr] Compiling unindent v0.1.11 [INFO] [stderr] Compiling num-format v0.4.4 [INFO] [stderr] Compiling rayon v1.7.0 [INFO] [stderr] Compiling ndarray v0.15.6 [INFO] [stderr] Compiling itertools v0.11.0 [INFO] [stderr] Compiling natord v1.0.9 [INFO] [stderr] Compiling linked-hash-map v0.5.6 [INFO] [stderr] Compiling maplit v1.0.2 [INFO] [stderr] Compiling libdeflate-sys v0.12.0 [INFO] [stderr] Compiling libz-sys v1.1.12 [INFO] [stderr] Compiling regex-automata v0.3.3 [INFO] [stderr] Compiling pyo3-macros-backend v0.19.1 [INFO] [stderr] Compiling pyo3-ffi v0.19.1 [INFO] [stderr] Compiling pyo3 v0.19.1 [INFO] [stderr] Compiling regex v1.9.1 [INFO] [stderr] Compiling serde_derive v1.0.171 [INFO] [stderr] Compiling pin-project-internal v1.1.2 [INFO] [stderr] Compiling thiserror-impl v1.0.43 [INFO] [stderr] Compiling libdeflater v0.12.0 [INFO] [stderr] Compiling pyo3-macros v0.19.1 [INFO] [stderr] Compiling pin-project v1.1.2 [INFO] [stderr] Compiling flume v0.10.14 [INFO] [stderr] Compiling flate2 v1.0.26 [INFO] [stderr] Compiling gzp v0.11.3 [INFO] [stderr] Compiling toml_datetime v0.6.3 [INFO] [stderr] Compiling serde_spanned v0.6.3 [INFO] [stderr] Compiling csv v1.2.2 [INFO] [stderr] Compiling toml_edit v0.19.12 [INFO] [stderr] Compiling prettytable v0.10.0 [INFO] [stderr] Compiling toml v0.7.6 [INFO] [stderr] Compiling readfish-tools v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stdout] --> src/lib.rs:1005:1 [INFO] [stdout] | [INFO] [stdout] 1005 | #[pymethods] [INFO] [stdout] | -^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | `PyClassImplCollector` is not local [INFO] [stdout] | `PyClassNewTextSignature` is not local [INFO] [stdout] | move the `impl` block outside of this function `trampoline` and up 4 bodies [INFO] [stdout] 1006 | impl ReadfishSummary { [INFO] [stdout] | --------------- [INFO] [stdout] | | [INFO] [stdout] | `ReadfishSummary` is not local [INFO] [stdout] | `ReadfishSummary` is not local [INFO] [stdout] | [INFO] [stdout] = note: the attribute macro `pymethods` defines the non-local `impl`, and may need to be changed [INFO] [stdout] = note: the attribute macro `pymethods` may come from an old version of the `pyo3_macros` crate, try updating your dependency with `cargo update -p pyo3_macros` [INFO] [stdout] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stdout] = note: `#[warn(non_local_definitions)]` on by default [INFO] [stdout] = note: this warning originates in the attribute macro `pymethods` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 2m 10s [INFO] running `Command { std: "docker" "inspect" "2ed17cc830d3d03d86c137db58d5ccdc69f95aa489adbbbb1f6b6997ead0d1f5", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "2ed17cc830d3d03d86c137db58d5ccdc69f95aa489adbbbb1f6b6997ead0d1f5", kill_on_drop: false }` [INFO] [stdout] 2ed17cc830d3d03d86c137db58d5ccdc69f95aa489adbbbb1f6b6997ead0d1f5 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/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" "RUSTDOCFLAGS=--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:b0b074c097205a61b89e8ad263052f976b2b332c4dc5f02aef1fe52501660d6e" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-04-13" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 422c5b765d68bbd21fea285cf8c34b83600ce7b19f9637b3553142ac1d8b8460 [INFO] running `Command { std: "docker" "start" "-a" "422c5b765d68bbd21fea285cf8c34b83600ce7b19f9637b3553142ac1d8b8460", kill_on_drop: false }` [INFO] [stderr] Compiling readfish-tools v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stdout] --> src/lib.rs:1005:1 [INFO] [stdout] | [INFO] [stdout] 1005 | #[pymethods] [INFO] [stdout] | -^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | `PyClassImplCollector` is not local [INFO] [stdout] | `PyClassNewTextSignature` is not local [INFO] [stdout] | move the `impl` block outside of this function `trampoline` and up 4 bodies [INFO] [stdout] 1006 | impl ReadfishSummary { [INFO] [stdout] | --------------- [INFO] [stdout] | | [INFO] [stdout] | `ReadfishSummary` is not local [INFO] [stdout] | `ReadfishSummary` is not local [INFO] [stdout] | [INFO] [stdout] = note: the attribute macro `pymethods` defines the non-local `impl`, and may need to be changed [INFO] [stdout] = note: the attribute macro `pymethods` may come from an old version of the `pyo3_macros` crate, try updating your dependency with `cargo update -p pyo3_macros` [INFO] [stdout] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stdout] = note: `#[warn(non_local_definitions)]` on by default [INFO] [stdout] = note: this warning originates in the attribute macro `pymethods` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stdout] --> src/lib.rs:1005:1 [INFO] [stdout] | [INFO] [stdout] 1005 | #[pymethods] [INFO] [stdout] | -^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | `PyClassImplCollector` is not local [INFO] [stdout] | `PyClassNewTextSignature` is not local [INFO] [stdout] | move the `impl` block outside of this function `trampoline` and up 4 bodies [INFO] [stdout] 1006 | impl ReadfishSummary { [INFO] [stdout] | --------------- [INFO] [stdout] | | [INFO] [stdout] | `ReadfishSummary` is not local [INFO] [stdout] | `ReadfishSummary` is not local [INFO] [stdout] | [INFO] [stdout] = note: the attribute macro `pymethods` defines the non-local `impl`, and may need to be changed [INFO] [stdout] = note: the attribute macro `pymethods` may come from an old version of the `pyo3_macros` crate, try updating your dependency with `cargo update -p pyo3_macros` [INFO] [stdout] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stdout] = note: `#[warn(non_local_definitions)]` on by default [INFO] [stdout] = note: this warning originates in the attribute macro `pymethods` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 4.67s [INFO] running `Command { std: "docker" "inspect" "422c5b765d68bbd21fea285cf8c34b83600ce7b19f9637b3553142ac1d8b8460", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "422c5b765d68bbd21fea285cf8c34b83600ce7b19f9637b3553142ac1d8b8460", kill_on_drop: false }` [INFO] [stdout] 422c5b765d68bbd21fea285cf8c34b83600ce7b19f9637b3553142ac1d8b8460 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/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" "RUSTDOCFLAGS=--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:b0b074c097205a61b89e8ad263052f976b2b332c4dc5f02aef1fe52501660d6e" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-04-13" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] 9e7da3d1dfed86ab99791da27372b106c64ba760ee6bb93d8cae909e8e190963 [INFO] running `Command { std: "docker" "start" "-a" "9e7da3d1dfed86ab99791da27372b106c64ba760ee6bb93d8cae909e8e190963", kill_on_drop: false }` [INFO] [stderr] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stderr] --> src/lib.rs:1005:1 [INFO] [stderr] | [INFO] [stderr] 1005 | #[pymethods] [INFO] [stderr] | -^^^^^^^^^^^ [INFO] [stderr] | | [INFO] [stderr] | `PyClassImplCollector` is not local [INFO] [stderr] | `PyClassNewTextSignature` is not local [INFO] [stderr] | move the `impl` block outside of this function `trampoline` and up 4 bodies [INFO] [stderr] 1006 | impl ReadfishSummary { [INFO] [stderr] | --------------- [INFO] [stderr] | | [INFO] [stderr] | `ReadfishSummary` is not local [INFO] [stderr] | `ReadfishSummary` is not local [INFO] [stderr] | [INFO] [stderr] = note: the attribute macro `pymethods` defines the non-local `impl`, and may need to be changed [INFO] [stderr] = note: the attribute macro `pymethods` may come from an old version of the `pyo3_macros` crate, try updating your dependency with `cargo update -p pyo3_macros` [INFO] [stderr] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stderr] = note: `#[warn(non_local_definitions)]` on by default [INFO] [stderr] = note: this warning originates in the attribute macro `pymethods` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stderr] [INFO] [stderr] warning: `readfish-tools` (lib) generated 1 warning [INFO] [stderr] warning: `readfish-tools` (lib test) generated 1 warning (1 duplicate) [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.21s [INFO] [stderr] Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/readfish_tools-3388769e23048927) [INFO] [stdout] [INFO] [stdout] running 50 tests [INFO] [stdout] test nanopore::tests::test_format_bases ... ok [INFO] [stdout] test nanopore::tests::test_get_coords ... ok [INFO] [stdout] test nanopore::tests::test_generate_flowcell_odd_even ... ok [INFO] [stdout] test paf::tests::test_barcode_absent ... ok [INFO] [stdout] test nanopore::tests::test_running_mean ... ok [INFO] [stdout] test paf::tests::test_barcode_present ... ok [INFO] [stdout] test paf::tests::test_channel ... ok [INFO] [stdout] test paf::tests::test_from_file_empty_file ... ok [INFO] [stdout] test paf::tests::test_from_file_invalid_paf ... ok [INFO] [stdout] test paf::tests::test_from_file_valid_paf ... ok [INFO] [stdout] test paf::tests::test_from_tuple ... ok [INFO] [stdout] test nanopore::tests::test_get_flowcell_array ... ok [INFO] [stdout] test paf::tests::test_from_tuple_no_barcode ... ok [INFO] [stdout] test paf::tests::test_read_id ... ok [INFO] [stdout] test nanopore::tests::test_generate_flowcell ... ok [INFO] [stdout] test readfish::tests::test_conf_validate_post_init ... ok [INFO] [stdout] test readfish::tests::read_toml ... ok [INFO] [stdout] test readfish::tests::test_generate_channel_map_barcode ... ok [INFO] [stdout] test readfish::tests::test_get_coord_contig ... ok [INFO] [stdout] test readfish::tests::test_get_csv_record_strand ... ok [INFO] [stdout] test readfish::tests::test_get_coord ... ok [INFO] [stdout] test paf::tests::test_paf_from_file ... ok [INFO] [stdout] test readfish::tests::test_get_regions_no_regions ... ok [INFO] [stdout] test readfish::tests::test_insert_into_targets ... ok [INFO] [stdout] test readfish::tests::test_load_barcoded_conf ... ok [INFO] [stdout] test readfish_io::tests::test_byte_counter_read ... ok [INFO] [stdout] test readfish::tests::test_make_targets ... ok [INFO] [stdout] test readfish_io::tests::test_consume_exact_small ... ok [INFO] [stdout] test readfish_io::tests::test_byte_counter_read_exact_past_end ... ok [INFO] [stdout] test readfish_io::tests::test_consume_exact_large ... ok [INFO] [stdout] test readfish::tests::test_merge_intervals ... ok [INFO] [stdout] test readfish_io::tests::test_byte_counter_read_past_end ... ok [INFO] [stdout] test readfish_io::tests::test_reader_seek ... ok [INFO] [stdout] test readfish_io::tests::test_byte_counter_new ... ok [INFO] [stdout] test readfish_io::tests::test_reader_seek_gz ... ok [INFO] [stdout] test tests::test_update_lengths ... ok [INFO] [stdout] test readfish_io::tests::test_reader ... ok [INFO] [stdout] test readfish::tests::test_get_conditions ... ok [INFO] [stdout] test readfish::tests::test_generate_channel_map ... ok [INFO] [stdout] test readfish::tests::test_get_region ... ok [INFO] [stdout] test readfish::tests::test_load_conf ... ok [INFO] [stdout] test readfish::tests::test_from_string ... ok [INFO] [stdout] test tests::test_parse_conf_file ... ok [INFO] [stdout] test nanopore::tests::test_get_coords_panics_size - should panic ... ok [INFO] [stdout] test nanopore::tests::test_get_flowcell_array_panic - should panic ... ok [INFO] [stdout] test paf::tests::test_from_file_nonexistent_file - should panic ... ok [INFO] [stdout] test readfish::tests::test_conf_validate_post_init_panic - should panic ... ok [INFO] [stdout] test nanopore::tests::test_get_coords_panics - should panic ... ok [INFO] [stdout] test sequencing_summary::tests::test_seq_sum_from_file ... ok [INFO] [stdout] test tests::test_parse_sequencing_summary ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 50 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 1.98s [INFO] [stdout] [INFO] [stderr] Running tests/integration_tests.rs (/opt/rustwide/target/debug/deps/integration_tests-ff70a08dcbb3fa7c) [INFO] [stdout] [INFO] [stdout] running 1 test [INFO] [stdout] +---------------------------+-------------+----------------+--------------+-------------+------------+-----------+-----------+-----------+------------+ [INFO] [stdout] | Condition | Total reads | # Off-target | # On-target | Total Yield | Off Target | On Target | Mean read | On target | Off target | [INFO] [stdout] | | | reads | reads | | Yield | yield | length | Mean read | Mean read | [INFO] [stdout] | | | | | | | | | length | length | [INFO] [stdout] +---------------------------+-------------+----------------+--------------+-------------+------------+-----------+-----------+-----------+------------+ [INFO] [stdout] | barcode05_NA12878_tst-170 | 4,236 | 4,210 (99.39%) | 26 (0.61%) | 3.90 Mb | 3.79 Mb | 111.62 Kb | 969 b | 4.29 Kb | 885 b | [INFO] [stdout] +---------------------------+-------------+----------------+--------------+-------------+------------+-----------+-----------+-----------+------------+ [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | Condition Name | barcode05_NA12878_tst-170 | | | | | | | | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | Contig | Contig Length | Read count | Yield | Mean | On Target | Off | Mean read | On target | Off target | [INFO] [stdout] | | | | | Read Length | Reads | Target Reads | length | Mean read | Mean read | [INFO] [stdout] | | | | | | | | | length | length | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr1 | 248,956,422 | 352 | 335.21 Kb | 944 b | 0 | 352 | 944 b | 0 b | 944 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr2 | 242,193,529 | 345 | 316.69 Kb | 915 b | 2 | 343 | 915 b | 6.93 Kb | 870 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr3 | 198,295,559 | 271 | 249.95 Kb | 927 b | 4 | 267 | 927 b | 3.73 Kb | 863 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr4 | 190,214,555 | 287 | 271.72 Kb | 963 b | 2 | 285 | 963 b | 6.06 Kb | 896 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr5 | 181,538,259 | 252 | 235.06 Kb | 921 b | 5 | 247 | 921 b | 3.36 Kb | 868 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr6 | 170,805,979 | 259 | 230.60 Kb | 883 b | 1 | 258 | 883 b | 3.55 Kb | 867 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr7 | 159,345,973 | 229 | 208.20 Kb | 895 b | 4 | 225 | 895 b | 2.18 Kb | 872 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr8 | 145,138,636 | 199 | 174.63 Kb | 866 b | 1 | 198 | 866 b | 198 b | 871 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr9 | 138,394,717 | 163 | 152.97 Kb | 948 b | 1 | 162 | 948 b | 8.43 Kb | 883 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr10 | 133,797,422 | 210 | 191.82 Kb | 918 b | 0 | 210 | 918 b | 0 b | 918 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr11 | 135,086,622 | 178 | 173.62 Kb | 986 b | 1 | 177 | 986 b | 8.40 Kb | 930 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr12 | 133,275,309 | 203 | 185.16 Kb | 914 b | 1 | 202 | 914 b | 7.79 Kb | 874 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr13 | 114,364,328 | 130 | 125.82 Kb | 977 b | 2 | 128 | 977 b | 4.76 Kb | 909 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr14 | 107,043,718 | 138 | 130.83 Kb | 942 b | 1 | 137 | 942 b | 6.40 Kb | 897 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr15 | 101,991,189 | 98 | 88.72 Kb | 904 b | 1 | 97 | 904 b | 943 b | 902 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr16 | 90,338,345 | 135 | 120.16 Kb | 889 b | 0 | 135 | 889 b | 0 b | 889 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr17 | 83,257,441 | 102 | 94.98 Kb | 926 b | 0 | 102 | 926 b | 0 b | 926 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr18 | 80,373,285 | 122 | 109.59 Kb | 901 b | 0 | 122 | 901 b | 0 b | 901 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr19 | 58,617,616 | 65 | 58.65 Kb | 903 b | 0 | 65 | 903 b | 0 b | 903 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr20 | 64,444,167 | 105 | 95.66 Kb | 901 b | 0 | 105 | 901 b | 0 b | 901 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr21 | 46,709,983 | 85 | 66.16 Kb | 771 b | 0 | 85 | 771 b | 0 b | 771 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chr22 | 50,818,468 | 57 | 52.35 Kb | 921 b | 0 | 57 | 921 b | 0 b | 921 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chrM | 16,569 | 9 | 7.51 Kb | 835 b | 0 | 9 | 835 b | 0 b | 835 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chrX | 156,040,895 | 224 | 205.49 Kb | 908 b | 0 | 224 | 908 b | 0 b | 908 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] | chrY | 57,227,415 | 18 | 17.53 Kb | 973 b | 0 | 18 | 973 b | 0 b | 973 b | [INFO] [stdout] +----------------+---------------+-------------+-----------+-------------+-----------+--------------+-----------+-----------+------------+ [INFO] [stdout] test test_region_based_paf_demultiplex ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 1 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 1.62s [INFO] [stdout] [INFO] [stderr] Doc-tests readfish_tools [INFO] [stdout] [INFO] [stdout] running 48 tests [INFO] [stdout] test src/lib.rs - ConditionSummary::get_or_add_contig (line 503) ... ignored [INFO] [stdout] test src/lib.rs - ReadfishSummary::parse_paf_from_iter (line 1060) ... ignored [INFO] [stdout] test src/lib.rs - ReadfishSummary::print_summary (line 1108) ... ignored [INFO] [stdout] test src/lib.rs - ReadfishSummary::print_summary (line 1138) ... ignored [INFO] [stdout] test src/lib.rs - Summary (line 542) ... ignored [INFO] [stdout] test src/lib.rs - Summary::conditions (line 793) ... ignored [INFO] [stdout] test src/lib.rs - _demultiplex_paf (line 844) ... ignored [INFO] [stdout] test src/nanopore.rs - nanopore (line 7) ... ignored [INFO] [stdout] test src/nanopore.rs - nanopore::format_bases (line 243) ... ignored [INFO] [stdout] test src/nanopore.rs - nanopore::generate_flowcell (line 172) ... ignored [INFO] [stdout] test src/nanopore.rs - nanopore::get_flowcell_array (line 110) ... ignored [INFO] [stdout] test src/paf.rs - paf::Paf (line 181) ... ignored [INFO] [stdout] test src/paf.rs - paf::Paf::demultiplex (line 272) ... ignored [INFO] [stdout] test src/paf.rs - paf::Paf::new (line 230) ... ignored [INFO] [stdout] test src/paf.rs - paf::_parse_paf_line (line 408) ... ignored [INFO] [stdout] test src/paf.rs - paf::open_paf_for_reading (line 332) ... ignored [INFO] [stdout] test src/readfish.rs - readfish::Conf::from_file (line 983) ... ignored [INFO] [stdout] test src/readfish.rs - readfish::Conf::from_string (line 931) ... ignored [INFO] [stdout] test src/readfish.rs - readfish::Conf::make_decision (line 1289) ... ignored [INFO] [stdout] test src/readfish.rs - readfish::Conf::new (line 1022) ... ignored [INFO] [stdout] test src/readfish.rs - readfish::Conf::validate_post_init (line 1077) ... ignored [INFO] [stdout] test src/readfish.rs - readfish::CsvRecord::get_coords (line 467) ... ignored [INFO] [stdout] test src/readfish.rs - readfish::CsvRecord::get_strand (line 508) ... ignored [INFO] [stdout] test src/readfish.rs - readfish::CsvRecord::has_coords (line 433) ... ignored [INFO] [stdout] test src/readfish.rs - readfish::Targets::_merge_intervals (line 819) ... ignored [INFO] [stdout] test src/readfish.rs - readfish::Targets::check_coords (line 885) ... ignored [INFO] [stdout] test src/readfish.rs - readfish::Targets::from_parsed_toml (line 696) ... ignored [INFO] [stdout] test src/readfish.rs - readfish::Targets::insert_into_targets (line 636) ... ignored [INFO] [stdout] test src/readfish.rs - readfish::Targets::new (line 591) ... ignored [INFO] [stdout] test src/readfish_io.rs - readfish_io::ByteCounter (line 32) ... ignored [INFO] [stdout] test src/readfish_io.rs - readfish_io::ByteCounter::bytes_read (line 93) ... ignored [INFO] [stdout] test src/readfish_io.rs - readfish_io::ByteCounter::new (line 68) ... ignored [INFO] [stdout] test src/readfish_io.rs - readfish_io::GzSeekable::consume_exact (line 177) ... ignored [INFO] [stdout] test src/readfish_io.rs - readfish_io::_get_reader_from_path (line 232) ... ignored [INFO] [stdout] test src/readfish_io.rs - readfish_io::_get_writer_from_path (line 348) ... ignored [INFO] [stdout] test src/readfish_io.rs - readfish_io::reader (line 267) ... ignored [INFO] [stdout] test src/readfish_io.rs - readfish_io::reader (line 276) ... ignored [INFO] [stdout] test src/readfish_io.rs - readfish_io::writer (line 390) ... ignored [INFO] [stdout] test src/sequencing_summary.rs - sequencing_summary::SeqSum (line 28) ... ignored [INFO] [stdout] test src/sequencing_summary.rs - sequencing_summary::SeqSum::from_file (line 140) ... ignored [INFO] [stdout] test src/sequencing_summary.rs - sequencing_summary::SeqSum::get_record (line 343) ... ignored [INFO] [stdout] test src/sequencing_summary.rs - sequencing_summary::SeqSum::roll_along_file (line 262) ... ignored [INFO] [stdout] test src/sequencing_summary.rs - sequencing_summary::SeqSumInfo (line 75) ... ignored [INFO] [stdout] test src/readfish.rs - readfish::Conf::generate_channel_map (line 1115) ... ok [INFO] [stdout] test src/nanopore.rs - nanopore::running_mean (line 282) ... ok [INFO] [stdout] test src/nanopore.rs - nanopore::get_coords (line 47) ... ok [INFO] [stdout] test src/lib.rs - ReadfishSummary::new (line 918) ... ok [INFO] [stdout] test src/lib.rs - MeanReadLengths::update_lengths (line 89) ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 5 passed; 0 failed; 43 ignored; 0 measured; 0 filtered out; finished in 3.83s [INFO] [stdout] [INFO] running `Command { std: "docker" "inspect" "9e7da3d1dfed86ab99791da27372b106c64ba760ee6bb93d8cae909e8e190963", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "9e7da3d1dfed86ab99791da27372b106c64ba760ee6bb93d8cae909e8e190963", kill_on_drop: false }` [INFO] [stdout] 9e7da3d1dfed86ab99791da27372b106c64ba760ee6bb93d8cae909e8e190963