[INFO] cloning repository https://github.com/juanfraitu1/Rustle
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/juanfraitu1/Rustle" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fjuanfraitu1%2FRustle", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fjuanfraitu1%2FRustle'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] abcf34e3c95b1e91370c1ee015f91e2ada36517c
[INFO] testing juanfraitu1/Rustle against try#b8e88e5ddf5521a9f43ee3f62a702388c713e4bb for pr-155114
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fjuanfraitu1%2FRustle" "/workspace/builds/worker-0-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc2/source'...
[INFO] [stderr] done.
[INFO] removed /workspace/builds/worker-0-tc2/source/.cargo/config.toml
[INFO] started tweaking git repo https://github.com/juanfraitu1/Rustle
[INFO] removed 0 missing tests
[INFO] finished tweaking git repo https://github.com/juanfraitu1/Rustle
[INFO] tweaked toml for git repo https://github.com/juanfraitu1/Rustle written to /workspace/builds/worker-0-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/juanfraitu1/Rustle on toolchain b8e88e5ddf5521a9f43ee3f62a702388c713e4bb
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+b8e88e5ddf5521a9f43ee3f62a702388c713e4bb" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/juanfraitu1/Rustle 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" "+b8e88e5ddf5521a9f43ee3f62a702388c713e4bb" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+b8e88e5ddf5521a9f43ee3f62a702388c713e4bb" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] a310aa87b25760f0224443c125443088c95bbfa5e86c98a97cfbe3e8e6b3d0dd
[INFO] running `Command { std: "docker" "start" "-a" "a310aa87b25760f0224443c125443088c95bbfa5e86c98a97cfbe3e8e6b3d0dd", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "a310aa87b25760f0224443c125443088c95bbfa5e86c98a97cfbe3e8e6b3d0dd", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "a310aa87b25760f0224443c125443088c95bbfa5e86c98a97cfbe3e8e6b3d0dd", kill_on_drop: false }`
[INFO] [stdout] a310aa87b25760f0224443c125443088c95bbfa5e86c98a97cfbe3e8e6b3d0dd
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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=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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+b8e88e5ddf5521a9f43ee3f62a702388c713e4bb" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] fab05c3bc320c5c5bf3b1e4f53ba993dba7f23c1fbe5edfe6a9bbc38c7e5563a
[INFO] running `Command { std: "docker" "start" "-a" "fab05c3bc320c5c5bf3b1e4f53ba993dba7f23c1fbe5edfe6a9bbc38c7e5563a", kill_on_drop: false }`
[INFO] [stderr]    Compiling crc32fast v1.5.0
[INFO] [stderr]    Compiling memchr v2.8.0
[INFO] [stderr]    Compiling proc-macro2 v1.0.106
[INFO] [stderr]    Compiling adler2 v2.0.1
[INFO] [stderr]    Compiling simd-adler32 v0.3.9
[INFO] [stderr]    Compiling quote v1.0.45
[INFO] [stderr]    Compiling byteorder v1.5.0
[INFO] [stderr]    Compiling unicode-ident v1.0.24
[INFO] [stderr]    Compiling zlib-rs v0.6.3
[INFO] [stderr]    Compiling libc v0.2.185
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling crossbeam-channel v0.5.15
[INFO] [stderr]    Compiling miniz_oxide v0.8.9
[INFO] [stderr]    Compiling equivalent v1.0.2
[INFO] [stderr]    Compiling bytes v1.11.1
[INFO] [stderr]    Compiling bstr v1.12.1
[INFO] [stderr]    Compiling lexical-util v1.0.7
[INFO] [stderr]    Compiling syn v2.0.117
[INFO] [stderr]    Compiling hashbrown v0.17.0
[INFO] [stderr]    Compiling zerocopy v0.8.48
[INFO] [stderr]    Compiling serde v1.0.228
[INFO] [stderr]    Compiling lexical-parse-integer v1.0.6
[INFO] [stderr]    Compiling lexical-write-integer v1.0.6
[INFO] [stderr]    Compiling utf8parse v0.2.2
[INFO] [stderr]    Compiling anstyle-parse v1.0.0
[INFO] [stderr]    Compiling lexical-parse-float v1.0.6
[INFO] [stderr]    Compiling noodles-core v0.15.0
[INFO] [stderr]    Compiling lexical-write-float v1.0.6
[INFO] [stderr]    Compiling indexmap v2.14.0
[INFO] [stderr]    Compiling num-integer v0.1.46
[INFO] [stderr]    Compiling anstyle-query v1.1.5
[INFO] [stderr]    Compiling allocator-api2 v0.2.21
[INFO] [stderr]    Compiling colorchoice v1.0.5
[INFO] [stderr]    Compiling zmij v1.0.21
[INFO] [stderr]    Compiling version_check v0.9.5
[INFO] [stderr]    Compiling bit-vec v0.8.0
[INFO] [stderr]    Compiling getrandom v0.3.4
[INFO] [stderr]    Compiling anstyle v1.0.14
[INFO] [stderr]    Compiling foldhash v0.1.5
[INFO] [stderr]    Compiling is_terminal_polyfill v1.70.2
[INFO] [stderr]    Compiling hashbrown v0.15.5
[INFO] [stderr]    Compiling ahash v0.8.12
[INFO] [stderr]    Compiling anstream v1.0.0
[INFO] [stderr]    Compiling num-bigint v0.4.6
[INFO] [stderr]    Compiling lexical-core v1.0.6
[INFO] [stderr]    Compiling getrandom v0.2.17
[INFO] [stderr]    Compiling noodles-core v0.17.0
[INFO] [stderr]    Compiling strsim v0.11.1
[INFO] [stderr]    Compiling heck v0.5.0
[INFO] [stderr]    Compiling clap_lex v1.1.0
[INFO] [stderr]    Compiling anyhow v1.0.102
[INFO] [stderr]    Compiling bitflags v2.11.1
[INFO] [stderr]    Compiling serde_json v1.0.149
[INFO] [stderr]    Compiling clap_builder v4.6.0
[INFO] [stderr]    Compiling rand_core v0.6.4
[INFO] [stderr]    Compiling num-iter v0.1.45
[INFO] [stderr]    Compiling num-complex v0.4.6
[INFO] [stderr]    Compiling noodles-fastq v0.19.0
[INFO] [stderr]    Compiling once_cell v1.21.4
[INFO] [stderr]    Compiling fixedbitset v0.5.7
[INFO] [stderr]    Compiling itoa v1.0.18
[INFO] [stderr]    Compiling num-rational v0.4.2
[INFO] [stderr]    Compiling flate2 v1.1.9
[INFO] [stderr]    Compiling num v0.4.3
[INFO] [stderr]    Compiling rustc-hash v2.1.2
[INFO] [stderr]    Compiling nonmax v0.5.5
[INFO] [stderr]    Compiling bytemuck v1.25.0
[INFO] [stderr]    Compiling rayon v1.12.0
[INFO] [stderr]    Compiling lru v0.12.5
[INFO] [stderr]    Compiling noodles-bgzf v0.33.0
[INFO] [stderr]    Compiling noodles-bgzf v0.41.0
[INFO] [stderr]    Compiling roaring v0.10.12
[INFO] [stderr]    Compiling serde_derive v1.0.228
[INFO] [stderr]    Compiling noodles-csi v0.40.0
[INFO] [stderr]    Compiling noodles-fasta v0.54.0
[INFO] [stderr]    Compiling clap_derive v4.6.1
[INFO] [stderr]    Compiling ppv-lite86 v0.2.21
[INFO] [stderr]    Compiling noodles-sam v0.66.0
[INFO] [stderr]    Compiling noodles v0.99.0
[INFO] [stderr]    Compiling rand_chacha v0.3.1
[INFO] [stderr]    Compiling memmap2 v0.9.10
[INFO] [stderr]    Compiling fxhash v0.2.1
[INFO] [stderr]    Compiling rand v0.8.6
[INFO] [stderr]    Compiling clap v4.6.1
[INFO] [stderr]    Compiling noodles-bam v0.70.0
[INFO] [stderr]    Compiling smallvec v1.15.1
[INFO] [stderr]    Compiling petgraph v0.8.3
[INFO] [stderr]    Compiling bincode v1.3.3
[INFO] [stderr]    Compiling noodles v0.85.0
[INFO] [stderr]    Compiling poasta v0.1.0
[INFO] [stderr]    Compiling rustle v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `print_predcluster_with_summary`
[INFO] [stdout]     --> src/rustle/pipeline.rs:3658:5
[INFO] [stdout]      |
[INFO] [stdout] 3658 |     print_predcluster_with_summary, suppress_near_duplicate_chains, PredclusterStageSummary,
[INFO] [stdout]      |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]      |
[INFO] [stdout]      = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::collections::HashSet`
[INFO] [stdout]     --> src/rustle/vg.rs:1473:9
[INFO] [stdout]      |
[INFO] [stdout] 1473 |     use std::collections::HashSet;
[INFO] [stdout]      |         ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `DetHashMap`
[INFO] [stdout]  --> src/rustle/vg_hmm/rescue.rs:3:40
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::types::{Bundle, BundleRead, DetHashMap, DetHashSet, JunctionStats, RunConfig};
[INFO] [stdout]   |                                        ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `is_tss`
[INFO] [stdout]     --> src/rustle/vg_hmm/rescue.rs:1434:68
[INFO] [stdout]      |
[INFO] [stdout] 1434 |         let refine_boundary = |i: usize, node_s: u64, node_e: u64, is_tss: bool| -> u64 {
[INFO] [stdout]      |                                                                    ^^^^^^ help: if this is intentional, prefix it with an underscore: `_is_tss`
[INFO] [stdout]      |
[INFO] [stdout]      = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `recompute_junction_stats_primary_only` is never used
[INFO] [stdout]     --> src/rustle/bundle.rs:2214:8
[INFO] [stdout]      |
[INFO] [stdout] 2214 | pub fn recompute_junction_stats_primary_only(bundle: &mut Bundle, config: &RunConfig) {
[INFO] [stdout]      |        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]      |
[INFO] [stdout]      = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `profile_viterbi_with_boundary` is never used
[INFO] [stdout]    --> src/rustle/vg_hmm/scorer.rs:408:4
[INFO] [stdout]     |
[INFO] [stdout] 408 | fn profile_viterbi_with_boundary(
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `noodles_bgzf as bgzf`
[INFO] [stdout]  --> src/bin/index_bam.rs:7:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | use noodles_bgzf as bgzf;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `noodles_sam::alignment::record::Cigar`
[INFO] [stdout]    --> src/bin/loo_assembly.rs:268:9
[INFO] [stdout]     |
[INFO] [stdout] 268 |     use noodles_sam::alignment::record::Cigar as _;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 2m 03s
[INFO] running `Command { std: "docker" "inspect" "fab05c3bc320c5c5bf3b1e4f53ba993dba7f23c1fbe5edfe6a9bbc38c7e5563a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "fab05c3bc320c5c5bf3b1e4f53ba993dba7f23c1fbe5edfe6a9bbc38c7e5563a", kill_on_drop: false }`
[INFO] [stdout] fab05c3bc320c5c5bf3b1e4f53ba993dba7f23c1fbe5edfe6a9bbc38c7e5563a
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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=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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+b8e88e5ddf5521a9f43ee3f62a702388c713e4bb" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] d24e255e0240ac8c37ca4279e27b3dc9ed6d7356d805c46a042ed9dba7d7cc02
[INFO] running `Command { std: "docker" "start" "-a" "d24e255e0240ac8c37ca4279e27b3dc9ed6d7356d805c46a042ed9dba7d7cc02", kill_on_drop: false }`
[INFO] [stderr]    Compiling bitflags v2.11.1
[INFO] [stderr]    Compiling once_cell v1.21.4
[INFO] [stderr]    Compiling rustix v1.1.4
[INFO] [stderr]    Compiling linux-raw-sys v0.12.1
[INFO] [stderr]    Compiling fastrand v2.4.1
[INFO] [stderr]    Compiling noodles-sam v0.66.0
[INFO] [stderr]    Compiling ahash v0.8.12
[INFO] [stderr]    Compiling poasta v0.1.0
[INFO] [stderr]    Compiling noodles-bam v0.70.0
[INFO] [stderr]    Compiling tempfile v3.27.0
[INFO] [stderr]    Compiling noodles v0.85.0
[INFO] [stderr]    Compiling rustle v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `print_predcluster_with_summary`
[INFO] [stdout]     --> src/rustle/pipeline.rs:3658:5
[INFO] [stdout]      |
[INFO] [stdout] 3658 |     print_predcluster_with_summary, suppress_near_duplicate_chains, PredclusterStageSummary,
[INFO] [stdout]      |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]      |
[INFO] [stdout]      = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::collections::HashSet`
[INFO] [stdout]     --> src/rustle/vg.rs:1473:9
[INFO] [stdout]      |
[INFO] [stdout] 1473 |     use std::collections::HashSet;
[INFO] [stdout]      |         ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `DetHashMap`
[INFO] [stdout]  --> src/rustle/vg_hmm/rescue.rs:3:40
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::types::{Bundle, BundleRead, DetHashMap, DetHashSet, JunctionStats, RunConfig};
[INFO] [stdout]   |                                        ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `print_predcluster_with_summary`
[INFO] [stdout]     --> src/rustle/pipeline.rs:3658:5
[INFO] [stdout]      |
[INFO] [stdout] 3658 |     print_predcluster_with_summary, suppress_near_duplicate_chains, PredclusterStageSummary,
[INFO] [stdout]      |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]      |
[INFO] [stdout]      = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::collections::HashSet`
[INFO] [stdout]     --> src/rustle/vg.rs:1473:9
[INFO] [stdout]      |
[INFO] [stdout] 1473 |     use std::collections::HashSet;
[INFO] [stdout]      |         ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `DetHashMap`
[INFO] [stdout]  --> src/rustle/vg_hmm/rescue.rs:3:40
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::types::{Bundle, BundleRead, DetHashMap, DetHashSet, JunctionStats, RunConfig};
[INFO] [stdout]   |                                        ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `is_tss`
[INFO] [stdout]     --> src/rustle/vg_hmm/rescue.rs:1434:68
[INFO] [stdout]      |
[INFO] [stdout] 1434 |         let refine_boundary = |i: usize, node_s: u64, node_e: u64, is_tss: bool| -> u64 {
[INFO] [stdout]      |                                                                    ^^^^^^ help: if this is intentional, prefix it with an underscore: `_is_tss`
[INFO] [stdout]      |
[INFO] [stdout]      = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `is_tss`
[INFO] [stdout]     --> src/rustle/vg_hmm/rescue.rs:1434:68
[INFO] [stdout]      |
[INFO] [stdout] 1434 |         let refine_boundary = |i: usize, node_s: u64, node_e: u64, is_tss: bool| -> u64 {
[INFO] [stdout]      |                                                                    ^^^^^^ help: if this is intentional, prefix it with an underscore: `_is_tss`
[INFO] [stdout]      |
[INFO] [stdout]      = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `recompute_junction_stats_primary_only` is never used
[INFO] [stdout]     --> src/rustle/bundle.rs:2214:8
[INFO] [stdout]      |
[INFO] [stdout] 2214 | pub fn recompute_junction_stats_primary_only(bundle: &mut Bundle, config: &RunConfig) {
[INFO] [stdout]      |        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]      |
[INFO] [stdout]      = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `profile_viterbi_with_boundary` is never used
[INFO] [stdout]    --> src/rustle/vg_hmm/scorer.rs:408:4
[INFO] [stdout]     |
[INFO] [stdout] 408 | fn profile_viterbi_with_boundary(
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `recompute_junction_stats_primary_only` is never used
[INFO] [stdout]     --> src/rustle/bundle.rs:2214:8
[INFO] [stdout]      |
[INFO] [stdout] 2214 | pub fn recompute_junction_stats_primary_only(bundle: &mut Bundle, config: &RunConfig) {
[INFO] [stdout]      |        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]      |
[INFO] [stdout]      = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `profile_viterbi_with_boundary` is never used
[INFO] [stdout]    --> src/rustle/vg_hmm/scorer.rs:408:4
[INFO] [stdout]     |
[INFO] [stdout] 408 | fn profile_viterbi_with_boundary(
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `noodles_sam::alignment::record::Cigar`
[INFO] [stdout]    --> src/bin/loo_assembly.rs:268:9
[INFO] [stdout]     |
[INFO] [stdout] 268 |     use noodles_sam::alignment::record::Cigar as _;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `noodles_sam::alignment::record::Cigar`
[INFO] [stdout]    --> src/bin/loo_assembly.rs:268:9
[INFO] [stdout]     |
[INFO] [stdout] 268 |     use noodles_sam::alignment::record::Cigar as _;
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `JunctionEdge`
[INFO] [stdout]  --> tests/regression/vg_hmm_em.rs:8:60
[INFO] [stdout]   |
[INFO] [stdout] 8 | use rustle::vg_hmm::family_graph::{ExonClass, FamilyGraph, JunctionEdge, NodeIdx};
[INFO] [stdout]   |                                                            ^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `DetHashMap`
[INFO] [stdout]  --> tests/regression/vg_hmm_rescue.rs:8:33
[INFO] [stdout]   |
[INFO] [stdout] 8 | use rustle::types::{DetHashSet, DetHashMap};
[INFO] [stdout]   |                                 ^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `noodles_bgzf as bgzf`
[INFO] [stdout]  --> src/bin/index_bam.rs:7:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | use noodles_bgzf as bgzf;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `noodles_bgzf as bgzf`
[INFO] [stdout]  --> src/bin/index_bam.rs:7:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | use noodles_bgzf as bgzf;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 1m 20s
[INFO] running `Command { std: "docker" "inspect" "d24e255e0240ac8c37ca4279e27b3dc9ed6d7356d805c46a042ed9dba7d7cc02", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "d24e255e0240ac8c37ca4279e27b3dc9ed6d7356d805c46a042ed9dba7d7cc02", kill_on_drop: false }`
[INFO] [stdout] d24e255e0240ac8c37ca4279e27b3dc9ed6d7356d805c46a042ed9dba7d7cc02
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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=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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+b8e88e5ddf5521a9f43ee3f62a702388c713e4bb" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] 14928eafb2324651caa06cf6a9ee2e4be051dc95d06eac1701db7882f675ad29
[INFO] running `Command { std: "docker" "start" "-a" "14928eafb2324651caa06cf6a9ee2e4be051dc95d06eac1701db7882f675ad29", kill_on_drop: false }`
[INFO] [stderr] warning: unused import: `print_predcluster_with_summary`
[INFO] [stderr]     --> src/rustle/pipeline.rs:3658:5
[INFO] [stderr]      |
[INFO] [stderr] 3658 |     print_predcluster_with_summary, suppress_near_duplicate_chains, PredclusterStageSummary,
[INFO] [stderr]      |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]      |
[INFO] [stderr]      = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::collections::HashSet`
[INFO] [stderr]     --> src/rustle/vg.rs:1473:9
[INFO] [stderr]      |
[INFO] [stderr] 1473 |     use std::collections::HashSet;
[INFO] [stderr]      |         ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `DetHashMap`
[INFO] [stderr]  --> src/rustle/vg_hmm/rescue.rs:3:40
[INFO] [stderr]   |
[INFO] [stderr] 3 | use crate::types::{Bundle, BundleRead, DetHashMap, DetHashSet, JunctionStats, RunConfig};
[INFO] [stderr]   |                                        ^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `is_tss`
[INFO] [stderr]     --> src/rustle/vg_hmm/rescue.rs:1434:68
[INFO] [stderr]      |
[INFO] [stderr] 1434 |         let refine_boundary = |i: usize, node_s: u64, node_e: u64, is_tss: bool| -> u64 {
[INFO] [stderr]      |                                                                    ^^^^^^ help: if this is intentional, prefix it with an underscore: `_is_tss`
[INFO] [stderr]      |
[INFO] [stderr]      = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: function `recompute_junction_stats_primary_only` is never used
[INFO] [stderr]     --> src/rustle/bundle.rs:2214:8
[INFO] [stderr]      |
[INFO] [stderr] 2214 | pub fn recompute_junction_stats_primary_only(bundle: &mut Bundle, config: &RunConfig) {
[INFO] [stderr]      |        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]      |
[INFO] [stderr]      = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: function `profile_viterbi_with_boundary` is never used
[INFO] [stderr]    --> src/rustle/vg_hmm/scorer.rs:408:4
[INFO] [stderr]     |
[INFO] [stderr] 408 | fn profile_viterbi_with_boundary(
[INFO] [stderr]     |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: `rustle` (lib) generated 6 warnings (run `cargo fix --lib -p rustle` to apply 4 suggestions)
[INFO] [stderr] warning: unused import: `noodles_sam::alignment::record::Cigar`
[INFO] [stderr]    --> src/bin/loo_assembly.rs:268:9
[INFO] [stderr]     |
[INFO] [stderr] 268 |     use noodles_sam::alignment::record::Cigar as _;
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: `rustle` (bin "loo_assembly") generated 1 warning
[INFO] [stderr] warning: unused import: `noodles_bgzf as bgzf`
[INFO] [stderr]  --> src/bin/index_bam.rs:7:5
[INFO] [stderr]   |
[INFO] [stderr] 7 | use noodles_bgzf as bgzf;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: `rustle` (bin "index_bam") generated 1 warning (run `cargo fix --bin "index_bam" -p rustle` to apply 1 suggestion)
[INFO] [stderr] warning: unused import: `DetHashMap`
[INFO] [stderr]  --> tests/regression/vg_hmm_rescue.rs:8:33
[INFO] [stderr]   |
[INFO] [stderr] 8 | use rustle::types::{DetHashSet, DetHashMap};
[INFO] [stderr]   |                                 ^^^^^^^^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: `rustle` (test "vg_hmm_rescue") generated 1 warning (run `cargo fix --test "vg_hmm_rescue" -p rustle` to apply 1 suggestion)
[INFO] [stderr] warning: `rustle` (bin "loo_assembly" test) generated 1 warning (1 duplicate)
[INFO] [stderr] warning: `rustle` (lib test) generated 6 warnings (6 duplicates)
[INFO] [stderr] warning: `rustle` (bin "index_bam" test) generated 1 warning (1 duplicate)
[INFO] [stderr] warning: unused import: `JunctionEdge`
[INFO] [stderr]  --> tests/regression/vg_hmm_em.rs:8:60
[INFO] [stderr]   |
[INFO] [stderr] 8 | use rustle::vg_hmm::family_graph::{ExonClass, FamilyGraph, JunctionEdge, NodeIdx};
[INFO] [stderr]   |                                                            ^^^^^^^^^^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: `rustle` (test "vg_hmm_em") generated 1 warning (run `cargo fix --test "vg_hmm_em" -p rustle` to apply 1 suggestion)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.28s
[INFO] [stderr]      Running unittests src/rustle/lib.rs (/opt/rustwide/target/debug/deps/rustle-b4d5c5717b94f936)
[INFO] [stdout] 
[INFO] [stdout] running 40 tests
[INFO] [stdout] test bitset::tests::contains_all ... ok
[INFO] [stdout] test bitset::tests::inline_insert_contains ... ok
[INFO] [stdout] test bitset::tests::gbvec_compat ... ok
[INFO] [stdout] test bitset::tests::grow_inline_to_large ... ok
[INFO] [stdout] test bitset::tests::from_iter_large ... ok
[INFO] [stdout] test bitset::tests::from_iter_basic ... ok
[INFO] [stdout] test bitset::tests::extend_basic ... ok
[INFO] [stdout] test bitset::tests::inline_intersects ... ok
[INFO] [stdout] test bitset::tests::inline_remove ... ok
[INFO] [stdout] test bitset::tests::inline_union_with ... ok
[INFO] [stdout] test bitset::tests::nodeset_alias ... ok
[INFO] [stdout] test bitset::tests::ones_iterator ... ok
[INFO] [stdout] test coord::tests::inclusive_half_open_length_compat ... ok
[INFO] [stdout] test coord::tests::inclusive_half_open_overlap_compat ... ok
[INFO] [stdout] test coord::tests::roundtrip_half_open_inclusive ... ok
[INFO] [stdout] test bitset::tests::inline_count_ones ... ok
[INFO] [stdout] test bitset::tests::large_basic ... ok
[INFO] [stdout] test killed_junctions::tests::cov_sign_window_longreads_subtracts_opposite_strand ... ok
[INFO] [stdout] test junction_correction::tests::test_higherr_merges_weak_nearby ... ok
[INFO] [stdout] test killed_junctions::tests::higherr_demotes_acceptor_variant ... ok
[INFO] [stdout] test killed_junctions::tests::higherr_demotes_donor_variant ... ok
[INFO] [stdout] test per_bnode_graph::tests::test_contiguous_bundlenodes ... ok
[INFO] [stdout] test per_bnode_graph::tests::test_disconnected_bundlenodes ... ok
[INFO] [stdout] test per_bnode_graph::tests::test_junction_connects_two_bundlenodes ... ok
[INFO] [stdout] test per_bnode_graph::tests::test_single_bundlenode ... ok
[INFO] [stdout] test pipeline::tests::bad_mm_neg_donor_uses_probe_base ... ok
[INFO] [stdout] test polya::tests::test_check_polya_window ... ok
[INFO] [stdout] test polya::tests::test_detect_polya_aligned_unaligned_base_specific ... ok
[INFO] [stdout] test polya::tests::test_detect_polya_aligned_unaligned_boundary_run ... ok
[INFO] [stdout] test polya::tests::test_detect_polya_aligned_unaligned_right_clip_boundary ... ok
[INFO] [stdout] test transcript_filter::tests::included_pred_skips_abutting_big_exon_before_alignment ... ok
[INFO] [stdout] test transcript_filter::tests::included_pred_treats_abutting_single_exons_as_non_overlapping ... ok
[INFO] [stdout] test transcript_filter::tests::retainedintron_requires_overlap_before_prev_exon_end ... ok
[INFO] [stdout] test transcript_filter::tests::retainedintron_skips_exon_ending_at_next_exon_start ... ok
[INFO] [stdout] test vg_hmm::positional::tests::revcomp_hash_matches_explicit_revcomp ... ok
[INFO] [stdout] test vg_hmm::positional::tests::cluster_tiles_merges_adjacent ... ok
[INFO] [stdout] test vg_hmm::positional::tests::exclude_known_paralogs_drops_overlapping ... ok
[INFO] [stdout] test vg_hmm::scorer::tests::banded_matches_unbanded_for_short_read ... ok
[INFO] [stdout] test vg_hmm::scorer::tests::viterbi_returns_correct_node_sequence ... ok
[INFO] [stdout] test vg_hmm::positional::tests::scan_finds_planted_seed ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 40 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.08s
[INFO] [stdout] 
[INFO] [stderr]      Running unittests src/bin/bam_header.rs (/opt/rustwide/target/debug/deps/bam_header-38a273667cd579b5)
[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] [stderr]      Running unittests src/bin/debug_poa.rs (/opt/rustwide/target/debug/deps/debug_poa-dc1bd0c8947b1054)
[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] [stderr]      Running unittests src/bin/dump_family_graph.rs (/opt/rustwide/target/debug/deps/dump_family_graph-0fb9bb6c59787fa0)
[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] [stderr]      Running unittests src/bin/filter_bam_by_as.rs (/opt/rustwide/target/debug/deps/filter_bam_by_as-0b0989be9e276fe4)
[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] [stderr]      Running unittests src/bin/index_bam.rs (/opt/rustwide/target/debug/deps/index_bam-9fb2e161243ec5e7)
[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] [stderr]      Running unittests src/bin/leave_one_out_rescue.rs (/opt/rustwide/target/debug/deps/leave_one_out_rescue-c80fef856c49fe48)
[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] [stderr]      Running unittests src/bin/loo_assembly.rs (/opt/rustwide/target/debug/deps/loo_assembly-189b482b27a28e86)
[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] [stderr]      Running unittests src/bin/roundtrip_family_graph.rs (/opt/rustwide/target/debug/deps/roundtrip_family_graph-f3f170c6c3c28773)
[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] [stderr]      Running unittests src/rustle/main.rs (/opt/rustwide/target/debug/deps/rustle-cad40e18a3f9dce0)
[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] [stderr]      Running tests/regression/test_parity_flow_iter_dump.rs (/opt/rustwide/target/debug/deps/test_parity_flow_iter_dump-5071e8c50e9897ae)
[INFO] [stdout] 
[INFO] [stdout] running 1 test
[INFO] [stdout] test flow_iter_dump_emits_monotone_iterations ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 1 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.18s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/regression/test_parity_graph_edges_dump.rs (/opt/rustwide/target/debug/deps/test_parity_graph_edges_dump-587568782ce85a55)
[INFO] [stdout] 
[INFO] [stdout] running 1 test
[INFO] [stderr]      Running tests/regression/vg_hmm_diagnostic.rs (/opt/rustwide/target/debug/deps/vg_hmm_diagnostic-07b32c192344320b)
[INFO] [stdout] test graph_edges_dump_produces_expected_schema ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 1 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.10s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 5 tests
[INFO] [stdout] test test_internal_below_threshold_chain ... ok
[INFO] [stdout] test test_internal_needs_external ... ok
[INFO] [stdout] test test_internal_seed_masked ... ok
[INFO] [stdout] test test_cigar_long_indel_detection ... ok
[INFO] [stdout] test test_external_classify_skip_if_no_minimap2 ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 5 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.02s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/regression/vg_hmm_em.rs (/opt/rustwide/target/debug/deps/vg_hmm_em-3084d97d0f405a23)
[INFO] [stdout] 
[INFO] [stdout] running 6 tests
[INFO] [stdout] test em_no_reweighting_when_no_multimappers ... ok
[INFO] [stdout] test em_skips_read_with_no_sequence_provided ... ok
[INFO] [stdout] test em_assigns_paralog_0_read_to_paralog_0 ... ok
[INFO] [stdout] test em_converges_with_many_reads_split_across_paralogs ... ok
[INFO] [stdout] test em_assigns_paralog_1_read_to_paralog_1 ... ok
[INFO] [stdout] test em_no_reweighting_when_family_too_small ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 6 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.03s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/regression/vg_hmm_family_graph.rs (/opt/rustwide/target/debug/deps/vg_hmm_family_graph-7f08736b45f5e4f7)
[INFO] [stdout] 
[INFO] [stdout] running 9 tests
[INFO] [stdout] test empty_family_graph_constructs ... ok
[INFO] [stdout] test build_family_graph_two_copy_smoke ... ok
[INFO] [stdout] test exon_class_carries_per_copy_sequences ... ok
[INFO] [stdout] test exon_extraction_returns_unique_sorted_intervals ... ok
[INFO] [stdout] test junction_edges_count_unique_copies_supporting_each_edge ... ok
[INFO] [stdout] test minimizer_jaccard_keeps_similar_sequences_together ... ok
[INFO] [stdout] test build_family_graph_fits_profiles_when_sequences_present ... ok
[INFO] [stdout] test position_overlap_clusters_partition_exons ... ok
[INFO] [stderr]      Running tests/regression/vg_hmm_integration_golga.rs (/opt/rustwide/target/debug/deps/vg_hmm_integration_golga-3a82cc6d684f6b03)
[INFO] [stderr]      Running tests/regression/vg_hmm_negative_control.rs (/opt/rustwide/target/debug/deps/vg_hmm_negative_control-2a84e3f206b201c3)
[INFO] [stdout] test minimizer_jaccard_splits_position_cluster_when_sequences_diverge ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 9 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 1 test
[INFO] [stdout] test hmm_mode_smoke_on_chr19 ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 1 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 3 tests
[INFO] [stdout] test empty_families_yield_no_rescue ... ok
[INFO] [stdout] test any_reads_yield_no_rescue_at_high_threshold ... ok
[INFO] [stdout] test poly_a_reads_yield_no_rescue ... ok
[INFO] [stderr]      Running tests/regression/vg_hmm_profile.rs (/opt/rustwide/target/debug/deps/vg_hmm_profile-9ca1394ed1e6ccc1)
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 3 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.12s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 7 tests
[INFO] [stdout] test fully_conserved_column_has_peaked_emission ... ok
[INFO] [stdout] test gappy_msa_increases_md_or_mi ... ok
[INFO] [stdout] test no_gaps_msa_makes_mm_dominant ... ok
[INFO] [stdout] test divergent_column_is_flatter_than_conserved ... ok
[INFO] [stdout] test empty_profile_hmm_constructs ... ok
[INFO] [stdout] test poa_msa_returns_equal_length_rows ... ok
[INFO] [stdout] test singleton_class_profile_has_one_hot_match_emissions ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 7 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s
[INFO] [stdout] 
[INFO] [stderr]      Running tests/regression/vg_hmm_rescue.rs (/opt/rustwide/target/debug/deps/vg_hmm_rescue-14506755e7d1dc1e)
[INFO] [stdout] 
[INFO] [stdout] running 20 tests
[INFO] [stdout] test paralog_offsets_project_onto_candidate_locus ... ok
[INFO] [stdout] test non_synthetic_bundle_leaves_transcript_flag_false ... ok
[INFO] [stdout] test paralog_exon_spans_returns_genomic_order_for_copy ... ok
[INFO] [stdout] test prefilter_read_empty_family_kmers_always_fails ... ok
[INFO] [stdout] test prefilter_read_fails_when_too_few_hits ... ok
[INFO] [stdout] test prefilter_read_passes_when_enough_hits ... ok
[INFO] [stdout] test prefilter_read_returns_consistent_passed_and_hits ... ok
[INFO] [stdout] test prefilter_read_short_read_fails ... ok
[INFO] [stdout] test representative_copy_picks_most_complete ... ok
[INFO] [stdout] test run_rescue_in_memory_empty_inputs_returns_empty ... ok
[INFO] [stdout] test run_rescue_in_memory_empty_reads_returns_empty ... ok
[INFO] [stdout] test run_rescue_in_memory_high_threshold_returns_empty ... ok
[INFO] [stdout] test synthesize_bundles_min_reads_drops_small_clusters ... ok
[INFO] [stdout] test synthesize_bundles_refined_falls_back_when_too_few_supporters ... ok
[INFO] [stdout] test synthesize_bundles_emits_synthetic_bundle_for_sufficient_cluster ... ok
[INFO] [stdout] test synthesize_bundles_refined_produces_synthetic_bundle_with_strand_aware_anchoring ... ok
[INFO] [stdout] test synthesize_bundles_two_clusters_emit_two_bundles ... ok
[INFO] [stdout] test synthetic_flag_propagates_from_bundle_to_transcripts ... ok
[INFO] [stdout] test run_rescue_in_memory_matching_read_scores_pass ... ok
[INFO] [stderr]      Running tests/regression/vg_hmm_scorer.rs (/opt/rustwide/target/debug/deps/vg_hmm_scorer-fef008d04207013d)
[INFO] [stdout] test synthesize_bundles_refined_keeps_internal_node_spans ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 20 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] running 9 tests
[INFO] [stderr]      Running tests/regression/vg_hmm_synthetic_ground_truth.rs (/opt/rustwide/target/debug/deps/vg_hmm_synthetic_ground_truth-708e7596553aa117)
[INFO] [stdout] test forward_against_path_distinguishes_paralogs_via_recover_paralog_path ... ok
[INFO] [stdout] test forward_against_path_constrained_score_finite_for_valid_path ... ok
[INFO] [stdout] test forward_against_path_returns_neginf_for_empty_path ... ok
[INFO] [stdout] test forward_against_path_full_path_matches_full_family_score ... ok
[INFO] [stdout] test forward_against_path_returns_neginf_for_out_of_range_node ... ok
[INFO] [stdout] test perfectly_matching_read_scores_higher_than_random ... ok
[INFO] [stdout] test recover_paralog_path_excludes_nodes_paralog_doesnt_contribute_to ... ok
[INFO] [stdout] test recover_paralog_path_returns_genomic_order ... ok
[INFO] [stdout] test family_forward_path_through_two_nodes ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 9 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 synthetic_fixture_files_are_present_and_non_empty ... ok
[INFO] [stderr] [VG] Loading genome for sequence-similarity family discovery...
[INFO] [stdout] test synthetic_fixture_runs_without_crash ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 2 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.03s
[INFO] [stdout] 
[INFO] [stderr]    Doc-tests rustle
[INFO] [stdout] 
[INFO] [stdout] running 1 test
[INFO] [stdout] test src/rustle/parity_decisions.rs - parity_decisions (line 10) ... FAILED
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout] 
[INFO] [stdout] ---- src/rustle/parity_decisions.rs - parity_decisions (line 10) stdout ----
[INFO] [stdout] error: expected one of `.`, `;`, `?`, `}`, or an operator, found `:`
[INFO] [stdout]   --> src/rustle/parity_decisions.rs:12:8
[INFO] [stdout]    |
[INFO] [stdout] 12 | {"step":"junction_accept","tool":"rustle","chrom":"NC_073243.2","start":15400361,"end":15402062,"strand":"-","payload":{"support":12...
[INFO] [stdout]    |        ^ expected one of `.`, `;`, `?`, `}`, or an operator
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 1 previous error
[INFO] [stdout] 
[INFO] [stdout] Couldn't compile the test.
[INFO] [stdout] 
[INFO] [stdout] failures:
[INFO] [stdout]     src/rustle/parity_decisions.rs - parity_decisions (line 10)
[INFO] [stdout] 
[INFO] [stdout] test result: FAILED. 0 passed; 1 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.05s
[INFO] [stdout] 
[INFO] [stderr] error: doctest failed, to rerun pass `--doc`
[INFO] running `Command { std: "docker" "inspect" "14928eafb2324651caa06cf6a9ee2e4be051dc95d06eac1701db7882f675ad29", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "14928eafb2324651caa06cf6a9ee2e4be051dc95d06eac1701db7882f675ad29", kill_on_drop: false }`
[INFO] [stdout] 14928eafb2324651caa06cf6a9ee2e4be051dc95d06eac1701db7882f675ad29
