[INFO] cloning repository https://github.com/KingofLaniakea/Straglr-rs [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/KingofLaniakea/Straglr-rs" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FKingofLaniakea%2FStraglr-rs", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FKingofLaniakea%2FStraglr-rs'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] af3897354bf6635d887b0cf1e1a93bd626783234 [INFO] testing KingofLaniakea/Straglr-rs against 1.95.0 for beta-1.96-1 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FKingofLaniakea%2FStraglr-rs" "/workspace/builds/worker-6-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-6-tc1/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/KingofLaniakea/Straglr-rs [INFO] finished tweaking git repo https://github.com/KingofLaniakea/Straglr-rs [INFO] tweaked toml for git repo https://github.com/KingofLaniakea/Straglr-rs written to /workspace/builds/worker-6-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/KingofLaniakea/Straglr-rs on toolchain 1.95.0 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.95.0" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/KingofLaniakea/Straglr-rs 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" "+1.95.0" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded nalgebra-macros v0.1.0 [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded simba v0.6.0 [INFO] [stderr] Downloaded custom_derive v0.1.7 [INFO] [stderr] Downloaded derive-new v0.6.0 [INFO] [stderr] Downloaded linear-map v1.2.0 [INFO] [stderr] Downloaded ieee754 v0.2.6 [INFO] [stderr] Downloaded bio-types v1.0.4 [INFO] [stderr] Downloaded clap v4.5.60 [INFO] [stderr] Downloaded derive-new v0.7.0 [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded statrs v0.16.1 [INFO] [stderr] Downloaded rust-htslib v0.48.0 [INFO] [stderr] Downloaded clap_builder v4.5.60 [INFO] [stderr] Downloaded nalgebra v0.29.0 [INFO] [stderr] Downloaded libz-sys v1.1.24 [INFO] [stderr] Downloaded curl-sys v0.4.85+curl-8.18.0 [INFO] [stderr] Downloaded hts-sys v2.2.0 [INFO] [stderr] Downloaded openssl-src v300.5.5+3.5.5 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+1.95.0" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] f701a688a327d03f2fe766224048e81923d9c35fafa2569c554b60acc0582d9c [INFO] running `Command { std: "docker" "start" "-a" "f701a688a327d03f2fe766224048e81923d9c35fafa2569c554b60acc0582d9c", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "f701a688a327d03f2fe766224048e81923d9c35fafa2569c554b60acc0582d9c", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f701a688a327d03f2fe766224048e81923d9c35fafa2569c554b60acc0582d9c", kill_on_drop: false }` [INFO] [stdout] f701a688a327d03f2fe766224048e81923d9c35fafa2569c554b60acc0582d9c [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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=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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+1.95.0" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 6e1d9fdbbeb6793eeaae806698ee40e2f9d901e2bf742928ec1bab058cca13c7 [INFO] running `Command { std: "docker" "start" "-a" "6e1d9fdbbeb6793eeaae806698ee40e2f9d901e2bf742928ec1bab058cca13c7", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.182 [INFO] [stderr] Compiling libm v0.2.16 [INFO] [stderr] Compiling glob v0.3.3 [INFO] [stderr] Compiling zerocopy v0.8.40 [INFO] [stderr] Compiling bytemuck v1.25.0 [INFO] [stderr] Compiling regex-syntax v0.8.10 [INFO] [stderr] Compiling minimal-lexical v0.2.1 [INFO] [stderr] Compiling libloading v0.8.9 [INFO] [stderr] Compiling bindgen v0.69.5 [INFO] [stderr] Compiling itertools v0.12.1 [INFO] [stderr] Compiling matrixmultiply v0.3.10 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling bitflags v2.11.0 [INFO] [stderr] Compiling rustc-hash v1.1.0 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling lazycell v1.3.0 [INFO] [stderr] Compiling smallvec v1.15.1 [INFO] [stderr] Compiling nom v7.1.3 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling regex-automata v0.4.14 [INFO] [stderr] Compiling rawpointer v0.2.1 [INFO] [stderr] Compiling thiserror-impl v1.0.69 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling safe_arch v0.7.4 [INFO] [stderr] Compiling percent-encoding v2.3.2 [INFO] [stderr] Compiling icu_normalizer v2.1.1 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling clang-sys v1.8.1 [INFO] [stderr] Compiling form_urlencoded v1.2.2 [INFO] [stderr] Compiling derive-new v0.6.0 [INFO] [stderr] Compiling clap_builder v4.5.60 [INFO] [stderr] Compiling clap_derive v4.5.55 [INFO] [stderr] Compiling derive-new v0.7.0 [INFO] [stderr] Compiling wide v0.7.33 [INFO] [stderr] Compiling idna_adapter v1.2.1 [INFO] [stderr] Compiling idna v1.1.0 [INFO] [stderr] Compiling nalgebra-macros v0.2.2 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling url v2.5.8 [INFO] [stderr] Compiling jobserver v0.1.34 [INFO] [stderr] Compiling getrandom v0.2.17 [INFO] [stderr] Compiling rand_core v0.6.4 [INFO] [stderr] Compiling thiserror v1.0.69 [INFO] [stderr] Compiling cc v1.2.56 [INFO] [stderr] Compiling approx v0.5.1 [INFO] [stderr] Compiling num-complex v0.4.6 [INFO] [stderr] Compiling num-integer v0.1.46 [INFO] [stderr] Compiling is-terminal v0.4.17 [INFO] [stderr] Compiling getrandom v0.4.2 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling cexpr v0.6.0 [INFO] [stderr] Compiling termcolor v1.4.1 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling once_cell v1.21.3 [INFO] [stderr] Compiling num-rational v0.4.2 [INFO] [stderr] Compiling tempfile v3.26.0 [INFO] [stderr] Compiling openssl-src v300.5.5+3.5.5 [INFO] [stderr] Compiling cmake v0.1.57 [INFO] [stderr] Compiling regex v1.12.3 [INFO] [stderr] Compiling simba v0.6.0 [INFO] [stderr] Compiling simba v0.8.1 [INFO] [stderr] Compiling clap v4.5.60 [INFO] [stderr] Compiling bio-types v1.0.4 [INFO] [stderr] Compiling env_logger v0.10.2 [INFO] [stderr] Compiling libz-sys v1.1.24 [INFO] [stderr] Compiling openssl-sys v0.9.111 [INFO] [stderr] Compiling bzip2-sys v0.1.13+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling curl-sys v0.4.85+curl-8.18.0 [INFO] [stderr] Compiling nalgebra-macros v0.1.0 [INFO] [stderr] Compiling ppv-lite86 v0.2.21 [INFO] [stderr] Compiling rand_chacha v0.3.1 [INFO] [stderr] Compiling rand v0.8.5 [INFO] [stderr] Compiling rand_distr v0.4.3 [INFO] [stderr] Compiling nalgebra v0.29.0 [INFO] [stderr] Compiling nalgebra v0.32.6 [INFO] [stderr] Compiling hts-sys v2.2.0 [INFO] [stderr] Compiling statrs v0.16.1 [INFO] [stderr] Compiling rust-htslib v0.48.0 [INFO] [stderr] Compiling straglr-rs v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: fields `genome_fasta` and `temp_files` are never read [INFO] [stdout] --> src/ins/finder.rs:40:5 [INFO] [stdout] | [INFO] [stdout] 38 | pub struct INSFinder { [INFO] [stdout] | --------- fields in this struct [INFO] [stdout] 39 | bam_path: String, [INFO] [stdout] 40 | genome_fasta: String, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 41 | config: INSFinderConfig, [INFO] [stdout] 42 | temp_files: HashSet, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `bam_path` and `genome_fasta` are never read [INFO] [stdout] --> src/tre/mod.rs:159:5 [INFO] [stdout] | [INFO] [stdout] 157 | pub struct TREFinder { [INFO] [stdout] | --------- fields in this struct [INFO] [stdout] 158 | /// BAM file path [INFO] [stdout] 159 | bam_path: String, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 160 | /// Reference genome FASTA path [INFO] [stdout] 161 | genome_fasta: String, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `etype` and `repeat_unit` are never read [INFO] [stdout] --> src/ins/mod.rs:26:9 [INFO] [stdout] | [INFO] [stdout] 12 | pub struct Insertion { [INFO] [stdout] | --------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 26 | pub etype: String, [INFO] [stdout] | ^^^^^ [INFO] [stdout] ... [INFO] [stdout] 30 | pub repeat_unit: Option, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Insertion` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `extract_neighbor_seqs` and `to_bed` are never used [INFO] [stdout] --> src/ins/mod.rs:58:12 [INFO] [stdout] | [INFO] [stdout] 33 | impl Insertion { [INFO] [stdout] | -------------- associated items in this implementation [INFO] [stdout] ... [INFO] [stdout] 58 | pub fn extract_neighbor_seqs(read_seq: &str, rpos: usize, ins_size: usize, flank_size: usize) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 83 | pub fn to_bed(&self, include_read: bool) -> String { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `flank_size`, `max_cov`, `nprocs`, `check_split_alignments`, `use_unpaired_clips`, and `debug` are never read [INFO] [stdout] --> src/ins/finder.rs:13:9 [INFO] [stdout] | [INFO] [stdout] 11 | pub struct INSFinderConfig { [INFO] [stdout] | --------------- fields in this struct [INFO] [stdout] 12 | pub min_size: u32, [INFO] [stdout] 13 | pub flank_size: u32, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] 14 | pub max_cov: u32, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] 15 | pub min_support: u32, [INFO] [stdout] 16 | pub nprocs: usize, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] 17 | pub check_split_alignments: bool, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] 18 | pub use_unpaired_clips: bool, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] 19 | pub debug: bool, [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `INSFinderConfig` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `genome_fasta` and `temp_files` are never read [INFO] [stdout] --> src/ins/finder.rs:40:5 [INFO] [stdout] | [INFO] [stdout] 38 | pub struct INSFinder { [INFO] [stdout] | --------- fields in this struct [INFO] [stdout] 39 | bam_path: String, [INFO] [stdout] 40 | genome_fasta: String, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 41 | config: INSFinderConfig, [INFO] [stdout] 42 | temp_files: HashSet, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `flank_size`, `nprocs`, and `include_partials` are never read [INFO] [stdout] --> src/tre/mod.rs:28:9 [INFO] [stdout] | [INFO] [stdout] 20 | pub struct TREFinderConfig { [INFO] [stdout] | --------------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 28 | pub flank_size: u32, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 32 | pub nprocs: usize, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 48 | pub include_partials: bool, [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `TREFinderConfig` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: multiple fields are never read [INFO] [stdout] --> src/tre/mod.rs:96:9 [INFO] [stdout] | [INFO] [stdout] 92 | pub struct TrfResult { [INFO] [stdout] | --------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 96 | pub end: i32, [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 100 | pub copy_number: f64, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] 101 | /// Consensus size [INFO] [stdout] 102 | pub consensus_size: i32, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] 103 | /// Percent matches [INFO] [stdout] 104 | pub percent_matches: f64, [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] 105 | /// Percent indels [INFO] [stdout] 106 | pub percent_indels: f64, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] 107 | /// Score [INFO] [stdout] 108 | pub score: i32, [INFO] [stdout] | ^^^^^ [INFO] [stdout] 109 | /// A count [INFO] [stdout] 110 | pub a_count: i32, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] 111 | /// C count [INFO] [stdout] 112 | pub c_count: i32, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] 113 | /// G count [INFO] [stdout] 114 | pub g_count: i32, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] 115 | /// T count [INFO] [stdout] 116 | pub t_count: i32, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] 117 | /// Entropy [INFO] [stdout] 118 | pub entropy: f64, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `TrfResult` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: multiple fields are never read [INFO] [stdout] --> src/tre/mod.rs:129:9 [INFO] [stdout] | [INFO] [stdout] 125 | pub struct BlastnResult { [INFO] [stdout] | ------------ fields in this struct [INFO] [stdout] ... [INFO] [stdout] 129 | pub subject_id: String, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 133 | pub alignment_length: i32, [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] 134 | /// Mismatches [INFO] [stdout] 135 | pub mismatches: i32, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] 136 | /// Gap openings [INFO] [stdout] 137 | pub gap_openings: i32, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 138 | /// Query start (1-based) [INFO] [stdout] 139 | pub query_start: i32, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] 140 | /// Query end (1-based) [INFO] [stdout] 141 | pub query_end: i32, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] 142 | /// Subject start (1-based) [INFO] [stdout] 143 | pub subject_start: i32, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] 144 | /// Subject end (1-based) [INFO] [stdout] 145 | pub subject_end: i32, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 149 | pub bit_score: f64, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] 150 | /// Query sequence [INFO] [stdout] 151 | pub query_seq: Option, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] 152 | /// Subject sequence [INFO] [stdout] 153 | pub subject_seq: Option, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `BlastnResult` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `bam_path` and `genome_fasta` are never read [INFO] [stdout] --> src/tre/mod.rs:159:5 [INFO] [stdout] | [INFO] [stdout] 157 | pub struct TREFinder { [INFO] [stdout] | --------- fields in this struct [INFO] [stdout] 158 | /// BAM file path [INFO] [stdout] 159 | bam_path: String, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 160 | /// Reference genome FASTA path [INFO] [stdout] 161 | genome_fasta: String, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `max_bad_cluster_size` is never read [INFO] [stdout] --> src/cluster/mod.rs:21:9 [INFO] [stdout] | [INFO] [stdout] 11 | pub struct ClusterParams { [INFO] [stdout] | ------------- field in this struct [INFO] [stdout] ... [INFO] [stdout] 21 | pub max_bad_cluster_size: usize, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `ClusterParams` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `genome_start`, `genome_end`, `repeat_seq`, and `fail_reason` are never read [INFO] [stdout] --> src/variant/mod.rs:22:9 [INFO] [stdout] | [INFO] [stdout] 10 | pub struct Allele { [INFO] [stdout] | ------ fields in this struct [INFO] [stdout] ... [INFO] [stdout] 22 | pub genome_start: i32, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 23 | /// Genome end position [INFO] [stdout] 24 | pub genome_end: i32, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 28 | pub repeat_seq: String, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 36 | pub fail_reason: Option, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Allele` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `ref_motif`, `ref_seq`, and `ref_cn` are never read [INFO] [stdout] --> src/variant/mod.rs:114:9 [INFO] [stdout] | [INFO] [stdout] 96 | pub struct Variant { [INFO] [stdout] | ------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 114 | pub ref_motif: String, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] 115 | /// Reference sequence [INFO] [stdout] 116 | pub ref_seq: String, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] 117 | /// Reference copy number [INFO] [stdout] 118 | pub ref_cn: f64, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Variant` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `split_tasks` is never used [INFO] [stdout] --> src/utils/mod.rs:9:8 [INFO] [stdout] | [INFO] [stdout] 9 | pub fn split_tasks(items: &[T], n: usize) -> Vec> { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `reverse_complement` is never used [INFO] [stdout] --> src/utils/mod.rs:34:8 [INFO] [stdout] | [INFO] [stdout] 34 | pub fn reverse_complement(seq: &str) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `merge_spans` is never used [INFO] [stdout] --> src/utils/mod.rs:49:8 [INFO] [stdout] | [INFO] [stdout] 49 | pub fn merge_spans(spans: &[(i32, i32)]) -> Vec<(i32, i32)> { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `complement_spans` is never used [INFO] [stdout] --> src/utils/mod.rs:72:8 [INFO] [stdout] | [INFO] [stdout] 72 | pub fn complement_spans(spans: &[(i32, i32)], _min: i32, _max: i32) -> Vec<(i32, i32)> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `create_temp_file` is never used [INFO] [stdout] --> src/utils/mod.rs:111:8 [INFO] [stdout] | [INFO] [stdout] 111 | pub fn create_temp_file(content: &str, _suffix: &str) -> std::io::Result { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parse_bed_line` is never used [INFO] [stdout] --> src/utils/mod.rs:118:8 [INFO] [stdout] | [INFO] [stdout] 118 | pub fn parse_bed_line(line: &str) -> Option<(String, i32, i32, Option)> { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `read_bed_file` is never used [INFO] [stdout] --> src/utils/mod.rs:133:8 [INFO] [stdout] | [INFO] [stdout] 133 | pub fn read_bed_file>(path: P) -> std::io::Result)>> { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 09s [INFO] running `Command { std: "docker" "inspect" "6e1d9fdbbeb6793eeaae806698ee40e2f9d901e2bf742928ec1bab058cca13c7", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "6e1d9fdbbeb6793eeaae806698ee40e2f9d901e2bf742928ec1bab058cca13c7", kill_on_drop: false }` [INFO] [stdout] 6e1d9fdbbeb6793eeaae806698ee40e2f9d901e2bf742928ec1bab058cca13c7 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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=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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+1.95.0" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 94ed528a90b961b1b48d265921c8c7d944d863338f7b5afa4aa77c70c3a949b5 [INFO] running `Command { std: "docker" "start" "-a" "94ed528a90b961b1b48d265921c8c7d944d863338f7b5afa4aa77c70c3a949b5", kill_on_drop: false }` [INFO] [stderr] Compiling straglr-rs v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: fields `genome_fasta` and `temp_files` are never read [INFO] [stdout] --> src/ins/finder.rs:40:5 [INFO] [stdout] | [INFO] [stdout] 38 | pub struct INSFinder { [INFO] [stdout] | --------- fields in this struct [INFO] [stdout] 39 | bam_path: String, [INFO] [stdout] 40 | genome_fasta: String, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 41 | config: INSFinderConfig, [INFO] [stdout] 42 | temp_files: HashSet, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `bam_path` and `genome_fasta` are never read [INFO] [stdout] --> src/tre/mod.rs:159:5 [INFO] [stdout] | [INFO] [stdout] 157 | pub struct TREFinder { [INFO] [stdout] | --------- fields in this struct [INFO] [stdout] 158 | /// BAM file path [INFO] [stdout] 159 | bam_path: String, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 160 | /// Reference genome FASTA path [INFO] [stdout] 161 | genome_fasta: String, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `genome_fasta` and `temp_files` are never read [INFO] [stdout] --> src/ins/finder.rs:40:5 [INFO] [stdout] | [INFO] [stdout] 38 | pub struct INSFinder { [INFO] [stdout] | --------- fields in this struct [INFO] [stdout] 39 | bam_path: String, [INFO] [stdout] 40 | genome_fasta: String, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 41 | config: INSFinderConfig, [INFO] [stdout] 42 | temp_files: HashSet, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `bam_path` and `genome_fasta` are never read [INFO] [stdout] --> src/tre/mod.rs:159:5 [INFO] [stdout] | [INFO] [stdout] 157 | pub struct TREFinder { [INFO] [stdout] | --------- fields in this struct [INFO] [stdout] 158 | /// BAM file path [INFO] [stdout] 159 | bam_path: String, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 160 | /// Reference genome FASTA path [INFO] [stdout] 161 | genome_fasta: String, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `etype` and `repeat_unit` are never read [INFO] [stdout] --> src/ins/mod.rs:26:9 [INFO] [stdout] | [INFO] [stdout] 12 | pub struct Insertion { [INFO] [stdout] | --------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 26 | pub etype: String, [INFO] [stdout] | ^^^^^ [INFO] [stdout] ... [INFO] [stdout] 30 | pub repeat_unit: Option, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Insertion` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `to_bed` is never used [INFO] [stdout] --> src/ins/mod.rs:83:12 [INFO] [stdout] | [INFO] [stdout] 33 | impl Insertion { [INFO] [stdout] | -------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 83 | pub fn to_bed(&self, include_read: bool) -> String { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `flank_size`, `max_cov`, `nprocs`, `check_split_alignments`, `use_unpaired_clips`, and `debug` are never read [INFO] [stdout] --> src/ins/finder.rs:13:9 [INFO] [stdout] | [INFO] [stdout] 11 | pub struct INSFinderConfig { [INFO] [stdout] | --------------- fields in this struct [INFO] [stdout] 12 | pub min_size: u32, [INFO] [stdout] 13 | pub flank_size: u32, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] 14 | pub max_cov: u32, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] 15 | pub min_support: u32, [INFO] [stdout] 16 | pub nprocs: usize, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] 17 | pub check_split_alignments: bool, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] 18 | pub use_unpaired_clips: bool, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] 19 | pub debug: bool, [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `INSFinderConfig` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `genome_fasta` and `temp_files` are never read [INFO] [stdout] --> src/ins/finder.rs:40:5 [INFO] [stdout] | [INFO] [stdout] 38 | pub struct INSFinder { [INFO] [stdout] | --------- fields in this struct [INFO] [stdout] 39 | bam_path: String, [INFO] [stdout] 40 | genome_fasta: String, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 41 | config: INSFinderConfig, [INFO] [stdout] 42 | temp_files: HashSet, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `flank_size`, `nprocs`, and `include_partials` are never read [INFO] [stdout] --> src/tre/mod.rs:28:9 [INFO] [stdout] | [INFO] [stdout] 20 | pub struct TREFinderConfig { [INFO] [stdout] | --------------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 28 | pub flank_size: u32, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 32 | pub nprocs: usize, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 48 | pub include_partials: bool, [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `TREFinderConfig` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: multiple fields are never read [INFO] [stdout] --> src/tre/mod.rs:96:9 [INFO] [stdout] | [INFO] [stdout] 92 | pub struct TrfResult { [INFO] [stdout] | --------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 96 | pub end: i32, [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 100 | pub copy_number: f64, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] 101 | /// Consensus size [INFO] [stdout] 102 | pub consensus_size: i32, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] 103 | /// Percent matches [INFO] [stdout] 104 | pub percent_matches: f64, [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] 105 | /// Percent indels [INFO] [stdout] 106 | pub percent_indels: f64, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] 107 | /// Score [INFO] [stdout] 108 | pub score: i32, [INFO] [stdout] | ^^^^^ [INFO] [stdout] 109 | /// A count [INFO] [stdout] 110 | pub a_count: i32, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] 111 | /// C count [INFO] [stdout] 112 | pub c_count: i32, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] 113 | /// G count [INFO] [stdout] 114 | pub g_count: i32, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] 115 | /// T count [INFO] [stdout] 116 | pub t_count: i32, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] 117 | /// Entropy [INFO] [stdout] 118 | pub entropy: f64, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `TrfResult` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: multiple fields are never read [INFO] [stdout] --> src/tre/mod.rs:129:9 [INFO] [stdout] | [INFO] [stdout] 125 | pub struct BlastnResult { [INFO] [stdout] | ------------ fields in this struct [INFO] [stdout] ... [INFO] [stdout] 129 | pub subject_id: String, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 133 | pub alignment_length: i32, [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] 134 | /// Mismatches [INFO] [stdout] 135 | pub mismatches: i32, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] 136 | /// Gap openings [INFO] [stdout] 137 | pub gap_openings: i32, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 138 | /// Query start (1-based) [INFO] [stdout] 139 | pub query_start: i32, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] 140 | /// Query end (1-based) [INFO] [stdout] 141 | pub query_end: i32, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] 142 | /// Subject start (1-based) [INFO] [stdout] 143 | pub subject_start: i32, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] 144 | /// Subject end (1-based) [INFO] [stdout] 145 | pub subject_end: i32, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 149 | pub bit_score: f64, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] 150 | /// Query sequence [INFO] [stdout] 151 | pub query_seq: Option, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] 152 | /// Subject sequence [INFO] [stdout] 153 | pub subject_seq: Option, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `BlastnResult` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `bam_path` and `genome_fasta` are never read [INFO] [stdout] --> src/tre/mod.rs:159:5 [INFO] [stdout] | [INFO] [stdout] 157 | pub struct TREFinder { [INFO] [stdout] | --------- fields in this struct [INFO] [stdout] 158 | /// BAM file path [INFO] [stdout] 159 | bam_path: String, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 160 | /// Reference genome FASTA path [INFO] [stdout] 161 | genome_fasta: String, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `max_bad_cluster_size` is never read [INFO] [stdout] --> src/cluster/mod.rs:21:9 [INFO] [stdout] | [INFO] [stdout] 11 | pub struct ClusterParams { [INFO] [stdout] | ------------- field in this struct [INFO] [stdout] ... [INFO] [stdout] 21 | pub max_bad_cluster_size: usize, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `ClusterParams` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `genome_start`, `genome_end`, `repeat_seq`, and `fail_reason` are never read [INFO] [stdout] --> src/variant/mod.rs:22:9 [INFO] [stdout] | [INFO] [stdout] 10 | pub struct Allele { [INFO] [stdout] | ------ fields in this struct [INFO] [stdout] ... [INFO] [stdout] 22 | pub genome_start: i32, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 23 | /// Genome end position [INFO] [stdout] 24 | pub genome_end: i32, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 28 | pub repeat_seq: String, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 36 | pub fail_reason: Option, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Allele` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `ref_motif` and `ref_seq` are never read [INFO] [stdout] --> src/variant/mod.rs:114:9 [INFO] [stdout] | [INFO] [stdout] 96 | pub struct Variant { [INFO] [stdout] | ------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 114 | pub ref_motif: String, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] 115 | /// Reference sequence [INFO] [stdout] 116 | pub ref_seq: String, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Variant` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `complement_spans` is never used [INFO] [stdout] --> src/utils/mod.rs:72:8 [INFO] [stdout] | [INFO] [stdout] 72 | pub fn complement_spans(spans: &[(i32, i32)], _min: i32, _max: i32) -> Vec<(i32, i32)> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `create_temp_file` is never used [INFO] [stdout] --> src/utils/mod.rs:111:8 [INFO] [stdout] | [INFO] [stdout] 111 | pub fn create_temp_file(content: &str, _suffix: &str) -> std::io::Result { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parse_bed_line` is never used [INFO] [stdout] --> src/utils/mod.rs:118:8 [INFO] [stdout] | [INFO] [stdout] 118 | pub fn parse_bed_line(line: &str) -> Option<(String, i32, i32, Option)> { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `read_bed_file` is never used [INFO] [stdout] --> src/utils/mod.rs:133:8 [INFO] [stdout] | [INFO] [stdout] 133 | pub fn read_bed_file>(path: P) -> std::io::Result)>> { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 2.44s [INFO] running `Command { std: "docker" "inspect" "94ed528a90b961b1b48d265921c8c7d944d863338f7b5afa4aa77c70c3a949b5", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "94ed528a90b961b1b48d265921c8c7d944d863338f7b5afa4aa77c70c3a949b5", kill_on_drop: false }` [INFO] [stdout] 94ed528a90b961b1b48d265921c8c7d944d863338f7b5afa4aa77c70c3a949b5 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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=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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+1.95.0" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] 9f1ee635240d24ee19c84d2dab9733983451835ec52add766bcb0e3a2b2fe25c [INFO] running `Command { std: "docker" "start" "-a" "9f1ee635240d24ee19c84d2dab9733983451835ec52add766bcb0e3a2b2fe25c", kill_on_drop: false }` [INFO] [stderr] warning: fields `genome_fasta` and `temp_files` are never read [INFO] [stderr] --> src/ins/finder.rs:40:5 [INFO] [stderr] | [INFO] [stderr] 38 | pub struct INSFinder { [INFO] [stderr] | --------- fields in this struct [INFO] [stderr] 39 | bam_path: String, [INFO] [stderr] 40 | genome_fasta: String, [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] 41 | config: INSFinderConfig, [INFO] [stderr] 42 | temp_files: HashSet, [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: fields `bam_path` and `genome_fasta` are never read [INFO] [stderr] --> src/tre/mod.rs:159:5 [INFO] [stderr] | [INFO] [stderr] 157 | pub struct TREFinder { [INFO] [stderr] | --------- fields in this struct [INFO] [stderr] 158 | /// BAM file path [INFO] [stderr] 159 | bam_path: String, [INFO] [stderr] | ^^^^^^^^ [INFO] [stderr] 160 | /// Reference genome FASTA path [INFO] [stderr] 161 | genome_fasta: String, [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: `straglr-rs` (lib) generated 2 warnings [INFO] [stderr] warning: `straglr-rs` (lib test) generated 2 warnings (2 duplicates) [INFO] [stderr] warning: fields `etype` and `repeat_unit` are never read [INFO] [stderr] --> src/ins/mod.rs:26:9 [INFO] [stderr] | [INFO] [stderr] 12 | pub struct Insertion { [INFO] [stderr] | --------- fields in this struct [INFO] [stderr] ... [INFO] [stderr] 26 | pub etype: String, [INFO] [stderr] | ^^^^^ [INFO] [stderr] ... [INFO] [stderr] 30 | pub repeat_unit: Option, [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `Insertion` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stderr] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stderr] [INFO] [stderr] warning: method `to_bed` is never used [INFO] [stderr] --> src/ins/mod.rs:83:12 [INFO] [stderr] | [INFO] [stderr] 33 | impl Insertion { [INFO] [stderr] | -------------- method in this implementation [INFO] [stderr] ... [INFO] [stderr] 83 | pub fn to_bed(&self, include_read: bool) -> String { [INFO] [stderr] | ^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: fields `flank_size`, `max_cov`, `nprocs`, `check_split_alignments`, `use_unpaired_clips`, and `debug` are never read [INFO] [stderr] --> src/ins/finder.rs:13:9 [INFO] [stderr] | [INFO] [stderr] 11 | pub struct INSFinderConfig { [INFO] [stderr] | --------------- fields in this struct [INFO] [stderr] 12 | pub min_size: u32, [INFO] [stderr] 13 | pub flank_size: u32, [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] 14 | pub max_cov: u32, [INFO] [stderr] | ^^^^^^^ [INFO] [stderr] 15 | pub min_support: u32, [INFO] [stderr] 16 | pub nprocs: usize, [INFO] [stderr] | ^^^^^^ [INFO] [stderr] 17 | pub check_split_alignments: bool, [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] 18 | pub use_unpaired_clips: bool, [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ [INFO] [stderr] 19 | pub debug: bool, [INFO] [stderr] | ^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `INSFinderConfig` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stderr] [INFO] [stderr] warning: fields `genome_fasta` and `temp_files` are never read [INFO] [stderr] --> src/ins/finder.rs:40:5 [INFO] [stderr] | [INFO] [stderr] 38 | pub struct INSFinder { [INFO] [stderr] | --------- fields in this struct [INFO] [stderr] 39 | bam_path: String, [INFO] [stderr] 40 | genome_fasta: String, [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] 41 | config: INSFinderConfig, [INFO] [stderr] 42 | temp_files: HashSet, [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: fields `flank_size`, `nprocs`, and `include_partials` are never read [INFO] [stderr] --> src/tre/mod.rs:28:9 [INFO] [stderr] | [INFO] [stderr] 20 | pub struct TREFinderConfig { [INFO] [stderr] | --------------- fields in this struct [INFO] [stderr] ... [INFO] [stderr] 28 | pub flank_size: u32, [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 32 | pub nprocs: usize, [INFO] [stderr] | ^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 48 | pub include_partials: bool, [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `TREFinderConfig` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stderr] [INFO] [stderr] warning: multiple fields are never read [INFO] [stderr] --> src/tre/mod.rs:96:9 [INFO] [stderr] | [INFO] [stderr] 92 | pub struct TrfResult { [INFO] [stderr] | --------- fields in this struct [INFO] [stderr] ... [INFO] [stderr] 96 | pub end: i32, [INFO] [stderr] | ^^^ [INFO] [stderr] ... [INFO] [stderr] 100 | pub copy_number: f64, [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] 101 | /// Consensus size [INFO] [stderr] 102 | pub consensus_size: i32, [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] 103 | /// Percent matches [INFO] [stderr] 104 | pub percent_matches: f64, [INFO] [stderr] | ^^^^^^^^^^^^^^^ [INFO] [stderr] 105 | /// Percent indels [INFO] [stderr] 106 | pub percent_indels: f64, [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] 107 | /// Score [INFO] [stderr] 108 | pub score: i32, [INFO] [stderr] | ^^^^^ [INFO] [stderr] 109 | /// A count [INFO] [stderr] 110 | pub a_count: i32, [INFO] [stderr] | ^^^^^^^ [INFO] [stderr] 111 | /// C count [INFO] [stderr] 112 | pub c_count: i32, [INFO] [stderr] | ^^^^^^^ [INFO] [stderr] 113 | /// G count [INFO] [stderr] 114 | pub g_count: i32, [INFO] [stderr] | ^^^^^^^ [INFO] [stderr] 115 | /// T count [INFO] [stderr] 116 | pub t_count: i32, [INFO] [stderr] | ^^^^^^^ [INFO] [stderr] 117 | /// Entropy [INFO] [stderr] 118 | pub entropy: f64, [INFO] [stderr] | ^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `TrfResult` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stderr] [INFO] [stderr] warning: multiple fields are never read [INFO] [stderr] --> src/tre/mod.rs:129:9 [INFO] [stderr] | [INFO] [stderr] 125 | pub struct BlastnResult { [INFO] [stderr] | ------------ fields in this struct [INFO] [stderr] ... [INFO] [stderr] 129 | pub subject_id: String, [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 133 | pub alignment_length: i32, [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] 134 | /// Mismatches [INFO] [stderr] 135 | pub mismatches: i32, [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] 136 | /// Gap openings [INFO] [stderr] 137 | pub gap_openings: i32, [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] 138 | /// Query start (1-based) [INFO] [stderr] 139 | pub query_start: i32, [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] 140 | /// Query end (1-based) [INFO] [stderr] 141 | pub query_end: i32, [INFO] [stderr] | ^^^^^^^^^ [INFO] [stderr] 142 | /// Subject start (1-based) [INFO] [stderr] 143 | pub subject_start: i32, [INFO] [stderr] | ^^^^^^^^^^^^^ [INFO] [stderr] 144 | /// Subject end (1-based) [INFO] [stderr] 145 | pub subject_end: i32, [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 149 | pub bit_score: f64, [INFO] [stderr] | ^^^^^^^^^ [INFO] [stderr] 150 | /// Query sequence [INFO] [stderr] 151 | pub query_seq: Option, [INFO] [stderr] | ^^^^^^^^^ [INFO] [stderr] 152 | /// Subject sequence [INFO] [stderr] 153 | pub subject_seq: Option, [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `BlastnResult` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stderr] [INFO] [stderr] warning: field `max_bad_cluster_size` is never read [INFO] [stderr] --> src/cluster/mod.rs:21:9 [INFO] [stderr] | [INFO] [stderr] 11 | pub struct ClusterParams { [INFO] [stderr] | ------------- field in this struct [INFO] [stderr] ... [INFO] [stderr] 21 | pub max_bad_cluster_size: usize, [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `ClusterParams` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stderr] [INFO] [stderr] warning: fields `genome_start`, `genome_end`, `repeat_seq`, and `fail_reason` are never read [INFO] [stderr] --> src/variant/mod.rs:22:9 [INFO] [stderr] | [INFO] [stderr] 10 | pub struct Allele { [INFO] [stderr] | ------ fields in this struct [INFO] [stderr] ... [INFO] [stderr] 22 | pub genome_start: i32, [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] 23 | /// Genome end position [INFO] [stderr] 24 | pub genome_end: i32, [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 28 | pub repeat_seq: String, [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 36 | pub fail_reason: Option, [INFO] [stderr] | ^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `Allele` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stderr] [INFO] [stderr] warning: fields `ref_motif` and `ref_seq` are never read [INFO] [stderr] --> src/variant/mod.rs:114:9 [INFO] [stderr] | [INFO] [stderr] 96 | pub struct Variant { [INFO] [stderr] | ------- fields in this struct [INFO] [stderr] ... [INFO] [stderr] 114 | pub ref_motif: String, [INFO] [stderr] | ^^^^^^^^^ [INFO] [stderr] 115 | /// Reference sequence [INFO] [stderr] 116 | pub ref_seq: String, [INFO] [stderr] | ^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `Variant` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stderr] [INFO] [stderr] warning: function `complement_spans` is never used [INFO] [stderr] --> src/utils/mod.rs:72:8 [INFO] [stderr] | [INFO] [stderr] 72 | pub fn complement_spans(spans: &[(i32, i32)], _min: i32, _max: i32) -> Vec<(i32, i32)> { [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `create_temp_file` is never used [INFO] [stderr] --> src/utils/mod.rs:111:8 [INFO] [stderr] | [INFO] [stderr] 111 | pub fn create_temp_file(content: &str, _suffix: &str) -> std::io::Result { [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `parse_bed_line` is never used [INFO] [stderr] --> src/utils/mod.rs:118:8 [INFO] [stderr] | [INFO] [stderr] 118 | pub fn parse_bed_line(line: &str) -> Option<(String, i32, i32, Option)> { [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: function `read_bed_file` is never used [INFO] [stderr] --> src/utils/mod.rs:133:8 [INFO] [stderr] | [INFO] [stderr] 133 | pub fn read_bed_file>(path: P) -> std::io::Result)>> { [INFO] [stderr] | ^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: `straglr-rs` (bin "straglr-rs" test) generated 15 warnings (1 duplicate) [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.23s [INFO] [stderr] Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/straglr_rs-2aaafb76b7ff8986) [INFO] [stdout] [INFO] [stdout] running 16 tests [INFO] [stdout] test cluster::tests::test_identical_points ... ok [INFO] [stdout] test ins::finder::tests::test_config_default ... ok [INFO] [stdout] test ins::tests::test_extract_neighbor_seqs ... ok [INFO] [stdout] test ins::tests::test_extract_neighbor_seqs_full ... ok [INFO] [stdout] test ins::tests::test_insertion_eid ... ok [INFO] [stdout] test tre::tests::test_patterns_match ... ok [INFO] [stdout] test tre::tests::test_trefinder_config_default ... ok [INFO] [stdout] test utils::tests::test_merge_spans ... ok [INFO] [stdout] test utils::tests::test_reverse_complement ... ok [INFO] [stdout] test utils::tests::test_split_tasks ... ok [INFO] [stdout] test vcf::tests::test_vcf_header ... ok [INFO] [stdout] test ins::tests::test_extract_neighbor_seqs_large_flank ... ok [INFO] [stdout] test cluster::tests::test_single_point ... ok [INFO] [stdout] test cluster::tests::test_two_clusters ... ok [INFO] [stdout] test variant::tests::test_allele_is_full ... ok [INFO] [stdout] test variant::tests::test_variant_creation ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 16 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] [stderr] Running unittests src/main.rs (/opt/rustwide/target/debug/deps/straglr_rs-3b5210cb5becc33c) [INFO] [stdout] [INFO] [stdout] running 16 tests [INFO] [stdout] test cluster::tests::test_single_point ... ok [INFO] [stdout] test cluster::tests::test_identical_points ... ok [INFO] [stdout] test ins::finder::tests::test_config_default ... ok [INFO] [stdout] test ins::tests::test_extract_neighbor_seqs ... ok [INFO] [stdout] test ins::tests::test_extract_neighbor_seqs_large_flank ... ok [INFO] [stdout] test ins::tests::test_insertion_eid ... ok [INFO] [stdout] test cluster::tests::test_two_clusters ... ok [INFO] [stdout] test tre::tests::test_trefinder_config_default ... ok [INFO] [stdout] test utils::tests::test_merge_spans ... ok [INFO] [stdout] test utils::tests::test_reverse_complement ... ok [INFO] [stdout] test variant::tests::test_variant_creation ... ok [INFO] [stdout] test utils::tests::test_split_tasks ... ok [INFO] [stdout] test variant::tests::test_allele_is_full ... ok [INFO] [stdout] test tre::tests::test_patterns_match ... ok [INFO] [stderr] Doc-tests straglr_rs [INFO] [stdout] test vcf::tests::test_vcf_header ... ok [INFO] [stdout] test ins::tests::test_extract_neighbor_seqs_full ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 16 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] running 0 tests [INFO] [stdout] [INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] running `Command { std: "docker" "inspect" "9f1ee635240d24ee19c84d2dab9733983451835ec52add766bcb0e3a2b2fe25c", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "9f1ee635240d24ee19c84d2dab9733983451835ec52add766bcb0e3a2b2fe25c", kill_on_drop: false }` [INFO] [stdout] 9f1ee635240d24ee19c84d2dab9733983451835ec52add766bcb0e3a2b2fe25c