[INFO] cloning repository https://github.com/JamesKane/DecodingUsTools [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/JamesKane/DecodingUsTools" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FJamesKane%2FDecodingUsTools", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FJamesKane%2FDecodingUsTools'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 07b5853bcc15aef1cfcaa4a9403988cc5f4b4e9c [INFO] checking JamesKane/DecodingUsTools against try#1f5783cbeb5da8b38566d718631d016891e9c912 for pr-142704 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FJamesKane%2FDecodingUsTools" "/workspace/builds/worker-7-tc2/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-7-tc2/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/JamesKane/DecodingUsTools on toolchain 1f5783cbeb5da8b38566d718631d016891e9c912 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1f5783cbeb5da8b38566d718631d016891e9c912" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/JamesKane/DecodingUsTools [INFO] finished tweaking git repo https://github.com/JamesKane/DecodingUsTools [INFO] tweaked toml for git repo https://github.com/JamesKane/DecodingUsTools written to /workspace/builds/worker-7-tc2/source/Cargo.toml [INFO] crate git repo https://github.com/JamesKane/DecodingUsTools 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" "+1f5783cbeb5da8b38566d718631d016891e9c912" "fetch" 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"/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+1f5783cbeb5da8b38566d718631d016891e9c912" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 87b35430bd5b58c65fecb63d90b90e460d8ec6de1552c67b052afaa3afc13818 [INFO] running `Command { std: "docker" "start" "-a" "87b35430bd5b58c65fecb63d90b90e460d8ec6de1552c67b052afaa3afc13818", kill_on_drop: false }` [INFO] [stderr] Compiling 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[INFO] [stderr] Checking toml_datetime v0.6.11 [INFO] [stderr] Checking serde_spanned v0.6.9 [INFO] [stderr] Checking csv v1.3.1 [INFO] [stderr] Checking multimap v0.10.0 [INFO] [stderr] Checking serde_urlencoded v0.7.1 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking icu_normalizer v1.5.0 [INFO] [stderr] Checking toml_edit v0.22.27 [INFO] [stderr] Checking idna_adapter v1.2.0 [INFO] [stderr] Checking idna v1.0.3 [INFO] [stderr] Checking url v2.5.4 [INFO] [stderr] Checking toml v0.8.23 [INFO] [stderr] Checking statrs v0.18.0 [INFO] [stderr] Checking bio v2.2.0 [INFO] [stderr] Checking tokio-native-tls v0.3.1 [INFO] [stderr] Checking hyper-tls v0.6.0 [INFO] [stderr] Checking reqwest v0.12.15 [INFO] [stderr] Checking rust-htslib v0.49.0 [INFO] [stderr] Checking decodingus-tools v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `std::io::Write` [INFO] [stdout] --> src/callable_loci/mod.rs:20:5 [INFO] [stdout] | [INFO] [stdout] 20 | use std::io::Write; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io::Write` [INFO] [stdout] --> src/callable_loci/mod.rs:20:5 [INFO] [stdout] | [INFO] [stdout] 20 | use std::io::Write; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `depth` [INFO] [stdout] --> src/haplogroup/mod.rs:153:40 [INFO] [stdout] | [INFO] [stdout] 153 | Some((called_base, depth, freq)) => { [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_depth` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `freq` [INFO] [stdout] --> src/haplogroup/mod.rs:153:47 [INFO] [stdout] | [INFO] [stdout] 153 | Some((called_base, depth, freq)) => { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_freq` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `depth` [INFO] [stdout] --> src/haplogroup/mod.rs:153:40 [INFO] [stdout] | [INFO] [stdout] 153 | Some((called_base, depth, freq)) => { [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_depth` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `freq` [INFO] [stdout] --> src/haplogroup/mod.rs:153:47 [INFO] [stdout] | [INFO] [stdout] 153 | Some((called_base, depth, freq)) => { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_freq` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `other` [INFO] [stdout] --> src/utils/sequence_processor.rs:39:39 [INFO] [stdout] | [INFO] [stdout] 39 | fn merge_processor(&mut self, other: &Self) -> Result<()> { [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_other` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `progress` [INFO] [stdout] --> src/utils/sequence_processor.rs:114:13 [INFO] [stdout] | [INFO] [stdout] 114 | progress: &ProgressBar, [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_progress` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `thread_id` [INFO] [stdout] --> src/utils/sequence_processor.rs:304:17 [INFO] [stdout] | [INFO] [stdout] 304 | for thread_id in 0..num_threads { [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_thread_id` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `e` [INFO] [stdout] --> src/utils/sequence_processor.rs:311:36 [INFO] [stdout] | [INFO] [stdout] 311 | if let Err(e) = worker_processor.process_sequence(&sequence) { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_e` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `other` [INFO] [stdout] --> src/utils/sequence_processor.rs:39:39 [INFO] [stdout] | [INFO] [stdout] 39 | fn merge_processor(&mut self, other: &Self) -> Result<()> { [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_other` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `record_count` [INFO] [stdout] --> src/utils/sequence_processor.rs:327:13 [INFO] [stdout] | [INFO] [stdout] 327 | record_count: u64, [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_record_count` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `progress` [INFO] [stdout] --> src/utils/sequence_processor.rs:114:13 [INFO] [stdout] | [INFO] [stdout] 114 | progress: &ProgressBar, [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_progress` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `progress` [INFO] [stdout] --> src/utils/sequence_processor.rs:372:13 [INFO] [stdout] | [INFO] [stdout] 372 | progress: &ProgressBar, [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_progress` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `thread_id` [INFO] [stdout] --> src/utils/sequence_processor.rs:304:17 [INFO] [stdout] | [INFO] [stdout] 304 | for thread_id in 0..num_threads { [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_thread_id` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `e` [INFO] [stdout] --> src/utils/sequence_processor.rs:311:36 [INFO] [stdout] | [INFO] [stdout] 311 | if let Err(e) = worker_processor.process_sequence(&sequence) { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_e` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `record_count` [INFO] [stdout] --> src/utils/sequence_processor.rs:327:13 [INFO] [stdout] | [INFO] [stdout] 327 | record_count: u64, [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_record_count` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `progress` [INFO] [stdout] --> src/utils/sequence_processor.rs:372:13 [INFO] [stdout] | [INFO] [stdout] 372 | progress: &ProgressBar, [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_progress` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `qc_depth` is assigned to, but never used [INFO] [stdout] --> src/callable_loci/profilers/contig_profiler.rs:53:17 [INFO] [stdout] | [INFO] [stdout] 53 | let mut qc_depth = 0; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_qc_depth` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `qc_depth` is assigned to, but never used [INFO] [stdout] --> src/callable_loci/profilers/contig_profiler.rs:53:17 [INFO] [stdout] | [INFO] [stdout] 53 | let mut qc_depth = 0; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_qc_depth` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `to_chromosome_names` is never used [INFO] [stdout] --> src/commands/region.rs:4:12 [INFO] [stdout] | [INFO] [stdout] 3 | impl Region { [INFO] [stdout] | ----------- method in this implementation [INFO] [stdout] 4 | pub fn to_chromosome_names(&self) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `save` is never used [INFO] [stdout] --> src/config/config.rs:40:12 [INFO] [stdout] | [INFO] [stdout] 23 | impl Config { [INFO] [stdout] | ----------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 40 | pub fn save(&self) -> Result<(), Box> { [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `stop` is never read [INFO] [stdout] --> src/haplogroup/types.rs:28:9 [INFO] [stdout] | [INFO] [stdout] 26 | pub struct ApiCoordinate { [INFO] [stdout] | ------------- field in this struct [INFO] [stdout] 27 | pub start: u32, [INFO] [stdout] 28 | pub stop: u32, [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `parent` is never read [INFO] [stdout] --> src/haplogroup/types.rs:60:16 [INFO] [stdout] | [INFO] [stdout] 58 | pub struct Haplogroup { [INFO] [stdout] | ---------- field in this struct [INFO] [stdout] 59 | pub(crate) name: String, [INFO] [stdout] 60 | pub(crate) parent: Option, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Haplogroup` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `GenomeAccession` is never constructed [INFO] [stdout] --> src/haplogroup/types.rs:143:12 [INFO] [stdout] | [INFO] [stdout] 143 | pub struct GenomeAccession { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `GenomeAccession` has derived impls for the traits `Debug` and `Clone`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `accessions` and `get_accession` are never used [INFO] [stdout] --> src/haplogroup/types.rs:151:12 [INFO] [stdout] | [INFO] [stdout] 150 | impl ReferenceGenome { [INFO] [stdout] | -------------------- methods in this implementation [INFO] [stdout] 151 | pub fn accessions(&self) -> Vec { [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 222 | pub fn get_accession(&self, common_name: &str) -> Option { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `id`, `quality`, and `metadata` are never read [INFO] [stdout] --> src/utils/sequence_processor.rs:8:13 [INFO] [stdout] | [INFO] [stdout] 6 | pub struct Sequence { [INFO] [stdout] | -------- fields in this struct [INFO] [stdout] 7 | pub data: Vec, [INFO] [stdout] 8 | pub id: Option, [INFO] [stdout] | ^^ [INFO] [stdout] 9 | pub quality: Option>, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] 10 | pub metadata: SequenceMetadata, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Sequence` has derived impls for the traits `Debug` and `Clone`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `is_mapped`, `chromosome`, and `position` are never read [INFO] [stdout] --> src/utils/sequence_processor.rs:15:13 [INFO] [stdout] | [INFO] [stdout] 14 | pub struct SequenceMetadata { [INFO] [stdout] | ---------------- fields in this struct [INFO] [stdout] 15 | pub is_mapped: bool, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] 16 | pub chromosome: Option, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] 17 | pub position: Option, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `SequenceMetadata` has derived impls for the traits `Debug` and `Clone`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `skipped` is never read [INFO] [stdout] --> src/utils/sequence_processor.rs:23:13 [INFO] [stdout] | [INFO] [stdout] 21 | pub struct ProcessingStats { [INFO] [stdout] | --------------- field in this struct [INFO] [stdout] 22 | pub processed: u64, [INFO] [stdout] 23 | pub skipped: u64, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `ProcessingStats` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `finalize` is never used [INFO] [stdout] --> src/utils/sequence_processor.rs:33:12 [INFO] [stdout] | [INFO] [stdout] 29 | pub trait SequenceProcessor: Send + Clone + 'static { [INFO] [stdout] | ----------------- method in this trait [INFO] [stdout] ... [INFO] [stdout] 33 | fn finalize(&mut self) -> Result<()> { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `read_sequences` is never used [INFO] [stdout] --> src/utils/sequence_processor.rs:51:12 [INFO] [stdout] | [INFO] [stdout] 44 | pub trait SequenceReader { [INFO] [stdout] | -------------- method in this trait [INFO] [stdout] ... [INFO] [stdout] 51 | fn read_sequences( [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `chunk_size` is never read [INFO] [stdout] --> src/utils/sequence_processor.rs:86:9 [INFO] [stdout] | [INFO] [stdout] 84 | pub struct BamReader { [INFO] [stdout] | --------- field in this struct [INFO] [stdout] 85 | reader: bam::Reader, [INFO] [stdout] 86 | chunk_size: usize, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `supported_builds` is never used [INFO] [stdout] --> src/vendor/mod.rs:15:8 [INFO] [stdout] | [INFO] [stdout] 9 | pub trait TreeProvider { [INFO] [stdout] | ------------ method in this trait [INFO] [stdout] ... [INFO] [stdout] 15 | fn supported_builds(&self) -> Vec; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `region` and `id` are never read [INFO] [stdout] --> src/vendor/ftdna.rs:21:9 [INFO] [stdout] | [INFO] [stdout] 11 | pub struct FtdnaVariant { [INFO] [stdout] | ------------ fields in this struct [INFO] [stdout] ... [INFO] [stdout] 21 | pub region: String, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] 22 | #[serde(default)] [INFO] [stdout] 23 | pub id: Option, [INFO] [stdout] | ^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `root`, `kits_count`, `sub_branches`, and `big_y_count` are never read [INFO] [stdout] --> src/vendor/ftdna.rs:58:5 [INFO] [stdout] | [INFO] [stdout] 50 | struct FtdnaNode { [INFO] [stdout] | --------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 58 | root: String, [INFO] [stdout] | ^^^^ [INFO] [stdout] 59 | #[serde(rename = "kitsCount")] [INFO] [stdout] 60 | kits_count: u32, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] 61 | #[serde(rename = "subBranches")] [INFO] [stdout] 62 | sub_branches: u32, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 63 | #[serde(rename = "bigYCount")] [INFO] [stdout] 64 | big_y_count: u32, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `stop` is never read [INFO] [stdout] --> src/vendor/decoding_us.rs:13:9 [INFO] [stdout] | [INFO] [stdout] 11 | pub struct ApiCoordinate { [INFO] [stdout] | ------------- field in this struct [INFO] [stdout] 12 | pub start: u32, [INFO] [stdout] 13 | pub stop: u32, [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `last_updated` and `is_backbone` are never read [INFO] [stdout] --> src/vendor/decoding_us.rs:33:9 [INFO] [stdout] | [INFO] [stdout] 27 | pub struct ApiNode { [INFO] [stdout] | ------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 33 | pub last_updated: String, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 34 | #[serde(rename = "isBackbone")] [INFO] [stdout] 35 | pub is_backbone: bool, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `deserialize_null_string` is never used [INFO] [stdout] --> src/vendor/decoding_us.rs:38:4 [INFO] [stdout] | [INFO] [stdout] 38 | fn deserialize_null_string<'de, D>(deserializer: D) -> Result [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `counts` is never read [INFO] [stdout] --> src/callable_loci/profilers/callable_profiler.rs:12:5 [INFO] [stdout] | [INFO] [stdout] 11 | pub struct CallableProfiler { [INFO] [stdout] | ---------------- field in this struct [INFO] [stdout] 12 | counts: [u64; 6], [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `finish` is never used [INFO] [stdout] --> src/callable_loci/profilers/contig_profiler.rs:82:12 [INFO] [stdout] | [INFO] [stdout] 19 | impl ContigProfiler { [INFO] [stdout] | ------------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 82 | pub fn finish(&self) { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `to_chromosome_names` is never used [INFO] [stdout] --> src/commands/region.rs:4:12 [INFO] [stdout] | [INFO] [stdout] 3 | impl Region { [INFO] [stdout] | ----------- method in this implementation [INFO] [stdout] 4 | pub fn to_chromosome_names(&self) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `save` is never used [INFO] [stdout] --> src/config/config.rs:40:12 [INFO] [stdout] | [INFO] [stdout] 23 | impl Config { [INFO] [stdout] | ----------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 40 | pub fn save(&self) -> Result<(), Box> { [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `stop` is never read [INFO] [stdout] --> src/haplogroup/types.rs:28:9 [INFO] [stdout] | [INFO] [stdout] 26 | pub struct ApiCoordinate { [INFO] [stdout] | ------------- field in this struct [INFO] [stdout] 27 | pub start: u32, [INFO] [stdout] 28 | pub stop: u32, [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `parent` is never read [INFO] [stdout] --> src/haplogroup/types.rs:60:16 [INFO] [stdout] | [INFO] [stdout] 58 | pub struct Haplogroup { [INFO] [stdout] | ---------- field in this struct [INFO] [stdout] 59 | pub(crate) name: String, [INFO] [stdout] 60 | pub(crate) parent: Option, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Haplogroup` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `GenomeAccession` is never constructed [INFO] [stdout] --> src/haplogroup/types.rs:143:12 [INFO] [stdout] | [INFO] [stdout] 143 | pub struct GenomeAccession { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `GenomeAccession` has derived impls for the traits `Debug` and `Clone`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `accessions` and `get_accession` are never used [INFO] [stdout] --> src/haplogroup/types.rs:151:12 [INFO] [stdout] | [INFO] [stdout] 150 | impl ReferenceGenome { [INFO] [stdout] | -------------------- methods in this implementation [INFO] [stdout] 151 | pub fn accessions(&self) -> Vec { [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 222 | pub fn get_accession(&self, common_name: &str) -> Option { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `id`, `quality`, and `metadata` are never read [INFO] [stdout] --> src/utils/sequence_processor.rs:8:13 [INFO] [stdout] | [INFO] [stdout] 6 | pub struct Sequence { [INFO] [stdout] | -------- fields in this struct [INFO] [stdout] 7 | pub data: Vec, [INFO] [stdout] 8 | pub id: Option, [INFO] [stdout] | ^^ [INFO] [stdout] 9 | pub quality: Option>, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] 10 | pub metadata: SequenceMetadata, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Sequence` has derived impls for the traits `Debug` and `Clone`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `is_mapped`, `chromosome`, and `position` are never read [INFO] [stdout] --> src/utils/sequence_processor.rs:15:13 [INFO] [stdout] | [INFO] [stdout] 14 | pub struct SequenceMetadata { [INFO] [stdout] | ---------------- fields in this struct [INFO] [stdout] 15 | pub is_mapped: bool, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] 16 | pub chromosome: Option, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] 17 | pub position: Option, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `SequenceMetadata` has derived impls for the traits `Debug` and `Clone`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `skipped` is never read [INFO] [stdout] --> src/utils/sequence_processor.rs:23:13 [INFO] [stdout] | [INFO] [stdout] 21 | pub struct ProcessingStats { [INFO] [stdout] | --------------- field in this struct [INFO] [stdout] 22 | pub processed: u64, [INFO] [stdout] 23 | pub skipped: u64, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `ProcessingStats` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `finalize` is never used [INFO] [stdout] --> src/utils/sequence_processor.rs:33:12 [INFO] [stdout] | [INFO] [stdout] 29 | pub trait SequenceProcessor: Send + Clone + 'static { [INFO] [stdout] | ----------------- method in this trait [INFO] [stdout] ... [INFO] [stdout] 33 | fn finalize(&mut self) -> Result<()> { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `read_sequences` is never used [INFO] [stdout] --> src/utils/sequence_processor.rs:51:12 [INFO] [stdout] | [INFO] [stdout] 44 | pub trait SequenceReader { [INFO] [stdout] | -------------- method in this trait [INFO] [stdout] ... [INFO] [stdout] 51 | fn read_sequences( [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `chunk_size` is never read [INFO] [stdout] --> src/utils/sequence_processor.rs:86:9 [INFO] [stdout] | [INFO] [stdout] 84 | pub struct BamReader { [INFO] [stdout] | --------- field in this struct [INFO] [stdout] 85 | reader: bam::Reader, [INFO] [stdout] 86 | chunk_size: usize, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `supported_builds` is never used [INFO] [stdout] --> src/vendor/mod.rs:15:8 [INFO] [stdout] | [INFO] [stdout] 9 | pub trait TreeProvider { [INFO] [stdout] | ------------ method in this trait [INFO] [stdout] ... [INFO] [stdout] 15 | fn supported_builds(&self) -> Vec; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `region` and `id` are never read [INFO] [stdout] --> src/vendor/ftdna.rs:21:9 [INFO] [stdout] | [INFO] [stdout] 11 | pub struct FtdnaVariant { [INFO] [stdout] | ------------ fields in this struct [INFO] [stdout] ... [INFO] [stdout] 21 | pub region: String, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] 22 | #[serde(default)] [INFO] [stdout] 23 | pub id: Option, [INFO] [stdout] | ^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `root`, `kits_count`, `sub_branches`, and `big_y_count` are never read [INFO] [stdout] --> src/vendor/ftdna.rs:58:5 [INFO] [stdout] | [INFO] [stdout] 50 | struct FtdnaNode { [INFO] [stdout] | --------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 58 | root: String, [INFO] [stdout] | ^^^^ [INFO] [stdout] 59 | #[serde(rename = "kitsCount")] [INFO] [stdout] 60 | kits_count: u32, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] 61 | #[serde(rename = "subBranches")] [INFO] [stdout] 62 | sub_branches: u32, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 63 | #[serde(rename = "bigYCount")] [INFO] [stdout] 64 | big_y_count: u32, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `stop` is never read [INFO] [stdout] --> src/vendor/decoding_us.rs:13:9 [INFO] [stdout] | [INFO] [stdout] 11 | pub struct ApiCoordinate { [INFO] [stdout] | ------------- field in this struct [INFO] [stdout] 12 | pub start: u32, [INFO] [stdout] 13 | pub stop: u32, [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `last_updated` and `is_backbone` are never read [INFO] [stdout] --> src/vendor/decoding_us.rs:33:9 [INFO] [stdout] | [INFO] [stdout] 27 | pub struct ApiNode { [INFO] [stdout] | ------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 33 | pub last_updated: String, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 34 | #[serde(rename = "isBackbone")] [INFO] [stdout] 35 | pub is_backbone: bool, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `deserialize_null_string` is never used [INFO] [stdout] --> src/vendor/decoding_us.rs:38:4 [INFO] [stdout] | [INFO] [stdout] 38 | fn deserialize_null_string<'de, D>(deserializer: D) -> Result [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `counts` is never read [INFO] [stdout] --> src/callable_loci/profilers/callable_profiler.rs:12:5 [INFO] [stdout] | [INFO] [stdout] 11 | pub struct CallableProfiler { [INFO] [stdout] | ---------------- field in this struct [INFO] [stdout] 12 | counts: [u64; 6], [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `finish` is never used [INFO] [stdout] --> src/callable_loci/profilers/contig_profiler.rs:82:12 [INFO] [stdout] | [INFO] [stdout] 19 | impl ContigProfiler { [INFO] [stdout] | ------------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 82 | pub fn finish(&self) { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 56s [INFO] running `Command { std: "docker" "inspect" "87b35430bd5b58c65fecb63d90b90e460d8ec6de1552c67b052afaa3afc13818", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "87b35430bd5b58c65fecb63d90b90e460d8ec6de1552c67b052afaa3afc13818", kill_on_drop: false }` [INFO] [stdout] 87b35430bd5b58c65fecb63d90b90e460d8ec6de1552c67b052afaa3afc13818