[INFO] cloning repository https://github.com/avalind/ossler [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/avalind/ossler" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Favalind%2Fossler", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Favalind%2Fossler'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 1800a6afdb9015433a8a92073db81faa9525e667 [INFO] checking avalind/ossler against master#bca37a20bd376ce3fd138e7cdee7fe704e0f8814 for pr-139493-3 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Favalind%2Fossler" "/workspace/builds/worker-0-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc1/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/avalind/ossler [INFO] finished tweaking git repo https://github.com/avalind/ossler [INFO] tweaked toml for git repo https://github.com/avalind/ossler written to /workspace/builds/worker-0-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/avalind/ossler on toolchain bca37a20bd376ce3fd138e7cdee7fe704e0f8814 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+bca37a20bd376ce3fd138e7cdee7fe704e0f8814" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/avalind/ossler 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" "+bca37a20bd376ce3fd138e7cdee7fe704e0f8814" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded ieee754 v0.2.6 [INFO] [stderr] Downloaded linear-map v1.2.0 [INFO] [stderr] Downloaded hdf5-derive v0.8.1 [INFO] [stderr] Downloaded hdf5-types v0.8.1 [INFO] [stderr] Downloaded bio-types v0.12.1 [INFO] [stderr] Downloaded hdf5-sys v0.8.1 [INFO] [stderr] Downloaded strum_macros v0.23.1 [INFO] [stderr] Downloaded anyhow v1.0.56 [INFO] [stderr] Downloaded hdf5 v0.8.1 [INFO] [stderr] Downloaded rust-htslib v0.38.2 [INFO] [stderr] Downloaded libc v0.2.123 [INFO] [stderr] Downloaded lzma-sys v0.1.17 [INFO] [stderr] Downloaded libz-sys v1.1.5 [INFO] [stderr] Downloaded curl-sys v0.4.53+curl-7.82.0 [INFO] [stderr] Downloaded hts-sys v2.0.2 [INFO] [stderr] Downloaded openssl-src v111.18.0+1.1.1n [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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:aa71247004a7fa38d13ec170f48f06cdedf5bc50b2a8645e56ed7e992e6fa513" "/opt/rustwide/cargo-home/bin/cargo" "+bca37a20bd376ce3fd138e7cdee7fe704e0f8814" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] bfc47d269dc1c68faa5c13c5b7103a7905ade8d47caa5320c8e3ab0cd40ac1dc [INFO] running `Command { std: "docker" "start" "-a" "bfc47d269dc1c68faa5c13c5b7103a7905ade8d47caa5320c8e3ab0cd40ac1dc", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "bfc47d269dc1c68faa5c13c5b7103a7905ade8d47caa5320c8e3ab0cd40ac1dc", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "bfc47d269dc1c68faa5c13c5b7103a7905ade8d47caa5320c8e3ab0cd40ac1dc", kill_on_drop: false }` [INFO] [stdout] bfc47d269dc1c68faa5c13c5b7103a7905ade8d47caa5320c8e3ab0cd40ac1dc [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:aa71247004a7fa38d13ec170f48f06cdedf5bc50b2a8645e56ed7e992e6fa513" "/opt/rustwide/cargo-home/bin/cargo" "+bca37a20bd376ce3fd138e7cdee7fe704e0f8814" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 84f06438a5b99a874bf7b79044613e7408d9446ac7d2289b5dc885d8b29c7718 [INFO] running `Command { std: "docker" "start" "-a" "84f06438a5b99a874bf7b79044613e7408d9446ac7d2289b5dc885d8b29c7718", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.123 [INFO] [stderr] Compiling pkg-config v0.3.25 [INFO] [stderr] Compiling proc-macro2 v1.0.37 [INFO] [stderr] Compiling syn v1.0.91 [INFO] [stderr] Compiling num-traits v0.2.14 [INFO] [stderr] Compiling libloading v0.7.3 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling regex v1.5.5 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling serde_derive v1.0.136 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Checking tinyvec v1.5.1 [INFO] [stderr] Compiling jobserver v0.1.24 [INFO] [stderr] Compiling glob v0.3.0 [INFO] [stderr] Compiling parking_lot_core v0.8.5 [INFO] [stderr] Compiling cc v1.0.73 [INFO] [stderr] Compiling unicode-segmentation v1.9.0 [INFO] [stderr] Compiling quote v1.0.18 [INFO] [stderr] Compiling serde v1.0.136 [INFO] [stderr] Checking matches v0.1.9 [INFO] [stderr] Compiling lock_api v0.4.7 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Checking instant v0.1.12 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Compiling hdf5-types v0.8.1 [INFO] [stderr] Checking unicode-bidi v0.3.7 [INFO] [stderr] Checking unicode-normalization v0.1.19 [INFO] [stderr] Compiling heck v0.3.3 [INFO] [stderr] Checking form_urlencoded v1.0.1 [INFO] [stderr] Compiling cmake v0.1.48 [INFO] [stderr] Compiling openssl-src v111.18.0+1.1.1n [INFO] [stderr] Checking matrixmultiply v0.3.2 [INFO] [stderr] Checking num-integer v0.1.44 [INFO] [stderr] Checking num-complex v0.4.0 [INFO] [stderr] Compiling libz-sys v1.1.5 [INFO] [stderr] Compiling openssl-sys v0.9.72 [INFO] [stderr] Compiling curl-sys v0.4.53+curl-7.82.0 [INFO] [stderr] Compiling lzma-sys v0.1.17 [INFO] [stderr] Compiling bzip2-sys v0.1.11+1.0.8 [INFO] [stderr] Compiling hts-sys v2.0.2 [INFO] [stderr] Checking idna v0.2.3 [INFO] [stderr] Compiling hdf5 v0.8.1 [INFO] [stderr] Checking ascii v1.0.0 [INFO] [stderr] Compiling anyhow v1.0.56 [INFO] [stderr] Checking ndarray v0.15.4 [INFO] [stderr] Checking url v2.2.2 [INFO] [stderr] Compiling hdf5-sys v0.8.1 [INFO] [stderr] Checking parking_lot v0.11.2 [INFO] [stderr] Checking csv-core v0.1.10 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Checking itertools v0.10.3 [INFO] [stderr] Compiling thiserror-impl v1.0.30 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling strum_macros v0.23.1 [INFO] [stderr] Compiling hdf5-derive v0.8.1 [INFO] [stderr] Checking thiserror v1.0.30 [INFO] [stderr] Checking bio-types v0.12.1 [INFO] [stderr] Checking bstr v0.2.17 [INFO] [stderr] Checking csv v1.1.6 [INFO] [stderr] Checking rust-htslib v0.38.2 [INFO] [stderr] Checking ossler v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `std::collections::HashMap` [INFO] [stdout] --> src/main.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use std::collections::HashMap; [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 imports: `*` and `TypeDescriptor as TD` [INFO] [stdout] --> src/main.rs:6:19 [INFO] [stdout] | [INFO] [stdout] 6 | use hdf5::types::{TypeDescriptor as TD, *}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Datatype`, `File`, and `H5Type` [INFO] [stdout] --> src/main.rs:7:12 [INFO] [stdout] | [INFO] [stdout] 7 | use hdf5::{File, H5Type, Datatype}; [INFO] [stdout] | ^^^^ ^^^^^^ ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ndarray::Array1` [INFO] [stdout] --> src/main.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use ndarray::Array1; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `csv::ReaderBuilder` [INFO] [stdout] --> src/main.rs:9:5 [INFO] [stdout] | [INFO] [stdout] 9 | use csv::ReaderBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashMap` [INFO] [stdout] --> src/record/snp.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use std::collections::HashMap; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ndarray::Array1` [INFO] [stdout] --> src/record/snp.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use ndarray::Array1; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `File` [INFO] [stdout] --> src/record/oschp.rs:2:12 [INFO] [stdout] | [INFO] [stdout] 2 | use hdf5::{File, H5Type}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `hdf5::types::VarLenAscii` [INFO] [stdout] --> src/record/oschp.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use hdf5::types::VarLenAscii; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `serde::Deserialize` [INFO] [stdout] --> src/record/manifest.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use serde::Deserialize; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashMap` [INFO] [stdout] --> src/main.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use std::collections::HashMap; [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 imports: `*` and `TypeDescriptor as TD` [INFO] [stdout] --> src/main.rs:6:19 [INFO] [stdout] | [INFO] [stdout] 6 | use hdf5::types::{TypeDescriptor as TD, *}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ ^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Datatype`, `File`, and `H5Type` [INFO] [stdout] --> src/main.rs:7:12 [INFO] [stdout] | [INFO] [stdout] 7 | use hdf5::{File, H5Type, Datatype}; [INFO] [stdout] | ^^^^ ^^^^^^ ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ndarray::Array1` [INFO] [stdout] --> src/main.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use ndarray::Array1; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `csv::ReaderBuilder` [INFO] [stdout] --> src/main.rs:9:5 [INFO] [stdout] | [INFO] [stdout] 9 | use csv::ReaderBuilder; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashMap` [INFO] [stdout] --> src/record/snp.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use std::collections::HashMap; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ndarray::Array1` [INFO] [stdout] --> src/record/snp.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use ndarray::Array1; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `File` [INFO] [stdout] --> src/record/oschp.rs:2:12 [INFO] [stdout] | [INFO] [stdout] 2 | use hdf5::{File, H5Type}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `hdf5::types::VarLenAscii` [INFO] [stdout] --> src/record/oschp.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use hdf5::types::VarLenAscii; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `serde::Deserialize` [INFO] [stdout] --> src/record/manifest.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use serde::Deserialize; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `segments` [INFO] [stdout] --> src/main.rs:27:9 [INFO] [stdout] | [INFO] [stdout] 27 | let segments = record::oschp::CopyNumberSegment::from_oschp_file(&handle)?; [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_segments` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `loh` [INFO] [stdout] --> src/main.rs:28:9 [INFO] [stdout] | [INFO] [stdout] 28 | let loh = record::oschp::LOHSegment::from_oschp_file(&handle)?; [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_loh` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `tab` [INFO] [stdout] --> src/main.rs:30:9 [INFO] [stdout] | [INFO] [stdout] 30 | let tab = transform::utils::build_chrom_table(&chroms); [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_tab` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: multiple fields are never read [INFO] [stdout] --> src/record/snp.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 5 | pub struct Marker { [INFO] [stdout] | ------ fields in this struct [INFO] [stdout] 6 | chrom: u8, [INFO] [stdout] | ^^^^^ [INFO] [stdout] 7 | position: u32, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 8 | lrr: f32, [INFO] [stdout] | ^^^ [INFO] [stdout] 9 | weighted_lrr: f32, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 10 | allelic_diff: f32, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 11 | baf: f32, [INFO] [stdout] | ^^^ [INFO] [stdout] 12 | call: u8, [INFO] [stdout] | ^^^^ [INFO] [stdout] 13 | conf: f32, [INFO] [stdout] | ^^^^ [INFO] [stdout] 14 | a_signal: f32, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 15 | b_signal: f32, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 16 | probe_name: String, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] 17 | a_allele: u8, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 18 | b_allele: u8, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Marker` has a derived impl for the trait `Debug`, but this is 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 `new` and `to_vcf_record` are never used [INFO] [stdout] --> src/record/snp.rs:22:12 [INFO] [stdout] | [INFO] [stdout] 21 | impl Marker { [INFO] [stdout] | ----------- associated items in this implementation [INFO] [stdout] 22 | pub fn new() -> Marker { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 65 | pub fn to_vcf_record(&self) { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stdout] --> src/record/oschp.rs:9:10 [INFO] [stdout] | [INFO] [stdout] 9 | #[derive(H5Type, Clone, Debug, Copy)] [INFO] [stdout] | ^----- [INFO] [stdout] | | [INFO] [stdout] | `H5Type` is not local [INFO] [stdout] | move the `impl` block outside of this constant `_IMPL_H5TYPE_FOR_Call` [INFO] [stdout] 10 | #[repr(C)] [INFO] [stdout] 11 | pub struct Call { [INFO] [stdout] | ---- `Call` is not local [INFO] [stdout] | [INFO] [stdout] = note: the derive macro `H5Type` defines the non-local `impl`, and may need to be changed [INFO] [stdout] = note: the derive macro `H5Type` may come from an old version of the `hdf5_derive` crate, try updating your dependency with `cargo update -p hdf5_derive` [INFO] [stdout] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stdout] = note: items in an anonymous const item (`const _: () = { ... }`) are treated as in the same scope as the anonymous const's declaration for the purpose of this lint [INFO] [stdout] = note: `#[warn(non_local_definitions)]` on by default [INFO] [stdout] = note: this warning originates in the derive macro `H5Type` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stdout] --> src/record/oschp.rs:29:10 [INFO] [stdout] | [INFO] [stdout] 29 | #[derive(H5Type, Clone, Debug, Copy)] [INFO] [stdout] | ^----- [INFO] [stdout] | | [INFO] [stdout] | `H5Type` is not local [INFO] [stdout] | move the `impl` block outside of this constant `_IMPL_H5TYPE_FOR_CopyNumber` [INFO] [stdout] 30 | #[repr(C)] [INFO] [stdout] 31 | pub struct CopyNumber { [INFO] [stdout] | ---------- `CopyNumber` is not local [INFO] [stdout] | [INFO] [stdout] = note: the derive macro `H5Type` defines the non-local `impl`, and may need to be changed [INFO] [stdout] = note: the derive macro `H5Type` may come from an old version of the `hdf5_derive` crate, try updating your dependency with `cargo update -p hdf5_derive` [INFO] [stdout] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stdout] = note: items in an anonymous const item (`const _: () = { ... }`) are treated as in the same scope as the anonymous const's declaration for the purpose of this lint [INFO] [stdout] = note: this warning originates in the derive macro `H5Type` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stdout] --> src/record/oschp.rs:47:10 [INFO] [stdout] | [INFO] [stdout] 47 | #[derive(H5Type, Clone, Debug, Copy)] [INFO] [stdout] | ^----- [INFO] [stdout] | | [INFO] [stdout] | `H5Type` is not local [INFO] [stdout] | move the `impl` block outside of this constant `_IMPL_H5TYPE_FOR_AllelicData` [INFO] [stdout] 48 | #[repr(C)] [INFO] [stdout] 49 | pub struct AllelicData { [INFO] [stdout] | ----------- `AllelicData` is not local [INFO] [stdout] | [INFO] [stdout] = note: the derive macro `H5Type` defines the non-local `impl`, and may need to be changed [INFO] [stdout] = note: the derive macro `H5Type` may come from an old version of the `hdf5_derive` crate, try updating your dependency with `cargo update -p hdf5_derive` [INFO] [stdout] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stdout] = note: items in an anonymous const item (`const _: () = { ... }`) are treated as in the same scope as the anonymous const's declaration for the purpose of this lint [INFO] [stdout] = note: this warning originates in the derive macro `H5Type` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stdout] --> src/record/oschp.rs:63:10 [INFO] [stdout] | [INFO] [stdout] 63 | #[derive(H5Type, Clone, Debug)] [INFO] [stdout] | ^----- [INFO] [stdout] | | [INFO] [stdout] | `H5Type` is not local [INFO] [stdout] | move the `impl` block outside of this constant `_IMPL_H5TYPE_FOR_CopyNumberSegment` [INFO] [stdout] 64 | #[repr(C)] [INFO] [stdout] 65 | pub struct CopyNumberSegment { [INFO] [stdout] | ----------------- `CopyNumberSegment` is not local [INFO] [stdout] | [INFO] [stdout] = note: the derive macro `H5Type` defines the non-local `impl`, and may need to be changed [INFO] [stdout] = note: the derive macro `H5Type` may come from an old version of the `hdf5_derive` crate, try updating your dependency with `cargo update -p hdf5_derive` [INFO] [stdout] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stdout] = note: items in an anonymous const item (`const _: () = { ... }`) are treated as in the same scope as the anonymous const's declaration for the purpose of this lint [INFO] [stdout] = note: this warning originates in the derive macro `H5Type` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stdout] --> src/record/oschp.rs:84:10 [INFO] [stdout] | [INFO] [stdout] 84 | #[derive(H5Type, Clone, Debug)] [INFO] [stdout] | ^----- [INFO] [stdout] | | [INFO] [stdout] | `H5Type` is not local [INFO] [stdout] | move the `impl` block outside of this constant `_IMPL_H5TYPE_FOR_LOHSegment` [INFO] [stdout] 85 | #[repr(C)] [INFO] [stdout] 86 | pub struct LOHSegment { [INFO] [stdout] | ---------- `LOHSegment` is not local [INFO] [stdout] | [INFO] [stdout] = note: the derive macro `H5Type` defines the non-local `impl`, and may need to be changed [INFO] [stdout] = note: the derive macro `H5Type` may come from an old version of the `hdf5_derive` crate, try updating your dependency with `cargo update -p hdf5_derive` [INFO] [stdout] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stdout] = note: items in an anonymous const item (`const _: () = { ... }`) are treated as in the same scope as the anonymous const's declaration for the purpose of this lint [INFO] [stdout] = note: this warning originates in the derive macro `H5Type` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stdout] --> src/record/oschp.rs:104:10 [INFO] [stdout] | [INFO] [stdout] 104 | #[derive(H5Type, Clone, Debug)] [INFO] [stdout] | ^----- [INFO] [stdout] | | [INFO] [stdout] | `H5Type` is not local [INFO] [stdout] | move the `impl` block outside of this constant `_IMPL_H5TYPE_FOR_ChromosomeSummary` [INFO] [stdout] 105 | #[repr(C)] [INFO] [stdout] 106 | pub struct ChromosomeSummary { [INFO] [stdout] | ----------------- `ChromosomeSummary` is not local [INFO] [stdout] | [INFO] [stdout] = note: the derive macro `H5Type` defines the non-local `impl`, and may need to be changed [INFO] [stdout] = note: the derive macro `H5Type` may come from an old version of the `hdf5_derive` crate, try updating your dependency with `cargo update -p hdf5_derive` [INFO] [stdout] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stdout] = note: items in an anonymous const item (`const _: () = { ... }`) are treated as in the same scope as the anonymous const's declaration for the purpose of this lint [INFO] [stdout] = note: this warning originates in the derive macro `H5Type` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `segments` [INFO] [stdout] --> src/main.rs:27:9 [INFO] [stdout] | [INFO] [stdout] 27 | let segments = record::oschp::CopyNumberSegment::from_oschp_file(&handle)?; [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_segments` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `loh` [INFO] [stdout] --> src/main.rs:28:9 [INFO] [stdout] | [INFO] [stdout] 28 | let loh = record::oschp::LOHSegment::from_oschp_file(&handle)?; [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_loh` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `tab` [INFO] [stdout] --> src/main.rs:30:9 [INFO] [stdout] | [INFO] [stdout] 30 | let tab = transform::utils::build_chrom_table(&chroms); [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_tab` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: multiple fields are never read [INFO] [stdout] --> src/record/snp.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 5 | pub struct Marker { [INFO] [stdout] | ------ fields in this struct [INFO] [stdout] 6 | chrom: u8, [INFO] [stdout] | ^^^^^ [INFO] [stdout] 7 | position: u32, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 8 | lrr: f32, [INFO] [stdout] | ^^^ [INFO] [stdout] 9 | weighted_lrr: f32, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 10 | allelic_diff: f32, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 11 | baf: f32, [INFO] [stdout] | ^^^ [INFO] [stdout] 12 | call: u8, [INFO] [stdout] | ^^^^ [INFO] [stdout] 13 | conf: f32, [INFO] [stdout] | ^^^^ [INFO] [stdout] 14 | a_signal: f32, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 15 | b_signal: f32, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 16 | probe_name: String, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] 17 | a_allele: u8, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 18 | b_allele: u8, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Marker` has a derived impl for the trait `Debug`, but this is 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 `new` and `to_vcf_record` are never used [INFO] [stdout] --> src/record/snp.rs:22:12 [INFO] [stdout] | [INFO] [stdout] 21 | impl Marker { [INFO] [stdout] | ----------- associated items in this implementation [INFO] [stdout] 22 | pub fn new() -> Marker { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 65 | pub fn to_vcf_record(&self) { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stdout] --> src/record/oschp.rs:9:10 [INFO] [stdout] | [INFO] [stdout] 9 | #[derive(H5Type, Clone, Debug, Copy)] [INFO] [stdout] | ^----- [INFO] [stdout] | | [INFO] [stdout] | `H5Type` is not local [INFO] [stdout] | move the `impl` block outside of this constant `_IMPL_H5TYPE_FOR_Call` [INFO] [stdout] 10 | #[repr(C)] [INFO] [stdout] 11 | pub struct Call { [INFO] [stdout] | ---- `Call` is not local [INFO] [stdout] | [INFO] [stdout] = note: the derive macro `H5Type` defines the non-local `impl`, and may need to be changed [INFO] [stdout] = note: the derive macro `H5Type` may come from an old version of the `hdf5_derive` crate, try updating your dependency with `cargo update -p hdf5_derive` [INFO] [stdout] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stdout] = note: items in an anonymous const item (`const _: () = { ... }`) are treated as in the same scope as the anonymous const's declaration for the purpose of this lint [INFO] [stdout] = note: `#[warn(non_local_definitions)]` on by default [INFO] [stdout] = note: this warning originates in the derive macro `H5Type` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stdout] --> src/record/oschp.rs:29:10 [INFO] [stdout] | [INFO] [stdout] 29 | #[derive(H5Type, Clone, Debug, Copy)] [INFO] [stdout] | ^----- [INFO] [stdout] | | [INFO] [stdout] | `H5Type` is not local [INFO] [stdout] | move the `impl` block outside of this constant `_IMPL_H5TYPE_FOR_CopyNumber` [INFO] [stdout] 30 | #[repr(C)] [INFO] [stdout] 31 | pub struct CopyNumber { [INFO] [stdout] | ---------- `CopyNumber` is not local [INFO] [stdout] | [INFO] [stdout] = note: the derive macro `H5Type` defines the non-local `impl`, and may need to be changed [INFO] [stdout] = note: the derive macro `H5Type` may come from an old version of the `hdf5_derive` crate, try updating your dependency with `cargo update -p hdf5_derive` [INFO] [stdout] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stdout] = note: items in an anonymous const item (`const _: () = { ... }`) are treated as in the same scope as the anonymous const's declaration for the purpose of this lint [INFO] [stdout] = note: this warning originates in the derive macro `H5Type` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stdout] --> src/record/oschp.rs:47:10 [INFO] [stdout] | [INFO] [stdout] 47 | #[derive(H5Type, Clone, Debug, Copy)] [INFO] [stdout] | ^----- [INFO] [stdout] | | [INFO] [stdout] | `H5Type` is not local [INFO] [stdout] | move the `impl` block outside of this constant `_IMPL_H5TYPE_FOR_AllelicData` [INFO] [stdout] 48 | #[repr(C)] [INFO] [stdout] 49 | pub struct AllelicData { [INFO] [stdout] | ----------- `AllelicData` is not local [INFO] [stdout] | [INFO] [stdout] = note: the derive macro `H5Type` defines the non-local `impl`, and may need to be changed [INFO] [stdout] = note: the derive macro `H5Type` may come from an old version of the `hdf5_derive` crate, try updating your dependency with `cargo update -p hdf5_derive` [INFO] [stdout] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stdout] = note: items in an anonymous const item (`const _: () = { ... }`) are treated as in the same scope as the anonymous const's declaration for the purpose of this lint [INFO] [stdout] = note: this warning originates in the derive macro `H5Type` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stdout] --> src/record/oschp.rs:63:10 [INFO] [stdout] | [INFO] [stdout] 63 | #[derive(H5Type, Clone, Debug)] [INFO] [stdout] | ^----- [INFO] [stdout] | | [INFO] [stdout] | `H5Type` is not local [INFO] [stdout] | move the `impl` block outside of this constant `_IMPL_H5TYPE_FOR_CopyNumberSegment` [INFO] [stdout] 64 | #[repr(C)] [INFO] [stdout] 65 | pub struct CopyNumberSegment { [INFO] [stdout] | ----------------- `CopyNumberSegment` is not local [INFO] [stdout] | [INFO] [stdout] = note: the derive macro `H5Type` defines the non-local `impl`, and may need to be changed [INFO] [stdout] = note: the derive macro `H5Type` may come from an old version of the `hdf5_derive` crate, try updating your dependency with `cargo update -p hdf5_derive` [INFO] [stdout] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stdout] = note: items in an anonymous const item (`const _: () = { ... }`) are treated as in the same scope as the anonymous const's declaration for the purpose of this lint [INFO] [stdout] = note: this warning originates in the derive macro `H5Type` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stdout] --> src/record/oschp.rs:84:10 [INFO] [stdout] | [INFO] [stdout] 84 | #[derive(H5Type, Clone, Debug)] [INFO] [stdout] | ^----- [INFO] [stdout] | | [INFO] [stdout] | `H5Type` is not local [INFO] [stdout] | move the `impl` block outside of this constant `_IMPL_H5TYPE_FOR_LOHSegment` [INFO] [stdout] 85 | #[repr(C)] [INFO] [stdout] 86 | pub struct LOHSegment { [INFO] [stdout] | ---------- `LOHSegment` is not local [INFO] [stdout] | [INFO] [stdout] = note: the derive macro `H5Type` defines the non-local `impl`, and may need to be changed [INFO] [stdout] = note: the derive macro `H5Type` may come from an old version of the `hdf5_derive` crate, try updating your dependency with `cargo update -p hdf5_derive` [INFO] [stdout] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stdout] = note: items in an anonymous const item (`const _: () = { ... }`) are treated as in the same scope as the anonymous const's declaration for the purpose of this lint [INFO] [stdout] = note: this warning originates in the derive macro `H5Type` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: non-local `impl` definition, `impl` blocks should be written at the same level as their item [INFO] [stdout] --> src/record/oschp.rs:104:10 [INFO] [stdout] | [INFO] [stdout] 104 | #[derive(H5Type, Clone, Debug)] [INFO] [stdout] | ^----- [INFO] [stdout] | | [INFO] [stdout] | `H5Type` is not local [INFO] [stdout] | move the `impl` block outside of this constant `_IMPL_H5TYPE_FOR_ChromosomeSummary` [INFO] [stdout] 105 | #[repr(C)] [INFO] [stdout] 106 | pub struct ChromosomeSummary { [INFO] [stdout] | ----------------- `ChromosomeSummary` is not local [INFO] [stdout] | [INFO] [stdout] = note: the derive macro `H5Type` defines the non-local `impl`, and may need to be changed [INFO] [stdout] = note: the derive macro `H5Type` may come from an old version of the `hdf5_derive` crate, try updating your dependency with `cargo update -p hdf5_derive` [INFO] [stdout] = note: an `impl` is never scoped, even when it is nested inside an item, as it may impact type checking outside of that item, which can be the case if neither the trait or the self type are at the same nesting level as the `impl` [INFO] [stdout] = note: items in an anonymous const item (`const _: () = { ... }`) are treated as in the same scope as the anonymous const's declaration for the purpose of this lint [INFO] [stdout] = note: this warning originates in the derive macro `H5Type` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 3m 14s [INFO] running `Command { std: "docker" "inspect" "84f06438a5b99a874bf7b79044613e7408d9446ac7d2289b5dc885d8b29c7718", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "84f06438a5b99a874bf7b79044613e7408d9446ac7d2289b5dc885d8b29c7718", kill_on_drop: false }` [INFO] [stdout] 84f06438a5b99a874bf7b79044613e7408d9446ac7d2289b5dc885d8b29c7718