[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#2886b36df4a646dd8d82fb65bf0c9d8d96c1f71a for pr-145113 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Favalind%2Fossler" "/workspace/builds/worker-3-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-3-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-3-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/avalind/ossler on toolchain 2886b36df4a646dd8d82fb65bf0c9d8d96c1f71a [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+2886b36df4a646dd8d82fb65bf0c9d8d96c1f71a" "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" "+2886b36df4a646dd8d82fb65bf0c9d8d96c1f71a" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Updating crates.io index [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded hdf5-derive v0.8.1 [INFO] [stderr] Downloaded bio-types v0.12.1 [INFO] [stderr] Downloaded hdf5-types v0.8.1 [INFO] [stderr] Downloaded hdf5 v0.8.1 [INFO] [stderr] Downloaded lzma-sys v0.1.17 [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-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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:ae6f63d130afcfff7f91f5ba9fdb2a74d52830289c6a2ea2d23a94dcfb480a0d" "/opt/rustwide/cargo-home/bin/cargo" "+2886b36df4a646dd8d82fb65bf0c9d8d96c1f71a" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 52f01605f469ed94356d3af70adc2904cc9f0e4c893526611aa532e34f1edd4e [INFO] running `Command { std: "docker" "start" "-a" "52f01605f469ed94356d3af70adc2904cc9f0e4c893526611aa532e34f1edd4e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "52f01605f469ed94356d3af70adc2904cc9f0e4c893526611aa532e34f1edd4e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "52f01605f469ed94356d3af70adc2904cc9f0e4c893526611aa532e34f1edd4e", kill_on_drop: false }` [INFO] [stdout] 52f01605f469ed94356d3af70adc2904cc9f0e4c893526611aa532e34f1edd4e [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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:ae6f63d130afcfff7f91f5ba9fdb2a74d52830289c6a2ea2d23a94dcfb480a0d" "/opt/rustwide/cargo-home/bin/cargo" "+2886b36df4a646dd8d82fb65bf0c9d8d96c1f71a" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] eab0ddb4cb2f0bbfc6800acf89435db9e84e602f2b727c7357feb1ccda28a9ce [INFO] running `Command { std: "docker" "start" "-a" "eab0ddb4cb2f0bbfc6800acf89435db9e84e602f2b727c7357feb1ccda28a9ce", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.123 [INFO] [stderr] Compiling pkg-config v0.3.25 [INFO] [stderr] Compiling autocfg v1.1.0 [INFO] [stderr] Compiling memchr v2.4.1 [INFO] [stderr] Compiling proc-macro2 v1.0.37 [INFO] [stderr] Compiling unicode-xid v0.2.2 [INFO] [stderr] Compiling syn v1.0.91 [INFO] [stderr] Compiling regex-syntax v0.6.25 [INFO] [stderr] Compiling cfg-if v1.0.0 [INFO] [stderr] Compiling rustversion v1.0.6 [INFO] [stderr] Compiling serde_derive v1.0.136 [INFO] [stderr] Checking tinyvec_macros v0.1.0 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Checking lazy_static v1.4.0 [INFO] [stderr] Compiling libloading v0.7.3 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Checking tinyvec v1.5.1 [INFO] [stderr] Compiling glob v0.3.0 [INFO] [stderr] Compiling parking_lot_core v0.8.5 [INFO] [stderr] Compiling serde v1.0.136 [INFO] [stderr] Compiling unicode-segmentation v1.9.0 [INFO] [stderr] Checking matches v0.1.9 [INFO] [stderr] Checking instant v0.1.12 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling heck v0.3.3 [INFO] [stderr] Checking percent-encoding v2.1.0 [INFO] [stderr] Checking smallvec v1.8.0 [INFO] [stderr] Compiling aho-corasick v0.7.18 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Checking unicode-bidi v0.3.7 [INFO] [stderr] Compiling jobserver v0.1.24 [INFO] [stderr] Compiling hdf5-types v0.8.1 [INFO] [stderr] Compiling cc v1.0.73 [INFO] [stderr] Compiling quote v1.0.18 [INFO] [stderr] Compiling num-traits v0.2.14 [INFO] [stderr] Compiling lock_api v0.4.7 [INFO] [stderr] Compiling num-integer v0.1.44 [INFO] [stderr] Checking scopeguard v1.1.0 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Checking matrixmultiply v0.3.2 [INFO] [stderr] Checking form_urlencoded v1.0.1 [INFO] [stderr] Compiling anyhow v1.0.56 [INFO] [stderr] Checking regex-automata v0.1.10 [INFO] [stderr] Compiling hdf5 v0.8.1 [INFO] [stderr] Checking ascii v1.0.0 [INFO] [stderr] Checking csv-core v0.1.10 [INFO] [stderr] Checking bitflags v1.3.2 [INFO] [stderr] Checking either v1.6.1 [INFO] [stderr] Checking ryu v1.0.9 [INFO] [stderr] Checking byteorder v1.4.3 [INFO] [stderr] Checking parking_lot v0.11.2 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Compiling paste v1.0.7 [INFO] [stderr] Checking itoa v0.4.8 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Compiling cmake v0.1.48 [INFO] [stderr] Compiling openssl-src v111.18.0+1.1.1n [INFO] [stderr] Checking itertools v0.10.3 [INFO] [stderr] Checking num-complex v0.4.0 [INFO] [stderr] Checking unicode-normalization v0.1.19 [INFO] [stderr] Compiling openssl-sys v0.9.72 [INFO] [stderr] Compiling bzip2-sys v0.1.11+1.0.8 [INFO] [stderr] Compiling curl-sys v0.4.53+curl-7.82.0 [INFO] [stderr] Compiling lzma-sys v0.1.17 [INFO] [stderr] Compiling hts-sys v2.0.2 [INFO] [stderr] Compiling libz-sys v1.1.5 [INFO] [stderr] Checking ndarray v0.15.4 [INFO] [stderr] Checking idna v0.2.3 [INFO] [stderr] Checking url v2.2.2 [INFO] [stderr] Checking regex v1.5.5 [INFO] [stderr] Compiling thiserror-impl v1.0.30 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling hdf5-sys v0.8.1 [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)]` 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)]` 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)]` 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)]` 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)]` 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)]` 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 1m 44s [INFO] running `Command { std: "docker" "inspect" "eab0ddb4cb2f0bbfc6800acf89435db9e84e602f2b727c7357feb1ccda28a9ce", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "eab0ddb4cb2f0bbfc6800acf89435db9e84e602f2b727c7357feb1ccda28a9ce", kill_on_drop: false }` [INFO] [stdout] eab0ddb4cb2f0bbfc6800acf89435db9e84e602f2b727c7357feb1ccda28a9ce