[INFO] cloning repository https://github.com/bluenote-1577/rs-liftover [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/bluenote-1577/rs-liftover" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Frs-liftover", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Frs-liftover'... 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cb6a9de2e356918992b34e859937cbdfdf49e03f72608c0b3006e461d867d834 [INFO] running `Command { std: "docker" "start" "-a" "cb6a9de2e356918992b34e859937cbdfdf49e03f72608c0b3006e461d867d834", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "cb6a9de2e356918992b34e859937cbdfdf49e03f72608c0b3006e461d867d834", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "cb6a9de2e356918992b34e859937cbdfdf49e03f72608c0b3006e461d867d834", kill_on_drop: false }` [INFO] [stdout] cb6a9de2e356918992b34e859937cbdfdf49e03f72608c0b3006e461d867d834 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+ed606620234c6b50f2414162c4bbabd5f4a925f3" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] b73ec97bdee632cd38fad454d4a17af16ecb1f039b89f1b0a40c48f3e28db34b [INFO] running `Command { std: "docker" "start" "-a" "b73ec97bdee632cd38fad454d4a17af16ecb1f039b89f1b0a40c48f3e28db34b", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.125 [INFO] [stderr] Compiling proc-macro2 v1.0.38 [INFO] [stderr] 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v0.10.0 [INFO] [stderr] Compiling libz-sys v1.1.6 [INFO] [stderr] Compiling openssl-sys v0.9.73 [INFO] [stderr] Compiling bzip2-sys v0.1.11+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.17 [INFO] [stderr] Compiling curl-sys v0.4.55+curl-7.83.1 [INFO] [stderr] Checking rand_distr v0.4.3 [INFO] [stderr] Compiling hts-sys v2.0.2 [INFO] [stderr] Checking url v2.2.2 [INFO] [stderr] Checking clap v3.1.18 [INFO] [stderr] Checking regex v1.5.5 [INFO] [stderr] Compiling thiserror-impl v1.0.31 [INFO] [stderr] Compiling nalgebra-macros v0.1.0 [INFO] [stderr] Compiling strum_macros v0.23.1 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling enum-map-derive v0.6.0 [INFO] [stderr] Compiling getset v0.1.2 [INFO] [stderr] Checking enum-map v1.1.1 [INFO] [stderr] Checking thiserror v1.0.31 [INFO] [stderr] Checking bio-types v0.12.1 [INFO] [stderr] Checking nalgebra v0.27.1 [INFO] [stderr] Checking bstr v0.2.17 [INFO] [stderr] Checking multimap v0.8.3 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking csv v1.1.6 [INFO] [stderr] Checking statrs v0.15.0 [INFO] [stderr] Checking bio v0.41.0 [INFO] [stderr] Checking rust-htslib v0.39.5 [INFO] [stderr] Checking rs-liftover v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `Header` [INFO] [stdout] --> src/parse_files.rs:6:32 [INFO] [stdout] | [INFO] [stdout] 6 | use rust_htslib::bam::header::{Header, HeaderRecord}; [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: `Deserialize` and `Serialize` [INFO] [stdout] --> src/parse_files.rs:9:13 [INFO] [stdout] | [INFO] [stdout] 9 | use serde::{Deserialize, Serialize}; [INFO] [stdout] | ^^^^^^^^^^^ ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs` [INFO] [stdout] --> src/parse_files.rs:11:5 [INFO] [stdout] | [INFO] [stdout] 11 | use std::fs; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io::prelude::*` [INFO] [stdout] --> src/parse_files.rs:14:5 [INFO] [stdout] | [INFO] [stdout] 14 | use std::io::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::sync::Mutex` [INFO] [stdout] --> src/parse_files.rs:17:5 [INFO] [stdout] | [INFO] [stdout] 17 | use std::sync::Mutex; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `App` and `SubCommand` [INFO] [stdout] --> src/main.rs:3:12 [INFO] [stdout] | [INFO] [stdout] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand}; [INFO] [stdout] | ^^^ ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Header` [INFO] [stdout] --> src/parse_files.rs:6:32 [INFO] [stdout] | [INFO] [stdout] 6 | use rust_htslib::bam::header::{Header, HeaderRecord}; [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: `Deserialize` and `Serialize` [INFO] [stdout] --> src/parse_files.rs:9:13 [INFO] [stdout] | [INFO] [stdout] 9 | use serde::{Deserialize, Serialize}; [INFO] [stdout] | ^^^^^^^^^^^ ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs` [INFO] [stdout] --> src/parse_files.rs:11:5 [INFO] [stdout] | [INFO] [stdout] 11 | use std::fs; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io::prelude::*` [INFO] [stdout] --> src/parse_files.rs:14:5 [INFO] [stdout] | [INFO] [stdout] 14 | use std::io::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::sync::Mutex` [INFO] [stdout] --> src/parse_files.rs:17:5 [INFO] [stdout] | [INFO] [stdout] 17 | use std::sync::Mutex; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `App` and `SubCommand` [INFO] [stdout] --> src/main.rs:3:12 [INFO] [stdout] | [INFO] [stdout] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand}; [INFO] [stdout] | ^^^ ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated struct `clap::App`: Replaced with `Command` [INFO] [stdout] --> src/main.rs:3:12 [INFO] [stdout] | [INFO] [stdout] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand}; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(deprecated)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated struct `clap::SubCommand`: Replaced with `Command::new` unless you intended the `Subcommand` trait [INFO] [stdout] --> src/main.rs:3:44 [INFO] [stdout] | [INFO] [stdout] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand}; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated unit variant `clap::AppSettings::ArgRequiredElseHelp`: Replaced with `Command::arg_required_else_help` and `Command::is_arg_required_else_help_set` [INFO] [stdout] --> src/main.rs:7:31 [INFO] [stdout] | [INFO] [stdout] 7 | .setting(AppSettings::ArgRequiredElseHelp) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated struct `clap::App`: Replaced with `Command` [INFO] [stdout] --> src/main.rs:3:12 [INFO] [stdout] | [INFO] [stdout] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand}; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(deprecated)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated struct `clap::SubCommand`: Replaced with `Command::new` unless you intended the `Subcommand` trait [INFO] [stdout] --> src/main.rs:3:44 [INFO] [stdout] | [INFO] [stdout] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand}; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated unit variant `clap::AppSettings::ArgRequiredElseHelp`: Replaced with `Command::arg_required_else_help` and `Command::is_arg_required_else_help_set` [INFO] [stdout] --> src/main.rs:7:31 [INFO] [stdout] | [INFO] [stdout] 7 | .setting(AppSettings::ArgRequiredElseHelp) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `header` found for struct `rust_htslib::bam::Reader` in the current scope [INFO] [stdout] --> src/parse_files.rs:184:53 [INFO] [stdout] | [INFO] [stdout] 184 | let mut header = bam::Header::from_template(bam.header()); [INFO] [stdout] | ^^^^^^ private field, not a method [INFO] [stdout] | [INFO] [stdout] ::: /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.39.5/src/bam/mod.rs:168:8 [INFO] [stdout] | [INFO] [stdout] 168 | fn header(&self) -> &HeaderView; [INFO] [stdout] | ------ the method is available for `rust_htslib::bam::Reader` here [INFO] [stdout] | [INFO] [stdout] = help: items from traits can only be used if the trait is in scope [INFO] [stdout] help: there is a method `read` with a similar name, but with different arguments [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.39.5/src/bam/mod.rs:116:5 [INFO] [stdout] | [INFO] [stdout] 116 | fn read(&mut self, record: &mut record::Record) -> Option>; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] help: trait `Read` which provides `header` is implemented but not in scope; perhaps you want to import it [INFO] [stdout] | [INFO] [stdout] 1 + use rust_htslib::bam::Read; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `header` found for struct `rust_htslib::bam::Reader` in the current scope [INFO] [stdout] --> src/parse_files.rs:184:53 [INFO] [stdout] | [INFO] [stdout] 184 | let mut header = bam::Header::from_template(bam.header()); [INFO] [stdout] | ^^^^^^ private field, not a method [INFO] [stdout] | [INFO] [stdout] ::: /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.39.5/src/bam/mod.rs:168:8 [INFO] [stdout] | [INFO] [stdout] 168 | fn header(&self) -> &HeaderView; [INFO] [stdout] | ------ the method is available for `rust_htslib::bam::Reader` here [INFO] [stdout] | [INFO] [stdout] = help: items from traits can only be used if the trait is in scope [INFO] [stdout] help: there is a method `read` with a similar name, but with different arguments [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.39.5/src/bam/mod.rs:116:5 [INFO] [stdout] | [INFO] [stdout] 116 | fn read(&mut self, record: &mut record::Record) -> Option>; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] help: trait `Read` which provides `header` is implemented but not in scope; perhaps you want to import it [INFO] [stdout] | [INFO] [stdout] 1 + use rust_htslib::bam::Read; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `records` found for struct `rust_htslib::bam::Reader` in the current scope [INFO] [stdout] --> src/parse_files.rs:198:20 [INFO] [stdout] | [INFO] [stdout] 198 | for rec in bam.records() { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] ::: /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.39.5/src/bam/mod.rs:126:8 [INFO] [stdout] | [INFO] [stdout] 126 | fn records(&mut self) -> Records<'_, Self>; [INFO] [stdout] | ------- the method is available for `rust_htslib::bam::Reader` here [INFO] [stdout] | [INFO] [stdout] = help: items from traits can only be used if the trait is in scope [INFO] [stdout] help: trait `Read` which provides `records` is implemented but not in scope; perhaps you want to import it [INFO] [stdout] | [INFO] [stdout] 1 + use rust_htslib::bam::Read; [INFO] [stdout] | [INFO] [stdout] help: there is a method `rc_records` with a similar name [INFO] [stdout] | [INFO] [stdout] 198 | for rec in bam.rc_records() { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0282]: type annotations needed [INFO] [stdout] --> src/parse_files.rs:199:22 [INFO] [stdout] | [INFO] [stdout] 199 | let record = rec.unwrap(); [INFO] [stdout] | ^^^ cannot infer type [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `records` found for struct `rust_htslib::bam::Reader` in the current scope [INFO] [stdout] --> src/parse_files.rs:198:20 [INFO] [stdout] | [INFO] [stdout] 198 | for rec in bam.records() { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] ::: /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.39.5/src/bam/mod.rs:126:8 [INFO] [stdout] | [INFO] [stdout] 126 | fn records(&mut self) -> Records<'_, Self>; [INFO] [stdout] | ------- the method is available for `rust_htslib::bam::Reader` here [INFO] [stdout] | [INFO] [stdout] = help: items from traits can only be used if the trait is in scope [INFO] [stdout] help: trait `Read` which provides `records` is implemented but not in scope; perhaps you want to import it [INFO] [stdout] | [INFO] [stdout] 1 + use rust_htslib::bam::Read; [INFO] [stdout] | [INFO] [stdout] help: there is a method `rc_records` with a similar name [INFO] [stdout] | [INFO] [stdout] 198 | for rec in bam.rc_records() { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0282]: type annotations needed [INFO] [stdout] --> src/parse_files.rs:199:22 [INFO] [stdout] | [INFO] [stdout] 199 | let record = rec.unwrap(); [INFO] [stdout] | ^^^ cannot infer type [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rayon::prelude` [INFO] [stdout] --> src/parse_files.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use rayon::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rayon::prelude` [INFO] [stdout] --> src/parse_files.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use rayon::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0282, E0599. [INFO] [stdout] [INFO] [stdout] For more information about an error, try `rustc --explain E0282`. [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0282, E0599. [INFO] [stdout] [INFO] [stdout] For more information about an error, try `rustc --explain E0282`. [INFO] [stdout] [INFO] [stderr] error: could not compile `rs-liftover` (bin "rs-liftover") due to 3 previous errors; 10 warnings emitted [INFO] [stderr] warning: build failed, waiting for other jobs to finish... [INFO] [stderr] error: could not compile `rs-liftover` (bin "rs-liftover" test) due to 3 previous errors; 10 warnings emitted [INFO] running `Command { std: "docker" "inspect" "b73ec97bdee632cd38fad454d4a17af16ecb1f039b89f1b0a40c48f3e28db34b", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "b73ec97bdee632cd38fad454d4a17af16ecb1f039b89f1b0a40c48f3e28db34b", kill_on_drop: false }` [INFO] [stdout] b73ec97bdee632cd38fad454d4a17af16ecb1f039b89f1b0a40c48f3e28db34b