[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'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] f54a6a838f3d2656e270465c5d5d14a3885d640c [INFO] building bluenote-1577/rs-liftover against master#44f415c1d617ebc7b931a243b7b321ef8a6ca47c for pr-142134-abi-ast-error [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Frs-liftover" "/workspace/builds/worker-5-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-5-tc1/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/bluenote-1577/rs-liftover on toolchain 44f415c1d617ebc7b931a243b7b321ef8a6ca47c [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+44f415c1d617ebc7b931a243b7b321ef8a6ca47c" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/bluenote-1577/rs-liftover [INFO] finished tweaking git repo https://github.com/bluenote-1577/rs-liftover [INFO] tweaked toml for git repo https://github.com/bluenote-1577/rs-liftover written to /workspace/builds/worker-5-tc1/source/Cargo.toml [INFO] crate git repo https://github.com/bluenote-1577/rs-liftover 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" "+44f415c1d617ebc7b931a243b7b321ef8a6ca47c" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded bio-types v0.12.1 [INFO] [stderr] Downloaded rust-htslib v0.39.5 [INFO] [stderr] Downloaded bio v0.41.0 [INFO] [stderr] Downloaded lzma-sys v0.1.17 [INFO] [stderr] Downloaded curl-sys v0.4.55+curl-7.83.1 [INFO] [stderr] Downloaded hts-sys v2.0.2 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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:eea15d5475069c3ef791f10c2c6b5af2ee421ef2da1e680ecce1cba46243983b" "/opt/rustwide/cargo-home/bin/cargo" "+44f415c1d617ebc7b931a243b7b321ef8a6ca47c" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] cb72e2c98392ff9e1a1b0387f0b72463b3d336c1b4e121f516d512627df07fa9 [INFO] running `Command { std: "docker" "start" "-a" "cb72e2c98392ff9e1a1b0387f0b72463b3d336c1b4e121f516d512627df07fa9", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "cb72e2c98392ff9e1a1b0387f0b72463b3d336c1b4e121f516d512627df07fa9", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "cb72e2c98392ff9e1a1b0387f0b72463b3d336c1b4e121f516d512627df07fa9", kill_on_drop: false }` [INFO] [stdout] cb72e2c98392ff9e1a1b0387f0b72463b3d336c1b4e121f516d512627df07fa9 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:eea15d5475069c3ef791f10c2c6b5af2ee421ef2da1e680ecce1cba46243983b" "/opt/rustwide/cargo-home/bin/cargo" "+44f415c1d617ebc7b931a243b7b321ef8a6ca47c" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] cfd8d592cb2e74fa9103588eec453b8c72743fd90a46539223e482703ba69995 [INFO] running `Command { std: "docker" "start" "-a" "cfd8d592cb2e74fa9103588eec453b8c72743fd90a46539223e482703ba69995", kill_on_drop: false }` [INFO] [stderr] Compiling autocfg v1.1.0 [INFO] [stderr] Compiling libc v0.2.125 [INFO] [stderr] Compiling proc-macro2 v1.0.38 [INFO] [stderr] Compiling unicode-xid v0.2.3 [INFO] [stderr] Compiling syn v1.0.94 [INFO] [stderr] Compiling pkg-config v0.3.25 [INFO] [stderr] Compiling libm v0.2.2 [INFO] [stderr] Compiling cfg-if v1.0.0 [INFO] [stderr] Compiling lazy_static v1.4.0 [INFO] [stderr] Compiling serde_derive v1.0.137 [INFO] [stderr] Compiling memchr v2.5.0 [INFO] [stderr] Compiling serde v1.0.137 [INFO] [stderr] Compiling version_check v0.9.4 [INFO] [stderr] Compiling crossbeam-utils v0.8.8 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling ppv-lite86 v0.2.16 [INFO] [stderr] Compiling rustversion v1.0.6 [INFO] [stderr] Compiling rawpointer v0.2.1 [INFO] [stderr] Compiling typenum v1.15.0 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] 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v0.5.2 [INFO] [stderr] Compiling clap_lex v0.2.0 [INFO] [stderr] Compiling regex v1.5.5 [INFO] [stderr] Compiling url v2.2.2 [INFO] [stderr] Compiling ndarray v0.15.4 [INFO] [stderr] Compiling ordered-float v1.1.1 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling fxhash v0.2.1 [INFO] [stderr] Compiling itertools v0.10.3 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling strsim v0.10.0 [INFO] [stderr] Compiling itoa v1.0.1 [INFO] [stderr] Compiling bitflags v1.3.2 [INFO] [stderr] Compiling bytecount v0.6.2 [INFO] [stderr] Compiling textwrap v0.15.0 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling termcolor v1.1.3 [INFO] [stderr] Compiling strum v0.23.0 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling triple_accel v0.4.0 [INFO] [stderr] Compiling clap v3.1.18 [INFO] [stderr] Compiling thiserror-impl v1.0.31 [INFO] [stderr] Compiling strum_macros v0.23.1 [INFO] [stderr] Compiling nalgebra-macros v0.1.0 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling nalgebra v0.27.1 [INFO] [stderr] Compiling enum-map-derive v0.6.0 [INFO] [stderr] Compiling thiserror v1.0.31 [INFO] [stderr] Compiling getset v0.1.2 [INFO] [stderr] Compiling enum-map v1.1.1 [INFO] [stderr] Compiling bio-types v0.12.1 [INFO] [stderr] Compiling bstr v0.2.17 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling multimap v0.8.3 [INFO] [stderr] Compiling csv v1.1.6 [INFO] [stderr] Compiling statrs v0.15.0 [INFO] [stderr] Compiling bio v0.41.0 [INFO] [stderr] Compiling rust-htslib v0.39.5 [INFO] [stderr] Compiling 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)]` 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: 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 variable: `aligned_pairs` [INFO] [stdout] --> src/parse_files.rs:214:17 [INFO] [stdout] | [INFO] [stdout] 214 | let aligned_pairs = record.aligned_pairs(); [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_aligned_pairs` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `curr_read_pos` [INFO] [stdout] --> src/parse_files.rs:224:17 [INFO] [stdout] | [INFO] [stdout] 224 | let curr_read_pos = cigar.leading_softclips(); [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_curr_read_pos` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `gap_len` [INFO] [stdout] --> src/parse_files.rs:229:21 [INFO] [stdout] | [INFO] [stdout] 229 | let mut gap_len = 0; [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_gap_len` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `new_start_pos` [INFO] [stdout] --> src/parse_files.rs:232:21 [INFO] [stdout] | [INFO] [stdout] 232 | let mut new_start_pos = 0; [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_new_start_pos` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:263:49 [INFO] [stdout] | [INFO] [stdout] 263 | if matches!(c, hts_Cigar::Match(u32)) [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:264:51 [INFO] [stdout] | [INFO] [stdout] 264 | || matches!(c, hts_Cigar::Ins(u32)) [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:265:51 [INFO] [stdout] | [INFO] [stdout] 265 | || matches!(c, hts_Cigar::Del(u32)) [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:270:59 [INFO] [stdout] | [INFO] [stdout] 270 | ... if matches!(c, hts_Cigar::Ins(u32)) [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:271:65 [INFO] [stdout] | [INFO] [stdout] 271 | ... || matches!(c, hts_Cigar::Match(u32)) [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:277:55 [INFO] [stdout] | [INFO] [stdout] 277 | if matches!(c, hts_Cigar::Ins(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:283:65 [INFO] [stdout] | [INFO] [stdout] 283 | ... if matches!(c, hts_Cigar::Match(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:301:65 [INFO] [stdout] | [INFO] [stdout] 301 | ... if matches!(c, hts_Cigar::Match(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:315:69 [INFO] [stdout] | [INFO] [stdout] 315 | ... && matches!(c, hts_Cigar::Match(u32)) [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:320:65 [INFO] [stdout] | [INFO] [stdout] 320 | ... if matches!(c, hts_Cigar::Match(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:323:63 [INFO] [stdout] | [INFO] [stdout] 323 | ... if matches!(c, hts_Cigar::Del(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:344:65 [INFO] [stdout] | [INFO] [stdout] 344 | ... if matches!(c, hts_Cigar::Match(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:347:63 [INFO] [stdout] | [INFO] [stdout] 347 | ... if matches!(c, hts_Cigar::Del(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `s1` [INFO] [stdout] --> src/parse_files.rs:358:17 [INFO] [stdout] | [INFO] [stdout] 358 | let s1 = &secondary_seqs_dict[&cinfo.secondary_name] [INFO] [stdout] | ^^ help: if this is intentional, prefix it with an underscore: `_s1` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `s2` [INFO] [stdout] --> src/parse_files.rs:360:17 [INFO] [stdout] | [INFO] [stdout] 360 | let s2 = &primary_seqs_dict[&cinfo.primary_name] [INFO] [stdout] | ^^ help: if this is intentional, prefix it with an underscore: `_s2` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `seq_len_from_cig` is assigned to, but never used [INFO] [stdout] --> src/parse_files.rs:365:21 [INFO] [stdout] | [INFO] [stdout] 365 | let mut seq_len_from_cig = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_seq_len_from_cig` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:368:53 [INFO] [stdout] | [INFO] [stdout] 368 | if matches!(cigar, hts_Cigar::Match(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:371:58 [INFO] [stdout] | [INFO] [stdout] 371 | } else if matches!(cigar, hts_Cigar::Ins(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:373:63 [INFO] [stdout] | [INFO] [stdout] 373 | } else if matches!(cigar, hts_Cigar::SoftClip(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/parse_files.rs:229:17 [INFO] [stdout] | [INFO] [stdout] 229 | let mut gap_len = 0; [INFO] [stdout] | ----^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/parse_files.rs:232:17 [INFO] [stdout] | [INFO] [stdout] 232 | let mut new_start_pos = 0; [INFO] [stdout] | ----^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [optimized + debuginfo] target(s) in 3m 01s [INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nalgebra v0.27.1 [INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1` [INFO] running `Command { std: "docker" "inspect" "cfd8d592cb2e74fa9103588eec453b8c72743fd90a46539223e482703ba69995", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "cfd8d592cb2e74fa9103588eec453b8c72743fd90a46539223e482703ba69995", kill_on_drop: false }` [INFO] [stdout] cfd8d592cb2e74fa9103588eec453b8c72743fd90a46539223e482703ba69995 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:eea15d5475069c3ef791f10c2c6b5af2ee421ef2da1e680ecce1cba46243983b" "/opt/rustwide/cargo-home/bin/cargo" "+44f415c1d617ebc7b931a243b7b321ef8a6ca47c" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 81c8232cc851434e4273a4acea9dab393fbc05dca1a7e5ef62db16d2c008529a [INFO] running `Command { std: "docker" "start" "-a" "81c8232cc851434e4273a4acea9dab393fbc05dca1a7e5ef62db16d2c008529a", kill_on_drop: false }` [INFO] [stderr] Compiling 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)]` 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: 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 variable: `aligned_pairs` [INFO] [stdout] --> src/parse_files.rs:214:17 [INFO] [stdout] | [INFO] [stdout] 214 | let aligned_pairs = record.aligned_pairs(); [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_aligned_pairs` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `curr_read_pos` [INFO] [stdout] --> src/parse_files.rs:224:17 [INFO] [stdout] | [INFO] [stdout] 224 | let curr_read_pos = cigar.leading_softclips(); [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_curr_read_pos` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `gap_len` [INFO] [stdout] --> src/parse_files.rs:229:21 [INFO] [stdout] | [INFO] [stdout] 229 | let mut gap_len = 0; [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_gap_len` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `new_start_pos` [INFO] [stdout] --> src/parse_files.rs:232:21 [INFO] [stdout] | [INFO] [stdout] 232 | let mut new_start_pos = 0; [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_new_start_pos` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:263:49 [INFO] [stdout] | [INFO] [stdout] 263 | if matches!(c, hts_Cigar::Match(u32)) [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:264:51 [INFO] [stdout] | [INFO] [stdout] 264 | || matches!(c, hts_Cigar::Ins(u32)) [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:265:51 [INFO] [stdout] | [INFO] [stdout] 265 | || matches!(c, hts_Cigar::Del(u32)) [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:270:59 [INFO] [stdout] | [INFO] [stdout] 270 | ... if matches!(c, hts_Cigar::Ins(u32)) [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:271:65 [INFO] [stdout] | [INFO] [stdout] 271 | ... || matches!(c, hts_Cigar::Match(u32)) [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:277:55 [INFO] [stdout] | [INFO] [stdout] 277 | if matches!(c, hts_Cigar::Ins(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:283:65 [INFO] [stdout] | [INFO] [stdout] 283 | ... if matches!(c, hts_Cigar::Match(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:301:65 [INFO] [stdout] | [INFO] [stdout] 301 | ... if matches!(c, hts_Cigar::Match(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:315:69 [INFO] [stdout] | [INFO] [stdout] 315 | ... && matches!(c, hts_Cigar::Match(u32)) [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:320:65 [INFO] [stdout] | [INFO] [stdout] 320 | ... if matches!(c, hts_Cigar::Match(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:323:63 [INFO] [stdout] | [INFO] [stdout] 323 | ... if matches!(c, hts_Cigar::Del(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:344:65 [INFO] [stdout] | [INFO] [stdout] 344 | ... if matches!(c, hts_Cigar::Match(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:347:63 [INFO] [stdout] | [INFO] [stdout] 347 | ... if matches!(c, hts_Cigar::Del(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `s1` [INFO] [stdout] --> src/parse_files.rs:358:17 [INFO] [stdout] | [INFO] [stdout] 358 | let s1 = &secondary_seqs_dict[&cinfo.secondary_name] [INFO] [stdout] | ^^ help: if this is intentional, prefix it with an underscore: `_s1` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `s2` [INFO] [stdout] --> src/parse_files.rs:360:17 [INFO] [stdout] | [INFO] [stdout] 360 | let s2 = &primary_seqs_dict[&cinfo.primary_name] [INFO] [stdout] | ^^ help: if this is intentional, prefix it with an underscore: `_s2` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `seq_len_from_cig` is assigned to, but never used [INFO] [stdout] --> src/parse_files.rs:365:21 [INFO] [stdout] | [INFO] [stdout] 365 | let mut seq_len_from_cig = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_seq_len_from_cig` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:368:53 [INFO] [stdout] | [INFO] [stdout] 368 | if matches!(cigar, hts_Cigar::Match(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:371:58 [INFO] [stdout] | [INFO] [stdout] 371 | } else if matches!(cigar, hts_Cigar::Ins(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `u32` [INFO] [stdout] --> src/parse_files.rs:373:63 [INFO] [stdout] | [INFO] [stdout] 373 | } else if matches!(cigar, hts_Cigar::SoftClip(u32)) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_u32` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/parse_files.rs:229:17 [INFO] [stdout] | [INFO] [stdout] 229 | let mut gap_len = 0; [INFO] [stdout] | ----^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/parse_files.rs:232:17 [INFO] [stdout] | [INFO] [stdout] 232 | let mut new_start_pos = 0; [INFO] [stdout] | ----^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `test` profile [optimized + debuginfo] target(s) in 0.73s [INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nalgebra v0.27.1 [INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1` [INFO] running `Command { std: "docker" "inspect" "81c8232cc851434e4273a4acea9dab393fbc05dca1a7e5ef62db16d2c008529a", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "81c8232cc851434e4273a4acea9dab393fbc05dca1a7e5ef62db16d2c008529a", kill_on_drop: false }` [INFO] [stdout] 81c8232cc851434e4273a4acea9dab393fbc05dca1a7e5ef62db16d2c008529a