[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] checking bluenote-1577/rs-liftover against master#385fa9d845dd326c6bbfd58c22244215e431948a for absurd-question-mark-desugar [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Frs-liftover" "/workspace/builds/worker-0-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc1/source'... [INFO] [stderr] done. 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"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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+385fa9d845dd326c6bbfd58c22244215e431948a" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] e55feed5a5e5fbd6f0b39f521bc712edfd481414f7dc713a62e28dff67311354 [INFO] running `Command { std: "docker" "start" "-a" "e55feed5a5e5fbd6f0b39f521bc712edfd481414f7dc713a62e28dff67311354", 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] Checking cfg-if v1.0.0 [INFO] [stderr] Checking 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[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)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `Record` is imported redundantly [INFO] [stdout] --> src/parse_files.rs:7:65 [INFO] [stdout] | [INFO] [stdout] 7 | use rust_htslib::bam::record::{Cigar as hts_Cigar, CigarString, Record}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] 8 | use rust_htslib::bam::*; [INFO] [stdout] | ------------------- the item `Record` is already imported here [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Deserialize`, `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`, `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: `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: the item `Record` is imported redundantly [INFO] [stdout] --> src/parse_files.rs:7:65 [INFO] [stdout] | [INFO] [stdout] 7 | use rust_htslib::bam::record::{Cigar as hts_Cigar, CigarString, Record}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] 8 | use rust_htslib::bam::*; [INFO] [stdout] | ------------------- the item `Record` is already imported here [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Deserialize`, `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`, `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: 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: 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] [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: 36 warnings emitted [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] [stdout] warning: 36 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [optimized + debuginfo] target(s) in 1m 43s [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" "e55feed5a5e5fbd6f0b39f521bc712edfd481414f7dc713a62e28dff67311354", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "e55feed5a5e5fbd6f0b39f521bc712edfd481414f7dc713a62e28dff67311354", kill_on_drop: false }` [INFO] [stdout] e55feed5a5e5fbd6f0b39f521bc712edfd481414f7dc713a62e28dff67311354