Dec 04 23:40:44.856 INFO checking TuBieJun/consensus against try#1df97983eb2057dc6a8f7eb364e263b51ae23230 for pr-56481 Dec 04 23:40:44.856 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56481/worker-5/try#1df97983eb2057dc6a8f7eb364e263b51ae23230:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-5/pr-56481/try#1df97983eb2057dc6a8f7eb364e263b51ae23230:/source:ro,Z" "-v" "/mnt/big/crater/work/local/cargo-home:/cargo-home:ro,Z" "-v" "/mnt/big/crater/work/local/rustup-home:/rustup-home:ro,Z" "-e" "USER_ID=1000" "-e" "SOURCE_DIR=/source" "-e" "USER_ID=1000" "-e" "CMD=cargo +1df97983eb2057dc6a8f7eb364e263b51ae23230-alt check --frozen --all --all-targets" "-e" "CARGO_TARGET_DIR=/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/cargo-home" "-e" "RUSTUP_HOME=/rustup-home" "-m" "1536M" "--network" "none" "crater"` Dec 04 23:40:45.337 INFO [stdout] e685c14beeb44f5ce68b2fb69a1d6ae7322015f76691ec5a744e103ebd656aec Dec 04 23:40:45.339 INFO running `"docker" "start" "-a" "e685c14beeb44f5ce68b2fb69a1d6ae7322015f76691ec5a744e103ebd656aec"` Dec 04 23:40:47.607 INFO [stderr] usermod: no changes Dec 04 23:40:47.742 INFO [stderr] Checking ieee754 v0.2.2 Dec 04 23:40:47.743 INFO [stderr] Compiling fs-utils v1.0.0 Dec 04 23:40:47.743 INFO [stderr] Checking itertools v0.6.5 Dec 04 23:40:49.719 INFO [stderr] Compiling rust-htslib v0.15.0 Dec 04 23:41:20.050 INFO [stderr] Checking consensus v0.1.0 (/source) Dec 04 23:41:22.588 INFO [stderr] warning: unused import: `std::env` Dec 04 23:41:22.588 INFO [stderr] --> src/main.rs:12:5 Dec 04 23:41:22.588 INFO [stderr] | Dec 04 23:41:22.588 INFO [stderr] 12 | use std::env; Dec 04 23:41:22.588 INFO [stderr] | ^^^^^^^^ Dec 04 23:41:22.588 INFO [stderr] | Dec 04 23:41:22.588 INFO [stderr] = note: #[warn(unused_imports)] on by default Dec 04 23:41:22.588 INFO [stderr] Dec 04 23:41:22.588 INFO [stderr] warning: unused import: `rust_htslib::prelude::*` Dec 04 23:41:22.588 INFO [stderr] --> src/main.rs:16:5 Dec 04 23:41:22.589 INFO [stderr] | Dec 04 23:41:22.589 INFO [stderr] 16 | use rust_htslib::prelude::*; Dec 04 23:41:22.589 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:22.589 INFO [stderr] Dec 04 23:41:22.589 INFO [stderr] warning: unused import: `std::io` Dec 04 23:41:22.589 INFO [stderr] --> src/main.rs:21:5 Dec 04 23:41:22.589 INFO [stderr] | Dec 04 23:41:22.589 INFO [stderr] 21 | use std::io; Dec 04 23:41:22.589 INFO [stderr] | ^^^^^^^ Dec 04 23:41:22.589 INFO [stderr] Dec 04 23:41:22.589 INFO [stderr] warning: unused import: `PathBuf` Dec 04 23:41:22.589 INFO [stderr] --> src/main.rs:25:23 Dec 04 23:41:22.589 INFO [stderr] | Dec 04 23:41:22.589 INFO [stderr] 25 | use std::path::{Path, PathBuf}; Dec 04 23:41:22.589 INFO [stderr] | ^^^^^^^ Dec 04 23:41:22.589 INFO [stderr] Dec 04 23:41:22.589 INFO [stderr] warning: unused import: `SubCommand` Dec 04 23:41:22.589 INFO [stderr] --> src/main.rs:26:22 Dec 04 23:41:22.589 INFO [stderr] | Dec 04 23:41:22.589 INFO [stderr] 26 | use clap::{Arg, App, SubCommand}; Dec 04 23:41:22.589 INFO [stderr] | ^^^^^^^^^^ Dec 04 23:41:22.589 INFO [stderr] Dec 04 23:41:22.589 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 04 23:41:22.589 INFO [stderr] --> src/main.rs:218:20 Dec 04 23:41:22.589 INFO [stderr] | Dec 04 23:41:22.589 INFO [stderr] 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Dec 04 23:41:22.589 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 04 23:41:22.589 INFO [stderr] | Dec 04 23:41:22.589 INFO [stderr] = note: #[warn(unused_parens)] on by default Dec 04 23:41:22.589 INFO [stderr] Dec 04 23:41:22.589 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 04 23:41:22.589 INFO [stderr] --> src/main.rs:239:16 Dec 04 23:41:22.589 INFO [stderr] | Dec 04 23:41:22.589 INFO [stderr] 239 | if (baseEach_percent_record.len() > 0) { Dec 04 23:41:22.589 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 04 23:41:22.589 INFO [stderr] Dec 04 23:41:22.883 INFO [stderr] warning: unused import: `std::io::prelude` Dec 04 23:41:22.883 INFO [stderr] --> src/main.rs:22:5 Dec 04 23:41:22.883 INFO [stderr] | Dec 04 23:41:22.883 INFO [stderr] 22 | use std::io::prelude::*; Dec 04 23:41:22.883 INFO [stderr] | ^^^^^^^^^^^^^^^^ Dec 04 23:41:22.883 INFO [stderr] Dec 04 23:41:22.903 INFO [stderr] warning: unused variable: `consensus_base` Dec 04 23:41:22.903 INFO [stderr] --> src/main.rs:139:9 Dec 04 23:41:22.903 INFO [stderr] | Dec 04 23:41:22.903 INFO [stderr] 139 | let consensus_base:Vec = Vec::new(); Dec 04 23:41:22.903 INFO [stderr] | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Dec 04 23:41:22.903 INFO [stderr] | Dec 04 23:41:22.903 INFO [stderr] = note: #[warn(unused_variables)] on by default Dec 04 23:41:22.903 INFO [stderr] Dec 04 23:41:22.903 INFO [stderr] warning: unused variable: `consensus_source_reads` Dec 04 23:41:22.903 INFO [stderr] --> src/main.rs:144:13 Dec 04 23:41:22.903 INFO [stderr] | Dec 04 23:41:22.903 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 04 23:41:22.903 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Dec 04 23:41:22.903 INFO [stderr] Dec 04 23:41:22.903 INFO [stderr] warning: unused variable: `chrom` Dec 04 23:41:22.903 INFO [stderr] --> src/main.rs:283:121 Dec 04 23:41:22.903 INFO [stderr] | Dec 04 23:41:22.903 INFO [stderr] 283 | fn block_consensus(pd:& mut HashMap, Vec, Vec, CigarStringView, bool)>>>, chrom: i32, use_check:bool, min_t_s: &u32, min_t_p: &f32, o_r1: & mut File, o_r2: & mut File, need_trim:bool) { Dec 04 23:41:22.903 INFO [stderr] | ^^^^^ help: consider using `_chrom` instead Dec 04 23:41:22.903 INFO [stderr] Dec 04 23:41:22.903 INFO [stderr] warning: value assigned to `new_seq_b` is never read Dec 04 23:41:22.903 INFO [stderr] --> src/main.rs:370:21 Dec 04 23:41:22.903 INFO [stderr] | Dec 04 23:41:22.903 INFO [stderr] 370 | let mut new_seq_b:Vec = Vec::new(); Dec 04 23:41:22.903 INFO [stderr] | ^^^^^^^^^ Dec 04 23:41:22.903 INFO [stderr] | Dec 04 23:41:22.903 INFO [stderr] = note: #[warn(unused_assignments)] on by default Dec 04 23:41:22.903 INFO [stderr] Dec 04 23:41:22.917 INFO [stderr] warning: variable does not need to be mutable Dec 04 23:41:22.917 INFO [stderr] --> src/main.rs:74:9 Dec 04 23:41:22.917 INFO [stderr] | Dec 04 23:41:22.917 INFO [stderr] 74 | let mut pair; Dec 04 23:41:22.917 INFO [stderr] | ----^^^^ Dec 04 23:41:22.917 INFO [stderr] | | Dec 04 23:41:22.917 INFO [stderr] | help: remove this `mut` Dec 04 23:41:22.917 INFO [stderr] | Dec 04 23:41:22.917 INFO [stderr] = note: #[warn(unused_mut)] on by default Dec 04 23:41:22.917 INFO [stderr] Dec 04 23:41:22.917 INFO [stderr] warning: variable does not need to be mutable Dec 04 23:41:22.917 INFO [stderr] --> src/main.rs:75:9 Dec 04 23:41:22.917 INFO [stderr] | Dec 04 23:41:22.917 INFO [stderr] 75 | let mut strand; Dec 04 23:41:22.917 INFO [stderr] | ----^^^^^^ Dec 04 23:41:22.917 INFO [stderr] | | Dec 04 23:41:22.917 INFO [stderr] | help: remove this `mut` Dec 04 23:41:22.917 INFO [stderr] Dec 04 23:41:22.917 INFO [stderr] warning: variable does not need to be mutable Dec 04 23:41:22.917 INFO [stderr] --> src/main.rs:76:9 Dec 04 23:41:22.917 INFO [stderr] | Dec 04 23:41:22.917 INFO [stderr] 76 | let mut aln_pos; Dec 04 23:41:22.917 INFO [stderr] | ----^^^^^^^ Dec 04 23:41:22.917 INFO [stderr] | | Dec 04 23:41:22.917 INFO [stderr] | help: remove this `mut` Dec 04 23:41:22.917 INFO [stderr] Dec 04 23:41:22.963 INFO [stderr] warning: variable does not need to be mutable Dec 04 23:41:22.963 INFO [stderr] --> src/main.rs:144:9 Dec 04 23:41:22.963 INFO [stderr] | Dec 04 23:41:22.963 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 04 23:41:22.963 INFO [stderr] | ----^^^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:22.963 INFO [stderr] | | Dec 04 23:41:22.963 INFO [stderr] | help: remove this `mut` Dec 04 23:41:22.963 INFO [stderr] Dec 04 23:41:22.963 INFO [stderr] warning: variable does not need to be mutable Dec 04 23:41:22.963 INFO [stderr] --> src/main.rs:151:9 Dec 04 23:41:22.963 INFO [stderr] | Dec 04 23:41:22.963 INFO [stderr] 151 | let mut top_cigar:&CigarStringView; Dec 04 23:41:22.963 INFO [stderr] | ----^^^^^^^^^ Dec 04 23:41:22.963 INFO [stderr] | | Dec 04 23:41:22.963 INFO [stderr] | help: remove this `mut` Dec 04 23:41:22.963 INFO [stderr] Dec 04 23:41:22.975 INFO [stderr] warning: variable does not need to be mutable Dec 04 23:41:22.975 INFO [stderr] --> src/main.rs:338:9 Dec 04 23:41:22.975 INFO [stderr] | Dec 04 23:41:22.975 INFO [stderr] 338 | let mut need_trim:bool; Dec 04 23:41:22.975 INFO [stderr] | ----^^^^^^^^^ Dec 04 23:41:22.975 INFO [stderr] | | Dec 04 23:41:22.975 INFO [stderr] | help: remove this `mut` Dec 04 23:41:22.975 INFO [stderr] Dec 04 23:41:22.975 INFO [stderr] warning: variable does not need to be mutable Dec 04 23:41:22.975 INFO [stderr] --> src/main.rs:355:9 Dec 04 23:41:22.975 INFO [stderr] | Dec 04 23:41:22.975 INFO [stderr] 355 | let mut chrom = 0; Dec 04 23:41:22.975 INFO [stderr] | ----^^^^^ Dec 04 23:41:22.975 INFO [stderr] | | Dec 04 23:41:22.975 INFO [stderr] | help: remove this `mut` Dec 04 23:41:22.975 INFO [stderr] Dec 04 23:41:22.987 INFO [stderr] warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Dec 04 23:41:22.987 INFO [stderr] --> src/main.rs:68:1 Dec 04 23:41:22.987 INFO [stderr] | Dec 04 23:41:22.987 INFO [stderr] 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Dec 04 23:41:22.987 INFO [stderr] 69 | | Dec 04 23:41:22.987 INFO [stderr] 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Dec 04 23:41:22.987 INFO [stderr] 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Dec 04 23:41:22.987 INFO [stderr] ... | Dec 04 23:41:22.987 INFO [stderr] 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Dec 04 23:41:22.987 INFO [stderr] 98 | | } Dec 04 23:41:22.987 INFO [stderr] | |_^ Dec 04 23:41:22.995 INFO [stderr] warning: unused import: `std::env` Dec 04 23:41:22.995 INFO [stderr] --> src/main.rs:12:5 Dec 04 23:41:22.995 INFO [stderr] | Dec 04 23:41:22.995 INFO [stderr] 12 | use std::env; Dec 04 23:41:22.995 INFO [stderr] | ^^^^^^^^ Dec 04 23:41:22.995 INFO [stderr] | Dec 04 23:41:22.995 INFO [stderr] = note: #[warn(unused_imports)] on by default Dec 04 23:41:22.995 INFO [stderr] Dec 04 23:41:22.995 INFO [stderr] warning: unused import: `rust_htslib::prelude::*` Dec 04 23:41:22.995 INFO [stderr] --> src/main.rs:16:5 Dec 04 23:41:22.995 INFO [stderr] | Dec 04 23:41:22.995 INFO [stderr] 16 | use rust_htslib::prelude::*; Dec 04 23:41:22.995 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:22.995 INFO [stderr] Dec 04 23:41:22.995 INFO [stderr] warning: unused import: `std::io` Dec 04 23:41:22.995 INFO [stderr] --> src/main.rs:21:5 Dec 04 23:41:22.995 INFO [stderr] | Dec 04 23:41:22.995 INFO [stderr] 21 | use std::io; Dec 04 23:41:22.995 INFO [stderr] | ^^^^^^^ Dec 04 23:41:22.995 INFO [stderr] Dec 04 23:41:22.995 INFO [stderr] warning: unused import: `PathBuf` Dec 04 23:41:22.995 INFO [stderr] --> src/main.rs:25:23 Dec 04 23:41:22.995 INFO [stderr] | Dec 04 23:41:22.995 INFO [stderr] 25 | use std::path::{Path, PathBuf}; Dec 04 23:41:22.995 INFO [stderr] | ^^^^^^^ Dec 04 23:41:22.995 INFO [stderr] Dec 04 23:41:22.995 INFO [stderr] warning: unused import: `SubCommand` Dec 04 23:41:22.995 INFO [stderr] --> src/main.rs:26:22 Dec 04 23:41:22.995 INFO [stderr] | Dec 04 23:41:22.995 INFO [stderr] 26 | use clap::{Arg, App, SubCommand}; Dec 04 23:41:22.995 INFO [stderr] | ^^^^^^^^^^ Dec 04 23:41:22.995 INFO [stderr] Dec 04 23:41:22.995 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 04 23:41:22.995 INFO [stderr] --> src/main.rs:218:20 Dec 04 23:41:22.995 INFO [stderr] | Dec 04 23:41:22.995 INFO [stderr] 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Dec 04 23:41:22.995 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 04 23:41:22.995 INFO [stderr] | Dec 04 23:41:22.995 INFO [stderr] = note: #[warn(unused_parens)] on by default Dec 04 23:41:22.995 INFO [stderr] Dec 04 23:41:22.995 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 04 23:41:22.995 INFO [stderr] --> src/main.rs:239:16 Dec 04 23:41:22.995 INFO [stderr] | Dec 04 23:41:22.995 INFO [stderr] 239 | if (baseEach_percent_record.len() > 0) { Dec 04 23:41:22.995 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 04 23:41:22.995 INFO [stderr] Dec 04 23:41:22.999 INFO [stderr] | Dec 04 23:41:22.999 INFO [stderr] = note: #[warn(non_snake_case)] on by default Dec 04 23:41:22.999 INFO [stderr] Dec 04 23:41:22.999 INFO [stderr] warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Dec 04 23:41:22.999 INFO [stderr] --> src/main.rs:147:9 Dec 04 23:41:22.999 INFO [stderr] | Dec 04 23:41:22.999 INFO [stderr] 147 | let mut baseEach_num_record = String::new(); Dec 04 23:41:22.999 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:22.999 INFO [stderr] Dec 04 23:41:22.999 INFO [stderr] warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Dec 04 23:41:22.999 INFO [stderr] --> src/main.rs:148:9 Dec 04 23:41:22.999 INFO [stderr] | Dec 04 23:41:22.999 INFO [stderr] 148 | let mut baseEach_percent_record = String::new(); Dec 04 23:41:22.999 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:22.999 INFO [stderr] Dec 04 23:41:22.999 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 04 23:41:22.999 INFO [stderr] --> src/main.rs:267:9 Dec 04 23:41:22.999 INFO [stderr] | Dec 04 23:41:22.999 INFO [stderr] 267 | o_buff.write(&member_record.2); Dec 04 23:41:22.999 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:22.999 INFO [stderr] | Dec 04 23:41:22.999 INFO [stderr] = note: #[warn(unused_must_use)] on by default Dec 04 23:41:22.999 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 04 23:41:22.999 INFO [stderr] Dec 04 23:41:22.999 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 04 23:41:22.999 INFO [stderr] --> src/main.rs:269:9 Dec 04 23:41:22.999 INFO [stderr] | Dec 04 23:41:22.999 INFO [stderr] 269 | o_buff.write(&member_record.0); Dec 04 23:41:22.999 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:22.999 INFO [stderr] | Dec 04 23:41:22.999 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 04 23:41:22.999 INFO [stderr] Dec 04 23:41:22.999 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 04 23:41:22.999 INFO [stderr] --> src/main.rs:272:9 Dec 04 23:41:22.999 INFO [stderr] | Dec 04 23:41:22.999 INFO [stderr] 272 | o_buff.write(&real_qual_temp); Dec 04 23:41:22.999 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:22.999 INFO [stderr] | Dec 04 23:41:22.999 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 04 23:41:22.999 INFO [stderr] Dec 04 23:41:22.999 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 04 23:41:22.999 INFO [stderr] --> src/main.rs:274:5 Dec 04 23:41:22.999 INFO [stderr] | Dec 04 23:41:22.999 INFO [stderr] 274 | o_buff.write(b"\n"); Dec 04 23:41:22.999 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:22.999 INFO [stderr] | Dec 04 23:41:22.999 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 04 23:41:22.999 INFO [stderr] Dec 04 23:41:22.999 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 04 23:41:23.000 INFO [stderr] --> src/main.rs:277:5 Dec 04 23:41:23.000 INFO [stderr] | Dec 04 23:41:23.000 INFO [stderr] 277 | o_buff.write(b"\n"); Dec 04 23:41:23.000 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:23.019 INFO [stderr] | Dec 04 23:41:23.019 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 04 23:41:23.019 INFO [stderr] Dec 04 23:41:23.019 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 04 23:41:23.019 INFO [stderr] --> src/main.rs:280:5 Dec 04 23:41:23.019 INFO [stderr] | Dec 04 23:41:23.019 INFO [stderr] 280 | o_buff.write(b"\n"); Dec 04 23:41:23.019 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:23.019 INFO [stderr] | Dec 04 23:41:23.019 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 04 23:41:23.019 INFO [stderr] Dec 04 23:41:23.019 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 04 23:41:23.019 INFO [stderr] --> src/main.rs:286:10 Dec 04 23:41:23.019 INFO [stderr] | Dec 04 23:41:23.019 INFO [stderr] 286 | for (key_dupGroup, pair_dup) in pd.iter() { Dec 04 23:41:23.019 INFO [stderr] | ^^^^^^^^^^^^ Dec 04 23:41:23.019 INFO [stderr] Dec 04 23:41:23.019 INFO [stderr] warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Dec 04 23:41:23.019 INFO [stderr] --> src/main.rs:357:9 Dec 04 23:41:23.019 INFO [stderr] | Dec 04 23:41:23.019 INFO [stderr] 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Dec 04 23:41:23.019 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:23.019 INFO [stderr] Dec 04 23:41:23.019 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 04 23:41:23.019 INFO [stderr] --> src/main.rs:387:17 Dec 04 23:41:23.019 INFO [stderr] | Dec 04 23:41:23.019 INFO [stderr] 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Dec 04 23:41:23.019 INFO [stderr] | ^^^^^^^^^^^^ Dec 04 23:41:23.019 INFO [stderr] Dec 04 23:41:23.179 INFO [stderr] warning: unused import: `std::io::prelude` Dec 04 23:41:23.179 INFO [stderr] --> src/main.rs:22:5 Dec 04 23:41:23.179 INFO [stderr] | Dec 04 23:41:23.179 INFO [stderr] 22 | use std::io::prelude::*; Dec 04 23:41:23.179 INFO [stderr] | ^^^^^^^^^^^^^^^^ Dec 04 23:41:23.179 INFO [stderr] Dec 04 23:41:23.189 INFO [stderr] warning: unused variable: `consensus_base` Dec 04 23:41:23.189 INFO [stderr] --> src/main.rs:139:9 Dec 04 23:41:23.189 INFO [stderr] | Dec 04 23:41:23.189 INFO [stderr] 139 | let consensus_base:Vec = Vec::new(); Dec 04 23:41:23.189 INFO [stderr] | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Dec 04 23:41:23.189 INFO [stderr] | Dec 04 23:41:23.189 INFO [stderr] = note: #[warn(unused_variables)] on by default Dec 04 23:41:23.189 INFO [stderr] Dec 04 23:41:23.189 INFO [stderr] warning: unused variable: `consensus_source_reads` Dec 04 23:41:23.189 INFO [stderr] --> src/main.rs:144:13 Dec 04 23:41:23.189 INFO [stderr] | Dec 04 23:41:23.189 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 04 23:41:23.189 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Dec 04 23:41:23.189 INFO [stderr] Dec 04 23:41:23.189 INFO [stderr] warning: unused variable: `chrom` Dec 04 23:41:23.189 INFO [stderr] --> src/main.rs:283:121 Dec 04 23:41:23.189 INFO [stderr] | Dec 04 23:41:23.189 INFO [stderr] 283 | fn block_consensus(pd:& mut HashMap, Vec, Vec, CigarStringView, bool)>>>, chrom: i32, use_check:bool, min_t_s: &u32, min_t_p: &f32, o_r1: & mut File, o_r2: & mut File, need_trim:bool) { Dec 04 23:41:23.189 INFO [stderr] | ^^^^^ help: consider using `_chrom` instead Dec 04 23:41:23.189 INFO [stderr] Dec 04 23:41:23.195 INFO [stderr] warning: value assigned to `new_seq_b` is never read Dec 04 23:41:23.195 INFO [stderr] --> src/main.rs:370:21 Dec 04 23:41:23.195 INFO [stderr] | Dec 04 23:41:23.195 INFO [stderr] 370 | let mut new_seq_b:Vec = Vec::new(); Dec 04 23:41:23.195 INFO [stderr] | ^^^^^^^^^ Dec 04 23:41:23.195 INFO [stderr] | Dec 04 23:41:23.195 INFO [stderr] = note: #[warn(unused_assignments)] on by default Dec 04 23:41:23.195 INFO [stderr] Dec 04 23:41:23.207 INFO [stderr] warning: variable does not need to be mutable Dec 04 23:41:23.207 INFO [stderr] --> src/main.rs:74:9 Dec 04 23:41:23.207 INFO [stderr] | Dec 04 23:41:23.207 INFO [stderr] 74 | let mut pair; Dec 04 23:41:23.207 INFO [stderr] | ----^^^^ Dec 04 23:41:23.207 INFO [stderr] | | Dec 04 23:41:23.207 INFO [stderr] | help: remove this `mut` Dec 04 23:41:23.207 INFO [stderr] | Dec 04 23:41:23.207 INFO [stderr] = note: #[warn(unused_mut)] on by default Dec 04 23:41:23.207 INFO [stderr] Dec 04 23:41:23.207 INFO [stderr] warning: variable does not need to be mutable Dec 04 23:41:23.207 INFO [stderr] --> src/main.rs:75:9 Dec 04 23:41:23.207 INFO [stderr] | Dec 04 23:41:23.207 INFO [stderr] 75 | let mut strand; Dec 04 23:41:23.207 INFO [stderr] | ----^^^^^^ Dec 04 23:41:23.207 INFO [stderr] | | Dec 04 23:41:23.207 INFO [stderr] | help: remove this `mut` Dec 04 23:41:23.207 INFO [stderr] Dec 04 23:41:23.207 INFO [stderr] warning: variable does not need to be mutable Dec 04 23:41:23.207 INFO [stderr] --> src/main.rs:76:9 Dec 04 23:41:23.207 INFO [stderr] | Dec 04 23:41:23.207 INFO [stderr] 76 | let mut aln_pos; Dec 04 23:41:23.207 INFO [stderr] | ----^^^^^^^ Dec 04 23:41:23.207 INFO [stderr] | | Dec 04 23:41:23.207 INFO [stderr] | help: remove this `mut` Dec 04 23:41:23.207 INFO [stderr] Dec 04 23:41:23.247 INFO [stderr] warning: variable does not need to be mutable Dec 04 23:41:23.247 INFO [stderr] --> src/main.rs:144:9 Dec 04 23:41:23.247 INFO [stderr] | Dec 04 23:41:23.247 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 04 23:41:23.247 INFO [stderr] | ----^^^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:23.247 INFO [stderr] | | Dec 04 23:41:23.247 INFO [stderr] | help: remove this `mut` Dec 04 23:41:23.247 INFO [stderr] Dec 04 23:41:23.247 INFO [stderr] warning: variable does not need to be mutable Dec 04 23:41:23.247 INFO [stderr] --> src/main.rs:151:9 Dec 04 23:41:23.247 INFO [stderr] | Dec 04 23:41:23.247 INFO [stderr] 151 | let mut top_cigar:&CigarStringView; Dec 04 23:41:23.247 INFO [stderr] | ----^^^^^^^^^ Dec 04 23:41:23.247 INFO [stderr] | | Dec 04 23:41:23.247 INFO [stderr] | help: remove this `mut` Dec 04 23:41:23.247 INFO [stderr] Dec 04 23:41:23.267 INFO [stderr] warning: variable does not need to be mutable Dec 04 23:41:23.267 INFO [stderr] --> src/main.rs:338:9 Dec 04 23:41:23.267 INFO [stderr] | Dec 04 23:41:23.267 INFO [stderr] 338 | let mut need_trim:bool; Dec 04 23:41:23.267 INFO [stderr] | ----^^^^^^^^^ Dec 04 23:41:23.267 INFO [stderr] | | Dec 04 23:41:23.267 INFO [stderr] | help: remove this `mut` Dec 04 23:41:23.267 INFO [stderr] Dec 04 23:41:23.267 INFO [stderr] warning: variable does not need to be mutable Dec 04 23:41:23.267 INFO [stderr] --> src/main.rs:355:9 Dec 04 23:41:23.267 INFO [stderr] | Dec 04 23:41:23.267 INFO [stderr] 355 | let mut chrom = 0; Dec 04 23:41:23.267 INFO [stderr] | ----^^^^^ Dec 04 23:41:23.267 INFO [stderr] | | Dec 04 23:41:23.267 INFO [stderr] | help: remove this `mut` Dec 04 23:41:23.267 INFO [stderr] Dec 04 23:41:23.287 INFO [stderr] warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Dec 04 23:41:23.287 INFO [stderr] --> src/main.rs:68:1 Dec 04 23:41:23.287 INFO [stderr] | Dec 04 23:41:23.287 INFO [stderr] 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Dec 04 23:41:23.287 INFO [stderr] 69 | | Dec 04 23:41:23.287 INFO [stderr] 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Dec 04 23:41:23.287 INFO [stderr] 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Dec 04 23:41:23.287 INFO [stderr] ... | Dec 04 23:41:23.287 INFO [stderr] 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Dec 04 23:41:23.287 INFO [stderr] 98 | | } Dec 04 23:41:23.287 INFO [stderr] | |_^ Dec 04 23:41:23.287 INFO [stderr] | Dec 04 23:41:23.287 INFO [stderr] = note: #[warn(non_snake_case)] on by default Dec 04 23:41:23.287 INFO [stderr] Dec 04 23:41:23.287 INFO [stderr] warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Dec 04 23:41:23.287 INFO [stderr] --> src/main.rs:147:9 Dec 04 23:41:23.287 INFO [stderr] | Dec 04 23:41:23.287 INFO [stderr] 147 | let mut baseEach_num_record = String::new(); Dec 04 23:41:23.287 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:23.287 INFO [stderr] Dec 04 23:41:23.287 INFO [stderr] warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Dec 04 23:41:23.287 INFO [stderr] --> src/main.rs:148:9 Dec 04 23:41:23.287 INFO [stderr] | Dec 04 23:41:23.287 INFO [stderr] 148 | let mut baseEach_percent_record = String::new(); Dec 04 23:41:23.287 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:23.287 INFO [stderr] Dec 04 23:41:23.289 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 04 23:41:23.289 INFO [stderr] --> src/main.rs:267:9 Dec 04 23:41:23.289 INFO [stderr] | Dec 04 23:41:23.289 INFO [stderr] 267 | o_buff.write(&member_record.2); Dec 04 23:41:23.289 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:23.289 INFO [stderr] | Dec 04 23:41:23.289 INFO [stderr] = note: #[warn(unused_must_use)] on by default Dec 04 23:41:23.289 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 04 23:41:23.289 INFO [stderr] Dec 04 23:41:23.289 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 04 23:41:23.289 INFO [stderr] --> src/main.rs:269:9 Dec 04 23:41:23.289 INFO [stderr] | Dec 04 23:41:23.289 INFO [stderr] 269 | o_buff.write(&member_record.0); Dec 04 23:41:23.289 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:23.289 INFO [stderr] | Dec 04 23:41:23.289 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 04 23:41:23.289 INFO [stderr] Dec 04 23:41:23.289 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 04 23:41:23.289 INFO [stderr] --> src/main.rs:272:9 Dec 04 23:41:23.289 INFO [stderr] | Dec 04 23:41:23.289 INFO [stderr] 272 | o_buff.write(&real_qual_temp); Dec 04 23:41:23.289 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:23.289 INFO [stderr] | Dec 04 23:41:23.289 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 04 23:41:23.289 INFO [stderr] Dec 04 23:41:23.289 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 04 23:41:23.289 INFO [stderr] --> src/main.rs:274:5 Dec 04 23:41:23.289 INFO [stderr] | Dec 04 23:41:23.289 INFO [stderr] 274 | o_buff.write(b"\n"); Dec 04 23:41:23.289 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:23.289 INFO [stderr] | Dec 04 23:41:23.289 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 04 23:41:23.289 INFO [stderr] Dec 04 23:41:23.289 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 04 23:41:23.289 INFO [stderr] --> src/main.rs:277:5 Dec 04 23:41:23.289 INFO [stderr] | Dec 04 23:41:23.289 INFO [stderr] 277 | o_buff.write(b"\n"); Dec 04 23:41:23.289 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:23.289 INFO [stderr] | Dec 04 23:41:23.289 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 04 23:41:23.289 INFO [stderr] Dec 04 23:41:23.289 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 04 23:41:23.289 INFO [stderr] --> src/main.rs:280:5 Dec 04 23:41:23.289 INFO [stderr] | Dec 04 23:41:23.289 INFO [stderr] 280 | o_buff.write(b"\n"); Dec 04 23:41:23.289 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:23.289 INFO [stderr] | Dec 04 23:41:23.289 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 04 23:41:23.289 INFO [stderr] Dec 04 23:41:23.289 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 04 23:41:23.289 INFO [stderr] --> src/main.rs:286:10 Dec 04 23:41:23.289 INFO [stderr] | Dec 04 23:41:23.289 INFO [stderr] 286 | for (key_dupGroup, pair_dup) in pd.iter() { Dec 04 23:41:23.289 INFO [stderr] | ^^^^^^^^^^^^ Dec 04 23:41:23.289 INFO [stderr] Dec 04 23:41:23.289 INFO [stderr] warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Dec 04 23:41:23.289 INFO [stderr] --> src/main.rs:357:9 Dec 04 23:41:23.289 INFO [stderr] | Dec 04 23:41:23.289 INFO [stderr] 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Dec 04 23:41:23.289 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^ Dec 04 23:41:23.289 INFO [stderr] Dec 04 23:41:23.289 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 04 23:41:23.289 INFO [stderr] --> src/main.rs:387:17 Dec 04 23:41:23.290 INFO [stderr] | Dec 04 23:41:23.290 INFO [stderr] 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Dec 04 23:41:23.290 INFO [stderr] | ^^^^^^^^^^^^ Dec 04 23:41:23.290 INFO [stderr] Dec 04 23:41:23.312 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 35.68s Dec 04 23:41:23.323 INFO [stderr] su: No module specific data is present Dec 04 23:41:24.386 INFO running `"docker" "inspect" "e685c14beeb44f5ce68b2fb69a1d6ae7322015f76691ec5a744e103ebd656aec"` Dec 04 23:41:24.697 INFO running `"docker" "rm" "-f" "e685c14beeb44f5ce68b2fb69a1d6ae7322015f76691ec5a744e103ebd656aec"` Dec 04 23:41:25.080 INFO [stdout] e685c14beeb44f5ce68b2fb69a1d6ae7322015f76691ec5a744e103ebd656aec