Dec 18 05:05:51.297 INFO checking TuBieJun/consensus against master#96d1334e567237b1507cd277938e7ae2de75ff51 for pr-54252 Dec 18 05:05:51.297 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-54252/worker-0/master#96d1334e567237b1507cd277938e7ae2de75ff51:/opt/crater/target:rw,Z" "-v" "/mnt/big/crater/work/ex/pr-54252/sources/master#96d1334e567237b1507cd277938e7ae2de75ff51/gh/TuBieJun/consensus:/opt/crater/workdir:ro,Z" "-v" "/mnt/big/crater/work/local/cargo-home:/opt/crater/cargo-home:ro,Z" "-v" "/mnt/big/crater/work/local/rustup-home:/opt/crater/rustup-home:ro,Z" "-e" "USER_ID=1000" "-e" "SOURCE_DIR=/opt/crater/workdir" "-e" "MAP_USER_ID=1000" "-e" "CARGO_TARGET_DIR=/opt/crater/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/crater/cargo-home" "-e" "RUSTUP_HOME=/opt/crater/rustup-home" "-w" "/opt/crater/workdir" "-m" "1536M" "--network" "none" "rustops/crates-build-env" "/opt/crater/cargo-home/bin/cargo" "+96d1334e567237b1507cd277938e7ae2de75ff51-alt" "check" "--frozen" "--all" "--all-targets"` Dec 18 05:05:51.764 INFO [stdout] f778842c924dff01f89562012fbf30bdd45d7fa4d8122fe74149ee00259c6b58 Dec 18 05:05:51.772 INFO running `"docker" "start" "-a" "f778842c924dff01f89562012fbf30bdd45d7fa4d8122fe74149ee00259c6b58"` Dec 18 05:05:53.432 INFO [stderr] Checking ieee754 v0.2.2 Dec 18 05:05:53.432 INFO [stderr] Compiling fs-utils v1.0.0 Dec 18 05:05:53.433 INFO [stderr] Compiling newtype_derive v0.1.6 Dec 18 05:05:54.792 INFO [stderr] Compiling rust-htslib v0.15.0 Dec 18 05:06:24.961 INFO [stderr] Checking consensus v0.1.0 (/opt/crater/workdir) Dec 18 05:06:25.583 INFO [stderr] warning: unused import: `std::env` Dec 18 05:06:25.584 INFO [stderr] --> src/main.rs:12:5 Dec 18 05:06:25.584 INFO [stderr] | Dec 18 05:06:25.584 INFO [stderr] 12 | use std::env; Dec 18 05:06:25.584 INFO [stderr] | ^^^^^^^^ Dec 18 05:06:25.584 INFO [stderr] | Dec 18 05:06:25.584 INFO [stderr] = note: #[warn(unused_imports)] on by default Dec 18 05:06:25.584 INFO [stderr] Dec 18 05:06:25.584 INFO [stderr] warning: unused import: `rust_htslib::prelude::*` Dec 18 05:06:25.584 INFO [stderr] --> src/main.rs:16:5 Dec 18 05:06:25.584 INFO [stderr] | Dec 18 05:06:25.584 INFO [stderr] 16 | use rust_htslib::prelude::*; Dec 18 05:06:25.584 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:25.584 INFO [stderr] Dec 18 05:06:25.584 INFO [stderr] warning: unused import: `std::io` Dec 18 05:06:25.584 INFO [stderr] --> src/main.rs:21:5 Dec 18 05:06:25.584 INFO [stderr] | Dec 18 05:06:25.584 INFO [stderr] 21 | use std::io; Dec 18 05:06:25.584 INFO [stderr] | ^^^^^^^ Dec 18 05:06:25.584 INFO [stderr] Dec 18 05:06:25.584 INFO [stderr] warning: unused import: `PathBuf` Dec 18 05:06:25.584 INFO [stderr] --> src/main.rs:25:23 Dec 18 05:06:25.584 INFO [stderr] | Dec 18 05:06:25.584 INFO [stderr] 25 | use std::path::{Path, PathBuf}; Dec 18 05:06:25.584 INFO [stderr] | ^^^^^^^ Dec 18 05:06:25.585 INFO [stderr] Dec 18 05:06:25.585 INFO [stderr] warning: unused import: `SubCommand` Dec 18 05:06:25.585 INFO [stderr] --> src/main.rs:26:22 Dec 18 05:06:25.585 INFO [stderr] | Dec 18 05:06:25.585 INFO [stderr] 26 | use clap::{Arg, App, SubCommand}; Dec 18 05:06:25.585 INFO [stderr] | ^^^^^^^^^^ Dec 18 05:06:25.585 INFO [stderr] Dec 18 05:06:25.585 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 18 05:06:25.585 INFO [stderr] --> src/main.rs:218:20 Dec 18 05:06:25.585 INFO [stderr] | Dec 18 05:06:25.585 INFO [stderr] 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Dec 18 05:06:25.585 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 18 05:06:25.585 INFO [stderr] | Dec 18 05:06:25.585 INFO [stderr] = note: #[warn(unused_parens)] on by default Dec 18 05:06:25.585 INFO [stderr] Dec 18 05:06:25.585 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 18 05:06:25.585 INFO [stderr] --> src/main.rs:239:16 Dec 18 05:06:25.585 INFO [stderr] | Dec 18 05:06:25.585 INFO [stderr] 239 | if (baseEach_percent_record.len() > 0) { Dec 18 05:06:25.585 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 18 05:06:25.585 INFO [stderr] Dec 18 05:06:25.866 INFO [stderr] warning: unused import: `std::env` Dec 18 05:06:25.866 INFO [stderr] --> src/main.rs:12:5 Dec 18 05:06:25.866 INFO [stderr] | Dec 18 05:06:25.866 INFO [stderr] 12 | use std::env; Dec 18 05:06:25.866 INFO [stderr] | ^^^^^^^^ Dec 18 05:06:25.866 INFO [stderr] | Dec 18 05:06:25.866 INFO [stderr] = note: #[warn(unused_imports)] on by default Dec 18 05:06:25.866 INFO [stderr] Dec 18 05:06:25.866 INFO [stderr] warning: unused import: `rust_htslib::prelude::*` Dec 18 05:06:25.866 INFO [stderr] --> src/main.rs:16:5 Dec 18 05:06:25.872 INFO [stderr] | Dec 18 05:06:25.872 INFO [stderr] 16 | use rust_htslib::prelude::*; Dec 18 05:06:25.872 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:25.872 INFO [stderr] Dec 18 05:06:25.872 INFO [stderr] warning: unused import: `std::io` Dec 18 05:06:25.872 INFO [stderr] --> src/main.rs:21:5 Dec 18 05:06:25.872 INFO [stderr] | Dec 18 05:06:25.872 INFO [stderr] 21 | use std::io; Dec 18 05:06:25.872 INFO [stderr] | ^^^^^^^ Dec 18 05:06:25.872 INFO [stderr] Dec 18 05:06:25.872 INFO [stderr] warning: unused import: `PathBuf` Dec 18 05:06:25.872 INFO [stderr] --> src/main.rs:25:23 Dec 18 05:06:25.872 INFO [stderr] | Dec 18 05:06:25.872 INFO [stderr] 25 | use std::path::{Path, PathBuf}; Dec 18 05:06:25.872 INFO [stderr] | ^^^^^^^ Dec 18 05:06:25.872 INFO [stderr] Dec 18 05:06:25.872 INFO [stderr] warning: unused import: `SubCommand` Dec 18 05:06:25.872 INFO [stderr] --> src/main.rs:26:22 Dec 18 05:06:25.872 INFO [stderr] | Dec 18 05:06:25.872 INFO [stderr] 26 | use clap::{Arg, App, SubCommand}; Dec 18 05:06:25.872 INFO [stderr] | ^^^^^^^^^^ Dec 18 05:06:25.872 INFO [stderr] Dec 18 05:06:25.872 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 18 05:06:25.872 INFO [stderr] --> src/main.rs:218:20 Dec 18 05:06:25.872 INFO [stderr] | Dec 18 05:06:25.872 INFO [stderr] 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Dec 18 05:06:25.872 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 18 05:06:25.872 INFO [stderr] | Dec 18 05:06:25.872 INFO [stderr] = note: #[warn(unused_parens)] on by default Dec 18 05:06:25.872 INFO [stderr] Dec 18 05:06:25.872 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 18 05:06:25.872 INFO [stderr] --> src/main.rs:239:16 Dec 18 05:06:25.872 INFO [stderr] | Dec 18 05:06:25.872 INFO [stderr] 239 | if (baseEach_percent_record.len() > 0) { Dec 18 05:06:25.872 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 18 05:06:25.872 INFO [stderr] Dec 18 05:06:25.880 INFO [stderr] warning: unused import: `std::io::prelude` Dec 18 05:06:25.880 INFO [stderr] --> src/main.rs:22:5 Dec 18 05:06:25.880 INFO [stderr] | Dec 18 05:06:25.880 INFO [stderr] 22 | use std::io::prelude::*; Dec 18 05:06:25.880 INFO [stderr] | ^^^^^^^^^^^^^^^^ Dec 18 05:06:25.880 INFO [stderr] Dec 18 05:06:25.891 INFO [stderr] warning: unused variable: `consensus_base` Dec 18 05:06:25.891 INFO [stderr] --> src/main.rs:139:9 Dec 18 05:06:25.891 INFO [stderr] | Dec 18 05:06:25.891 INFO [stderr] 139 | let consensus_base:Vec = Vec::new(); Dec 18 05:06:25.891 INFO [stderr] | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Dec 18 05:06:25.891 INFO [stderr] | Dec 18 05:06:25.897 INFO [stderr] = note: #[warn(unused_variables)] on by default Dec 18 05:06:25.897 INFO [stderr] Dec 18 05:06:25.897 INFO [stderr] warning: unused variable: `consensus_source_reads` Dec 18 05:06:25.897 INFO [stderr] --> src/main.rs:144:13 Dec 18 05:06:25.897 INFO [stderr] | Dec 18 05:06:25.897 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 18 05:06:25.897 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Dec 18 05:06:25.897 INFO [stderr] Dec 18 05:06:25.898 INFO [stderr] warning: unused variable: `chrom` Dec 18 05:06:25.898 INFO [stderr] --> src/main.rs:283:121 Dec 18 05:06:25.898 INFO [stderr] | Dec 18 05:06:25.898 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 18 05:06:25.898 INFO [stderr] | ^^^^^ help: consider using `_chrom` instead Dec 18 05:06:25.898 INFO [stderr] Dec 18 05:06:25.898 INFO [stderr] warning: value assigned to `new_seq_b` is never read Dec 18 05:06:25.898 INFO [stderr] --> src/main.rs:370:21 Dec 18 05:06:25.898 INFO [stderr] | Dec 18 05:06:25.898 INFO [stderr] 370 | let mut new_seq_b:Vec = Vec::new(); Dec 18 05:06:25.898 INFO [stderr] | ^^^^^^^^^ Dec 18 05:06:25.898 INFO [stderr] | Dec 18 05:06:25.898 INFO [stderr] = note: #[warn(unused_assignments)] on by default Dec 18 05:06:25.898 INFO [stderr] Dec 18 05:06:25.916 INFO [stderr] warning: variable does not need to be mutable Dec 18 05:06:25.916 INFO [stderr] --> src/main.rs:74:9 Dec 18 05:06:25.916 INFO [stderr] | Dec 18 05:06:25.916 INFO [stderr] 74 | let mut pair; Dec 18 05:06:25.916 INFO [stderr] | ----^^^^ Dec 18 05:06:25.916 INFO [stderr] | | Dec 18 05:06:25.916 INFO [stderr] | help: remove this `mut` Dec 18 05:06:25.916 INFO [stderr] | Dec 18 05:06:25.916 INFO [stderr] = note: #[warn(unused_mut)] on by default Dec 18 05:06:25.916 INFO [stderr] Dec 18 05:06:25.916 INFO [stderr] warning: variable does not need to be mutable Dec 18 05:06:25.916 INFO [stderr] --> src/main.rs:75:9 Dec 18 05:06:25.916 INFO [stderr] | Dec 18 05:06:25.916 INFO [stderr] 75 | let mut strand; Dec 18 05:06:25.916 INFO [stderr] | ----^^^^^^ Dec 18 05:06:25.916 INFO [stderr] | | Dec 18 05:06:25.916 INFO [stderr] | help: remove this `mut` Dec 18 05:06:25.916 INFO [stderr] Dec 18 05:06:25.916 INFO [stderr] warning: variable does not need to be mutable Dec 18 05:06:25.916 INFO [stderr] --> src/main.rs:76:9 Dec 18 05:06:25.917 INFO [stderr] | Dec 18 05:06:25.917 INFO [stderr] 76 | let mut aln_pos; Dec 18 05:06:25.917 INFO [stderr] | ----^^^^^^^ Dec 18 05:06:25.917 INFO [stderr] | | Dec 18 05:06:25.917 INFO [stderr] | help: remove this `mut` Dec 18 05:06:25.917 INFO [stderr] Dec 18 05:06:25.968 INFO [stderr] warning: variable does not need to be mutable Dec 18 05:06:25.968 INFO [stderr] --> src/main.rs:144:9 Dec 18 05:06:25.968 INFO [stderr] | Dec 18 05:06:25.969 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 18 05:06:25.969 INFO [stderr] | ----^^^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:25.969 INFO [stderr] | | Dec 18 05:06:25.969 INFO [stderr] | help: remove this `mut` Dec 18 05:06:25.969 INFO [stderr] Dec 18 05:06:25.969 INFO [stderr] warning: variable does not need to be mutable Dec 18 05:06:25.969 INFO [stderr] --> src/main.rs:151:9 Dec 18 05:06:25.970 INFO [stderr] | Dec 18 05:06:25.970 INFO [stderr] 151 | let mut top_cigar:&CigarStringView; Dec 18 05:06:25.970 INFO [stderr] | ----^^^^^^^^^ Dec 18 05:06:25.970 INFO [stderr] | | Dec 18 05:06:25.970 INFO [stderr] | help: remove this `mut` Dec 18 05:06:25.980 INFO [stderr] Dec 18 05:06:25.984 INFO [stderr] warning: variable does not need to be mutable Dec 18 05:06:25.984 INFO [stderr] --> src/main.rs:338:9 Dec 18 05:06:25.984 INFO [stderr] | Dec 18 05:06:25.984 INFO [stderr] 338 | let mut need_trim:bool; Dec 18 05:06:25.984 INFO [stderr] | ----^^^^^^^^^ Dec 18 05:06:25.984 INFO [stderr] | | Dec 18 05:06:25.984 INFO [stderr] | help: remove this `mut` Dec 18 05:06:25.985 INFO [stderr] Dec 18 05:06:25.988 INFO [stderr] warning: variable does not need to be mutable Dec 18 05:06:25.988 INFO [stderr] --> src/main.rs:355:9 Dec 18 05:06:25.988 INFO [stderr] | Dec 18 05:06:25.988 INFO [stderr] 355 | let mut chrom = 0; Dec 18 05:06:25.988 INFO [stderr] | ----^^^^^ Dec 18 05:06:25.988 INFO [stderr] | | Dec 18 05:06:25.988 INFO [stderr] | help: remove this `mut` Dec 18 05:06:25.988 INFO [stderr] Dec 18 05:06:26.004 INFO [stderr] warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Dec 18 05:06:26.004 INFO [stderr] --> src/main.rs:68:1 Dec 18 05:06:26.004 INFO [stderr] | Dec 18 05:06:26.005 INFO [stderr] 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Dec 18 05:06:26.005 INFO [stderr] 69 | | Dec 18 05:06:26.005 INFO [stderr] 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Dec 18 05:06:26.005 INFO [stderr] 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Dec 18 05:06:26.005 INFO [stderr] ... | Dec 18 05:06:26.005 INFO [stderr] 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Dec 18 05:06:26.005 INFO [stderr] 98 | | } Dec 18 05:06:26.005 INFO [stderr] | |_^ Dec 18 05:06:26.008 INFO [stderr] | Dec 18 05:06:26.008 INFO [stderr] = note: #[warn(non_snake_case)] on by default Dec 18 05:06:26.008 INFO [stderr] Dec 18 05:06:26.008 INFO [stderr] warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Dec 18 05:06:26.008 INFO [stderr] --> src/main.rs:147:9 Dec 18 05:06:26.008 INFO [stderr] | Dec 18 05:06:26.008 INFO [stderr] 147 | let mut baseEach_num_record = String::new(); Dec 18 05:06:26.008 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:26.008 INFO [stderr] Dec 18 05:06:26.008 INFO [stderr] warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Dec 18 05:06:26.008 INFO [stderr] --> src/main.rs:148:9 Dec 18 05:06:26.008 INFO [stderr] | Dec 18 05:06:26.008 INFO [stderr] 148 | let mut baseEach_percent_record = String::new(); Dec 18 05:06:26.008 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:26.008 INFO [stderr] Dec 18 05:06:26.008 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 18 05:06:26.008 INFO [stderr] --> src/main.rs:267:9 Dec 18 05:06:26.008 INFO [stderr] | Dec 18 05:06:26.008 INFO [stderr] 267 | o_buff.write(&member_record.2); Dec 18 05:06:26.008 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:26.008 INFO [stderr] | Dec 18 05:06:26.008 INFO [stderr] = note: #[warn(unused_must_use)] on by default Dec 18 05:06:26.009 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 18 05:06:26.009 INFO [stderr] Dec 18 05:06:26.009 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 18 05:06:26.009 INFO [stderr] --> src/main.rs:269:9 Dec 18 05:06:26.009 INFO [stderr] | Dec 18 05:06:26.009 INFO [stderr] 269 | o_buff.write(&member_record.0); Dec 18 05:06:26.009 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:26.009 INFO [stderr] | Dec 18 05:06:26.010 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 18 05:06:26.010 INFO [stderr] Dec 18 05:06:26.010 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 18 05:06:26.010 INFO [stderr] --> src/main.rs:272:9 Dec 18 05:06:26.010 INFO [stderr] | Dec 18 05:06:26.010 INFO [stderr] 272 | o_buff.write(&real_qual_temp); Dec 18 05:06:26.010 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:26.010 INFO [stderr] | Dec 18 05:06:26.010 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 18 05:06:26.010 INFO [stderr] Dec 18 05:06:26.010 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 18 05:06:26.010 INFO [stderr] --> src/main.rs:274:5 Dec 18 05:06:26.011 INFO [stderr] | Dec 18 05:06:26.011 INFO [stderr] 274 | o_buff.write(b"\n"); Dec 18 05:06:26.011 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:26.016 INFO [stderr] | Dec 18 05:06:26.016 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 18 05:06:26.016 INFO [stderr] Dec 18 05:06:26.016 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 18 05:06:26.016 INFO [stderr] --> src/main.rs:277:5 Dec 18 05:06:26.016 INFO [stderr] | Dec 18 05:06:26.016 INFO [stderr] 277 | o_buff.write(b"\n"); Dec 18 05:06:26.016 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:26.016 INFO [stderr] | Dec 18 05:06:26.016 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 18 05:06:26.016 INFO [stderr] Dec 18 05:06:26.016 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 18 05:06:26.016 INFO [stderr] --> src/main.rs:280:5 Dec 18 05:06:26.016 INFO [stderr] | Dec 18 05:06:26.016 INFO [stderr] 280 | o_buff.write(b"\n"); Dec 18 05:06:26.016 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:26.016 INFO [stderr] | Dec 18 05:06:26.016 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 18 05:06:26.016 INFO [stderr] Dec 18 05:06:26.016 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 18 05:06:26.016 INFO [stderr] --> src/main.rs:286:10 Dec 18 05:06:26.016 INFO [stderr] | Dec 18 05:06:26.016 INFO [stderr] 286 | for (key_dupGroup, pair_dup) in pd.iter() { Dec 18 05:06:26.016 INFO [stderr] | ^^^^^^^^^^^^ Dec 18 05:06:26.016 INFO [stderr] Dec 18 05:06:26.016 INFO [stderr] warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Dec 18 05:06:26.016 INFO [stderr] --> src/main.rs:357:9 Dec 18 05:06:26.016 INFO [stderr] | Dec 18 05:06:26.016 INFO [stderr] 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Dec 18 05:06:26.016 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:26.016 INFO [stderr] Dec 18 05:06:26.016 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 18 05:06:26.016 INFO [stderr] --> src/main.rs:387:17 Dec 18 05:06:26.016 INFO [stderr] | Dec 18 05:06:26.016 INFO [stderr] 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Dec 18 05:06:26.016 INFO [stderr] | ^^^^^^^^^^^^ Dec 18 05:06:26.016 INFO [stderr] Dec 18 05:06:26.056 INFO [stderr] warning: unused import: `std::io::prelude` Dec 18 05:06:26.056 INFO [stderr] --> src/main.rs:22:5 Dec 18 05:06:26.056 INFO [stderr] | Dec 18 05:06:26.056 INFO [stderr] 22 | use std::io::prelude::*; Dec 18 05:06:26.056 INFO [stderr] | ^^^^^^^^^^^^^^^^ Dec 18 05:06:26.056 INFO [stderr] Dec 18 05:06:26.080 INFO [stderr] warning: unused variable: `consensus_base` Dec 18 05:06:26.080 INFO [stderr] --> src/main.rs:139:9 Dec 18 05:06:26.080 INFO [stderr] | Dec 18 05:06:26.080 INFO [stderr] 139 | let consensus_base:Vec = Vec::new(); Dec 18 05:06:26.080 INFO [stderr] | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Dec 18 05:06:26.080 INFO [stderr] | Dec 18 05:06:26.080 INFO [stderr] = note: #[warn(unused_variables)] on by default Dec 18 05:06:26.080 INFO [stderr] Dec 18 05:06:26.080 INFO [stderr] warning: unused variable: `consensus_source_reads` Dec 18 05:06:26.080 INFO [stderr] --> src/main.rs:144:13 Dec 18 05:06:26.080 INFO [stderr] | Dec 18 05:06:26.080 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 18 05:06:26.080 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Dec 18 05:06:26.080 INFO [stderr] Dec 18 05:06:26.080 INFO [stderr] warning: unused variable: `chrom` Dec 18 05:06:26.080 INFO [stderr] --> src/main.rs:283:121 Dec 18 05:06:26.080 INFO [stderr] | Dec 18 05:06:26.080 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 18 05:06:26.080 INFO [stderr] | ^^^^^ help: consider using `_chrom` instead Dec 18 05:06:26.080 INFO [stderr] Dec 18 05:06:26.084 INFO [stderr] warning: value assigned to `new_seq_b` is never read Dec 18 05:06:26.084 INFO [stderr] --> src/main.rs:370:21 Dec 18 05:06:26.084 INFO [stderr] | Dec 18 05:06:26.084 INFO [stderr] 370 | let mut new_seq_b:Vec = Vec::new(); Dec 18 05:06:26.084 INFO [stderr] | ^^^^^^^^^ Dec 18 05:06:26.084 INFO [stderr] | Dec 18 05:06:26.084 INFO [stderr] = note: #[warn(unused_assignments)] on by default Dec 18 05:06:26.084 INFO [stderr] Dec 18 05:06:26.089 INFO [stderr] warning: variable does not need to be mutable Dec 18 05:06:26.089 INFO [stderr] --> src/main.rs:74:9 Dec 18 05:06:26.089 INFO [stderr] | Dec 18 05:06:26.089 INFO [stderr] 74 | let mut pair; Dec 18 05:06:26.089 INFO [stderr] | ----^^^^ Dec 18 05:06:26.089 INFO [stderr] | | Dec 18 05:06:26.089 INFO [stderr] | help: remove this `mut` Dec 18 05:06:26.089 INFO [stderr] | Dec 18 05:06:26.096 INFO [stderr] = note: #[warn(unused_mut)] on by default Dec 18 05:06:26.097 INFO [stderr] Dec 18 05:06:26.097 INFO [stderr] warning: variable does not need to be mutable Dec 18 05:06:26.097 INFO [stderr] --> src/main.rs:75:9 Dec 18 05:06:26.097 INFO [stderr] | Dec 18 05:06:26.097 INFO [stderr] 75 | let mut strand; Dec 18 05:06:26.097 INFO [stderr] | ----^^^^^^ Dec 18 05:06:26.097 INFO [stderr] | | Dec 18 05:06:26.097 INFO [stderr] | help: remove this `mut` Dec 18 05:06:26.097 INFO [stderr] Dec 18 05:06:26.097 INFO [stderr] warning: variable does not need to be mutable Dec 18 05:06:26.097 INFO [stderr] --> src/main.rs:76:9 Dec 18 05:06:26.097 INFO [stderr] | Dec 18 05:06:26.097 INFO [stderr] 76 | let mut aln_pos; Dec 18 05:06:26.097 INFO [stderr] | ----^^^^^^^ Dec 18 05:06:26.097 INFO [stderr] | | Dec 18 05:06:26.097 INFO [stderr] | help: remove this `mut` Dec 18 05:06:26.097 INFO [stderr] Dec 18 05:06:26.140 INFO [stderr] warning: variable does not need to be mutable Dec 18 05:06:26.140 INFO [stderr] --> src/main.rs:144:9 Dec 18 05:06:26.140 INFO [stderr] | Dec 18 05:06:26.140 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 18 05:06:26.140 INFO [stderr] | ----^^^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:26.140 INFO [stderr] | | Dec 18 05:06:26.140 INFO [stderr] | help: remove this `mut` Dec 18 05:06:26.140 INFO [stderr] Dec 18 05:06:26.141 INFO [stderr] warning: variable does not need to be mutable Dec 18 05:06:26.141 INFO [stderr] --> src/main.rs:151:9 Dec 18 05:06:26.141 INFO [stderr] | Dec 18 05:06:26.141 INFO [stderr] 151 | let mut top_cigar:&CigarStringView; Dec 18 05:06:26.141 INFO [stderr] | ----^^^^^^^^^ Dec 18 05:06:26.141 INFO [stderr] | | Dec 18 05:06:26.141 INFO [stderr] | help: remove this `mut` Dec 18 05:06:26.141 INFO [stderr] Dec 18 05:06:26.160 INFO [stderr] warning: variable does not need to be mutable Dec 18 05:06:26.160 INFO [stderr] --> src/main.rs:338:9 Dec 18 05:06:26.160 INFO [stderr] | Dec 18 05:06:26.160 INFO [stderr] 338 | let mut need_trim:bool; Dec 18 05:06:26.160 INFO [stderr] | ----^^^^^^^^^ Dec 18 05:06:26.160 INFO [stderr] | | Dec 18 05:06:26.160 INFO [stderr] | help: remove this `mut` Dec 18 05:06:26.160 INFO [stderr] Dec 18 05:06:26.160 INFO [stderr] warning: variable does not need to be mutable Dec 18 05:06:26.160 INFO [stderr] --> src/main.rs:355:9 Dec 18 05:06:26.160 INFO [stderr] | Dec 18 05:06:26.160 INFO [stderr] 355 | let mut chrom = 0; Dec 18 05:06:26.160 INFO [stderr] | ----^^^^^ Dec 18 05:06:26.160 INFO [stderr] | | Dec 18 05:06:26.160 INFO [stderr] | help: remove this `mut` Dec 18 05:06:26.160 INFO [stderr] Dec 18 05:06:26.172 INFO [stderr] warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Dec 18 05:06:26.172 INFO [stderr] --> src/main.rs:68:1 Dec 18 05:06:26.172 INFO [stderr] | Dec 18 05:06:26.172 INFO [stderr] 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Dec 18 05:06:26.172 INFO [stderr] 69 | | Dec 18 05:06:26.172 INFO [stderr] 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Dec 18 05:06:26.172 INFO [stderr] 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Dec 18 05:06:26.172 INFO [stderr] ... | Dec 18 05:06:26.172 INFO [stderr] 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Dec 18 05:06:26.172 INFO [stderr] 98 | | } Dec 18 05:06:26.172 INFO [stderr] | |_^ Dec 18 05:06:26.172 INFO [stderr] | Dec 18 05:06:26.172 INFO [stderr] = note: #[warn(non_snake_case)] on by default Dec 18 05:06:26.172 INFO [stderr] Dec 18 05:06:26.172 INFO [stderr] warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Dec 18 05:06:26.172 INFO [stderr] --> src/main.rs:147:9 Dec 18 05:06:26.172 INFO [stderr] | Dec 18 05:06:26.172 INFO [stderr] 147 | let mut baseEach_num_record = String::new(); Dec 18 05:06:26.172 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:26.172 INFO [stderr] Dec 18 05:06:26.172 INFO [stderr] warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Dec 18 05:06:26.172 INFO [stderr] --> src/main.rs:148:9 Dec 18 05:06:26.172 INFO [stderr] | Dec 18 05:06:26.172 INFO [stderr] 148 | let mut baseEach_percent_record = String::new(); Dec 18 05:06:26.172 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:26.172 INFO [stderr] Dec 18 05:06:26.176 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 18 05:06:26.176 INFO [stderr] --> src/main.rs:267:9 Dec 18 05:06:26.176 INFO [stderr] | Dec 18 05:06:26.176 INFO [stderr] 267 | o_buff.write(&member_record.2); Dec 18 05:06:26.176 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:26.176 INFO [stderr] | Dec 18 05:06:26.176 INFO [stderr] = note: #[warn(unused_must_use)] on by default Dec 18 05:06:26.176 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 18 05:06:26.176 INFO [stderr] Dec 18 05:06:26.176 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 18 05:06:26.176 INFO [stderr] --> src/main.rs:269:9 Dec 18 05:06:26.176 INFO [stderr] | Dec 18 05:06:26.176 INFO [stderr] 269 | o_buff.write(&member_record.0); Dec 18 05:06:26.176 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:26.176 INFO [stderr] | Dec 18 05:06:26.176 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 18 05:06:26.176 INFO [stderr] Dec 18 05:06:26.177 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 18 05:06:26.177 INFO [stderr] --> src/main.rs:272:9 Dec 18 05:06:26.177 INFO [stderr] | Dec 18 05:06:26.177 INFO [stderr] 272 | o_buff.write(&real_qual_temp); Dec 18 05:06:26.177 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:26.177 INFO [stderr] | Dec 18 05:06:26.177 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 18 05:06:26.177 INFO [stderr] Dec 18 05:06:26.177 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 18 05:06:26.177 INFO [stderr] --> src/main.rs:274:5 Dec 18 05:06:26.177 INFO [stderr] | Dec 18 05:06:26.177 INFO [stderr] 274 | o_buff.write(b"\n"); Dec 18 05:06:26.177 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:26.177 INFO [stderr] | Dec 18 05:06:26.177 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 18 05:06:26.177 INFO [stderr] Dec 18 05:06:26.177 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 18 05:06:26.177 INFO [stderr] --> src/main.rs:277:5 Dec 18 05:06:26.177 INFO [stderr] | Dec 18 05:06:26.177 INFO [stderr] 277 | o_buff.write(b"\n"); Dec 18 05:06:26.177 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:26.177 INFO [stderr] | Dec 18 05:06:26.177 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 18 05:06:26.177 INFO [stderr] Dec 18 05:06:26.177 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 18 05:06:26.177 INFO [stderr] --> src/main.rs:280:5 Dec 18 05:06:26.177 INFO [stderr] | Dec 18 05:06:26.177 INFO [stderr] 280 | o_buff.write(b"\n"); Dec 18 05:06:26.177 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:26.177 INFO [stderr] | Dec 18 05:06:26.177 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 18 05:06:26.177 INFO [stderr] Dec 18 05:06:26.177 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 18 05:06:26.177 INFO [stderr] --> src/main.rs:286:10 Dec 18 05:06:26.177 INFO [stderr] | Dec 18 05:06:26.177 INFO [stderr] 286 | for (key_dupGroup, pair_dup) in pd.iter() { Dec 18 05:06:26.177 INFO [stderr] | ^^^^^^^^^^^^ Dec 18 05:06:26.177 INFO [stderr] Dec 18 05:06:26.177 INFO [stderr] warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Dec 18 05:06:26.177 INFO [stderr] --> src/main.rs:357:9 Dec 18 05:06:26.177 INFO [stderr] | Dec 18 05:06:26.177 INFO [stderr] 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Dec 18 05:06:26.177 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^ Dec 18 05:06:26.177 INFO [stderr] Dec 18 05:06:26.177 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 18 05:06:26.177 INFO [stderr] --> src/main.rs:387:17 Dec 18 05:06:26.177 INFO [stderr] | Dec 18 05:06:26.177 INFO [stderr] 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Dec 18 05:06:26.177 INFO [stderr] | ^^^^^^^^^^^^ Dec 18 05:06:26.177 INFO [stderr] Dec 18 05:06:26.220 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 32.88s Dec 18 05:06:26.931 INFO running `"docker" "inspect" "f778842c924dff01f89562012fbf30bdd45d7fa4d8122fe74149ee00259c6b58"` Dec 18 05:06:27.206 INFO running `"docker" "rm" "-f" "f778842c924dff01f89562012fbf30bdd45d7fa4d8122fe74149ee00259c6b58"` Dec 18 05:06:27.520 INFO [stdout] f778842c924dff01f89562012fbf30bdd45d7fa4d8122fe74149ee00259c6b58