Nov 28 10:38:35.725 INFO checking TuBieJun/consensus against master#0b9f19dff1347e29bf4362ab5a8fab84b43023b5 for pr-56074 Nov 28 10:38:35.725 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56074/worker-6/master#0b9f19dff1347e29bf4362ab5a8fab84b43023b5:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-6/pr-56074/master#0b9f19dff1347e29bf4362ab5a8fab84b43023b5:/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 +0b9f19dff1347e29bf4362ab5a8fab84b43023b5-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"` Nov 28 10:38:36.273 INFO [stdout] da8f58bce1641486fbe85c9be2073d206db1cbdffe9624d7767e6737037acbea Nov 28 10:38:36.281 INFO running `"docker" "start" "-a" "da8f58bce1641486fbe85c9be2073d206db1cbdffe9624d7767e6737037acbea"` Nov 28 10:38:38.600 INFO [stderr] usermod: no changes Nov 28 10:38:38.808 INFO [stderr] Checking ieee754 v0.2.2 Nov 28 10:38:38.808 INFO [stderr] Compiling fs-utils v1.0.0 Nov 28 10:38:38.808 INFO [stderr] Checking itertools v0.6.5 Nov 28 10:38:40.706 INFO [stderr] Compiling rust-htslib v0.15.0 Nov 28 10:39:09.208 INFO [stderr] Checking consensus v0.1.0 (/source) Nov 28 10:39:11.465 INFO [stderr] warning: unused import: `std::env` Nov 28 10:39:11.465 INFO [stderr] --> src/main.rs:12:5 Nov 28 10:39:11.465 INFO [stderr] | Nov 28 10:39:11.465 INFO [stderr] 12 | use std::env; Nov 28 10:39:11.465 INFO [stderr] | ^^^^^^^^ Nov 28 10:39:11.465 INFO [stderr] | Nov 28 10:39:11.465 INFO [stderr] = note: #[warn(unused_imports)] on by default Nov 28 10:39:11.465 INFO [stderr] Nov 28 10:39:11.465 INFO [stderr] warning: unused import: `rust_htslib::prelude::*` Nov 28 10:39:11.465 INFO [stderr] --> src/main.rs:16:5 Nov 28 10:39:11.465 INFO [stderr] | Nov 28 10:39:11.465 INFO [stderr] 16 | use rust_htslib::prelude::*; Nov 28 10:39:11.465 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:11.465 INFO [stderr] Nov 28 10:39:11.465 INFO [stderr] warning: unused import: `std::io` Nov 28 10:39:11.465 INFO [stderr] --> src/main.rs:21:5 Nov 28 10:39:11.465 INFO [stderr] | Nov 28 10:39:11.465 INFO [stderr] 21 | use std::io; Nov 28 10:39:11.465 INFO [stderr] | ^^^^^^^ Nov 28 10:39:11.465 INFO [stderr] Nov 28 10:39:11.465 INFO [stderr] warning: unused import: `PathBuf` Nov 28 10:39:11.465 INFO [stderr] --> src/main.rs:25:23 Nov 28 10:39:11.465 INFO [stderr] | Nov 28 10:39:11.465 INFO [stderr] 25 | use std::path::{Path, PathBuf}; Nov 28 10:39:11.465 INFO [stderr] | ^^^^^^^ Nov 28 10:39:11.465 INFO [stderr] Nov 28 10:39:11.465 INFO [stderr] warning: unused import: `SubCommand` Nov 28 10:39:11.465 INFO [stderr] --> src/main.rs:26:22 Nov 28 10:39:11.465 INFO [stderr] | Nov 28 10:39:11.465 INFO [stderr] 26 | use clap::{Arg, App, SubCommand}; Nov 28 10:39:11.465 INFO [stderr] | ^^^^^^^^^^ Nov 28 10:39:11.465 INFO [stderr] Nov 28 10:39:11.465 INFO [stderr] warning: unnecessary parentheses around `if` condition Nov 28 10:39:11.465 INFO [stderr] --> src/main.rs:218:20 Nov 28 10:39:11.465 INFO [stderr] | Nov 28 10:39:11.466 INFO [stderr] 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Nov 28 10:39:11.466 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Nov 28 10:39:11.466 INFO [stderr] | Nov 28 10:39:11.466 INFO [stderr] = note: #[warn(unused_parens)] on by default Nov 28 10:39:11.466 INFO [stderr] Nov 28 10:39:11.466 INFO [stderr] warning: unnecessary parentheses around `if` condition Nov 28 10:39:11.466 INFO [stderr] --> src/main.rs:239:16 Nov 28 10:39:11.466 INFO [stderr] | Nov 28 10:39:11.466 INFO [stderr] 239 | if (baseEach_percent_record.len() > 0) { Nov 28 10:39:11.466 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Nov 28 10:39:11.466 INFO [stderr] Nov 28 10:39:11.740 INFO [stderr] warning: unused import: `std::io::prelude` Nov 28 10:39:11.741 INFO [stderr] --> src/main.rs:22:5 Nov 28 10:39:11.741 INFO [stderr] | Nov 28 10:39:11.742 INFO [stderr] 22 | use std::io::prelude::*; Nov 28 10:39:11.742 INFO [stderr] | ^^^^^^^^^^^^^^^^ Nov 28 10:39:11.742 INFO [stderr] Nov 28 10:39:11.748 INFO [stderr] warning: unused variable: `consensus_base` Nov 28 10:39:11.748 INFO [stderr] --> src/main.rs:139:9 Nov 28 10:39:11.748 INFO [stderr] | Nov 28 10:39:11.748 INFO [stderr] 139 | let consensus_base:Vec = Vec::new(); Nov 28 10:39:11.748 INFO [stderr] | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Nov 28 10:39:11.748 INFO [stderr] | Nov 28 10:39:11.748 INFO [stderr] = note: #[warn(unused_variables)] on by default Nov 28 10:39:11.748 INFO [stderr] Nov 28 10:39:11.748 INFO [stderr] warning: unused variable: `consensus_source_reads` Nov 28 10:39:11.748 INFO [stderr] --> src/main.rs:144:13 Nov 28 10:39:11.748 INFO [stderr] | Nov 28 10:39:11.748 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Nov 28 10:39:11.748 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Nov 28 10:39:11.748 INFO [stderr] Nov 28 10:39:11.748 INFO [stderr] warning: unused variable: `chrom` Nov 28 10:39:11.748 INFO [stderr] --> src/main.rs:283:121 Nov 28 10:39:11.748 INFO [stderr] | Nov 28 10:39:11.748 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) { Nov 28 10:39:11.748 INFO [stderr] | ^^^^^ help: consider using `_chrom` instead Nov 28 10:39:11.749 INFO [stderr] Nov 28 10:39:11.749 INFO [stderr] warning: value assigned to `new_seq_b` is never read Nov 28 10:39:11.749 INFO [stderr] --> src/main.rs:370:21 Nov 28 10:39:11.749 INFO [stderr] | Nov 28 10:39:11.749 INFO [stderr] 370 | let mut new_seq_b:Vec = Vec::new(); Nov 28 10:39:11.749 INFO [stderr] | ^^^^^^^^^ Nov 28 10:39:11.749 INFO [stderr] | Nov 28 10:39:11.749 INFO [stderr] = note: #[warn(unused_assignments)] on by default Nov 28 10:39:11.749 INFO [stderr] Nov 28 10:39:11.768 INFO [stderr] warning: variable does not need to be mutable Nov 28 10:39:11.768 INFO [stderr] --> src/main.rs:74:9 Nov 28 10:39:11.768 INFO [stderr] | Nov 28 10:39:11.768 INFO [stderr] 74 | let mut pair; Nov 28 10:39:11.768 INFO [stderr] | ----^^^^ Nov 28 10:39:11.768 INFO [stderr] | | Nov 28 10:39:11.768 INFO [stderr] | help: remove this `mut` Nov 28 10:39:11.768 INFO [stderr] | Nov 28 10:39:11.768 INFO [stderr] = note: #[warn(unused_mut)] on by default Nov 28 10:39:11.768 INFO [stderr] Nov 28 10:39:11.768 INFO [stderr] warning: variable does not need to be mutable Nov 28 10:39:11.768 INFO [stderr] --> src/main.rs:75:9 Nov 28 10:39:11.768 INFO [stderr] | Nov 28 10:39:11.768 INFO [stderr] 75 | let mut strand; Nov 28 10:39:11.768 INFO [stderr] | ----^^^^^^ Nov 28 10:39:11.768 INFO [stderr] | | Nov 28 10:39:11.768 INFO [stderr] | help: remove this `mut` Nov 28 10:39:11.768 INFO [stderr] Nov 28 10:39:11.768 INFO [stderr] warning: variable does not need to be mutable Nov 28 10:39:11.768 INFO [stderr] --> src/main.rs:76:9 Nov 28 10:39:11.769 INFO [stderr] | Nov 28 10:39:11.769 INFO [stderr] 76 | let mut aln_pos; Nov 28 10:39:11.769 INFO [stderr] | ----^^^^^^^ Nov 28 10:39:11.769 INFO [stderr] | | Nov 28 10:39:11.769 INFO [stderr] | help: remove this `mut` Nov 28 10:39:11.769 INFO [stderr] Nov 28 10:39:11.781 INFO [stderr] warning: unused import: `std::env` Nov 28 10:39:11.781 INFO [stderr] --> src/main.rs:12:5 Nov 28 10:39:11.781 INFO [stderr] | Nov 28 10:39:11.781 INFO [stderr] 12 | use std::env; Nov 28 10:39:11.781 INFO [stderr] | ^^^^^^^^ Nov 28 10:39:11.781 INFO [stderr] | Nov 28 10:39:11.781 INFO [stderr] = note: #[warn(unused_imports)] on by default Nov 28 10:39:11.781 INFO [stderr] Nov 28 10:39:11.781 INFO [stderr] warning: unused import: `rust_htslib::prelude::*` Nov 28 10:39:11.781 INFO [stderr] --> src/main.rs:16:5 Nov 28 10:39:11.781 INFO [stderr] | Nov 28 10:39:11.781 INFO [stderr] 16 | use rust_htslib::prelude::*; Nov 28 10:39:11.781 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:11.781 INFO [stderr] Nov 28 10:39:11.781 INFO [stderr] warning: unused import: `std::io` Nov 28 10:39:11.781 INFO [stderr] --> src/main.rs:21:5 Nov 28 10:39:11.781 INFO [stderr] | Nov 28 10:39:11.781 INFO [stderr] 21 | use std::io; Nov 28 10:39:11.781 INFO [stderr] | ^^^^^^^ Nov 28 10:39:11.781 INFO [stderr] Nov 28 10:39:11.781 INFO [stderr] warning: unused import: `PathBuf` Nov 28 10:39:11.781 INFO [stderr] --> src/main.rs:25:23 Nov 28 10:39:11.781 INFO [stderr] | Nov 28 10:39:11.781 INFO [stderr] 25 | use std::path::{Path, PathBuf}; Nov 28 10:39:11.781 INFO [stderr] | ^^^^^^^ Nov 28 10:39:11.781 INFO [stderr] Nov 28 10:39:11.781 INFO [stderr] warning: unused import: `SubCommand` Nov 28 10:39:11.781 INFO [stderr] --> src/main.rs:26:22 Nov 28 10:39:11.781 INFO [stderr] | Nov 28 10:39:11.781 INFO [stderr] 26 | use clap::{Arg, App, SubCommand}; Nov 28 10:39:11.781 INFO [stderr] | ^^^^^^^^^^ Nov 28 10:39:11.781 INFO [stderr] Nov 28 10:39:11.781 INFO [stderr] warning: unnecessary parentheses around `if` condition Nov 28 10:39:11.781 INFO [stderr] --> src/main.rs:218:20 Nov 28 10:39:11.781 INFO [stderr] | Nov 28 10:39:11.781 INFO [stderr] 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Nov 28 10:39:11.781 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Nov 28 10:39:11.781 INFO [stderr] | Nov 28 10:39:11.781 INFO [stderr] = note: #[warn(unused_parens)] on by default Nov 28 10:39:11.781 INFO [stderr] Nov 28 10:39:11.781 INFO [stderr] warning: unnecessary parentheses around `if` condition Nov 28 10:39:11.781 INFO [stderr] --> src/main.rs:239:16 Nov 28 10:39:11.781 INFO [stderr] | Nov 28 10:39:11.781 INFO [stderr] 239 | if (baseEach_percent_record.len() > 0) { Nov 28 10:39:11.781 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Nov 28 10:39:11.781 INFO [stderr] Nov 28 10:39:11.852 INFO [stderr] warning: variable does not need to be mutable Nov 28 10:39:11.852 INFO [stderr] --> src/main.rs:144:9 Nov 28 10:39:11.852 INFO [stderr] | Nov 28 10:39:11.852 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Nov 28 10:39:11.852 INFO [stderr] | ----^^^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:11.852 INFO [stderr] | | Nov 28 10:39:11.852 INFO [stderr] | help: remove this `mut` Nov 28 10:39:11.852 INFO [stderr] Nov 28 10:39:11.852 INFO [stderr] warning: variable does not need to be mutable Nov 28 10:39:11.852 INFO [stderr] --> src/main.rs:151:9 Nov 28 10:39:11.852 INFO [stderr] | Nov 28 10:39:11.852 INFO [stderr] 151 | let mut top_cigar:&CigarStringView; Nov 28 10:39:11.852 INFO [stderr] | ----^^^^^^^^^ Nov 28 10:39:11.852 INFO [stderr] | | Nov 28 10:39:11.852 INFO [stderr] | help: remove this `mut` Nov 28 10:39:11.852 INFO [stderr] Nov 28 10:39:11.884 INFO [stderr] warning: variable does not need to be mutable Nov 28 10:39:11.884 INFO [stderr] --> src/main.rs:338:9 Nov 28 10:39:11.884 INFO [stderr] | Nov 28 10:39:11.884 INFO [stderr] 338 | let mut need_trim:bool; Nov 28 10:39:11.884 INFO [stderr] | ----^^^^^^^^^ Nov 28 10:39:11.884 INFO [stderr] | | Nov 28 10:39:11.884 INFO [stderr] | help: remove this `mut` Nov 28 10:39:11.884 INFO [stderr] Nov 28 10:39:11.884 INFO [stderr] warning: variable does not need to be mutable Nov 28 10:39:11.884 INFO [stderr] --> src/main.rs:355:9 Nov 28 10:39:11.884 INFO [stderr] | Nov 28 10:39:11.884 INFO [stderr] 355 | let mut chrom = 0; Nov 28 10:39:11.884 INFO [stderr] | ----^^^^^ Nov 28 10:39:11.884 INFO [stderr] | | Nov 28 10:39:11.884 INFO [stderr] | help: remove this `mut` Nov 28 10:39:11.884 INFO [stderr] Nov 28 10:39:11.897 INFO [stderr] warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Nov 28 10:39:11.897 INFO [stderr] --> src/main.rs:68:1 Nov 28 10:39:11.897 INFO [stderr] | Nov 28 10:39:11.897 INFO [stderr] 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Nov 28 10:39:11.897 INFO [stderr] 69 | | Nov 28 10:39:11.897 INFO [stderr] 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Nov 28 10:39:11.897 INFO [stderr] 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Nov 28 10:39:11.897 INFO [stderr] ... | Nov 28 10:39:11.897 INFO [stderr] 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Nov 28 10:39:11.897 INFO [stderr] 98 | | } Nov 28 10:39:11.897 INFO [stderr] | |_^ Nov 28 10:39:11.897 INFO [stderr] | Nov 28 10:39:11.897 INFO [stderr] = note: #[warn(non_snake_case)] on by default Nov 28 10:39:11.897 INFO [stderr] Nov 28 10:39:11.897 INFO [stderr] warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Nov 28 10:39:11.897 INFO [stderr] --> src/main.rs:147:9 Nov 28 10:39:11.897 INFO [stderr] | Nov 28 10:39:11.897 INFO [stderr] 147 | let mut baseEach_num_record = String::new(); Nov 28 10:39:11.897 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:11.897 INFO [stderr] Nov 28 10:39:11.897 INFO [stderr] warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Nov 28 10:39:11.897 INFO [stderr] --> src/main.rs:148:9 Nov 28 10:39:11.897 INFO [stderr] | Nov 28 10:39:11.897 INFO [stderr] 148 | let mut baseEach_percent_record = String::new(); Nov 28 10:39:11.897 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:11.897 INFO [stderr] Nov 28 10:39:11.897 INFO [stderr] warning: unused `std::result::Result` that must be used Nov 28 10:39:11.897 INFO [stderr] --> src/main.rs:267:9 Nov 28 10:39:11.897 INFO [stderr] | Nov 28 10:39:11.897 INFO [stderr] 267 | o_buff.write(&member_record.2); Nov 28 10:39:11.897 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:11.897 INFO [stderr] | Nov 28 10:39:11.897 INFO [stderr] = note: #[warn(unused_must_use)] on by default Nov 28 10:39:11.897 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Nov 28 10:39:11.897 INFO [stderr] Nov 28 10:39:11.897 INFO [stderr] warning: unused `std::result::Result` that must be used Nov 28 10:39:11.897 INFO [stderr] --> src/main.rs:269:9 Nov 28 10:39:11.897 INFO [stderr] | Nov 28 10:39:11.897 INFO [stderr] 269 | o_buff.write(&member_record.0); Nov 28 10:39:11.897 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:11.897 INFO [stderr] | Nov 28 10:39:11.897 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Nov 28 10:39:11.897 INFO [stderr] Nov 28 10:39:11.897 INFO [stderr] warning: unused `std::result::Result` that must be used Nov 28 10:39:11.897 INFO [stderr] --> src/main.rs:272:9 Nov 28 10:39:11.897 INFO [stderr] | Nov 28 10:39:11.897 INFO [stderr] 272 | o_buff.write(&real_qual_temp); Nov 28 10:39:11.897 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:11.897 INFO [stderr] | Nov 28 10:39:11.897 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Nov 28 10:39:11.897 INFO [stderr] Nov 28 10:39:11.897 INFO [stderr] warning: unused `std::result::Result` that must be used Nov 28 10:39:11.897 INFO [stderr] --> src/main.rs:274:5 Nov 28 10:39:11.897 INFO [stderr] | Nov 28 10:39:11.897 INFO [stderr] 274 | o_buff.write(b"\n"); Nov 28 10:39:11.897 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:11.897 INFO [stderr] | Nov 28 10:39:11.897 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Nov 28 10:39:11.897 INFO [stderr] Nov 28 10:39:11.897 INFO [stderr] warning: unused `std::result::Result` that must be used Nov 28 10:39:11.898 INFO [stderr] --> src/main.rs:277:5 Nov 28 10:39:11.898 INFO [stderr] | Nov 28 10:39:11.898 INFO [stderr] 277 | o_buff.write(b"\n"); Nov 28 10:39:11.898 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:11.898 INFO [stderr] | Nov 28 10:39:11.898 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Nov 28 10:39:11.898 INFO [stderr] Nov 28 10:39:11.898 INFO [stderr] warning: unused `std::result::Result` that must be used Nov 28 10:39:11.898 INFO [stderr] --> src/main.rs:280:5 Nov 28 10:39:11.898 INFO [stderr] | Nov 28 10:39:11.898 INFO [stderr] 280 | o_buff.write(b"\n"); Nov 28 10:39:11.898 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:11.898 INFO [stderr] | Nov 28 10:39:11.898 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Nov 28 10:39:11.898 INFO [stderr] Nov 28 10:39:11.898 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Nov 28 10:39:11.898 INFO [stderr] --> src/main.rs:286:10 Nov 28 10:39:11.898 INFO [stderr] | Nov 28 10:39:11.898 INFO [stderr] 286 | for (key_dupGroup, pair_dup) in pd.iter() { Nov 28 10:39:11.898 INFO [stderr] | ^^^^^^^^^^^^ Nov 28 10:39:11.898 INFO [stderr] Nov 28 10:39:11.898 INFO [stderr] warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Nov 28 10:39:11.898 INFO [stderr] --> src/main.rs:357:9 Nov 28 10:39:11.898 INFO [stderr] | Nov 28 10:39:11.898 INFO [stderr] 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Nov 28 10:39:11.898 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:11.898 INFO [stderr] Nov 28 10:39:11.898 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Nov 28 10:39:11.898 INFO [stderr] --> src/main.rs:387:17 Nov 28 10:39:11.898 INFO [stderr] | Nov 28 10:39:11.898 INFO [stderr] 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Nov 28 10:39:11.898 INFO [stderr] | ^^^^^^^^^^^^ Nov 28 10:39:11.898 INFO [stderr] Nov 28 10:39:12.012 INFO [stderr] warning: unused import: `std::io::prelude` Nov 28 10:39:12.012 INFO [stderr] --> src/main.rs:22:5 Nov 28 10:39:12.012 INFO [stderr] | Nov 28 10:39:12.012 INFO [stderr] 22 | use std::io::prelude::*; Nov 28 10:39:12.012 INFO [stderr] | ^^^^^^^^^^^^^^^^ Nov 28 10:39:12.012 INFO [stderr] Nov 28 10:39:12.024 INFO [stderr] warning: unused variable: `consensus_base` Nov 28 10:39:12.024 INFO [stderr] --> src/main.rs:139:9 Nov 28 10:39:12.024 INFO [stderr] | Nov 28 10:39:12.024 INFO [stderr] 139 | let consensus_base:Vec = Vec::new(); Nov 28 10:39:12.024 INFO [stderr] | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Nov 28 10:39:12.024 INFO [stderr] | Nov 28 10:39:12.024 INFO [stderr] = note: #[warn(unused_variables)] on by default Nov 28 10:39:12.024 INFO [stderr] Nov 28 10:39:12.024 INFO [stderr] warning: unused variable: `consensus_source_reads` Nov 28 10:39:12.024 INFO [stderr] --> src/main.rs:144:13 Nov 28 10:39:12.024 INFO [stderr] | Nov 28 10:39:12.024 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Nov 28 10:39:12.024 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Nov 28 10:39:12.024 INFO [stderr] Nov 28 10:39:12.024 INFO [stderr] warning: unused variable: `chrom` Nov 28 10:39:12.024 INFO [stderr] --> src/main.rs:283:121 Nov 28 10:39:12.024 INFO [stderr] | Nov 28 10:39:12.025 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) { Nov 28 10:39:12.025 INFO [stderr] | ^^^^^ help: consider using `_chrom` instead Nov 28 10:39:12.025 INFO [stderr] Nov 28 10:39:12.025 INFO [stderr] warning: value assigned to `new_seq_b` is never read Nov 28 10:39:12.025 INFO [stderr] --> src/main.rs:370:21 Nov 28 10:39:12.025 INFO [stderr] | Nov 28 10:39:12.025 INFO [stderr] 370 | let mut new_seq_b:Vec = Vec::new(); Nov 28 10:39:12.025 INFO [stderr] | ^^^^^^^^^ Nov 28 10:39:12.025 INFO [stderr] | Nov 28 10:39:12.025 INFO [stderr] = note: #[warn(unused_assignments)] on by default Nov 28 10:39:12.025 INFO [stderr] Nov 28 10:39:12.036 INFO [stderr] warning: variable does not need to be mutable Nov 28 10:39:12.036 INFO [stderr] --> src/main.rs:74:9 Nov 28 10:39:12.036 INFO [stderr] | Nov 28 10:39:12.036 INFO [stderr] 74 | let mut pair; Nov 28 10:39:12.036 INFO [stderr] | ----^^^^ Nov 28 10:39:12.036 INFO [stderr] | | Nov 28 10:39:12.036 INFO [stderr] | help: remove this `mut` Nov 28 10:39:12.036 INFO [stderr] | Nov 28 10:39:12.036 INFO [stderr] = note: #[warn(unused_mut)] on by default Nov 28 10:39:12.036 INFO [stderr] Nov 28 10:39:12.036 INFO [stderr] warning: variable does not need to be mutable Nov 28 10:39:12.036 INFO [stderr] --> src/main.rs:75:9 Nov 28 10:39:12.036 INFO [stderr] | Nov 28 10:39:12.036 INFO [stderr] 75 | let mut strand; Nov 28 10:39:12.036 INFO [stderr] | ----^^^^^^ Nov 28 10:39:12.036 INFO [stderr] | | Nov 28 10:39:12.036 INFO [stderr] | help: remove this `mut` Nov 28 10:39:12.036 INFO [stderr] Nov 28 10:39:12.036 INFO [stderr] warning: variable does not need to be mutable Nov 28 10:39:12.037 INFO [stderr] --> src/main.rs:76:9 Nov 28 10:39:12.037 INFO [stderr] | Nov 28 10:39:12.037 INFO [stderr] 76 | let mut aln_pos; Nov 28 10:39:12.037 INFO [stderr] | ----^^^^^^^ Nov 28 10:39:12.037 INFO [stderr] | | Nov 28 10:39:12.037 INFO [stderr] | help: remove this `mut` Nov 28 10:39:12.037 INFO [stderr] Nov 28 10:39:12.076 INFO [stderr] warning: variable does not need to be mutable Nov 28 10:39:12.076 INFO [stderr] --> src/main.rs:144:9 Nov 28 10:39:12.076 INFO [stderr] | Nov 28 10:39:12.076 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Nov 28 10:39:12.076 INFO [stderr] | ----^^^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:12.076 INFO [stderr] | | Nov 28 10:39:12.076 INFO [stderr] | help: remove this `mut` Nov 28 10:39:12.076 INFO [stderr] Nov 28 10:39:12.076 INFO [stderr] warning: variable does not need to be mutable Nov 28 10:39:12.076 INFO [stderr] --> src/main.rs:151:9 Nov 28 10:39:12.076 INFO [stderr] | Nov 28 10:39:12.076 INFO [stderr] 151 | let mut top_cigar:&CigarStringView; Nov 28 10:39:12.076 INFO [stderr] | ----^^^^^^^^^ Nov 28 10:39:12.076 INFO [stderr] | | Nov 28 10:39:12.076 INFO [stderr] | help: remove this `mut` Nov 28 10:39:12.076 INFO [stderr] Nov 28 10:39:12.088 INFO [stderr] warning: variable does not need to be mutable Nov 28 10:39:12.088 INFO [stderr] --> src/main.rs:338:9 Nov 28 10:39:12.088 INFO [stderr] | Nov 28 10:39:12.088 INFO [stderr] 338 | let mut need_trim:bool; Nov 28 10:39:12.088 INFO [stderr] | ----^^^^^^^^^ Nov 28 10:39:12.088 INFO [stderr] | | Nov 28 10:39:12.088 INFO [stderr] | help: remove this `mut` Nov 28 10:39:12.088 INFO [stderr] Nov 28 10:39:12.088 INFO [stderr] warning: variable does not need to be mutable Nov 28 10:39:12.088 INFO [stderr] --> src/main.rs:355:9 Nov 28 10:39:12.088 INFO [stderr] | Nov 28 10:39:12.088 INFO [stderr] 355 | let mut chrom = 0; Nov 28 10:39:12.088 INFO [stderr] | ----^^^^^ Nov 28 10:39:12.088 INFO [stderr] | | Nov 28 10:39:12.088 INFO [stderr] | help: remove this `mut` Nov 28 10:39:12.088 INFO [stderr] Nov 28 10:39:12.105 INFO [stderr] warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Nov 28 10:39:12.105 INFO [stderr] --> src/main.rs:68:1 Nov 28 10:39:12.105 INFO [stderr] | Nov 28 10:39:12.105 INFO [stderr] 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Nov 28 10:39:12.105 INFO [stderr] 69 | | Nov 28 10:39:12.105 INFO [stderr] 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Nov 28 10:39:12.105 INFO [stderr] 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Nov 28 10:39:12.105 INFO [stderr] ... | Nov 28 10:39:12.105 INFO [stderr] 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Nov 28 10:39:12.105 INFO [stderr] 98 | | } Nov 28 10:39:12.105 INFO [stderr] | |_^ Nov 28 10:39:12.105 INFO [stderr] | Nov 28 10:39:12.105 INFO [stderr] = note: #[warn(non_snake_case)] on by default Nov 28 10:39:12.105 INFO [stderr] Nov 28 10:39:12.105 INFO [stderr] warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Nov 28 10:39:12.105 INFO [stderr] --> src/main.rs:147:9 Nov 28 10:39:12.105 INFO [stderr] | Nov 28 10:39:12.105 INFO [stderr] 147 | let mut baseEach_num_record = String::new(); Nov 28 10:39:12.105 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:12.105 INFO [stderr] Nov 28 10:39:12.105 INFO [stderr] warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Nov 28 10:39:12.105 INFO [stderr] --> src/main.rs:148:9 Nov 28 10:39:12.105 INFO [stderr] | Nov 28 10:39:12.105 INFO [stderr] 148 | let mut baseEach_percent_record = String::new(); Nov 28 10:39:12.105 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:12.105 INFO [stderr] Nov 28 10:39:12.105 INFO [stderr] warning: unused `std::result::Result` that must be used Nov 28 10:39:12.105 INFO [stderr] --> src/main.rs:267:9 Nov 28 10:39:12.105 INFO [stderr] | Nov 28 10:39:12.105 INFO [stderr] 267 | o_buff.write(&member_record.2); Nov 28 10:39:12.105 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:12.105 INFO [stderr] | Nov 28 10:39:12.105 INFO [stderr] = note: #[warn(unused_must_use)] on by default Nov 28 10:39:12.105 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Nov 28 10:39:12.105 INFO [stderr] Nov 28 10:39:12.105 INFO [stderr] warning: unused `std::result::Result` that must be used Nov 28 10:39:12.105 INFO [stderr] --> src/main.rs:269:9 Nov 28 10:39:12.105 INFO [stderr] | Nov 28 10:39:12.105 INFO [stderr] 269 | o_buff.write(&member_record.0); Nov 28 10:39:12.105 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:12.105 INFO [stderr] | Nov 28 10:39:12.105 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Nov 28 10:39:12.105 INFO [stderr] Nov 28 10:39:12.105 INFO [stderr] warning: unused `std::result::Result` that must be used Nov 28 10:39:12.105 INFO [stderr] --> src/main.rs:272:9 Nov 28 10:39:12.105 INFO [stderr] | Nov 28 10:39:12.105 INFO [stderr] 272 | o_buff.write(&real_qual_temp); Nov 28 10:39:12.105 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:12.105 INFO [stderr] | Nov 28 10:39:12.105 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Nov 28 10:39:12.105 INFO [stderr] Nov 28 10:39:12.105 INFO [stderr] warning: unused `std::result::Result` that must be used Nov 28 10:39:12.105 INFO [stderr] --> src/main.rs:274:5 Nov 28 10:39:12.105 INFO [stderr] | Nov 28 10:39:12.105 INFO [stderr] 274 | o_buff.write(b"\n"); Nov 28 10:39:12.105 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:12.105 INFO [stderr] | Nov 28 10:39:12.105 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Nov 28 10:39:12.105 INFO [stderr] Nov 28 10:39:12.105 INFO [stderr] warning: unused `std::result::Result` that must be used Nov 28 10:39:12.105 INFO [stderr] --> src/main.rs:277:5 Nov 28 10:39:12.105 INFO [stderr] | Nov 28 10:39:12.105 INFO [stderr] 277 | o_buff.write(b"\n"); Nov 28 10:39:12.105 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:12.105 INFO [stderr] | Nov 28 10:39:12.105 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Nov 28 10:39:12.105 INFO [stderr] Nov 28 10:39:12.105 INFO [stderr] warning: unused `std::result::Result` that must be used Nov 28 10:39:12.105 INFO [stderr] --> src/main.rs:280:5 Nov 28 10:39:12.105 INFO [stderr] | Nov 28 10:39:12.105 INFO [stderr] 280 | o_buff.write(b"\n"); Nov 28 10:39:12.105 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:12.105 INFO [stderr] | Nov 28 10:39:12.105 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Nov 28 10:39:12.105 INFO [stderr] Nov 28 10:39:12.105 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Nov 28 10:39:12.105 INFO [stderr] --> src/main.rs:286:10 Nov 28 10:39:12.106 INFO [stderr] | Nov 28 10:39:12.106 INFO [stderr] 286 | for (key_dupGroup, pair_dup) in pd.iter() { Nov 28 10:39:12.106 INFO [stderr] | ^^^^^^^^^^^^ Nov 28 10:39:12.106 INFO [stderr] Nov 28 10:39:12.106 INFO [stderr] warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Nov 28 10:39:12.106 INFO [stderr] --> src/main.rs:357:9 Nov 28 10:39:12.106 INFO [stderr] | Nov 28 10:39:12.106 INFO [stderr] 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Nov 28 10:39:12.106 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^ Nov 28 10:39:12.106 INFO [stderr] Nov 28 10:39:12.106 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Nov 28 10:39:12.106 INFO [stderr] --> src/main.rs:387:17 Nov 28 10:39:12.106 INFO [stderr] | Nov 28 10:39:12.106 INFO [stderr] 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Nov 28 10:39:12.106 INFO [stderr] | ^^^^^^^^^^^^ Nov 28 10:39:12.106 INFO [stderr] Nov 28 10:39:12.133 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 33.50s Nov 28 10:39:12.138 INFO [stderr] su: No module specific data is present Nov 28 10:39:13.104 INFO running `"docker" "inspect" "da8f58bce1641486fbe85c9be2073d206db1cbdffe9624d7767e6737037acbea"` Nov 28 10:39:13.444 INFO running `"docker" "rm" "-f" "da8f58bce1641486fbe85c9be2073d206db1cbdffe9624d7767e6737037acbea"` Nov 28 10:39:13.828 INFO [stdout] da8f58bce1641486fbe85c9be2073d206db1cbdffe9624d7767e6737037acbea