Dec 02 02:35:00.848 INFO testing TuBieJun/consensus against 1.30.1 for beta-1.31-5
Dec 02 02:35:00.848 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/beta-1.31-5/worker-3/1.30.1:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-3/beta-1.31-5/1.30.1:/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 +1.30.1 build --frozen" "-e" "CARGO_TARGET_DIR=/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/cargo-home" "-e" "RUSTUP_HOME=/rustup-home" "-m" "1536M" "--network" "none" "crater"`
Dec 02 02:35:01.373 INFO [stdout] 729fd849bdee80081370ec222f87ae563a48a202fbef0ed317b61d351f7599f6
Dec 02 02:35:01.375 INFO running `"docker" "start" "-a" "729fd849bdee80081370ec222f87ae563a48a202fbef0ed317b61d351f7599f6"`
Dec 02 02:35:03.914 INFO [stderr] usermod: no changes
Dec 02 02:35:04.083 INFO [stderr]    Compiling custom_derive v0.1.7
Dec 02 02:35:04.087 INFO [stderr]    Compiling ieee754 v0.2.2
Dec 02 02:35:04.127 INFO [stderr]    Compiling fs-utils v1.0.0
Dec 02 02:35:04.143 INFO [stderr]    Compiling itertools v0.6.5
Dec 02 02:35:04.195 INFO [stderr]    Compiling newtype_derive v0.1.6
Dec 02 02:35:07.667 INFO [stderr]    Compiling rust-htslib v0.15.0
Dec 02 02:35:41.675 INFO [stderr]    Compiling consensus v0.1.0 (/source)
Dec 02 02:35:43.495 INFO [stderr] warning: unused import: `std::env`
Dec 02 02:35:43.495 INFO [stderr]   --> src/main.rs:12:5
Dec 02 02:35:43.495 INFO [stderr]    |
Dec 02 02:35:43.495 INFO [stderr] 12 | use std::env;
Dec 02 02:35:43.495 INFO [stderr]    |     ^^^^^^^^
Dec 02 02:35:43.495 INFO [stderr]    |
Dec 02 02:35:43.495 INFO [stderr]    = note: #[warn(unused_imports)] on by default
Dec 02 02:35:43.495 INFO [stderr] 
Dec 02 02:35:43.495 INFO [stderr] warning: unused import: `rust_htslib::prelude::*`
Dec 02 02:35:43.495 INFO [stderr]   --> src/main.rs:16:5
Dec 02 02:35:43.495 INFO [stderr]    |
Dec 02 02:35:43.495 INFO [stderr] 16 | use rust_htslib::prelude::*;
Dec 02 02:35:43.495 INFO [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:43.495 INFO [stderr] 
Dec 02 02:35:43.495 INFO [stderr] warning: unused import: `std::io`
Dec 02 02:35:43.495 INFO [stderr]   --> src/main.rs:21:5
Dec 02 02:35:43.495 INFO [stderr]    |
Dec 02 02:35:43.495 INFO [stderr] 21 | use std::io;
Dec 02 02:35:43.495 INFO [stderr]    |     ^^^^^^^
Dec 02 02:35:43.495 INFO [stderr] 
Dec 02 02:35:43.495 INFO [stderr] warning: unused import: `PathBuf`
Dec 02 02:35:43.495 INFO [stderr]   --> src/main.rs:25:23
Dec 02 02:35:43.495 INFO [stderr]    |
Dec 02 02:35:43.495 INFO [stderr] 25 | use std::path::{Path, PathBuf};
Dec 02 02:35:43.495 INFO [stderr]    |                       ^^^^^^^
Dec 02 02:35:43.495 INFO [stderr] 
Dec 02 02:35:43.495 INFO [stderr] warning: unused import: `SubCommand`
Dec 02 02:35:43.495 INFO [stderr]   --> src/main.rs:26:22
Dec 02 02:35:43.495 INFO [stderr]    |
Dec 02 02:35:43.495 INFO [stderr] 26 | use clap::{Arg, App, SubCommand};
Dec 02 02:35:43.495 INFO [stderr]    |                      ^^^^^^^^^^
Dec 02 02:35:43.495 INFO [stderr] 
Dec 02 02:35:43.495 INFO [stderr] warning: unnecessary parentheses around `if` condition
Dec 02 02:35:43.495 INFO [stderr]    --> src/main.rs:218:20
Dec 02 02:35:43.495 INFO [stderr]     |
Dec 02 02:35:43.495 INFO [stderr] 218 |                 if (num_position[&(i as usize)] == num_position[&(0 as usize)]) {
Dec 02 02:35:43.495 INFO [stderr]     |                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses
Dec 02 02:35:43.495 INFO [stderr]     |
Dec 02 02:35:43.495 INFO [stderr]     = note: #[warn(unused_parens)] on by default
Dec 02 02:35:43.495 INFO [stderr] 
Dec 02 02:35:43.495 INFO [stderr] warning: unnecessary parentheses around `if` condition
Dec 02 02:35:43.495 INFO [stderr]    --> src/main.rs:239:16
Dec 02 02:35:43.495 INFO [stderr]     |
Dec 02 02:35:43.495 INFO [stderr] 239 |             if (baseEach_percent_record.len() > 0) {
Dec 02 02:35:43.495 INFO [stderr]     |                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses
Dec 02 02:35:43.495 INFO [stderr] 
Dec 02 02:35:43.723 INFO [stderr] warning: unused import: `std::io::prelude`
Dec 02 02:35:43.723 INFO [stderr]   --> src/main.rs:22:5
Dec 02 02:35:43.723 INFO [stderr]    |
Dec 02 02:35:43.723 INFO [stderr] 22 | use std::io::prelude::*;
Dec 02 02:35:43.723 INFO [stderr]    |     ^^^^^^^^^^^^^^^^
Dec 02 02:35:43.723 INFO [stderr] 
Dec 02 02:35:43.775 INFO [stderr] warning: unused variable: `consensus_base`
Dec 02 02:35:43.775 INFO [stderr]    --> src/main.rs:139:9
Dec 02 02:35:43.775 INFO [stderr]     |
Dec 02 02:35:43.775 INFO [stderr] 139 |     let consensus_base:Vec<u8> = Vec::new();
Dec 02 02:35:43.775 INFO [stderr]     |         ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead
Dec 02 02:35:43.775 INFO [stderr]     |
Dec 02 02:35:43.780 INFO [stderr]     = note: #[warn(unused_variables)] on by default
Dec 02 02:35:43.780 INFO [stderr] 
Dec 02 02:35:43.780 INFO [stderr] warning: unused variable: `consensus_source_reads`
Dec 02 02:35:43.780 INFO [stderr]    --> src/main.rs:144:13
Dec 02 02:35:43.780 INFO [stderr]     |
Dec 02 02:35:43.780 INFO [stderr] 144 |     let mut consensus_source_reads = String::new();
Dec 02 02:35:43.780 INFO [stderr]     |             ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead
Dec 02 02:35:43.780 INFO [stderr] 
Dec 02 02:35:43.780 INFO [stderr] warning: unused variable: `chrom`
Dec 02 02:35:43.780 INFO [stderr]    --> src/main.rs:283:121
Dec 02 02:35:43.780 INFO [stderr]     |
Dec 02 02:35:43.780 INFO [stderr] 283 | fn  block_consensus(pd:& mut HashMap<String, HashMap<String, Vec<(Vec<u8>, Vec<u8>, Vec<u8>, 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 02 02:35:43.780 INFO [stderr]     |                                                                                                                         ^^^^^ help: consider using `_chrom` instead
Dec 02 02:35:43.780 INFO [stderr] 
Dec 02 02:35:43.783 INFO [stderr] warning: value assigned to `new_seq_b` is never read
Dec 02 02:35:43.783 INFO [stderr]    --> src/main.rs:370:21
Dec 02 02:35:43.783 INFO [stderr]     |
Dec 02 02:35:43.783 INFO [stderr] 370 |             let mut new_seq_b:Vec<u8> = Vec::new();
Dec 02 02:35:43.783 INFO [stderr]     |                     ^^^^^^^^^
Dec 02 02:35:43.783 INFO [stderr]     |
Dec 02 02:35:43.783 INFO [stderr]     = note: #[warn(unused_assignments)] on by default
Dec 02 02:35:43.783 INFO [stderr] 
Dec 02 02:35:43.799 INFO [stderr] warning: variable does not need to be mutable
Dec 02 02:35:43.799 INFO [stderr]   --> src/main.rs:74:9
Dec 02 02:35:43.799 INFO [stderr]    |
Dec 02 02:35:43.799 INFO [stderr] 74 |     let mut pair;
Dec 02 02:35:43.799 INFO [stderr]    |         ----^^^^
Dec 02 02:35:43.799 INFO [stderr]    |         |
Dec 02 02:35:43.799 INFO [stderr]    |         help: remove this `mut`
Dec 02 02:35:43.799 INFO [stderr]    |
Dec 02 02:35:43.799 INFO [stderr]    = note: #[warn(unused_mut)] on by default
Dec 02 02:35:43.799 INFO [stderr] 
Dec 02 02:35:43.799 INFO [stderr] warning: variable does not need to be mutable
Dec 02 02:35:43.799 INFO [stderr]   --> src/main.rs:75:9
Dec 02 02:35:43.799 INFO [stderr]    |
Dec 02 02:35:43.799 INFO [stderr] 75 |     let mut strand;
Dec 02 02:35:43.799 INFO [stderr]    |         ----^^^^^^
Dec 02 02:35:43.799 INFO [stderr]    |         |
Dec 02 02:35:43.799 INFO [stderr]    |         help: remove this `mut`
Dec 02 02:35:43.799 INFO [stderr] 
Dec 02 02:35:43.799 INFO [stderr] warning: variable does not need to be mutable
Dec 02 02:35:43.799 INFO [stderr]   --> src/main.rs:76:9
Dec 02 02:35:43.799 INFO [stderr]    |
Dec 02 02:35:43.799 INFO [stderr] 76 |     let mut aln_pos;
Dec 02 02:35:43.799 INFO [stderr]    |         ----^^^^^^^
Dec 02 02:35:43.799 INFO [stderr]    |         |
Dec 02 02:35:43.799 INFO [stderr]    |         help: remove this `mut`
Dec 02 02:35:43.799 INFO [stderr] 
Dec 02 02:35:43.843 INFO [stderr] warning: variable does not need to be mutable
Dec 02 02:35:43.843 INFO [stderr]    --> src/main.rs:144:9
Dec 02 02:35:43.843 INFO [stderr]     |
Dec 02 02:35:43.843 INFO [stderr] 144 |     let mut consensus_source_reads = String::new();
Dec 02 02:35:43.843 INFO [stderr]     |         ----^^^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:43.843 INFO [stderr]     |         |
Dec 02 02:35:43.843 INFO [stderr]     |         help: remove this `mut`
Dec 02 02:35:43.843 INFO [stderr] 
Dec 02 02:35:43.843 INFO [stderr] warning: variable does not need to be mutable
Dec 02 02:35:43.843 INFO [stderr]    --> src/main.rs:151:9
Dec 02 02:35:43.843 INFO [stderr]     |
Dec 02 02:35:43.843 INFO [stderr] 151 |     let mut top_cigar:&CigarStringView;
Dec 02 02:35:43.843 INFO [stderr]     |         ----^^^^^^^^^
Dec 02 02:35:43.843 INFO [stderr]     |         |
Dec 02 02:35:43.843 INFO [stderr]     |         help: remove this `mut`
Dec 02 02:35:43.843 INFO [stderr] 
Dec 02 02:35:43.859 INFO [stderr] warning: variable does not need to be mutable
Dec 02 02:35:43.859 INFO [stderr]    --> src/main.rs:338:9
Dec 02 02:35:43.859 INFO [stderr]     |
Dec 02 02:35:43.859 INFO [stderr] 338 |     let mut need_trim:bool;
Dec 02 02:35:43.859 INFO [stderr]     |         ----^^^^^^^^^
Dec 02 02:35:43.859 INFO [stderr]     |         |
Dec 02 02:35:43.859 INFO [stderr]     |         help: remove this `mut`
Dec 02 02:35:43.859 INFO [stderr] 
Dec 02 02:35:43.859 INFO [stderr] warning: variable does not need to be mutable
Dec 02 02:35:43.859 INFO [stderr]    --> src/main.rs:355:9
Dec 02 02:35:43.859 INFO [stderr]     |
Dec 02 02:35:43.859 INFO [stderr] 355 |     let mut chrom = 0;
Dec 02 02:35:43.859 INFO [stderr]     |         ----^^^^^
Dec 02 02:35:43.859 INFO [stderr]     |         |
Dec 02 02:35:43.859 INFO [stderr]     |         help: remove this `mut`
Dec 02 02:35:43.859 INFO [stderr] 
Dec 02 02:35:43.859 INFO [stderr] warning: function `bamLineParse` should have a snake case name such as `bam_line_parse`
Dec 02 02:35:43.859 INFO [stderr]   --> src/main.rs:68:1
Dec 02 02:35:43.859 INFO [stderr]    |
Dec 02 02:35:43.859 INFO [stderr] 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){
Dec 02 02:35:43.859 INFO [stderr] 69 | |
Dec 02 02:35:43.859 INFO [stderr] 70 | |     let qname_str = String::from_utf8_lossy(record.qname()).to_string();
Dec 02 02:35:43.859 INFO [stderr] 71 | |     let temp_v:Vec<&str> = qname_str.split('#').collect();
Dec 02 02:35:43.859 INFO [stderr] ...  |
Dec 02 02:35:43.859 INFO [stderr] 97 | |     (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos)
Dec 02 02:35:43.859 INFO [stderr] 98 | | }
Dec 02 02:35:43.859 INFO [stderr]    | |_^
Dec 02 02:35:43.859 INFO [stderr]    |
Dec 02 02:35:43.859 INFO [stderr]    = note: #[warn(non_snake_case)] on by default
Dec 02 02:35:43.859 INFO [stderr] 
Dec 02 02:35:43.859 INFO [stderr] warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record`
Dec 02 02:35:43.859 INFO [stderr]    --> src/main.rs:147:9
Dec 02 02:35:43.859 INFO [stderr]     |
Dec 02 02:35:43.859 INFO [stderr] 147 |     let mut baseEach_num_record = String::new();
Dec 02 02:35:43.859 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:43.859 INFO [stderr] 
Dec 02 02:35:43.859 INFO [stderr] warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record`
Dec 02 02:35:43.859 INFO [stderr]    --> src/main.rs:148:9
Dec 02 02:35:43.859 INFO [stderr]     |
Dec 02 02:35:43.859 INFO [stderr] 148 |     let mut baseEach_percent_record = String::new();
Dec 02 02:35:43.859 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:43.859 INFO [stderr] 
Dec 02 02:35:43.860 INFO [stderr] warning: unused `std::result::Result` which must be used
Dec 02 02:35:43.860 INFO [stderr]    --> src/main.rs:267:9
Dec 02 02:35:43.860 INFO [stderr]     |
Dec 02 02:35:43.860 INFO [stderr] 267 |         o_buff.write(&member_record.2);
Dec 02 02:35:43.860 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:43.860 INFO [stderr]     |
Dec 02 02:35:43.860 INFO [stderr]     = note: #[warn(unused_must_use)] on by default
Dec 02 02:35:43.860 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 02 02:35:43.860 INFO [stderr] 
Dec 02 02:35:43.860 INFO [stderr] warning: unused `std::result::Result` which must be used
Dec 02 02:35:43.860 INFO [stderr]    --> src/main.rs:269:9
Dec 02 02:35:43.860 INFO [stderr]     |
Dec 02 02:35:43.860 INFO [stderr] 269 |         o_buff.write(&member_record.0);
Dec 02 02:35:43.860 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:43.860 INFO [stderr]     |
Dec 02 02:35:43.860 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 02 02:35:43.860 INFO [stderr] 
Dec 02 02:35:43.861 INFO [stderr] warning: unused `std::result::Result` which must be used
Dec 02 02:35:43.861 INFO [stderr]    --> src/main.rs:272:9
Dec 02 02:35:43.861 INFO [stderr]     |
Dec 02 02:35:43.861 INFO [stderr] 272 |         o_buff.write(&real_qual_temp);
Dec 02 02:35:43.861 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:43.861 INFO [stderr]     |
Dec 02 02:35:43.861 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 02 02:35:43.862 INFO [stderr] 
Dec 02 02:35:43.862 INFO [stderr] warning: unused `std::result::Result` which must be used
Dec 02 02:35:43.862 INFO [stderr]    --> src/main.rs:274:5
Dec 02 02:35:43.862 INFO [stderr]     |
Dec 02 02:35:43.862 INFO [stderr] 274 |     o_buff.write(b"\n");
Dec 02 02:35:43.862 INFO [stderr]     |     ^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:43.862 INFO [stderr]     |
Dec 02 02:35:43.862 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 02 02:35:43.862 INFO [stderr] 
Dec 02 02:35:43.862 INFO [stderr] warning: unused `std::result::Result` which must be used
Dec 02 02:35:43.862 INFO [stderr]    --> src/main.rs:277:5
Dec 02 02:35:43.862 INFO [stderr]     |
Dec 02 02:35:43.862 INFO [stderr] 277 |     o_buff.write(b"\n");
Dec 02 02:35:43.862 INFO [stderr]     |     ^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:43.862 INFO [stderr]     |
Dec 02 02:35:43.862 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 02 02:35:43.862 INFO [stderr] 
Dec 02 02:35:43.862 INFO [stderr] warning: unused `std::result::Result` which must be used
Dec 02 02:35:43.862 INFO [stderr]    --> src/main.rs:280:5
Dec 02 02:35:43.862 INFO [stderr]     |
Dec 02 02:35:43.862 INFO [stderr] 280 |     o_buff.write(b"\n");
Dec 02 02:35:43.862 INFO [stderr]     |     ^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:43.862 INFO [stderr]     |
Dec 02 02:35:43.862 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 02 02:35:43.862 INFO [stderr] 
Dec 02 02:35:43.862 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group`
Dec 02 02:35:43.862 INFO [stderr]    --> src/main.rs:286:10
Dec 02 02:35:43.862 INFO [stderr]     |
Dec 02 02:35:43.862 INFO [stderr] 286 |     for (key_dupGroup, pair_dup) in pd.iter() {
Dec 02 02:35:43.862 INFO [stderr]     |          ^^^^^^^^^^^^
Dec 02 02:35:43.863 INFO [stderr] 
Dec 02 02:35:43.863 INFO [stderr] warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group`
Dec 02 02:35:43.863 INFO [stderr]    --> src/main.rs:357:9
Dec 02 02:35:43.863 INFO [stderr]     |
Dec 02 02:35:43.863 INFO [stderr] 357 |     let mut position_dupGroup: HashMap<String, HashMap<String, Vec<(Vec<u8>, Vec<u8>, Vec<u8>, CigarStringView, bool)>>> = HashMap::new();
Dec 02 02:35:43.863 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:43.863 INFO [stderr] 
Dec 02 02:35:43.867 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group`
Dec 02 02:35:43.867 INFO [stderr]    --> src/main.rs:387:17
Dec 02 02:35:43.867 INFO [stderr]     |
Dec 02 02:35:43.867 INFO [stderr] 387 |             let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size);
Dec 02 02:35:43.867 INFO [stderr]     |                 ^^^^^^^^^^^^
Dec 02 02:35:43.867 INFO [stderr] 
Dec 02 02:35:47.688 INFO [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 43.74s
Dec 02 02:35:47.693 INFO [stderr] su: No module specific data is present
Dec 02 02:35:48.835 INFO running `"docker" "inspect" "729fd849bdee80081370ec222f87ae563a48a202fbef0ed317b61d351f7599f6"`
Dec 02 02:35:49.212 INFO running `"docker" "rm" "-f" "729fd849bdee80081370ec222f87ae563a48a202fbef0ed317b61d351f7599f6"`
Dec 02 02:35:49.517 INFO [stdout] 729fd849bdee80081370ec222f87ae563a48a202fbef0ed317b61d351f7599f6
Dec 02 02:35:49.521 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/beta-1.31-5/worker-3/1.30.1:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-3/beta-1.31-5/1.30.1:/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 +1.30.1 test --frozen --no-run" "-e" "CARGO_TARGET_DIR=/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/cargo-home" "-e" "RUSTUP_HOME=/rustup-home" "-m" "1536M" "--network" "none" "crater"`
Dec 02 02:35:50.051 INFO [stdout] a5d779cb6956f47ac55f4a28e37ad59efb2ad006a9e4376cf5d1aa426190a3b2
Dec 02 02:35:50.057 INFO running `"docker" "start" "-a" "a5d779cb6956f47ac55f4a28e37ad59efb2ad006a9e4376cf5d1aa426190a3b2"`
Dec 02 02:35:51.678 INFO [stderr] usermod: no changes
Dec 02 02:35:51.780 INFO [stderr]    Compiling consensus v0.1.0 (/source)
Dec 02 02:35:53.695 INFO [stderr] warning: unused import: `std::env`
Dec 02 02:35:53.695 INFO [stderr]   --> src/main.rs:12:5
Dec 02 02:35:53.695 INFO [stderr]    |
Dec 02 02:35:53.695 INFO [stderr] 12 | use std::env;
Dec 02 02:35:53.695 INFO [stderr]    |     ^^^^^^^^
Dec 02 02:35:53.695 INFO [stderr]    |
Dec 02 02:35:53.695 INFO [stderr]    = note: #[warn(unused_imports)] on by default
Dec 02 02:35:53.695 INFO [stderr] 
Dec 02 02:35:53.695 INFO [stderr] warning: unused import: `rust_htslib::prelude::*`
Dec 02 02:35:53.695 INFO [stderr]   --> src/main.rs:16:5
Dec 02 02:35:53.695 INFO [stderr]    |
Dec 02 02:35:53.695 INFO [stderr] 16 | use rust_htslib::prelude::*;
Dec 02 02:35:53.695 INFO [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:53.695 INFO [stderr] 
Dec 02 02:35:53.696 INFO [stderr] warning: unused import: `std::io`
Dec 02 02:35:53.696 INFO [stderr]   --> src/main.rs:21:5
Dec 02 02:35:53.696 INFO [stderr]    |
Dec 02 02:35:53.696 INFO [stderr] 21 | use std::io;
Dec 02 02:35:53.696 INFO [stderr]    |     ^^^^^^^
Dec 02 02:35:53.696 INFO [stderr] 
Dec 02 02:35:53.696 INFO [stderr] warning: unused import: `PathBuf`
Dec 02 02:35:53.696 INFO [stderr]   --> src/main.rs:25:23
Dec 02 02:35:53.696 INFO [stderr]    |
Dec 02 02:35:53.696 INFO [stderr] 25 | use std::path::{Path, PathBuf};
Dec 02 02:35:53.696 INFO [stderr]    |                       ^^^^^^^
Dec 02 02:35:53.696 INFO [stderr] 
Dec 02 02:35:53.696 INFO [stderr] warning: unused import: `SubCommand`
Dec 02 02:35:53.696 INFO [stderr]   --> src/main.rs:26:22
Dec 02 02:35:53.696 INFO [stderr]    |
Dec 02 02:35:53.696 INFO [stderr] 26 | use clap::{Arg, App, SubCommand};
Dec 02 02:35:53.696 INFO [stderr]    |                      ^^^^^^^^^^
Dec 02 02:35:53.696 INFO [stderr] 
Dec 02 02:35:53.696 INFO [stderr] warning: unnecessary parentheses around `if` condition
Dec 02 02:35:53.696 INFO [stderr]    --> src/main.rs:218:20
Dec 02 02:35:53.696 INFO [stderr]     |
Dec 02 02:35:53.696 INFO [stderr] 218 |                 if (num_position[&(i as usize)] == num_position[&(0 as usize)]) {
Dec 02 02:35:53.696 INFO [stderr]     |                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses
Dec 02 02:35:53.696 INFO [stderr]     |
Dec 02 02:35:53.696 INFO [stderr]     = note: #[warn(unused_parens)] on by default
Dec 02 02:35:53.696 INFO [stderr] 
Dec 02 02:35:53.696 INFO [stderr] warning: unnecessary parentheses around `if` condition
Dec 02 02:35:53.696 INFO [stderr]    --> src/main.rs:239:16
Dec 02 02:35:53.696 INFO [stderr]     |
Dec 02 02:35:53.696 INFO [stderr] 239 |             if (baseEach_percent_record.len() > 0) {
Dec 02 02:35:53.696 INFO [stderr]     |                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses
Dec 02 02:35:53.696 INFO [stderr] 
Dec 02 02:35:53.836 INFO [stderr] warning: unused import: `std::io::prelude`
Dec 02 02:35:53.836 INFO [stderr]   --> src/main.rs:22:5
Dec 02 02:35:53.836 INFO [stderr]    |
Dec 02 02:35:53.836 INFO [stderr] 22 | use std::io::prelude::*;
Dec 02 02:35:53.836 INFO [stderr]    |     ^^^^^^^^^^^^^^^^
Dec 02 02:35:53.836 INFO [stderr] 
Dec 02 02:35:53.863 INFO [stderr] warning: unused variable: `consensus_base`
Dec 02 02:35:53.863 INFO [stderr]    --> src/main.rs:139:9
Dec 02 02:35:53.863 INFO [stderr]     |
Dec 02 02:35:53.863 INFO [stderr] 139 |     let consensus_base:Vec<u8> = Vec::new();
Dec 02 02:35:53.863 INFO [stderr]     |         ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead
Dec 02 02:35:53.863 INFO [stderr]     |
Dec 02 02:35:53.863 INFO [stderr]     = note: #[warn(unused_variables)] on by default
Dec 02 02:35:53.863 INFO [stderr] 
Dec 02 02:35:53.863 INFO [stderr] warning: unused variable: `consensus_source_reads`
Dec 02 02:35:53.863 INFO [stderr]    --> src/main.rs:144:13
Dec 02 02:35:53.863 INFO [stderr]     |
Dec 02 02:35:53.863 INFO [stderr] 144 |     let mut consensus_source_reads = String::new();
Dec 02 02:35:53.863 INFO [stderr]     |             ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead
Dec 02 02:35:53.863 INFO [stderr] 
Dec 02 02:35:53.863 INFO [stderr] warning: unused variable: `chrom`
Dec 02 02:35:53.863 INFO [stderr]    --> src/main.rs:283:121
Dec 02 02:35:53.863 INFO [stderr]     |
Dec 02 02:35:53.863 INFO [stderr] 283 | fn  block_consensus(pd:& mut HashMap<String, HashMap<String, Vec<(Vec<u8>, Vec<u8>, Vec<u8>, 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 02 02:35:53.863 INFO [stderr]     |                                                                                                                         ^^^^^ help: consider using `_chrom` instead
Dec 02 02:35:53.863 INFO [stderr] 
Dec 02 02:35:53.863 INFO [stderr] warning: value assigned to `new_seq_b` is never read
Dec 02 02:35:53.863 INFO [stderr]    --> src/main.rs:370:21
Dec 02 02:35:53.863 INFO [stderr]     |
Dec 02 02:35:53.863 INFO [stderr] 370 |             let mut new_seq_b:Vec<u8> = Vec::new();
Dec 02 02:35:53.863 INFO [stderr]     |                     ^^^^^^^^^
Dec 02 02:35:53.863 INFO [stderr]     |
Dec 02 02:35:53.863 INFO [stderr]     = note: #[warn(unused_assignments)] on by default
Dec 02 02:35:53.863 INFO [stderr] 
Dec 02 02:35:53.871 INFO [stderr] warning: variable does not need to be mutable
Dec 02 02:35:53.871 INFO [stderr]   --> src/main.rs:74:9
Dec 02 02:35:53.871 INFO [stderr]    |
Dec 02 02:35:53.871 INFO [stderr] 74 |     let mut pair;
Dec 02 02:35:53.871 INFO [stderr]    |         ----^^^^
Dec 02 02:35:53.871 INFO [stderr]    |         |
Dec 02 02:35:53.871 INFO [stderr]    |         help: remove this `mut`
Dec 02 02:35:53.871 INFO [stderr]    |
Dec 02 02:35:53.871 INFO [stderr]    = note: #[warn(unused_mut)] on by default
Dec 02 02:35:53.871 INFO [stderr] 
Dec 02 02:35:53.871 INFO [stderr] warning: variable does not need to be mutable
Dec 02 02:35:53.871 INFO [stderr]   --> src/main.rs:75:9
Dec 02 02:35:53.871 INFO [stderr]    |
Dec 02 02:35:53.871 INFO [stderr] 75 |     let mut strand;
Dec 02 02:35:53.871 INFO [stderr]    |         ----^^^^^^
Dec 02 02:35:53.871 INFO [stderr]    |         |
Dec 02 02:35:53.871 INFO [stderr]    |         help: remove this `mut`
Dec 02 02:35:53.871 INFO [stderr] 
Dec 02 02:35:53.871 INFO [stderr] warning: variable does not need to be mutable
Dec 02 02:35:53.871 INFO [stderr]   --> src/main.rs:76:9
Dec 02 02:35:53.871 INFO [stderr]    |
Dec 02 02:35:53.871 INFO [stderr] 76 |     let mut aln_pos;
Dec 02 02:35:53.871 INFO [stderr]    |         ----^^^^^^^
Dec 02 02:35:53.871 INFO [stderr]    |         |
Dec 02 02:35:53.871 INFO [stderr]    |         help: remove this `mut`
Dec 02 02:35:53.871 INFO [stderr] 
Dec 02 02:35:53.895 INFO [stderr] warning: variable does not need to be mutable
Dec 02 02:35:53.895 INFO [stderr]    --> src/main.rs:144:9
Dec 02 02:35:53.895 INFO [stderr]     |
Dec 02 02:35:53.895 INFO [stderr] 144 |     let mut consensus_source_reads = String::new();
Dec 02 02:35:53.895 INFO [stderr]     |         ----^^^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:53.895 INFO [stderr]     |         |
Dec 02 02:35:53.895 INFO [stderr]     |         help: remove this `mut`
Dec 02 02:35:53.895 INFO [stderr] 
Dec 02 02:35:53.895 INFO [stderr] warning: variable does not need to be mutable
Dec 02 02:35:53.895 INFO [stderr]    --> src/main.rs:151:9
Dec 02 02:35:53.895 INFO [stderr]     |
Dec 02 02:35:53.895 INFO [stderr] 151 |     let mut top_cigar:&CigarStringView;
Dec 02 02:35:53.895 INFO [stderr]     |         ----^^^^^^^^^
Dec 02 02:35:53.895 INFO [stderr]     |         |
Dec 02 02:35:53.895 INFO [stderr]     |         help: remove this `mut`
Dec 02 02:35:53.895 INFO [stderr] 
Dec 02 02:35:53.911 INFO [stderr] warning: variable does not need to be mutable
Dec 02 02:35:53.911 INFO [stderr]    --> src/main.rs:338:9
Dec 02 02:35:53.911 INFO [stderr]     |
Dec 02 02:35:53.911 INFO [stderr] 338 |     let mut need_trim:bool;
Dec 02 02:35:53.911 INFO [stderr]     |         ----^^^^^^^^^
Dec 02 02:35:53.911 INFO [stderr]     |         |
Dec 02 02:35:53.911 INFO [stderr]     |         help: remove this `mut`
Dec 02 02:35:53.911 INFO [stderr] 
Dec 02 02:35:53.911 INFO [stderr] warning: variable does not need to be mutable
Dec 02 02:35:53.911 INFO [stderr]    --> src/main.rs:355:9
Dec 02 02:35:53.911 INFO [stderr]     |
Dec 02 02:35:53.911 INFO [stderr] 355 |     let mut chrom = 0;
Dec 02 02:35:53.911 INFO [stderr]     |         ----^^^^^
Dec 02 02:35:53.911 INFO [stderr]     |         |
Dec 02 02:35:53.911 INFO [stderr]     |         help: remove this `mut`
Dec 02 02:35:53.911 INFO [stderr] 
Dec 02 02:35:53.911 INFO [stderr] warning: function `bamLineParse` should have a snake case name such as `bam_line_parse`
Dec 02 02:35:53.911 INFO [stderr]   --> src/main.rs:68:1
Dec 02 02:35:53.911 INFO [stderr]    |
Dec 02 02:35:53.911 INFO [stderr] 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){
Dec 02 02:35:53.911 INFO [stderr] 69 | |
Dec 02 02:35:53.911 INFO [stderr] 70 | |     let qname_str = String::from_utf8_lossy(record.qname()).to_string();
Dec 02 02:35:53.911 INFO [stderr] 71 | |     let temp_v:Vec<&str> = qname_str.split('#').collect();
Dec 02 02:35:53.911 INFO [stderr] ...  |
Dec 02 02:35:53.911 INFO [stderr] 97 | |     (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos)
Dec 02 02:35:53.911 INFO [stderr] 98 | | }
Dec 02 02:35:53.911 INFO [stderr]    | |_^
Dec 02 02:35:53.911 INFO [stderr]    |
Dec 02 02:35:53.911 INFO [stderr]    = note: #[warn(non_snake_case)] on by default
Dec 02 02:35:53.911 INFO [stderr] 
Dec 02 02:35:53.911 INFO [stderr] warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record`
Dec 02 02:35:53.911 INFO [stderr]    --> src/main.rs:147:9
Dec 02 02:35:53.911 INFO [stderr]     |
Dec 02 02:35:53.911 INFO [stderr] 147 |     let mut baseEach_num_record = String::new();
Dec 02 02:35:53.911 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:53.911 INFO [stderr] 
Dec 02 02:35:53.911 INFO [stderr] warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record`
Dec 02 02:35:53.911 INFO [stderr]    --> src/main.rs:148:9
Dec 02 02:35:53.911 INFO [stderr]     |
Dec 02 02:35:53.911 INFO [stderr] 148 |     let mut baseEach_percent_record = String::new();
Dec 02 02:35:53.911 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:53.911 INFO [stderr] 
Dec 02 02:35:53.911 INFO [stderr] warning: unused `std::result::Result` which must be used
Dec 02 02:35:53.911 INFO [stderr]    --> src/main.rs:267:9
Dec 02 02:35:53.911 INFO [stderr]     |
Dec 02 02:35:53.911 INFO [stderr] 267 |         o_buff.write(&member_record.2);
Dec 02 02:35:53.911 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:53.911 INFO [stderr]     |
Dec 02 02:35:53.911 INFO [stderr]     = note: #[warn(unused_must_use)] on by default
Dec 02 02:35:53.911 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 02 02:35:53.911 INFO [stderr] 
Dec 02 02:35:53.912 INFO [stderr] warning: unused `std::result::Result` which must be used
Dec 02 02:35:53.912 INFO [stderr]    --> src/main.rs:269:9
Dec 02 02:35:53.912 INFO [stderr]     |
Dec 02 02:35:53.912 INFO [stderr] 269 |         o_buff.write(&member_record.0);
Dec 02 02:35:53.912 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:53.912 INFO [stderr]     |
Dec 02 02:35:53.912 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 02 02:35:53.912 INFO [stderr] 
Dec 02 02:35:53.916 INFO [stderr] warning: unused `std::result::Result` which must be used
Dec 02 02:35:53.916 INFO [stderr]    --> src/main.rs:272:9
Dec 02 02:35:53.916 INFO [stderr]     |
Dec 02 02:35:53.916 INFO [stderr] 272 |         o_buff.write(&real_qual_temp);
Dec 02 02:35:53.916 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:53.916 INFO [stderr]     |
Dec 02 02:35:53.916 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 02 02:35:53.916 INFO [stderr] 
Dec 02 02:35:53.916 INFO [stderr] warning: unused `std::result::Result` which must be used
Dec 02 02:35:53.916 INFO [stderr]    --> src/main.rs:274:5
Dec 02 02:35:53.916 INFO [stderr]     |
Dec 02 02:35:53.916 INFO [stderr] 274 |     o_buff.write(b"\n");
Dec 02 02:35:53.916 INFO [stderr]     |     ^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:53.916 INFO [stderr]     |
Dec 02 02:35:53.916 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 02 02:35:53.916 INFO [stderr] 
Dec 02 02:35:53.916 INFO [stderr] warning: unused `std::result::Result` which must be used
Dec 02 02:35:53.916 INFO [stderr]    --> src/main.rs:277:5
Dec 02 02:35:53.916 INFO [stderr]     |
Dec 02 02:35:53.916 INFO [stderr] 277 |     o_buff.write(b"\n");
Dec 02 02:35:53.916 INFO [stderr]     |     ^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:53.916 INFO [stderr]     |
Dec 02 02:35:53.916 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 02 02:35:53.916 INFO [stderr] 
Dec 02 02:35:53.916 INFO [stderr] warning: unused `std::result::Result` which must be used
Dec 02 02:35:53.916 INFO [stderr]    --> src/main.rs:280:5
Dec 02 02:35:53.916 INFO [stderr]     |
Dec 02 02:35:53.916 INFO [stderr] 280 |     o_buff.write(b"\n");
Dec 02 02:35:53.916 INFO [stderr]     |     ^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:53.916 INFO [stderr]     |
Dec 02 02:35:53.916 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Dec 02 02:35:53.916 INFO [stderr] 
Dec 02 02:35:53.916 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group`
Dec 02 02:35:53.916 INFO [stderr]    --> src/main.rs:286:10
Dec 02 02:35:53.916 INFO [stderr]     |
Dec 02 02:35:53.916 INFO [stderr] 286 |     for (key_dupGroup, pair_dup) in pd.iter() {
Dec 02 02:35:53.916 INFO [stderr]     |          ^^^^^^^^^^^^
Dec 02 02:35:53.916 INFO [stderr] 
Dec 02 02:35:53.916 INFO [stderr] warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group`
Dec 02 02:35:53.916 INFO [stderr]    --> src/main.rs:357:9
Dec 02 02:35:53.916 INFO [stderr]     |
Dec 02 02:35:53.916 INFO [stderr] 357 |     let mut position_dupGroup: HashMap<String, HashMap<String, Vec<(Vec<u8>, Vec<u8>, Vec<u8>, CigarStringView, bool)>>> = HashMap::new();
Dec 02 02:35:53.916 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^
Dec 02 02:35:53.916 INFO [stderr] 
Dec 02 02:35:53.916 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group`
Dec 02 02:35:53.916 INFO [stderr]    --> src/main.rs:387:17
Dec 02 02:35:53.916 INFO [stderr]     |
Dec 02 02:35:53.916 INFO [stderr] 387 |             let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size);
Dec 02 02:35:53.916 INFO [stderr]     |                 ^^^^^^^^^^^^
Dec 02 02:35:53.916 INFO [stderr] 
Dec 02 02:35:54.523 INFO [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 2.82s
Dec 02 02:35:54.531 INFO [stderr] su: No module specific data is present
Dec 02 02:35:55.527 INFO running `"docker" "inspect" "a5d779cb6956f47ac55f4a28e37ad59efb2ad006a9e4376cf5d1aa426190a3b2"`
Dec 02 02:35:55.871 INFO running `"docker" "rm" "-f" "a5d779cb6956f47ac55f4a28e37ad59efb2ad006a9e4376cf5d1aa426190a3b2"`
Dec 02 02:35:56.197 INFO [stdout] a5d779cb6956f47ac55f4a28e37ad59efb2ad006a9e4376cf5d1aa426190a3b2
Dec 02 02:35:56.203 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/beta-1.31-5/worker-3/1.30.1:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-3/beta-1.31-5/1.30.1:/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 +1.30.1 test --frozen" "-e" "CARGO_TARGET_DIR=/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/cargo-home" "-e" "RUSTUP_HOME=/rustup-home" "-m" "1536M" "--network" "none" "crater"`
Dec 02 02:35:56.740 INFO [stdout] 8efd4f6445010f4b6cdc58a1762458205acee2a8edd38d7eaa27848ec93a382f
Dec 02 02:35:56.743 INFO running `"docker" "start" "-a" "8efd4f6445010f4b6cdc58a1762458205acee2a8edd38d7eaa27848ec93a382f"`
Dec 02 02:35:58.294 INFO [stderr] usermod: no changes
Dec 02 02:35:58.375 INFO [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 0.05s
Dec 02 02:35:58.405 INFO [stderr]      Running /target/debug/deps/consensus-9beff4282fad8d60
Dec 02 02:35:58.419 INFO [stdout] 
Dec 02 02:35:58.419 INFO [stdout] running 0 tests
Dec 02 02:35:58.419 INFO [stdout] 
Dec 02 02:35:58.419 INFO [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out
Dec 02 02:35:58.419 INFO [stdout] 
Dec 02 02:35:58.419 INFO [stderr] su: No module specific data is present
Dec 02 02:35:59.697 INFO running `"docker" "inspect" "8efd4f6445010f4b6cdc58a1762458205acee2a8edd38d7eaa27848ec93a382f"`
Dec 02 02:35:59.935 INFO running `"docker" "rm" "-f" "8efd4f6445010f4b6cdc58a1762458205acee2a8edd38d7eaa27848ec93a382f"`
Dec 02 02:36:00.247 INFO [stdout] 8efd4f6445010f4b6cdc58a1762458205acee2a8edd38d7eaa27848ec93a382f
